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McAlpine C, Isabelle M, Broad R, Naidoo R, Liddle A, Duperret E, Noto P, Wang R, Batrakou D, Middha S, Evans C. Abstract 892: Afamitresgene autoleucel (afami-cel; formerly ADP-A2M4) demonstrates durable clinical responses by inducing broad immune engagement with anti-tumor activity. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-892] [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: 04/07/2023]
Abstract
Abstract
Afami-cel is a mixed CD4+ CD8+ autologous T-cell therapy engineered to target the cancer testis antigen melanoma-associated antigen A4 in HLA-A*02-positive patients with advanced/metastatic synovial sarcoma or myxoid/round cell liposarcoma (MRCLS). Pooled data from the Phase 1 (NCT03132922) and Phase 2 (SPEARHEAD-1, NCT04044768) trials of afami-cel showed an acceptable benefit to risk profile with an overall response rate of 36.2% and a median duration of response of 52.0 weeks.1 To support the continued investigation of potential mechanisms of durable anti-tumor activity, we previously showed that afami-cel induces broad and enduring peripheral cytokine responses2 and that afami-cel tumoral infiltration is associated with increased presence of activated and proliferative cytotoxic T-cells in the tumor microenvironment.3 Here, we report the results of translational analyses exploring the cooperation between afami-cel-induced innate and adaptive immune responses pooled from the Phase 1 and 2 trials. Methods included measurement of 92 biomarkers related to apoptosis, chemotaxis, metabolism, tumor immunity promotion/suppression, and vascular/tissue remodeling in pre- and post-infusion serum samples from 38 patients. We also conducted multiplex immunofluorescence and gene set variation analysis of Reactome immune system pathway categories and microenvironment cell populations in RNA sequencing data from pre- and post-infusion biopsies from ≥15 patients. Serum analyses showed that patients with a clinical benefit as defined by RECIST v1.1 had significantly greater post-infusion levels of chemotactic markers (Kruskal-Wallis; p<0.05 for partial response [PR] compared to progressive disease, p<0.01 for PR compared to stable disease), indicating higher signaling related to immune-cell recruitment towards lesions. Tumor analyses showed increased expression of genes associated with innate and adaptive immunity, and cytokine signaling, in post-infusion biopsies, including T-cell receptor signaling-related expression, which was consistent with relatively greater spatial protein detection of pro-immune infiltrate. This profile was associated with longer progression-free survival. In conclusion, our data suggest that afami-cel induces peripheral and tumoral innate and adaptive immune responses, a hallmark of durable anti-tumor activity. Updated patient sample data will be presented. 1. D'Angelo SP, et al. J Clin Oncol. 2022;40:16_suppl:11562. 2. D’Angelo SP, et al. Poster 146 presented at: CTOS 2021; Virtual. 3. Van Tine, BA et al. Paper 61 presented at: CTOS 2022; Vancouver, BC, Canada.
Citation Format: Cheryl McAlpine, Martin Isabelle, Robyn Broad, Revashnee Naidoo, Ashley Liddle, Elizabeth Duperret, Paul Noto, Ruoxi Wang, Dzmitry Batrakou, Sumit Middha, Chris Evans. Afamitresgene autoleucel (afami-cel; formerly ADP-A2M4) demonstrates durable clinical responses by inducing broad immune engagement with anti-tumor activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 892.
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Affiliation(s)
| | | | - Robyn Broad
- 1Adaptimmune, Abingdon, Oxfordshire, United Kingdom
| | | | | | | | | | - Ruoxi Wang
- 1Adaptimmune, Abingdon, Oxfordshire, United Kingdom
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Vanderbilt CM, Bowman AS, Middha S, Petrova-Drus K, Tang YW, Chen X, Wang Y, Chang J, Rekhtman N, Busam KJ, Gupta S, Hameed M, Arcila ME, Ladanyi M, Berger MF, Dogan S, Zehir A. Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data. J Mol Diagn 2022; 24:515-528. [PMID: 35331965 PMCID: PMC9127461 DOI: 10.1016/j.jmoldx.2022.01.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/27/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
This study is the largest analysis of DNA viruses in solid tumors with associated genomics. To achieve this, a novel method for discovery of DNA viruses from matched tumor/normal next-generation sequencing samples was developed and validated. This method performed comparably to reference methods for the detection of high-risk (HR) human papilloma virus (HPV) (area under the receiver operating characteristic curve = 0.953). After virus identification in 48,148 consecutives samples from 42,846 unique patients, novel virus tumor associations were established by segregating tumor types to determine whether each DNA virus was enriched in each of the tumor types compared with the remaining cohort. All firmly established solid tumor-virus associations (eg, HR HPV in cervical cancer) were confirmed, and the novel associations discovered included: human herpes virus 6 in neuroblastoma, human herpes virus 7 in esophagogastric cancer, and HPV42 in digital papillary adenocarcinoma. These associations were confirmed in an independent validation cohort. HR HPV- and Epstein-Barr virus-associated tumors showed newly discovered genomic associations, including a lower tumor mutation burden. The study demonstrated the ability to study the role of DNA viruses in human cancer from clinical genomics data and established the largest cohort that can be utilized as a validation set for future discovery efforts.
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Affiliation(s)
- Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi-Wei Tang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xin Chen
- Atila Biosystems Inc., Mountain View, California
| | | | - Jason Chang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sounak Gupta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Meera Hameed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Gupta S, Vanderbilt CM, Lin YT, Benhamida JK, Jungbluth AA, Rana S, Momeni-Boroujeni A, Chang JC, Mcfarlane T, Salazar P, Mullaney K, Middha S, Zehir A, Gopalan A, Bale TA, Ganly I, Arcila ME, Benayed R, Berger MF, Ladanyi M, Dogan S. A Pan-Cancer Study of Somatic TERT Promoter Mutations and Amplification in 30,773 Tumors Profiled by Clinical Genomic Sequencing. J Mol Diagn 2020; 23:253-263. [PMID: 33285287 DOI: 10.1016/j.jmoldx.2020.11.003] [Citation(s) in RCA: 5] [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] [Received: 06/24/2020] [Revised: 10/15/2020] [Accepted: 11/10/2020] [Indexed: 01/20/2023] Open
Abstract
TERT gene promoter mutations are known in multiple cancer types. Other TERT alterations remain poorly characterized. Sequencing data from 30,773 tumors analyzed by a hybridization capture next-generation sequencing assay (Memorial Sloan Kettering Cancer Center Integrated Mutation Profiling of Actionable Cancer Targets) were analyzed for the presence of TERT alterations. Promoter rearrangements (500 bases upstream of the transcriptional start site), hypermethylation (n = 57), and gene expression (n = 155) were evaluated for a subset of cases. Mutually exclusive and recurrent promoter mutations were identified at three hot spots upstream of the transcriptional start site in 11.3% of cases (-124: 74%; -146: 24%; and -138: <2%). Mutually exclusive amplification events were identified in another 2.3% of cases, whereas mutually exclusive rearrangements proximal to the TERT gene were seen in 24 cases. The highest incidence of TERT promoter mutations was seen in cutaneous melanoma (82%), whereas amplification events significantly outnumbered promoter mutations in well-differentiated/dedifferentiated liposarcoma (14.1% versus 2.4%) and adrenocortical carcinoma (13.6% versus 4.5%). Gene expression analysis suggests that the highest levels of gene expression are seen in cases with amplifications and rearrangements. Hypermethylation events upstream of the TERT coding sequence were not mutually exclusive with known pathogenic alterations. Studies aimed at defining the prevalence and prognostic impact of TERT alterations should incorporate other pathogenic TERT alterations as these may impact telomerase function.
