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I. Jurisica
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P3.01 - Poster Session with Presenters Present (ID 469)
- Event: WCLC 2016
- Type: Poster Presenters Present
- Track: Biology/Pathology
- Presentations: 2
- Moderators:
- Coordinates: 12/07/2016, 14:30 - 15:45, Hall B (Poster Area)
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P3.01-019 - Desmoplasia is Associated with Poor Prognosis and Carcinoma-Associated Fibroblast Heterogeneity in Non-Small Cell Lung Cancer (ID 5281)
14:30 - 14:30 | Author(s): I. Jurisica
- Abstract
Background:
Cancer-associated fibroblasts (CAFs) are known to influence tumor development, progression and metastasis. Their characteristics and prognostic role in non-small cell lung cancer (NSCLC) patients have been recognized. However, the functional heterogeneity of CAFs between patients and its genetic basis is less understood.
Methods:
Two pathologists scored for desmoplasia on Hematoxylin-Eosin stained sections of resected lung tumors from two patient cohorts: one consisting of 171 NSCLC patients (128 adenocarcinoma, 43 squamous carcinoma) and the second of 24 primary cultures of CAFs. Percent area of desmoplasia among total tumor stroma was used to define high desmoplasia (HD) versus low desmoplasia (LD). The desmoplasia and survival analysis were assessed for 171 NSCLC patients. Gene expression data on RNA extracted from CAFs in contracted gels following 24 hours incubation was obtained using Illumina Human HT-12v4 Bead Chips array and was preprocessed and normalized using RMA and values were log2 transformed. Significant genes whose expression is strongly correlated (Spearman correlation coefficient and p value) with percent of desmoplasia were identified in both cohorts. The gene set enrichment analysis (GSEA) was applied to test for the enrichment of CAF cohort significant genes in 171 NSCLC cohort. Additionally, CAF significant genes were subjected to pathway enrichment analysis using Pathway Data Integration Portal ver. 2.5 (http://ophid.utoronto.ca/pahtDIP).
Results:
The prognosis of adenocarcinoma patients with HD had poorer outcome in comparison to the patients with LD (disease free survival at 3 years 34% vs. 75% p=0.00045 and relapse rate 41% vs. 14%, p=0.0051). In the CAF cohort, the number of genes that are significantly associated with desmoplasia for enrichment are 356. Using GSEA, these genes were enriched in 171 NSCLC cohort (with a p value of 0.045). Protein-protein interaction (PPI) partners of these 356 genes were acquired using Integrated Interaction Database – IID (version 2016-03, http://dcv.uhnres.utoronto.ca/iid/). Obtained genes were then ranked according to their degree, i.e., number of PPIs. Top 44 (top 1%) of the genes were then selected to pathway enrichment analysis using pathDIP version 2.5. 245 pathways that significantly enriched by these 44 genes (FDR < 0.01) were obtained. Many of these pathways are known to be involved in lung cancer.
Conclusion:
We demonstrated that the prognosis of lung adenocarcinoma patients with HD had poorer outcome in comparison to the patients with LD. Furthermore, PPI analysis of CAF genes associated with HD reveals enrichment of many cancer-related pathways, suggesting their high relevance to lung cancer.
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P3.01-049 - ELF3 Overexpression Leads to Oncogenic Reprogramming of Protein Interactions Exposing Therapeutically Actionable Targets (ID 5807)
14:30 - 14:30 | Author(s): I. Jurisica
- Abstract
Background:
Emerging evidence has implicated ELF3 involvement in cancer signaling pathways. To determine the biological basis to pursue ELF3 as a novel therapeutic target, we investigated the role of ELF3 in lung adenocarcinoma (LUAD). Using a multi-omics approach in two independent cohorts of LUAD we (a) discover genetic mechanisms driving aberrant expression of this oncogene, (b) identify the protein-protein-interaction (PPI) partners of ELF3, and (c) determine the specific functions of ELF3 in LUAD using model systems.
Methods:
Comprehensive, multi-omic data was collected from the BC Cancer Research Centre (BCCRC), The Cancer Genome Atlas (TCGA), and several mouse models of LUAD tumourigenesis. ELF3 cellular localization was visualized by immunofluorescence. ELF3 knock-down and overexpression was achieved by lentiviral vector delivery for in vitro and in vivo assays. Physical protein-protein interaction (PPI) networks obtained from IID were overlaid onto cancer and non-malignant gene expression data from TCGA and 11 restructured datasets from Gene Expression Omnibus. PPIs were interrogated to investigate malignancy-associated ELF3 interactions. Pathway analysis was performed using pathDIP. Survival analysis was performed using the log-rank method.
Results:
ELF3 was significantly overexpressed in both cohorts, remarkably in >70% of cases (p=1.64E-21). However, mutation of known upstream regulators was not sufficient to explain the frequency of ELF3 overexpression. Instead, the ELF3 locus underwent frequent (>80%) genetic alteration including focal amplification and promoter hypomethylation, which corresponded with increased expression. ELF3 was predominantly localized to the nucleus, consistent with its transcription factor function. Analysis of PPI networks indicated highly LUAD-specific ELF3 interactions whereby loss and gain of interactions lead to reprogramming of LUAD transcriptional networks, including loss of TNFα pathway, and gain of TGFβ pathway, PI3K pathway, and translesion (DNA repair) pathway interactions. Furthermore, EGFR, KRAS, and MYC transgenic models of LUAD tumourigenesis all displayed a marked increase (6 to 8-fold) in ELF3 expression signifying its importance to LUAD of varied genetic backgrounds. In culture, ELF3 regulated proliferation, viability and anchorage-independent growth. In animal models, ELF3 knock-down cells underwent negative clonal selection, suggesting ELF3 expression is beneficial to tumour growth. Clinically, high expression of ELF3 was associated with poor survival regardless of tumour stage.
Conclusion:
Overexpression of ELF3 reprograms protein-protein-interactions in LUAD leading to the activation of cancer-specific pathways, and producing oncogenic phenotypes. Depletion of ELF3 with shRNAs reverses tumour cell growth, suggesting ELF3 is a promising therapeutic target. In addition to ELF3, interruption of cancer-specific PPIs also represents a therapeutically actionable strategy.
