1
|
Harrold E, Keane F, Walch H, Chou JF, Sinopoli J, Palladino S, Al-Rawi DH, Chadalavada K, Manca P, Chalasani S, Yang J, Cercek A, Shia J, Capanu M, Bakhoum SF, Schultz N, Chatila WK, Yaeger R. Molecular and Clinical Determinants of Acquired Resistance and Treatment Duration for Targeted Therapies in Colorectal Cancer. Clin Cancer Res 2024:741877. [PMID: 38502113 DOI: 10.1158/1078-0432.ccr-23-4005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/19/2024] [Accepted: 03/15/2024] [Indexed: 03/20/2024]
Abstract
PURPOSE Targeted therapies have improved outcomes for patients with metastatic colorectal cancer, but their impact is limited by rapid emergence of resistance. We hypothesized that an understanding of the underlying genetic mechanisms and intrinsic tumor features that mediate resistance to therapy will guide new therapeutic strategies and ultimately allow the prevention of resistance. EXPERIMENTAL DESIGN We assembled a series of 52 patients with paired pre-treatment and progression samples who received therapy targeting EGFR (n=17), BRAF V600E (n=17), KRAS G12C (n=15), or amplified HER2 (n=3) to identify molecular and clinical factors associated with time on treatment (TOT). RESULTS All patients stopped treatment for progression and TOT did not vary by oncogenic driver (p=0.5). Baseline disease burden (≥3 versus <3 sites, p=0.02), the presence of hepatic metastases (p=0.02), and gene amplification on baseline tissue (p=0.03) were each associated with shorter TOT. We found evidence of chromosomal instability (CIN) at progression in patients with baseline MAPK pathway amplifications and those with acquired gene amplifications. At resistance, copy number changes (p=0.008) and high number (≥5) of acquired alterations (p=0.04) were associated with shorter TOT. Patients with hepatic metastases demonstrated both higher number of emergent alterations at resistance and enrichment of mutations involving receptor tyrosine kinases. CONCLUSIONS Our genomic analysis suggests that high baseline CIN or effective induction of enhanced mutagenesis on targeted therapy underlies rapid progression. Longer response appears to result from a progressive acquisition of genomic or chromosomal instability in the underlying cancer or from the chance event of a new resistance alteration.
Collapse
Affiliation(s)
- Emily Harrold
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Fergus Keane
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Henry Walch
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Joanne F Chou
- Memorial Sloan Kettering Cancer Center, NYC, United States
| | - Jenna Sinopoli
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Silvia Palladino
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Duaa H Al-Rawi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Paolo Manca
- Memorial Sloan Kettering Cancer Center, New York, United States
| | - Sree Chalasani
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Jessica Yang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Marinela Capanu
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Samuel F Bakhoum
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Nikolaus Schultz
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Walid K Chatila
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| |
Collapse
|
2
|
Feng Y, Yuan Q, Newsome RC, Robinson T, Bowman RL, Zuniga AN, Hall KN, Bernsten CM, Shabashvili DE, Krajcik KI, Gunaratne C, Zaroogian ZJ, Venugopal K, Casellas Roman HL, Levine RL, Chatila WK, Yaeger R, Riva A, Jobin C, Kopinke D, Avram D, Guryanova OA. Hematopoietic-specific heterozygous loss of Dnmt3a exacerbates colitis-associated colon cancer. J Exp Med 2023; 220:e20230011. [PMID: 37615936 PMCID: PMC10450614 DOI: 10.1084/jem.20230011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/12/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Clonal hematopoiesis (CH) is defined as clonal expansion of mutant hematopoietic stem cells absent diagnosis of a hematologic malignancy. Presence of CH in solid tumor patients, including colon cancer, correlates with shorter survival. We hypothesized that bone marrow-derived cells with heterozygous loss-of-function mutations of DNMT3A, the most common genetic alteration in CH, contribute to the pathogenesis of colon cancer. In a mouse model that combines colitis-associated colon cancer (CAC) with experimental CH driven by Dnmt3a+/Δ, we found higher tumor penetrance and increased tumor burden compared with controls. Histopathological analysis revealed accentuated colonic epithelium injury, dysplasia, and adenocarcinoma formation. Transcriptome profiling of colon tumors identified enrichment of gene signatures associated with carcinogenesis, including angiogenesis. Treatment with the angiogenesis inhibitor axitinib eliminated the colon tumor-promoting effect of experimental CH driven by Dnmt3a haploinsufficiency and rebalanced hematopoiesis. This study provides conceptually novel insights into non-tumor-cell-autonomous effects of hematopoietic alterations on colon carcinogenesis and identifies potential therapeutic strategies.
Collapse
Affiliation(s)
- Yang Feng
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Qingchen Yuan
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Rachel C. Newsome
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Troy Robinson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ashley N. Zuniga
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kendra N. Hall
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Cassandra M. Bernsten
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Daniil E. Shabashvili
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kathryn I. Krajcik
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Chamara Gunaratne
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Zachary J. Zaroogian
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Kartika Venugopal
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Heidi L. Casellas Roman
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K. Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Christian Jobin
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| | - Daniel Kopinke
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
| | - Dorina Avram
- Department of Anatomy and Cell Biology, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
- Immunology Department, Moffitt Cancer Center, Tampa, FL, USA
| | - Olga A. Guryanova
- Department of Pharmacology and Therapeutics, University of FloridaCollege of Medicine, Gainesville, FL, USA
- University of FloridaHealth Cancer Center, Gainesville, FL, USA
| |
Collapse
|
3
|
Tagore M, Hergenreder E, Perlee SC, Cruz NM, Menocal L, Suresh S, Chan E, Baron M, Melendez S, Dave A, Chatila WK, Nsengimana J, Koche RP, Hollmann TJ, Ideker T, Studer L, Schietinger A, White RM. GABA Regulates Electrical Activity and Tumor Initiation in Melanoma. Cancer Discov 2023; 13:2270-2291. [PMID: 37553760 PMCID: PMC10551668 DOI: 10.1158/2159-8290.cd-23-0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Oncogenes can initiate tumors only in certain cellular contexts, which is referred to as oncogenic competence. In melanoma, whether cells in the microenvironment can endow such competence remains unclear. Using a combination of zebrafish transgenesis coupled with human tissues, we demonstrate that GABAergic signaling between keratinocytes and melanocytes promotes melanoma initiation by BRAFV600E. GABA is synthesized in melanoma cells, which then acts on GABA-A receptors in keratinocytes. Electron microscopy demonstrates specialized cell-cell junctions between keratinocytes and melanoma cells, and multielectrode array analysis shows that GABA acts to inhibit electrical activity in melanoma/keratinocyte cocultures. Genetic and pharmacologic perturbation of GABA synthesis abrogates melanoma initiation in vivo. These data suggest that GABAergic signaling across the skin microenvironment regulates the ability of oncogenes to initiate melanoma. SIGNIFICANCE This study shows evidence of GABA-mediated regulation of electrical activity between melanoma cells and keratinocytes, providing a new mechanism by which the microenvironment promotes tumor initiation. This provides insights into the role of the skin microenvironment in early melanomas while identifying GABA as a potential therapeutic target in melanoma. See related commentary by Ceol, p. 2128. This article is featured in Selected Articles from This Issue, p. 2109.
Collapse
Affiliation(s)
- Mohita Tagore
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emiliano Hergenreder
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, New York
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, New York
- Weill Graduate School of Medical Sciences of Cornell University, New York, New York
| | - Sarah C. Perlee
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelly M. Cruz
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Menocal
- Weill Graduate School of Medical Sciences of Cornell University, New York, New York
| | - Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maayan Baron
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Stephanie Melendez
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Asim Dave
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K. Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeremie Nsengimana
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Travis J. Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, New York
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard M. White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
4
|
Kasago IS, Chatila WK, Lezcano CM, Febres-Aldana CA, Schultz N, Vanderbilt C, Dogan S, Bartlett EK, D'Angelo SP, Tap WD, Singer S, Ladanyi M, Shoushtari AN, Busam KJ, Hameed M. Undifferentiated and Dedifferentiated Metastatic Melanomas Masquerading as Soft Tissue Sarcomas: Mutational Signature Analysis and Immunotherapy Response. Mod Pathol 2023; 36:100165. [PMID: 36990277 PMCID: PMC10698871 DOI: 10.1016/j.modpat.2023.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023]
Abstract
The distinction between undifferentiated melanoma (UM) or dedifferentiated melanoma (DM) from undifferentiated or unclassifiable sarcoma can be difficult and requires the careful correlation of clinical, pathologic, and genomic findings. In this study, we examined the utility of mutational signatures to identify patients with UM/DM with particular attention as to whether this distinction matters for treatment because the survival of patients with metastatic melanoma has dramatically improved with immunologic therapy, whereas durable responses are less frequent in sarcomas. We identified 19 cases of UM/DM that were initially reported as unclassified or undifferentiated malignant neoplasm or sarcoma and submitted for targeted next-generation sequencing analysis. These cases were confirmed as UM/DM by harboring melanoma driver mutations, UV signature, and high tumor mutation burden. One case of DM showed melanoma in situ. Meanwhile, 18 cases represented metastatic UM/DM. Eleven patients had a prior history of melanoma. Thirteen of 19 (68%) of the tumors were immunohistochemically completely negative for 4 melanocytic markers (S100, SOX10, HMB45, and MELAN-A). All cases harbored a dominant UV signature. Frequent driver mutations involved BRAF (26%), NRAS (32%), and NF1 (42%). In contrast, the control cohort of undifferentiated pleomorphic sarcomas (UPS) of deep soft tissue exhibited a dominant aging signature in 46.6% (7/15) without evidence of UV signature. The median tumor mutation burden for DM/UM vs UPS was 31.5 vs 7.0 mutations/Mb (P < .001). A favorable response to immune checkpoint inhibitor therapy was observed in 66.6% (12/18) of patients with UM/DM. Eight patients exhibited a complete response and were alive with no evidence of disease at the last follow-up (median 45.5 months). Our findings support the usefulness of the UV signature in discriminating DM/UM vs UPS. Furthermore, we present evidence suggesting that patients with DM/UM and UV signatures can benefit from immune checkpoint inhibitor therapy.
Collapse
Affiliation(s)
- Israel S Kasago
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cecilia M Lezcano
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edmund K Bartlett
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sandra P D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
5
|
Vos EL, Maron SB, Krell RW, Nakauchi M, Fiasconaro M, Capanu M, Walch HS, Chatila WK, Schultz N, Ilson DH, Janjigian YY, Ku GY, Yoon SS, Coit DG, Vanderbilt CM, Tang LH, Strong VE. Survival of Locally Advanced MSI-high Gastric Cancer Patients Treated With Perioperative Chemotherapy: A Retrospective Cohort Study. Ann Surg 2023; 277:798-805. [PMID: 35766391 PMCID: PMC9797619 DOI: 10.1097/sla.0000000000005501] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To evaluate the efficacy of chemotherapy in patients with microsatellite instability (MSI)-high gastric cancer. BACKGROUND Although MSI-high gastric cancer is associated with a superior prognosis, recent studies question the benefit of perioperative chemotherapy in this population. METHODS Locally advanced gastric adenocarcinoma patients who either underwent surgery alone or also received neoadjuvant, perioperative, or adjuvant chemotherapy between 2000 and 2018 were eligible. MSI status, determined by next-generation sequencing or mismatch repair protein immunohistochemistry, was determined in 535 patients. Associations among MSI status, chemotherapy administration, overall survival (OS), disease-specific survival, and disease-free survival were assessed. RESULTS In 535 patients, 82 (15.3%) had an MSI-high tumor and ∼20% better OS, disease-specific survival, and disease-free survival. Grade 1 (90%-100%) pathological response to neoadjuvant chemotherapy was found in 0 of 40 (0%) MSI-high tumors versus 43 of 274 (16%) MSS. In the MSI-high group, the 3-year OS rate was 79% with chemotherapy versus 88% with surgery alone ( P =0.48). In the MSS group, this was 61% versus 59%, respectively ( P =0.96). After multivariable interaction analyses, patients with MSI-high tumors had superior survival compared with patients with MSS tumors whether given chemotherapy (hazard ratio=0.53, 95% confidence interval: 0.28-0.99) or treated with surgery alone (hazard ratio=0.15, 95% confidence interval: 0.02-1.17). CONCLUSIONS MSI-high locally advanced gastric cancer was associated with superior survival compared with MSS overall, despite worse pathological chemotherapy response. In patients with MSI-high gastric cancer who received chemotherapy, the survival rate was ∼9% worse compared with surgery alone, but chemotherapy was not significantly associated with survival.
Collapse
Affiliation(s)
- Elvira L Vos
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven B Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert W Krell
- Department of Surgery, Brooke Army Medical Center, Fort Sam Houston, TX
| | - Masaya Nakauchi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Megan Fiasconaro
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Henry S Walch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sam S Yoon
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Laura H Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
6
|
Klemen ND, Court CM, Fernandes MC, Walch HS, Chatila WK, Saadat LV, Maron S, Crane C, Shia J, Cercek A, Gönen M, Schultz ND, Garcia Aguilar J, Jarnagin WR, D'Angelica MI. Local Therapy for Oligoprogression or Consolidation in High Mutational Burden Stage 4 Colorectal Cancer Treated With PD-1 or PD-L1 Blockade. Ann Surg Oncol 2022; 29:8373-8382. [PMID: 35930112 PMCID: PMC9649851 DOI: 10.1245/s10434-022-12095-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 06/12/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Immune checkpoint blockade (ICI) of programmed cell death protein 1 (PD-1) or PD-1 ligand (PD-L1) can induce durable responses in patients who have colorectal cancer (CRC) with a high tumor mutational burden (TMB). Two recurring clinical dilemmas show how to manage oligoprogressive disease and stable disease after ICI. METHODS A cohort study was conducted to analyze patients with metastatic CRC who underwent PD-1 or PD-L1 blockade. Tumors were mismatch repair (MMR) deficient or had more than 25 mutations per megabase. Patients were identified who had local therapy (surgery, ablation, or radiotherapy) for one to three sites of progressive disease (PD) or surgery to consolidate SD. The study evaluated clinical and biologic factors associated with patient selection, outcomes, and pathologic response rates. RESULTS From 2014 to 2020, treatment was administered to 111 patients with ICI. Of these 111 patients, 19 (17%) survived fewer than 6 months, whereas to date, 50 have not had progression of disease. The remaining 42 patients experienced PD, and 16 (38%) were treated with local therapy for oligoprogression. Selection for local therapy was associated with response to ICI. The 2-year progression-free survival (PFS) after local therapy was 62%. Finally, 6 of the 50 patients without PD had consolidation of SD, and 5 had complete or near complete pathologic responses. CONCLUSIONS Oligoprogression, a frequent pattern of failure after ICI, can be managed effectively with local therapy. In contrast, it may not be necessary to consolidate SD for selected patients. Further research is essential to define management algorithms better and to explore heterogeneity in response patterns.
