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Devalben Patel



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    MA18 - Advances in Diagnosis of Common Types of NSCLC (ID 145)

    • Event: WCLC 2019
    • Type: Mini Oral Session
    • Track: Pathology
    • Presentations: 1
    • Now Available
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      MA18.07 - Identification of Neuroendocrine Transformation in Anaplastic Lymphoma Kinase Rearranged (ALK+) Tumors After Tyrosine Kinase Inhibitors (Now Available) (ID 1137)

      11:30 - 13:00  |  Author(s): Devalben Patel

      • Abstract
      • Presentation
      • Slides

      Background

      Acquired resistance after ALK tyrosine kinase inhibitors treatment has multiple known mechanisms: new mutations or gene amplifications, bypass signaling and rarely neuroendocrine histological transformation. Here we describe results of a program utilizing routine biopsy post-progression in ALK+ patients for clinical and research purposes.

      Method

      Since 2014, ALK+ lung cancer patients treated at the Princess Margaret Cancer Centre have undergone routine biopsies at disease progression time points upon failure of an ALK-tyrosine kinase inhibitor (TKI) for both clinical purposes and research purposes, in particular to obtain tissue for primary derived xenograft (PDX) engraftment.

      Result

      All 9/9 patients consented for research sampling during clinical biopsy procedures (median 2 extra cores/passes); 2 patients were biopsied more than once; 3 PDX models from 2 patients have engrafted; 3 additional models are too early to assess engraftment. Engraftment occurred in patients with clinically aggressive tumors and poor survival outcomes. In this process, we identified 2 patients with neuroendocrine transformation post-second generation ALK TKI: (a) a 59 yo Asian female, never smoker, diagnosed six years prior with metastatic disease, heavily pretreated with crizotinib (12 months), pemetrexed (16 months), ceritinib (25 months), alectinib (6 months) and brigatinib (3 months); post-alectinib biopsy showed no transformation, while post-brigatinib liver biopsy demonstrated transformation to large cell neuroendocrine carcinoma; (b) a 75 yo Caucasian female, never smoker, diagnosed eight months prior and started on alectinib with a partial response, progressed in a single site; endobronchial biopsy demonstrated high grade neuroendocrine transformation. Both biopsies were positive for neuroendocrine markers (chromogranin and synaptophysin), TTF-1 and diffusely co-expressed ALK on immunohistochemistry. Assessment of PDX engraftment of these models is ongoing.

      Conclusion

      Routine combined clinical and research biopsy of ALK+ patients at time of TKI failure helped to identify these recent cases of neuroendocrine transformation as a possible mode of resistance and provide tissue for model development. This is the first time that ALK+ transformation to large cell neuroendocrine carcinoma is reported in the literature. (PP, AFF, SNMF, LN contributed equally).

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    P1.01 - Advanced NSCLC (ID 158)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Advanced NSCLC
    • Presentations: 1
    • Now Available
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
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      P1.01-70 - Dominant Circulating Myeloid Populations Are Associated with Poor Response in NSCLC Treated with 1st Line PD-1 Monotherapy (Now Available) (ID 2295)

      09:45 - 18:00  |  Author(s): Devalben Patel

      • Abstract
      • Slides

      Background

      Immune subpopulations within the tumor microenvironment (TME) play a central role in determining response to checkpoint inhibitors. Myeloid derived suppressor cells (MDSC), a heterogeneous population of immature myeloid cells, have a predominantly immunosuppressive role by stimulating T regulatory cells. We hypothesize that elevated myeloid-to-lymphocyte measures in the peripheral blood predict for greater numbers of myeloid derived suppressor cells in the TME and worse outcomes.

      Method

      We identified all advanced NSCLC patients treated with immunotherapy between 2010-2019 at the Princess Margaret Cancer Center. Patients who received first line monotherapy with a PD-1 inhibitor were reviewed for clinical information including age, sex, histology, stage, smoking status, ethnicity, PD-L1 expression and tumor genotype. Myeloid cells lines analyzed included neutrophils, monocytes and platelets, expressed as ratios to peripheral lymphocytes. Multivariate analyses were conducted using the cox and logistic regression models to adjust for confounders.

      Result

      We identified 75 patients who were eligible for analysis. Disproportionate increases in the different myeloid cell types were highly correlated with each other (all Pearson’s rho>0.8) and the neutrophil to lymphocyte ratio (NLR) was selected as representative. A high NLR (>5) was associated with shorter time-to-treatment-failure (median TTF 9.7 vs 29.4 months) that remained significant after adjusting for confounders including PD-L1 and presence of liver metastases (p=0.004). High NLR was also an independent predictor of poor OS (median 11.3 vs 56.8 months, HR 3.02, p=0.04). Although NLR was not predictive of radiographic response, there was a trend to association with a rapidly progressive phenotype defined by primary progressive disease and a duration of therapy ≤2 months (p=0.06). Other predictive factors included the presence of liver metastases, which was associated with a worse OS (HR3.37 p=0.05) but not TTF (p=0.14). An association was also seen between NLR and liver metastases (mean NLR 6.6 vs 25.2 in the absence and presence of liver metastases respectively, p<0.001).

