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Van Andel Research Institute<br />

<strong>Scientific</strong> <strong>Report</strong> <strong>2013</strong>

Van Andel Research Institute<br />

<strong>Scientific</strong> <strong>Report</strong> <strong>2013</strong><br />

Cryosection of a mouse calvaria.<br />

In using tissue-specific knock-out mouse models, the promoter must have precise<br />

specificity. Here we used the mTmG reporter model to demonstrate that Ocn-Cre<br />

expresses specifically in the bone cells. Top panel: Cells were stained with DAPI (blue) for<br />

nucleic acids. Bone cells are expressing GFP (green), while all other cells are expressing Tomato<br />

(red). Lower panel: A differential interference contrast image with DAPI stain of the same area.<br />

Photo by Alex Zhong of the Williams laboratory.

Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Published March <strong>2013</strong>.<br />

Copyright <strong>2013</strong> by the Van Andel Institute; all rights reserved.<br />

Van Andel Institute, 333 Bostwick Avenue, N.E.<br />

Grand Rapids, Michigan 49503, U.S.A.<br />


VARI | <strong>2013</strong><br />

Introduction 1<br />

Laboratory <strong>Report</strong>s<br />

Arthur S. Alberts, Ph.D.<br />

Cell Structure and Signal Integration 6<br />

William H. Baer II, M.D., Pharm.D.<br />

VARI-ClinXus, LLC 8<br />

John F. Bender, Pharm.D.<br />

Clinical Operations 10<br />

Patrik Brundin, M.D., Ph.D.<br />

Translational Parkinson’s Disease Research 11<br />

Ting-Tung (Anthony) Chang, Ph.D.<br />

Small-Animal Imaging Facility/Translational Imaging 14<br />

Nicholas S. Duesbery, Ph.D.<br />

Cancer and Developmental Cell Biology 16<br />

Bryn Eagleson, B.S., RLATG<br />

Vivarium and Transgenics 19<br />

Table of Contents<br />

Kyle A. Furge, Ph.D.<br />

Interdisciplinary Renal Oncology 22<br />

Brian B. Haab, Ph.D.<br />

Cancer Immunodiagnostics 25<br />

Galen H. Hostetter, M.D.<br />

Analytical Pathology 28<br />

Scott D. Jewell, Ph.D.<br />

Program for Biospecimen Science 30<br />

Xiaohong Li, Ph.D.<br />

Tumor Microenvironment and Metastasis 34<br />

Jeffrey P. MacKeigan, Ph.D.<br />

Systems Biology 35<br />

Karsten Melcher, Ph.D.<br />

Structural Biology and Biochemistry 38<br />

Cindy K. Miranti, Ph.D.<br />

Integrin Signaling and Tumorigenesis 41<br />

Mark W. Neff, Ph.D.<br />

Canine Genetics and Genomics 44<br />

Brian J. Nickoloff, M.D., Ph.D.<br />

Cutaneous Oncology 46<br />

Giselle S. Sholler, M.D.<br />

Neuroblastoma Translational Research 47<br />

Matthew Steensma, M.D.<br />

Musculoskeletal Oncology 49<br />

Steven J. Triezenberg, Ph.D.<br />

Transcriptional Regulation 51<br />

Jeremy M. Van Raamsdonk, Ph.D.<br />

Aging and Neurodegenerative Disease 54<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Laboratory <strong>Report</strong>s, continued<br />

George F. Vande Woude, Ph.D.<br />

Molecular Oncology 57<br />

Craig P. Webb, Ph.D.<br />

Translational Medicine 60<br />

Michael Weinreich, Ph.D.<br />

Genome Integrity and Tumorigenesis 63<br />

Bart O. Williams, Ph.D.<br />

Cell Signaling and Carcinogenesis 66<br />

H. Eric Xu, Ph.D.<br />

Structural Sciences 70<br />

Awards for <strong>Scientific</strong> Achievement 73<br />

Jay Van Andel Award for Outstanding Achievement in Parkinson’s<br />

Disease Research<br />

Han-Mo Koo Memorial Award<br />

Postdoctoral Fellowship Program 76<br />

List of Fellows<br />

Student Programs 78<br />

Grand Rapids Area Pre-College Engineering Program<br />

Summer Student Internship Program<br />

VARI Seminar Series 82<br />

2011 – 2012 Seminars<br />

Van Andel Research Institute Organization 85<br />

Boards<br />

Office of the Director<br />

VAI Administrative Organization<br />


Introduction<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Introduction<br />

Phase II of the Van Andel Institute building, which opened in late 2009, added 240,000 square feet to the Institute, nearly<br />

tripling the available laboratory space, and it garnered LEED Platinum status from the United States Green Building Council.<br />

This expansion enabled the start of a major new initiative into the study of neurodegenerative diseases and provided the<br />

infrastructure to establish the Van Andel Research Institute (VARI) Center for Neurodegenerative Science. The Center is led by<br />

Dr. Patrik Brundin, one of the world’s leading researchers in the field of Parkinson’s disease, who arrived from Lund University<br />

in Sweden in January 2012. Dr. Brundin holds the Jay Van Andel Endowed Chair in Parkinson’s Research and also serves as<br />

VARI Associate Director.<br />

The VARI investigator staff welcomed two other distinguished members into its ranks in 2012. Jeremy Van Raamsdonk’s<br />

research focuses on aging, Parkinson’s disease, and Huntington’s disease. He heads the Laboratory of Aging and Neurodegenerative<br />

Disease, and in his translational research, positive results from studies in worm and mouse models will be used to<br />

identify therapeutic targets for clinical trials. Xiaohong Li leads the Laboratory for Tumor Microenvironment and Metastasis. Her<br />

research focuses on the role of stromal transforming growth factor (TGF-b) in the microenvironment of primary and metastatic<br />

tumor sites and its effect on bone metastases, with the aim of developing early diagnostic and treatment strategies for breast<br />

and prostate cancer metastasis to bone.<br />

The Institute hosted world-renowned researchers in 2012 and honored two of them for their contributions to science. In May<br />

2012, Dr. Phillip A. Sharp was the first recipient of the Institute’s Han-Mo Koo Memorial Award. Dr. Sharp received the 1993<br />

Nobel Prize in Physiology or Medicine for his discovery of RNA splicing, which fundamentally changed the understanding of<br />

gene structure. Much of his research has focused on the molecular biology of gene expression relevant to cancer. The Han-Mo<br />

Koo Award recipients are selected on the basis of their scientific achievements and contributions to human health and research.<br />

The award is named for one of VAI’s founding scientists who, in 2004 at the age of 40, succumbed to aggressive NK T-cell<br />

lymphoma, a rare form of cancer.<br />

The Van Andel Institute held the “Grand Challenges in Parkinson’s Disease” symposium in September 2012, gathering experts<br />

from nearly a dozen nations to present the latest research on this devastating disease. Dr. Ted Dawson of Johns Hopkins<br />

University and Dr. Roger Barker of the University of Cambridge provided keynote addresses. During the symposium, the<br />

Institute presented the inaugural Jay Van Andel Award for Outstanding Achievement in Parkinson’s Disease Research to Dr.<br />

Andrew B. Singleton of the National Institutes of Health. Dr. Singleton’s research focuses on the genetic causes of Parkinson’s<br />

disease, and he is actively studying the consequences of gene alterations in the context of the aging brain.<br />

VARI researchers in 2012 had much success in terms of funded grant proposals and sponsored research. Major grants<br />

included the following:<br />

• a four-year R01 renewal from the National Institutes of Health (NIH) to Bart Williams for the project entitled “Analyzing<br />

the Role of Wnt Signaling in Bone Development”;<br />

• a five-year R01 award to Cindy Miranti for a project on “The Role of a6b1 Integrin in Prostate Cancer”;<br />

• a three-year R01 award to Karsten Melcher for “Structural and Functional Analysis of a Dynamic ABA Signaling<br />

Complex”; and<br />

• a five-year NIH U01 award to Brian Haab for a project on “Targeted Glycomics and Affinity Reagents for Cancer<br />

Biomarker Development”.<br />


VARI | <strong>2013</strong><br />

In addition, Scott Jewell received several major contracts for the Program for Biospecimen Science, including one for “Research<br />

Studies in Cancer and Normal Tissue Acquisition and Processing Variables”. The Program for Biospecimen Science also<br />

became one of only seven biorepositories in the nation accredited by the College of American Pathologists (CAP), based on the<br />

results of an on-site inspection as part of the CAP Accreditation Program.<br />

VARI has announced an agreement with Dako, the Danish-based, worldwide supplier of cancer diagnostic tools, to license,<br />

manufacture, and distribute cancer diagnostics utilizing the MET4 antibody. This antibody, which detects the MET gene in<br />

human tumors, works exceptionally well in classical diagnostic procedures. MET4 was developed by the laboratories of George<br />

F. Vande Woude and Brian Cao of VARI and Beatrice Knudsen, formerly of the Fred Hutchinson Cancer Research Center.<br />

Among VARI research publications in 2012 was “Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C<br />

phosphatases”, co-authored by Fen-Fen Soon, Karsten Melcher, and Eric Xu and published in a January 2012 edition of<br />

Science. Abscisic acid (ABA) is a crucial plant hormone involved in stress adaptation. Activation of the signaling pathway<br />

for ABA includes the phosphorylation of pathway proteins by a SnRK kinase. In this paper, the authors determined that the<br />

SnRK kinase is turned off by the direct binding of the kinase activation loop into the catalytic cleft of a PP2C phosphatase<br />

as part of a two-step inactivation mechanism. The kinase is turned on when it is displaced from the phosphatase by the<br />

ABA hormone receptor complex. That displacement is the result of the similarity in PP2C recognition between the kinase<br />

molecule and the complex, which allows facile regulation of the kinase’s activity. This study provides a new paradigm of<br />

kinase–phosphatase regulation.<br />

Thanks to the achievements of new and existing programs, Van Andel Institute anticipates the continued growth and success<br />

of its research programs into cancer and neurodegenerative disease in <strong>2013</strong> and beyond. This growing intellectual capital<br />

complements the expansion of the Institute’s state-of-the-art facilities. At full capacity, Phase II will support a $125 million<br />

annual research operation that will expand the number of laboratories to more than 50 and provide some 550 additional jobs.<br />

Such growth is made possible, in part, by the Institute’s wide network of dedicated supporters. Thanks to the generous<br />

endowment of the Van Andel family, 100% of donor contributions go directly to the laboratories where VARI scientists seek<br />

discoveries leading to improved treatments for patients. That’s 100% to Research, Discovery, and Hope!<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />


Laboratory <strong>Report</strong>s<br />


Arthur S. Alberts, Ph.D.<br />

Laboratory of Cell Structure and Signal Integration<br />

Dr. Alberts received his Ph.D. in physiology and pharmacology from the<br />

School of Medicine at the University of California, San Diego in 1993. From<br />

1994-1997, he was an HHMI postdoctoral scholar in Richard Treisman’s lab<br />

at the Imperial Cancer Research Fund in London. Prior to joining VARI, he<br />

was in the laboratory of Frank McCormick at the University of California, San<br />

Francisco. Dr. Alberts joined VARI in January 2000; he was promoted in 2006<br />

to Associate Professor and to Professor in 2009. Dr. Alberts also directs the<br />

Flow Cytometry core facility.<br />

From left: Lash-Van Wyhe, Schepers, Goosen, Schumacher, Becker, Alberts, Howard, Rybski, LaGrone, Turner<br />

Staff Students Visiting Scientists<br />

Susan Goosen, M.B.A.<br />

Leanne Lash-Van Wyhe, Ph.D.<br />

Heather Schumacher, MT(ASCP)<br />

Lisa Becker<br />

Andrew Howard, B.A.<br />

Chantice LaGrone<br />

Kristin Rybski<br />

Alison Schepers<br />

Sarah Sternberger, M.S.<br />

Julie Davis Turner, Ph.D.<br />

Brad Wallar, Ph.D.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

• To investigate the genetic and molecular basis of disease arising from defects in the cell infrastructure, which comprises<br />

the microtubule and microfilament cytoskeletons.<br />

• To gain a full understanding of how cells spatially and temporally organize the signaling networks that are required for cell<br />

growth control and differentiation.<br />

We place a basic research focus on the intersection of Rho and Wnt signaling to the nucleus and on the cytoskeletal remodeling<br />

apparatus. We place a translational focus on targeted therapies that reinforce and/or repair the cell infrastructure.<br />

Our disease focus is the blood cancers that arise from cells of the bone marrow. We use genetic models of these diseases to<br />

test ideas generated by our molecular studies. These models will inform the development of novel diagnostic and therapeutic<br />

tools for treating these cancers.<br />

Recent Publications<br />

Touré, Fatouma, Günter Fritz, Qing Li, Vivek Rai, Gurdip Daffu, Yu Shan Zou, Rosa Rosario, Ravichandran Ramasamy,<br />

Arthur S. Alberts, Shi Fang Yan, et al. 2012. Formin mDia1 mediates vascular remodeling via integration of oxidative and signal<br />

transduction pathways. Circulation Research 110(10): 1279–1293.<br />

Alberts, Art, and Michael Way. 2011. Actin motility: formin a SCAry tail. Current Biology 21(1): R27–R30.<br />

He, Yuanzheng, Yong Xu, Chenghai Zhang, Xiang Gao, Karl J. Dykema, Katie R. Martin, Jiyuan Ke, Eric A. Hudson, Sok Kean<br />

Khoo, James H. Resau, et al. 2011. Identification of a lysosomal pathway that modulates glucocorticoid signaling and the<br />

inflammatory response. Science Signaling 4(180): ra44.<br />

Thomas, S.G., S.D.J. Calaminus, L.M. Machesky, A.S. Alberts, and S.P. Watson. 2011. G-protein coupled and ITAM receptor<br />

regulation of the formin FHOD1 through Rho kinase in platelets. Journal of Thrombosis and Haemostasis 9(8): 1648–1651.<br />


William H. Baer II, M.D., Pharm.D.<br />

VARI-ClinXus, LLC<br />

Dr. Baer joined ClinXus in 2009 as Executive Director and Chief Medical<br />

Officer. When ClinXus became VARI-ClinXus LLC in January 2011, Dr. Baer<br />

was appointed as an Associate Professor within VARI. Dr. Baer received<br />

his pharmacy degree from Duquesne University, the Pharm.D. from the<br />

West Virginia University, and his M.D. from West Virginia University School<br />

of Medicine. He practices internal medicine at Grand Valley Medical<br />

Specialists. His areas of interest and research development include<br />

pharmacogenetics, disease prevention and wellness, obesity, and nutrition.<br />

From left: Baer, Eckhardt, Rogers<br />

Staff<br />

Elizabeth Eckhardt, B.S.<br />

Lisa Moore, M.S.<br />

Daniel Rogers, B.S., CCRC<br />

Heidi Smith-Green, RN, B.S.N., B.S.W.<br />

Emily Vander Molen, B.A., CHRC, CIP<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

VARI-ClinXus, LLC, is a West Michigan translational research organization dedicated to benefiting human health and improving<br />

patient’s lives through early-phase and molecular-based trials that are fundamental to personalized medicine. VARI-ClinXus<br />

works with community partner institutions that are highly credentialed in areas of health care, early clinical development, clinical<br />

research, and academics. Through our network, we are able to provide client organizations with the many advantages of<br />

collective expertise to facilitate innovative clinical trials of diagnostics, devices, and biological agents and bring them to market<br />

in a more efficient time frame. We offer an integrated suite of services that includes protocol and project design, clinical trial<br />

development and implementation, state-of-the-art patient facilities and support, extensive molecular profiling capabilities, and<br />

a full breadth of integrated IT infrastructure.<br />

The comprehensive expertise of our partner institutions extends across a wide range of specialties, with an emphasis on<br />

oncologic and neurodegenerative medicine. Current partners include Advanced Radiology Services, Borgess Research<br />

Institute, Bronson Healthcare, Cancer and Hematology Centers of West Michigan, Ferris State University, Grand Valley Medical<br />

Specialists, Grand Valley State University, Innovative Analytics, Jasper Clinical Research & Development, Metro Health Hospital,<br />

Michigan Institute for Clinical & Health Research, Michigan State University, MPI Research, Saint Mary’s Health Care, and<br />

Spectrum Health hospitals.<br />

We have partnered with the Critical Path Institute’s Predictive Safety Testing Consortium (PSTC) in several capacities, and we<br />

provide clinical advice and support for PSTC’s clinical efforts in the evaluation and qualification of new biomarkers to assist in<br />

the safety of drug development. The PSTC’s mission is to bring pharmaceutical companies together to validate each other’s<br />

safety testing methods.<br />


John F. Bender, Pharm.D.<br />

Clinical Operations<br />

Dr. Bender holds a B.S. in biology from Mount Saint Mary’s College, a<br />

B.S. in pharmacy from the University of Maryland, and a Pharm.D. from<br />

the University of Utah. He worked at Parke-Davis as director of clinical<br />

research – oncology for over 20 years. Dr. Bender also served as senior<br />

vice-president of clinical research and of research and development at<br />

two biopharmaceutical companies in San Diego that focused on cancer<br />

treatments. He is currently the Clinical Operations Director at the Van Andel<br />

Research Institute. He is also an Adjunct Assistant Professor of Clinical<br />

Pharmacy with the Ferris State College of Pharmacy in Grand Rapids.<br />

Research Interests<br />

As VARI Clinical Operations Director, Dr. Bender coordinates the development of oncology clinical trials to accelerate<br />

translational research studies in Grand Rapids. He provides translational research support to VARI research, with active<br />

projects currently in eight labs. An effort underway is to establish a clinical trial center for VARI. Dr. Bender has an effective<br />

network of colleagues within Michigan and beyond, and he fosters productive interactions between VARI researchers,<br />

outside investigators, and the pharmaceutical and clinical communities.<br />

Staff<br />

Ashley Rodriguez<br />


Patrik Brundin, M.D., Ph.D.<br />

Laboratory for Translational Parkinson’s Disease Research<br />

Dr. Brundin earned both his M.D. and Ph.D. at Lund University, Sweden.<br />

He has over 30 years of experience with neurodegenerative diseases, has<br />

some 300 publications, and is in the top 0.5% of cited researchers in the<br />

field. Much of his research has addressed disease mechanisms in cell<br />

culture and animal models of Parkinson’s disease. In addition to managing<br />

laboratories at VARI and in Lund, Sweden, he is Associate Director of VARI<br />

and the co-editor-in-chief of the Journal of Parkinson’s Disease.<br />

From left: Kaufman, Beauvais, Brundin, Steiner, Cousineau, Ghosh<br />

Staff<br />

Genevieve Beauvais, Ph.D.<br />

Kim Cousineau, B.S.<br />

Martha Escobar, Ph.D.<br />

Anamitra Ghosh, Ph.D.<br />

Darcy Kaufman, M.S.<br />

Jennifer Steiner, Ph.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

The Laboratory for Translational Parkinson’s Disease Research studies cellular and rodent models of neurodegenerative<br />

disease. We currently focus on several projects that might lead us to our ultimate goals of 1) understanding why Parkinson’s<br />

disease (PD) develops and 2) discovering new methods of treatment that could stop or slow disease progression.<br />

We expect that these experiments will reveal how genetic and other factors are associated with PD pathology.<br />

Many rodent models of PD are based on treating the animals with neurotoxins such as 1-methyl-4-phenyl-1,2,3,6-<br />

tetrahydropyridine (MPTP) or 6-hydroxydopamine. These toxins lead to select neuronal degeneration within days in brain<br />

areas relevant to PD. However, we know that the development of PD in humans is a decades-long process of neuron<br />

death, unlike the short time line of days in these models. We have initiated work in a mouse that lacks one copy of a gene<br />

known to be expressed in midbrain dopaminergic neurons and that exhibits a progressive degeneration of these cells.<br />

As a consequence, the neurons’ slow degeneration over many weeks into adulthood more closely mirrors PD. In our<br />

studies, we are carefully analyzing the morphological and neurochemical changes in the degenerating dopamine neurons<br />

and trying to understand the changes in gene expression in the cells during the process. We believe these mice will be a<br />

highly relevant model of PD, and we are now planning to treat them with potentially neuroprotective agents over several<br />

weeks in attempts to slow down the degenerative process.<br />

We are also using a transformed cell line derived from the immature human ventral midbrain. We can differentiate these<br />

cells into mature dopaminergic neurons that exhibit the expected electrical activity and synthesize dopamine. We have<br />

previously identified the sensitivity of these human midbrain neurons to cellular toxins or stresses. This unique dopaminergic<br />

cell line serves as a starting point for many of our studies with both neurotoxins and neuroprotective agents. We aim to<br />

determine whether known neuroprotective drugs, some of which are currently in clinical trials, rescue these dopaminergic<br />

cells from PD-relevant challenges. If these human cells respond positively to these drugs, then we will test the agents in<br />

the mouse models described earlier. For example, disturbances in mitochondrial function are hypothesized to play an<br />

important role in the development of PD. Therefore we will explore whether drugs that modulate mitochondrial function<br />

can protect against neurodegeneration. Our current experiments using the genetic mouse models and toxin-based<br />

mouse models of PD described above will help us decide whether these mitochondrial modulators may be efficacious in<br />

the clinic.<br />

In order to study how PD develops, we also study the spreading of abnormal a-synuclein (a-syn) protein. The transmission<br />

of a-syn-associated pathology from cell to cell throughout the nervous system is believed to drive the clinical disease<br />

state and underlie several PD symptoms, including nonmotor symptoms. We are interested in identifying the mechanisms<br />

underlying intercellular a-syn transfer and transport in order to clarify their role(s) in the development of PD.<br />

We will partly focus on inter/intracellular transfer involving exosomes. We plan to perform studies using exosomes isolated<br />

under specific conditions (e.g., overexpression of a-syn) to determine whether exosomes play a role in a-syn transfer and<br />

aggregation. We will also explore the fate of a-syn that has been taken up by neurons. Thus, we will attempt to clarify<br />

how the imported a-syn is processed inside the cells and under what conditions it is transported between brain regions<br />

in rodents.<br />

In addition, we plan to use Caenorhabditis elegans to identify genes that control a-syn transfer between cells. We<br />

will generate transgenic C. elegans strains that will allow us to study a-syn transfer between neurons with the help of<br />

fluorescent markers.<br />


VARI | <strong>2013</strong><br />

Recent Publications<br />

Brundin, Patrik, and Jeffrey H. Kordower. In press. Neuropathology in transplants in Parkinson’s disease: implications for<br />

disease pathogenesis and the future of cell therapy. In Functional Neural Transplantation III, Amsterdam: Elsevier.<br />

Rey, Nolwen L., Elodie Angot, Christopher Dunning, Jennifer A. Steiner, and Patrik Brundin. In press. Accumulating evidence<br />

suggests that Parkinson’s disease is a prion-like disorder. In Research and Perspectives in Alzheimer’s Disease, Berlin: Springer.<br />

Tomé, Carla M. Lema, Trevor Tyson, Nolwen L. Rey, Stefan Grathwohl, Markus Britschgi, and Patrik Brundin. In press.<br />

Inflammation and a-synuclein’s prion-like behavior in Parkinson’s disease — is there a link? Molecular Neurobiology.<br />

Angot, Elodie, Jennifer A. Steiner, Carla M. Lema Tomé, Peter Ekström, Bengt Mattsson, Anders Björklund, and Patrik Brundin.<br />

2012. Alpha-synuclein cell-to-cell transfer and seeding in grafted dopaminergic neurons in vivo. PLoS One 7(6): e39465.<br />