Collapse
Affiliation(s)
- Nicholas D Klemen
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Colin M Court
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | | | - Henry S Walch
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lily V Saadat
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Steven Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chris Crane
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus D Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael I D'Angelica
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
| |
Collapse
|
7
|
Datta J, Narayan RR, Goldman DA, Chatila WK, Gonen M, Strong J, Balachandran VP, Drebin JA, Kingham TP, Jarnagin WR, Schultz N, Kemeny NE, D'Angelica MI. Distinct Genomic Profiles are Associated With Conversion to Resection and Survival in Patients With Initially Unresectable Colorectal Liver Metastases Treated With Systemic and Hepatic Artery Chemotherapy. Ann Surg 2022; 276:e474-e482. [PMID: 33214457 PMCID: PMC8502489 DOI: 10.1097/sla.0000000000004613] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE To examine genomic correlates of conversion to resection (CTR and overall survival (OS) in patients with initially unresectable colorectal liver metastasis (IU-CRLM) treated with combination systemic and hepatic artery infusion (HAI) chemotherapy. BACKGROUND In patients presenting with IU-CRLM, combination systemic and HAI chemotherapy enables CTR with associated long-term OS in a subset of patients. Genomic correlates of CTR and OS in IU-CRLM have not been previously explored. METHODS Specimens from IU-CRLM patients receiving systemic/HAI chemotherapy (2003-2017) were submitted for next-generation sequencing. Fisher Exact test assessed associations with CTR, and Kaplan-Meier/Cox methods assessed associations with OS from HAI initiation. RESULTS Of 128 IU-CRLM patients, 51 (40%) underwent CTR at median 6 months (range: 3-35) from HAI initiation. CTR and persistently unresectable cohorts differed significantly in preoperative systemic chemotherapy exposure, node-positive primary status, and size of largest liver metastasis. Median and 5-year OS was 66 months and 51%. CTR was associated with prolonged survival (time-dependent HR 0.23,95% CI: 0.12-0.46, P < 0.001). The most frequently altered genes were APC (81%), TP53 (77%), and KRAS (37%). Oncogenic mutations in SOX9 and BRAF were associated with CTR. BRAF mutations, any RAS pathway alterations, and co-altered RAS/RAF-TP53 mutations wereassociated with worse survival. Classification and regression tree analysis defined prognostically relevant clusters of genomic risk to reveal co-altered RAS/RAF-TP53 as the highest risk subgroup. Co-altered RAS/RAF-TP53 remained independently associated with worse survival (HR 2.52, 95% CI: 1.37-4.64, P = 0.003) after controlling for CTR, number of liver metastases, and preoperative extrahepatic disease. CONCLUSIONS Distinct genomic profiles are associated with CTR and survival in patients with IU-CRLM treated with HAI/systemic chemotherapy. Presence of SOX9, BRAF , and co-altered RAS/RAF- TP53 mutations are promising biomarkers that, when validated in larger datasets, may impact treatment of IU-CRLM patients.
Collapse
Affiliation(s)
- Jashodeep Datta
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Raja R. Narayan
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Surgery, Stanford University School of Medicine, Stanford, CA
| | - Debra A. Goldman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid K. Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - James Strong
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vinod P. Balachandran
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey A. Drebin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - T. Peter Kingham
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William R. Jarnagin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nancy E. Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael I. D'Angelica
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
8
|
Vanderbilt CM, Chatila WK, Khalil DN, Chen CT, Kim JK, Wu F, Schultz N, Weiser MR, Garcia-Aguilar J, Sanchez-Vega F. Abstract 3058: Characterization of the tumor microbiome in patients with locally advanced rectal cancer treated with neoadjuvant therapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The gut microbiota is a component of the tumor microenvironment that has the potential to influence sensitivity or resistance to neoadjuvant therapy through modulation of the host immune response in patients diagnosed with locally advanced rectal cancer (LARC, stage II-III).
We performed DNA and RNA sequencing of pre-treatment endoscopic biopsies from 89 LARC patients treated with neoadjuvant therapy (NAT). Our cohort included 84 microsatellite stable and 5 microsatellite unstable (MSI) patients. We identified the presence of microbial species by mapping non-human RNA read sequences to a large catalogue of viral and bacterial microorganisms. Our methodology has been validated and determined to have comparable accuracy to reference microbial tests for both viruses and bacteria. We analyzed correlations between presence of specific microbial species and (1) clinicopathological variables such as age, stage, anatomic location and MSI status, (2) genomic variables such as tumor mutational burden, chromosomal instability and somatic alterations and (3) response to NAT. We identified 152 species with at least 100 mapped reads in 10% or more of our cohort. The median number of species per patient was 37 [IQR 16-66], with only 6/89, 7% patients having no detected species at all. The most frequently detected species included well-known intestinal bacteria such as Escherichia coli, Fusobacterium nucleatum, Faecalibacterium prausnitzii and several members of the Bacteroides genus. The Parvimonas micra coccus was more often detected in tumors from the lower rectum (13/22, 59%, 0-4 cm from the anal verge) than the middle (8/36, 22%, 4-8 cm) and upper rectum (5/30, 17%, 8-12 cm) (p<0.01). Several species from the Gordonia and Rhodococcus genera were associated with increased tumor mutational burden (p<0.001) and significantly higher numbers of mapped reads in samples from the CMS1 molecular subtype (p<0.01), which is enriched in MSI tumors. RNA-Seq based estimates of neutrophil abundance were positively correlated with detection of several Ruminococcus and Prevotella species (p<0.001), highlighting the cross-talk between host immunity and microbiota. Opportunistic bacteria previously reported to benefit from a patient’s weakened immune system such as Williamsia muralis and several species of Agrobacterium were associated with lower rates of complete response (30% vs. 15%, n.s.) and significantly shorter disease free survival following NAT (3-year disease free survival was 25% in 8 Williamsia positive patients vs. 42% in 12 Agrobacterium fabrum patients vs. 87% in the rest of the cohort; pairwise log-rank p<0.001). Our data shows that standard RNA sequencing platforms can be used to detect microbial species in endoscopic biopsies from LARC patients and that the presence of specific species is associated with clinical and genomic features of translational relevance.
Citation Format: Chad M. Vanderbilt, Walid K. Chatila, Danny N. Khalil, Chin-Tung Chen, Jin K. Kim, Fan Wu, Nikolaus Schultz, Martin R. Weiser, Julio Garcia-Aguilar, Francisco Sanchez-Vega. Characterization of the tumor microbiome in patients with locally advanced rectal cancer treated with neoadjuvant therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3058.
Collapse
Affiliation(s)
| | | | | | | | | | - Fan Wu
- 1Memorial Sloan Kettering, New York, NY
| | | | | | | | | |
Collapse
|
9
|
Bandlamudi C, Chatila WK, Smith SA, Nandakumar S, Bielski C, Nguyen B, Walch HS, Kreitzer CK, Arora KS, Ngoc TT, Mehine M, Ostrovnaya I, de Bruijn I, Woo HJ, Kundra R, Fong CJ, Rana S, Zhao G, Zhang M, Zucker MR, Zhang H, Ptashkin R, Brannon R, Reznik E, Gao J, Arcila ME, Benayed R, Chakravarty D, Solit D, Donoghue MT, Ladanyi M, Schultz ND, Berger MF, Zehir A. Abstract 3628: Comprehensive identification of lineage associated cancer genes in 122 histologies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although the majority of cancer genes show a high degree of specificity for certain lineages, genomic profiling of cancer patients routinely identify alterations in genes that are atypical to the presented cancer type but are canonical drivers in a different lineage. It is often unclear if these atypical drivers arose early in tumorigenesis or were acquired during progression. A complete understanding of lineage associated genes (LAGs) will enable better interpretation of the molecular etiology of each diagnosed tumor.
Here, we used a cohort of 38,912 patients across 122 cancer histologies (each with 50 or more patients) profiled for somatic alterations (mutations, copy number alterations and gene fusions) using the MSK-IMPACT assay. Tumors with TMB > 15 were already excluded. All alterations were classified as drivers using OncoKB. Allele-specific copy number calls were assessed using FACETS.
Overall, 95% of patients harbored at least one oncogenic alteration, with a median of 4 drivers per tumor. We observed widespread prevalence of drivers across lineages with each gene mutated in a median of 36 different lineages. Conversely, a median of 103 genes were mutated at least once in each lineage. Hypothesizing that cancer genes are influenced by cell of origin, we sought to identify lineages harboring significantly higher rates of drivers in a given gene compared to its pancancer driver rate. We identified 1781 significant (adjusted P < 0.05) gene and lineage associations, and an additional 109 involving genes mutated at >10% in the respective lineages but which did not reach significance were also included. Lineage-agnostic genes such as TP53 and CDKN2A were associated with a broad spectrum of lineages (90 and 55, respectively). However, overall, each gene we profiled was found to be associated with a median of 3 distinct lineages. For example, while BRAF drivers are found in nearly all histologies (n=91), it is enriched for drivers in only 8 lineages: melanoma (acral and cutaneous), thyroid (poorly differentiated, anaplastic and papillary) and bowel (mucinous adenocarc. of colon/rectum, colon adenocarc. and neuroendocrine carc. of colon/rectum). In all, nearly a third of all drivers were observed in non-associated lineages.
We next compared the somatic properties of drivers among genes in associated lineages vs. the same genes in non-associated lineages. We observed that mutations in LAGs were more often clonal (83% vs. 73%, associated vs. non-associated, P = 0) and showed enrichment for mutant allele imbalance in oncogenes (40% vs. 23%, P = 2e-111) and biallelic inactivation in tumor suppressor LAGs (71% vs. 58%, P = 4e-130). Furthermore, 93% of all OncoKB Level 1/2/3A actionable alterations, which are classified based on their histology, were in LAGs. In conclusion, our findings enable classification of drivers that are relevant for lineage-specific malignant transformation and advance our understanding of tumor biology.
Citation Format: Chaitanya Bandlamudi, Walid K. Chatila, Shaleigh A. Smith, Subhiksha Nandakumar, Craig Bielski, Bastien Nguyen, Henry S. Walch, Christoph K. Kreitzer, Kanika S. Arora, Tran Thinh Ngoc, Miika Mehine, Irina Ostrovnaya, Ino de Bruijn, Hyung Jun Woo, Ritika Kundra, Christopher J. Fong, Satshil Rana, Gaofei Zhao, Mingxuan Zhang, Mark R. Zucker, Hongxin Zhang, Ryan Ptashkin, Rose Brannon, Eduard Reznik, JianJiong Gao, Maria E. Arcila, Ryma Benayed, Debyani Chakravarty, David Solit, Mark T. Donoghue, Marc Ladanyi, Nikolaus D. Schultz, Michael F. Berger, Ahmet Zehir. Comprehensive identification of lineage associated cancer genes in 122 histologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3628.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Miika Mehine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyung Jun Woo
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Satshil Rana
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaofei Zhao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rose Brannon
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eduard Reznik
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - JianJiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - David Solit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
10
|
Walch H, Luthra A, Chatila WK, Wu F, Chakravarty D, Chen CT, Sood R, Omer DM, Smith JJ, Schultz N, Ganesh K, Garcia-Aguilar J, Yaeger R, Sanchez-Vega F. Abstract 3634: Integrative analysis of the contribution of genomic and clinical factors to worse clinical outcomes in non-Hispanic Black patients with colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Non-Hispanic Black (NHB) patients have higher incidence and higher mortality from colorectal cancer (CRC) than non-Hispanic white (NHW) patients. The extent to which this aggressive behavior in NHB patients is driven by differences in cancer genomics is presently unknown.
We analyzed clinical and genomic data from 3,963 CRC patients treated at Memorial Sloan Kettering, including 336 (8%) NHB and 3,627 (92%) NHW patients. Tumors were sequenced using the clinical MSK-IMPACT test, a targeted next-generation DNA sequencing assay that identifies mutations, copy number changes and structural rearrangements in 341-505 genes using solid tissue and matched blood.
No significant differences by race were observed for stage at diagnosis or sex. While the difference in median age at diagnosis was small (53.4 for NHB vs. 55 years for NHW patients, p=0.012), significantly fewer NHB patients were diagnosed after 65 years of age (17% vs. 27%, p=0.001). Right-sided colon tumors were more common among NHB patients (37% vs. 25%, p=0.02); the proportion of rectal tumors was similar in both racial groups (31% in NHB vs. 34% in NHW patients, n.s.). Hypermutated tumors, including tumors with microsatellite instability (MSI) and POLE hypermutants, were more frequent among NHW patients (12% vs. 8%, p=0.02). Right-sided tumors were more frequently MSI/hypermutated in the NHW patients (27% vs. 13%, p=0.008), whereas no differences by race were observed for left-sided colon (5% vs. 1%, n.s.) or rectal primaries (4% vs. 5%, n.s.).
Genomic analysis of the non-hypermutated tumors revealed no significant differences in tumor mutational burden or fraction of genome altered between racial groups. Tumors in NHB patients were enriched in KRAS mutations (60% vs. 45%, p<0.001), but G12C mutations accounted only for 3% of all driver KRAS mutations in NHB patients vs. 8% of all driver mutations in NHW patients (p=0.01). BRAF mutations were more frequent in non-hypermutated NHW patients (7% vs. 3%, p=0.006), but the overall frequency of RTK/RAS pathway alterations was higher in the NHB group (74% vs. 66%, p=0.004).
Even though all patients were treated at the same single institution during the study, NHB patients had shorter overall survival (OS) from the time of sequencing (median 28 months [95% CI 25-38] vs. 50 months [95% CI 47-53], p<0.001). NHB patients also had worse OS [HR 1.64, CI 1.3 - 2.1, p<0.001] in a multivariate analysis using Cox Proportional-Hazards and accounting for age at diagnosis, stage at diagnosis, body mass index, primary tumor location, MSI status and oncogenic alterations in APC, TP53, KRAS, SMAD4, and BRAF.
Our data confirms that NHB patients with CRC have worse clinical outcomes than NHW patients. Clinically relevant differences in the frequency of alterations in cancer driver genes are observed based on racial origin, but they do not fully explain the difference in survival.
Citation Format: Henry Walch, Anisha Luthra, Walid K. Chatila, Fan Wu, Debyani Chakravarty, Chin-Tung Chen, Rupa Sood, Dana M. Omer, Jesse J. Smith, Nikolaus Schultz, Karuna Ganesh, Julio Garcia-Aguilar, Rona Yaeger, Francisco Sanchez-Vega. Integrative analysis of the contribution of genomic and clinical factors to worse clinical outcomes in non-Hispanic Black patients with colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3634.
