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Vibha Raghavan
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OA08 - Advanced Models and "Omics" for Therapeutic Development (ID 133)
- Event: WCLC 2019
- Type: Oral Session
- Track: Biology
- Presentations: 1
- Now Available
- Moderators:Luis M Montuenga, Julie George
- Coordinates: 9/09/2019, 11:00 - 12:30, Interlaken (1988)
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OA08.01 - Organoid Cultures as Novel Preclinical Models of Non-Small Cell Lung Cancer (Now Available) (ID 2115)
11:00 - 12:30 | Author(s): Vibha Raghavan
- Abstract
- Presentation
Background
There is an unmet need to develop novel clinically relevant models of NSCLC to accelerate identification of drug targets and our understanding of the disease. Organoids, which are cells grown in three-dimensional environments in Matrigel, have emerged as novel preclinical models of cancer. Recently protocols for generating NSCLC organoids have been reported, but the growth, and molecular features of organoids as compared to their matching primary patient tumor or patient-derived xenografts (PDX) remain vague.
Method
Thirty surgically resected NSCLC patient tumor and 35 PDX tissue of lung adenocarcinoma and squamous cell carcinoma subtypes were processed for organoid establishment. Organoids and matching tumor tissues were characterized by histology and immunohistochemistry, and molecularly profiled by whole exome and RNA-sequencing. Subcutaneous injection of organoids in vivo was performed to confirm tumorgenicity. Organoids were subjected to drug testing and drug response was verified in the matched PDX.
Result
Using a novel culture condition that our laboratory developed, we have collected tumor samples from 16 primary and 13 PDX samples of adenocarcinoma (n=29) and 14 primary and 22 PDX samples of squamous cell carcinoma (n=36). Over 85% (57/65) of our patient and PDX tumor tissues formed organoids that exhibited a wide range of short-term (<3 months) and long-term (>3 months) growth. Specifically, the success rate of establishing short-term and long-term models are 74% (48/65) and 14% (9/65), respectively. The long-term propagable organoids recapitulated the histology of the patient and PDX tumor. They also retained the ability to form xenograft in NOD-SCID mice. The organoids preserved mutation, copy number aberrations and global gene expression profile of the parental tumors. We additionally showed the utility of short-term and long-term organoids for identifying biomarkers of sensitivity to drugs and combinational targeted therapies.
Conclusion
NSCLC organoids are novel patient-derived ex-vivo tumor models for anti-cancer drug screening and biomarker discovery, thus could be incorporated into novel drug discovery pipelines. Further efforts are ongoing to increase the success rate of establishing long-term organoid lines.
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P2.03 - Biology (ID 162)
- Event: WCLC 2019
- Type: Poster Viewing in the Exhibit Hall
- Track: Biology
- Presentations: 2
- Moderators:
- Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
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P2.03-11 - Impact of Ethnicity on Outcome in Never Smokers with EGFR and ALK Wildtype (EGFR/ALK-Wildtype) Lung Adenocarcinomas (ID 2035)
10:15 - 18:15 | Author(s): Vibha Raghavan
- Abstract
Background
EGFR-mutations and ALK-rearrangements are frequent in lung adenocarcinoma (LUAD) samples from never smoker patients. Nevertheless, up to a quarter of all LUAD cases in never smokers are EGFR/ALK-wildtype: these patients have limited therapeutic options and few well-established clinical and molecular predictors of outcome. Our main objectives here were to investigate the prognostic impact of ethnicity in never smoker patients with EGFR/ALK-wildtype LUAD and seek for specific somatic events correlated to ethnical background in these patients.
Method
We included 85 samples from lifetime never-smoker patients with EGFR/ALK-wildtype LUAD collected from surgical resection with curative intent. Stages 1/2/3 were identified in 56 (66%)/15 (18%)/14 (16%) samples. A subset of those samples (n=46), with similar stage distribution, had snap-frozen tumor and paired-adjacent tissue available and were submitted to paired-end whole-exome sequencing. Fisher’s exact and Chi-squared tests were used to compare specific mutations between Asians vs non-Asians. Recurrence-free-survival (RFS) was calculated based on the Kaplan-Meier method; Cox modeling was used to generate hazard ratios (HR), adjusted for key clinical features.