Jeon, Iksoo, Nayeon Lee, Jia-Yi Li, In-Hyun Park, Kyoung Sun Park, Jisook Moon, Soung Han Shim, Chunggab Choi,<br />

Da-Jeong Chang, Jihye Kwon, et al. 2012. Neuronal properties, in vivo effects, and pathology of a Huntington’s disease<br />

patient-derived induced pluripotent stem cells. Stem Cells 30(9): 2054–2062.<br />

Paul, Gesine, Ilknur Özen, Nicolaj S. Christophersen, Thomas Reinbothe, Johan Bengzon, Edward Visse, Kararina Jansson,<br />

Karin Dannaeus, Catarina Henriques-Oliveira, Laurent Roybon, et al. 2012. The adult human brain harbors multipotent<br />

perivascular mesenchymal stem cells. PLoS One 7(4): e35577.<br />

Tyson, Trevor, and Patrik Brundin. 2012. VPS41-mediated neuroprotection in a Caenorhabditis elegans model of Parkinson’s<br />

disease. Future Neurology 7(3): 255–258.<br />


Ting-Tung (Anthony) Chang, Ph.D.<br />

Small-Animal Imaging Facility/Laboratory of Translational Imaging<br />

Dr. Chang received a B.S. degree in medical imaging and radiological<br />

sciences from Chang Gung University (Taoyuan, Taiwan) and his Ph.D.<br />

degree in medical physics (CAMPEP), specializing in diagnostic imaging<br />

physics, from the University of Texas Health Science Center at San Antonio.<br />

He received advanced imaging training at Yale University and at the<br />

Vanderbilt University Institute of Imaging Science. Dr. Chang joined VARI in<br />

2010 as a Research Assistant Professor and Director of the Small-Animal<br />

Imaging Facility.<br />

From left: Bozio, Dieffenbach, Dykstra, Peck, Li, Holly, Chang, Nelson<br />

Staff<br />

Students<br />

Visiting Scientist<br />

Adjunct Faculty<br />

Shihong Li, Ph.D.<br />

Amy Nelson<br />

Anderson Peck, M.S.E.<br />

Ryan Bozio, B.S.<br />

Zachary Dieffenbach<br />

Michael Dykstra<br />

Brittany Holly<br />

Yasmeen Robinson<br />

Samhita Rhodes, Ph.D.<br />

Ewa Komorowska-Timek, M.D.<br />

Zheng (Jim) Wang, Ph.D.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

The Small-Animal Imaging Facility provides novel imaging and image analysis tools for use with biology specimens and small<br />

animals. Our instruments include digital X-ray, high-resolution microCT, microSPECT/CT, microPET/CT, micro-ultrasound, and<br />

optical imaging. Our research focuses on the development of new preclinical imaging technologies that can offer significant<br />

anatomic and functional information to biomedical investigators.<br />

The Laboratory of Translational Imaging aims at developing imaging technologies capable of monitoring organ/tissue activity<br />

at the molecular level. We intend these developments to be highly translatable into clinical use, especially for tumor early<br />

detection and staging. Combining tracer development, imaging analysis, and genomic information, we are dedicated to collecting<br />

medically useful information through novel, non-invasive imaging technologies that will advance the goal of personalized<br />

precision medicine.<br />

Recent Publications<br />

Flaten, Gøril Eide, Ting-Tung Chang, William T. Phillips, Martin Brandl, Ande Bao, and Beth Goins. In press. Liposomal<br />

formulations of poorly soluble camptothecin: drug retention and biodistribution. Journal of Liposome Research.<br />

Figure 1<br />

Figure 1. Three-dimensional imaging<br />

of a kidney cyst in vivo using contrastenhanced<br />

computed tomography (CT).<br />


Nicholas S. Duesbery, Ph.D.<br />

Laboratory of Cancer and Developmental Cell Biology<br />

Dr. Duesbery received a B.Sc. (Hon.) in biology (1987) from Queen’s<br />

University, Canada, and both his M.Sc. (1990) and Ph.D. (1996) degrees<br />

in zoology from the University of Toronto under the supervision of Yoshio<br />

Masui. Before his appointment at VARI in 1999, he was a postdoctoral<br />

fellow in George Vande Woude’s laboratory at the National Cancer Institute,<br />

Frederick Cancer Research and Development Center, Maryland. Dr.<br />

Duesbery was promoted to Associate Professor in 2006, and he chairs<br />

VARI’s Council for Research Affairs.<br />

From left: Duesbery, Boguslawski, Bromberg-White, Lewis, Kuk, Andersen, Bhattacharya, Naidu<br />

Staff<br />

Nicholas Andersen, Ph.D.<br />

Poulomi Bhattacharya, Ph.D.<br />

Elissa Boguslawski<br />

Jenn Bromberg-White, Ph.D.<br />

Kara Kits, Ph.D.<br />

Diana Lewis, A.S.<br />

Students<br />

Cynthia Kuk, B.S.<br />

Agni Naidu, B.S., B.A.<br />

Adjunct Faculty<br />

Christopher Chambers, M.D., Ph.D.<br />

Lou Glazer, M.D.<br />

Barbara Kitchell, D.V.M., Ph.D., DACVIM<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

Our lab is interested in a family of related proteins called the mitogen-activated protein kinase kinases (MKKs). MKKs are<br />

evolutionarily conserved, regulatory protein kinases that play pivotal roles in a wide variety of developmental cellular processes,<br />

including growth, division, and differentiation. Our lab is specifically interested in the roles of these kinases in the developmental<br />

and pathologic growth of blood vessels.<br />

More than a decade ago we showed that blocking the activity of MKKs in tumors caused decreased blood flow and tumor<br />

regression. Since then we have used a variety of experimental approaches to understand how the loss of MKK activity affects<br />

the growth of blood vessels. Most recently we discovered that MKK activity was essential for the regrowth of blood vessels in a<br />

mouse model of diabetic retinopathy. Our results suggest that the inhibition of MKK activity may be a good strategy for treating<br />

eye diseases such as proliferative diabetic retinopathy or wet macular degeneration. We are currently exploring this possibility<br />

in collaboration with Grand Rapids ophthalmologist Dr. Louis Glazer.<br />

In some cases the abnormal growth of cells that form blood vessels results in cancer. These tumors, called angiosarcomas,<br />

are an extremely rare but deadly form of cancer for which there is no effective treatment. In collaboration with Dr. Barbara<br />

Kitchell at the Michigan State University College of Veterinary Medicine, Dr. Laurence Baker at the University of Michigan, and<br />

Dr. Gary Schwartz at the Memorial Sloan – Kettering Cancer Center, we have discovered that MKK activity plays an essential<br />

role in the growth of these tumors. On-going studies in our lab are using unique mouse models we have developed to identify<br />

combinatorial approaches for treating these tumors.<br />

While excessive blood vessel growth is characteristic of cancer and retinal diseases, decreased blood flow is a crucial factor<br />

in peripheral arterial disease. This disease, often associated with obesity, diabetes, and smoking, is caused by blood vessel<br />

obstruction and a diminished ability to grow or expand existing blood vessels. Together with Dr. Christopher Chambers, a<br />

cardiovascular surgeon at the Meijer Heart and Vascular Institute, we have begun an exciting new research project involving<br />

human clinical samples to investigate the molecular biology of peripheral arterial disease.<br />

The goals of the lab in the coming years are to<br />

• Define the key roles of MKKs in developmental and pathologic growth of blood vessels, using models of retinal disease<br />

and peripheral arterial disease<br />

• Identify novel anti-angiogenic targets<br />

• Discover and validate genetic and biochemical drivers of site-specific disease in angiosarcoma<br />

• Translate these findings to improve the clinical care of patients.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Figure 1<br />

Figure 1: MKK activity is essential for blood vessel growth. In a model that mimics diabetic retinopathy, blood vessels in these<br />

mouse retina whole mounts show regrowth following oxygen deprivation (left panel). Such regrowth is prevented (right panel)<br />

in retinas treated with anthrax lethal toxin, an MKK inhibitor. Such inhibitors may have utility in treating human eye diseases<br />

such as proliferative diabetic retinopathy. Photographs by Jennifer Bromberg-White (Bromberg-White et al., 2011, Investigative<br />

Ophthalmology and Visual Science 52: 8979); ©Association for Research in Vision and Ophthalmology.<br />

Recent Publications<br />

Bromberg-White, Jennifer L., Nicholas J. Andersen, and Nicholas S. Duesbery. 2012. MEK genomics in development and<br />

disease. Briefings in Functional Genomics 11(4): 300–310.<br />

Andersen, Nicholas, Roe Froman, B. Ketchell, and Nicholas S. Duesbery. 2011. Angiosarcoma: clinical and molecular<br />

aspects. In Soft Tissue Sarcoma, Austria: I-Tech Education and Publishing, pp. 149–174.<br />

Bromberg-White, Jennifer L., Elissa Boguslawski, Daniel Hekman, Eric J. Kort, and Nicholas S. Duesbery. 2011. Persistent<br />

inhibition of oxygen-induced retinal neovascularization by anthrax lethal toxin. Investigative Ophthalmology and Visual<br />

Science 52(12): 8979–8992.<br />

Lee, Chih-Shia, Karl J. Dykema, Danielle M. Hawkins, David M. Cherba, Craig P. Webb, Kyle A. Furge, and Nicholas S.<br />

Duesbery. 2011. MEK2 is sufficient but not necessary for proliferation and anchorage-independent growth of SK-MEL-28<br />

melanoma cells. PLoS One 6(2): e17165.<br />


Bryn Eagleson, B.S., RLATG<br />

Vivarium and Laboratory of Transgenics<br />

Ms. Eagleson began her career in laboratory animal services with Litton<br />

Bionetics at the National Cancer Institute’s Frederick Cancer Research and<br />

Development Center (NCI-FCRDC) in Maryland. She later worked at the<br />

Johnson & Johnson Biotechnology Center in San Diego, California. In 1988,<br />

she returned to the NCI-FCRDC as manager of the transgenic mouse colony.<br />

In 1999, Ms. Eagleson was recruited to VARI as the Vivarium Director and<br />

Transgenics Special Program Manager. She has a B.S. degree in psychology<br />

from the University of Maryland University College. Ms. Eagleson is a member<br />

of the IACUC and has served two terms as its chair.<br />

Standing, from left: Kefene, Guikema, Boguslawski, Post, Ramsey, Meringa, Baumann, B. Eagleson, Timmer, Stroben, Vrbis, K. Eagleson,<br />

Brady, Ehrke Kneeling, from left: Kempston, Rackham, Brandow, Holzgen<br />

Research<br />

Technicians<br />

Laboratory<br />

Animal Technicians<br />

Animal Caretaker<br />

Staff<br />

Audra Guikema, B.S., LVT<br />

Tristan Kempston, B.S.<br />

Kristen Baumann, B.S.<br />

Elissa Boguslawski<br />

Susan Budnick, B.S.<br />

Lisa Kefene, B.S.<br />

Tina Meringa, A.S.<br />

Janelle Post, B.S.<br />

Lisa Ramsey, A.S., LVT<br />

Sylvia Timmer, Vivarium Supervisor<br />

Crystal Brady<br />

Neil Brandow<br />

Kendra Eagleson<br />

Crystal Ehrke<br />

Katie Holzgen<br />

Mat Rackham<br />

Brandon Stroben<br />

Ashlee Vrbis<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

The goal of the VARI vivarium and transgenics core is to develop, provide, and support high-quality mouse modeling services<br />

for the VARI investigators, collaborators, and the greater research community. The vivarium is a state-of-the-art facility that<br />

includes a high-level containment barrier. All procedures are conducted according to the NIH Guide for the Care and Use<br />

of Laboratory Animals. Because we understand the importance of excellence in animal care to producing quality research,<br />

we are committed to the highest quality in animal standards, and the Van Andel Research Institute is an AAALAC-accredited<br />

institution. The staff provides rederivation, surgery, dissection, necropsy, breeding, weaning, tail biopsies, sperm and embryo<br />

cryopreservation, animal data management, and health-status monitoring. Transgenic mouse models are produced on request<br />

for project-specific needs.<br />

Transgenics<br />

Fertilized eggs contain two pronuclei, one that is derived from the egg and contains the maternal genetic material and one<br />

derived from the sperm that contains the paternal genetic material. As development proceeds, these two pronuclei fuse,<br />

the genetic material mixes, and the cell proceeds to divide and develop into an embryo. Transgenic mice are produced by<br />

injecting small quantities of foreign DNA (the transgene) into a pronucleus of a one-cell fertilized egg. DNA microinjected into a<br />

pronucleus randomly integrates into the mouse genome and will theoretically be present in every cell of the resulting organism.<br />

Expression of the transgene is controlled by elements called promoters that are genetically engineered into the transgenic<br />

DNA. Depending on the selection of the promoter, the transgene can be expressed in every cell of the mouse or in specific cell<br />

populations such as neurons, skin cells, or blood cells. Temporal expression of the transgene during development can also<br />

be controlled by genetic engineering. These transgenic mice are excellent models for studying the expression and function of<br />

the transgene in vivo.<br />

Gene targeting<br />

Mouse models are produced using gene-targeting technology, a well-established, powerful method for inserting specific<br />

genetic changes into the mouse genome. The resulting mice can be used to study the effects of these changes in the complex<br />

biological environment of a living organism. The genetic changes can include the introduction of a gene into a specific site in<br />

the genome (gene “knock-in”) or the inactivation of a gene already in the genome (gene “knock-out”). Since these mutations<br />

are introduced into the reproductive cells known as the germline, they can be used to study the developmental aspects of gene<br />

function associated with inherited genetic diseases.<br />

The vivarium and transgenics lab can also produce mouse models in which the gene of interest is inactivated in a target organ<br />

or cell line instead of in the entire animal. These models, known as conditional knock-outs, are particularly useful in studying<br />

genes that, if missing, cause the mouse to die as an embryo.<br />

Our gene-targeting service encompasses three major procedures: DNA electroporation, clone expansion and cryopreservation,<br />

and microinjection. Gene targeting is initiated by mutating the genomic DNA of interest and inserting it into mouse embryonic<br />

stem (ES) cells via electroporation. The mutated gene integrates into the genome and, by a process called homologous<br />

recombination, replaces one of the two wild-type copies of the gene in the ES cells. Clones are identified, isolated, and<br />

cryopreserved, and genomic DNA is extracted from each clone and delivered to the client for analysis. Correctly targeted ES<br />

cell clones are thawed, established into tissue culture, and cryopreserved in liquid nitrogen. Gene-targeting mutations are<br />

introduced by microinjection of the pluripotent ES cell clones into 3.5-day-old mouse embryos (blastocysts). These embryos,<br />

containing a mixture of wild-type and mutant ES cells, develop into mice called chimeras. The offspring of chimeras that inherit<br />

the mutated gene are heterozygotes possessing one copy of the mutated gene. The heterozygous mice are bred together to<br />

produce “knock-out mice” that completely lack the normal gene and have two copies of the mutant gene.<br />


VARI | <strong>2013</strong><br />

Embryo/sperm cryopreservation<br />

We provide cryopreservation services for archiving and reconstituting valuable mouse strains. These cost-effective procedures<br />

decrease the need to continuously breed valuable mouse models, and they provide added insurance against the loss of custom<br />

mouse lines due to disease outbreak or a catastrophic event. Mouse embryos at various stages of development, as well as<br />

mouse sperm, can be cryopreserved and stored in liquid nitrogen; they can be thawed and used, respectively, by implantation<br />

into the oviducts of recipient mice or by in vitro fertilization of oocytes.<br />

Rederivation<br />

Mice harboring pathogens can negatively affect research results, and they may pass on those pathogens to other mice within<br />

the colony. Strain rederivation, by embryo transfer, is a management tool to clean a mouse line from pathogen infection or to<br />

import mice into a barrier facility from outside the vivarium. At VARI, any mice imported from an outside research institution are<br />

rederived to ensure the specific pathogen-free status of the animals coming in, and also to ensure that our existing research<br />

models remain pathogen-free.<br />


Kyle A. Furge, Ph.D.<br />

Laboratory of Interdisciplinary Renal Oncology<br />

Dr. Furge received his Ph.D. in biochemistry from the Vanderbilt University<br />

School of Medicine in 2000. Prior to obtaining his degree, he worked as<br />

a software engineer at YSI, Inc., where he wrote operating systems for<br />

remote environmental sensors. Dr. Furge did his postdoctoral work in the<br />

laboratory of George Vande Woude. He joined VARI in June 2001 and was<br />

promoted to Assistant Professor in May 2005. Dr. Furge also heads the<br />

Kidney Cancer Research Program.<br />

From left: Ooi, Petillo, Furge, Dykema<br />

Staff<br />

Karl Dykema, B.A.<br />

Aikseng Ooi, Ph.D.<br />

David Petillo, Ph.D.<br />

Adjunct Faculty<br />

Richard Kahnoski, M.D.<br />

Brian Lane, M.D., Ph.D.<br />

Bin Teh, M.D., Ph.D.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

Renal cell carcinoma (RCC) is the most common type of cancer that arises within the adult kidney, and the tumors can be<br />

separated into categories based on the morphology of their cells. Clear cell RCC is the most common subtype, constituting<br />

70–80% of renal tumors. Papillary RCC, which can be divided into type 1 and type 2, is the next most common subtype,<br />

representing 10–15%. Chromophobe RCC represents about 5% of renal tumors; other renal cell carcinomas are either unclassifiable<br />

by conventional means or represent rare subtypes. The latter include transitional cell carcinoma of the renal pelvis, renal<br />

medullary tumor, tubulocystic carcinoma, Xp11.2 translocation-associated tumor, collecting duct tumor, adult Wilms tumor,<br />

mixed epithelial and stromal tumor/cystic nephroma, and the usually benign renal oncocytoma and angiomyolipoma.<br />

Several decades of kidney cancer research indicate that the genetic mutations that accumulate within the tumor cells differ<br />

depending on the particular subtype. Overall, the laboratory is interested in identifying the genetic mutations present in renal<br />

cancer cells and in understanding how the different mutations transform normal cells into cancerous cells. We also want to<br />

understand the features associated with the most aggressive renal tumors.<br />

The analysis of papillary type 2 tumors (PRCC2) is one current focus. This is an aggressive subtype that has no effective<br />

treatment. Individuals who inherit a rare germline mutation in the fumarate hydratase gene (FH) are predisposed to develop this<br />

cancer. However, most PRCC2 tumors arise in the general population and do not contain that mutation. The genetic defects<br />

that lead to formation of sporadic PRCC2 tumors in the general population are not known.<br />

We have recently discovered that the transcription factors NRF1 and NRF2 (nuclear factor–erythroid-related factors 1 and<br />

2) are activated in type 2 papillary RCC but not other subtypes of RCC. NRFs are key mediators of the adaptive detoxification<br />

response, and they regulate the many aspects of cellular detoxification and cell metabolism. NRF1 and NRF2 become<br />

activated as cells are exposed to electrophilic and reactive oxygen insults. NRFs then activate the transcription of a crucial set<br />

of enzymes that promotes cell survival by clearing toxic metabolites and xenobiotics.<br />

The FH mutations present in hereditary PRCC2 tumors result in high levels of intercellular fumarate. We have found that the<br />

NRF transcription factors become activated as fumarate, a reactive molecule, chemically modifies proteins at their exposed<br />

cysteine residues, a process termed succination (Figure 1). The modification of proteins by fumarate leads to NRF activation<br />

in these tumors. Sporadic PRCC2 tumors frequently lack FH mutations, so the mechanisms by which NRF is activated in<br />

these tumors is unclear. Both the mechanism by which NRF activation occurs in PRCC2 tumors and the functional connection<br />

between NRF activation and tumor cell survival are current focuses of the laboratory.<br />

We are also interested in the genetic mechanisms that give rise to the chromophobe subtype of renal tumors. Individuals who<br />

inherit a rare germline mutation in the folliculin gene (FLCN) are predisposed to chromophobe renal cancer. The mRNA profiles<br />

of tumors from such individuals gave clues that FLCN has a role in the energy sensing network, particularly in mitochondrial<br />

function. The connection between FLCN loss of function and tumor cell development is another focus.<br />

The tools that we use to study renal tumor development include a blend of computational modeling, molecular biology, and<br />

genetics. The genetic analysis of tumor cells typically includes the analysis of large amounts of DNA sequencing, mRNA<br />

expression profiling, and DNA copy number data. Therefore, we develop and apply new computational tools that can assist in<br />

extracting the significant biological information from these data sets, with a goal of understanding how cancer cells differ from<br />

normal cells at the molecular level.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Figure 1<br />

Figure 1: Mechanism of NRF2 activation in hereditary papillary renal cell carcinoma. NRF2 is a transcription factor that can<br />

migrate to the nucleus and activate the transcription of detoxification genes such as AKR1B10. Low levels of NRF2 are maintained<br />

by KEAP1 and CUL3. KEAP1 and CUL3 are required for NRF2 ubiquitination and degradation. This process is disrupted in cells<br />

with fumarate hydratase (FH) mutations. The normal biochemical activity of fumarate hydratase and succinate dehydrogenase are<br />

shown as part of the mitochondrial TCA cycle. In cells with FH mutation, excess fumarate is exported from the mitochondria and<br />

reacts with cysteine residues on KEAP1 (rounded rectangle). Modified KEAP1 is ubiquitinated and degraded. This prevents NRF2<br />

from being degraded, and so nuclear levels of NRF2 increase.<br />

Recent Publications<br />

Farber, Leslie J., Kyle Furge, and Bin Tean Teh. 2012. Renal cell carcinoma deep sequencing: recent developments.<br />

Current Oncology <strong>Report</strong>s 14(3): 240–248.<br />

Klomp, Jeff A., and Kyle A. Furge. 2012. Genome-wide matching of genes to cellular roles using guilt-by-association<br />

models derived from single sample analysis. BMC Research Notes 5: 370.<br />

Ong, Choon Kiat, Chutima Subimerb, Chawalit Pairojkul, Sopit Wongkham, Ioana Cutcutache, Willie Yu, John R. McPherson,<br />

George E. Allen, Cedric Chuan Young Ng, Bernice Huimin Wong, et al. 2012. Exome sequencing of liver fluke-associated<br />

cholangiocarcinoma. Nature Genetics 44(6): 690–693.<br />

Zhang, Yu-Wen, Ben Staal, Karl J. Dykema, Kyle A. Furge, and George F. Vande Woude. 2012. Cancer-type regulation of<br />

MIG-6 expression by inhibitors of methylation and histone deacetylation. PLoS One 7(6): e38955.<br />


Brian B. Haab, Ph.D.<br />

Laboratory of Cancer Immunodiagnostics<br />

Dr. Haab earned his Ph.D. in chemistry from the University of California,<br />

Berkeley in 1998, after which he was a postdoctoral fellow in the laboratory<br />

of Patrick Brown in the Department of Biochemistry at Stanford University.<br />

Dr. Haab joined VARI in May 2000 and was promoted to Associate Professor<br />

in 2007.<br />

From left, front row: Nelson, Partyka, Bartlam, Tang, Brouhard, Ma; back row: McDonald, Curnutte, Sinha, Haab, Cao, Westra<br />