Collapse
Affiliation(s)
| | | | | | - Fan Wu
- 1Memorial Sloan Kettering, New York, NY
| | | | | | - Rupa Sood
- 1Memorial Sloan Kettering, New York, NY
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Nigam A, Chatila WK, Krishnamoorthy GP, Ho AL, Fagin JA, Schultz ND, Untch BR. Abstract 1181: PTEN loss-of-function mutations prevalent in HRAS-mutant cancers results in resistance to targeted therapy. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The clinical development of farnesyltransferase inhibitors (FTIs) as targeted therapy for HRAS-mutant cancers has demonstrated mixed responses dependent on cancer type. Co-occurring mutations may affect tumor response, supported by previous studies demonstrating that NF1 mutations confer resistance to HRAS inhibition by the FTI tipifarnib in thyroid cancer mouse models. We aimed to determine if PI3K pathway activating mutations altered responses to targeted therapy in HRAS-mutant cancers.
Methods: Targeted sequencing data from MSK-IMPACT cohort and DFCI-GENIE (Version 9.0) database was used to investigate co-mutations amongst HRAS-mutant cancers. Fisher’s exact test was used to determine co-altered mutations found predominantly in HRAS-mutant cancers relative to respective KRAS- and NRAS-mutant cancers. ‘RASless’ (KRASlox/HRASKO/NRASKO) mouse embryonic fibroblasts (MEFs) were obtained that in the presence of 600nM tamoxifen (4OHT) resulted in a KRAS knock-out. ‘Rasless’ MEFs were transfected with HRASG13R to create a system for testing sensitivity to FTIs in the presence or absence of WT KRAS, or with concurrent PTEN loss generated by CRISPR-Cas9 technology.
Results: A greater proportion of HRAS-mutant cancers had co-altered mutations (48.8%) in genes encoding effectors in the MAPK, PI3K or RTK pathways compared to KRAS- and NRAS-mutant cancers (41.4% and 38.4%, respectively; p<0.05). PTEN mutations were more prevalent in HRAS-mutant NSCLC (21%) compared to KRAS- and NRAS-mutant NSCLC (1% and 2%, respectively; p<0.05). Non-transfected MEFs were sensitized to tipifarnib by introduction of a HRASG13R allele in non-4OHT (IC50: MEF= >3uM, HRASG13R = 324.7nM) and 4OHT (IC50: MEF= >3uM, HRASG13R= 0.62nM; p<0.001) conditions, indicating that WT KRAS confers a relative resistance to the inhibitory effects of the FTI on HRAS. PTEN loss-of-function mutations led to tipifarnib resistance in HRASG13R MEFs in the absence (IC50: >3uM; p<0.001) or presence of 4OHT (IC50: 213.6nM; p<0.001). Combined treatment of HRASG13R/PTEN MEFs with the PIK3CB-specific inhibitor AZD8186 and tipifarnib sensitized cells in non-4OHT (IC50- 100nM:100nM Tipifarnib:AZD8186) and 4OHT (IC50- 100nM:10nM Tipifarnib:AZD8186) conditions.
Conclusions: Co-altered mutations of MAPK, PI3K or RTK effectors are found more commonly in HRAS than in KRAS or NRAS-mutant cancers. Co-alteration of PTEN preferentially associated with HRAS-mutations in NSCLC. Deletion of PTEN resulted in resistance to FTI targeted therapy in vitro. Co-altered mutations may predict sensitivity and resistance to FTIs and guide clinical trial design.
Citation Format: Aradhya Nigam, Walid K. Chatila, Gnana P. Krishnamoorthy, Alan L. Ho, James A. Fagin, Nikolaus D. Schultz, Brian R. Untch. PTEN loss-of-function mutations prevalent in HRAS-mutant cancers results in resistance to targeted therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1181.
Collapse
Affiliation(s)
- Aradhya Nigam
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Alan L. Ho
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | |
Collapse
|
12
|
Ozer M, Ranganathan M, Lecomte N, Schvartzman JM, Walch HS, Chatila WK, Hong J, Carlo MI, Walsh MF, Sheehan M, Mandelker D, Ceyhan-Birsoy O, Maio A, Kemel Y, Iacobuzio-Donahue CA, O'Reilly EM, Yu KH. Concurrent Germline BRCA1/ 2 and Mismatch Repair Mutations in Young-Onset Pancreatic and Colorectal Cancer: The Importance of Comprehensive Germline and Somatic Characterization to Inform Therapeutic Options. JCO Precis Oncol 2022; 6:e2100560. [PMID: 35675575 PMCID: PMC9200400 DOI: 10.1200/po.21.00560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 02/07/2022] [Accepted: 04/20/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Megha Ranganathan
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Nicolas Lecomte
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Juan M. Schvartzman
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Henry S. Walch
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Walid K. Chatila
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Jungeui Hong
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Maria I. Carlo
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Michael F. Walsh
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Margaret Sheehan
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Ozge Ceyhan-Birsoy
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Anna Maio
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Christine A. Iacobuzio-Donahue
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Eileen M. O'Reilly
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
- Weill Cornell Medical College, New York, NY
| | - Kenneth H. Yu
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
- Weill Cornell Medical College, New York, NY
| |
Collapse
|
13
|
Mathur D, Taylor BP, Chatila WK, Scher HI, Schultz N, Razavi P, Xavier JB. Optimal Strategy and Benefit of Pulsed Therapy Depend On Tumor Heterogeneity and Aggressiveness at Time of Treatment Initiation. Mol Cancer Ther 2022; 21:831-843. [PMID: 35247928 PMCID: PMC9081172 DOI: 10.1158/1535-7163.mct-21-0574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/20/2021] [Accepted: 02/18/2022] [Indexed: 11/16/2022]
Abstract
Therapeutic resistance is a fundamental obstacle in cancer treatment. Tumors that initially respond to treatment may have a preexisting resistant subclone or acquire resistance during treatment, making relapse theoretically inevitable. Here, we investigate treatment strategies that may delay relapse using mathematical modeling. We find that for a single-drug therapy, pulse treatment-short, elevated doses followed by a complete break from treatment-delays relapse compared with continuous treatment with the same total dose over a length of time. For tumors treated with more than one drug, continuous combination treatment is only sometimes better than sequential treatment, while pulsed combination treatment or simply alternating between the two therapies at defined intervals delays relapse the longest. These results are independent of the fitness cost or benefit of resistance, and are robust to noise. Machine-learning analysis of simulations shows that the initial tumor response and heterogeneity at the start of treatment suffice to determine the benefit of pulsed or alternating treatment strategies over continuous treatment. Analysis of eight tumor burden trajectories of breast cancer patients treated at Memorial Sloan Kettering Cancer Center shows the model can predict time to resistance using initial responses to treatment and estimated preexisting resistant populations. The model calculated that pulse treatment would delay relapse in all eight cases. Overall, our results support that pulsed treatments optimized by mathematical models could delay therapeutic resistance.
Collapse
Affiliation(s)
- Deepti Mathur
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bradford P. Taylor
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K. Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Howard I. Scher
- Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joao B. Xavier
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
14
|
Nguyen B, Fong C, Luthra A, Smith SA, DiNatale RG, Nandakumar S, Walch H, Chatila WK, Madupuri R, Kundra R, Bielski CM, Mastrogiacomo B, Donoghue MTA, Boire A, Chandarlapaty S, Ganesh K, Harding JJ, Iacobuzio-Donahue CA, Razavi P, Reznik E, Rudin CM, Zamarin D, Abida W, Abou-Alfa GK, Aghajanian C, Cercek A, Chi P, Feldman D, Ho AL, Iyer G, Janjigian YY, Morris M, Motzer RJ, O'Reilly EM, Postow MA, Raj NP, Riely GJ, Robson ME, Rosenberg JE, Safonov A, Shoushtari AN, Tap W, Teo MY, Varghese AM, Voss M, Yaeger R, Zauderer MG, Abu-Rustum N, Garcia-Aguilar J, Bochner B, Hakimi A, Jarnagin WR, Jones DR, Molena D, Morris L, Rios-Doria E, Russo P, Singer S, Strong VE, Chakravarty D, Ellenson LH, Gopalan A, Reis-Filho JS, Weigelt B, Ladanyi M, Gonen M, Shah SP, Massague J, Gao J, Zehir A, Berger MF, Solit DB, Bakhoum SF, Sanchez-Vega F, Schultz N. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell 2022; 185:563-575.e11. [PMID: 35120664 PMCID: PMC9147702 DOI: 10.1016/j.cell.2022.01.003] [Citation(s) in RCA: 190] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/21/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma, and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high-grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.
Collapse
Affiliation(s)
- Bastien Nguyen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anisha Luthra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh A Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renzo G DiNatale
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA; Urology and Renal Transplantation Service, Virginia Mason Medical Center, Seattle, WA, USA
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ramyasree Madupuri
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College at Cornell University, New York, NY, USA
| | - Brooke Mastrogiacomo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrienne Boire
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Neurology and Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Harding
- Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darren Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopakumar Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert J Motzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael A Postow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nitya P Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - William Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernard Bochner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abraham Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Rios-Doria
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joan Massague
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
15
|
Moy RH, Walch HS, Mattar M, Chatila WK, Molena D, Strong VE, Tang LH, Maron SB, Coit DG, Jones DR, Hechtman JF, Solit DB, Schultz N, de Stanchina E, Janjigian YY. Defining and Targeting Esophagogastric Cancer Genomic Subsets With Patient-Derived Xenografts. JCO Precis Oncol 2022; 6:e2100242. [PMID: 35138918 PMCID: PMC8865520 DOI: 10.1200/po.21.00242] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 10/26/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Comprehensive genomic profiling has defined key oncogenic drivers and distinct molecular subtypes in esophagogastric cancer; however, the number of clinically actionable alterations remains limited. To establish preclinical models for testing genomically driven therapeutic strategies, we generated and characterized a large collection of esophagogastric cancer patient-derived xenografts (PDXs). MATERIALS AND METHODS We established a biobank of 98 esophagogastric cancer PDX models derived from primary tumors and metastases. Clinicopathologic features of each PDX and the corresponding patient sample were annotated, including stage at diagnosis, treatment history, histology, and biomarker profile. To identify oncogenic DNA alterations, we analyzed and compared targeted sequencing performed on PDX and parent tumor pairs. We conducted xenotrials in genomically defined models with oncogenic drivers. RESULTS From April 2010 to June 2019, we implanted 276 patient tumors, of which 98 successfully engrafted (35.5%). This collection is enriched for PDXs derived from patients with human epidermal growth factor receptor 2-positive esophagogastric adenocarcinoma (62 models, 63%), the majority of which were refractory to standard therapies including trastuzumab. Factors positively correlating with engraftment included advanced stage, metastatic origin, intestinal-type histology, and human epidermal growth factor receptor 2-positivity. Mutations in TP53 and alterations in receptor tyrosine kinases (ERBB2 and EGFR), RAS/PI3K pathway genes, cell-cycle mediators (CDKN2A and CCNE1), and CDH1 were the predominant oncogenic drivers, recapitulating clinical tumor sequencing. We observed antitumor activity with rational combination strategies in models established from treatment-refractory disease. CONCLUSION The Memorial Sloan Kettering Cancer Center PDX collection recapitulates the heterogeneity of esophagogastric cancer and is a powerful resource to investigate mechanisms driving tumor progression, identify predictive biomarkers, and develop therapeutic strategies for molecularly defined subsets of esophagogastric cancer.
Collapse
Affiliation(s)
- Ryan H. Moy
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Present address: Department of Medicine, Columbia University Medical Center, New York, NY
| | - Henry S. Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marissa Mattar
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid K. Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vivian E. Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Laura H. Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven B. Maron
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel G. Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B. Solit
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Y. Janjigian
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| |
Collapse
|
16
|
Cercek A, Chatila WK, Yaeger R, Walch H, Fernandes GDS, Krishnan A, Palmaira L, Maio A, Kemel Y, Srinivasan P, Bandlamudi C, Salo-Mullen E, Tejada PR, Belanfanti K, Galle J, Joseph V, Segal N, Varghese A, Reidy-Lagunes D, Shia J, Vakiani E, Mondaca S, Mendelsohn R, Lumish MA, Steinruecke F, Kemeny N, Connell L, Ganesh K, Markowitz A, Nash G, Guillem J, Smith JJ, Paty PB, Zhang L, Mandelker D, Birsoy O, Robson M, Offit K, Taylor B, Berger M, Solit D, Weiser M, Saltz LB, Aguilar JG, Schultz N, Diaz LA, Stadler ZK. A Comprehensive Comparison of Early-Onset and Average-Onset Colorectal Cancers. J Natl Cancer Inst 2021; 113:1683-1692. [PMID: 34405229 PMCID: PMC8634406 DOI: 10.1093/jnci/djab124] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/29/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The causative factors for the recent increase in early-onset colorectal cancer (EO-CRC) incidence are unknown. We sought to determine if early-onset disease is clinically or genomically distinct from average-onset colorectal cancer (AO-CRC). METHODS Clinical, histopathologic, and genomic characteristics of EO-CRC patients (2014-2019), divided into age 35 years and younger and 36-49 years at diagnosis, were compared with AO-CRC (50 years and older). Patients with mismatch repair deficient tumors, CRC-related hereditary syndromes, and inflammatory bowel disease were excluded from all but the germline analysis. All statistical tests were 2-sided. RESULTS In total, 759 patients with EO-CRC (35 years, n = 151; 36-49 years, n = 608) and AO-CRC (n = 687) were included. Left-sided tumors (35 years and younger = 80.8%; 36-49 years = 83.7%; AO = 63.9%; P < .001 for both comparisons), rectal bleeding (35 years and younger = 41.1%; 36-49 years = 41.0%; AO = 25.9%; P = .001 and P < .001, respectively), and abdominal pain (35 years and younger = 37.1%; 36-49 years = 34.0%; AO = 26.8%; P = .01 and P = .005, respectively) were more common in EO-CRC. Among microsatellite stable tumors, we found no differences in histopathologic tumor characteristics. Initially, differences in TP53 and Receptor Tyrosine Kinase signaling pathway (RTK-RAS)alterations were noted by age. However, on multivariate analysis including somatic gene analysis and tumor sidedness, no statistically significant differences at the gene or pathway level were demonstrated. Among advanced microsatellite stable CRCs, chemotherapy response and survival were equivalent by age cohorts. Pathogenic germline variants were identified in 23.3% of patients 35 years and younger vs 14.1% of AO-CRC (P = .01). CONCLUSIONS EO-CRCs are more commonly left-sided and present with rectal bleeding and abdominal pain but are otherwise clinically and genomically indistinguishable from AO-CRCs. Aggressive treatment regimens based solely on the age at CRC diagnosis are not warranted.
