Journal Thoracic Oncology

Abstracts Journal of Thoracic Oncology • Volume 12 Issue S1 January 2017
into XG and non-XG-forming groups with 100% accuracy. However, the roles
of the selected features (1 miRNA and 11 mRNAs) in the metastasis of SQCC
are not well defined. GO annotation of the identified mRNAs in ADC revealed
enrichment of biological processes related to B cell differentiation, wound
healing and regulation of the immune response and signalling pathway, while
catabolic and metabolic processes were enriched in SQ. Conclusion: The use of
single-dimensional data to classify patients into different prognostic groups
may not be sufficient in the presence of heterogeneous patient populations.
Integrative analysis of multi-omic data can provide greater insights into
clinically relevant genetic aberrations, which can be used to improve the
molecular classification of NSCLC.
Keywords: mRNA, patient-derived xenografts, miRNA, Prognosis
POSTER SESSION 1 - P1.05: EARLY STAGE NSCLC
TRANSLATIONAL RESEARCH & BIOMARKERS –
MONDAY, DECEMBER 5, 2016
P1.05-007 ANALYSIS OF RNA SEQUENCING DATA ALONG WITH PET
SUV-MAX CAN DISCOVER NOVEL GENE SETS WHICH CAN PREDICT
SURGICAL OUTCOME OF NSCLC
Yoohwa Hwang 1 , Yoo Jin Jung 1 , Sae Bom Lee 1 , Yoon Ho Kim 1 , Kwanyong Hyun 2 ,
Samina Park 2 , Hyun Joo Lee 2 , In Kyu Park 2 , Chang Hyun Kang 2 , Young Tae Kim 2
1 Thoracic and Cardiovascular Surgery, Seoul National University Hospital, Seoul/
Korea, Republic of, 2 Department of Thoracic and Cardiovascular Surgery, Seoul
National University Hospital, Seoul/Korea, Republic of
Background: Recent development of NGS technology provides a better
understanding on the molecular mechanism of the cancer. A comprehensive
analysis algorism of NGS data along with various clinical phenotypes and
clinical outcome may lead discovery of novel molecular mechanism of cancer
biology. It has been suggested that the preoperative SUV of the PET-CT
is related to the aggressiveness of the cancer. We hypothesized that the
identification of genes that were related to the PET SUV-max would lead a
discovery of novel genes which could predict long-term outcomes of patients
of non-small cell lung cancer. Methods: We set a 51 adenocarcinoma and a 101
squamous cell carcinoma patients cohort, whose cancer and normal tissue
whole transcriptome sequencing data were available. The RNA sequencing
fastq files were aligned on the reference genome (http://grch37.ensembl.
org/) and the differential expressions were analyzed using tuxedo protocol
(TopHat 2.0, Cufflinks 2.2.1). Visualizations of differential expressions
were presented with CummeRbund R-package. Results: Based on the
preoperative PET-CT SUV-max, patients were classified as “Low” (SUV≤3),
“Intermediate” (SUV 3-10), and “High” (SUV>10) groups. Using the tuxedo RNA
analysis tools, we selected 31 genes which showed significantly different
expression of RNAs between “Low” and “High” groups in adenocarcinoma and
between “Intermediate” and “High” groups in squamous cell carcinoma. By
comparing expression levels of those 31 genes according to the development
of recurrence, we could identify two sets of genes (COL2A1, BPIFB2, RYR2,
F7, HPX, AC022596.6 and H19 for adenocarcinoma; BPIFB2, AC022596.6,
ANKRD18B, GCLC, HHIPL2, COL2A1 and DPP10 for squamous cell carcinoma)
which were related to the development of recurrence.
POSTER SESSION 1 - P1.05: EARLY STAGE NSCLC
TRANSLATIONAL RESEARCH & BIOMARKERS –
MONDAY, DECEMBER 5, 2016
P1.05-008 DETECTION OF EGFR MUTATIONS IN PULMONARY VEIN
AND PERIPHERAL BLOOD PLASMA CELL-FREE DNA FOR ANALYSIS
OF SURGICAL TREATMENT IN EARLY-STAGE NSCLC
Chengliang Yang 1 , Dan Yang 1 , Bo Dong 2 , Xin Meng 2 , Yong-Yu Liu 3
1 Department of Thoracic Oncology, Shenyang Tenth People’s Hospital & Shenyang
Chest Hospital, Shenyang/China, 2 Laboratory of Lung Cancer, Shenyang Tenth
People’s Hospital & Shenyang Chest Hospital, Shenyang/China, 3 Department of
Thoracic Surgery, Shenyang Tenth People’s Hospital & Shenyang Chest Hospital,
Shenyang/China
Background: Free circulating DNA (cfDNA) has been known for several
decades. These small DNA fragments are released into the circulation from
nucleated cells through necrosis, apoptosis and/or active secretion. Use
of blood plasma cfDNA to detect mutations has spread widely as a form
of liquid biopsy. However, it remains unclear which types of samples are
appropriate for detecting tumor cell-free DNA in these biopsies. We compared
the abundance of EGFR mutations in peripheral blood and pulmonary vein
plasma cell-free DNA from patients with early-stage NSCLC. Methods: In this
study, primary lung tumors and matched presurgery peripheral blood plasma
samples and intraoperative pulmonary vein blood samples were collected
from patients with early-stage NSCLC (n=89). We detected EGFR mutations
(exon19 deletion, L858R, G719X, S768I and T790M) in 89 early-stage lung
cancer samples using droplet digital PCR (ddPCR) and amplification refractory
mutation system (ARMS). EGFR mutation abundance was determined and
analyzed to reveal potential impact of samples types. Results: Presurgery
peripheral blood plasma samples (n=89) and intraoperative pulmonary vein
blood samples (n=89) matched tumor tissue samples (n=89) were analyzed
for EGFR mutations using ddPCR and ARMS respectively. Of the 41 EGFR
mutations detected in tumor tissues by ARMS, 37 of the corresponding
mutations were detected in presurgical peripheral blood plasma cfDNA and
intraoperative pulmonary vein cfDNA, whereas 4 mutations were found
in plasma from patients with EGFR wild-type tumors (sensitivity 80.49%,
specificity 91.67%).Free circulating DNA was identified in the plasma of
pulmonary venous blood and peripheral blood in thirty-seven patients. Of the
37 cases of EGFR mutation positive plasma samples, ddPCR identified a higher
mutation abundance of pulmonary venous samples than peripheral blood
(1.05% vs. 0.12%, p = 0.007). Conclusion: This study demonstrates accurate
mutation detection in plasma using ddPCR, and that cfDNA can be detected
in presurgical peripheral blood and intraoperative pulmonary vein in patients
with early-stage lung cancer. Our results suggest that pulmonary venous blood
can be obtained from the resected specimen, thus facilitating the detection
of cfDNA. Future studies can now address whether monitoring the change
of EGFR mutation abundance after surgery identifies patients at risk for
recurrence, which could guide therapy decisions for individual NSCLC patients.
Keywords: plasma, pulmonary vein, lung cancer, cell-free DNA
Conclusion: Our results suggest that it is necessary to set a comprehensive
analysis algorithm of the NGS data along with various clinical phenotypes of
the patients, for the discovery of clinically meaningful molecular mechanisms
of the cancer.
Keywords: NSCLC, transcriptome, NGS, recurrence
S318 Journal of Thoracic Oncology • Volume 12 Issue S1 January 2017