Staff<br />

Betsy Brouhard, B.S.<br />

Zheng Cao, Ph.D.<br />

Bryan Curnutte, B.S.<br />

Amy Nelson<br />

Katie Partyka, B.S.<br />

Huiyuan Tang, Ph.D.<br />

Students<br />

Heather Bartlam, B.S.<br />

Yinjiao Ma, M.S.<br />

Mitch McDonald<br />

Arkadeep Sinha, B.S.<br />

Hannah Westra<br />

Visiting Scientist<br />

David Nowack, Ph.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

The Haab laboratory studies pancreatic cancer, with the aims of identifying molecular factors that characterize and promote<br />

cancer progression and of using this information to more accurately diagnose and guide the treatment of pancreatic cancer.<br />

Diagnostics for pancreatic cancers<br />

Modern medicine increasingly relies on detailed molecular information to make accurate diagnoses and treatment decisions.<br />

A molecular-level understanding of healthy versus diseased human tissue promises to provide much more information about<br />

the patient than conventional clinical approaches. The development of improved tools for assessing pancreatic cancer is one<br />

of our main goals.<br />

For certain patients, there are serious difficulties in distinguishing pancreatic cancer from benign conditions of the pancreas.<br />

Some patients have abnormalities that are difficult to diagnose using imaging and biopsy procedures, and the diagnostic<br />

work-up process can be highly invasive, costly, and even after using all available methods, inconclusive. A blood test that could<br />

clearly resolve the differences between malignant and benign conditions of the pancreas would alleviate this situation.<br />

We are working to develop such a blood test based on changes to the carbohydrates (glycans) that are abnormally produced<br />

in pancreatic cancers. These structures are attached to a variety of proteins, some of which are secreted and detectable in<br />

the blood. An FDA-approved test is available for the CA 19-9 antigen, the most common carbohydrate antigen made by<br />

pancreatic cancers, but that test has limited value because some 20% of cancers produce low amounts of CA 19-9. Our<br />

studies have shown that the cancers that do not produce much CA 19-9 instead overproduce other structures, and we<br />

propose that assays to detect the alternate structures plus the CA 19-9 antigen will accurately identify a higher percentage of<br />

cancer patients. We are working with our clinical collaborators at the University of Pittsburgh, the University of Michigan, and<br />

in Grand Rapids to test this strategy.<br />

Another diagnostic problem is found with patients who have fluid-filled openings, known as pancreatic cysts, within their<br />

pancreas. Some cysts are unlikely to ever develop into cancer, while others may progress rapidly to cancer. Current diagnostic<br />

methods can not clearly differentiate these types. We are working with our collaborators to analyze the proteins and<br />

carbohydrates in fluid collected from the cysts, which could result in tests to determine which patients should have those<br />

cysts removed.<br />

We also are applying these approaches to related problems in pancreatic cancer, such as determining which patients should<br />

have surgery as opposed to chemotherapy only, and monitoring how well a patient is responding to treatment. A future goal<br />

is to use our new markers to detect incipient disease among people at a high risk for developing pancreatic cancer, such as<br />

those with predisposing genetic characteristics.<br />

Glycans in pancreatic ductal adenocarcinoma<br />

The goals described above will be advanced by further characterizing the changes in glycans as cancer cells develop and<br />

by understanding the cellular processes that result in those changes. We are using novel tools (described below) as well as<br />

powerful mass-spectrometry methods to compare the carbohydrates between tumors that produce CA 19-9 and those that do<br />

not. In addition, we are controlling the production of CA 19-9 in cultured cells or in mouse hosts to identify what carbohydrate<br />

structures are produced when CA 19-9 production is reduced. That control is based on manipulating specific genes involved<br />

in the production of CA 19-9. Our aim is to determine which genes are most important in producing the glycan structures.<br />


VARI | <strong>2013</strong><br />

Genetics and phenotypes of cancer cell subsets<br />

Not all cancer cells within a tumor are equivalent. The more advanced and aggressive cells are proposed to be primarily<br />

responsible for the migration and spread of cancer (metastasis) and for resistance to chemotherapeutics. An improved understanding<br />

of the molecular characteristics and origins of these subtypes could help to specifically eliminate them.<br />

We have approached this problem by comparing the molecular characteristics of pancreatic cancer cells that appear mesenchymal<br />

(migratory) to those that appear epithelial (stationary), and we have identified several consistent differences. One<br />

difference is the overexpression of the cell surface protein MRC2 in mesenchymal-like cancer cells. MRC2 has a primary<br />

function of helping cells to recognize and degrade the extracellular matrix that surrounds them. We now are investigating<br />

whether MRC2 is specifically up-regulated in pancreatic cancer cells that are transitioning to a mesenchymal state.<br />

Another difference is in the particular genetic alterations characteristic of mesenchymal-like cancer cells. We are determining<br />

which of those alterations are most prevalent in primary tumors and which contribute to the behavioral changes of the cancer<br />

cells. We plan to build on these studies to improve methods for assessing and treating pancreatic cancer.<br />

New tools for studying specific carbohydrate structures<br />

We are developing novel methods for studying carbohydrates in human tissue samples. In particular, we are developing new<br />

molecular reagents that bind specific carbohydrate structures and so can be used to detect and measure them. Such reagents<br />

are unavailable for many carbohydrates that may be overexpressed in cancer tissue. We are using new bioinformatics methods<br />

developed by us and collaborators that allow us to search publicly available information on naturally occurring proteins that<br />

have carbohydrate-binding properties. Once we identify potentially useful reagents, we test them with our antibody and protein<br />

array technologies, optimize them, and then evaluate them in the analysis of carbohydrates in clinical specimens. These tools<br />

have value for our pancreatic cancer studies and the potential for broader scientific use in various glycobiology studies.<br />

Recent Publications<br />

Haab, B. 2012. Using lectins in biomarker research: addressing the limitations of sensitivity and availability. Proteomics<br />

Clinical Applications 6(7-8): 346–350.<br />

Partyka, Katie, Kevin A. Maupin, Randall E. Brand, and Brian B. Haab. 2012. Diverse monoclonal antibodies against the<br />

CA 19-9 antigen show variation in binding specificity with consequences for clinical interpretation. Proteomics 12(13):<br />

2212–2220.<br />

Partyka, Katie, Mitchell McDonald, Kevin A. Maupin, Randall Brand, Richard Kwon, Diane M. Simeone, Peter Allen, and Brian<br />

B. Haab. 2012. Comparison of surgical and endoscopic sample collection for pancreatic cyst fluid biomarker identification.<br />

Journal of Proteome Research 11(5): 2904–2911.<br />

Maupin, Kevin A., Daniel Liden, and Brian B. Haab. 2011. The fine specificity of mannose-binding and galactose-binding<br />

lectins revealed using outlier motif analysis of glycan array data. Glycobiology 22(1): 160–169.<br />

Yue, Tingting, Kevin A. Maupin, Brian Fallon, Lin Li, Katie Partyka, Michelle A. Anderson, Dean E. Brenner, Karen Kaul,<br />

Herbert Zeh, A. James Moser, et al. 2011. Enhanced discrimination of malignant from benign pancreatic disease by<br />

measuring the CA 19-9 antigen on specific protein carriers. PLoS One 6(12): e29180.<br />


Galen H. Hostetter, M.D.<br />

Laboratory of Analytical Pathology<br />

Dr. Hostetter received his M.D. degree from the University of Pennsylvania<br />

in 1993, and he is board-certified in pathology. He has completed medical<br />

and cancer genetics fellowships at the National Institutes of Health. His<br />

primary research interest has been applications of genomic assays and<br />

validation in clinical samples using tissue microarrays. He was staff<br />

pathologist at the Translational Genomics Research Institute (TGen) from<br />

2003 to 2011. Dr. Hostetter joined VARI in 2011 as an Assistant Professor<br />

and head of the Laboratory of Analytical Pathology within the Program for<br />

Biospecimen Science (PBS).<br />

Staff<br />

Bree Berghuis, B.S., HTL(ASCP), QIHC<br />

Eric Hudson, B.S.<br />

Lisa Turner, B.S., ST(ASCP), QIHC<br />

Students<br />

Eric Edewaard<br />

Peter Varlan<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

As head of the Laboratory of Analytical Pathology, Dr. Hostetter provides histology and pathology review for a wide range<br />

of tissue-based studies performed in VARI laboratories. Services provided include high-quality histology, diagnostic tissue<br />

review, morphometric analysis, immunohistochemistry, in situ hybridization, tissue microarrays, digital imaging and analysis<br />

by light, and spectral and confocal microscopy. Arcturus integrated laser-capture microdissection, isolation of nucleic acids<br />

and proteins from cells and tissue, and whole-cell antibody-specific isolation/purification are also provided. Zeiss and Nikon<br />

confocal microscopes are used. The Zeiss 510 multi-photon scope is equipped with both a Ti-sapphire pulse laser and a<br />

Meta-detector, which enables investigators to view simultaneously as many as eight fluorophores at the cellular and molecular<br />

level. The Nikon A1 confocal system provides static and live-cell imaging. The lab also has a CRi Nuance spectral imaging<br />

system to enable researchers to quantify chromic-dyed histological preparations.<br />

Dr. Hostetter’s research addresses the effects of preanalytic variables in the collection and transport of biosamples. Ongoing<br />

research includes the development and validation of novel liquid-based collection media with a focus on macroanalyte yield and<br />

integrity. This research contributes to the emerging field of biospecimen science and will determine the extent of experimental<br />

biases related to macroanalyte integrity, an ever-constant challenge in both the research laboratory and the clinical laboratory.<br />

Interactions with various core facilities and services include macroanalyte (DNA, RNA, protein) extractions suitable for<br />

downstream assays, with a focus on optimized and standardized protocols. Dr. Hostetter works closely with the excellent<br />

histotechnical staff within the PBS to provide top-quality, accurate, and interpretable results for use in clinical applications.<br />

For example, an immunohistochemical assay on a tissue section detects expression of a candidate protein identified in the<br />

research laboratory; the result is validated with an automated immunostainer that mimics the workflow in the hospital pathology<br />

department, thereby translating research findings into potential clinical care practices. Additionally, tissue microarrays can<br />

be used to determine the prevalence of a given expressed protein in specific tumor types, and standardized measures of<br />

staining intensity can be determined using high-resolution digital image scanners and semi-quantitative algorithms. Interactive<br />

collaborative efforts with clinical partners of VARI provide continuing opportunities and challenges that focus on improving<br />

patient care.<br />

Recent Publications<br />

Demeure, Michael J., Elizabeth Stephen, Shripad Sinari, David Mount, Steven Gately, Paul Gonzales, Galen Hostetter, Richard<br />

Komorowski, Jeff Kiefer, Clive S. Grant, et al. 2012. Preclinical investigation of nanoparticle albumin-bound paclitaxel as a<br />

potential treatment for adrenocortical cancer. Annals of Surgery 255(1): 140–146.<br />

Stephens, Bret, Stephen P. Anthony, Haiyong Han, Jeffrey Kiefer, Galen Hostetter, Michael Barrett, and Daniel D. Von Hoff.<br />

2012. Molecular characterization of a patient’s small cell carcinoma of the ovary of the hypercalcemic type. Journal of Cancer<br />

3: 58–66.<br />

Weiss, Glen J., Winnie S. Liang, Tyler Izatt, Shilpi Arora, Irene Cherni, Robert N. Raju, Galen Hostetter, Ahmet Kurdoglu,<br />

Alexis Christoforides, Shripad Sinari, et al. 2012. Paired tumor and normal whole genome sequencing of metastatic olfactory<br />

neuroblastoma. PLoS One 7(5): e37029.<br />

Whitsett, Timothy G., Emily Cheng, Landon Inge, Kaushal Asrani, Nathan M. Jameson, Galen Hostetter, Glen J. Weiss,<br />

Christopher B. Kingsley, Joseph C. Loftus, Ross Bremner, et al. 2012. Elevated expression of Fn14 in non-small cell<br />

lung cancer correlates with activated EGFR and promotes tumor cell migration and invasion. American Journal of Pathology<br />

181(1): 111–120.<br />


Scott D. Jewell, Ph.D.<br />

Program for Biospecimen Science<br />

Dr. Jewell received his M.S. and Ph.D. degrees in experimental pathology<br />

and immunology from The Ohio State University. He has more than<br />

25 years of experience in biorepository and biospecimen services and<br />

pathology laboratory services. Dr. Jewell previously served as director<br />

for the Human Tissue Resource Network and associate director of the<br />

OSU Comprehensive Cancer Center’s Biorepository and Biospecimen<br />

Resource. He joined VARI in 2010 as a Professor and Director of Program<br />

for Biospecimen Science.<br />

Front row, from left: Khoo, Wiesner, Hilsabeck, Berghuis, Turner, Noyes Back rows, from left: Christensen, Blanski, Koeman, Webster,<br />

Feenstra, Hudson, Hostetter, Beck, Filkins, Rohrer, Harbach, Watkins, Jewell<br />

Staff<br />

John Beck, B.S.<br />

Bree Berghuis, B.S., HTL(ASCP), QIHC<br />

Alexander Blanski, B.S.<br />

Carrie Christensen, B.S.<br />

Kristin Feenstra, B.S.<br />

Dana Filkins, B.A., CAPM<br />

Phil Harbach, M.S.<br />

Renee Hilsabeck, B.S.<br />

Eric Hudson, B.S.<br />

Sok Kean Khoo, Ph.D.<br />

Julie Koeman, B.S., CG(ASCP)<br />

Dan Maxim, B.S.<br />

Sabrina Noyes, B.S.<br />

Dan Rohrer, B.S., M.B.A.<br />

Lisa Turner, B.S., HT(ASCP), QIHC<br />

Anthony Watkins<br />

Timothy Webster, B.A.<br />

Cathy Wiesner, M.S.<br />

Students<br />

Eric Edewaard<br />

Mary Goyings<br />

Adriane Shorkey<br />

Katie Uhl<br />

Peter Varlan<br />

Adjunct Faculty<br />

Sandra Cottingham, M.D., Ph.D.<br />

James Resau, Ph.D.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

Biospecimen science uses evidence-based approaches to study the effects of collection, processing, and storage on the<br />

biological parameters of biospecimens in an effort to establish best practices for the collection and control of high-quality<br />

human biospecimens for research. In our Program for Biospecimen Science (PBS), two broad categories of interest are the<br />

pre- and post-analytical variables that can alter in vivo biological assessments. Model systems are used for the study of the<br />

variables that can arise in biospecimen management, and we are working to establish in vitro and in vivo tissue models that<br />

can be used to answer specific questions.<br />

Laboratory of Analytical Pathology<br />

The Laboratory of Analytical Pathology, directed by Galen Hostetter, M.D., provides histology and morphometric analysis using<br />

immunohistochemistry, in situ hybridization, tissue microarray technology, digital imaging and analysis by light and spectral<br />

microscopy, confocal microscopy, and diagnostic tissue evaluation. The lab can visualize cells and their components with<br />

striking clarity, and the images enable researchers to determine where in a cell particular molecules are located and to quantify<br />

the molecules through imaging analysis software. See p. 28 for a complete description.<br />

Laboratory of Microarray Technology<br />

The Laboratory of Microarray Technology is directed by Sok Kean Khoo, Ph.D. It provides gene expression arrays, miRNA<br />

arrays, and array CGH using the Agilent microarray platform and cDNA platform capabilities. Microarray technology plays an<br />

important part in the discovery of genetic signatures, copy number variations, and biomarkers. Genomic DNA or total RNA<br />

from a wide range of tissues, including blood and fresh or frozen tissues, can be analyzed. Agilent microarrays in array formats<br />

from 4 x 44,000 to 1 x 1 million are used, and whole-genome gene expression (GE) arrays, exon arrays, miRNA arrays, and<br />

array CGH are available. Human, mouse, rat, and canine arrays are most frequently processed, but the lab offers GE and<br />

custom arrays for more than 20 plant and animal model organisms. Recently the lab has successfully developed a microarray<br />

gene expression technique for RNA from newborn blood spots. This technique can detect thousands of gene signatures using<br />

low-resolution arrays, enabling clinical research into the origins, epidemiology, and diagnosis of pediatric diseases.<br />

Cytogenetics Core facility<br />

Julie Koeman, CG (ASCP), directs the Cytogenetics Core facility, which uses both cytogenetic and molecular genetic techniques<br />

to identify structural and numerical chromosomal aberrations associated with mammalian disease. Information about the loss<br />

or gain of a gene or about gene amplification can be generated from many sample types, and that information can be used to<br />

validate microarray data. Cytogenetic techniques can also be used for species identification, which is especially valuable when<br />

working with tumor xenograft models. The cytogenetic services include fluorescence in situ hybridization (FISH), custom FISH<br />

probe production, spectral karyotyping (SKY), transgene localization, routine karyotyping (G-banding), chromosomal breakage<br />

studies, and mouse embryonic stem cell trisomy 8 screening.<br />

Biorepository services<br />

Dan Rohrer directs the operations of the biorepository, including database tracking and management of biospecimen<br />

inventory; biospecimen kit development and manufacturing; shipping and tracking services; procurement of surgical tissue and<br />

biospecimens from patient populations; quality control assessment of operations for the collection and banking of biospecimens;<br />

and biospecimen project management. The VARI biorepository contains approximately 2,000 frozen human tissues and a<br />

paraffin block archive of human diagnostic tissues currently exceeding 800,000 blocks. Tissue acquisition is in collaboration with<br />

West Michigan hospitals, providing fresh-frozen and paraffin-embedded surgical tissues and blood from consenting patients. The<br />

biorepository is designed to provide human tumors to investigators with IRB-approved basic and translational research projects.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Comprehensive biospecimen resource for the NCI Cancer Human Biobank<br />

The Cancer Human Biobank (caHUB) includes biospecimen source sites, a comprehensive biospecimen resource, a pathology<br />

resource center, and a comprehensive data resource to implement the collection and management of high-quality biospecimens<br />

for NCI and NIH projects such as the Genotype-Tissue Expression (GTEx) program. VARI’s Program for Biospecimen Science<br />

was awarded funding as the comprehensive biospecimen resource for the caHUB. Using a stringent quality management<br />

program and project-specific standard operating procedures, we produce biospecimen kits for the collection and management<br />

of human tissues and pathology services for caHUB projects. In 2011 and 2012, our Program was awarded major contracts<br />

to support the caHUB projects.<br />

Biospecimen resource for the Multiple Myeloma Research Foundation CoMMpass study<br />

The Multiple Myeloma Research Foundation launched a genomics study, CoMMpass SM , in collaboration with the Translational<br />

Genomics Research Institute (TGen), our Program for Biospecimen Science, and Spectrum Health Medical Center. The primary<br />

aim of CoMMpass is to collect biospecimens from 1,000 multiple myeloma patients for genomic analysis to assess changes<br />

associated with major clinical events, treatment response, and disease progression. This data will fuel therapeutic target<br />

discovery, drug development, and biomarker validation. Biospecimen kits are designed by the VARI PBS for the collection<br />

of bone marrow aspirate and peripheral blood. The kits, which are tracked from design through shipment and use, maintain<br />

biospecimens at 2–8 °C during shipment to Spectrum, where they are characterized by flow cytometry and BRAF sequencing<br />

in a clinical diagnostic laboratory. The PBS isolates CD138 + tumor cells and nucleic acids from patient samples for molecular<br />

sequencing and analysis at TGen. CoMMpass biospecimen management includes kit design, distribution, tracking, processing,<br />

and biobanking. Since July 2011, 200 patient cases have been processed, of which 28 have completed full genomic analysis.<br />

In 2011 the PBS was awarded an eight-year contract for this project.<br />

Recent Publications<br />

Jewell, Scott D. 2012. Perspective on biorepository return of results and incidental findings. Minnesota Journal of Law,<br />

Science and Technology 13(2): 655–667.<br />

Resau, James H., Nhan T. Ho, Karl Dykema, Matthew S. Faber, Julia V. Busik, Radoslav Z. Nickolov, Kyle A. Furge, Nigel<br />

Paneth, Scott Jewell, and Sok Kean Khoo. 2012. Evaluation of sex-specific gene expression in archived dried blood spots<br />

(DBS). International Journal of Molecular Sciences 13(8): 9599–9608.<br />

Glaser, Ronald, Rebecca Andridge, Eric V. Yang, Arwa Y. Shana’ah, Michael Di Gregorio, Min Chen, Sheri L. Johnson,<br />

Lawrence A. De Renne, David R. Lambert, Scott D. Jewell, et al. 2011. Tumor site immune markers associated with risk for<br />

subsequent basal cell carcinomas. PLoS One 6(9): e25160.<br />

Moore, Helen M., Andrea Kelly, Scott D. Jewell, Lisa M. McShane, Douglas P. Clark, Renata Greenspan, Pierre Hainaut,<br />

Daniel F. Hayes, Paula Kim, Elizabeth Mansfield, et al. 2011. Biospecimen reporting for improved study quality. Biopreservation<br />

and Biobanking 9(1): 57–70.<br />


Figure 1 Figure 2<br />

Figure 3<br />

Differentiated prostate<br />

epithelial cells.<br />

Figure 1 shows basal cells (the lowest layer of cells) stained for integrin a6; the red<br />

stain is largely on the periphery of the cells. Figure 2 shows secretory cells (the upper<br />

layer), which have differentiated from the basal cells. The green stain in the secretory cells,<br />

which have lost integrin expression, is for the ING4 molecule in the nucleus. Figure 3 shows a<br />

composite image of both stains, plus DAPI stain (blue) for DNA.<br />

Images by Penny Berger and Elly Park of the Miranti lab.<br />


Xiaohong Li, Ph.D.<br />

Laboratory for Tumor Microenvironment and Metastasis<br />

Dr. Li received her Ph.D. from the Chinese Academy of Sciences in Beijing<br />

in 2000, and she moved to Vanderbilt University in the same year. Dr. Li<br />

was a postdoctoral fellow in the laboratory of David Ong until 2005 and in<br />

the laboratory of Neil Bhowmick from 2005 to 2009. She was promoted to<br />

research assistant professor in the Department of Urologic Surgery in 2009.<br />

Dr. Li joined VARI as an Assistant Professor in September 2012.<br />

Research Interests<br />

The laboratory is committed to understanding cancer and metastasis. We study not only the cancer cells, but also the<br />

contributions of the tumor microenvironment, aiming to develop early diagnostic and treatment strategies for breast and<br />

prostate cancer metastasis to bone. Our research focuses on the role of stromal transforming growth factor (TGF-b) in the<br />

microenvironment of primary and metastatic tumor sites, as well as its effects in bone metastases, and on the development<br />

of animal models of cancer-induced osteolytic and osteoblastic bone disease.<br />

We have recently been funded by the Department of Defense Prostate Cancer Research Program to study the influence<br />

of the primary microenvironment on the development of prostate cancer osteoblastic bone lesions. The objectives are to<br />

determine the contribution of prostate mesenchymal TGF-b to lesion development and to determine whether chemokines<br />

induced by the loss of TGF-b signaling mediate prostate cancer bone metastasis. Other developing projects include the<br />

creation of animal models for studying prostate osteoblastic bone metastases and mechanisms; study of the role of TGF-b on<br />

the development of breast cancer-induced osteolytic bone lesions; and the evaluation of anti-TGF-b combination therapies<br />

on cancer-induced bone disease.<br />

Staff<br />

Priscilla Lee, B.S.<br />

Diana Lewis, A.S.<br />

Jared Murdoch, B.S.<br />


Jeffrey P. MacKeigan, Ph.D.<br />

Laboratory of Systems Biology<br />

Dr. MacKeigan received his Ph.D. in microbiology and immunology at the<br />

University of North Carolina Lineberger Comprehensive Cancer Center in<br />

2002, followed by a postdoctoral fellowship with John Blenis at Harvard<br />

Medical School. In 2004, he joined Novartis Institutes for Biomedical<br />

Research in Cambridge, Massachusetts, as an investigator and project<br />

leader in the Molecular and Developmental Pathways expertise platform.<br />

Dr. MacKeigan, who joined VARI in 2006, is an Associate Professor.<br />

From left: MacKeigan, Niemi, Burgenske, Martin, Westrate, Doppel, Lanning, Goodall, Looyenga, Fogg, May, Nelson, Karnes, Kauffman<br />