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Affiliation(s)
- Sounak Gupta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yun-Te Lin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Satshil Rana
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tiffany Mcfarlane
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology, 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
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tejus A Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- 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.
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Abida W, Cheng ML, Armenia J, Middha S, Autio KA, Vargas HA, Rathkopf D, Morris MJ, Danila DC, Slovin SF, Carbone E, Barnett ES, Hullings M, Hechtman JF, Zehir A, Shia J, Jonsson P, Stadler ZK, Srinivasan P, Laudone VP, Reuter V, Wolchok JD, Socci ND, Taylor BS, Berger MF, Kantoff PW, Sawyers CL, Schultz N, Solit DB, Gopalan A, Scher HI. Analysis of the Prevalence of Microsatellite Instability in Prostate Cancer and Response to Immune Checkpoint Blockade. JAMA Oncol 2020; 5:471-478. [PMID: 30589920 DOI: 10.1001/jamaoncol.2018.5801] [Citation(s) in RCA: 382] [Impact Index Per Article: 95.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance The anti-programmed cell death protein 1 (PD-1) antibody pembrolizumab is approved by the US Food and Drug Administration for the treatment of microsatellite instability-high (MSI-H) or mismatch repair-deficient (dMMR) solid tumors, but the prevalence of MSI-H/dMMR prostate cancer and the clinical utility of immune checkpoint blockade in this disease subset are unknown. Objective To define the prevalence of MSI-H/dMMR prostate cancer and the clinical benefit of anti-PD-1/programmed cell death 1 ligand 1 (PD-L1) therapy in this molecularly defined population. Design, Setting, and Participants In this case series, 1551 tumors from 1346 patients with prostate cancer undergoing treatment at Memorial Sloan Kettering Cancer Center were prospectively analyzed using a targeted sequencing assay from January 1, 2015, through January 31, 2018. Patients had a diagnosis of prostate cancer and consented to tumor molecular profiling when a tumor biopsy was planned or archival tissue was available. For each patient, clinical outcomes were reported, with follow-up until May 31, 2018. Main Outcomes and Measures Tumor mutation burden and MSIsensor score, a quantitative measure of MSI, were calculated. Mutational signature analysis and immunohistochemistry for MMR protein expression were performed in select cases. Results Among the 1033 patients who had adequate tumor quality for MSIsensor analysis (mean [SD] age, 65.6 [9.3] years), 32 (3.1%) had MSI-H/dMMR prostate cancer. Twenty-three of 1033 patients (2.2%) had tumors with high MSIsensor scores, and an additional 9 had indeterminate scores with evidence of dMMR. Seven of the 32 MSI-H/dMMR patients (21.9%) had a pathogenic germline mutation in a Lynch syndrome-associated gene. Six patients had more than 1 tumor analyzed, 2 of whom displayed an acquired MSI-H phenotype later in their disease course. Eleven patients with MSI-H/dMMR castration-resistant prostate cancer received anti-PD-1/PD-L1 therapy. Six of these (54.5%) had a greater than 50% decline in prostate-specific antigen levels, 4 of whom had radiographic responses. As of May 2018, 5 of the 6 responders (5 of 11 total [45.5%]) were still on therapy for as long as 89 weeks. Conclusions and Relevance The MSI-H/dMMR molecular phenotype is uncommon yet therapeutically meaningful in prostate cancer and can be somatically acquired during disease evolution. Given the potential for durable responses to anti-PD-1/PD-L1 therapy, these findings support the use of prospective tumor sequencing to screen all patients with advanced prostate cancer for MSI-H/dMMR. Because not all patients with the MSI-H/dMMR phenotype respond, further studies should explore mechanisms of resistance.
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Affiliation(s)
- Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen A Autio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael J Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel C Danila
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Susan F Slovin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Carbone
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ethan S Barnett
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melanie Hullings
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, 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.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vincent P Laudone
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Victor Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Bioinformatics Core, 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 and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and 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
| | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, 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 and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Suehara Y, Alex D, Bowman A, Middha S, Zehir A, Chakravarty D, Wang L, Jour G, Nafa K, Hayashi T, Jungbluth AA, Frosina D, Slotkin E, Shukla N, Meyers P, Healey JH, Hameed M, Ladanyi M. Clinical Genomic Sequencing of Pediatric and Adult Osteosarcoma Reveals Distinct Molecular Subsets with Potentially Targetable Alterations. Clin Cancer Res 2019. [PMID: 31175097 DOI: 10.1158/1078‐0432.ccr‐18‐4032] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE Although multimodal chemotherapy has improved outcomes for patients with osteosarcoma, the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of osteosarcoma samples could identify potentially actionable alterations.Experimental Design: We analyzed genomic data from 71 osteosarcoma samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel next-generation sequencing assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which levels 1 to 3 were considered clinically actionable. RESULTS We found at least one potentially actionable alteration in 14 of 66 patients (21%), including amplification of CDK4 (n = 9, 14%: level 2B) and/or MDM2 (n = 9, 14%: level 3B), and somatic truncating mutations/deletions in BRCA2 (n = 3, 5%: level 2B) and PTCH1 (n = 1, level 3B). In addition, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR, and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by IHC. In another largely nonoverlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS We found potentially clinically actionable alterations in approximately 21% of patients with osteosarcoma. In addition, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically based algorithm for directing patients with osteosarcoma to clinical trial options.
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Affiliation(s)
- Yoshiyuki Suehara
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anita Bowman
- Department of Pathology, 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
| | - Debyani Chakravarty
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - George Jour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, 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
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6
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Mandal R, Samstein RM, Lee KW, Havel JJ, Wang H, Krishna C, Sabio EY, Makarov V, Kuo F, Blecua P, Ramaswamy AT, Durham JN, Bartlett B, Ma X, Srivastava R, Middha S, Zehir A, Hechtman JF, Morris LG, Weinhold N, Riaz N, Le DT, Diaz LA, Chan TA. Genetic diversity of tumors with mismatch repair deficiency influences anti-PD-1 immunotherapy response. Science 2019; 364:485-491. [PMID: 31048490 DOI: 10.1126/science.aau0447] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 04/09/2019] [Indexed: 12/12/2022]
Abstract
Tumors with mismatch repair deficiency (MMR-d) are characterized by sequence alterations in microsatellites and can accumulate thousands of mutations. This high mutational burden renders tumors immunogenic and sensitive to programmed cell death-1 (PD-1) immune checkpoint inhibitors. Yet, despite their tumor immunogenicity, patients with MMR-deficient tumors experience highly variable responses, and roughly half are refractory to treatment. We present experimental and clinical evidence showing that the degree of microsatellite instability (MSI) and resultant mutational load, in part, underlies the variable response to PD-1 blockade immunotherapy in MMR-d human and mouse tumors. The extent of response is particularly associated with the accumulation of insertion-deletion (indel) mutational load. This study provides a rationale for the genome-wide characterization of MSI intensity and mutational load to better profile responses to anti-PD-1 immunotherapy across MMR-deficient human cancers.
