Integrated genomic and DNA methylation analyses of non-small cell lung cancer patients with brain metastases

Integrated genomic and DNA methylation analyses of non-small cell lung cancer patients with brain metastases

Annals of Oncology 30 (Supplement 5): v602–v660, 2019 doi:10.1093/annonc/mdz260 NSCLC, METASTATIC 1478O Results of the ASCEND-7 phase II study evalu...

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Annals of Oncology 30 (Supplement 5): v602–v660, 2019 doi:10.1093/annonc/mdz260

NSCLC, METASTATIC 1478O

Results of the ASCEND-7 phase II study evaluating ALK inhibitor (ALKi) ceritinib in patients (pts) with ALK1 non-small cell lung cancer (NSCLC) metastatic to the brain

Background: Ceritinib is approved for the treatment of pts with metastatic ALKþ NSCLC. In previous studies (ASCEND-1 to 5), ceritinib was highly active in ALKþ NSCLC pts with reported intracranial responses in pts with measurable baseline brain lesions. ASCEND-7 (NCT02336451) was designed to specifically study intracranial effects of ceritinib and we report here efficacy and safety in pts with ALKþ NSCLC metastatic to the brain (Arms 1-4). Methods: Eligible pts had, WHO performance status 0-2, ALK þ (FISH) NSCLC, with active brain metastases (BM) either newly diagnosed or progressive, and 1 extracranial measurable lesion using RECIST v1.1. Pts may have been pretreated with chemotherapy and/or crizotinib (ALK inhibitor [ALKi]). Pts were assigned to arms 1 to 4 depending on prior treatment (refer to below table). Primary endpoint was investigator assessed whole body overall response rate (CR or PR) and key secondary endpoint was investigator assessed disease control rate (CR or PR or SD). Intracranial responses and extracranial responses were assessed using modified RECIST 1.1 and RECIST 1.1, respectively. Results: As of 6-Feb-2019, 138 pts were treated in Arms 1-4 (Arm 1: 42; Arm 2: 40; Arm 3: 12; Arm 4: 44), and all the pts discontinued the treatment. Median follow-up for whole body progression free survival was 5.49 months across Arm 1-4. Efficacy endpoints by investigator assessment are reported in the below Table. Most common AEs (>50% all grades in any of the Arms 1-4) regardless of causality were diarrhoea, nausea, ALT increased, vomiting, AST increased, decreased appetite. Majority of these AEs was grade 1/2. Conclusions: Efficacy of ceritinib, either in pts with or without a prior exposure to crizotinib, as reported in other studies, is confirmed in this study where only pts with active brain metastases were eligible. Safety profile of ceritinib in these pts remain consistent to what was reported earlier. Clinical trial identification: NCT02336451. Editorial acknowledgement: Shiva Krishna Rachamadugu, Novartis Healthcare Pvt Ltd, Hyderabad, India. Legal entity responsible for the study: Novartis Pharmaceuticals Corporation. Funding: Novartis Pharmaceuticals Corporation. Disclosure: L.Q. Chow: Advisory / Consultancy, Consultation Honoraria/Review panel: Amgen; Advisory / Consultancy, Research grant / Funding (institution): Novartis; Advisory / Consultancy, Research grant / Funding (institution): Merck; Research grant / Funding (institution): Lilly/Imclone; Advisory / Consultancy, Research grant / Funding (institution): Bristol-Myers Squibb; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca/MedImmune ; Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Research grant / Funding (institution): Incyte; Advisory / Consultancy: Takeda; Research grant / Funding (institution): VentiRx; Advisory / Consultancy: Sanofi-Genzyme; Advisory / Consultancy, Research grant / Funding (institution): Seattle Genetics; Advisory / Consultancy, Research grant / Funding (institution): Dynavax; Advisory / Consultancy, Research grant / Funding (institution): Genentech; Advisory / Consultancy: Synthorx; Research grant / Funding (institution): Alkermes. F. Barlesi: Honoraria (self), Research grant / Funding (institution): AstraZeneca, Bayer; Honoraria (self), Research grant / Funding (institution): Bristol-Myers Squibb; Honoraria (self), Research grant / Funding (institution): Boehringer– Ingelheim; Honoraria (self), Research grant / Funding (institution): Eli Lilly Oncology; Honoraria (self), Research grant / Funding (institution): F. Hoffmann–La Roche Ltd; Honoraria (self), Research grant / Funding (institution): Novartis; Honoraria (self), Research grant / Funding (institution): Merck; Honoraria (self), Research grant / Funding (institution): MSD; Honoraria (self), Research grant / Funding (institution): Pierre Fabre; Honoraria (self), Research grant / Funding (institution): Pfizer; Honoraria (self), Research grant / Funding (institution): Takeda; Research grant / Funding