Staff<br />

Nicole Doppel, B.S.<br />

Vanessa Fogg, Ph.D.<br />

Audra Kauffman, M.S.<br />

Nate Lanning, Ph.D.<br />

Brendan Looyenga, Ph.D.<br />

Katie Martin, Ph.D.<br />

Brett May, B.S.<br />

Amy Nelson<br />

Students<br />

Dani Burgenske, B.S.<br />

Megan Goodall, B.S.<br />

Matt Harder<br />

Jonathan Karnes, M.S.<br />

Natalie Niemi, Ph.D.<br />

Anna Plantinga<br />

Aaron Sayfie<br />

Laura Westrate, B.A., B.S.<br />

Visiting Scientist<br />

Aaron Putzke, Ph.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

“Systems biology” integrates multiple disciplines such as biochemistry, mathematics, and genetics to investigate unanswered<br />

biological questions. The Laboratory of Systems Biology focuses on identifying and understanding the genes and signaling<br />

pathways that, when mutated, contribute to the pathophysiology of cancer and neurodegeneration. The lab has two major<br />

research programs: cancer metabolism and the PI3K-mTOR autophagy signaling network. We employ tools such as RNA<br />

interference (RNAi), quantitative proteomics, and in silico screening to investigate the kinases and phosphatases that mediate<br />

the pro-apoptotic and cell survival functions of mitochondria, as well as those that regulate lipid signaling and autophagy. The<br />

laboratory’s primary scientific objectives are to investigate the molecular details of cancer and Parkinson’s disease; develop<br />

therapeutics for high-priority targets; and reposition drugs for use against cancer and neurodegenerative diseases.<br />

Cancer metabolism and cellular energetics<br />

Evasion of apoptosis is a significant problem in a variety of cancers. In order to identify novel regulators of apoptosis, the lab<br />

performed an RNAi screen against all kinases and phosphatases in the human genome. A possible regulator we identified<br />

was MK-STYX (encoded by the STYXL1 gene), a catalytically inactive phosphatase with homology to the MAPK phosphatases.<br />

Despite this homology, MK-STYX knockdown failed to modulate MAPK signaling in response to growth factors or apoptotic<br />

stimuli. Rather, RNAi-mediated knockdown of MK-STYX prevented cells from undergoing apoptosis induced by cellular<br />

stressors, activating mitochondrial-dependent apoptosis. This MK-STYX phenotype mimicked the loss of Bax and Bak, two<br />

potent guardians of mitochondrial apoptotic potential: cells without MK-STYX expression were unable to release cytochrome c.<br />

The overexpression of pro-apoptotic Bcl-2 proteins was unable to trigger cytochrome c release in MK-STYX knockdown cells,<br />

placing the apoptotic deficiency at the level of mitochondrial outer membrane permeabilization (MOMP).<br />

MK-STYX localizes to the mitochondria, but it is neither released from the mitochondria upon apoptotic stress nor localized<br />

proximal to the machinery currently known to control MOMP. Thus, MK-STYX regulates the chemoresistance potential of<br />

cancer cells through the control of MOMP, but in distinct fashion from currently characterized mechanisms. Additionally, we<br />

have determined that MK-STYX interacts with a mitochondrial phosphatase, PTPMT1. The loss of PTPMT1 in MK-STYX<br />

knockdown cells resensitizes the cells to chemotherapy and cytochrome c release, demonstrating a genetic interaction between<br />

these two proteins. Ongoing studies are focused on characterizing this MK-STYX–PTPMT1 interaction and on gaining insight<br />

into the metabolic and apoptotic capacity of cancer cells.<br />

A wealth of experimental evidence clearly connects the regulation of cellular metabolism with the development of cancer.<br />

Metabolic changes in cancer cells are considered a key event in the transition from a normal cell to a cancer cell. Such changes<br />

cause cancer cells to be metabolically reprogrammed to provide the fuel and energy required for rapid proliferation. To identify<br />

genes crucial for cancer cell metabolism, we developed a novel, high-throughput method to comprehensively screen all known<br />

nuclear-encoded genes whose protein products localize to mitochondria. Our screen also included other metabolic genes and<br />

used cellular ATP levels as a readout. The screen was performed under both glycolytic and oxidative phosphorylation-restricted<br />

conditions to define genes contributing to ATP production in each bioenergetic state. We identified several genes that drive<br />

cancer cell bioenergetics and upon which cancer cells rely for survival and proliferation. A substantial proportion of the genes<br />

we identified as novel targets were dysregulated in tumors from glioma patients, and their expression and copy number status<br />

significantly correlated with patient survival. Current experiments seek to answer questions about the cellular interactions<br />

involving these target genes and how these interactions affect the metabolic programs of normal and cancer cells.<br />


VARI | <strong>2013</strong><br />

PI3K-mTOR and the autophagy signaling network<br />

Autophagy is a cellular recycling program essential for homeostasis and survival during cytotoxic stress. When cancer cells<br />

encounter environmental stressors such as nutrient starvation or chemotherapy, autophagy is dramatically up-regulated,<br />

resulting in cellular adaptation to the stress and subsequent survival. The autophagy process, which has an emerging role<br />

in disease etiology and treatment, is executed in four stages through the coordinated action of more than 30 proteins. An<br />

effective strategy for studying this complicated process involves the construction and analysis of computational models. When<br />

developed and refined from experimental knowledge, these models can be used to interrogate signaling pathways, formulate<br />

novel hypotheses about systems, and make predictions about cell signaling changes induced by specific interventions.<br />

In conjunction with collaborators at Los Alamos National Laboratory, we developed a computational model describing<br />

autophagic vesicle dynamics in a mammalian system. We used time-resolved live-cell microscopy to measure the synthesis<br />

and turnover of autophagic vesicles in single cells. The stochastically simulated model was consistent with data acquired<br />

during conditions of both basal and chemically induced autophagy. The model was tested by genetic modulation of the<br />

autophagic machinery and it accurately predicted the vesicle dynamics observed experimentally. Furthermore, the model<br />

generated an unforeseen prediction about vesicle size that is consistent with both published findings and our experimental<br />

observations. Thus, we have developed an accurate and useful model that can serve as the foundation for future efforts to<br />

quantitatively characterize autophagy. Ongoing efforts include building and refining a computational model of autophagy<br />

that will make reliable predictions about complex cancer cell behavior; verifying the predictions in cellular and preclinical<br />

models; and ultimately using the model to develop effective strategies for therapeutically targeting autophagy in cancer.<br />

Recent Publications<br />

Martin, Katie R., Dipak Barua, Audra L. Kauffman, Laura M. Westrate, Richard G. Posner, William S. Hlavacek, and Jeffrey P.<br />

MacKeigan. <strong>2013</strong>. Computational model for autophagic vesicle dynamics in single cells. Autophagy 9(1): 74–92.<br />

Niemi, Natalie M., Nathan J. Lanning, Laura M. Westrate, and Jeffrey P. MacKeigan. <strong>2013</strong>. Downregulation of the mitochondrial<br />

phosphatase PTPMT1 is sufficient to promote cancer cell death. PLoS One 8(1): e53803.<br />

Klionsky, Daniel J., Fabio C. Abdalla, Hagai Abeliovich, Robert T. Abraham, Abraham Acevedo-Arozena, Khosrow Adeli,<br />

Lotta Agholme, Maria Aganello, Patrizia Agostinis, Julio A. Aguirre-Ghiso, et al. 2012. Guidelines for the use and interpretation<br />

of assays for monitoring autophagy. Autophagy 8(4): 445–544.<br />

Looyenga, Brendan D., Danielle Hutchings, Irene Cherni, Chris Kingsley, Glen J. Weiss, and Jeffrey P. MacKeigan.<br />

2012. STAT3 is activated by JAK2 independent of key oncogenic driver mutations in non-small cell lung carcinoma.<br />

PLoS One 7(2): e30820.<br />

Looyenga, Brendan D., and Jeffrey P. MacKeigan. 2012. Characterization of differential protein tethering at the plasma<br />

membrane in response to epidermal growth factor signaling. Journal of Proteome Research 11(6): 3101–3111.<br />

Stark, Mitchell S., Susan L. Woods, Michael G. Gartside, Vanessa F. Bonazzi, Ken Dutton-Regester, Lauren G. Aoude, Donald<br />

Chow, Chris Sereduk, Natalie M. Niemi, Nanyun Tang, et al. 2012. Frequent somatic mutations in MAP3K5 and MAP3K9 in<br />

metastatic melanoma identified by exome sequencing. Nature Genetics 44(2): 165–169.<br />


Karsten Melcher, Ph.D.<br />

Laboratory of Structural Biology and Biochemistry<br />

Dr. Melcher earned his master’s in biology and his Ph.D. in biochemistry from<br />

the Eberhard Karls Universität in Tübingen, Germany, after which he was a<br />

postdoctoral fellow at the University of Texas Southwestern Medical Center<br />

in Dallas. He has been an independent investigator at the University of<br />

Ulster in Coleraine, U.K., and at Goethe University in Frankfurt. Dr. Melcher<br />

was recruited to VARI in 2007, serving as a Research Scientist within the<br />

Laboratory of Structural Sciences. In 2011, he became Assistant Professor<br />

and head of the Laboratory of Structural Biology and Biochemistry.<br />

From left: deWaal, Zhou, Li, Wang, Melcher, Kovach, Merrill, Weber<br />

Staff<br />

Amanda Kovach, B.S.<br />

Stephanie Weber, B.S.<br />

Xiaoyin (Edward) Zhou, Ph.D.<br />

Students<br />

Parker deWaal<br />

Xiaodan Li, B.S.<br />

Nate Merrill, B.S.<br />

Lili Wang, B.S.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

The Laboratory of Structural Biology and Biochemistry studies the structure and function of proteins that have central roles in<br />

cellular signaling. To do so, we employ X-ray crystallography in combination with biochemical and cellular methods to identify<br />

structural mechanisms of signaling at high resolution.<br />

In addition to their fundamental physiological roles, most signaling proteins are also important targets of therapeutic drugs. Determination<br />

of the three-dimensional structures of protein–drug complexes at atomic resolution allows a detailed understanding<br />

of how a drug binds its target and modifies its activity. This knowledge allows the rational design of new and better drugs<br />

against diseases such as diabetes, cancer, and neurological disorders.<br />

Two areas of focus in the lab are the adenosine-monophosphate (AMP)-activated protein kinase (AMPK), a cellular energy and<br />

nutrient sensor, and the receptors and key signaling proteins for a plant hormone, abscisic acid (ABA).<br />

AMP-activated protein kinase<br />

Cells use ATP to drive energy-consuming cellular processes such as muscle contraction, cell growth, and neuronal excitation.<br />

AMPK is a three-subunit protein kinase that functions as a sensor of the energy status in human cells. Its kinase activity is<br />

triggered by energy stress (i.e., a drop in the ratio of ATP to AMP/ADP), activating ATP-generating pathways and reducing<br />

energy-consuming programs.<br />

To adjust energy balance, AMPK regulates<br />

• Almost all cellular metabolic processes (activation of ATP-generating pathways such as glucose and fatty acid uptake<br />

and catabolism, and inhibition of energy-consuming pathways such as the synthesis of glycogen, fatty acids, cholesterol,<br />

proteins, and ribosomal RNA)<br />

• Whole-body energy balance (appetite regulation in the hypothalamus via leptin, adiponectin, ghrelin, and cannabinoids)<br />

• Many nonmetabolic processes (cell growth and proliferation, mitochondrial homeostasis, autophagy, aging, neuronal<br />

activity, and cell polarity).<br />

Due to its central roles in the uptake and metabolism of glucose and fatty acids, AMPK is an important pharmacological target<br />

for the treatment of diabetes and obesity. Moreover, AMPK activation restrains the growth and metabolism of tumor cells and<br />

has thus become an exciting new target for cancer therapy. In this project we strive to determine the structural mechanisms<br />

of AMPK regulation by direct binding of AMP, ADP, ATP, drugs, and glycogen, in order to provide a structural framework for the<br />

rational design of new therapeutic AMPK modulators.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Abscisic acid<br />

Abscisic acid is an ancient signaling molecule that is found in plants, fungi, and metazoans ranging from sponges to humans.<br />

In plants, ABA is an essential hormone and is also the central regulator protecting plants against abiotic stresses such as<br />

drought, cold, and high salinity. These stresses—most prominently, the scarcity of fresh water—are major limiting factors in<br />

crop production and therefore major contributors to malnutrition.<br />

Malnutrition affects an estimated one billion people and contributes to more than 50% of human disease worldwide, including<br />

cancer and infectious diseases. We have determined the structure of ABA receptors in the free state and bound to ABA. Using<br />

computational receptor docking experiments, we have identified and verified synthetic small-molecule receptor activators as<br />

new chemical scaffolds toward the development of new, environmentally friendly, and affordable compounds that will protect<br />

plants against abiotic stresses. We have also identified the structural mechanism of the core ABA signaling pathway, which will<br />

allow modulation of this pathway through genetic engineering of crop plants.<br />

Recent Publications<br />

Pal, Kuntal, Karsten Melcher, and H. Eric Xu. 2012. Structure and mechanism for recognition of peptide hormones by<br />

Class B G-protein-coupled receptors. Acta Pharmacologica Sinica 33(3): 300–311.<br />

Soon, Fen-Fen, Ley-Moy Ng, X. Edward Zhou, Graham M. West, Amanda Kovach, M. H. Eileen Tan, Kelly M. Suino-Powell,<br />

Yuanzheng He, Yong Xu, Michael J. Chalmers, et al. 2012. Molecular mimicry regulates ABA signaling by SnRK2 kinases and<br />

PP2C phosphatases. Science 335(6064): 85–88.<br />

Soon, Fen-Fen, Kelly M. Suino-Powell, Jun Li, Eu-Leong Yong, H. Eric Xu, and Karsten Melcher. 2012. Abscisic acid signaling:<br />

thermal stability shift assays as tool to analyze hormone perception and signal transduction. PLoS One 7(10): e47857.<br />

Zhou, X. Edward, Karsten Melcher, and H. Eric Xu. 2012. Structure and activation of rhodopsin. Acta Pharmacologica Sinica<br />

33(3): 291–299.<br />

Zhou, X. Edward, Fen-Fen Soon, Ley-Moy Ng, Amanda Kovach, Kelly M. Suino-Powell, Jun Li, Eu-Leong Yong, Jian-Kang Zhu,<br />

H. Eric Xu, and Karsten Melcher. 2012. Catalytic mechanism and kinase interactions of ABA-signaling PP2C phosphatases.<br />

Plant Signaling & Behavior 7(5): 581–588.<br />

Ng, Ley-Moy, Fen-Fen Soon, X. Edward Zhou, Graham M. West, Amanda Kovach, Kelly M. Suino-Powell, Michael J. Chalmers,<br />

Jun Li, Eu-Leong Yong, Jian-Kang Zhu, et al. 2011. Structural basis for basal activity and autoactivation of abscisic acid (ABA)<br />

signaling SnRK2 kinases. Proceedings of the National Academy of Sciences U.S.A. 108(52): 21259–21264.<br />

Zhi, Xiaoyong, X. Edward Zhou, Karsten Melcher, Daniel L. Motola, Verena Gelmedin, John Hawdon, Steven A. Kliewer, David<br />

J. Mangelsdorf, and H. Eric Xu. 2011. Structural conservation of ligand binding reveals a bile acid–like signaling pathway in<br />

nematodes. Journal of Biological Chemistry 287(7): 4894–4903.<br />


Cindy K. Miranti, Ph.D.<br />

Laboratory of Integrin Signaling and Tumorigenesis<br />

Dr. Miranti received her M.S. in microbiology from Colorado State University<br />

and her Ph.D. in biochemistry from Harvard Medical School. She was<br />

a postdoctoral fellow in the laboratory of Dr. Joan Brugge at ARIAD<br />

Pharmaceuticals, Cambridge, Massachusetts and in the Department of<br />

Cell Biology at Harvard Medical School. Dr. Miranti joined VARI in January<br />

2000, where she is currently an Associate Professor. She is also an Adjunct<br />

Professor in the Department of Physiology at Michigan State University.<br />

From left: Frank, Cooper, Zarif, Berger, Nollett, Hildebrandt, Schulz, Miranti, Park<br />

Staff<br />

Penny Berger, B.S.<br />

Elly Park, Ph.D.<br />

Veronique Schulz, B.S.<br />

Students<br />

Alexis Bergsma, B.S.<br />

Jason Cooper, B.S.<br />

Amanda Erwin<br />

Sander Frank, B.A.<br />

Erin Hildebrandt, B.S.<br />

Eric Nollet, B.S.<br />

Jelani Zarif, M.S.<br />

Teacher Intern<br />

Erin Combs, M.S.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

Our objective is to understand how cell adhesion and the tumor microenvironment promote prostate cancer progression and<br />

metastasis. Our work focuses on three major questions: 1) how do the androgen receptor (AR) and integrin interactions with<br />

the tumor microenvironment cooperate to promote prostate cancer bone metastasis? 2) how do oncogenes disrupt integrin<br />

signaling and prostate epithelial differentiation to promote tumorigenesis? and 3) how does the metastasis suppressor gene<br />

CD82/KAI1 regulate the tumor microenvironment to suppress prostate cancer metastasis? Our strategy is to develop cell- and<br />

animal-based models that accurately reflect the in vivo biology of human prostate cancer as observed in the clinic and use them<br />

to develop therapeutic strategies for prostate cancer.<br />

The AR/a6b1 integrin axis<br />

The human prostate gland contains basal cells which express and use integrins to adhere to laminin matrix. Basal cells<br />

do not express AR, but they differentiate into AR-expressing secretory cells that detach from matrix and lose integrin<br />

expression. In prostate cancer, the AR-expressing tumor cells retain abnormal expression of integrin a6b1. We hypothesize<br />

that abnormal cross-talk between AR and integrin a6b1 is crucial for prostate cancer development and progression to<br />

castration-resistant disease.<br />

We found that AR binds directly to the integrin a6 promoter to stimulate its transcription, while simultaneously decreasing the<br />

expression of other integrins. Control of integrin a6 expression by AR requires the fusion gene, TMPRSS2-Erg, suggesting<br />

cross-talk between AR and Erg. We discovered that AR stimulation of a6b1 expression activates a laminin-dependent survival<br />

pathway involving NF-kB/RelA activation and subsequent increased transcription of Bcl-xL.<br />

To understand the mechanisms that promote the survival of castration-resistant cancer, we screened tumors cells for NF-kB<br />

target genes whose expression depends on AR and integrin a6b1. We identified and validated BNIP3 as such a gene.<br />

BNIP3 expression is higher in castration-resistant cells and correlates with disease progression and poor patient outcome.<br />

Furthermore, loss of BNIP3 induces cell death. BNIP3 promotes mitochondrial-specific degradation through autophagy, and<br />

we hypothesize that BNIP3 promotes the emergence and survival of castration-resistant tumors by enhancing such mitophagy.<br />

The loss of Pten, which leads to enhanced PI3K signaling, occurs in 60% of advanced prostate cancers; however, PI3K<br />

inhibitors are not effective in patients. When plated on laminin to engage integrin a6b1, tumor cells were resistant to PI3K<br />

inhibition. Blocking PI3K in combination with blocking AR, integrin a6b1, RelA, or Bcl-xL resensitized the cells to such inhibition.<br />

Thus, interactions with the tumor microenvironment through AR/a6b1 is an important mechanism by which prostate tumor<br />

cells escape their reliance on PI3K signaling, and disrupting this pathway will be necessary for effectively blocking prostate<br />

cancer in vivo.<br />

Differentiation and oncogenesis<br />

The prostate cancer field is hampered by the lack of cell models that reflect in vivo events. We developed an in vitro differentiation<br />

model in which basal epithelial cells are differentiated into secretory cells that behave similarly to those in vivo. As is seen in<br />

vivo, the secretory cells are marked by their loss of integrin expression and loss of adhesion to matrix. In fact, the competency<br />

to activate AR requires the loss of matrix adhesion. Differentiation is accompanied by a dramatic increase in E-cadherin expression<br />

and increased cell-cell adhesion. At the same time, there is a switch in the basal cells from dependence on integrins and<br />

MAPK for survival, to E-cadherin and PI3K in the secretory cells.<br />


VARI | <strong>2013</strong><br />

Based on our observations that differentiation begins prior to complete loss of integrin a6b1 and that Myc controls integrin<br />

a6b1 transcription in epithelial cells, we hypothesize that prostate oncogenesis occurs within a subpopulation of transiently<br />

differentiating cells in which AR is partially stabilized but the cells still retain a6b1. Using normal cells engineered to overexpress<br />

two known prostate oncogenes, Myc and TMPRSS2/Erg, and an shRNA to Pten, we generated tumorigenic cells that coexpress<br />

integrin a6b1 and AR. Surprisingly, these oncogene-modified cells were unable to differentiate. Thus, we developed<br />

an in vitro model for studying prostate tumorigenesis that recapitulates many of its in vivo aspects and links prostate cancer to<br />

defects in differentiation.<br />

CD82/KAI1<br />

CD82/KAI1 is encoded by a metastasis suppressor gene whose loss in primary prostate tumors correlates with poor patient<br />

prognosis. CD82 is one of 33 tetraspanins whose functions remain enigmatic but are linked to cell adhesion. Our hypothesis is<br />

that CD82 suppresses metastasis by limiting signal transduction pathways that promote integrin-based migration and invasion<br />

while simultaneously increasing cell-cell adhesion.<br />

CD82 suppresses both integrin- and ligand-based activation of the tyrosine kinases Met and Src; it also suppresses their<br />

ability to stimulate prostate tumor cell migration and invasion in vitro, as well as metastasis in vivo. Other tetraspanins, CD9<br />

and CD151, are required for CD82-dependent suppression of Met. CD82 expression also increases E-cadherin-based<br />

cell-cell adhesion. Several CD82 mutants were generated to decipher how CD82 suppresses Met-dependent metastasis and<br />

promotes cell-cell adhesion.<br />

The reexpression of CD82 in metastatic tumor cells is sufficient to suppress metastasis. However, using a conditional null<br />

CD82 mutant mouse, we found that loss of CD82 alone in a mouse primary prostate tumor model was not sufficient to induce<br />

metastasis. To address the possibility that loss of other genes is also needed, we are crossing floxed CD82 mice with mice that<br />

are null for another metastasis suppressor gene, RKIP. RKIP regulates miRNAs that are involved in controlling Myc and MAPK<br />

signaling, pathways that are not influenced by CD82.<br />

We generated CD82-null mice to better understand the normal function of CD82. The most striking phenotype is enhanced<br />

platelet clotting and reduced bleeding, as well as a twofold increase in total platelets. The increase in platelets is due to<br />

changes in megakaryocyte differentiation, which is controlled by tyrosine kinase and cytokine signaling and is tightly linked to<br />

the cytoskeleton. CD82-null mice also have increased bone density, defects in toll receptor signaling, and reduced capacity to<br />

stimulate T-cell signaling. Thus, the in vivo data support our in vitro work, suggesting the major function of CD82 is to regulate<br />

cell signaling, and further suggesting CD82 regulates cell differentiation.<br />