      Conclusion

      A disproportionate increase in peripheral immune myeloid populations may represent a systemic, myeloid-driven, immunosuppressive state that is significantly associated with primary refractory disease, rapid progression, and poor survival. A subset of about 50 patients with biobanked tissue are presently being analyzed using multiplex immunofluorescence to assess for MDSCs in the TME to correlate with peripheral blood findings.

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    P1.14 - Targeted Therapy (ID 182)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Targeted Therapy
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
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      P1.14-07 - Genomic Profiling of Liquid Biopsies During 2nd/3rd Generation ALK Inhibitor Therapy to Identify Novel Mechanisms of Resistance (ID 804)

      09:45 - 18:00  |  Author(s): Devalben Patel

      • Abstract

      Background

      Second- and third-generation ALK inhibitors each have diverse mechanisms of resistance. Only a fraction of resistance is due to secondary mutations of the ALK gene. Altered bypass tracts are likely the case in some other instances. Genomic alterations of other genes and pathways may be a third mechanism of resistance. Repeat liquid biopsies during the course of patients’ treatments can provide a minimally invasive method for sampling cancer-specific genomic information that leads to improved treatment selection.

      Method

      In the Lung Cancer Clinic of the Princess Margaret Cancer Centre, serial plasma samples were collected from six lung cancer patients with ALK rearrangement at multiple serial clinic visits pre- and post- progression on next-generation ALK inhibitors. We focused on next generation agents, as there has been previous focus on crizotinib resistance mechanisms already. Cell-free DNA (cfDNA) was extracted (median: 50 ng; range: 20-2760 ng) and profiled using a next-generation sequencing (NGS) platform with Geneseeq Prime 425-gene panel at a mean coverage depth of 4747X (and a deduplicated mean coverage depth of 2160X).

      Result

      Somatic alterations from plasma cfDNA were detected in all six patients at various time points with three patients having detectable ALK alterations. Systemic progression (2/2 patients) correlated well with the ability of liquid biopsies to detect somatic mutations, while central nervous system (CNS)-predominant progression did not (4/4 patients). One patient, after disease progression on ceritinib, alectinib and brigatinib, exhibited variable allele fractions (AFs) of ALK G1202R mutation in cfDNA. The levels of G1202R decreased and ultimately became undetectable, corresponding to the patient’s clinical response to lorlatinib. In a patient who exhibited significant systemic progression, a massive increase in mutation AFs and many newly acquired mutations were detected in the cfDNA, including NOTCH1, DICER1, BRCA2, TP53, CDKN2A, ERBB3, and FAT1mutations. However, the increase in the number of co-mutations was not related to increases in the amount of extracted cfDNA.

      Conclusion

      Broad panel-based NGS of plasma cfDNA enabled noninvasive detection of systemic (but not CNS-predominant) progression during second and subsequent generation ALK inhibitor treatment, and can identify known and putative mechanisms of resistance for treatment decision-making.

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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): Devalben Patel

      • 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)

      figure 1.jpg

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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): Devalben Patel

      • 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.

      oncoprint wes.png

      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).

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    P2.14 - Targeted Therapy (ID 183)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Targeted Therapy
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
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      P2.14-62 - Early, Subclinical SCLC Transformation in Patients with EGFR Mutant Lung Cancer Receiving Osimertinib, Detected Through Cell-Free DNA (ID 812)

      10:15 - 18:15  |  Author(s): Devalben Patel

      • Abstract

      Background

      Liquid biopsies provide a convenient approachfor serial sampling and real-time disease monitoring, leading to the early detection of treatment response, disease progression and drug-resistance. Here,we present genomic profiling of serial liquid biopsies from seven lung cancer patients with activatingEGFRmutations receiving osimertinib in clinical practice.

      Method

      At Princess Margaret Cancer Centre, in the Lung Cancer Outpatient Clinics, plasma samples were obtained from each patient at defined clinical visits (between ~1–5 months in-between visits). Cell-free DNA (cfDNA; with a median of 57 ng; range: 3.5 to 3806 ng) was extracted from plasma samples and profiled using targeted capture next-generation sequencing with the Geneseeq Prime 425-gene panel, at a mean coverage depth of 4892X (with a deduplicated mean coverage depth of 2108X).

      Result

      Systemic tumour burden correlated with the detection of genomic alterations in cfDNA: Four of four of the patients with low tumour burden, despite minor disease progression, exhibited minimal EGFR and co-mutation allele frequencies (AFs). Conversely, significant increases in systemic (but not central nervous system) tumour burden led to increases in driver and co-mutation AFs (two our of three patients). EGFR C797S mutation and inactivating mutations in RB1 and TP53 were detected in the cfDNA of one patient nearly four months prior to the development of small cell lung cancer (SCLC) transformation confirmed on tissue biopsy with distinct transformed and untransformed areas. Both of the specific RB1 and TP53 mutations found in cfDNA have been previously associated with SCLC. Subsequent combination cisplatin-etoposide chemoradiation resulted in temporary complete remission of the transformed SCLC, corresponding to loss of RB1 mutation detection by cfDNA testing.

      Conclusion

      Profiling of plasma cfDNA using hybrid capture deep sequencing of a large gene panel can detect early subclinical transformation of EGFR-mutated lung cancer into small cell lung cancer (i.e., neuroendocrine transformation), leading to earlier diagnosis and management of the transformed disease. Serial liquid biopsy profiling can also be used to monitor disease progression. However, detection sensitivity of tumour cfDNA largely depends on systemic tumour burden.