Collapse
Affiliation(s)
- Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Asha Krishnan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lerie Palmaira
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prince R Tejada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kimeisha Belanfanti
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vijai Joseph
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Neil Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diane Reidy-Lagunes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robin Mendelsohn
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa A Lumish
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Felix Steinruecke
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nancy Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Louise Connell
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnold Markowitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Garrett Nash
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jose Guillem
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Joshua Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Phillip B Paty
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
17
|
Alatise OI, Knapp GC, Sharma A, Chatila WK, Arowolo OA, Olasehinde O, Famurewa OC, Omisore AD, Komolafe AO, Olaofe OO, Katung AI, Ibikunle DE, Egberongbe AA, Olatoke SA, Agodirin SO, Adesiyun OA, Adeyeye A, Kolawole OA, Olakanmi AO, Arora K, Constable J, Shah R, Basunia A, Sylvester B, Wu C, Weiser MR, Seier K, Gonen M, Stadler ZK, Kemel Y, Vakiani E, Berger MF, Chan TA, Solit DB, Shia J, Sanchez-Vega F, Schultz N, Brennan M, Smith JJ, Kingham TP. Molecular and phenotypic profiling of colorectal cancer patients in West Africa reveals biological insights. Nat Commun 2021; 12:6821. [PMID: 34819518 PMCID: PMC8613248 DOI: 10.1038/s41467-021-27106-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
Understanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is vital to addressing the regions rising burden of disease. Tissue from unselected Nigerian patients was analyzed with a multigene, next-generation sequencing assay. The rate of microsatellite instability is significantly higher among Nigerian CRC patients (28.1%) than patients from The Cancer Genome Atlas (TCGA, 14.2%) and Memorial Sloan Kettering Cancer Center (MSKCC, 8.5%, P < 0.001). In microsatellite-stable cases, tumors from Nigerian patients are less likely to have APC mutations (39.1% vs. 76.0% MSKCC P < 0.001) and WNT pathway alterations (47.8% vs. 81.9% MSKCC, P < 0.001); whereas RAS pathway alteration is more prevalent (76.1% vs. 59.6%, P = 0.03). Nigerian CRC patients are also younger and more likely to present with rectal disease (50.8% vs. 33.7% MSKCC, P < 0.001). The findings suggest a unique biology of CRC in Nigeria, which emphasizes the need for regional data to guide diagnostic and treatment approaches for patients in West Africa. Understanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is important for early detection and treatment. Here, the authors use a multigene next-generation sequencing panel to identify genomic differences in Nigerian CRCs compared to those from TCGA and MSKCC cohorts.
Collapse
Affiliation(s)
- Olusegun Isaac Alatise
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Gregory C Knapp
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Division of General Surgery, Department of Surgery, Dalhousie University, Halifax, NS, Canada
| | - Avinash Sharma
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Marie-Jose and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Olukayode A Arowolo
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Olalekan Olasehinde
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Olusola C Famurewa
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Adeleye D Omisore
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Akinwumi O Komolafe
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Olaejinrinde O Olaofe
- Faculty of Clinical Sciences, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Aba I Katung
- Federal Medical Centre, Owo, Ondo State, Nigeria
| | | | | | - Samuel A Olatoke
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Sulaiman O Agodirin
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Olusola A Adesiyun
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Ademola Adeyeye
- Department of Surgery, University of Ilorin Teaching Hospital, Ilorin, Nigeria
| | - Oladapo A Kolawole
- Department of Surgery, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Akinwumi O Olakanmi
- Department of Surgery, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - Kanika Arora
- Marie-Jose and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeremy Constable
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronak Shah
- Marie-Jose and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Azfar Basunia
- Marie-Jose and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brooke Sylvester
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chao Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin R Weiser
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ken Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Clinical Genetics Service and the Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Murray Brennan
- Bobst International Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Joshua Smith
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - T Peter Kingham
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
18
|
Kemeny NE, Chou JF, Capanu M, Chatila WK, Shi H, Sanchez-Vega F, Kingham TP, Connell LC, Jarnagin WR, D'Angelica MI. A Randomized Phase II Trial of Adjuvant Hepatic Arterial Infusion and Systemic Therapy With or Without Panitumumab After Hepatic Resection of KRAS Wild-type Colorectal Cancer. Ann Surg 2021; 274:248-254. [PMID: 33938493 PMCID: PMC9351589 DOI: 10.1097/sla.0000000000004923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE/BACKGROUND The purpose was to determine whether adding Pmab versus no Pmab to an adjuvant regimen of hepatic arterial infusion (HAI) of floxuridine (FUDR) plus systemic (SYS) leucovorin, fluorouracil, and irinotecan (FOLFIRI) improves 15-month recurrence-free survival for patients with RAS wild-type colorectal cancer. Secondary endpoints included overall survival, toxicity, and influence of predictive biomarkers. METHODS This phase II trial randomized patients with KRAS wild-type resected colorectal liver metastases to adjuvant HAI FUDR + SYS FOLFIRI +/- Pmab (NCT01312857). Patients were stratified by clinical risk score and previous chemotherapy. Based on an exact binomial design, if one arm had ≥24 patients alive and disease-free at 15 months that regimen was considered promising for further investigation. RESULTS Seventy-five patients were randomized. Patient characteristics and toxicity were not different in the 2 arms, except for rash in +Pmab arm. Grade 3/4 elevation in bilirubin or alkaline phosphatase did not differ in the 2 arms. Twenty-five (69%; 95% CI, 53-82) patients in the Pmab arm versus 18 (47%; 95% CI, 32-63) patients in the arm without Pmab were alive and recurrence-free at 15 months. Only the Pmab arm met the decision rule, while the other arm did not. After median follow-up of 56.6 months, 3-year recurrence-free survival was 57% (95% CI, 43-76) and 42% (95% CI, 29-61), and 3-year overall survival was 97% (95% CI, 90-99) and 91% (95% CI, 83-99), +/- Pmab, respectively. CONCLUSIONS The addition of Pmab to HAI FUDR + SYS FOLFIRI showed promising activity without increased biliary toxicity and should be further investigated in a larger trial.
Collapse
Affiliation(s)
- Nancy E Kemeny
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joanne F Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid K Chatila
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongyu Shi
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Thomas Peter Kingham
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Louise Catherine Connell
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William R Jarnagin
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael I D'Angelica
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
19
|
Li J, Duran MA, Dhanota N, Chatila WK, Bettigole SE, Kwon J, Sriram RK, Humphries MP, Salto-Tellez M, James JA, Hanna MG, Melms JC, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li HW, Martin ML, Dorsaint P, Cavallo JA, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su SSM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF. Metastasis and Immune Evasion from Extracellular cGAMP Hydrolysis. Cancer Discov 2021; 11:1212-1227. [PMID: 33372007 PMCID: PMC8102348 DOI: 10.1158/2159-8290.cd-20-0387] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/30/2020] [Accepted: 12/11/2020] [Indexed: 12/21/2022]
Abstract
Cytosolic DNA is characteristic of chromosomally unstable metastatic cancer cells, resulting in constitutive activation of the cGAS-STING innate immune pathway. How tumors co-opt inflammatory signaling while evading immune surveillance remains unknown. Here, we show that the ectonucleotidase ENPP1 promotes metastasis by selectively degrading extracellular cGAMP, an immune-stimulatory metabolite whose breakdown products include the immune suppressor adenosine. ENPP1 loss suppresses metastasis, restores tumor immune infiltration, and potentiates response to immune checkpoint blockade in a manner dependent on tumor cGAS and host STING. Conversely, overexpression of wild-type ENPP1, but not an enzymatically weakened mutant, promotes migration and metastasis, in part through the generation of extracellular adenosine, and renders otherwise sensitive tumors completely resistant to immunotherapy. In human cancers, ENPP1 expression correlates with reduced immune cell infiltration, increased metastasis, and resistance to anti-PD-1/PD-L1 treatment. Thus, cGAMP hydrolysis by ENPP1 enables chromosomally unstable tumors to transmute cGAS activation into an immune-suppressive pathway. SIGNIFICANCE: Chromosomal instability promotes metastasis by generating chronic tumor inflammation. ENPP1 facilitates metastasis and enables tumor cells to tolerate inflammation by hydrolyzing the immunotransmitter cGAMP, preventing its transfer from cancer cells to immune cells.This article is highlighted in the In This Issue feature, p. 995.
Collapse
Affiliation(s)
- Jun Li
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mercedes A Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ninjit Dhanota
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | | | - John Kwon
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roshan K Sriram
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Matthew P Humphries
- Precision Medicine Centre of Excellence, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Manuel Salto-Tellez
- Precision Medicine Centre of Excellence, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
- Medical Sciences Division, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Jacqueline A James
- Precision Medicine Centre of Excellence, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
| | - Matthew G Hanna
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Johannes C Melms
- Columbia Center for Translational Immunology, New York, New York
- Division of Hematology and Oncology, Columbia University Medical Center, New York, New York
| | - Sreeram Vallabhaneni
- Laboratory for Systems Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, United Kingdom
| | - Ieva Usaite
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, United Kingdom
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, United Kingdom
| | - Rohan Bareja
- Englander Institute for Precision Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Hao Wei Li
- Columbia Center for Translational Immunology, New York, New York
| | - Maria Laura Martin
- Englander Institute for Precision Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Princesca Dorsaint
- Englander Institute for Precision Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Julie-Ann Cavallo
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peng Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chantal Pauli
- Institute for Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Lee Gottesdiener
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin J DiPardo
- Department of Surgery, University of California, Los Angeles, California
| | - Travis J Hollmann
- Medical Sciences Division, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Taha Merghoub
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Anusha Kalbasi
- Department of Radiation Oncology, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California
| | - Neil Vasan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jedd D Wolchok
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, United Kingdom
| | - Alexander N Shoushtari
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Eileen E Parkes
- Precision Medicine Centre of Excellence, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, United Kingdom
- Medical Sciences Division, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Benjamin Izar
- Columbia Center for Translational Immunology, New York, New York
- Division of Hematology and Oncology, Columbia University Medical Center, New York, New York
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
20
|
Gorelick AN, Kim M, Chatila WK, La K, Hakimi AA, Berger MF, Taylor BS, Gammage PA, Reznik E. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA. Nat Metab 2021; 3:558-570. [PMID: 33833465 PMCID: PMC9304985 DOI: 10.1038/s42255-021-00378-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/03/2021] [Indexed: 12/21/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes protein subunits and translational machinery required for oxidative phosphorylation (OXPHOS). Using repurposed whole-exome sequencing data, in the present study we demonstrate that pathogenic mtDNA mutations arise in tumours at a rate comparable to those in the most common cancer driver genes. We identify OXPHOS complexes as critical determinants shaping somatic mtDNA mutation patterns across tumour lineages. Loss-of-function mutations accumulate at an elevated rate specifically in complex I and often arise at specific homopolymeric hotspots. In contrast, complex V is depleted of all non-synonymous mutations, suggesting that impairment of ATP synthesis and mitochondrial membrane potential dissipation are under negative selection. Common truncating mutations and rarer missense alleles are both associated with a pan-lineage transcriptional programme, even in cancer types where mtDNA mutations are comparatively rare. Pathogenic mutations of mtDNA are associated with substantial increases in overall survival of colorectal cancer patients, demonstrating a clear functional relationship between genotype and phenotype. The mitochondrial genome is therefore frequently and functionally disrupted across many cancers, with major implications for patient stratification, prognosis and therapeutic development.
Collapse
Affiliation(s)
- Alexander N Gorelick
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Minsoo Kim
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konnor La
- Laboratory of Metabolic Regulation and Genetics, Rockefeller University, New York, NY, USA
| | - A Ari Hakimi
- Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Payam A Gammage
- CRUK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
21
|
Sihag S, Nussenzweig SC, Walch HS, Hsu M, Tan KS, Sanchez-Vega F, Chatila WK, De La Torre SA, Patel A, Janjigian YY, Maron S, Ku GY, Tang LH, Hechtman J, Shah PM, Wu AJ, Jones DR, Molena D, Solit DB, Schultz N, Berger MF. Next-Generation Sequencing of 487 Esophageal Adenocarcinomas Reveals Independently Prognostic Genomic Driver Alterations and Pathways. Clin Cancer Res 2021; 27:3491-3498. [PMID: 33795256 DOI: 10.1158/1078-0432.ccr-20-4707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/05/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE To delineate recurrent oncogenic driver alterations and dysregulated pathways in esophageal adenocarcinoma and to assess their prognostic value. EXPERIMENTAL DESIGN We analyzed a large cohort of patients with lower esophageal and junctional adenocarcinoma, prospectively sequenced by MSK-IMPACT with high-quality clinical annotation. Patients were subdivided according to treatment intent, curative versus palliative, which closely mirrored clinical staging. Genomic features, alterations, and pathways were examined for association with overall survival using Cox proportional hazard models, adjusted for relevant clinicopathologic factors knowable at the time of diagnosis. RESULTS Analysis of 487 patients revealed 16 oncogenic driver alterations, mostly amplifications, present in ≥5% of patients. Patients in the palliative-intent cohort, compared with those in the curative-intent cohort, were more likely to have metastatic disease, ERBB2 amplifications, Cell-cycle and RTK-RAS pathway alterations, as well as a higher fraction of genome altered and rate of whole-genome doubling. In multivariable analyses, CDKN2A alterations, SMAD4 alterations, KRAS amplifications, Cell-cycle and TGFβ pathways, and overall number of oncogenic drivers were independently associated with worse overall survival. ERBB2 amplification was associated with improved survival, presumably due to trastuzumab therapy. CONCLUSIONS Our study suggests that higher levels of genomic instability are associated with more advanced disease in esophageal adenocarcinoma. Furthermore, CDKN2A, KRAS, and SMAD4 represent prognostic biomarkers, given their strong association with poor survival.
Collapse
Affiliation(s)
- Smita Sihag
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Samuel C Nussenzweig
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Henry S Walch
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meier Hsu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francisco Sanchez-Vega
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sergio A De La Torre
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Assem Patel
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura H Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pari M Shah
- Department of Gastroenterology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Abraham J Wu
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
22
|
Bielska AA, Chatila WK, Walch H, Schultz N, Stadler ZK, Shia J, Reidy-Lagunes D, Yaeger R. Tumor Mutational Burden and Mismatch Repair Deficiency Discordance as a Mechanism of Immunotherapy Resistance. J Natl Compr Canc Netw 2021; 19:130-133. [PMID: 33545685 DOI: 10.6004/jnccn.2020.7680] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 10/27/2020] [Indexed: 11/17/2022]
Abstract
Lynch syndrome is a heritable cancer syndrome caused by a heterozygous germline mutation in DNA mismatch repair (MMR) genes. MMR-deficient (dMMR) tumors are particularly sensitive to immune checkpoint inhibitors, an effect attributed to the higher mutation rate in these cancers. However, approximately 15% to 30% of patients with dMMR cancers do not respond to immunotherapy. This report describes 3 patients with Lynch syndrome who each had 2 primary malignancies: 1 with dMMR and a high tumor mutational burden (TMB), and 1 with dMMR but, unexpectedly, a low TMB. Two of these patients received immunotherapy for their TMB-low tumors but experienced no response. We have found that not all Lynch-associated dMMR tumors have a high TMB and propose that tumors with dMMR and TMB discordance may be resistant to immunotherapy. The possibility of dMMR/TMB discordance should be considered, particularly in less-typical Lynch cancers, in which TMB evaluation could guide the use of immune checkpoint inhibitors.