Recent Publications<br />

Nollet, Eric A., and Cindy K. Miranti. In press. Integrin and matrix regulation of autophagy and mitophagy. In Autophagy,<br />

Yannick Bailly, ed. New York: InTech.<br />

Klionsky, Daniel J., Fabio C. Abdalla, Hagai Abeliovich, Robert T. Abraham, Abraham Acevedo-Arozena, Khosrow Adeli,<br />

Lotta Agholme, Maria Aganello, et al. 2012. Guidelines for the use and interpretation of assays for monitoring autophagy.<br />

Autophagy 8(4): 445–544.<br />

Lamb, Laura E., Jelani C. Zarif, and Cindy K. Miranti. 2011. The androgen receptor induces integrin a6b1 to promote<br />

prostate tumor cell survival via NF-kB and Bcl-xL independently of PI3K signaling. Cancer Research 71(7): 2739–2749.<br />


Mark W. Neff, Ph.D.<br />

Laboratory of Canine Genetics and Genomics<br />

Dr. Neff received his Ph.D. in biological sciences from the University of<br />

Virginia and completed a postdoctoral fellowship in canine genetics and<br />

genomics at the University of California, Berkeley. Most recently, he served<br />

as associate director of the Veterinary Genetics Laboratory at the University<br />

of California, Davis. Dr. Neff joined VARI in 2009 as an Associate Professor<br />

and Director of the Program for Canine Health and Performance.<br />

From left: Minard, Neff, Hodges, Kefene, Borgman, Roemer<br />

Staff<br />

Lisa Kefene, B.S.<br />

Michelle Minard<br />

Students<br />

Andrew Borgman, B.S.<br />

Jenea Chesnic<br />

Daniel Hodges, M.A.<br />

Alex Roemer<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

I apply a classical genetic perspective and genomic discovery platforms to a unique animal model. Dogs suffer the same inherited<br />

disorders as humans, including cancers and neurodegenerative diseases. In veterinary medicine, canine disorders are detected<br />

with human diagnostics and treated with human medicines, so it stands to reason that naturally occurring diseases in the dog are<br />

models of human disease counterparts. Genetic analysis can identify, in an unbiased way and owing to the strengths of breed<br />

isolates, the causal mechanisms underlying complex disease susceptibilities. DNA risk signatures enable predictive genetic<br />

epidemiology with corresponding clinical benefits—early intervention and prevention—and they inform on aberrant biological<br />

processes. Clinical trials can be performed more rapidly, more powerfully, and more economically in veterinary medicine owing to<br />

lesser regulatory constraints and accelerated patient time frames. Pet dogs also serve as a model for lifestyle management (e.g.,<br />

exercise, appetite, and behavioral modification), creating the opportunity to offset inherited risks. The dog is arguably the best<br />

patient model for evidence-based, personalized, and preventive medicine. Over the years, our group has developed the subject<br />

recruitment, genomic, and statistical analysis pipelines needed for advancing robust, informative, and efficient experiments<br />

in canine genetics research. Just as importantly, we have developed strong relationships with the dog owner and breeder<br />

community, without which research in this field would not be possible.<br />

Our lab studies naturally occurring diseases in the dog. We apply the perspective of genetics and the tools of genomics to<br />

tie complex phenotypes to causal genotypes. We exploit the strengths of breeds as genetic isolates to identify identicalby-descent<br />

mutations from within large ancestral haplotype blocks. These mutations can then be functionally characterized<br />

in model organisms or cell culture. Our collaborations over the past two years have included projects on osteosarcoma,<br />

hemangiosarcoma, essential head tremor, obsessive-compulsive disorder, agoraphobic-like behavior, cervical spondylopathy,<br />

adult onset hearing loss, and idiopathic pulmonary fibrosis.<br />

Recent Publications<br />

Wong, A.K., A.L. Ruhe, K.R. Robertson, E.R. Loew, D.C. Williams, and M.W. Neff. In press. A de novo mutation in KIT causes<br />

white spotting in a subpopulation of German Shepherd dogs. Animal Genetics.<br />

Neff, Mark W., John S. Beck, Julie M. Koeman, Elissa Boguslawski, Lisa Kefene, Andrew Borgman, and Alison L. Ruhe. 2012.<br />

Partial deletion of the sulfate transporter SLC13A1 is associated with an osteochondrodysplasia in the miniature poodle breed.<br />

PLoS One 7(12): e51917.<br />

Wong, Aaron K., Alison L. Ruhe, Shameek Biswas, Kathryn R. Robertson, Ammar Ali, Joshua M. Akey, and Mark W. Neff. 2012.<br />

Marker panels for genealogy-based mapping, breed demographics, and inference-of-ancestry in the dog. Animal Biotechnology<br />

23(4): 241–252.<br />

Yokoyama, Jennifer S., Ernest T. Lam, Alison L. Ruhe, Carolyn A. Erdmann, Kathryn R. Robertson, Aubrey A. Webb,<br />

D. Colette Williams, Melanie L. Chang, Marjo K. Hytönen, Hannes Lohi, et al. 2012. Variations in genes related to cochlear<br />

biology is strongly associated with adult-onset deafness in Border collies. PLoS Genetics 8(9): e1002898.<br />


Brian J. Nickoloff, M.D., Ph.D.<br />

Laboratory of Cutaneous Oncology<br />

Dr. Nickoloff received his M.D. and Ph.D. (biochemistry) from Wayne State<br />

University, and he completed an internship in Internal Medicine at Harbor<br />

General – UCLA Hospital. He is the former director of the Skin Disease<br />

Research Laboratory at Loyola University Chicago Medical Center. In<br />

2003, he became the director of Loyola’s Oncology Institute and deputy<br />

director of the Cardinal Bernardin Cancer Center. In 2011, he relocated to<br />

Grand Rapids to become Professor and Division Director of Dermatology at<br />

the College of Human Medicine, Michigan State University. He also holds<br />

an appointment as Professor and head of the Laboratory of Cutaneous<br />

Oncology at the Van Andel Research Institute. Most recently he became<br />

the Medical Director of Dermatopathology at St. Mary’s Hospital in the Skin<br />

Cancer Clinic.<br />

Research Interests<br />

Our primary interest is in finding new and better methods for diagnosing melanoma using genomics and treatment options<br />

in the setting of personalized medicine. Current efforts focus on overcoming treatment resistance and relapse in melanoma<br />

patients treated with targeted therapy. We are using human metastatic melanoma xenografts in immunodeficient mice.<br />

We have established a vemurafenib-resistant model system and also combination therapies to overcome this resistance.<br />

Another project is exploring the altered metabolomics in melanoma, using PET/CT imaging to develop novel approaches for<br />

targeting BRAF mutant and wild-type tumors.<br />

Recent Publications<br />

Monsma, David J., Noel R. Monks, David M. Cherba, Dawna Dylewski, Emily Eugster, Jahn Hailey, Sujata Srikanth, Stephanie<br />

B. Scott, Patrick J. Richardson, Robin E. Everts, et al. 2012. Genomic characterization of explant tumorgraft models derived<br />

from fresh patient tumor tissue. Journal of Translational Medicine 10: 125.<br />

Nickoloff, Brian J., and George Vande Woude. 2012. Hepatocyte growth factor in the neighborhood reverses resistance to<br />

BRAF inhibitor in melanoma. Pigment Cell & Melanoma Research 25(6): 758–761.<br />

Qin, Jianzhong, Hong Xin, and Brian J. Nickoloff. 2012. Specifically targeting ERK1 or ERK2 kills melanoma cells. Journal of<br />

Translational Medicine 10: 15.<br />


Giselle S. Sholler, M.D.<br />

Laboratory of Neuroblastoma Translational Research<br />

Dr. Sholler received her M.S. in microbiology and immunology from McGill<br />

University, Montreal, Quebec, and her M.D. from New York Medical<br />

College. She worked in the Division of Pediatric Hematology/Oncology at<br />

the University of Vermont before joining VAI in 2011 as Associate Professor<br />

and Co-Director of the Pediatric Oncology Program. Dr. Sholler has a joint<br />

appointment with the Helen DeVos Children’s Hospital as the Haworth<br />

Family Director of the Innovative Therapeutics Clinic in the Division of<br />

Pediatric Oncology.<br />

From left: Sholler, Ellis, Dutta, Vander Werff, McClung, Bender, Eckardt, Kendzicky, Zhao<br />

Staff<br />

Mary Bender, RN<br />

Genevieve Bergendahl, RN, B.S.N.<br />

Akshita Dutta, M.S.<br />

Alexandra Eckardt, B.S.<br />

Ellen Ellis<br />

Ann Kendzicky, B.S.<br />

Heather McClung, Ph.D.<br />

Alyssa Vander Werff, M.S.<br />

Ping Zhao, Ph.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

Our laboratory is committed to pushing forward cures for childhood cancers by identifying and exploiting new therapies<br />

for neuroblastoma and medulloblastoma, which continue to be therapeutic challenges in pediatrics. Our research aims at<br />

understanding the specific biological and genomic profiles of patients and using the information from patient-derived xenograft<br />

models and laboratory studies to identify and deliver new therapies to, and improve outcomes for, children with relapsed<br />

disease. Through the Neuroblastoma and Medulloblastoma Translational Research Consortium, which Dr. Sholler chairs,<br />

clinical trials are being conducted, for example, on molecular guided therapy for refractory/recurrent neuroblastoma and on<br />

a-diflouromethylornithine (DFMO) for patients with high-risk neuroblastoma in remission.<br />

Recent Publications<br />

Eslin, Don, Umesh T. Sankpal, Chris Lee, Robert M. Sutphin, Pius Maliakal, Erika Currier, Giselle Sholler, Moeez Khan, and<br />

Riyaz Basha. In press. Tolfenamic acid inhibits neuroblastoma cell proliferation and induces apoptosis: a novel therapeutic<br />

agent for neuroblastoma. Molecular Carcinogenesis.<br />

Sholler, Giselle L. Saulnier, William Ferguson, Genevieve Bergendahl, Erika Currier, Shannon R. Lenox, Jeffrey Bond,<br />

Marni Slavik, William Roberts, Deanna Mitchell, Don Eslin, et al. In press. A pilot trial testing the feasibility of using molecularguided<br />

therapy in patients with recurrent neuroblastoma. Journal of Cancer Therapy.<br />

Sun, Yujing, Girja Shukla, Stephanie C. Pero, Erika Currier, Giselle Sholler, and David Krag. 2012. Single tumor imaging with<br />

multiple antibodies targeting different antigens. BioTechniques Rapid Dispatches, doi 10.2144/000113855.<br />


Matthew Steensma, M.D.<br />

Laboratory of Musculoskeletal Oncology<br />

Dr. Steensma received his BA from Hope College and his M.D. from Wayne<br />

State University School of Medicine in Detroit. He was admitted into the<br />

fellowship program in musculoskeletal surgical oncology at Memorial<br />

Sloan-Kettering Cancer Center in New York, obtaining subspecialty training<br />

in surgical management of musculoskeletal tumors. Upon completion of<br />

this training, Dr. Steensma worked in the laboratory of Dr. Steve Goldring,<br />

one of the world’s leading orthopaedic researchers. There Dr. Steensma<br />

further developed his interest in understanding the molecular and cellular<br />

mechanisms underlying bone and soft-tissue sarcomas. Dr. Steensma is<br />

a practicing physician, treating patients in his musculoskeletal oncology<br />

clinic, and he joined VARI in 2010 as an Assistant Professor.<br />

From left: Steensma, Scholten, Kampfshulte, Ringler, Peacock, Pelle<br />

Staff<br />

Diana Lewis, A.S.<br />

Jacqueline Peacock, Ph.D.<br />

Jonathan Ringler, M.S.<br />

Students<br />

Kevin Kampfshulte, B.A.<br />

D.J. Scholten, B.A.<br />

Visiting Scientist<br />

Dominic Pelle, M.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

Our laboratory is particularly interested in defining the mechanisms of tumor initiation and disease progression for a rare type<br />

of cancer called sarcoma. In doing so, we seek to identify novel diagnostic and therapeutic targets for the disease. The lab<br />

centers its efforts around two disease entities: the primary bone cancer, called osteosarcoma, and Type 1 neurofibromatosis<br />

(NF1), also called Von Recklinghausen’s disease.<br />

Osteosarcoma affects predominantly children and young adults; it arises directly from bone and is highly aggressive. Advances<br />

in treatment have been slow over the last four decades, particularly with respect to metastatic osteosarcoma, which is largely<br />

incurable. Our lab is studying mechanisms whereby certain cells within the primary tumor resist chemotherapy, spread to<br />

a distant site, and reinitiate tumor formation (i.e., the process of metastasis). This subpopulation resembles mesenchymal<br />

stem cells in that they are capable of continuous self-renewal and multipotent differentiation. As a group, these cells are often<br />

referred to as tumor-initiating cells. The role of the microenvironment in the formation of these cells within the primary tumor and<br />

metastatic lesions is poorly understood. We are examining the effect of up-regulated hypoxia-inducible factor (HIF) signaling<br />

on tumor-initiating cell formation to determine whether HIF antagonists are useful adjuncts in preventing latent recurrence of<br />

osteosarcoma. We are also conducting genomic profiling studies of osteosarcomas to identify novel biomarkers and drug<br />

targets. This work is in collaboration with Drs. Craig Webb and Giselle Scholler. By comparing gene expression and mutational<br />

profiles of tumor-initiating cells with those of the bulk tumor, we aim to identify novel therapeutic targets specific to the most<br />

treatment-resistant cell populations.<br />

NF1 is an inherited disease that predisposes the affected individuals to both benign and malignant tumors. The lifetime incidence<br />

of sarcoma development in NF1 is about 10%, which is nearly 10,000-fold higher than for non-affected individuals. NF1-related<br />

sarcomas are highly aggressive and do not respond well to chemotherapy. Individuals with NF1 carry a mutation in one of<br />

two copies of the gene encoding neurofibromin (NF1), which results in deregulated RAS signaling. Loss of the second copy of<br />

NF1 is necessary for cancer to develop, but other factors have also been shown to be important for malignant transformation.<br />

Specifically, the lab is examining how HGF/MET signal activation drives both neurofibroma and neurofibrosarcoma development<br />

in the context of NF1. This work is being accomplished using novel, genetically engineered mouse models. Through a<br />

collaboration with Craig Webb, we are also applying a systems biology approach for analyzing clinical samples in anticipation<br />

of an NF1 personalized medicine trial.<br />

Recent Publications<br />

Steensma, Matthew, and John H. Healey. In press. Trends in the surgical treatment of pathologic proximal femur fractures<br />

among Musculoskeletal Tumor Society members. Clinical Orthopaedics and Related Research.<br />

Steensma, M.R., and C. Morris. In press. Ewing’s sarcoma. In Orthopaedic Knowledge Update, S. Biermann, ed. Rosemont,<br />

IL: American Academy of Orthopaedic Surgeons.<br />

Valkenburg, Kenneth C., Matthew R. Steensma, Bart O. Williams, and Zhendong Zhong. In press. Skeletal metastasis:<br />

treatments, mouse models, and Wnt signaling. Chinese Journal of Cancer.<br />

Zhong, Zhendong, Bart O. Williams, and Matthew R. Steensma. 2012. The activation of b-catenin by Gas contributes to the<br />

etiology of phenotypes seen in fibrous dysplasia and McCune-Albright syndrome. IBMS BoneKEy 9: 113.<br />


Steven J. Triezenberg, Ph.D.<br />

Laboratory of Transcriptional Regulation<br />

Dr. Triezenberg received his bachelor’s degree in biology and education at<br />

Calvin College in Grand Rapids, Michigan. His Ph.D. training in cell and<br />

molecular biology at the University of Michigan was followed by postdoctoral<br />

research with Steven L. McKnight at the Carnegie Institution of Washington.<br />

Dr. Triezenberg was a faculty member of the Department of Biochemistry<br />

and Molecular Biology at Michigan State University for more than 18 years,<br />

where he also served as associate director of the Graduate Program in Cell<br />

and Molecular Biology. In 2006, Dr. Triezenberg was recruited to VAI as the<br />

founding President and Dean of the Van Andel Institute Graduate School<br />

and as a researcher in VARI. He succeeded Dr. Gordon Van Harn as the<br />

Director of the Van Andel Education Institute in January 2009.<br />

From left: Akuli, Testori, Triezenberg, Klomp, Alberts, Thellman, Pikaart<br />

Staff<br />

Amy Akuli<br />

Glen Alberts, B.S.<br />

Jennifer Klomp, M.S.<br />

Marian Testori, B.S.<br />

Students<br />

Jamie Grit<br />

Nikki Thellman, D.V.M.<br />

Visiting Scientist<br />

Michael Pikaart, Ph.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

Our research is focused on the mechanisms that control whether genes are turned on or turned off inside cells. The genetic<br />

information encoded in DNA must first be copied, in the form of RNA, before it can be translated into the proteins that do<br />

most of the work in a cell. Some genes must be expressed more or less constantly throughout the life of any eukaryotic cell,<br />

while others must be turned on (or turned off) in particular cells either at specific times or in response to a specific signal or<br />

event. Regulation of gene expression helps determine how a given cell will function. Our laboratory explores the mechanisms<br />

that regulate the first step in that flow, the process known as transcription. We use infection by herpes simplex virus as an<br />

experimental context for exploring the mechanisms of transcriptional activation in human cells.<br />

Transcriptional activation during herpes simplex virus infection<br />

Herpes simplex virus type 1 (HSV-1) causes the common cold sore or fever blister. The initial lytic or productive infection by<br />

HSV-1 results in the obvious symptoms in the skin and mucosa, typically in or around the mouth. After the initial infection<br />

resolves, HSV-1 finds its way into nerve cells, where the virus can hide in a latent mode for long times—essentially for the<br />

lifetime of the host organism. Occasionally, some trigger event (such as emotional stress, damage to the nerve from a<br />

sunburn, or a root canal operation) will cause the latent virus to reactivate, producing new viruses in the nerve cell and sending<br />

those viruses back to the skin to cause a recurrence of the cold sore.<br />

The DNA genome of HSV-1 encodes approximately 80 different proteins. However, the virus does not have its own machinery<br />

for expressing those genes; instead, the virus must divert the gene expression machinery of the host cell. That process is<br />

triggered by a viral regulatory protein designated VP16, whose function is to stimulate transcription of the first viral genes to<br />

be expressed in the infected cell (the immediate-early, or IE, genes).<br />

Chromatin-modifying coactivators in herpes virus infections: a paradox leads to a hypothesis<br />

and yields an unexpected answer<br />

The strands of DNA in which the human genome is encoded are much longer than the diameter of a typical human cell. To<br />

help fit the DNA into the space of a cell, eukaryotic DNA is typically packaged as chromatin, in which the DNA is wrapped<br />

around “spools” of histone proteins, and these spools are then further arranged into higher-order structures. This elaborate<br />

packaging creates a problem when access is needed to the information carried in the DNA, such as when particular genes<br />

need to be expressed. This problem is solved in part by chromatin-modifying coactivator proteins, which either chemically<br />

change the histone proteins or else slide or remove them.<br />

Transcriptional activator proteins such as VP16 can recruit these chromatin-modifying coactivator proteins to target genes.<br />

We have shown this to be true for the viral genes that VP16 activates during an active infection. Curiously, however, the DNA<br />

of herpes simplex virus is not wrapped in histones inside the viral particle, and it also seems to stay relatively free of histones<br />

inside the infected cell. That observation leads to a paradox: why would VP16 recruit chromatin-modifying coactivators to the<br />

viral DNA, if the viral DNA doesn’t have much chromatin to modify?<br />

We took several approaches to test whether the coactivators recruited to viral DNA by the VP16 activation domain really<br />

play a significant role in transcriptional activation. In some experiments, we knocked down expression of given coactivators<br />

using short interfering RNAs (siRNAs). In other experiments, we used cell lines that have mutations disrupting the expression<br />

or activity of a given coactivator. We expected to find that viral gene expression was inhibited, but the experiments yielded<br />

unexpected results: in each case, expression of the viral genes was essentially unaffected. We were forced to conclude that<br />

our initial hypothesis was wrong; the coactivators, although present, are not required for viral gene expression during lytic<br />

infection.<br />


VARI | <strong>2013</strong><br />

The death of one hypothesis, however, gives life to new ideas. After the initial infection of a cold sore subsides, herpes simplex<br />

virus establishes a life-long latent infection in sensory neurons. In the latent state, the viral genome is essentially quiet; very<br />

few viral genes are expressed. Moreover, the viral genome becomes packaged in chromatin much like the silent genes of<br />

the host cell. So our new hypothesis is that the coactivators recruited by VP16 are required to reactivate the viral genes from<br />

the latent or quiescent state. We now have evidence that VP16 is likely the very first viral gene to be expressed during the<br />

reactivation process. We want to test whether the ability of VP16 to recruit coactivators is essential for subsequent events<br />

of reactivation. We will test this hypothesis both in quiescent infections in cultured cells and in animal models with genuinely<br />

latent herpesvirus infections.<br />

Regulating the regulatory proteins: posttranslational modifications of VP16<br />

The activity of a given protein is not only dependent on being expressed at the right time, but also on chemical modifications<br />

of its amino acids and on its interactions with other proteins. Proteins can be posttranslationally modified by adding chemical<br />

groups including phosphates, sugars, methyl or acetyl groups, lipids, or small proteins such as ubiquitin. Each of these<br />

modifications might affect the protein in different ways, including how the protein folds, how it interacts with other proteins,<br />

and how stable it remains in the cell.<br />

We know that VP16 can be phosphorylated, and we have already defined several sites within the VP16 protein where<br />

this happens. We are now testing whether these modifications matter for how VP16 functions, either as a transcriptional<br />

activator protein or as a structural protein of the HSV-1 virion. In some experiments, we create mutations that either prevent<br />

phosphorylation or that introduce an amino acid that mimics phosphorylation, and then we test the effects of these mutations<br />

on VP16 functions. In other experiments, we inhibit the enzymes that apply the modifications (for phosphorylation, these<br />

enzymes are known as protein kinases). We expect that this work will lead to new ideas about ways that we can selectively<br />

inhibit modification of VP16 using small-molecule drugs, and thereby prevent or shorten the infection process by HSV.<br />

Recent Publications<br />

Danaher, Robert J., Ross K. Cook, Chunmei Wang, Steven J. Triezenberg, Robert J. Jacob, and Craig S. Miller. In press.<br />

C-terminal trans-activation sub-region of VP-16 is uniquely required for forskolin-induced herpes simplex virus type 1<br />

reactivation from quiescently infected-PC12 cells but not for replication in neuronally differentiated-PC12 cells. Journal of<br />

Neurovirology.<br />

Silva, Lindsey, Hyung Suk Oh, Lynne Chang, Zhipeng Yan, Steven J. Triezenberg, and David M. Knipe. 2012. Roles of the<br />

nuclear lamina in stable nuclear association and assembly of a herpesviral transactivator complex on viral immediate-early<br />

genes. mBio 3(1): e00300–11.<br />

Sawtell, Nancy M., Steven J. Triezenberg, and Richard L. Thompson. 2011. VP16 serine 375 is a critical determinant of<br />

herpes simplex virus exit from latency in vivo. Journal of Neurovirology 17(6): 546–551.<br />