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Integrated genomic and DNA methylation analyses of non-small cell lung cancer patients with brain metastases

Y. Fan1, Y. Xu1, Z. Huang1, K. Chen1, H. Han-Zhang2, J. Ye2, N. Han1, L. Gong1, X. Xu1, H. Lu1, J. Qin1, F. Xie1 1 Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China, 2Burning Rock Biotech, Guangzhou, China Background: Brain metastases (BM), with a dismal prognosis, are a common and lethal complication of non-small cell lung cancer. Recognition of its genomic and epigenomic landscape is very necessary. Methods: Capture-based targeted sequencing for somatic mutation profiling was performed on 27 treatment-naı¨ve advanced NSCLC patients with paired lung primary and BM lesions using a pane consisting of 520 cancer related genes. DNA methylation analyses was performed on same samples using a DNA methylation panel consisting of 100,000 CpG sites. Results: Collectively, we identified 370 (291 SNVsþIndels, 78 CNVs and 1 rearrangement) and 574 (245 SNVsþIndels, 327 CNVs and 2 rearrangements) mutations from lung primary lesions and BM, respectively. Among them, 242 mutations were shared; 128 were lung primary-specific and 332 were BM-specific. Among the BM specific mutations, a majority of them (82%, 272/332) were copy number variations (CNVs). Only 16% of CNVs were shared by lung lesions and BM. The concordance for SNVs and indels were much higher-54% between the two sources of tissues. Furthermore, we observed a much higher concordance rate (79%) in TP53 and classic lung cancer driver genes than other genes (p < 0.001), indicating that they might be stem mutations. Next, we performed pathway analysis of genes that were only mutated in BM and revealed an enrichment of genes participating in PI3K-AKT and focal adhesion pathways. Our DNA methylation analysis revealed distinct methylation patterns with 268 blocks that are significantly differentially methylated between primary lung lesions and BM. Among them, 211 blocks were hypermethylated in BM and the remaining 57 blocks were hypermethylated in lung lesions. These blocks were enrichment in genes participating in cell adhesion, Rap1 signaling and calcium signaling pathways. Conclusions: We revealed diverse somatic mutation and DNA methylation profiles between lung primary lesions and BM. BM had significantly more unique CNVs. A great concordance was observed for classic lung cancer driver genes and TP53. Our study provided a comprehensive view of genomic and DNA methylation profiling for lung primary lesions and BM, paving the avenue for the development of targeted therapies for treating BM. Legal entity responsible for the study: The authors.

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L.Q. Chow1, F. Barlesi2, E.M. Bertino3, M.J. van den Bent4, H. Wakelee5, P.Y. Wen6, CH. Chiu7, S. Orlov8, M. Majem9, R. Chiari10, M. McKeage11, C-J. Yu12, F.K. Hurtado13, P. Cazorla Arratia14, Y. Song15, F. Branle16, M. Shi14, D-W. Kim17 1 Dept. of Oncology, University of Washington, Seattle, WA, USA, 2Dept. of Multidisciplinary Oncology and Therapeutic Innovations, Aix Marseille University, CNRS, INSERM, CRCM, APHM, Marseille, France, 3Dept. of Internal Medicine - Medical Oncology, The Ohio State University Medical Center, Columbus, OH, USA, 4Dept. of Neurologie, Erasmus MC Daniel den Hoed Cancer Center, Rotterdam, Netherlands, 5 Dept. of Medicine/Oncology, Stanford University, Stanford, CA, USA, 6Dept. of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA, 7Dept. of Chest Medicine, Taipei Veterans General Hospital, Taipei City, Taiwan, 8Dept. of Oncology, State Pavlov Medical University, Saint-Petersburg, Russian Federation, 9Dept. of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain, 10Dept. of Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy, 11 Dept. of Pharmacology and Clinical Pharmacology, and Auckland Cancer Society Research Centre, University of Auckland, Auckland, New Zealand, 12Dept. of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan, 13Dept. of Translational Medicine, Novartis Institutes for Biomedical Research, East Hanover, NJ, USA, 14Dept. of Clinical Development, Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA, 15 Dept. of Biostatistics, Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA, 16 Dept. of Drug Development, Novartis AG, Basel, Switzerland, 17Dept. of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea