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Affiliation(s)
- Rajarsi Mandal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD 21287, USA.,Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert M Samstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ken-Wing Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hao Wang
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Erich Y Sabio
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fengshen Kuo
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Pedro Blecua
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Apoorva T Ramaswamy
- Department of Otolaryngology-Head and Neck Surgery, Weill Cornell New York Presbyterian Hospital, New York, NY 10065, USA
| | - Jennifer N Durham
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.,Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA
| | - Bjarne Bartlett
- Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA
| | - Xiaoxiao Ma
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Raghvendra Srivastava
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Luc Gt Morris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dung T Le
- Bloomberg-Kimmel Institute for Cancer Immunotherapy at Johns Hopkins, Baltimore, MD 21287, USA.,Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA.,Swim Across America Laboratory at Johns Hopkins, Baltimore, MD 21287, USA
| | - Luis A Diaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. .,Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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7
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Srinivasan P, Bandlamudi C, Shia J, Latham AS, Jonsson P, Penson A, Middha S, Hechtman J, Zehir A, Richards A, Chawan S, Kemel Y, Mandelker D, Zhang L, Hyman D, Ladanyi M, Robson M, Offit K, Solit D, Taylor B, Berger M, Stadler Z. Abstract 4158: Dissecting the role of zygosity and lineage in Lynch Syndrome-associated microsatellite Instability. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4158] [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
Lynch syndrome (LS) is an inherited condition leading to an increased risk of developing colorectal cancer and other select malignancies. LS patients have germline alterations in mismatch repair (MMR) genes and their tumors often demonstrate microsatellite instability (MSI). With the advent of immune checkpoint blockade, this is of both prognostic and therapeutic significance. Nevertheless, the factors that dictate the presence of the MSI phenotype in tumors diagnosed in LS patients are poorly understood. We integrated germline pathogenicity with somatic alterations in 17,152 prospectively sequenced advanced cancer patients to determine how zygosity and lineage shape the presence and intensity of the somatic MSI phenotype in LS patients. Overall, we identified 117 LS patients (0.68%) with one of 46 distinct cancer types, 111 of which had sufficient purity for somatic assessment. The tumors of 72% (80/111) of these patients had biallelic inactivation of the germline allele as assessed by integrating high-precision mutant allele fractions with allele-specific DNA copy number analysis or, in select low purity tumors, confirmatory immunohistochemistry. Among patients with biallelic inactivation, 73% (58/80) had MSI positive tumors whereas, only 1/31 (3%) of heterozygous tumors were MSI positive, indicating that biallelic inactivation of the germline allele was obligate to drive the somatic MSI phenotype (p-value=5.4e-12). Lineage appears, however, to condition this dependence of MSI status on biallelic inactivation. Leveraging the prevalence of germline MMR mutations in our cohort, zygosity enrichment, and literature curation of MMR penetrance, we classified cancer types as either conventionally Lynch-associated or not. Notably, despite the presence of biallelic inactivation, MSI was not seen in LS patients whose cancers were not conventionally Lynch-associated such as breast, lung, and thyroid cancers among others. The nature and degree of the MSI phenotype also varied as a function of underlying genotype in these patients. Despite comparable mutational burdens, MSH6 germline carriers that were somatic biallelic had lower MSI scores, lower rates of frameshift indels and higher rates of missense mutations than patients with biallelic mutations in other MMR genes. Collectively, these data suggest that the presence of MSI is dictated by lineage-dependent selection for biallelic inactivation in LS tumors, and emerges to differing degrees driven by the underlying genotype, which together has implications for the immunogenicity of resulting tumors and the biomarker of greatest response to immune checkpoint blockade. By expanding our prospective cohort to >30,000 patients with advanced cancer and integrating clinical response to immunotherapy, we will further explore gene-specific variability in MSI patterns observed in LS patients and its effects on outcome and therapeutic response.
Citation Format: Preethi Srinivasan, Chaitanya Bandlamudi, Jinru Shia, Alicia S. Latham, Philip Jonsson, Alexander Penson, Sumit Middha, Jackie Hechtman, Ahmet Zehir, Allison Richards, Shweta Chawan, Yelena Kemel, Diana Mandelker, Liying Zhang, David Hyman, Marc Ladanyi, Mark Robson, Kenneth Offit, David Solit, Barry Taylor, Michael Berger, Zsofia Stadler. Dissecting the role of zygosity and lineage in Lynch Syndrome-associated microsatellite Instability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4158.
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Affiliation(s)
| | | | - Jinru Shia
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Sumit Middha
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Shweta Chawan
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Kemel
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Liying Zhang
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Hyman
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Robson
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Solit
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry Taylor
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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8
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Suehara Y, Alex D, Bowman A, Middha S, Zehir A, Chakravarty D, Wang L, Jour G, Nafa K, Hayashi T, Jungbluth AA, Frosina D, Slotkin E, Shukla N, Meyers P, Healey JH, Hameed M, Ladanyi M. Clinical Genomic Sequencing of Pediatric and Adult Osteosarcoma Reveals Distinct Molecular Subsets with Potentially Targetable Alterations. Clin Cancer Res 2019; 25:6346-6356. [PMID: 31175097 DOI: 10.1158/1078-0432.ccr-18-4032] [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: 12/12/2018] [Revised: 04/25/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Although multimodal chemotherapy has improved outcomes for patients with osteosarcoma, the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of osteosarcoma samples could identify potentially actionable alterations.Experimental Design: We analyzed genomic data from 71 osteosarcoma samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel next-generation sequencing assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which levels 1 to 3 were considered clinically actionable. RESULTS We found at least one potentially actionable alteration in 14 of 66 patients (21%), including amplification of CDK4 (n = 9, 14%: level 2B) and/or MDM2 (n = 9, 14%: level 3B), and somatic truncating mutations/deletions in BRCA2 (n = 3, 5%: level 2B) and PTCH1 (n = 1, level 3B). In addition, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR, and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by IHC. In another largely nonoverlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS We found potentially clinically actionable alterations in approximately 21% of patients with osteosarcoma. In addition, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically based algorithm for directing patients with osteosarcoma to clinical trial options.