Jeremy M. Van Raamsdonk, Ph.D.<br />

Laboratory of Aging and Neurodegenerative Disease<br />

Jeremy Van Raamsdonk received a B.Sc. (Honours) in biochemistry from<br />

the University of British Columbia in 1993. After completing an M.Sc.<br />

in medical science at McMaster University in 1999, he returned to the<br />

University of British Columbia to complete a Ph.D. in medical genetics in<br />

2005. Subsequently, he became a postdoctoral fellow in the Department<br />

of Biology at McGill University until joining the Van Andel Research Institute<br />

as an Assistant Professor in 2012.<br />

Staff<br />

Kim Cousineau, B.S.<br />

Keith Dufendach, B.S.<br />

Megan Senchuk, Ph.D.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

As the average human life span continues to rise, the likelihood of an individual developing a neurodegenerative disease also<br />

increases. Thus, there is an increasing need to understand the aging process and its role in the development of age-onset<br />

disorders such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease. Research in this laboratory is focused<br />

on gaining insight into the aging process and the pathogenesis of such diseases. In addition to the obvious benefit to the<br />

individual, this work has the potential to be a great benefit to society by decreasing health care costs and helping to maintain<br />

productivity and independence to a later age.<br />

Oxidative stress and longevity<br />

The widely accepted free radical theory of aging (FRTA) proposes that aging results from the accumulation of oxidative damage<br />

caused by reactive oxygen species (ROS) generated during normal metabolism. Recent work in the worm Caenorhabditis<br />

elegans has indicated that the relationship between ROS and life span is more complex than anticipated. Decreasing the antioxidant<br />

defense through the deletion of individual, or combinations of, superoxide dismutase (SOD) genes does not decrease<br />

life span. This is contrary to expectations, because SOD is an enzyme that decreases the levels of ROS. In fact, quintuplemutant<br />

worms lacking all five sod genes live as long as wild-type worms, despite a markedly increased sensitivity to oxidative<br />

stress. Thus, it appears that while oxidative damage increases with age, it does not cause aging.<br />

Recent evidence suggests that increased levels of superoxide can act as a pro-survival signal that leads to increased longevity.<br />

This is demonstrated by the fact that either deletion of the mitochondrial superoxide dismutase gene sod-2 or treatment of<br />

wild-type worms with the superoxide generator paraquat results in increased life span. The fact that sod quintuple-mutant<br />

worms exhibit a normal life span despite markedly increased sensitivity to oxidative stress suggests a balance between<br />

superoxide-mediated pro-survival signaling and the toxic effects of superoxide.<br />

Thus, one of the main goals of this work is to elucidate the mechanism by which superoxide-mediated pro-survival signaling<br />

leads to increased longevity: how increased levels of superoxide trigger the signal, how the signal is transmitted, and what<br />

changes that the signal introduces lead to increased life span. These experiments use a combination of genetic mutants and<br />

RNA interference to gain insight into the signaling mechanism.<br />

The role of aging in neurodegenerative disease<br />

Advancing age is the greatest risk factor for the development of neurodegenerative disease. In the familial forms of these<br />

diseases, the mutation that causes the disease is present from birth, and yet the symptoms do not appear for several decades.<br />

This suggests that changes during normal aging may make cells more susceptible to the disease-causing mutations. This<br />

is supported by the fact that the onset of these disorders in animal models is proportional to the life span of the organism,<br />

indicating disease progression according to biological age and not chronological time. In fact, multiple changes are known<br />

to occur during normal aging that likely reduce the ability of cells to protect themselves against the effects of toxic diseasecausing<br />

proteins. In support of this concept, interventions that are known to extend life span, such as caloric restriction, have<br />

shown benefit in both worm and mouse models of Huntington’s disease. Thus, by gaining insight into the aging process<br />

and examining its role in the pathogenesis of neurodegenerative disease, it may be possible to develop treatments for these<br />

devastating disorders.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Huntington’s disease (HD) is an adult-onset neurodegenerative disorder characterized by motor dysfunction, cognitive deficits,<br />

and neuropsychiatric abnormalities. Disease onset typically occurs between the ages of 35 and 55 and progresses inevitably<br />

to death approximately 15 years later. The disease is caused by a trinucleotide CAG repeat expansion in the HD gene, which<br />

codes for the protein huntingtin (HTT). The CAG repeat sequence is translated into a polyglutamine tract in the HTT protein,<br />

and thus HD belongs to a group of at least nine polyglutamine toxicity disorders. Interestingly, while the size of the CAG repeat<br />

is polymorphic in unaffected individuals (ranging from 9 to 35 repeats), the disease range begins at precisely 35 CAG repeats,<br />

and the severity of the disease is correlated with the length of the repeat.<br />

Both worms and mouse models of HD have been created through transgenic expression of varying lengths of the huntingtin<br />

protein with a disease-length polyglutamine tract. The worm models express the mutant polyglutamine sequence either in<br />

body wall muscle or in neurons. These worms exhibit numerous abnormal phenotypes—including decreased life span, slow<br />

development, and decreased mobility—that are not observed in worms expressing a normal length repeat. Mouse models of<br />

HD have been shown to recapitulate almost all features of human HD, including motor deficits, cognitive deficits, and selective<br />

neurodegeneration.<br />

Our project examines 1) whether genes that increase life span will be beneficial in worm models of HD (i.e., will the increased<br />

longevity imparted by the aging gene reduce the severity of the polyglutamine toxicity phenotypes?), and 2) whether specific<br />

changes that take place during normal aging and that have been implicated in neurodegenerative disease contribute to pathogenesis<br />

in worm models of HD (i.e., do the higher levels of oxidative stress in older individuals contribute to pathogenesis?).<br />

Both of these objectives are being studied using two complementary approaches: genetic crosses to generate double mutants,<br />

and specific knockdown of gene expression using RNAi. The results from the worm screen will be used to prioritize the genes<br />

that will be studied in mouse models, which provide more physiologically accurate models of HD.<br />

Similar experiments are being conducted in animal models of Parkinson’s disease. By comparing the results, it will be possible<br />

to identify both overlapping and disease-specific mechanisms in these two neurodegenerative disorders.<br />


George F. Vande Woude, Ph.D.<br />

Laboratory of Molecular Oncology<br />

Dr. Vande Woude received his M.S. and Ph.D. degrees from Rutgers<br />

University. In 1972, he joined the National Cancer Institute as head of the<br />

Human Tumor Studies and Virus Tumor Biochemistry sections. In 1983, he<br />

became director of the Advanced Bioscience Laboratories–Basic Research<br />

Program at the Frederick Cancer Research and Development Center, a<br />

position he held until 1998. From 1995, Dr. Vande Woude first served as<br />

special advisor to the director, and then as director, of the Division of Basic<br />

Sciences at NCI. In 1999, he was recruited as the founding Director of<br />

VARI. In 2009, Dr. Vande Woude stepped down as Director while retaining<br />

his leadership of the Laboratory of Molecular Oncology as a Distinguished<br />

<strong>Scientific</strong> Fellow and Professor. Dr. Vande Woude is a member of the National<br />

Academy of Sciences (1993) and a Fellow of the American Academy of Arts<br />

and Sciences (2006).<br />

From left: Xie, Graveel, Su, Gao, Kang, Essenburg, Vande Woude, Linklater, Yerrum, Staal, Johnson, Zhang, Kaufman<br />

Staff<br />

Student<br />

Adjunct Faculty<br />

Curt Essenburg, B.S.<br />

Chongfeng Gao, Ph.D.<br />

Carrie Graveel, Ph.D.<br />

Jennifer Johnson, M.S.<br />

Liang Kang, B.S.<br />

Dafna Kaufman, M.S.<br />

Eric Linklater, B.S.<br />

Ben Staal, M.S.<br />

Yanli Su, A.M.A.T.<br />

Qian Xie, M.D., Ph.D.<br />

Smitha Yerrum, M.S.<br />

Yu-Wen Zhang, M.D., Ph.D<br />

Caroline Muhoro<br />

Brian Cao, M.D.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

Targeting the MET pathway in glioblastoma<br />

Glioblastoma multiforme (GBM) is one of the most devastating cancers. Its hallmark is the invasiveness of the tumor cells<br />

infiltrating into normal brain parenchyma, making it virtually impossible to remove the tumor completely by surgery and inevitably<br />

leading to recurrent disease. Progress in understanding GBM pathobiology and in developing novel antitumor therapies could<br />

be greatly accelerated with animal model systems that display characteristics similar to human GBM and that enable noninvasive<br />

tumor imaging in real time. We have established GBM patient-derived xenograft models that preserve tumor genotypes<br />

and phenotypes during in vivo passage, and we have isolated stem cell–like cancer populations for preclinical testing of drugs<br />

to block tumor growth and invasion. High-throughput, real-time, non-invasive imaging using bioluminescence (BLI) technology<br />

can detect orthotopic brain tumor growth before and after treatment. These studies have led to the conclusion that GBM with<br />

HGF-autocrine activation acts as if it were MET addicted and displays very high sensitivity to MET inhibitors. A combination of<br />

MET inhibitor and the EGFR inhibitor erlotinib showed better anti-tumor efficacy than either drug alone. We are planning further<br />

in vivo drug combination studies to try to develop drug strategies that will be more effective in treating MET expression in MET<br />

paracrine tumor systems.<br />

The role of MET in aggressive breast cancers<br />

Understanding the signaling pathways that drive aggressive breast cancers is crucial to the development of effective therapeutics.<br />

High expression of the oncogene MET is associated with decreased survival in breast cancer, yet the role it plays in the<br />

various breast cancer subtypes is unclear. We are investigating the role of MET in breast cancer progression and metastasis.<br />

Using a mouse model and analyses of human tissues, we have found that high MET expression correlates with estrogen<br />

receptor-negative/ERBB2-negative tumors and with basal breast cancers. We believe that MET is a key in the development<br />

of aggressive breast cancer subtypes and may be a significant therapeutic target. Currently, we are investigating how MET<br />

signaling interacts with the ERBB family of receptors in the progression and therapeutic resistance of ERBB2-positive and<br />

triple-negative breast cancers.<br />

MET as a therapeutic target in human cancers<br />

Aberrant activation of the HGF-MET signaling pathway is found in many human cancers, and it promotes cell proliferation,<br />

invasion and metastasis. Targeting this pathway is a promising approach to cancer intervention. We are using our unique<br />

human-HGF transgenic SCID mice to explore how effective such targeting may be in treating human cancers such as non-small<br />

cell lung cancer both in vitro and in vivo. Various MET drugs have been developed, and we are interested in identifying parallel<br />

pathways that cross-talk with MET or that are crucial in driving cancer cell resistance to MET drugs. We are also studying the<br />

benefits of combination treatments using MET inhibitors together with agents such as EGFR inhibitors.<br />

The role of Mig-6 in cancer and joint disease<br />

Mig6 is a tumor suppressor gene that functions as a negative feedback regulator in receptor tyrosine kinase signaling, either<br />

by direct binding to EGFR/ERBB family receptors or by interactions with signaling molecules downstream of the RTKs. Mig-6<br />

plays an important role in stress responses and tissue homeostasis, and its disruption in mice results in the development of<br />

neoplasia and degenerative joint disease. We have shown that Mig6 can be epigenetically silenced and differentially regulated<br />

in lung cancer and melanoma cells. Currently, we are investigating the roles and mechanisms of Mig-6 in cancer development<br />

and in the maintenance of joint homeostasis.<br />


VARI | <strong>2013</strong><br />

Tumor phenotypic switching: mechanism and therapeutic implications<br />

In human carcinomas, acquisition of an invasive phenotype requires a breakdown of intercellular junctions with neighboring<br />

cells, a process termed the epithelial-to-mesenchymal transition (E-MT). Paradoxically, metastatic carcinomas often exhibit<br />

an epithelial phenotype, leading to the hypothesis that E-MT is a transient process induced by microenvironmental factors.<br />

Upon arriving at secondary sites, the mesenchymal cells revert to an epithelial phenotype (mesenchymal-to-epithelial transition;<br />

M-ET). Typically, human carcinoma tissues and cells exhibit extensive heterogeneity in both phenotype and genotype,<br />

suggesting a role for genetic instability in cell type determination. To test this possibility, we have developed methods to isolate<br />

phenotypic variants from epithelial or mesenchymal subclones of carcinoma cell lines, as well as to identify subclones that<br />

switch phenotypically. We have explored the signal pathway underlying E-MT/M-ET phenotypic switching by gene expression<br />

analysis, spectral karyotyping (SKY), and fluorescent in situ hybridization (FISH). We found that changes in chromosome<br />

content are associated with phenotypic switching. We further showed that these changes dictated the expression of specific<br />

genes, which in E-MT events are mesenchymal and in M-ET events are epithelial. Our results suggest that chromosome<br />

instability can provide the diversity of gene expression needed for tumor cells to switch phenotype.<br />

Recent Publications<br />

Gherardi, Ermanno, Walter Birchmeier, Carmen Birchmeier, and George Vande Woude. 2012. Targeting MET in cancer:<br />

rationale and progress. Nature Reviews Cancer 12(2): 89–103.<br />

Kentsis, Alex, Casie Reed, Kim L. Rice, Takaomi Sanda, Scott J. Rodig, Eleni Tholouli, Amanda Christie, Peter J.M. Valk,<br />

Ruud Delwel, Vu Ngo, et al. 2012. Autocrine activation of the MET receptor tyrosine kinase in acute myeloid leukemia.<br />

Nature Medicine 18(7): 1118–1122.<br />

Nickoloff, Brian J., and George Vande Woude. 2012. Hepatocyte growth factor in the neighborhood reverses resistance to<br />

BRAF inhibitor in melanoma. Pigment Cell & Melanoma Research 25(6): 758–761.<br />

Xie, Qian, George F. Vande Woude, and Michael E. Berens. 2012. RTK inhibition: looking for the right pathways toward a<br />

miracle. Future Oncology 8(11): 1397–1400.<br />

Zhang, Yu-Wen, Ben Staal, Karl J. Dykema, Kyle A. Furge, and George F. Vande Woude. 2012. Cancer-type regulation of<br />

MIG-6 expression by inhibitors of methylation and histone deacetylation. PLoS One 7(6): e38955.<br />

Xie, Qian, Robert Bradley, Liang Kang, Julie Koeman, Maria Libera Ascierto, Andrea Worschech, Valeria De Giorgi, Ena Want,<br />

Lisa Kefene, Yanli Su, et al. 2011. Hepatocyte growth factor (HGF) autocrine activation predicts sensitivity to MET inhibition in<br />

glioblastoma. Proceedings of the National Academy of Sciences U.S.A. 109(2): 570–575.<br />

Xie, Qian, Robert Wondergem, Yuehai Shen, Greg Cavey, Jiyuan Ke, Ryan Thompson, Robert Bradley, Jennifer Daugherty-<br />

Holtrop, Yong Xu, Edwin Chen, et al. 2011. Benzoquinone ansamycin 17AAG binds to mitochondrial voltage-dependent anion<br />

channel and inhibits cell invasion. Proceedings of the National Academy of Sciences U.S.A. 108(10): 4105–4110.<br />


Craig P. Webb, Ph.D.<br />

Laboratory for Translational Medicine<br />

Dr. Webb received his Ph.D. in cell biology from the University of East Anglia,<br />

England, in 1995. From 1995 to 1999, he was a postdoctoral fellow with<br />

George Vande Woude at the National Cancer Institute–Frederick Cancer<br />

Research and Development Center, Maryland. Dr. Webb joined VARI in<br />

October 1999 and was promoted to Professor in 2008. He is also co-<br />

Director of the Pediatric Cancer Translational Research Program.<br />

From left: Webb, Moon, Popkie, Davidson, Eugster, Dylewski, Orey, Monsma, Scott, Montroy, Monks, Cherba, Mooney<br />

Staff<br />

Students<br />

Visiting<br />

Scientists<br />

Adjunct<br />

Faculty<br />

David Cherba, Ph.D.<br />

Paula Davidson, M.S.<br />

Dawna Dylewski, B.S.<br />

Emily Eugster, M.S.<br />

Noel Monks, Ph.D.<br />

David Monsma, Ph.D.<br />

Rob Montroy, B.E.<br />

Lori Moon, M.B.A.<br />

Anthony Popkie, Ph.D.<br />

Stephanie Scott, B.S.<br />

Marie Mooney, M.S.<br />

Stephen Orey, B.S.<br />

Jessica Foley, M.D.<br />

Eric Kort, M.D.<br />

Debra Weist, Ph.D.<br />

Eric Lester, M.D.<br />

Laurence McCahill, M.D.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

The Laboratory of Translational Medicine (LTM) is a multidisciplinary group with both basic and applied research components.<br />

Our basic research is focused on deciphering the molecular basis of solid tumor metastasis, with particular emphasis on the<br />

role of the putative cancer stem cell and tumor-host interactions during the early establishment and subsequent progression<br />

of metastases in critical organs such as the liver and lung. We focus on pancreatic cancer, triple-negative breast cancer,<br />

melanoma, adult and pediatric brain tumors, and pediatric osteosarcoma. Our applied research efforts have resulted from<br />

our development of the translational research infrastructure needed to permit real-time, precision medicine (PMed) clinical<br />

trials for patients with metastatic and/or refractory disease. Through our expertise and resources in bioinformatics, genomics,<br />

preclinical models, clinical trial design, and regulatory affairs, the lab is currently supporting prospective PMed trials in pediatric<br />

and adult human patients, as well as in canines with advanced-stage tumors. Given these collective capabilities, the laboratory<br />

is initiating collaborative efforts to repurpose existing drugs for specific patient populations.<br />

Pancreatic cancer<br />

Pancreatic cancer (PCa) is the fourth leading cause of cancer-related mortality in the United States, with an estimated 37,000<br />

deaths per year and a dismal 5-year survival of less than 6% that has not improved greatly over the past 30 years. As in<br />

other cancers, the development of secondary metastases within critical organs, notably the liver, accounts for the majority of<br />

PCa-related morbidity and mortality. Identifying the key determinants that drive the early establishment and progression of liver<br />

metastases is paramount to improving long-term outcomes for patients. Current efforts within the LTM include investigating<br />

the interaction between PCa cells and the host macrophages (Kupffer cells) and stellate cells within the micro-metastatic niche<br />

of the liver.<br />

Metastatic melanoma<br />

Patients who develop metastatic melanoma (MM) have a poor prognosis, with a median survival of 6–9 months and a 3-year<br />

survival rate of 10–15%. The tumors of approximately 40% of MM patients harbor an activating mutation in the BRAF gene<br />

which confers sensitivity to B-Raf inhibitors such as the recently approved agent vemurafenib. Through the award of a Stand-<br />

Up-2-Cancer grant, we are enhancing the lab’s PMed bioinformatics framework to incorporate next-generation sequencing and<br />

phosphoproteomic technologies. The goal of this project is to identify, in real time, the key molecular drivers of B-Raf wild-type<br />

MM and align these findings to a series of experimental agents from biopharmaceutical companies; patients will be treated on<br />

the basis of these real-time findings.<br />

In patients whose MM harbors an oncogenic BRAF mutation, the tumors initially show an impressive response to B-Raf<br />

inhibitors such as vemurafenib. However, the synchronous regrowth of tumors after a period of treatment is a common<br />

occurrence. To investigate the molecular mechanism of drug resistance, the lab has developed a large number of primary patient<br />

tumorgrafts for many solid tumors (including MM) that closely resemble the patient’s tumor at the molecular, histopathological,<br />

and treatment-response levels. These models preserve a number of key aspects of the tumor-host microenvironment. We are<br />

using these tumorgraft models to investigate the role that the innate immune systems play in the onset of drug resistance in<br />

MM and developing combination treatment strategies to treat vemurafenib-resistant MM.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Triple-negative breast cancer<br />

The breast cancers referred to as triple negative (ER – , PR – , HER2 – ) represent a highly aggressive subtype for which no effective<br />

therapies exist. Thus, patients with triple-negative breast cancer (TNBrCa) have a poor prognosis. Within a heterogeneous<br />

tumor there resides a subpopulation of cells with stem cell–like properties known as cancer stem cells (CSCs). According to<br />

the CSC hypothesis, a hierarchical tumor organization exists in which deregulated, self-renewing CSCs drive tumorigenesis.<br />

CSCs are believed to be the key malignant cell contributing to metastasis and drug resistance, and targeting these cells<br />

therefore represents an excellent therapeutic opportunity against multiple tumor types including TNBrCa. Through a Komen<br />

Promise grant, the lab is working to characterize the CSCs from TNBrCa patients of different ethnic backgrounds at the genetic,<br />

epigenetic, and genomic levels to identify candidate targets for therapy.<br />

Adult and pediatric glioblastoma<br />

Glioblastoma (GBM) represents a group of highly aggressive and often recurrent brain tumors that affect both adults and<br />

children. Adult and pediatric GBM are largely indistinguishable by morphology or pathology, and their treatment regimens have<br />

been similar, with overall poor success. Some recent molecular characterization of GBMs from the two patient populations<br />

suggests that the molecular drivers of disease may be quite distinct, warranting different treatment considerations. Efforts in<br />

the lab include the identification of key signaling pathways in both adult and pediatric GBM and the evaluation of combinational<br />

treatment strategies for each.<br />

Osteosarcoma<br />

Osteosarcoma (OSA) is the most common primary bone malignancy in children, with a high rate of local recurrence and<br />

metastasis to the lungs. We have recently initiated efforts to characterize the CSCs within pediatric OSA with the goal of<br />

identifying CSC-directed therapies. These efforts will soon be expanded to implement a prospective PMed clinical trial in<br />

pediatric patients with OSA. As the most common primary bone tumor in dogs, canine OSA is comparable to the human<br />

disease at many levels, including its high propensity to metastasize to the lungs. We are also assessing our PMed approach<br />

for canine OSA patients to determine the feasibility of genomically profiling the disease in real time to support therapy selection<br />

by veterinarians.<br />

Recent Publications<br />

Sholler, Giselle L. Saulnier, William Ferguson, Genevieve Bergendahl, Erika Currier, Shannon R. Lenox, Jeffrey Bond,<br />

Marni Slavik, William Roberts, Deanna Mitchell, Don Eslin, et al. In press. A pilot trial testing the feasibility of using molecularguided<br />

therapy in patients with recurrent neuroblastoma. Journal of Cancer Therapy.<br />

Mazzarella, Richard, and Craig P. Webb. 2012. Computational and bioinformatic strategies for drug repositioning. In Drug<br />

Repositioning: Bringing New Life to Shelved Assets and Existing Drugs, Michael J. Barratt and Donald E. Frail, eds. New York:<br />

Wiley and Sons, pp. 91–128.<br />

Monsma, David J., Noel R. Monks, David M. Cherba, Dawna Dylewski, Emily Eugster, Hailey Jahn, Sujata Srikanth,<br />

Stephanie B. Scott, Patrick J. Richardson, Robin E. Everts, et al. 2012. Genomic characterization of explant tumorgraft<br />

models derived from fresh patient tumor tissue. Journal of Translational Medicine 10: 125.<br />

Lee, Chih-Shia, Karl J. Dykema, Danielle M. Hawkins, David M. Cherba, Craig P. Webb, Kyle A. Furge, and Nicholas S. Duesbery.<br />