Collapse
Affiliation(s)
- Agata A Bielska
- 1Department of Medicine, Memorial Sloan Kettering Cancer Center
| | - Walid K Chatila
- 2Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College; and.,3Marie-Josée and Henry R. Kravis Center for Molecular Oncology
| | - Henry Walch
- 3Marie-Josée and Henry R. Kravis Center for Molecular Oncology
| | - Nikolaus Schultz
- 3Marie-Josée and Henry R. Kravis Center for Molecular Oncology.,4Department of Epidemiology and Biostatistics.,5Human Oncology and Pathogenesis Program, and
| | | | - Jinru Shia
- 6Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Rona Yaeger
- 1Department of Medicine, Memorial Sloan Kettering Cancer Center
| |
Collapse
|
23
|
Shoushtari AN, Chatila WK, Arora A, Sanchez-Vega F, Kantheti HS, Rojas Zamalloa JA, Krieger P, Callahan MK, Betof Warner A, Postow MA, Momtaz P, Nair S, Ariyan CE, Barker CA, Brady MS, Coit DG, Rosen N, Chapman PB, Busam KJ, Solit DB, Panageas KS, Wolchok JD, Schultz N. Therapeutic Implications of Detecting MAPK-Activating Alterations in Cutaneous and Unknown Primary Melanomas. Clin Cancer Res 2021; 27:2226-2235. [PMID: 33509808 DOI: 10.1158/1078-0432.ccr-20-4189] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/17/2020] [Accepted: 01/21/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Cutaneous and unknown primary melanomas frequently harbor alterations that activate the MAPK pathway. Whether MAPK driver detection beyond BRAF V600 is clinically relevant in the checkpoint inhibitor era is unknown. EXPERIMENTAL DESIGN Patients with melanoma were prospectively offered tumor sequencing of 341-468 genes. Oncogenic alterations in 28 RTK-RAS-MAPK pathway genes were used to construct MAPK driver groups. Time to treatment failure (TTF) was determined for patients who received first-line programmed cell death protein 1 (PD-1) monotherapy, nivolumab plus ipilimumab, or subsequent genomically matched targeted therapies. A Cox proportional hazards model was constructed for TTF using driver group and clinical variables. RESULTS A total of 670 of 696 sequenced melanomas (96%) harbored an oncogenic RTK-RAS-MAPK pathway alteration; 33% had ≥1 driver. Nine driver groups varied by clinical presentation and mutational burden. TTF of PD-1 monotherapy (N = 181) varied by driver, with worse outcomes for NRAS Q61 and BRAF V600 versus NF1 or other alterations (median 4.2, 7.5, 22, and not reached; P < 0.0001). Driver group remained significant, independent of tumor mutational burden and clinical features. TTF did not vary by driver for nivolumab plus ipilimumab (N = 141). Among 172 patients with BRAF V600 wild-type melanoma who progressed on checkpoint blockade, 27 were treated with genomically matched therapy, and eight (30%) derived clinical benefit lasting ≥6 months. CONCLUSIONS Targeted capture multigene sequencing can detect oncogenic RTK-RAS-MAPK pathway alterations in almost all cutaneous and unknown primary melanomas. TTF of PD-1 monotherapy varies by mechanism of ERK activation. Oncogenic kinase fusions can be successfully targeted in immune checkpoint inhibitor-refractory melanoma.
Collapse
Affiliation(s)
- Alexander N Shoushtari
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Walid K Chatila
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Arshi Arora
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Francisco Sanchez-Vega
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Havish S Kantheti
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Penina Krieger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Margaret K Callahan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Allison Betof Warner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Michael A Postow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Parisa Momtaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Suresh Nair
- Lehigh Valley Medical Center, Bethlehem, Pennsylvania
| | - Charlotte E Ariyan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher A Barker
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mary Susan Brady
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Paul B Chapman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Katherine S Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
24
|
Alatise OI, Knapp GC, Sharma A, Chatila WK, Olasehinde O, Omisore AD, Katung A, Olatoke SA, Kingham T. Abstract IA35: Novel biological insights into colorectal cancer from West Africa. Cancer Epidemiol Biomarkers Prev 2020. [DOI: 10.1158/1538-7755.disp20-ia35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
The burden of colorectal cancer (CRC) is increasing in West Africa. Understanding the molecular and clinicopathologic profile of the region’s CRC patients is vital to optimizing early detection and therapeutic regimens. Clinicopathologic data from consecutive patients from a multicenter, prospectively maintained Nigerian CRC database were compared to a contemporary cohort from Memorial Sloan Kettering Cancer Center (MSKCC). Fresh-frozen tissue from Nigerian patients was analyzed with a multigene, next-generation sequencing assay, along with immunohistochemistry and methylation analyses; data were compared to molecular data from MSKCC and The Cancer Genome Atlas (TCGA) cohorts. Adult patients with histologically confirmed colorectal adenocarcinoma enrolled in a Nigerian CRC database from April 2013-November 2018 were included. All adult patients with colorectal adenocarcinoma diagnosed from January-June 2013 were included in the MSKCC cohort. Somatic and germline next-generation sequencing of cancer-associated genes, immunohistochemistry, and methylation analyses were performed. The primary outcomes were microsatellite instability status, somatic and germline mutation frequency, and overall survival. The median age at diagnosis was 55.8 years in the Nigerian cohort (n=380) and 60.0 years in the MSKCC cohort (n=458) (p<0.001). The rate of microsatellite instability was 28.1% in the Nigerian cohort (18/64), compared to 14.2% and 8.5% in the TCGA (65/459) and MSKCC (97/1145) cohorts, respectively (p<0.001). In microsatellite-stable cases, tumors from Nigerian patients were less likely to have APC mutations (39.1% vs. 76.0% p<0.001) and WNT pathway alterations (47.8% vs. 81.9%, p<0.001), and more likely to have RAS pathway alterations (76.1% vs. 59.6%, p=0.03) compared to MSKCC patients. Overall survival was significantly longer for MSKCC vs. Nigerian patients (not reached vs. 12 months, p<0.001). The biology of CRC in Nigeria appears to be distinct from that in high-income countries, emphasizing the need for regional data to guide diagnostic and treatment approaches for patients in West Africa.
Citation Format: Olusegun I. Alatise, Gregory C. Knapp, Avinash Sharma, Walid K. Chatila, Olalekan Olasehinde, Adeleye D. Omisore, Aba Katung, Samuel A. Olatoke, T.Peter Kingham. Novel biological insights into colorectal cancer from West Africa [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr IA35.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Aba Katung
- 4Federal Medical Center Owo, Owo, Nigeria,
| | | | | |
Collapse
|
25
|
Mondaca S, Walch H, Nandakumar S, Chatila WK, Schultz N, Yaeger R. Specific Mutations in APC, but Not Alterations in DNA Damage Response, Associate With Outcomes of Patients With Metastatic Colorectal Cancer. Gastroenterology 2020; 159:1975-1978.e4. [PMID: 32730818 PMCID: PMC7680360 DOI: 10.1053/j.gastro.2020.07.041] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 01/27/2023]
Abstract
In an integrated genomic and clinical analysis, we evaluate the effects of Wnt and DNA damage response pathway alterations on metastatic colorectal cancer.
Collapse
Affiliation(s)
- Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Henry Walch
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Subhiksha Nandakumar
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid K. Chatila
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Tri-I nstitutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY
| | - Nikolaus Schultz
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
26
|
Yang C, Sanchez-Vega F, Chang JC, Chatila WK, Shoushtari AN, Ladanyi M, Travis WD, Busam KJ, Rekhtman N. Lung-only melanoma: UV mutational signature supports origin from occult cutaneous primaries and argues against the concept of primary pulmonary melanoma. Mod Pathol 2020; 33:2244-2255. [PMID: 32581366 PMCID: PMC8386291 DOI: 10.1038/s41379-020-0594-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/28/2020] [Accepted: 05/28/2020] [Indexed: 01/14/2023]
Abstract
Primary pulmonary melanoma (PPM) is an entity recognized by the thoracic WHO classification. However, given the absence of native melanocytes in the lung and the known phenomenon of regression of cutaneous melanomas, the existence of PPM has remained controversial. Herein we investigate clinicopathologic and genomic features of lung-only melanomas with the goal to clarify their site of origin. We identified 10 melanomas involving exclusively lung with no current or previous cutaneous, uveal, or mucosal primaries. Four patients had solitary lesions with mean size of 5.1 cm (range 3.0-10.1 cm), meeting the criteria of PPM. Four patients had 2-3 lesions and 2 patients had >10 lesions. All cases underwent targeted next-generation sequencing interrogating up to 468 cancer genes, which revealed mean tumor mutation burden of 42.6 per megabase (range 1.8 to 126) and frequent mutations involving BRAF, NRAS, NF1, KIT, and KRAS - a genomic profile typical of UV-associated cutaneous melanoma. Mutational signature was assessable for eight cases harboring >20 mutations. This revealed that all evaluable cases harbored a dominant UV signature. In addition, one nonevaluable case harbored a GG > AA TERT promoter variant that is highly specific for UV-mutagenesis. As control groups, using the same methodology, a dominant UV signature was identified in 97% (470/486) of cutaneous melanomas, whereas no lung adenocarcinoma (n = 291) exhibited this signature. Notably, the clinical and pathologic features of solitary melanomas, especially those with large size and epithelioid morphology, closely mimicked primary lung carcinomas, highlighting a major potential for misdiagnosis. In conclusion, presence of a UV signature provides direct evidence that nearly all lung-only melanomas in this series, including solitary lesions meeting the strict criteria of PPM, represent metastases from occult cutaneous melanomas. This suggests that lung-only melanomas should be considered as likely metastatic even in the absence of a known primary melanoma elsewhere.
Collapse
Affiliation(s)
- Chen Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Klaus J Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
27
|
Adileh M, Yuval JB, Walch HS, Chatila WK, Yaeger R, Garcia-Aguilar J, Schultz N, Paty PB, Cercek A, Nash GM. Correction to: Primary Tumor Location and Outcomes After Cytoreductive Surgery and Intraperitoneal Chemotherapy for Peritoneal Metastases of Colorectal Origin. Ann Surg Oncol 2020; 27:987. [PMID: 33001300 DOI: 10.1245/s10434-020-09191-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In the original article there is a reference missing, in addition to its citations in the text. The reference is as follows.
Collapse
Affiliation(s)
- Mohammad Adileh
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan B Yuval
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry S Walch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia-Aguilar
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip B Paty
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Garrett M Nash
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
28
|
Adileh M, Yuval JB, Walch HS, Chatila WK, Yaeger R, Garcia-Aguilar J, Schultz N, Paty PB, Cercek A, Nash GM. Primary Tumor Location and Outcomes After Cytoreductive Surgery and Intraperitoneal Chemotherapy for Peritoneal Metastases of Colorectal Origin. Ann Surg Oncol 2020; 28:1109-1117. [PMID: 32844293 DOI: 10.1245/s10434-020-08993-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The aim of this study is to evaluate outcomes in patients with peritoneal metastasis of colorectal cancer (pmCRC) who underwent cytoreductive surgery and intraperitoneal chemotherapy (CRS/IPC) in relation to the location of the primary tumor. Regional therapy, including cytoreductive surgery and intraperitoneal chemotherapy, has been associated with improved survival in patients with pmCRC. Location of the primary tumor has been shown to be prognostic in patients with metastasis. PATIENTS AND METHODS A retrospective review was performed for all patients who underwent complete cytoreduction and intraperitoneal chemotherapy from 2010 to 2017, examining patient and tumor characteristics, overall and recurrence-free survival, recurrence patterns, and tumor mutational profiles. RESULTS Ninety-three patients were included in the study: 49 (53%) with a right-sided and 44 (47%) with a left-sided primary tumor. Patients with a right-sided tumor had significantly shorter recurrence-free survival (median, 6.3 months; 95% CI, 4.7-8.1 months vs 12.3 months; 95% CI, 3.6-21.7 months; P = 0.02) and overall survival (median, 36.6 months; 95% CI, 26.4-46.9 months vs 83.3 months; 95% CI 44.2-122.4 months; P = 0.03). BRAF and KRAS mutations were more frequent in right-sided tumors, and APC and TP53 mutations were more frequent in left-sided tumors, which were more chromosomally instable. BRAF mutations were associated with early recurrence. CONCLUSIONS Tumor sidedness is a predictor of oncological outcomes after CRS/IPC. Tumor sidedness and molecular characteristics should be considered when counseling patients regarding expected outcomes and when selecting or stratifying pmCRC patients for clinical trials of regional therapy.