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Affiliation(s)
- Yoshiyuki Suehara
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anita Bowman
- Department of Pathology, 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
| | - Debyani Chakravarty
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - George Jour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, 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
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9
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Dogan S, Xu B, Middha S, Vanderbilt CM, Bowman AS, Migliacci J, Morris LGT, Seshan VE, Ganly I. Identification of prognostic molecular biomarkers in 157 HPV-positive and HPV-negative squamous cell carcinomas of the oropharynx. Int J Cancer 2019; 145:3152-3162. [PMID: 31093971 DOI: 10.1002/ijc.32412] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/23/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
The incidence of oropharyngeal squamous cell carcinoma (OPSCC) has been increasing due to high-risk HPV infection. We explored the significance of genetic alterations in HPV-positive (HPV-P) and HPV-negative (HPV-N) OPSCC patients on long-term outcome. A total of 157 cases of primary resected OPSCC diagnosed from 1978 to 2005 were subjected to a targeted exome sequencing by MSK-IMPACT™ interrogating somatic mutations in 410 cancer-related genes. Mutational profiles were correlated to recurrence and survival outcomes. OPSCC included 47% HPV-positive (HPV-P) and 53% HPV-negative (HPV-N) tumors arising in the base of tongue (BOT, 43%), palatine tonsil (30%) and soft palate (SP, 27%). HPV negative status, SP location and smoking were associated with poorer outcome. Poorer overall survival was found in NOTCH1-mutated HPV-P (p = 0.039), and in SOX2-amplified HPV-N cases (p = 0.036). Chromosomal arm gains in 8p and 8q, and 16q loss were more common in HPV-P (p = 0.005, 0.04 and 0.01, respectively), while 9p, 18q and 21q losses were more frequent in HPV-N OPSCC (p = 0.006, 0.002 and 0.01, respectively). Novel, potentially functional JAK3, MYC and EP300 intragenic deletions were found in HPV-P, and FOXP1, CDKN2A, CCND1 and RUNX1 intragenic deletions and one FGFR3 inversion were detected in HPV-N tumors. HPV-N/TP53-wild-type OPSCC harbored recurrent mutations in NOTCH1/3/4 (39%), PIK3CA, FAT1 and TERT. In comparison to their oral and laryngeal counterparts, HPV-N OPSCC were genetically distinct. In OPSCC, HPV status, tumor subsite and smoking determine outcome. Risk-stratification can be further refined based on the mutational signature, namely, NOTCH1 and SOX2 mutation status.
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Affiliation(s)
- Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jocelyn Migliacci
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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10
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Xu B, Reznik E, Tuttle RM, Knauf J, Fagin JA, Katabi N, Dogan S, Aleynick N, Seshan V, Middha S, Enepekides D, Casadei GP, Solaroli E, Tallini G, Ghossein R, Ganly I. Outcome and molecular characteristics of non-invasive encapsulated follicular variant of papillary thyroid carcinoma with oncocytic features. Endocrine 2019; 64:97-108. [PMID: 30689169 PMCID: PMC6657696 DOI: 10.1007/s12020-019-01848-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 12/10/2018] [Accepted: 01/17/2019] [Indexed: 02/01/2023]
Abstract
PURPOSE In 2016, non-invasive encapsulated follicular variant of papillary thyroid carcinoma (NI-EFVPTC) was renamed as noninvasive thyroid follicular neoplasm with papillary-like nuclear features (NIFTP). However, as the study cohort did not mention tumors with oncocytic features, such lesions are still labeled by some as FVPTC. It is therefore crucial to evaluate the outcome and molecular profile of oncocytic NI-EFVPTC. METHODS A multi-institutional clinico-pathologic review was conducted to select 61 patients having oncocytic NI-EFVPTC. A detailed molecular profile was carried out in 15 patients. RESULTS Oncocytic NI-EFVPTCs predominantly affected women in their 50s. There was no distant metastasis, lymph node metastases, or structural recurrence in the entire cohort. Among patients with ≥5 years of FU, all 33 individuals did not recur with a median FU of 10.2 years. Oncocytic NI-EFVPTC commonly had RAS (33%) mutations, a high frequency of mitochondrial DNA mutations (67%) and multiple chromosomal gains/losses (53%). No fusion genes were detected. CONCLUSIONS Oncocytic NI-EFVPTC, when stringently selected for, lacks metastasis at presentation and follows an extremely indolent clinical course, even when treated conservatively with lobectomy alone without RAI therapy. These tumors share a similar mutational profile as NIFTP, FVPTC, and follicular neoplasm and are predominantly RAS-related. Like Hurthle cell neoplasms, they harbor a high frequency of mitochondrial DNA mutations, which contribute to the oncocytic cytomorphology. However, they lack the widespread chromosomal alterations observed in Hurthle cell carcinoma. Consideration should be given to include oncocytic NI-EFVPTCs as NIFTP in order to avoid overtreatment of these highly indolent tumors.
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Affiliation(s)
- Bin Xu
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - R Michael Tuttle
- Department of Medicine, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Jeffrey Knauf
- Department of Medicine, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - James A Fagin
- Department of Medicine, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Nathaniel Aleynick
- Department of Pathology, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer center, New York, NY, USA
| | - Danny Enepekides
- Department of Otolaryngology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | | | | | - Giovanni Tallini
- Department of Experimental, Diagnostic and Specialty Medicine-Anatomic Pathology, University of Bologna School of Medicine, Bologna, Italy
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer center, New York, NY, USA.
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer center, New York, NY, USA.
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11
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Middha S, Yaeger R, Shia J, Stadler ZK, King S, Guercio S, Paroder V, Bates DDB, Rana S, Diaz LA, Saltz L, Segal N, Ladanyi M, Zehir A, Hechtman JF. Majority of B2M-Mutant and -Deficient Colorectal Carcinomas Achieve Clinical Benefit From Immune Checkpoint Inhibitor Therapy and Are Microsatellite Instability-High. JCO Precis Oncol 2019; 3. [PMID: 31008436 DOI: 10.1200/po.18.00321] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Microsatellite instability-high (MSI-H) colorectal carcinomas (CRCs) show high rates of response to immune checkpoint inhibitors (IOs). B2M mutations and protein loss have been proposed as causes of resistance to IOs, yet they are enriched in MSI-H CRC. We aimed to characterize B2M-mutant, IO-naive CRC. PATIENTS AND METHODS All CRCs with results for Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets, a next-generation sequencing assay that interrogates > 400 genes for mutations as well as MSI status, were surveyed for B2M mutations. All B2M-mutant CRCs were assessed for expression of B2M, major histocompatibility complex class I, and programmed death-1 ligand (PD-L1) via immunohistochemistry and average CD3+ and CD8+ tumor-infiltrating lymphocyte counts against a control group of MSI-H B2M wild-type CRCs. RESULTS Fifty-nine (3.4%) of 1,751 patients with CRC harbored B2M mutations, with 84% (77 of 92) of the mutations predicted to be truncating. B2M mutations were significantly enriched in MSI-H CRCs, with 44 (24%) of 182 MSI-H CRCs harboring B2M mutations (P < .001). Thirty-two of 44 B2M-mutant CRCs with available material (73%) had complete loss of B2M expression, whereas all 26 CRCs with wild-type B2M retained expression (P < .001). B2M mutation status was not associated with major histocompatibility complex class I expression, KRAS or BRAF mutation, tumor-infiltrating lymphocyte level, or PD-L1 expression after adjustment for MSI status. Of 13 patients with B2M-mutant CRC who received programmed death-1 or PD-L1 IOs, 11 (85%) achieved clinical benefit, defined as stable disease or partial response using Response Evaluation Criteria in Solid Tumors criteria. CONCLUSION B2M mutations occur in approximately 24% of MSI-H CRCs and are usually associated with loss of B2M expression. Most patients with B2M-mutant MSI-H CRC with loss of protein expression obtain clinical benefit from IOs.