2011. MEK2 is sufficient but not necessary for proliferation and anchorage-independent growth of SK-MEL-28 melanoma<br />

cells. PLoS One 6(2): e17165.<br />


Michael Weinreich, Ph.D.<br />

Laboratory of Genome Integrity and Tumorigenesis<br />

Dr. Weinreich received his Ph.D. in biochemistry from the University of<br />

Wisconsin–Madison, after which he was a postdoctoral fellow in the<br />

laboratory of Bruce Stillman, director of Cold Spring Harbor Laboratory,<br />

New York. Dr. Weinreich joined VARI in March 2000 and is currently an<br />

Associate Professor.<br />

From left: Weinreich, Chang, Minard, Chen, Kenworthy, Tiwari<br />

Staff<br />

FuJung Chang, M.S.<br />

Jessica Kenworthy, B.S.<br />

Michelle Minard<br />

Kanchan Tiwari, M.S.<br />

Students<br />

Ying-Chou Chen, M.S.<br />

Nanda Kumar Sasi, B.S.<br />

Sandya Subramanian<br />

Raymond Yeow<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Research Interests<br />

The goal of our research is to understand how cells stably and accurately maintain their genetic information. Many diseases,<br />

including cancer, are caused by mutations in DNA, and it is now clear that the development of cancer requires multiple<br />

independent mutations. Early mutations often impair cellular surveillance mechanisms (checkpoints) that maintain genetic<br />

stability, and, in the absence of such checkpoints, additional mutations and genetic alterations become more frequent. This<br />

cumulative burden can ultimately lead to cancer as cells escape the normal growth and proliferation controls. Genetic instability<br />

also explains why cancer treatments often fail: tumors have such high mutation rates that they can readily develop resistance<br />

to chemotherapeutic drugs.<br />

The two-subunit Dbf4-dependent kinase (DDK) that we study (also known as Cdc7-Dbf4 protein kinase) is critical for the<br />

accurate replication and segregation of chromosomes. DDK is required for the initiation of DNA replication at multiple independent<br />

origins throughout the genome. It accomplishes this by phosphorylating and activating the MCM helicase, previously<br />

loaded in an inactive form at all origins during G1 phase. It is clear that DDK also affects replication fork stability and DNA<br />

repair processes during S phase, although the mechanisms for these activities are poorly understood. We recently reported<br />

that Dbf4 interacts with the yeast Polo-like kinase, Cdc5, to maintain the spindle position checkpoint. Polo kinases are master<br />

regulators of mitotic events. For example, Cdc5 promotes the loss of chromosome cohesion during metaphase, entry into<br />

anaphase, spindle elongation, exit from mitosis, and cytokinesis. Because of its essential role during mitosis, Cdc5 is the target<br />

of multiple checkpoint mechanisms to ensure the accurate segregation of chromosomes. We found that DDK inhibits Cdc5<br />

when the mitotic spindle apparatus is not properly aligned between mother and daughter cells. Loss of this regulation can<br />

cause a significant increase in chromosome mis-segregation events and cell death.<br />

The DNA damage and replication checkpoints are critical regulators of chromosome stability. The checkpoints facilitate repair<br />

of DNA damage, suppress late-origin firing, and also prevent premature entry into mitosis, which would be catastrophic with<br />

damaged or incompletely replicated chromosomes. The Rad53 protein kinase of yeast, the ortholog of the human tumor suppressor<br />

Chk2, is an essential regulator of these checkpoints and directly interacts with Dbf4. Rad53 phosphorylates Dbf4 to<br />

prevent the activation of late origins when replication forks stall, and our genetic data imply that Rad53 and DDK also cooperate<br />

in another (unknown) pathway that is essential for cell survival.<br />

We have recently investigated the basis of the molecular interaction between Dbf4 and Rad53. Rad53 likely binds Dbf4 using<br />

multiple protein-protein contacts in the Dbf4 N-terminus. Interestingly, loss of the Rad53-Dbf4 regulation leads to activation of<br />

late-origin firing during periods of replication stress. It is unknown how Rad53 phosphorylation prevents late-origin activation,<br />

since we have shown that Rad53 phosphorylation does not disrupt the Dbf4-Cdc7 interaction and results in only a modest<br />

decrease in DDK activity. The Rad53 protein binds to the Dbf4 N-terminus but phosphorylates critical residues in the Dbf4<br />

C-terminus to prevent late-origin activation.<br />

In summary, work over the last several years has shown that Dbf4 acts as a molecular scaffold to bind three separate protein<br />

kinases: Cdc7, Cdc5, and Rad53 (Figure 1). Binding of Cdc7 occurs through essential middle and C-terminal Dbf4 residues.<br />

Binding of Cdc5 and Rad53 occurs through Dbf4 N-terminal residues that have evolved a checkpoint effector role to mediate<br />

the response to DNA damage, replication fork stalling, and chromosome segregation defects. Many different types of tumors<br />

show increased levels of DDK, and inhibiting DDK causes the death of many types of tumor cells, but not normal cells. Because<br />

the ability of DDK to control multiple aspects of chromosome metabolism is likely conserved, it is crucial to understand these<br />

pathways in order to further the development of highly effective chemotherapeutic agents and interventions.<br />


VARI | <strong>2013</strong><br />

Figure 1<br />

Figure 1: Dbf4 is a molecular scaffold for three protein kinases and controls genome integrity at multiple levels. Dbf4 binds Cdc7<br />

kinase through C-terminal sequences to initiate DNA replication. Dbf4 binds Cdc5 (Polo kinase) and Rad53 (Chk2 kinase) through<br />

adjacent N-terminal sequences to control cell cycle progression in response to spindle and/or genomic stresses.<br />

Recent Publications<br />

Chang, FuJung, Caitlin D. May, Timothy Hoggard, Jeremy Miller, Catherine A. Fox, and Michael Weinreich. 2011. Highresolution<br />

analysis of four efficient yeast replication origins reveals new insights into the ORC and putative MCM binding<br />

elements. Nucleic Acids Research 39(15): 6523–6535.<br />


Bart O. Williams, Ph.D.<br />

Laboratory of Cell Signaling and Carcinogenesis<br />

Dr. Williams received his Ph.D. in biology from Massachusetts Institute of<br />

Technology in 1996 under the supervision of Tyler Jacks. He joined VARI in<br />

July 1999 and was promoted to Associate Professor in 2006. Prior to his<br />

recruitment, he was a postdoctoral fellow at the National Institutes of Health<br />

in the laboratory of Harold Varmus.<br />

From left: Valkenburg, Maupin, Zahatnansky, Van Wieren, Williams, Burgers, Haider, Joiner, Diegel, Lewis, Droscha<br />

Staff<br />

Students<br />

Adjunct Faculty<br />

Travis Burgers, Ph.D.<br />

Cassie Diegel, B.S.<br />

Danese Joiner, Ph.D.<br />

Diana Lewis, A.S.<br />

Emily Van Wieren, B.S.<br />

Juraj Zahatnansky, M.D.<br />

Alex Zhong, Ph.D.<br />

Casey Droscha, B.S.<br />

Rida Haider, M.S.<br />

Kevin Maupin, B.S.<br />

Ken Valkenberg, B.S.<br />

Clifford Jones, M.D.<br />

Madhuri Kakarala, M.D., Ph.D.<br />

Charlotta Lindvall, M.D., Ph.D.<br />

Debra Sietsema, Ph.D., RN<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

Our laboratory is interested in understanding how alterations in the Wnt signaling pathway cause human disease. Wnt signaling is<br />

an evolutionarily conserved process that functions in the differentiation of most tissues within the body. Wnt proteins initiate several<br />

signaling pathways, including one that results in the activation of the b-catenin protein and its downstream signaling targets.<br />

Given its central role in growth and differentiation, it is not surprising that alterations in the Wnt pathway are among the most<br />

common events associated with human cancer. In addition, other human diseases including osteoporosis, cardiovascular<br />

disease, neurodegenerative diseases, and diabetes have been linked to altered regulation of this pathway. Our main approach<br />

toward gaining insights into the mechanisms of Wnt signaling in development and disease is to create and characterize<br />

genetically engineered mouse models. We have pursued studies in three key areas outlined below. In addition, we are<br />

interested in understanding the molecular mechanisms by which specificity is generated by Wnts.<br />

Wnt signaling in skeletal development and disease<br />

A specific focus of our work is characterizing the role of Wnt signaling in skeletal development and disease. Mutations in the<br />

Wnt receptor Lrp5 have been causally linked to alterations in human bone development. Several years ago, we characterized<br />

a mouse strain carrying a germline deletion in Lrp5 and found that it recapitulated the low-bone-density phenotype seen in<br />

human patients who have a LRP5 deficiency. We further found that mice carrying germline deletions in both Lrp5 and the<br />

related Lrp6 protein have even more-severe defects in bone density. We next created mice carrying an osteoblast-specific<br />

deletion of b-catenin. Those mice have severely diminished bone mass and elevated osteoclastogenesis associated with<br />

changes in the expression of RANKL and osteoprotegerin. Our next step was to create and evaluate mice carrying osteoblastspecific<br />

deletions of Lrp6 and Lrp5. We have found that mice carrying deletions in either gene alone have reduced bone mass,<br />

and mice lacking both genes in osteoblasts have more-severe phenotypes.<br />

More recent studies have focused on gaining insight into the cell type(s) that secrete the Wnts necessary for normal bone<br />

development. Our strategy has used mice carrying osteoblast-specific deletions of the Wntless/Gpr177 (Wls) gene. Wls<br />

encodes a protein specifically required for secretion of all mammalian Wnts, and a mouse strain carrying a Wls allele that<br />

can be conditionally inactivated was developed by our collaborator, Richard Lang. We have generated mice carrying an<br />

osteoblast-specific deletion of this gene and found that mature osteoblasts are a crucial source of the Wnts required for normal<br />

skeletal development.<br />

Current work is also focusing on evaluating the roles of Wnt signaling in osteoarthritis and fracture repair, as well examining how<br />

other signaling pathways integrate with Wnt/b-catenin signaling to control osteoblast differentiation and function. Two such<br />

examples are the effects of parafibromin on regulating transcriptional outputs through its interaction with b-catenin and the<br />

potential role of galectin-3 in this process.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Wnt signaling in mammary development and cancer<br />

Activation of the Wnt signaling pathway has been linked to the development of some types of breast tumors. We are using<br />

genetically engineered mouse models to assess the roles of Wnt signaling in mammary development and carcinogenesis.<br />

Mice carrying conditional deletions of Lrp5 and / or Lrp6 in mammary epithelial cells have been developed and are being<br />

characterized. We are evaluating the role that activation of Wnt signaling plays in establishing and maintaining tumor-initiating<br />

cells within the mammary gland. We are also examining the source of Wnts necessary for normal mammary development and<br />

for the maintenance of some types of breast tumors.<br />

Wnt signaling in prostate development and cancer<br />

A hallmark of advanced prostate cancer is the development of skeletal osteoblastic metastases. The association of Wnt<br />

signaling with bone growth makes Wnt signaling an attractive candidate for explaining some phenotypes associated with<br />

advanced prostate cancer. As a first step to understanding the role of Wnt signaling in prostate carcinogenesis, we have<br />

generated mice carrying prostate-epithelial-specific deletion of Apc. We have found that mice carrying conditional deletions<br />

induced by either probasin-Cre or Nkx3.1-Cre develop prostate tumors having similar latency and pathology. Further, we are<br />

directly examining the role of Wnt signaling by assessing the effects of inhibiting the secretion of Wnts in models of skeletal<br />

metastases. We also have a specific interest in examining the role of Wnt5a in this process.<br />

Recent Publications<br />

Joiner, Danese M., Jiyuan Ke, Zhendong Zhong, H. Eric Xu, and Bart O. Williams. <strong>2013</strong>. LRP5 and LRP6 in development and<br />

disease. Trends in Endocrinology and Metabolism 24(1): 31–39.<br />

Fortin, Shannon P., Matthew J. Ennis, Cassie A. Schumacher, Cassandra R. Zylstra-Diegel, Bart O. Williams, Julianna T.D. Ross,<br />

Jeffrey A. Winkles, Joseph C. Loftus, Marc H. Symons, and Nhan L. Tran. 2012. Cdc42 and the guanine nucleotide exchange<br />

factors Ect2 and Trio mediate Fn14-Rac1-induced migration and invasion of glioblastoma cells. Molecular Cancer Research<br />

10(7): 958–968.<br />

Ke, Jiyuan, Chenghai Zhang, Kaleeckal G. Harikumar, Cassandra R. Zylstra-Diegel, Liren Wang, Laura E. Mowry, Laurence J.<br />

Miller, Bart O. Williams, and H. Eric Xu. 2012. Modulation of b-catenin signaling by glucagon receptor activation. PLoS One<br />

7(3): e33676.<br />

Li, Yi, Andrea Ferris, Brian C. Lewis, Sandra Orsulic, Bart O. Williams, Eric C. Holland, and Stephen H. Hughes. 2012. The<br />

RCAS/TVA somatic gene transfer method in modeling human cancer. In Genetically Engineered Mice for Cancer Research,<br />

Jeffrey E. Green and Thomas Ried, eds. Berlin: Springer Verlag, pp. 83–112.<br />

Zhong, Zhendong., and Bart O. Williams. 2012. Integration of cellular adhesion and Wnt signaling: interactions between<br />

N-cadherin and LRP5 and their role in regulating bone mass. Journal of Bone and Mineral Research 27(9): 1849–1851.<br />

Zhong, Zhendong, Bart O. Williams, and Matthew R. Steensma. 2012. The activation of b-catenin by Gas contributes to the<br />

etiology of phenotypes seen in fibrous dysplasia and McCune-Albright syndrome. IBMS BoneKEy 9: 113.<br />

Zhong, Zhendong, Cassandra R. Zylstra-Diegel, Cassie A. Schumacher, Jacob J. Baker, April C. Carpenter, Sujata Rao, Wei<br />

Yao, Min Guan, Jill A. Helms, Nancy E. Lane, et al. 2012. Wntless functions in mature osteoblasts to regulate bone mass.<br />

Proceedings of the National Academy of Sciences U.S.A. 109(33): E2197–E2204.<br />


Improving<br />

pancreatic<br />

cancer markers.<br />

These plots show two sets of results from a test of<br />

new markers to aid in the accurate diagnosis of pancreatic<br />

cancer. The current best marker (data set M1) is the total amount<br />

of a glycan called CA 19-9. We are testing a combination panel of the<br />

CA 19-9 assay with two additional markers (data sets M2 and M3) of CA<br />

19-9 bound to specific proteins. Each column represents a patient sample, and<br />

a yellow square indicates a higher level of a marker than normal. If any of the panel<br />

markers are elevated in a given sample, the sample is classified as cancer, indicated by a<br />

yellow square in the bottom (classification) row. The three-marker panel has more true positives<br />

(TP) and fewer false negatives (FN) than the CA 19-9 assay alone, while maintaining low false-positive<br />

(FP) and high true-negative (TN) results. Plots provided by the Haab laboratory.

H. Eric Xu, Ph.D.<br />

Laboratory of Structural Sciences<br />

Dr. Xu went to Duke University and the University of Texas Southwestern<br />

Medical Center, where he earned his Ph.D. in molecular biology and<br />

biochemistry. Following a postdoctoral fellowship with Carl Pabo at<br />

MIT, he moved to GlaxoWellcome in 1996 as a research investigator of<br />

nuclear receptor drug discovery. Dr. Xu joined VARI in July 2002 and<br />

was promoted to Professor in March 2007. Dr. Xu is also the Primary<br />

Investigator and Distinguished Director of the VARI/SIMM Research<br />

Center in Shanghai, China.<br />

From left: Zhi, Gao, Ke, Cheng, Sridharamurthy, Lili Wang, Weber, Xu, Kang, He, Pal, Li, Liren Wang, Hou, deWaal<br />

Staff<br />

Xiang Gao, Ph.D.<br />

Yuanzheng (Ajian) He, Ph.D.<br />

Yanyong Kang, Ph.D.<br />

Jiyuan Ke, Ph.D.<br />

Kuntal Pal, Ph.D.<br />

Kelly Powell, B.S.<br />

Stephanie Weber, B.S.<br />

Xiaoyong Zhi, Ph.D.<br />

Students<br />

Hao Cheng, B.S.<br />

Parker deWaal<br />

Li Hou, M.S.<br />

Xiaodan Li, B.S.<br />

Madhuri Sridharamurthy, B.S.<br />

Lili Wang, B.S.<br />

Liren Wang, B.S.<br />

Zhongshan Wu, B.S.<br />


VARI | <strong>2013</strong><br />

Research Interests<br />

Hormone signaling is essential to eukaryotic life. Our research is focused on the signaling mechanisms of physiologically<br />

important hormones, striving to solve fundamental questions that have a broad impact on human health and disease. The<br />

overall goal of my research program is to seek new biological paradigms through structural and functional analysis of key<br />

hormone signaling complexes and to develop therapeutic applications using the structural information we obtain. My current<br />

research programs are focused on two families of proteins, the nuclear hormone receptors and the G protein–coupled<br />

receptors, because these proteins, beyond their fundamental roles in biology, are important drug targets for treating major<br />

human diseases.<br />

Nuclear hormone receptors<br />

Nuclear hormone receptors are a large family comprising ligand-regulated and DNA-binding transcriptional factors, which<br />

include receptors for classic steroid hormones such as estrogen, progesterone, androgens, and glucocorticoids, as well as<br />

receptors for peroxisome proliferator activators, vitamin D, vitamin A, and thyroid hormones. One distinguishing fact about<br />

these classic receptors is that they are among the most successful targets in the history of drug discovery. Every receptor has<br />

one or more cognate synthetic ligands being used as medicines. Nuclear receptors also include a class of “orphan” receptors<br />

for which no ligand has been identified. In the last five years, we have developed the following projects centering on the<br />

structural biology of nuclear receptors.<br />

Peroxisome proliferator–activated receptors<br />

The peroxisome proliferator–activated receptors (PPAR a, d, and g) are the key regulators of glucose and fatty acid homeostasis<br />

and as such are important therapeutic targets for treating cardiovascular disease, diabetes, and cancer. Millions of patients<br />

have benefited from treatment with the novel PPARg ligands rosiglitazone and pioglitazone for type II diabetes. To understand<br />

the molecular basis of ligand-mediated signaling by PPARs, we have determined crystal structures of each PPAR’s ligandbinding<br />

domain (LBD) bound to many diverse ligands, including fatty acids, the lipid-lowering drugs called fibrates, and the<br />

new generation of anti-diabetic drugs, the glitazones. We have also determined the crystal structures of these receptors<br />

bound to co-activators or co-repressors, and the crystal structure of PPARg bound to a nitrated fatty acid. These structures<br />

have provided a framework for understanding the mechanisms of agonists and antagonists, as well as the recruitment of<br />

co-activators and co-repressors in gene activation and repression. Furthermore, these structures serve as a molecular basis<br />

for understanding the potency, selectivity, and binding mode of diverse ligands, and have provided crucial insights for designing<br />

the next generation of PPAR medicines. We have discovered a number of natural ligands of PPARg, and our plan is to test<br />

their physiological roles in glucose and insulin regulation, to unravel their molecular and structural mechanisms of action, and<br />

to develop them into therapeutics for diabetes and dislipidemia.<br />

The human glucocorticoid receptor<br />

The human glucocorticoid receptor (GR), the prototype steroid hormone receptor, is crucial for a wide spectrum of human<br />

physiology including immune/inflammatory responses, metabolic homeostasis, and control of blood pressure. GR is a wellestablished<br />

target for drugs, and those drugs have an annual market of over $10 billion. GR ligands such as dexamethasone<br />

(Dex) and fluticasone propionate (FP) are used to treat asthma, leukemia, and autoimmune diseases. However, the clinical use<br />

of these ligands is limited by undesirable side effects partly associated with their receptor cross-reactivity or low potency. The<br />

discovery of potent and more-selective GR ligands—called “dissociated glucocorticoids”, which can separate the good effects<br />

from the bad—remains an intensive goal of pharmaceutical research.<br />

We have determined a number of crystal structures of GR bound to unique ligands and have found an unexpected regulatory<br />

mechanism: GR degradation by lysosomes. We also are studying the molecular and structural mechanisms of the dissociated<br />

glucocorticoids identified by our research.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Structural genomics of nuclear receptor ligand-binding domains<br />

The LBD of a nuclear receptor contains key structural elements that mediate ligand-dependent regulation of the receptors<br />

and as such has been the focus of intense structural studies. Crystal structures for more than half of the 48 human nuclear<br />

receptors have been determined. These structures have illustrated the details of ligand binding, the conformational changes<br />

induced by agonists and antagonists, the basis of dimerization, and the mechanism of co-activator and co-repressor binding.<br />

The structures also have provided many surprises regarding the identity of ligands, the size and shape of the ligand-binding<br />

pockets, and the structural implications of the receptor signaling pathways. There are only a few orphan nuclear receptors for<br />

which the LBD structure remains unsolved; in the past few years, we have determined the crystal structures of those for CAR,<br />

SHP, SF-1, COUP-TFII, and LRH-1. Our structures have helped to identify new ligands and signaling mechanisms for orphan<br />

nuclear receptors.<br />

G protein–coupled receptors (GPCRs)<br />

The GPCRs form the largest family of receptors in the human genome. They receive a diverse set of signals carried by photons,<br />

ions, small chemicals, peptides, and large protein hormones. These receptors account for over 40% of drug targets, but their<br />

structures remain a challenge, because they are seven-transmembrane receptors. There are only a few crystal structures<br />

for class A GPCRs, and many important questions regarding GPCR ligand binding and activation remain unanswered. From<br />

our standpoint, GPCRs are similar to nuclear hormone receptors with respect to regulation by protein-ligand and proteinprotein<br />

interactions. Currently my group is focused on class B GPCRs, which includes receptors for parathyroid hormone<br />

(PTH), corticotropin-releasing factor (CRF), glucagon, and glucagon-like peptide-1. We have determined crystal structures<br />

of the ligand binding domain of the PTH receptor and the CRF receptor, and we are developing hormone analogs for treating<br />

osteoporosis, depression, and diabetes. In addition, we are developing a mammalian overexpression system and plan to use<br />

it to express full-length GPCRs for crystallization and structural studies.<br />

Recent Publications<br />

Ke, Jiyuan, Chenghai Zhang, Kaleeckal G. Harikumar, Cassandra R. Zylstra-Diegel, Liren Wang, Laura E. Mowry, Laurence<br />

J. Miller, Bart O. Williams, and H. Eric Xu. 2012. Modulation of b-catenin signaling by glucagon receptor activation.<br />

PLoS One 7(3): e33676.<br />

Pal, Kuntal, Karsten Melcher, and H. Eric Xu. 2012. Structure and mechanism for recognition of peptide hormones by Class<br />

B G-protein-coupled receptors. Acta Pharmacologica Sinica 33(3): 300–311.<br />

Soon, Fen-Fen, Ley-Moy Ng, X. Edward Zhou, Graham M. West, Amanda Kovach, M.H. Eileen Tan, Kelly M. Suino-Powell,<br />

Yuanzheng He, Yong Xu, Michael J. Chalmers, et al. 2012. Molecular mimicry regulates ABA signaling by SnRK2 kinases<br />

and PP2C phosphatases. Science 335(6064): 85–88.<br />

Soon, Fen-Fen, Kelly M. Suino-Powell, Jun Li, Eu-Leong Yong, H. Eric Xu, and Karsten Melcher. 2012. Abscisic acid signaling:<br />

thermal stability shift assays as tool to analyze hormone perception and signal transduction. PLoS One 7(10): e47857.<br />

Yu, Shanghai, and H. Eric Xu. 2012. Couple dynamics: PPARg and its ligand partners. Structure 20(1): 2–4.<br />

Zhou, X. Edward, Fen-Fen Soon, Ley-Moy Ng, Amanda Kovach, Kelly M. Suino-Powell, Jun Li, Eu-Leong Yong, Jian-Kang<br />

