Virtual Library

Start Your Search

Marc Ladanyi



Author of

  • +

    MA12 - New Frontiers from Pathology to Genomics (ID 138)

    • Event: WCLC 2019
    • Type: Mini Oral Session
    • Track: Mesothelioma
    • Presentations: 1
    • Now Available
    • +

      MA12.10 - Novel Germline Mutations in DNA-Damage Repair and DNA Replication Identified in Patients with Malignant Pleural Mesothelioma (MPM) (Now Available) (ID 1419)

      14:00 - 15:30  |  Author(s): Marc Ladanyi

      • Abstract
      • Presentation
      • Slides

      Background

      Recent efforts to characterize the germline genetic landscape of MPM have uncovered a surprising prevalence of pathogenic variants in DNA-damage sensing and repair genes. Increasingly, next-generation sequencing has helped bring new insight into critical mutations or pathways involved in the development of MPM. Additionally, observations from these studies could direct new screening, prevention, and therapeutic approaches for patients and families.

      Method

      With IRB approval, we performed deidentified analysis on 87 additional cancer-predisposing genes on our NGS platform among patients with MPM previously consented to a BAP1 germline testing protocol. Additionally, germline variants in an additional 380 genes associated with somatic alterations in cancer, but not associated with hereditary cancer predisposition, were screened for loss of function variant or pathogenic entries in ClinVar. All variants were reviewed according to the American College of Medical Genetics and Genomics and Association for Molecular Pathology consensus guidelines. Founder mutations were excluded. Clinicopathologic information was also collected. Comparisons were done using Fisher’s exact test. P values <0.05 were considered significant.

      Result

      Of 88 patients with MPM analyzed, 11% (10/88) had pathogenic variants. Clinical characteristics such as age, sex, histology, and self-reported asbestos exposure, were similar between patients with and without pathogenic variants (Table 1). Pathogenic variants previously unreported in mesothelioma were identified: MSH3 1/88 (1%; 95% CI: 0-7%), BARD1 1/88 (1%; 95% CI: 0-7%), and RECQL4 2/88 (2%; 95% CI: 0-8%). We also identified pathogenic variants previously associated with mesothelioma: BAP1 in 3/88 (3%; 95% CI: 1-10%), BRCA2 1/88 (1%; 95% CI: 0-7%), and MRE11A 1/88 (1%; 95% CI: 0-7%). One patient had a potentially pathogenic alteration in SHQ1, which has not been associated with a heightened susceptibility to cancer. Patients with germline pathogenic variants were more likely to have more than 2 first-degree family members with cancer compared to those without germline mutations (40% vs 13%; p = 0.049).

      Conclusion

      While the overall incidence of germline mutations identified is similar to prior reports, we identified germline pathogenic alterations in three DNA damage repair and replication genes not previously reported in mesothelioma. Furthermore, we describe a novel germline alteration in SHQ1, which has not been reported with hereditary cancer predisposition. Whether these variants increase the risk of mesothelioma is still under investigation, but given the high rate of germline pathogenic variant in individuals with pleural mesothelioma, germline testing for hereditary cancer susceptibility should be considered in all patients with MPM.

      wclc2019.mesobap1.table-min.jpg

      Only Members that have purchased this event or have registered via an access code will be able to view this content. To view this presentation, please login, select "Add to Cart" and proceed to checkout. If you would like to become a member of IASLC, please click here.

      Only Active Members that have purchased this event or have registered via an access code will be able to view this content. To view this presentation, please login or select "Add to Cart" and proceed to checkout.

  • +

    P1.01 - Advanced NSCLC (ID 158)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Advanced NSCLC
    • Presentations: 1
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
    • +

      P1.01-122 - A Clinical Utility Study of Plasma DNA Next Generation Sequencing Guided Treatment of Uncommon Drivers in Advanced Non-Small-Cell Lung Cancers (ID 2997)

      09:45 - 18:00  |  Author(s): Marc Ladanyi

      • Abstract
      • Slides

      Background

      Although EGFR and ALK testing in non-small-cell lung cancers (NSCLC) is now considered standard practice, next generation sequencing (NGS) for extended molecular testing of uncommon drivers is often difficult to perform in the community due to factors surrounding tissue adequacy, availability and turnaround time. We set out to prospectively determine the clinical utility of plasma ctDNA NGS in detecting uncommon actionable drivers and their plasma guided treatment response.

      Method

      Patients with advanced NSCLC who were driver unknown after routine EGFR and ALK testing were eligible. Patients were enrolled prospectively at Memorial Sloan Kettering Cancer Center (NY, USA) and Northern Cancer Institute (Sydney, Australia). Peripheral blood (10-20mL) was collected and sent to Resolution Bioscience (Kirkland, WA) for targeted ctDNA NGS using a bias-corrected hybrid-capture 21 gene assay in a CLIA laboratory achieving a mean unique read of at least 3000x and sensitivity above 0.1%. Clinical endpoints included detection of uncommon oncogenic drivers defined as actionable alterations in ROS1, RET, BRAF, MET, HER2, turnaround time, concordance with tissue NGS when available, and plasma guided treatment outcome.