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Affiliation(s)
- Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sarah King
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Satshil Rana
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luis A Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Leonard Saltz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neil Segal
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
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12
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Cocco E, Benhamida J, Middha S, Zehir A, Mullaney K, Shia J, Yaeger R, Zhang L, Wong D, Villafania L, Nafa K, Scaltriti M, Drilon A, Saltz L, Schram AM, Stadler ZK, Hyman DM, Benayed R, Ladanyi M, Hechtman JF. Colorectal Carcinomas Containing Hypermethylated MLH1 Promoter and Wild-Type BRAF/KRAS Are Enriched for Targetable Kinase Fusions. Cancer Res 2019; 79:1047-1053. [PMID: 30643016 DOI: 10.1158/0008-5472.can-18-3126] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/16/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023]
Abstract
Kinase fusions are rare and poorly characterized in colorectal carcinoma, yet they present unique opportunities for targeted therapy. In this study, we characterized kinase fusions from patients with advanced colorectal carcinoma who had MSK-IMPACT testing of their tumors between January 2014 and June 2018. Patients were analyzed for the presence of fusions, microsatellite instability (MSI), and RAS/BRAF mutations. Mismatch repair (MMR), IHC, and promoter hypermethylation status of MLH1 (MLH1ph) in microsatellite instability-high (MSI-H) colorectal carcinoma with fusions were investigated. Fusion transcripts were confirmed using a targeted RNA-seq panel assay. Of 2,314 colorectal carcinomas with MSK-IMPACT testing, 21 harbored kinase fusions. Overall 57% (12/21) of colorectal carcinoma fusions were MSI-H/MMR-D. Loss of MLH1 and MLH1ph was confirmed in all 12 and all 10 cases with available material, respectively. Fusions were present in 5% of MSI-H/MMR-D colorectal carcinoma compared with 0.4% of MSS/MMR-P colorectal carcinoma (P < 0.001) and 15% of MSI-H/MMR-D colorectal carcinoma with wild-type RAS/BRAF. Of 24 total MLH1-deficient colorectal carcinomas with MLH1ph and wild-type RAS/BRAF, 10 (42%) harbored kinase fusions. Kinase fusions in MSI-H colorectal carcinoma were associated with sporadic MLH1ph rather than with Lynch syndrome, and these patients may be eligible for kinase inhibitors, particularly following resistance or toxicity in response to immunotherapy. These findings identify a molecular subset of colorectal carcinoma with kinase fusions that may be responsive to kinase inhibitors.Significance: A high frequency of targetable kinase fusions in BRAF/RAS wild-type, MSI-H colorectal carcinoma offers a rationale for routine screening to identify patients with colorectal carcinoma with kinase fusions that may be responsive to kinase inhibitors.See related commentary by Valeri, p. 1041.
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Affiliation(s)
- Emiliano Cocco
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Department of Pathology, 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
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Donna Wong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liliana Villafania
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maurizio Scaltriti
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Leonard Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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13
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Hechtman JF, Middha S, Stadler ZK, Zehir A, Berger MF, Vakiani E, Weiser MR, Ladanyi M, Saltz LB, Klimstra DS, Shia J. Universal screening for microsatellite instability in colorectal cancer in the clinical genomics era: new recommendations, methods, and considerations. Fam Cancer 2018; 16:525-529. [PMID: 28405781 DOI: 10.1007/s10689-017-9993-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
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14
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Latham A, Srinivasan P, Kemel Y, Shia J, Bandlamudi C, Mandelker D, Middha S, Hechtman J, Zehir A, Dubard-Gault M, Tran C, Stewart C, Sheehan M, Penson A, DeLair D, Yaeger R, Vijai J, Mukherjee S, Galle J, Dickson MA, Janjigian Y, O'Reilly EM, Segal N, Saltz LB, Reidy-Lagunes D, Varghese AM, Bajorin D, Carlo MI, Cadoo K, Walsh MF, Weiser M, Aguilar JG, Klimstra DS, Diaz LA, Baselga J, Zhang L, Ladanyi M, Hyman DM, Solit DB, Robson ME, Taylor BS, Offit K, Berger MF, Stadler ZK. Microsatellite Instability Is Associated With the Presence of Lynch Syndrome Pan-Cancer. J Clin Oncol 2018; 37:286-295. [PMID: 30376427 DOI: 10.1200/jco.18.00283] [Citation(s) in RCA: 358] [Impact Index Per Article: 59.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Microsatellite instability (MSI) and/or mismatch repair deficiency (MMR-D) testing has traditionally been performed in patients with colorectal (CRC) and endometrial cancer (EC) to screen for Lynch syndrome (LS)-associated cancer predisposition. The recent success of immunotherapy in high-frequency MSI (MSI-H) and/or MMR-D tumors now supports testing for MSI in all advanced solid tumors. The extent to which LS accounts for MSI-H across heterogeneous tumor types is unknown. Here, we establish the prevalence of LS across solid tumors according to MSI status. METHODS MSI status was determined using targeted next-generation sequencing, with tumors classified as MSI-H, MSI-indeterminate, or microsatellite-stable. Matched germline DNA was analyzed for mutations in LS-associated mismatch repair genes ( MLH1, MSH2, MSH6, PMS2, EPCAM). In patients with LS with MSI-H/I tumors, immunohistochemical staining for MMR-D was assessed. RESULTS Among 15,045 unique patients (more than 50 cancer types), LS was identified in 16.3% (53 of 326), 1.9% (13 of 699), and 0.3% (37 of 14,020) of patients with MSI-H, MSI-indeterminate, and microsatellite-stable tumors, respectively ( P < .001). Among patients with LS with MSI-H/I tumors, 50% (33 of 66) had tumors other than CRC/EC, including urothelial, prostate, pancreas, adrenocortical, small bowel, sarcoma, mesothelioma, melanoma, gastric, and germ cell tumors. In these patients with non-CRC/EC tumors, 45% (15 of 33) did not meet LS genetic testing criteria on the basis of personal/family history. Immunohistochemical staining of LS-positive MSI-H/I tumors demonstrated MMR-D in 98.2% (56 of 57) of available cases. CONCLUSION MSI-H/MMR-D is predictive of LS across a much broader tumor spectrum than currently appreciated. Given implications for cancer surveillance and prevention measures in affected families, these data support germline genetic assessment for LS for patients with an MSI-H/MMR-D tumor, regardless of cancer type or family cancer history.