Zhu, H. Eric Xu, and Karsten Melcher. 2012. Catalytic mechanism and kinase interactions of ABA-signaling PP2C<br />

phosphatases. Plant Signaling & Behavior 7(5): 581–588.<br />


Awards for <strong>Scientific</strong> Achievement

VARI | <strong>2013</strong><br />

Jay Van Andel Award for Outstanding<br />

Achievement in Parkinson’s Disease Research<br />

This award was established to honor distinguished researchers in the field of Parkinson’s disease and is named after Van Andel<br />

Institute founder Jay Van Andel, who passed away in 2004 after a long struggle with the disease.<br />

Awardees are selected on the basis of their scientific achievements and renown as a leader in Parkinson’s research or in<br />

research on closely related neurodegenerative disorders.<br />

Award Recipient<br />

Andrew B. Singleton, Ph.D.<br />

Dr. Andrew Singleton during his lecture as the inaugural Jay Van Andel<br />

Award recipient.<br />


VARI | <strong>2013</strong><br />

Han-Mo Koo Memorial Award<br />

Dr. Han-Mo Koo joined the Van Andel Research Institute in 1999 as one of its founding investigators. Heading the Laboratory of<br />

Cancer Pharmacogenetics, Dr. Koo established important projects focused on identifying genetic targets for anti-cancer drugs<br />

against melanoma and pancreatic cancer, and he worked tirelessly to contribute to the Institute’s mission to improve health and<br />

enhance lives. In May 2004, Dr. Koo passed away following a six-month battle with cancer. To honor his memory and scientific<br />

contributions, the Han-Mo Koo Memorial Award and Lecture was established in 2010.<br />

Awardees are selected based upon their scientific achievements and their contributions to human health and research that align<br />

with the scientific legacy of Han-Mo Koo.<br />

Award Recipient<br />

Phillip A. Sharp, Ph.D.<br />

Dr. Phillip Sharp delivering the inaugural Han-Mo Koo Memorial Lecture.<br />


Postdoctoral Fellowship Program<br />


VARI | <strong>2013</strong><br />

Postdoctoral Fellowship Program<br />

The Van Andel Research Institute provides postdoctoral training opportunities to Ph.D. scientists beginning their research careers.<br />

The fellowships help promising scientists advance their knowledge and research experience while at the same time supporting<br />

the research endeavors of VARI. The fellowships are funded by the laboratories to which the fellow is assigned; by the VARI<br />

Office of the Director; or by outside agencies. Each fellow is assigned to a scientific investigator who oversees the progress and<br />

direction of research. Fellows who worked in VARI laboratories in 2012 are listed below.<br />

Nicholas Andersen<br />

University of Iowa<br />

VARI mentor: Nicholas Duesberry<br />

Genevieve Beauvais<br />

University of Paris Descartes<br />

VARI mentor: Patrik Brundin<br />

Poulomi Bhattacharya<br />

Illinois State University<br />

VARI mentor: Nicholas Duesberry<br />

Travis Burgers<br />

University of Wisconsin–Madison<br />

VARI mentor: Bart Williams<br />

Zheng Cao<br />

University of Maryland, College Park<br />

VARI mentor: Brian Haab<br />

Vanessa Fogg<br />

Washington University in St. Louis<br />

VARI mentor: Jeffrey MacKeigan<br />

Anamitra Ghosh<br />

Iowa State University<br />

VARI mentor: Patrik Brundin<br />

Danese Joiner<br />

University of Michigan<br />

VARI mentor: Bart Williams<br />

Yanyong Kang<br />

Institute of Biophysics, Chinese Academy<br />

of Sciences<br />

VARI mentor: Eric Xu<br />

Nate Lanning<br />

University of Michigan<br />

VARI mentor: Jeffrey MacKeigan<br />

Leanne Lash-Van Whye<br />

University of Texas Medical Branch,<br />

Galveston<br />

VARI mentor: Arthur Alberts<br />

Heather McClung<br />

Wayne State University<br />

VARI mentor: Giselle Sholler<br />

Aikseng Ooi<br />

University of Malaya, Kuala Lumpur<br />

VARI mentor: Kyle Furge<br />

Kuntal Pal<br />

National University of Singapore<br />

VARI mentor: Eric Xu<br />

Electa Park<br />

Louisiana State University Health Sciences<br />

Center, New Orleans<br />

VARI mentor: Cindy Miranti<br />

Jackie Peacock<br />

University of Miami<br />

VARI mentor: Matthew Steensma<br />

Anthony Popkie<br />

The Ohio State University<br />

VARI mentor: Craig Webb<br />

Juliana Sacoman<br />

Michigan State University<br />

VARI mentor: Jeffrey MacKeigan<br />

Huiyan Tang<br />

Michigan State University<br />

VARI mentor: Brian Haab<br />

Xiaoyong Zhi<br />

University of Texas Southwestern Medical<br />

Center<br />

VARI mentor: Eric Xu<br />

Alex Zhong<br />

Sun Yat-sen University, Guangzhou, China<br />

VARI mentor: Bart Williams<br />

From left: Ghosh, Cao, Burgers, Pal, Lanning, McClung, Popkie, Peacock, Kang, Fogg, Park, Joiner, Lash-Van Wyhe, Ooi, Sacoman, Beauvais<br />


Student Programs<br />


VARI | <strong>2013</strong><br />

Grand Rapids Area Pre-College Engineering Program<br />

The Grand Rapids Area Pre-College Engineering Program (GRAPCEP) is administered by Davenport University and is sponsored<br />

and funded by VAEI. The program is designed to provide selected high school students, who have plans to major in science<br />

or genetic engineering in college, with the opportunity to work in a research laboratory. In addition to research methods, the<br />

students also learn workplace success skills such as teamwork and leadership. The four 2012 GRAPCEP students from<br />

Creston High School were<br />

Jamilah Fields (Hostetter/Jewell)<br />

Jasmine Jones (Weinreich)<br />

Chantice LaGrone (Alberts)<br />

Yasmeen Robinson (Chang)<br />

From left: LaGrone, Robinson, Jones, Fields<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Summer Student Internship Program<br />

The VARI student internships were established to provide college students with an opportunity to work with professional researchers<br />

in their fields of interst, to use state-of-the-art equipment and technologies, and to learn valuable interpersonal and<br />

communications skills. At the completion of the 10-week program, the students summarize their projects in an oral presentation<br />

or poster.<br />

From January through August 2012, the Van Andel Institure hosted more than 49 students from over 16 colleges and universities<br />

in formal summer internships under the Frederik and Lena Meijer Student Internship Program and in other student positions during<br />

the year. An asterisk (*) indicates a Meijer student intern.<br />

Standing, from left: Dieffenbach, Langerak, Sayfie, Grit, Dykstra, Dills, Edewaard, Shorkey, deWaal, Uhl, Varlan, Reimink, Muhoro, Hanchon,<br />

M. Smith, Searose-Xu, Subramanian, Orey, Rybski.<br />

Kneeling, from left: McMasters, Parker, Vanderlinde, Bergsma, Goyings, Westra, Waslawski, Hotaling, Quinn.<br />


VARI | <strong>2013</strong><br />

Aquinas College, Grand Rapids, Michigan<br />

Lauren Smith* (Sholler)<br />

Calvin College, Grand Rapids, Michigan<br />

Eric Edewaard (Jewell)<br />

Caroline Muhoro (Vande Woude)<br />

Anna Plantinga* (MacKeigan)<br />

Allison Schepers (Alberts)<br />

Tyler Spiering (Williams)<br />

Central Michigan University, Mount Pleasant, Michigan<br />

Amanda Erwin* (Miranti)<br />

Sabrina Parker* (Office of the Director)<br />

Adriane Shorkey (Jewell)<br />

Grand Valley State University, Allendale, Michigan<br />

Andrew Borgman (Neff)<br />

Jenea Chesnic (Neff)<br />

Michael Dykstra* (Chang)<br />

Daniel Hodges (Neff)<br />

Kevin Kampfschulte, B.S. (Steensma)<br />

Justin Langerak (Duesbery)<br />

Mitch McDonald (Haab)<br />

Brittany Holly (Chang)<br />

Stephen Orey (Webb)<br />

Alexander Roemer (Neff)<br />

Katie Uhl (Jewell)<br />

Hannah Westra* (Haab)<br />

Raymond Yeow (Weinreich)<br />

Hope College, Holland, Michigan<br />

Jamie Grit* (Triezenberg)<br />

Aaron Sayfie (MacKeigan)<br />

Mallory Smith (Steensma)<br />

Emily Van Wieren (Williams)<br />

Huston Tillotson University, Austin, Texas<br />

Nahome Bete (Haab)<br />

Johns Hopkins University, Baltimore, Maryland<br />

Sandya Subramanian* (Weinreich)<br />

Kalamazoo College, Kalamazoo, Michigan<br />

Parker de Waal (Xu)<br />

Mary Goyings* (Jewell)<br />

Livingstone College, Salisbury, North Carolina<br />

Ashley McMasters (Melcher)<br />

Loyola University, Chicago, Illinois<br />

Hudson Hotaling* (Williams)<br />

Monique Quinn* (Steensma)<br />

Michigan State University, East Lansing<br />

Zach Dieffenbach (Chang)<br />

Kelvin Searose-Xu (Melcher)<br />

Sheila Waslawski* (Duesbery)<br />

Michigan Technological University, Houghton<br />

Nathan Dills* (Melcher)<br />

University of Mannheim, Germany<br />

Lisa Becker (Alberts)<br />

University of Michigan, Ann Arbor<br />

Alexis Bergsma (Miranti)<br />

Kristin Rybski* (Alberts)<br />

Vanderbilt University, Nashville, Tennessee<br />

Peter Varlan* (Jewell)<br />

Other Van Andel Institute Interns<br />

Calvin College, Grand Rapids, Michigan<br />

Calvin Wiersma (Finance)<br />

Davenport University, Grand Rapids, Michigan<br />

Sarah Kozal (Development)<br />

Andrew Lau (Finance)<br />

Ferris State University, Big Rapids, Michigan<br />

Sheri Orlekoski (Compliance)<br />

Grand Valley State University, Allendale, Michigan<br />

Jordan Hanchon (Finance)<br />

Christina Middaugh (Van Andel Education Institute)<br />

Jessica Reimink (Finance)<br />

Holly Vanderlinde (Development)<br />

University of Michigan, Ann Arbor<br />

Ellen Junewick (Business Development)<br />


VARI Seminar Series<br />


VARI | <strong>2013</strong><br />

VARI Seminar Series<br />

September 2011<br />

Brooke McCartney, Carnegie Mellon University<br />

“At the intersection of Wnt signaling and cytoskeletal dynamics: a model systems approach to the<br />

study of the enigmatic tumor suppressor adenomatous polyposis coli”<br />

W. James Nelson, Stanford University<br />

“Evolution of epithelia and cadherin-based cell-cell adhesion”<br />

October<br />

Dan Klinosky, University of Michigan<br />

“If you only have time to attend one talk today on autophagy, this is the one”<br />

Robert Maki, Mount Sinai School of Medicine<br />

“Slugs, snails, and puppy dogs’ tails: what sarcomas are made of and how they are treated”<br />

November<br />

Dinshaw Patel, Memorial Sloan – Kettering Cancer Center<br />

“Structural biology of gene and epigenetic regulation”<br />

Andrew Dillin, Salk Institute for Biological Studies<br />

“Immortality, stem cells, and humoral signals of longevity”<br />

Alan Hall, Memorial Sloan – Kettering Cancer Center<br />

“Rho GTPases controlling epithelial morphogenesis and migration”<br />

Jennifer Cross, University of Virginia<br />

“The inflammatory cytokine MIF is an immune-modulating therapeutic target in tumor growth<br />

and metastasis”<br />

February 2012<br />

March<br />

Shylam Biswal, Johns Hopkins University<br />

“Nrf2 as a target for cancer therapy”<br />

Regis J. O’Keefe, University of Rochester<br />

“Stem cell populations and their regulation in bone repair”<br />

Di Chen, Rush University Medical Center<br />

“TGF-b signaling and osteoarthritis”<br />

David Marc Virshup, Duke University<br />

“Regulating Wnts at the source — basic biology and potential therapy”<br />

April<br />

May<br />

Aik Choon Tan, University of Colorado<br />

“Translational bioinformatics: from bytes to bench and back”<br />

Vicki Rosen, Harvard University<br />

“BMP-2 links appositional bone growth and fracture repair”<br />

Phillip A. Sharp, Massachusetts Institutte of Technology<br />

Han-Mo Koo Memorial Lecture<br />

“Transcription and functions of microRNAs and other non-coding RNAs”<br />

Tom Shenk, Princeton University<br />

“Metabolomic analysis: fat management by human cytomegalovirus”<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

June<br />

Richard Youle, National Institutes of Health<br />

“Molecular mechanisms of mitochondrial quality control through autophagy in Parkinson’s disease”<br />

July<br />

Collin Duckett, University of California, Los Angeles<br />

“IAP proteins in neoplasia and immunodeficiency”<br />

Anna Wu, David Geffen School of Medicine at UCLA<br />

“Engineered antibodies for immunoPET detection of cancer”<br />

August<br />

Hideho Okada, University of Pittsburgh<br />

“Type-1 polarizing vaccines for adult and pediatric gliomas”<br />

Sean Culter, University of California, Riverside<br />

“Chemical and genetic dissection of ABA signaling”<br />

Jennifer Gillette, University of New Mexico<br />

“Regulation of hematopoietic stem cell communication with the bone marrow niche”<br />

Bill Weis, Stanford University<br />

“The interplay of a-catenin and the actin cytoskeleton in cell adhesion and cell polarity”<br />

September<br />

Ralph J. DeBerardinis, M.D., Ph.D., University of Texas Southwestern Medical Center<br />

“Cancer metabolism — biological insights and translational opportunities”<br />

C. Titus Brown, Michigan State University<br />

“An efficient framework for throwing away most of your next-gen sequencing data”<br />

November<br />

Roger K. Sunahara, Univeristy of Michigan Medical School<br />

“Structural basis for G protein activation by GPCRs”<br />

John Kuriyan, University of California, Berkeley<br />

“Allosteric mechanisms in the activation of the EGF receptor”<br />

December<br />

Prasad Jallepalli, Memorial Sloan–Kettering Cancer Center<br />

“Surfing mitosis and cell division with chemical genetics”<br />


Van Andel Research Institute Organization<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

David L. Van Andel,<br />

Chairman and CEO, Van Andel Institute<br />

VARI Board of Trustees<br />

David L. Van Andel, Chairman and CEO<br />

James Fahner, M.D.<br />

W. Gary Tarpley, Ph.D.<br />

George F. Vande Woude, Ph.D.<br />

Board of <strong>Scientific</strong> Advisors<br />

The Board of <strong>Scientific</strong> Advisors advises the CEO and the Board of Trustees, providing recommendations and suggestions<br />

regarding the overall goals and scientific direction of VARI. The members are<br />

Michael S. Brown, M.D., Chairman<br />

Richard Axel, M.D.<br />

Joseph L. Goldstein, M.D.<br />

Tony Hunter, Ph.D.<br />

Phillip A. Sharp, Ph.D.<br />

<strong>Scientific</strong> Advisory Board<br />

The <strong>Scientific</strong> Advisory Board advises the VARI Director, providing recommendations and suggestions specific to the<br />

ongoing research. It also coordinates and oversees the scientific review process for the Institute’s research programs.<br />

The members are<br />

Alan Bernstein, Ph.D.<br />

Joan Brugge, Ph.D.<br />

Webster Cavenee, Ph.D.<br />

Frank McCormick, Ph.D.<br />


VARI | <strong>2013</strong><br />

Office of the Director<br />

Van Andel Research Institute<br />

Research Leadership Council<br />

Patrick Brundin, M.D., Ph.D.<br />

George Vande Woude, Ph.D.<br />

Jana Hall, Ph.D., M.B.A.<br />

Office Staff<br />

John Bender, Clinical Operations Director<br />

Kim Cousineau, Senior Administrative Assistant<br />

Jens Forsberg, <strong>Scientific</strong> Project Leader<br />

Laura Holman, Executive Assistant<br />

Jennifer Holtrop, <strong>Scientific</strong> Administrator<br />

David Nadziejka, Science Editor<br />

Aaron Patrick, Administrative Manager<br />

Bonnie Petersen, Senior Administrative Assistant<br />

Beth Resau, Senior Administrative Assistant<br />

Ashley Rodriguez, Administrative Assistant<br />

From left: Petersen, Holtrop, Bender, Forsberg, Patrick, Rodriguez, Resau, Cousineau, Holman<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Van Andel Institute Administrative Organization<br />

The departments listed below provide administrative support to both the Van Andel Research Institute and the Van Andel<br />

Education Institute.<br />

Executive<br />

David Van Andel, Chairman and CEO<br />

Jana Hall, Ph.D., M.B.A., Chief Operations Officer<br />

David Whitescarver, Vice President and Chief Legal Officer<br />

Christy Goss, Executive Assistant<br />

Ann Schoen, Executive Assistant<br />

Business Development<br />

Jerry Callahan, Ph.D., M.B.A., Vice President<br />

Marilyn Becker<br />

Andrea DeJonge<br />

Thomas DeKoning<br />

Carolyn Hudson, Ph.D.<br />

Brent Mulder, Ph.D., M.B.A.<br />

Norma Torres<br />

Compliance<br />

Gwenn Oki, Director<br />

Paula Williamson DeBoe<br />

Angie Jason<br />

Stacy Kuiken<br />

Shelly Novakowski<br />

Sheri Orlekoski<br />

Development, Marketing, and Communications<br />

Love Collins III, Vice President<br />

Tim Hawkins<br />

Sarah Hop<br />

Nancy Kooienga<br />

Sarah Lamb<br />

Gerilyn May<br />

Patrick Placzkowski<br />

Angie Stumpo<br />

Anthony Thompson<br />

Nicky Wilkerson<br />

Nadina Williams<br />

Facilities<br />

Samuel Pinto, Manager<br />

Amber Baldwin<br />

Rob Cairns<br />

Maria Cavasos<br />

Jeff Cooling<br />

Deb Dale<br />

Jason Dawes<br />

Guadalupe Delgado<br />

Ken DeYoung<br />

Kristi Gentry<br />

Matthew Jump<br />

Todd Katerberg<br />

Facilities (continued)<br />

Tracy Lewis<br />

Lewis Lipsey<br />

Maria Lopez<br />

Dave Marvin<br />

Samantha Meekie<br />

Jeanette Mendez<br />

Kevin Morton<br />

Angela Nobel<br />

Karen Pittman<br />

Richard Sal<br />

Jose Santos<br />

Amber TenBrink<br />

Richard Ulrich<br />

Pete VanConant<br />

Jeff Wilbourn<br />

Finance<br />

Timothy Myers, Vice President and Chief Financial Officer<br />

Heather Zak, Controller<br />

Stephanie Birgy<br />

Theresa Brown<br />

Cory Cooper<br />

Raji Daniel<br />

Sandi Dulmes<br />

Katie Helder<br />

Rich Herrick<br />

Angie Lawrence<br />

Susan Raymond<br />

Cindy Turner<br />

Jamie VanPortfleet<br />

Grants and Contracts<br />

David Ross, Director<br />

Sara ONeal, Manager<br />

Marilyn Becker<br />

Anita Boven<br />

Nathan Gras<br />

Kathy Koehler<br />

Tanja Lumpp<br />

Michele Quick<br />

Human Resources<br />

Linda Zarzecki, Vice President<br />

Stacey Booth<br />

Margie Hoving<br />

Eric Miller<br />

Pamela Murray<br />

Carol Sheldon<br />

John Shereda<br />


VARI | <strong>2013</strong><br />

Information Technology<br />

Bryon Campbell, Ph.D., Chief Information Officer<br />

David Drolett, Manager<br />

Candy Wilkerson, Manager<br />

Sandra Badini<br />

Bill Baillod<br />

Terry Ballard<br />

Tom Barney<br />

Phil Bott<br />

James Clinthorne<br />

Dan DeVries<br />

Marianne Evans<br />

Kenneth Hoekman<br />

Kim Jeffries<br />

Jason Kotecki<br />

Ben Lewitt<br />

Deb Marshall<br />

Randy Mathieu<br />

Matt McFarlane<br />

Thad Roelofs<br />

Ken Selleck<br />

Investments Office<br />

Kathy Vogelsang, Chief Investment Officer<br />

Benjamin Carlson<br />

Ted Heilman<br />

Karla Mysels<br />

Materials Management<br />

Richard M. Disbrow, CPM, Director<br />

Eddie Cortadillo, Supervisor<br />

Bob Sadowski, Supervisor<br />

Matt Donahue<br />

Susanne Dubois<br />

Heather Frazee<br />

Chris Kutschinski<br />

Shannon Moore<br />

Monono Negash<br />

Amy Poplaski<br />

Marlene Sal<br />

John Waldon<br />

Security<br />

Kevin Denhof, CPP, Director<br />

Amy Davis<br />

Kate Harrison<br />

Andriana Vincent<br />

Chris Wilson<br />

Contract Support<br />

Jodi Tyron, Librarian<br />

(Grand Valley State University)<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Van Andel Institute<br />

Van Andel Institute Board of Trustees<br />

David Van Andel, Chairman<br />

Michael Jandernoa<br />

John C. Kennedy<br />

Ralph W. Hauenstein (emeritus)<br />

Board of <strong>Scientific</strong> Advisors<br />

Michael S. Brown, M.D., Chairman<br />

Richard Axel, M.D.<br />

Joseph L. Goldstein, M.D.<br />

Tony Hunter, Ph.D.<br />

Phillip A. Sharp, Ph.D.<br />

Van Andel Research Institute<br />

Board of Trustees<br />

David Van Andel, Chairman<br />

James Fahner, M.D.<br />

W. Gary Tarpley, Ph.D.<br />

George F. Vande Woude, Ph.D.<br />

Chief Executive Officer<br />

David Van Andel<br />

Van Andel Education Institute<br />

Board of Trustees<br />

David Van Andel, Chairman<br />

Donald W. Maine<br />

Juan R. Olivarez, Ph.D.<br />

Gordon Van Harn, Ph.D.<br />

Van Andel Research Institute<br />

Research Director<br />

Open<br />

Van Andel Education Institute<br />

Director<br />

Steven J. Triezenberg, Ph.D.<br />

Chief Administrative Officer<br />

and General Counsel<br />

David Whitescarver<br />

VP Development,<br />

Communications,<br />

and Marketing<br />

Love Collins III<br />

Chief Operations Officer<br />

Jana Hall, Ph.D., M.B.A.<br />

VP Human Resources<br />

Linda Zarzecki<br />

VP and Chief Financial Officer<br />

Timothy Myers<br />

VP Business Development<br />

Jerry Callahan, Ph.D.<br />


VARI | <strong>2013</strong><br />

The Van Andel Institute and its affiliated organizations (collectively the “Institute”) support and comply with applicable laws prohibiting<br />

discrimination based on race, color, national origin, religion, gender, age, disability, height, weight, marital status, U.S. military veteran status, or<br />

other personal characteristics covered by applicable law. The Institute also makes reasonable accommodations required by law. The Institute’s<br />

policy in this regard covers all aspects of the employment relationship, including recruiting, hiring, training, and promotion.<br />


Van Andel Research Institute | <strong>Scientific</strong> <strong>Report</strong><br />

Printed by Wolverine Printing Company<br />


333 Bostwick Avenue, N.E., Grand Rapids, Michigan 49503<br />

Phone 616.234.5000 Fax 616.234.5001 www.vai.org

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