Collapse
Affiliation(s)
- Mohammad Adileh
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan B Yuval
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry S Walch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia-Aguilar
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Philip B Paty
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Garrett M Nash
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
29
|
Janjigian YY, Maron SB, Chatila WK, Millang B, Chavan SS, Alterman C, Chou JF, Segal MF, Simmons MZ, Momtaz P, Shcherba M, Ku GY, Zervoudakis A, Won ES, Kelsen DP, Ilson DH, Nagy RJ, Lanman RB, Ptashkin RN, Donoghue MTA, Capanu M, Taylor BS, Solit DB, Schultz N, Hechtman JF. First-line pembrolizumab and trastuzumab in HER2-positive oesophageal, gastric, or gastro-oesophageal junction cancer: an open-label, single-arm, phase 2 trial. Lancet Oncol 2020; 21:821-831. [PMID: 32437664 DOI: 10.1016/s1470-2045(20)30169-8] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Addition of trastuzumab to first-line chemotherapy improves overall survival in patients with HER2-positive metastatic gastric cancer. We assessed the safety and activity of pembrolizumab in combination with trastuzumab and chemotherapy in first-line HER2-positive metastatic oesophagogastric (gastric, oesophageal, or gastroesophageal junction) cancer. METHODS This study was an investigator-initiated, open-label, non-randomised, single-arm, single centre, phase 2 trial in patients aged 18 years or older with HER2-positive metastatic oesophagogastric cancer. Eligible patients had measurable or evaluable non-measurable disease, Eastern Cooperative Oncology Group performance status of 0, 1, or 2, and left ventricular ejection fraction of at least 53%. Patients were eligible to receive an initial induction cycle of 200 mg flat dose of intravenous pembrolizumab and 8 mg/kg loading dose of intravenous trastuzumab. For subsequent cycles, patients received 130 mg/m2 of intravenous oxaliplatin or 80 mg/m2 of cisplatin on day 1, 850 mg/m2 of oral capecitabine twice a day for 2 weeks followed by 1 week off (or intravenous 5-fluorouracil, 800 mg/m2 per day on days 1-5), and a 200 mg flat dose of intravenous pembrolizumab, and 6 mg/kg of trastuzumab, administered on day 1 of each 3-week cycle. The primary endpoint was 6-month progression-free survival, defined as the proportion of patients alive and free of progression at 6 months, assessed in patients who received at least one dose of trastuzumab and pembrolizumab. The regimen would be considered worthy of further investigation if 26 or more of 37 patients were progression-free at 6 months. This trial is registered with ClinicalTrials.gov, NCT02954536, and is ongoing, but closed to enrolment. FINDINGS Between Nov 11, 2016, and Jan 23, 2019, 37 patients were enrolled. At the time of data cutoff on Aug 6, 2019, median follow-up among survivors was 13·0 months (IQR 11·7-23·5). The primary endpoint was achieved; 26 (70%; 95% CI 54-83) of 37 patients were progression-free at 6 months. The most common treatment-related adverse event of any grade was neuropathy, which was reported in 36 (97%) of 37 patients. The most common grade 3 or 4 adverse events were lymphocytopenia (seven [19%] patients with grade 3 and two [5%] with grade 4), grade 3 decreased electrolytes (six [16%] patients), and grade 3 anaemia (four [11%] patients). Serious adverse events occurred in two patients patients (both grade 3 nephritis leading to treatment discontinuation). Four patients discontinued pembrolizumab because of immune-related adverse events. There were no treatment-related deaths. INTERPRETATION Pembrolizumab can be safely combined with trastuzumab and chemotherapy and has promising activity in HER2-positive metastatic oesophagogastric cancer. A randomised phase 3 clinical trial assessing the efficacy and safety of pembrolizumab versus placebo in combination with trastuzumab and chemotherapy in first-line HER2-positive metastatic oesophagogastric cancer is underway. FUNDING Merck & Co.
Collapse
Affiliation(s)
- Yelena Y Janjigian
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Steven B Maron
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Walid K Chatila
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Brittanie Millang
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carly Alterman
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joanne F Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michal F Segal
- Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Z Simmons
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parisa Momtaz
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina Shcherba
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geoffrey Y Ku
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Alice Zervoudakis
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth S Won
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David P Kelsen
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David H Ilson
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
30
|
Datta J, Smith JJ, Chatila WK, McAuliffe JC, Kandoth C, Vakiani E, Frankel TL, Ganesh K, Wasserman I, Lipsyc-Sharf M, Guillem J, Nash GM, Paty PB, Weiser MR, Saltz LB, Berger MF, Jarnagin WR, Balachandran V, Kingham TP, Kemeny NE, Cercek A, Garcia-Aguilar J, Taylor BS, Viale A, Yaeger R, Solit DB, Schultz N, D'Angelica MI. Coaltered Ras/B-raf and TP53 Is Associated with Extremes of Survivorship and Distinct Patterns of Metastasis in Patients with Metastatic Colorectal Cancer. Clin Cancer Res 2019; 26:1077-1085. [PMID: 31719050 DOI: 10.1158/1078-0432.ccr-19-2390] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/27/2019] [Accepted: 11/08/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE We aimed to investigate genomic correlates underlying extremes of survivorship in metastatic colorectal cancer and their applicability in informing survival in distinct subsets of patients with metastatic colorectal cancer. EXPERIMENTAL DESIGN We examined differences in oncogenic somatic alterations between metastatic colorectal cancer cohorts demonstrating extremes of survivorship following complete metastasectomy: ≤2-year (n = 17) and ≥10-year (n = 18) survivors. Relevant genomic findings, and their association with overall survival (OS), were validated in two independent datasets of 935 stage IV and 443 resected stage I-IV patients. RESULTS In the extremes-of-survivorship cohort, significant co-occurrence of KRAS hotspot mutations and TP53 alterations was observed in ≤2-year survivors (P < 0.001). When validating these findings in the independent cohort of 935 stage IV patients, incorporation of the cumulative effect of any oncogenic Ras/B-raf (i.e., either KRAS, NRAS, or BRAF) and TP53 alteration generated three prognostic clusters: (i) TP53-altered alone (median OS, 132 months); (ii) Ras/B-raf-altered alone (65 months) or Ras/B-raf- and TP53 pan-wild-type (60 months); and (iii) coaltered Ras/B-raf-TP53 (40 months; P < 0.0001). Coaltered Ras/B-raf-TP53 was independently associated with mortality (HR, 2.47; 95% confidence interval, 1.91-3.21; P < 0.001). This molecular profile predicted survival in the second independent cohort of 443 resected stage I-IV patients. Coaltered Ras/B-raf-TP53 was associated with worse OS in patients with liver (n = 490) and lung (n = 172) but not peritoneal surface (n = 149) metastases. Moreover, coaltered Ras/B-raf-TP53 tumors were significantly more likely to involve extrahepatic metastatic sites with limited salvage options. CONCLUSIONS Genomic analysis of extremes of survivorship following colorectal cancer metastasectomy identifies a prognostic role for coaltered Ras/B-raf-TP53 and its association with distinct patterns of colorectal cancer metastasis.
Collapse
Affiliation(s)
- Jashodeep Datta
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
- Department of Surgery, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Miami, Florida
| | - J Joshua Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John C McAuliffe
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Montefiore Medical Center, Bronx, New York
| | - Cyriac Kandoth
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy L Frankel
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Karuna Ganesh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isaac Wasserman
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marla Lipsyc-Sharf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jose Guillem
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Garrett M Nash
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip B Paty
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vinod Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - T Peter Kingham
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy E Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael I D'Angelica
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
31
|
Smith JJ, Chatila WK, Sanchez-Vega F, Datta J, Connell LC, Szeglin BC, Basunia A, Boucher TM, Hauser H, Wasserman I, Wu C, Cercek A, Hechtman JF, Madden C, Jarnagin WR, Garcia-Aguilar J, D'Angelica MI, Yaeger R, Schultz N, Kemeny NE. Genomic stratification beyond Ras/B-Raf in colorectal liver metastasis patients treated with hepatic arterial infusion. Cancer Med 2019; 8:6538-6548. [PMID: 31503397 PMCID: PMC6825986 DOI: 10.1002/cam4.2415] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 12/15/2022] Open
Abstract
Background Resection of colorectal liver metastases (CLM) can cure disease, but many patients with extensive disease cannot be fully resected and others recur following surgery. Hepatic arterial infusion (HAI) chemotherapy can convert extensive liver disease to a resectable state or decrease recurrence risk, but response varies and no biomarkers currently exist to identify patients most likely to benefit. Methods We performed a retrospective cohort study of CLM patients receiving HAI chemotherapy whose tumors underwent MSK‐IMPACT sequencing. The frequency of oncogenic alterations and their association with overall survival (OS) and objective response rate were analyzed at the individual gene and signaling pathway levels. Results Three hundred and seventy patients met inclusion criteria: 189 (51.1%) who underwent colorectal liver metastasectomy followed by HAI + systemic therapy (Adjuvant cohort), and 181 (48.9%) with unresectable CLM (Metastatic cohort) who received HAI + systemic therapy, consisting of 63 (34.8%) with extrahepatic disease and 118 (65.2%) with liver‐restricted disease. Genomic alterations were similar in each cohort, and no individual gene or pathway was significantly associated with objective response. Patients in the adjuvant cohort with concurrent Ras/B‐Raf alteration and SMAD4 inactivation had worse prognosis while in the metastatic cohort patients with co‐alteration of Ras/B‐Raf and TP53 had worse OS. Similar findings were observed in a validation cohort. Conclusions Concurrently altered Ras/B‐Raf and SMAD4 mutations were associated with worse survival in resectable patients, while concurrent Ras/B‐Raf and TP53 alterations were associated with worse survival in unresectable patients. The mutual exclusivity of Ras/B‐Raf, SMAD4, and TP53 may have prognostic value for CLM patients receiving HAI.
Collapse
Affiliation(s)
- J Joshua Smith
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA.,Human Oncology and Pathogenesis Program, MSKCC, New York City, New York, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, MSKCC, New York City, New York, USA.,Center for Molecular Oncology, MSKCC, New York City, New York, USA.,Tri-Institutional Program in Computational Biology & Medicine, New York City, New York, USA
| | - Francisco Sanchez-Vega
- Human Oncology and Pathogenesis Program, MSKCC, New York City, New York, USA.,Center for Molecular Oncology, MSKCC, New York City, New York, USA
| | - Jashodeep Datta
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA.,Department of Surgery, Hepatopancreatobiliary Service, MSKCC, New York City, New York, USA
| | | | - Bryan C Szeglin
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA
| | - Azfar Basunia
- Human Oncology and Pathogenesis Program, MSKCC, New York City, New York, USA.,Center for Molecular Oncology, MSKCC, New York City, New York, USA
| | | | - Haley Hauser
- Department of Medicine, MSKCC, New York City, New York, USA
| | - Isaac Wasserman
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA
| | - Chao Wu
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA.,Human Oncology and Pathogenesis Program, MSKCC, New York City, New York, USA
| | - Andrea Cercek
- Department of Medicine, MSKCC, New York City, New York, USA
| | | | - Chris Madden
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA
| | - William R Jarnagin
- Department of Surgery, Hepatopancreatobiliary Service, MSKCC, New York City, New York, USA
| | - Julio Garcia-Aguilar
- Department of Surgery, Colorectal Service, Memorial Sloan Kettering Cancer Center (MSKCC), New York City, New York, USA
| | - Michael I D'Angelica
- Department of Surgery, Hepatopancreatobiliary Service, MSKCC, New York City, New York, USA
| | - Rona Yaeger
- Department of Medicine, MSKCC, New York City, New York, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, MSKCC, New York City, New York, USA.,Center for Molecular Oncology, MSKCC, New York City, New York, USA.,Department of Epidemiology & Biostatistics, MSKCC, New York City, New York, USA
| | - Nancy E Kemeny
- Department of Medicine, MSKCC, New York City, New York, USA
| |
Collapse
|
32
|
Zhou J, Sanchez-Vega F, Caso R, Tan KS, Brandt WS, Jones GD, Yan S, Adusumilli PS, Bott M, Huang J, Isbell JM, Sihag S, Molena D, Rusch VW, Chatila WK, Rekhtman N, Yang F, Ladanyi M, Solit DB, Berger MF, Schultz N, Jones DR. Analysis of Tumor Genomic Pathway Alterations Using Broad-Panel Next-Generation Sequencing in Surgically Resected Lung Adenocarcinoma. Clin Cancer Res 2019; 25:7475-7484. [PMID: 31455678 DOI: 10.1158/1078-0432.ccr-19-1651] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/22/2019] [Accepted: 08/23/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE The majority of broad-panel tumor genomic profiling has used a gene-centric approach, although much of that data is unused in clinical decision making. We hypothesized that a pathway-centric approach using next-generation sequencing (NGS), combined with conventional clinicopathologic features, may better predict disease-free survival (DFS) in early stage lung adenocarcinoma. EXPERIMENTAL DESIGN Utilizing our prospectively maintained database, we analyzed 492 patients with primary, untreated, completely surgically resected lung adenocarcinoma. Ten canonical pathways were analyzed using broad-panel NGS. The correlations of DFS and number (and type) of pathway (NPA) were analyzed using the Kaplan-Meier method and log-rank test. Associations between altered pathways and clinicopathologic variables, as well as identification of actionable therapeutic strategies were explored. RESULTS Median NPA for the cohort was two (range, 0-5). Smoking status, solid morphologic appearance on preoperative CT, maximal standardized uptake value, pathologic tumor size, aggressive histologic subtype, lymphovascular invasion, visceral pleural invasion, and positive lymph nodes were significantly associated with NPA (P < 0.05). Of 543 actionable genetic alterations identified, 455 (84%) were within the RTK/RAS pathway. A total of 86 tumors had actionable therapeutic genomic alterations in >1 pathway. On multivariable analysis, higher NPA was significantly associated with worse DFS (HR, 1.31; P = 0.014). CONCLUSIONS NPA and specific pathway alterations are associated with clinicopathologic features in patients with surgically resected lung adenocarcinoma. Cell cycle, Hippo, TGFβ, and p53 pathway alterations are associated with poor DFS. Finally, NPA is an independent risk factor for poor DFS in our cohort.See related commentary by Blakely, p. 7269.
Collapse
Affiliation(s)
- Jian Zhou
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Thoracic Department, Peking University People's Hospital, Beijing, China
| | - Francisco Sanchez-Vega
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Raul Caso
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay See Tan
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Whitney S Brandt
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gregory D Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shi Yan
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Bott
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James Huang
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James M Isbell
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Smita Sihag
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Valerie W Rusch
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fan Yang
- Thoracic Department, Peking University People's Hospital, Beijing, China
| | - Marc Ladanyi
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Thoracic Surgery Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York. .,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
33
|
Vedanayagam J, Chatila WK, Aksoy BA, Majumdar S, Skanderup AJ, Demir E, Schultz N, Sander C, Lai EC. Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis. Nat Commun 2019; 10:3682. [PMID: 31417090 PMCID: PMC6695490 DOI: 10.1038/s41467-019-11610-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 07/25/2019] [Indexed: 11/09/2022] Open
Abstract
Somatic mutations in the RNase IIIb domain of DICER1 arise in cancer and disrupt the cleavage of 5' pre-miRNA arms. Here, we characterize an unstudied, recurrent, mutation (S1344L) in the DICER1 RNase IIIa domain in tumors from The Cancer Genome Atlas (TCGA) project and MSK-IMPACT profiling. RNase IIIa/b hotspots are absent from most cancers, but are notably enriched in uterine cancers. Systematic analysis of TCGA small RNA datasets show that DICER1 RNase IIIa-S1344L tumors deplete 5p-miRNAs, analogous to RNase IIIb hotspot samples. Structural and evolutionary coupling analyses reveal constrained proximity of RNase IIIa-S1344 to the RNase IIIb catalytic site, rationalizing why mutation of this site phenocopies known hotspot alterations. Finally, examination of DICER1 hotspot endometrial tumors reveals derepression of specific miRNA target signatures. In summary, comprehensive analyses of DICER1 somatic mutations and small RNA data reveal a mechanistic aspect of pre-miRNA processing that manifests in specific cancer settings.