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Affiliation(s)
- Alicia Latham
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Yelena Kemel
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Sumit Middha
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Rona Yaeger
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Joseph Vijai
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jesse Galle
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark A Dickson
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Yelena Janjigian
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Eileen M O'Reilly
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Neil Segal
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Leonard B Saltz
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Diane Reidy-Lagunes
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Anna M Varghese
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Dean Bajorin
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Maria I Carlo
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Karen Cadoo
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Michael F Walsh
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Martin Weiser
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Julio Garcia Aguilar
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | | | - Luis A Diaz
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Jose Baselga
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Liying Zhang
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M Hyman
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - David B Solit
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Mark E Robson
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | | | - Kenneth Offit
- 1 Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
| | - Zsofia K Stadler
- 1 Memorial Sloan Kettering Cancer Center, New York, NY.,2 Weill Cornell Medical College, New York, NY
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15
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Razavi P, Chang MT, Xu G, Bandlamudi C, Ross DS, Vasan N, Cai Y, Bielski CM, Donoghue MTA, Jonsson P, Penson A, Shen R, Pareja F, Kundra R, Middha S, Cheng ML, Zehir A, Kandoth C, Patel R, Huberman K, Smyth LM, Jhaveri K, Modi S, Traina TA, Dang C, Zhang W, Weigelt B, Li BT, Ladanyi M, Hyman DM, Schultz N, Robson ME, Hudis C, Brogi E, Viale A, Norton L, Dickler MN, Berger MF, Iacobuzio-Donahue CA, Chandarlapaty S, Scaltriti M, Reis-Filho JS, Solit DB, Taylor BS, Baselga J. The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers. Cancer Cell 2018; 34:427-438.e6. [PMID: 30205045 PMCID: PMC6327853 DOI: 10.1016/j.ccell.2018.08.008] [Citation(s) in RCA: 568] [Impact Index Per Article: 94.7] [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: 12/11/2017] [Revised: 07/15/2018] [Accepted: 08/09/2018] [Indexed: 02/06/2023]
Abstract
We integrated the genomic sequencing of 1,918 breast cancers, including 1,501 hormone receptor-positive tumors, with detailed clinical information and treatment outcomes. In 692 tumors previously exposed to hormonal therapy, we identified an increased number of alterations in genes involved in the mitogen-activated protein kinase (MAPK) pathway and in the estrogen receptor transcriptional machinery. Activating ERBB2 mutations and NF1 loss-of-function mutations were more than twice as common in endocrine resistant tumors. Alterations in other MAPK pathway genes (EGFR, KRAS, among others) and estrogen receptor transcriptional regulators (MYC, CTCF, FOXA1, and TBX3) were also enriched. Altogether, these alterations were present in 22% of tumors, mutually exclusive with ESR1 mutations, and associated with a shorter duration of response to subsequent hormonal therapies.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Antineoplastic Agents, Hormonal/pharmacology
- Antineoplastic Agents, Hormonal/therapeutic use
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms, Male/drug therapy
- Breast Neoplasms, Male/genetics
- Breast Neoplasms, Male/pathology
- Drug Resistance, Neoplasm/genetics
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression Regulation, Neoplastic
- Genomics
- Humans
- MAP Kinase Signaling System/genetics
- Male
- Middle Aged
- Mutation
- Neurofibromin 1/genetics
- Neurofibromin 1/metabolism
- Prospective Studies
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
- Young Adult
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Affiliation(s)
- Pedram Razavi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Guotai Xu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Neil Vasan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanyan Cai
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Craig M Bielski
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, 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
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alexander Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Fresia Pareja
- Department of Pathology, 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
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, 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
| | - Ruchi Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lillian M Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Komal Jhaveri
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shanu Modi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tiffany A Traina
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chau Dang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wen Zhang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department 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
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, 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
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Clifford Hudis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Edi Brogi
- Department of Pathology, 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
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maura N Dickler
- Department of Medicine, 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; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge S Reis-Filho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; 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.
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Epidemiology and Biostatistics, 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.
| | - José Baselga
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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16
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Hechtman JF, Abou-Alfa GK, Stadler ZK, Mandelker DL, Roehrl MHA, Zehir A, Vakiani E, Middha S, Klimstra DS, Shia J. Somatic HNF1A mutations in the malignant transformation of hepatocellular adenomas: a retrospective analysis of data from MSK-IMPACT and TCGA. Hum Pathol 2018; 83:1-6. [PMID: 30121369 DOI: 10.1016/j.humpath.2018.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023]
Abstract
Mutations of Hepatocyte-Nuclear-Factor-1-Homeobox-A (HNF1A) gene and loss of Liver-Fatty-Acid-Binding-Protein (LFABP) are well documented in hepatocellular adenoma. However, the role of HNF1A mutations in hepatocellular carcinoma remains to be determined. In this study, all hepatocellular neoplasms evaluated by our institutional Memorial Sloan Kettering-Integrated Mutational Profiling of Actionable Clinical Targets assay or the Cancer Genome Atlas sequencing, and cases reported in the literature, were queried for HNF1A mutations. Together, 11 of 672 (1.6%) hepatocellular carcinomas harbored HNF1A mutations. The single case from our institution (n = 153) was extremely well differentiated, arising in a background of adenomatosis. Both the adenoma and carcinoma component contained the same 2 somatic HNF1A mutations (p. E32* and L214Q), with loss of LFABP. From the literature, 2 of 146 (1.4%) hepatocellular carcinomas had HNF1A mutations, and both arose in a background of adenomatosis. Information on pre-existing adenoma for the remaining cases (8/373, from The Cancer Genome Atlas) was not available. HNF1A mutations in carcinomas were associated with negative viral hepatitis status (p = .004), mutually exclusive with catenin beta-1 (CTNNB1) hotspot mutations, and trended to occur more in females (p = .06) and without cirrhosis (p = .03). Grade was not associated with HNF1A status (p = .28). Somatic HNF1A mutations occur in approximately 1% to 2% of hepatocellular carcinoma, often in a background of adenomatosis. Our findings suggest that malignant transformation of HNF1A-mutated hepatocellular adenoma occurs, albeit infrequently. Hepatocellular adenomas with HNF1A mutation or adenomatosis with loss of LFABP warrant thorough sampling and examination.
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Affiliation(s)
- Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Diana L Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michael H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Weill Cornell Medical College, New York, NY 10065, USA.