(institution): AbbVie; Research grant / Funding (institution): ACEA; Research grant / Funding (institution): Amgen; Research grant / Funding (institution): Eisai; Research grant / Funding (institution): Genentech; Research grant / Funding (institution): Ipsen; Research grant / Funding (institution): Loxo; Research grant / Funding (institution): MedImmune and Sanofi-Aventis; Non-remunerated activity/ies: Principal Investigator for AstraZeneca, BMS, Merck, Pierre Fabre and F. Hoffmann-La Roche, Ltd, sponsored trials (or ISR). E.M. Bertino: Advisory / Consultancy: Takeda; Speaker Bureau / Expert testimony: Pfizer. M.J. van den Bent: Honoraria (self): Celgene, Agios, Boehringer, BMS, AbbVie ; Research grant / Funding (institution): AbbVie. H. Wakelee: Honoraria (self): Novartis, AstraZeneca; Advisory / Consultancy, NOT compensated: Merck, Takeda, Genentech/Roche: AstraZeneca, Xcovery, Janssen; Research grant / Funding (institution): ACEA Biosciences, Arrys Therapeutics, AstraZeneca/MedImmune, Bayer (under Suki and not me), BMS, Celgene, Clovis Oncology, Exelixis, Genentech/Roche, Gilead, Lilly, Merck, Novartis, Pfizer, Pharmacyclics, Xcovery; Travel / Accommodation / Expenses: AstraZeneca; Officer / Board of Directors: International Association for the Study of Lung Cancer (IASLC). P.Y. Wen: Advisory / Consultancy: Agios, AstraZeneca, Beigene, Eli Lilly, Genentech/Roche, Karyopharm, Kazia, MediciNova, Merck, Novartis, Oncoceutics, Sanofi-Aventis, VBI Vaccines, Tocagen; Speaker Bureau / Expert testimony: Merck, Prime Oncology; Research grant / Funding (institution): Agios, AstraZeneca, Beigene, Eli Lilly, Genentech/Roche, Karyopharm, Kazia, MediciNova, Merck, Novartis, Oncoceutics, Sanofi-Aventis, VBI Vaccines. C. Chiu: Honoraria (self): AstraZeneca, Boehringer Ingelheim, Bristol-Myers Squibb, Chugai Pharmaceutical, Eli Lilly, Merck Sharp & Dohme, Novartis, Ono Pharmaceutical, Pfizer, Roche, and Takeda. M. Majem: Advisory / Consultancy: Roche, MSD, AstraZeneca, Boehringer, Tesaro, Takeda, Pierre Fabre; Speaker Bureau / Expert testimony: Roche, BMS, MSD, AstraZeneca, Boehringer Hellsin, Pierre Fabre, Amgen; Research grant / Funding (self): BMS; Travel / Accommodation / Expenses: BMS, MSD, AstraZeneca, Lilly. R. Chiari: Honoraria (self): AstraZeneca, Boehringer Ingelheim, Bristol-Myers Squibb, Novartis, Pfizer, Roche, and Takeda. M. McKeage: Advisory / Consultancy: Novartis, Pfizer; Research grant / Funding (institution): Novartis, Pfizer, Roche. C. Yu: Honoraria (self): Roche, AstraZeneca, Ono pharma, Boehringer Ingelheim ; Advisory / Consultancy: Roche, AstraZeneca, Ono pharma, Boehringer Ingelheim. F.K. Hurtado: Shareholder / Stockholder / Stock options, Full / Part-time employment: Novartis. P. Cazorla Arratia: Shareholder / Stockholder / Stock options, Full / Part-time employment: Novartis. Y. Song: Shareholder / Stockholder / Stock options, Full / Part-time employment: Novartis. F. Branle: Honoraria (self), Shareholder / Stockholder / Stock options, Full / Part-time employment: Novartis. M. Shi: Shareholder / Stockholder / Stock options, Full / Part-time employment: Novartis. D. Kim: Research grant / Funding (institution): Alpha Biopharma, AstraZeneca/MedImmune, Hanmi, Janssen, Merus, Mirati Therapeutics, MSD, Novartis, ONO Pharmaceutical, Pfizer, Roche/Genentech, Takeda, TP Therapeutics, Xcovery, and Yuhan. All other authors have declared no conflicts of interest.

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Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.

Volume 30 | Supplement 5 | October 2019

doi:10.1093/annonc/mdz260 | v603