Collapse
Affiliation(s)
- Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Walid K Chatila
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Bülent Arman Aksoy
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.,Immunology and Microbiology Department, Medical University of South Carolina, Charleston, SC, 29412, USA
| | - Sonali Majumdar
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Anders Jacobsen Skanderup
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Computational and Systems Biology, Agency for Science Technology and Research, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Emek Demir
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.,Oregon Health and Science University, Computational Biology Program, Portland, OR, 97239, USA
| | - Nikolaus Schultz
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Chris Sander
- Department of Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,cBio Center, Dana-Farber Cancer Institute, Boston, MA, 02115, USA. .,Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. .,Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, 10065, USA.
| |
Collapse
|
34
|
Greally M, Chou JF, Chatila WK, Margolis M, Capanu M, Hechtman JF, Tuvy Y, Kundra R, Daian F, Ladanyi M, Kelsen DP, Ilson DH, Berger MF, Tang LH, Solit DB, Diaz LA, Schultz N, Janjigian YY, Ku GY. Clinical and Molecular Predictors of Response to Immune Checkpoint Inhibitors in Patients with Advanced Esophagogastric Cancer. Clin Cancer Res 2019; 25:6160-6169. [PMID: 31337644 DOI: 10.1158/1078-0432.ccr-18-3603] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 04/15/2019] [Accepted: 07/12/2019] [Indexed: 12/27/2022]
Abstract
PURPOSE Immune checkpoint inhibitors (ICI) are effective in only a minority of patients with esophagogastric cancer (EGC). Here, we aimed to identify predictors of durable clinical benefit to ICI in EGC. EXPERIMENTAL DESIGN Patients with advanced EGC treated with ICIs at Memorial Sloan Kettering Cancer Center (New York, NY) were identified. Clinicopathologic variables were assessed. In patients profiled by MSK-IMPACT-targeted sequencing, outcomes were correlated with tumor genomic features. RESULTS One-hundred sixty-one patients were treated with ICIs (110 with anti-PD-1/PD-L1 antibodies and 51 with anti-CTLA-4 and PD-1/PD-L1 antibodies). The median progression-free survival (PFS) and overall survival (OS) were 1.7 and 4.9 months, respectively. Greater number of disease sites (≥3), liver metastases, treatment with ≥3 prior therapies and ECOG performance status ≥2 were associated with poorer PFS and OS. Patients treated with combination ICI and those with PD-L1-positive tumors had improved outcomes. There was no difference in outcomes between patients treated with antibiotics during or in the 2 months preceding ICI treatment versus those who were not. Occurrence of irAEs was associated with improved OS. In genomically profiled tumors (n = 89), survival was associated with increasing tumor mutation burden (TMB). However, in multivariable analyses and when microsatellite unstable (MSI) patients were excluded, a significant association was no longer observed. CONCLUSIONS In patients with advanced EGC, heavily pretreated patients, those with high-volume disease and/or poor PS were less likely to benefit from ICI. irAEs were associated with improved OS. TMB correlated with improved survival, but this association was not observed when MSI-high patients were excluded.
Collapse
Affiliation(s)
- Megan Greally
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F Chou
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Margolis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marinela Capanu
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yaelle Tuvy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ritika Kundra
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Foysal Daian
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura H Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
35
|
Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet 2019; 51:1194. [PMID: 31152158 DOI: 10.1038/s41588-019-0451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie A M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Celine Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christopher E Barbieri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zafeiris Zafeiriou
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Susana Miranda
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Tolonen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Johann S de Bono
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
36
|
Mondaca S, Walch HS, Nandakumar S, Chatila WK, Hechtman JF, Cercek A, Diaz LA, Sanchez-Vega F, Kemeny NE, Segal NH, Stadler ZK, Varghese AM, Vakiani E, Ladanyi M, Berger MF, Solit DB, Shia J, Saltz LB, Schultz ND, Yaeger R. Influence of WNT and DNA damage response pathway alterations on outcomes in patients with unresectable metastatic colorectal cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.3585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3585 Background: We assembled a large series of consecutive patients with unresectable metastatic colorectal cancer (mCRC) to identify genomic biomarkers of response and survival. Methods: Patients with unresectable mCRC treated at Memorial Sloan Kettering with genomic tumor profiling between 2014 and 2017 were included. Patients who underwent upfront metastasectomy or received neoadjuvant/conversion chemotherapy were excluded. Clinical information was retrieved from electronic medical records, and we evaluated associations between genomic profiles with progression free survival (PFS) on first-line chemotherapy and overall survival (OS). Categorical data were analyzed by Fisher exact test and time-to-event data were analyzed by Cox proportional hazards models. Results: Of 1453 mCRCs profiled in this period, 471 patients met the study criteria. Median age was 59 years (range, 18 to 95), and 73% of patients were stage IV at diagnosis. Most tumors (91%) were microsatellite stable (MSS). The most frequent first-line regimen was FOLFOX +/- bevacizumab (66%). Among MSS patients treated with oxaliplatin-containing regimens (n = 305), 7% harbored alterations in genes associated with DNA damage response (DDR) (BRCA1, BRCA2, ATM, PALB2). DDR gene alterations were not associated with PFS (P = 0.94) nor were different quartiles of large-state transitions (P = 0.54). Genomic alterations that significantly varied by duration of response included BRAF (16%, 10%, and 5% for PFS < 6 months, 6-12 months, and > 12 months, respectively) and APC (62%, 74%, and 80% for PFS < 6 months, 6-12 months, and > 12 months, respectively). APC mutation, single or dual, was associated with significantly longer PFS (HR 0.67) and OS (HR 0.59) in multivariate analysis versus no WNT pathway alteration or alterations in other WNT pathway genes (RNF43, AXIN2, CTNNB1). Conclusions: In unresectable mCRC patients, mutations in APC were associated with better outcomes; absence of an APC alteration or the occurrence of other WNT pathway alterations was associated with shorter survival. Somatic alterations in DDR genes were not associated with outcomes in mCRC patients receiving oxaliplatin-containing regimen.
Collapse
Affiliation(s)
- Sebastian Mondaca
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Henry S Walch
- Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Subhiksha Nandakumar
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York City, NY
| | - Luis A. Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Neil Howard Segal
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Rona Yaeger
- Memorial Sloan-Kettering Cancer Center, New York, NY
| |
Collapse
|
37
|
Shoushtari AN, Sanchez-Vega F, Kantheti H, Callahan MK, Postow MA, Barker CA, Chatila WK, Jonsson P, Ariyan CE, Brady MS, Coit DG, Nair S, Chapman PB, Busam KJ, Solit DB, Wolchok JD, Schultz N. Therapeutic implications of a novel driver classification system for cutaneous and unknown primary melanomas. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.9539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9539 Background: Cutaneous and “unknown primary” melanomas frequently harbor alterations that activate the Mitogen Activated Protein Kinase (MAPK) pathway, and are often classified as BRAF, NRAS, NF1 mutant, or “triple wild type.” Multigene sequencing may identify additional oncogenic drivers, but the clinical impact of this information is unknown. Methods: Patients with BRAF inhibitor naïve melanoma underwent prospective tumor molecular profiling using a targeted capture-based assay (MSK-IMPACT), and demographic and treatment data were collected. Time to treatment failure was assessed for patients who received frontline PD-1 monotherapy or nivolumab plus ipilimumab. Results: 576 patients were successfully sequenced. 533 samples (96%) harbored a known or presumed oncogenic mutation in 1 of 28 genes in the RTK-RAS-MAPK pathway. 187 tumors (32%) had two or more drivers in this pathway, and the rates of driver co-alterations varied widely by specific driver. A hierarchical classification of 9 driver groups (BRAF V600E; V600K/R/M; BRAF non-V600; NRAS Q61; Other RAS; NF1; KIT; Other driver; Unknown driver) was significantly associated with tumor mutational burden, primary melanoma site, and patient age. Time to treatment failure varied by driver class and site of primary melanoma for PD-1 monotherapy but not nivolumab plus ipilimumab. 150 patients with BRAF V600 wild-type melanoma required systemic therapy after progression on checkpoint blockade. 21 were given genomically matched therapy, and 5/21 had clinical benefit for ≥6 months. Complete and durable responses were observed with TRK and ROS1 inhibitors in patients with NTRK1/2/3 and ROS1 fusion positive tumors. Conclusions: Oncogenic alterations in the RTK-RAS-MAPK pathway can be detected using targeted capture NGS in the vast majority of cutaneous and unknown primary melanomas. A hierarchical classification of 9 driver groups revealed clinically relevant melanoma subsets with varying clinical outcomes to PD-1 monotherapy. Select patients with oncogenic kinase fusions can achieve durable therapeutic benefit with targeted inhibitors of these rare drivers.
Collapse
Affiliation(s)
| | | | | | - Margaret K. Callahan
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Won E, Basunia A, Chatila WK, Hechtman JF, Chou JF, Ku GY, Chalasani SB, Boyar MS, Goldberg Z, Desai AM, Tuvy Y, Berger MF, Tang L, Kelsen DP, Schattner M, Ilson DH, Capanu M, Solit DB, Schultz N, Janjigian YY. Efficacy of Combined VEGFR1-3, PDGFα/β, and FGFR1-3 Blockade Using Nintedanib for Esophagogastric Cancer. Clin Cancer Res 2019; 25:3811-3817. [PMID: 30952642 DOI: 10.1158/1078-0432.ccr-18-3789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/13/2019] [Accepted: 03/26/2019] [Indexed: 01/31/2023]
Abstract
PURPOSE VEGFR2-directed therapy is commonly used to treat metastatic esophagogastric cancer, but disease progresses in most patients within months. Therapeutic resistance is likely mediated in part by co-occurring amplifications of the genes for multiple oncogenic receptor tyrosine kinases (RTK). We therefore tested the efficacy of combined inhibition of VEGFR1-3, PDGFα/β, and FGFR1-3 using nintedanib. PATIENTS AND METHODS Patients with metastatic esophagogastric adenocarcinoma and disease progression on first-line chemotherapy were treated with nintedanib 200 mg twice daily. The primary endpoint was progression-free survival (PFS) at 6 months; secondary endpoints included tumor response and safety. Tumor biopsies were profiled by targeted capture next-generation sequencing (NGS) to identify molecular predictors of drug response. RESULTS The study achieved its primary endpoint; 6 of 32 patients (19%) were progression-free at 6 months. With a median follow-up of 14.5 months among survivors, median overall survival (OS) was 14.2 months [95% confidence interval (CI), 10.8 months-NR]. Nintedanib was well tolerated; grade ≥ 3 toxicities were uncommon and included grade 3 hypertension (15%) and liver enzyme elevation (4%). FGFR2 alterations were identified in 18% of patients but were not predictive of clinical outcome on nintedanib therapy. Alterations in cell-cycle pathway genes were associated with worse median PFS (1.61 months for patients with cell-cycle pathway alterations vs. 2.66 months for patients without, P = 0.019). CONCLUSIONS Nintedanib treatment resulted in modest disease stabilization in patients with metastatic esophagogastric cancer. Alterations in cell-cycle pathway genes and increased global copy-number alteration (CNA) burden warrant further study as prognostic or predictive biomarkers.
Collapse
Affiliation(s)
- Elizabeth Won
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Azfar Basunia
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Tri-Institutional Program in Computational Biology & Medicine, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Sree B Chalasani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Michelle S Boyar
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Zoe Goldberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Avni M Desai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Yaelle Tuvy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Michael F Berger
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mark Schattner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Weill Cornell Medical College, New York, New York
| |
Collapse
|
39
|
Sanchez-Vega F, Chatila WK, Ganesh K, Penson A, Camacho N, Jonsson P, Reznik E, Gao J, Yaeger R, Berger MF, Taylor BS, Schultz N. Abstract 3024: Genomic characterization of organ-specific metastasis from prospective clinical sequencing of 20,000 cancer patients. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We investigated genomic differences in sequenced biopsies of patients with metastatic cancer to identify associations between somatic alterations and anatomic site of metastasis.
We analyzed data from 20,000 patients treated at Memorial Sloan Kettering Cancer Center, covering >50 cancer types and >20 metastatic sites. Tumors were sequenced using MSK-IMPACT, a targeted sequencing assay that identifies somatic mutations, copy number changes and structural rearrangements in 468 cancer genes using tumor and matched normal DNA. We identified tumor types such as prostate cancer, lung adenocarcinoma, uterine endometrioid carcinoma, head and neck cancer and gastrointestinal stromal tumors, for which the primary biopsies differed significantly from the metastatic biopsies at the genomic level, suggesting a need for sample stratification in clinical studies. We also identified site-specific enrichment of individual somatic alterations for tumors from the same cancer type, including therapeutically relevant targets. For example, when evaluating patients with esophagogastric cancer, we found an enrichment of HER2 amplified tumors, which are candidates for trastuzumab therapy, in sequenced lung metastases as opposed to biopsies sequenced at other metastatic sites (8/16, 50% vs. 20/145, 14%; p<0.001). Looking at sequenced metastases of lung adenocarcinoma (n=468), we found that brain metastases (n=34) exhibit increased aneuploidy (median fraction of genome altered 0.55 vs. 0.44; p<0.001, purity-controlled results) and adrenal gland metastases (n=21) exhibit increased mutational burden (13.3 mut/Mb vs. 6.1 mut/Mb; p<0.001) when compared to metastases sequenced at other anatomic sites. Other examples of novel findings include enrichment of amplifications in the MITF-ETV1 pathway in melanoma patients with brain metastatic disease (13/63, 21% vs. 10/234, 4%; p<0.001) and enrichment of 20q chromosomal amplifications in patients with microsatellite stable colorectal tumors that exhibit oligo-metastatic (as opposed to poly-metastatic) patterns at first time of metastasis diagnosis (158/223, 71% vs. 28/58, 48%; p=0.002).
We provide a detailed analysis of associations between genomic features and metastatic patterns within a clinical sequencing setting. Our work has the potential to directly influence the management of patients with metastatic cancer by enabling clinicians to (a) estimate the risk of future metastasis based on the genomic profile of early stage tumors, (b) choose the appropriate site for biopsy in cases where mutation identification will influence the selection of targeted therapy, (c) optimize the use and frequency of imaging modalities for metastasis surveillance and (d) investigate and functionally characterize novel genomic alterations that have a role in metastasis and can lead to improved therapies.
Citation Format: Francisco Sanchez-Vega, Walid K. Chatila, Karuna Ganesh, Alexander Penson, Niedzica Camacho, Philip Jonsson, Ed Reznik, Jianjiong Gao, Rona Yaeger, Michael F. Berger, Barry S. Taylor, Nikolaus Schultz. Genomic characterization of organ-specific metastasis from prospective clinical sequencing of 20,000 cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3024.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ed Reznik
- Memorial Sloan Kettering, New York, NY
| | | | | | | | | | | |
Collapse
|
40
|
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La K, Dimitriadoy S, Liu DL, Kantheti HS, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Berger AH, Bivona TG, Lazar AJ, Hammer G, Giordano T, Kwong L, McArthur G, Huang C, Frederick MJ, McCormick F, Meyerson M, Network TCGAR, Allen EV, Cherniack AD, Ciriello G, Sander C, Schultz N. Abstract 3302: The molecular landscape of oncogenic signaling pathways in The Cancer Genome Atlas. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Over the past decade, The Cancer Genome Atlas (TCGA) has profiled more than 11,000 tumors spanning 33 distinct cancer types. The TCGA PanCanAtlas is a collaborative project by the TCGA Research Network that aims to address relevant overarching questions in oncology based on a cross-cancer analysis of the full, uniformly reprocessed TCGA data set. Here, we present results from our analysis of genetic alterations in mitogenic signaling pathways across cancer.