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17
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Soumerai TE, Donoghue MTA, Bandlamudi C, Srinivasan P, Chang MT, Zamarin D, Cadoo KA, Grisham RN, O'Cearbhaill RE, Tew WP, Konner JA, Hensley ML, Makker V, Sabbatini P, Spriggs DR, Troso-Sandoval TA, Charen AS, Friedman C, Gorsky M, Schweber SJ, Middha S, Murali R, Chiang S, Park KJ, Soslow RA, Ladanyi M, Li BT, Mueller J, Weigelt B, Zehir A, Berger MF, Abu-Rustum NR, Aghajanian C, DeLair DF, Solit DB, Taylor BS, Hyman DM. Clinical Utility of Prospective Molecular Characterization in Advanced Endometrial Cancer. Clin Cancer Res 2018; 24:5939-5947. [PMID: 30068706 DOI: 10.1158/1078-0432.ccr-18-0412] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/18/2018] [Accepted: 07/25/2018] [Indexed: 01/22/2023]
Abstract
PURPOSE Advanced-stage endometrial cancers have limited treatment options and poor prognosis, highlighting the need to understand genetic drivers of therapeutic vulnerabilities and/or prognostic predictors. We examined whether prospective molecular characterization of recurrent and metastatic disease can reveal grade and histology-specific differences, facilitating enrollment onto clinical trials. EXPERIMENTAL DESIGN We integrated prospective clinical sequencing and IHC data with detailed clinical and treatment histories for 197 tumors, profiled by MSK-IMPACT from 189 patients treated at Memorial Sloan Kettering Cancer Center. RESULTS Patients had advanced disease and high-grade histologies, with poor progression-free survival on first-line therapy (PFS1). When matched for histology and grade, the genomic landscape was similar to that of primary untreated disease profiled by TCGA. Using multiple complementary genomic and mutational signature-based methods, we identified patients with microsatellite instability (MSI), even when standard MMR protein IHC staining failed. Tumor and matched normal DNA sequencing identified rare pathogenic germline mutations in BRCA2 and MLH1. Clustering the pattern of DNA copy-number alterations revealed a novel subset characterized by heterozygous losses across the genome and significantly worse outcomes compared with other clusters (median PFS1 9.6 months vs. 17.0 and 17.4 months; P = 0.006). Of the 68% of patients harboring potentially actionable mutations, 27% were enrolled to matched clinical trials, of which 47% of these achieved clinical benefit. CONCLUSIONS Prospective clinical sequencing of advanced endometrial cancer can help refine prognosis and aid treatment decision making by simultaneously detecting microsatellite status, germline predisposition syndromes, and potentially actionable mutations. A small overall proportion of all patients tested received investigational, genomically matched therapy as part of clinical trials.
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Affiliation(s)
- Tara E Soumerai
- 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
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Preethi Srinivasan
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill-Cornell Medical College, Cornell University, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen A Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Rachel N Grisham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Roisin E O'Cearbhaill
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - William P Tew
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Jason A Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Martee L Hensley
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Vicky Makker
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Paul Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - David R Spriggs
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Tiffany A Troso-Sandoval
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | | | - Claire Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Mila Gorsky
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Sarah J Schweber
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Jennifer Mueller
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- 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
| | - Michael F Berger
- Marie-Josée and 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
| | - Nadeem R Abu-Rustum
- Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Deborah F DeLair
- Department of Pathology, 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.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée and 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
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
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18
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Srinivasan P, Tran C, Reichel J, Patel JA, Hasan M, Meng F, Jing X, Middha S, Zehir A, Yaeger RD, Reidy D, Tsui D, Stadler Z, Berger MF. Abstract 3656: Detecting MSI in plasma: Implications for early detection of lynch associated tumors. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3656] [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: 11/16/2022]
Abstract
Abstract
Lynch Syndrome (LS) is characterized by germline mutations in mismatch repair pathway genes. The increased cancer susceptibility risk in these patients and the association of these tumors with microsatellite instability (MSI) provides a transformative opportunity for early detection of cancer in these patients. The presence of microsatellite unstable DNA fragments or zygosity changes of the MMR mutations in the plasma of LS patients is predictive of the presence of cancer. Here we describe an approach to detect MSI from plasma cell-free DNA (cfDNA) of LS associated cancer patients. First, to determine the background rate of MSI in cfDNA of microsatellite stable patients, we screened plasma samples collected from a large number of advanced cancer patients using MSK-IMPACT, a custom sequencing assay targeting 468 cancer genes encompassing ~1.5 megabases. MSK-IMPACT is approved by the NYS Department of Health and authorized by the FDA for clinical testing, including MSI assessment based on more than 1,000 microsatellite regions covered by the assay, and has been used to profile more than 20,000 patients at our institution. We were also able to confirm the ability to detect MSI in cfDNA in a small cohort of plasma samples collected from patients with MSI High tumors, and determine thresholds to delineate MSI from MSS cases from plasma. Using MSK-IMPACT, we detected MSI in the plasma of four patients with advanced MSI-H cancer, including one with confirmed LS. Three of these were patients with confirmed MSI signature from tumor tissue (one prostate cancer and two colorectal cancers. The fourth patient with prostate cancer had no tissue available for sequencing, though MSI was independently confirmed. To improve the sensitivity to detect MSI in patients with earlier stage disease where the fraction of tumor-derived cfDNA is lower, we have developed a novel targeted panel with optimized sequencing process and informatics, incorporating a set of highly informative microsatellite regions as well as SNPs to assess tumor-specific zygosity changes in mismatch repairs pathway genes. Through this work, we demonstrate the ability of our assay to detect MSI in plasma cfDNA with high sensitivity.
Citation Format: Preethi Srinivasan, Christina Tran, Jonathan Reichel, Juber Ahamad Patel, Maysun Hasan, Fanli Meng, Xiaohong Jing, Sumit Middha, Ahmet Zehir, Rona D. Yaeger, Diane Reidy, Dana Tsui, Zsofia Stadler, Michael F. Berger. Detecting MSI in plasma: Implications for early detection of lynch associated tumors [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 3656.
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Affiliation(s)
| | | | | | | | - Maysun Hasan
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fanli Meng
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Xiaohong Jing
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Diane Reidy
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana Tsui
- Memorial Sloan Kettering Cancer Center, New York, NY
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19
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Latham Schwark A, Srinivasan P, Kemel Y, Shia J, Bandlamudi C, Mandelker D, Dubard-Gault M, Tran C, Middha S, Hechtman JF, Penson A, Varghese AM, Zhang L, Robson ME, Solit DB, Diaz LA, Taylor BS, Offit K, Berger MF, Stadler ZK. Pan-cancer microsatellite instability to predict for presence of Lynch syndrome. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.18_suppl.lba1509] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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
LBA1509 Background: The success of immunotherapy in microsatellite unstable (MSI-H) and/or DNA mismatch repair deficient (MMR-D) tumors has resulted in routine MSI-H/MMR-D testing in advanced solid tumors. Unlike colorectal (CRC) and endometrial cancer (EC), where this has long been undertaken, the characterization of Lynch syndrome (LS) across heterogeneous MSI-H/MMR-D tumors is unknown. Methods: Through a targeted NGS panel, MSI status was determined via MSIsensor. Scores of < 3, ≥3 to < 10, or ≥10 designated Microsatellite stable (MSS), MSI-Indeterminate (MSI-I) or MSI-H status, respectively. Germline mutations were assessed in MLH1, MSH2, MSH6, PMS2, EPCAM. Immunohistochemical staining (IHC) for MMR-D and tumor signatures in LS patients were assessed. Clinical variables were correlated with MSI and compared via Chi square or T-test. Results: Of 15,045 tumors spanning > 50 cancers , 93.2% were MSS, 4.6% MSI-I, and 2.2% MSI-H. Germline mutations were identified in 0.3% (37/14,020), 1.9% (13/699), and 16.3% (53/326) in the MSS, MSI-I, and MSI-H groups, respectively (p-value < 0.001). 25% of 1,025 MSI-H/MSI-I tumors were CRC/EC, but 50% (33/66) of LS patients had MSI-H/MSI-I tumors less commonly or not previously associated with LS (mesothelioma, sarcoma, adrenocortical, melanoma, ovarian germ cell). LS pts with MSI-H/MSI-I non-CRC/EC tumors only met testing criteria in 63.6% of cases, had lower MSIsensor scores, and were more likely to be MSI-I (MSI-I: non-CRC/EC, 30.3% (10/33) vs CRC/EC 9.1% (3/33); p-value = 0.03). IHC was completed in 86.4% (57/66) of LS MSI-H/MSI-I tumors, with 98.3% MMR-D-concordance. Of LS pts with MSS tumors, 78% had MSH6/PMS2 mutations, but 71% of LS pts with MSI-H/MSI-I tumors had MLH1/MSH2/EPCAM mutations(p-value < 0.001). 89% (33/37) of MSS tumors of LS pts had non-MMR-D signatures. Conclusions: MSI-H/MMR-D is predictive of LS across tumor types and suggests a more heterogeneous spectrum of LS-associated cancers than previously appreciated. Nearly 40% of LS pts with MSI-H/MMR-D non-CRC/EC tumors did not meet clinical criteria for genetic testing, suggesting that MSI-H/MMR-D tumors, regardless of cancer type or family history, should prompt germline testing for the evaluation of LS.