      Result

      614 patients were prospectively accrued. Plasma NGS detected an uncommon oncogenic driver in 7% (45/614) of patients including ROS1, RET fusions, BRAF, MET exon 14 and HER2 exon 20 mutations, of whom 3% (20/614) were matched to targeted therapy producing 12 partial responses. Mean turnaround time for plasma NGS was significantly shorter than tissue NGS (10 vs 25 days, P <0.0001). 399 patients had concurrent tissue NGS results available for concordance analysis; Overall concordance, defined as the proportion of patients for whom an uncommon driver was uniformly detected or absent in both plasma and tissue NGS, was 94.7% (378/399, 95% confidence interval [CI] 92.1 – 96.7%). Among patients who tested plasma NGS positive for uncommon drivers, 87.5% (28/32, 95% CI 71.0-96.5%) were concordant on tissue NGS, and among patients tested tissue NGS positive for uncommon driver, 62.2% (28/45, 95% CI 46.5-76.2%) were concordant on plasma NGS.

      Conclusion

      Plasma NGS uncovered uncommon oncogenic drivers with faster turnaround time than tissue NGS, directly matched patients to targeted therapy and produced clinical responses independent of tissue results. A positive finding of an oncogenic driver in plasma is highly specific and can immediately guide treatment, but a negative finding may still require tissue biopsy. Our findings provide prospective evidence to support a “blood first” approach in molecular diagnostics for the care of patients with NSCLC.

      Only Active Members that have purchased this event or have registered via an access code will be able to view this content. To view this presentation, please login or select "Add to Cart" and proceed to checkout.

  • +

    P1.14 - Targeted Therapy (ID 182)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Targeted Therapy
    • Presentations: 3
    • Now Available
    • Moderators:
    • Coordinates: 9/08/2019, 09:45 - 18:00, Exhibit Hall
    • +

      P1.14-06 - Tissue-Based Molecular and Histologic Landscape of Acquired Resistance to Osimertinib in Patients with EGFR-Mutant Lung Cancers (ID 1392)

      09:45 - 18:00  |  Author(s): Marc Ladanyi

      • Abstract
      • Slides

      Background

      Even though osimertinib (osi) is now the initial treatment for patients with EGFR-mutant lung cancers, our knowledge about mechanisms of resistance (MOR) is largely derived from patients who received osi after acquiring EGFR T790M on treatment with another EGFR inhibitor. Other studies of osi resistance have mainly reported genotyping of plasma which suboptimally detects lineage plasticity, copy number changes, and chromosomal rearrangements.

      Method

      To identify MOR to osi and characterize clinical, molecular and histologic factors associated with duration of response, we identified patients with EGFR-mutant lung cancers who had targeted next-generation sequencing (MSK-IMPACT) performed on tumor tissue obtained before treatment and after developing resistance to osi received as either first-line or later line EGFR-TKI.

      Result

      From January 2016 to March 2019, we collected paired pre-treatment and resistance specimens from 53 patients (1st line osi: 21. Osi after prior TKI: 32). MOR are summarized in the table. Histologic transformation was identified in 18% of 1st line cases and 17% of all cases. When osi was given as initial treatment, with median follow up of 18 months, early emerging MOR rarely included on-target resistance mechanisms (acquired EGFR G724S in 1/21). Other acquired alterations representing potential resistance mechanisms not listed in the table included CCNE1 and MYC amplifications, and mutations in MTOR A1098S and MET H1094Y.

      First line (n = 21)

      Osi after prior TKI

      (n = 32)

      All

      (n = 53)

      Squamous transformation

      3

      3

      6

      Neuroendocrine transformation

      1

      2

      3

      On target mutation (EGFR C797X or other)

      1

      9

      10

      Loss of EGFR T790M only

      -

      8

      8

      Fusions (ALK, RET, BRAF)

      0

      3

      3

      Amplifications (HER2, MET, EGFR)

      2

      3

      4

      Off target mutations (KRAS, BRAF, HER2)

      1

      2

      3

      Conclusion

      In this analysis of MOR identified on NGS from tumor tissue, we found a spectrum of resistance mechanisms to osi. By evaluating tissue rather than plasma we provide data on histologic transformation (including squamous cell transformation). Subsequent studies are needed to assess patients with a longer time on initial osi as early progressors may have different MOR, with off-target MOR emerging earlier and on-target resistance mutations later.