Genetic alterations in signaling pathways that control cell cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations and copy-number changes in 9,125 tumor samples profiled by TCGA, we analyzed the mechanisms and patterns of alterations in 10 canonical pathways: cell cycle, Hippo, Myc, Notch, beta-catenin / WNT, PI-3-Kinase / Akt, receptor-tyrosine kinase / RAS / MAP-kinase signaling, TP53, and TGF-beta signaling, as well as oxidative stress response. For each of these pathways, we propose an expert-curated description (or “template”) that includes the relevant (altered) genes and the connections between them, as well as a detailed catalogue of the driver mutations and copy number changes with known oncogenic relevance. We provide a high-level map of pathway alteration frequencies across tissues and relevant cancer subtypes as well as detailed frequencies of alteration at the gene level for each individual pathway. We also investigate relationships of co-occurrence and mutual exclusivity across pathways and evaluate therapeutic implications, including drug combinations. Forty-nine percent of tumors had at least one potentially targetable alteration in the evaluated pathways, and 31% of tumors had multiple targetable alterations, making them candidates for combination therapy.
Our work delineates the full landscape of oncogenic alterations in mitogenic signaling pathways across cancer, and the pathway templates as well as the richly annotated data set that we provide will constitute an invaluable public resource for future use by the cancer genomics and precision oncology communities.
Citation Format: Francisco Sanchez-Vega, Marco Mina, Joshua Armenia, Walid K. Chatila, Augustin Luna, Konnor La, Sofia Dimitriadoy, David L. Liu, Havish S. Kantheti, Zachary Heins, Angelica Ochoa, Benjamin Gross, Jianjiong Gao, Hongxin Zhang, Ritika Kundra, Cyriac Kandoth, Istemi Bahceci, Leonard Dervishi, Ugur Dogrusoz, Wanding Zhou, Hui Shen, Peter W. Laird, Alice H. Berger, Trever G. Bivona, Alexander J. Lazar, Gary Hammer, Thomas Giordano, Lawrence Kwong, Grant McArthur, Chenfei Huang, Mitchell J. Frederick, Frank McCormick, Matthew Meyerson, The Cancer Genome Atlas Research Network, Eliezer Van Allen, Andrew D. Cherniack, Giovanni Ciriello, Chris Sander, Nikolaus Schultz. The molecular landscape of oncogenic signaling pathways in The Cancer Genome Atlas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3302.
Collapse
Affiliation(s)
| | - Marco Mina
- 2University of Lausanne, Lausanne, Switzerland
| | | | | | | | - Konnor La
- 1Memorial Sloan Kettering, New York, NY
| | | | - David L. Liu
- 5Broad Institute of Harvard and MIT, Cambridge, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Hui Shen
- 8Van Andel Research Institute, Grand Rapids, MI
| | | | | | | | | | | | | | - Lawrence Kwong
- 11The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Rizvi H, Plodkowski AJ, Tenet M, Halpenny D, Long N, Sauter JL, Sanchez-Vega F, Chatila WK, Schultz N, Ladanyi M, Arbour KC, Chaft JE, Hellmann MD. Clinical and molecular features predicting long-term response (LTR) to anti-PD-(L)1 based therapy in patients with NSCLC. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.9022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Hira Rizvi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Megan Tenet
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Niamh Long
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | |
Collapse
|
42
|
Fernandes GDS, Chatila WK, Yaeger R, Mendelsohn RB, Stadler ZK, Segal NH, Varghese AM, Lagunes DR, Diaz LA, Shia J, Vakiani E, Hechtman JF, Schultz N, Berger MF, Hyman DM, Solit DB, Saltz LB, Garcia-Aguilar J, Cercek A. Genomic landscape, clinical characteristics and outcomes of early onset (EO) compared with average onset (AO) colorectal cancer (CRC). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Luis A. Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
43
|
Greally M, Chatila WK, Margolis M, Hechtman JF, Tuvy Y, Kundra R, Ladanyi M, Kelsen DP, Ilson DH, Berger MF, Tang LH, Solit DB, Schultz N, Janjigian YY, Ku GY. Tumor mutation burden (TMB) and immune-related adverse events (irAEs) compared to antibiotic (abx) use to predict for response to immune checkpoint inhibitors in esophagogastric cancer (EGC). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.4056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Megan Greally
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Yaelle Tuvy
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Paul Kelsen
- Memorial Sloan Kettering Cancer Center/Weill Cornell Medical College, New York, NY
| | | | | | - Laura H. Tang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | |
Collapse
|
44
|
Mondaca S, Chatila WK, Hechtman JF, Bates D, Cercek A, Segal NH, Stadler ZK, Varghese AM, Berger MF, Capanu M, Shia J, Schultz N, Saltz LB, Yaeger R. FOLFCIS regimen for treatment of cancer of the anal canal. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | - David Bates
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
45
|
Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. The long tail of oncogenic drivers in prostate cancer. Nat Genet 2018; 50:645-651. [PMID: 29610475 PMCID: PMC6107367 DOI: 10.1038/s41588-018-0078-z] [Citation(s) in RCA: 523] [Impact Index Per Article: 87.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 01/26/2018] [Indexed: 01/05/2023]
Abstract
Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway. We find that the incidence of significantly mutated genes (SMGs) follows a long-tail distribution, with many genes mutated in less than 3% of cases. We identify a total of 97 SMGs, including 70 not previously implicated in prostate cancer, such as the ubiquitin ligase CUL3 and the transcription factor SPEN. Finally, comparing primary and metastatic prostate cancer identifies a set of genomic markers that may inform risk stratification.
Collapse
Affiliation(s)
- Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie A M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Celine Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christopher E Barbieri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zafeiris Zafeiriou
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Susana Miranda
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Tolonen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Johann S de Bono
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA
- Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
46
|
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 2018; 173:321-337.e10. [PMID: 29625050 PMCID: PMC6070353 DOI: 10.1016/j.cell.2018.03.035] [Citation(s) in RCA: 1709] [Impact Index Per Article: 284.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 02/28/2018] [Accepted: 03/15/2018] [Indexed: 02/08/2023]
Abstract
Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFβ signaling, p53 and β-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these pathways, and 57% percent of tumors had at least one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy.
Collapse
Affiliation(s)
- Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marco Mina
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Joshua Armenia
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Augustin Luna
- cBio Center, Dana-Farber Cancer Institute, Boston, MA; Department of Cell Biology, Harvard Medical School, Boston, MA
| | - Konnor C La
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - David L Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | | | - Sadegh Saghafinia
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Foysal Daian
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Qingsong Gao
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Matthew H Bailey
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Wen-Wei Liang
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Steven M Foltz
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | | | - Li Ding
- Department of Medicine and McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zachary Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Cyriac Kandoth
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Istemi Bahceci
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Leonard Dervishi
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Ugur Dogrusoz
- Computer Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Wanding Zhou
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids Michigan, 49503, USA
| | - Hui Shen
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids Michigan, 49503, USA
| | - Peter W Laird
- Van Andel Research Institute, 333 Bostwick Ave NE, Grand Rapids Michigan, 49503, USA
| | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Chen Wang
- Department of Health Sciences Research and Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN, 55905, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Department of Neurology and Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Alice H Berger
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Trever G Bivona
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, California 94143, USA
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine & Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd-Unit 85, Houston, Texas 77030, USA
| | - Gary D Hammer
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, Endocrine Oncology Program, University of Michigan, Ann Arbor, Michigan, MI 48105, USA
| | - Thomas Giordano
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI; Department of Internal Medicine, Division of Metabolism, Endocrinology & Diabetes, University of Michigan Medical School, Ann Arbor, MI; Comprehensive Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Grant McArthur
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; University of Melbourne, Melbourne, VIC, Australia
| | - Chenfei Huang
- Dept. of Otolaryngology, Baylor College of Medicine, USA
| | - Aaron D Tward
- University of California, San Francisco Department of Otolaryngology-Head and Neck Surgery. 2233 Post Street, San Francisco, CA, 94143, USA
| | | | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1450 3rd Street, San Francisco, CA 94143, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, US
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland and Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Chris Sander
- cBio Center, Dana-Farber Cancer Institute, Boston, MA; Department of Cell Biology, Harvard Medical School, Boston, MA.
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
47
|
Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep 2018; 23:172-180.e3. [PMID: 29617658 PMCID: PMC5918694 DOI: 10.1016/j.celrep.2018.03.046] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 02/23/2018] [Accepted: 03/12/2018] [Indexed: 12/25/2022] Open
Abstract
Precision oncology uses genomic evidence to match patients with treatment but often fails to identify all patients who may respond. The transcriptome of these "hidden responders" may reveal responsive molecular states. We describe and evaluate a machine-learning approach to classify aberrant pathway activity in tumors, which may aid in hidden responder identification. The algorithm integrates RNA-seq, copy number, and mutations from 33 different cancer types across The Cancer Genome Atlas (TCGA) PanCanAtlas project to predict aberrant molecular states in tumors. Applied to the Ras pathway, the method detects Ras activation across cancer types and identifies phenocopying variants. The model, trained on human tumors, can predict response to MEK inhibitors in wild-type Ras cell lines. We also present data that suggest that multiple hits in the Ras pathway confer increased Ras activity. The transcriptome is underused in precision oncology and, combined with machine learning, can aid in the identification of hidden responders.
Collapse
Affiliation(s)
- Gregory P Way
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Francisco Sanchez-Vega
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Konnor La
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Joshua Armenia
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid K Chatila
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Augustin Luna
- cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chris Sander
- cBio Center, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marco Mina
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yolanda Sanchez
- Department of Molecular Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
48
|
Yaeger R, Chatila WK, Lipsyc MD, Hechtman JF, Cercek A, Sanchez-Vega F, Jayakumaran G, Middha S, Zehir A, Donoghue MTA, You D, Viale A, Kemeny N, Segal NH, Stadler ZK, Varghese AM, Kundra R, Gao J, Syed A, Hyman DM, Vakiani E, Rosen N, Taylor BS, Ladanyi M, Berger MF, Solit DB, Shia J, Saltz L, Schultz N. Clinical Sequencing Defines the Genomic Landscape of Metastatic Colorectal Cancer. Cancer Cell 2018; 33:125-136.e3. [PMID: 29316426 PMCID: PMC5765991 DOI: 10.1016/j.ccell.2017.12.004] [Citation(s) in RCA: 507] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/26/2017] [Accepted: 12/09/2017] [Indexed: 02/07/2023]
Abstract
Metastatic colorectal cancers (mCRCs) are clinically heterogeneous, but the genomic basis of this variability remains poorly understood. We performed prospective targeted sequencing of 1,134 CRCs. We identified splice alterations in intronic regions of APC and large in-frame deletions in CTNNB1, increasing oncogenic WNT pathway alterations to 96% of CRCs. Right-sided primary site in microsatellite stable mCRC was associated with shorter survival, older age at diagnosis, increased mutations, and enrichment of oncogenic alterations in KRAS, BRAF, PIK3CA, AKT1, RNF43, and SMAD4 compared with left-sided primaries. Left-sided tumors frequently had no identifiable genetic alteration in mitogenic signaling, but exhibited higher mitogenic ligand expression. Our results suggest different pathways to tumorigenesis in right- and left-sided microsatellite stable CRC that may underlie clinical differences.
Collapse
Affiliation(s)
- Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marla D Lipsyc
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jaclyn F Hechtman
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gowtham Jayakumaran
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sumit Middha
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daoqi You
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nancy Kemeny
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neil H Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Aijazuddin Syed
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Efsevia Vakiani
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Ladanyi
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jinru Shia
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Leonard Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| |
Collapse
|
49
|
Janjigian YY, Sanchez-Vega F, Jonsson P, Chatila WK, Hechtman JF, Ku GY, Riches JC, Tuvy Y, Kundra R, Bouvier N, Vakiani E, Gao J, Heins ZJ, Gross BE, Kelsen DP, Zhang L, Strong VE, Schattner M, Gerdes H, Coit DG, Bains M, Stadler ZK, Rusch VW, Jones DR, Molena D, Shia J, Robson ME, Capanu M, Middha S, Zehir A, Hyman DM, Scaltriti M, Ladanyi M, Rosen N, Ilson DH, Berger MF, Tang L, Taylor BS, Solit DB, Schultz N. Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer. Cancer Discov 2018; 8:49-58. [PMID: 29122777 PMCID: PMC5813492 DOI: 10.1158/2159-8290.cd-17-0787] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022]
Abstract
The incidence of esophagogastric cancer is rapidly rising, but only a minority of patients derive durable benefit from current therapies. Chemotherapy as well as anti-HER2 and PD-1 antibodies are standard treatments. To identify predictive biomarkers of drug sensitivity and mechanisms of resistance, we implemented prospective tumor sequencing of patients with metastatic esophagogastric cancer. There was no association between homologous recombination deficiency defects and response to platinum-based chemotherapy. Patients with microsatellite instability-high tumors were intrinsically resistant to chemotherapy but more likely to achieve durable responses to immunotherapy. The single Epstein-Barr virus-positive patient achieved a durable, complete response to immunotherapy. The level of ERBB2 amplification as determined by sequencing was predictive of trastuzumab benefit. Selection for a tumor subclone lacking ERBB2 amplification, deletion of ERBB2 exon 16, and comutations in the receptor tyrosine kinase, RAS, and PI3K pathways were associated with intrinsic and/or acquired trastuzumab resistance. Prospective genomic profiling can identify patients most likely to derive durable benefit to immunotherapy and trastuzumab and guide strategies to overcome drug resistance.Significance: Clinical application of multiplex sequencing can identify biomarkers of treatment response to contemporary systemic therapies in metastatic esophagogastric cancer. This large prospective analysis sheds light on the biological complexity and the dynamic nature of therapeutic resistance in metastatic esophagogastric cancers. Cancer Discov; 8(1); 49-58. ©2017 AACR.See related commentary by Sundar and Tan, p. 14See related article by Pectasides et al., p. 37This article is highlighted in the In This Issue feature, p. 1.
Collapse
Affiliation(s)
- Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York.
| | - Francisco Sanchez-Vega
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Jamie C Riches
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Yaelle Tuvy
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Ritika Kundra
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jianjiong Gao
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zachary J Heins
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin E Gross
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark Schattner
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Hans Gerdes
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manjit Bains
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Valerie W Rusch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Michael F Berger
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|