Result
Most patients in the cohort were female (63/85, 74%); the median age was 68 years; median follow-up was 51 months. According to self-reports, 19/85 (22%) and 66/85 (78%) patients identified as Asians and non-Asians, respectively; no major clinical and pathologic differences were identified between these populations. Five-year recurrence free survival was significantly lower for Asians compared to non-Asians (50% vs. 78%, adjusted HR = 2.9; CI = 1.1-7.8, p=0.02), Figure 1. Among somatic events, in-frame deletions in CNPY3 (Toll-like receptor-specific co-chaperone for HSP90B1) were more frequent in Asians (30%) compared to non-Asians (18%). In contrast, DDX11 missense mutations (21% vs 0%; nucleic acid binding protein involved in genome stability), NOTCH2 multi-hits and frame-shift deletions (7% vs 1%), and KRAS missense mutations (7% vs 0%) were more frequently altered in non-Asians than in Asians.
Conclusion
In our cohort of never-smoker patients with EGFR/ALK-wildtype LUAD, Asian patients showed higher relapse rates than non-Asians. We identified differentially mutated genes by ethnicity that may partly account for these differences in outcome. (SNMF and AFF contributed equally)
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P2.03-37 - Genomic Landscape of EGFR/ALK Wild-Type Lung Adenocarcinomas in Never-Smokers and Importance of Epithelial-Mesenchymal-Transition (ID 1283)
10:15 - 18:15 | Author(s): Vibha Raghavan
- Abstract
Background
The molecular landscape of EGFR/ALK wild-type Lung Adenocarcinomas in never-smokers is poorly understood. Never-smokers usually have low PD-L1 expression and low Tumor Mutation Burden, challenging treatment strategies when no known driver-mutations are found. To identify putative driver mutations, we compared whole exome sequencing (WES) results in the EGFR/ALK wild-type Lung Adenocarcinoma in the never smokers Toronto cohort with a corresponding EGFR/ALK wild-type Lung Adenocarcinoma group of smokers from TCGA.
Method
For never-smokers with resected EGFR/ALK wild-type Lung Adenocarcinomas, frozen tumor and paired-normal-lung were evaluated by WES at a mean coverage of 238x. The paired-end reads were aligned using BWA and were further processed using the standard GATK pipeline. Somatic mutations and indels were identified using MuTect and VarScan, respectively. We compared mutations from our cohort to the TCGA smokers who had EGFR/ALK wild-type Lung Adenocarcinomas from publicly available data (TCGA) to identify genes at least 10% more frequently mutated in never smokers compared to the TCGA cohort.
Result
In our cohort with 45 never-smoker patients, 80% were females; median age was 70y; 29% were Asians; Stage I/II/III+ were 71%/15%/13%; after a median follow-up of 69 months, 24% had recurred. Median non-synonymous Tumor Mutation Burden was 1.3mut/Mb in never-smokers. We identified 39 genes that were more frequently mutated in never-smokers vs smokers, including some known tumor suppressor genes. The most prevalent genes included ADAM21 missense mutations (21% vs 1%; adj p=0.003), NOTCH2 frame-shift deletions and multi-hit mutations (40% vs 17%; adj p=0.04), MST1 missense mutations and in-frame deletions (13% vs 0%; adj p=0.008), ZMIZ2 frame-shift insertions (13% vs 0%; adj p=0.008) and FOXD4 missense mutations (10% vs 0%; adj p=0.02). Many of these differentially mutated genes have been previously associated to epithelial-mesenchymal-transition signaling pathways. Conversely and as expected, KRAS, TP53, STK11 and KEAP1 were more frequently mutated in the TCGA smokers EGFR/ALK wild-type Lung Adenocarcinomas cohort.
Conclusion
We identified multiple genes, particularly involved in the epithelial-mesenchymal-transition signaling pathways that are over-represented in never-smokers with EGFR/ALK wild-type Lung Adenocarcinomas, when compared to smokers with EGFR/ALK wild-type Lung Adenocarcinomas. This is a novel finding with potential clinical importance. Validation studies, analyzing epithelial-mesenchymal-transition signaling activation pathways on the EGFR/ALK wild-type Lung Adenocarcinomas never smokers population are needed to best identify the actual role in carcinogenesis and metastasis, guiding future treatment strategies. (AFF and SNMF contributed equally).