      Only Active Members that have purchased this event or have registered via an access code will be able to view this content. To view this presentation, please login or select "Add to Cart" and proceed to checkout.

    • +

      P1.14-12 - A Novel Activating MAP2K1 In-Frame Deletion Mediates Acquired Resistance to ROS1 TKIs in a Patient with ROS1 Fusion-Positive NSCLC (ID 2450)

      09:45 - 18:00  |  Author(s): Marc Ladanyi

      • Abstract

      Background

      ROS1 tyrosine kinase inhibitors (TKIs) such as crizotinib, entrectinib and lorlatinib provide significant benefit in non-small cell lung cancer (NSCLC) patients with ROS1 fusions. As observed with all targeted therapies however, resistance arises. With the widespread adoption of large panel next generation sequencing (NGS) at the time of acquired resistance (AR), our appreciation of novel off-target mechanisms continues to grow. Detecting additional mechanisms of acquired resistance (AR) is crucial to find novel therapies and improve patient outcomes.

      Method

      We reviewed targeted large-panel sequencing data (using the MSK-IMPACT assay) of paired pre-treatment and post-progression samples from patients treated with ROS1 TKIs. Genetic alterations hypothesized to confer AR were modeled in a patient-derived cell line (LUAD-0003, expressing EZR/ROS1) as well as isogenic human (HBEC) and murine (NIH-3T3) cell lines. ROS1 fusions were expressed in these cells either by cDNA overexpression (CD74/ROS1, SLC34A2/ROS1) or CRISPR-Cas9-mediated genomic engineering (EZR/ROS1). Using these cell line models, alterations in drug sensitivity and downstream signal pathways were examined. We also explored possible therapeutic strategies to overcome the drug resistance caused by the novel AR mechanisms examined in this study.

      Result

      We identified a patient with NSCLC harboring a MAP2K1 (MEK1) variant encoding an in-frame deletion of amino acids E41-L54 (MEK1del) in a sample taken at the time of resistance to lorlatinib (after 9 months’ treatment). This mutation was not detected in the pre-TKI sample. Induction of ROS1 fusions in HBEC and NIH-3T3 cells increased the sensitivity of these cells to ROS1 TKIs and stimulated activation of MEK/ERK signaling in comparison with AKT signaling, suggesting the importance of the RAS-MAPK pathway in driving ROS1 fusion-positive cancers. Underscoring the importance of the RAS-MAPK pathway in ROS1-mediated tumorigenesis, we identified three patients (pancreatic, salivary, and breast cancer) with a ROS1 fusion and NF1 loss-of-function mutation concurrently, in TKI-naïve samples. Expression of MEK1del in HBEC and NIH-3T3 cells harboring ROS1 fusions, and knockdown of NF1 in LUAD-0003, activated ERK signaling and conferred resistance to ROS1 TKIs. Combined targeting of ROS1 (crizotinib, lorlatinib) and MEK (selumetinib, trametinib) inhibited growth of cells expressing both ROS1 fusion and MEK1del.

      Conclusion

      Our results suggest that the activation of the RAS-MAPK pathway plays a critical role in tumorigenesis mediated by ROS1 fusions, and that activating mutations in this pathway can drive AR to ROS1 TKIs. Combined inhibition of ROS1 and MEK is a potential therapeutic strategy that should be explored clinically.

    • +

      P1.14-50 - A Phase 2 Trial of Cabozantinib in ROS1-Rearranged Lung Adenocarcinoma (Now Available) (ID 2753)

      09:45 - 18:00  |  Author(s): Marc Ladanyi

      • Abstract
      • Slides

      Background

      To date, no ROS1 inhibitor is approved for the treatment of ROS1-rearranged lung cancers after progression on crizotinib. Progression on crizotinib can be mediated by the acquisition of ROS1 kinase domain mutations (e.g. ROS1G2032R or ROS1D2033N). Cabozantinib is a highly potent ROS1 tyrosine kinase inhibitor that has superior activity over lorlatinib against these mutations. We evaluated the activity of cabozantinib in patients with ROS1-rearranged lung cancers on a phase 2 trial.

      Method

      In this single-center, open-label, Simon two-stage, phase 2 study, eligible patients had ROS1-rearranged unresectable/metastatic non-small cell lung cancer, a Karnofsky performance status >70%, and measurable disease. ROS1 fusion was identified by local testing in a CLIA-compliant environment. Cabozantinib was dosed at 60 mg once daily. The primary endpoint was objective response (RECIST v1.1). In the first stage of this trial, 1 response was required to move to the second stage. Secondary endpoints included safety.

      Result

      Six patients received cabozantinib in the ongoing first stage of this study. All patients had >1 prior ROS1 inhibitor. The median age was 59 years; all were never smokers. The best response to therapy was: 1 partial response (-92%, confirmed), 1 unconfirmed partial response (-31%), and 4 stable disease. All patients had disease regression (-7 % to -92%); no patients had primary progressive disease. The only patient with a confirmed partial response was a patient whose cancer acquired a ROS1D2033N solvent front mutation after crizotinib. None of the other five ROS1 inhibitor pre-treated patients (who did not have a confirmed response) had a known on-target acquired resistance mutation in their cancer. After progression on cabozantinib (9.1 months after therapy initiation), the patient whose cancer harbored the ROS1D2033N mutation acquired a METD1228N kinase domain mutation on paired sequencing of pre-cabozantinib and post-progression tumor. The most common grade 3 treatment-related adverse events were hypertension (50%), and mucositis, palmar-plantar erythrodysesthesia, and hypophosphatemia (each in 17%). Most patients (83%) required a dose reduction.

      Conclusion

      Cabozantinib can re-establish disease control in ROS1-rearranged lung cancers after progression on a prior ROS1 inhibitor. The first stage of this ongoing trial met its prespecified endpoint for efficacy to move into the second stage. Response was only observed in the setting of a known ROS1 kinase domain resistance mutation.

      Only Active Members that have purchased this event or have registered via an access code will be able to view this content. To view this presentation, please login or select "Add to Cart" and proceed to checkout.

  • +

    P2.03 - Biology (ID 162)

    • Event: WCLC 2019
    • Type: Poster Viewing in the Exhibit Hall
    • Track: Biology
    • Presentations: 1
    • Now Available
    • Moderators:
    • Coordinates: 9/09/2019, 10:15 - 18:15, Exhibit Hall
    • +

      P2.03-26 - Elucidating Mechanisms of Resistance to Targeted Therapies in Mutant EGFR or KRAS Driven Lung Adenocarcinoma Harboring Dual Loss of p53 and RB1 (Now Available) (ID 2004)

      10:15 - 18:15  |  Author(s): Marc Ladanyi

      • Abstract
      • Slides

      Background

      Inactivation of the two canonical tumor suppressors, p53 and RB1, is a genetic hallmark of small-cell lung cancer (SCLC). In contrast, lung adenocarcinomas (LUADs) preferentially harbor alterations in the p16 pathway over RB1. Nonetheless, despite being rare, concurrent loss of p53 and RB1 occurs in a subset of LUADs and this is hypothesized to be necessary for the histological transformation of LUAD to SCLC, observed during treatment with tyrosine kinase inhibitors (TKIs). However, whether the dual loss of p53 and RB1 is sufficient for this histological transformation remains unknown. Furthermore, loss of RB1 in LUADs with EGFR mutations is associated with poor response to TKIs in the absence of SCLC transformation. Here, we aimed to explore how loss of p53/RB1 affects the biology of p16 pathway-altered LUAD, particularly in the context of acquired resistance mechanisms to targeted therapies.

      Method

      Four TP53-mutated LUAD cell lines were used: two EGFR mutation-positive (PC9 and H1975) and two KRAS mutation-positive (H1792 and H358). All these cell lines possess p16 pathway alterations: p16 (CDKN2A) mutations in PC9 and H1975, CDK4 amplification in H1792, and silenced p16 in H358. Inactivation of RB1 was carried out using CRISPR-Cas9 and RB1 knockout monoclonal cells were established. Cell proliferative and clonogenic abilities were assessed. In addition, osimertinib-resistant (PC9 and H1975) and trametinib-resistant (H1792 and H358) cells were generated (initial high dose and/or stepwise dose escalation methods). Acquired resistance mechanisms were evaluated by MSK-IMPACT profiling.

      Result

      Two RB1 knockout clones were established for each cell line. No advantageous effects were observed for proliferative and clonogenic abilities after RB1 knockout. Although loss of p53 and RB1 has been reported to result in lineage shift in prostate cancer through the upregulation of SOX2, deregulation of SOX2 expression was not observed upon RB1 knockout in the TP53-mutant LUAD cells. In addition, although loss of RB1 caused a modest reduction in osimertinib and trametinib sensitivities of H1975 and H358 cells, respectively, no effect was observed in PC9 and H1792 cells. After becoming resistant to osimertinib or trametinib, transformation to SCLC was not observed. Individual resistance mechanisms are currently being assessed by MSK-IMPACT.

      Conclusion

      Dual loss of p53 and RB1 caused no advantageous effects in TP53-mutated and p16 pathway-altered LUAD cells and did not initiate transformation to SCLC as a resistance mechanism to targeted therapies. TP53/RB1 deficiency-related acquired resistance mechanisms to osimertinib or trametinib will be further explored and presented.

      Only Active Members that have purchased this event or have registered via an access code will be able to view this content. To view this presentation, please login or select "Add to Cart" and proceed to checkout.