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Affiliation(s)
| | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Luis A. Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
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20
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Abida W, Cheng ML, Armenia J, Middha S, Autio KA, Rathkopf DE, Morris MJ, Danila DC, Slovin SF, Carbone E, Hullings M, Hechtman JF, Reuter VE, Berger MF, Kantoff PW, Sawyers CL, Schultz N, Solit DB, Gopalan A, Scher HI. Microsatellite instability in prostate cancer and response to immune checkpoint blockade. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.5020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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)
- Wassim Abida
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Emily Carbone
- Memorial Sloan Kettering Cancer Center, New York, NY
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21
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Karyadi DM, Geybels MS, Karlins E, Decker B, McIntosh L, Hutchinson A, Kolb S, McDonnell SK, Hicks B, Middha S, FitzGerald LM, DeRycke MS, Yeager M, Schaid DJ, Chanock SJ, Thibodeau SN, Berndt SI, Stanford JL, Ostrander EA. Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes. Oncotarget 2018; 8:1495-1507. [PMID: 27902461 PMCID: PMC5341753 DOI: 10.18632/oncotarget.13646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 09/20/2016] [Accepted: 11/07/2016] [Indexed: 12/30/2022] Open
Abstract
Prostate cancer (PCa) susceptibility is defined by a continuum from rare, high-penetrance to common, low-penetrance alleles. Research to date has concentrated on identification of variants at the ends of that continuum. Taking an alternate approach, we focused on the important but elusive class of low-frequency, moderately penetrant variants by performing disease model-based variant filtering of whole exome sequence data from 75 hereditary PCa families. Analysis of 341 candidate risk variants identified nine variants significantly associated with increased PCa risk in a population-based, case-control study of 2,495 men. In an independent nested case-control study of 7,121 men, there was risk association evidence for TANGO2 p.Ser17Ter and the established HOXB13 p.Gly84Glu variant. Meta-analysis combining the case-control studies identified two additional variants suggestively associated with risk, OR5H14 p.Met59Val and CHAD p.Ala342Asp. The TANGO2 and HOXB13 variants co-occurred in cases more often than expected by chance and never in controls. Finally, TANGO2 p.Ser17Ter was associated with aggressive disease in both case-control studies separately. Our analyses identified three new PCa susceptibility alleles in the TANGO2, OR5H14 and CHAD genes that not only segregate in multiple high-risk families but are also of importance in altering disease risk for men from the general population. This is the first successful study to utilize sequencing in high-risk families for the express purpose of identifying low-frequency, moderately penetrant PCa risk mutations.
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Affiliation(s)
- Danielle M Karyadi
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Milan S Geybels
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric Karlins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.,Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brennan Decker
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Laura McIntosh
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Suzanne Kolb
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sumit Middha
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Melissa S DeRycke
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stephen N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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22
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Javier BM, Yaeger R, Wang L, Sanchez-Vega F, Zehir A, Middha S, Sadowska J, Vakiani E, Shia J, Klimstra D, Ladanyi M, Iacobuzio-Donahue CA, Hechtman JF. Recurrent, truncating SOX9 mutations are associated with SOX9 overexpression, KRAS mutation, and TP53 wild type status in colorectal carcinoma. Oncotarget 2018; 7:50875-50882. [PMID: 27248473 PMCID: PMC5239443 DOI: 10.18632/oncotarget.9682] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 04/26/2016] [Accepted: 05/22/2016] [Indexed: 11/25/2022] Open
Abstract
PURPOSE The extent to which the developmental transcription factor SOX9 functions as an oncogene or tumor suppressor in colorectal carcinoma (CRC) is debatable. We aimed to clarify the effect of SOX9 mutations on SOX9 protein expression and their association with known molecular subtypes and clinical characteristics in advanced CRC. EXPERIMENTAL DESIGN Next generation sequencing data (MSK-IMPACT) from CRC patients was used to interrogate SOX9, KRAS, NRAS, BRAF, TP53, APC, and PIK3CA. Mutant and wild type (WT) SOX9 cases underwent immunohistochemical (IHC) staining to assess protein expression. SOX9 allele-specific copy number was assessed by Affymetrix Oncoscan array. RESULTS SOX9 was mutated in 38 of 353 (10.7%) CRC, of which 82% were frameshift or nonsense. Compared to SOX9 WT, SOX9 mutation was strongly associated with coexistent mutant KRAS (p=0.0001) and WT TP53 (p=0.0004). SOX9 was overexpressed in both SOX9 mutant and WT CRC. Among SOX9 mutants, the highest expression was noted for truncating exon 3 mutants (mean H scores 239±105 versus 147±119, p value=0.02). Further, SOX9 truncating mutants with loss of the WT allele demonstrated protein overexpression indicating the WT protein was not required for protein stabilization. CONCLUSIONS SOX9 is overexpressed in CRC, including those with recurrent distal truncating mutations. The latter has structural similarity to the oncogenic isoform MiniSOX9, which is distally truncated due to aberrant splicing. This information suggests that truncated SOX9 has oncogenic features. SOX9 mutations are highly enriched in KRAS mutant and TP53 wild type CRC; and may provide a therapeutic target in approximately 11% of CRC.
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Affiliation(s)
- Breanna M Javier
- 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
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lu Wang
- 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
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justyna Sadowska
- 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
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Klimstra
- 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.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- 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
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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23
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Scheid AD, Van Keulen VP, Felts SJ, Neier SC, Middha S, Nair AA, Techentin RW, Gilbert BK, Jen J, Neuhauser C, Zhang Y, Pease LR. Gene Expression Signatures Characterized by Longitudinal Stability and Interindividual Variability Delineate Baseline Phenotypic Groups with Distinct Responses to Immune Stimulation. J Immunol 2018; 200:1917-1928. [PMID: 29352003 DOI: 10.4049/jimmunol.1701099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/12/2017] [Indexed: 11/19/2022]
Abstract
Human immunity exhibits remarkable heterogeneity among individuals, which engenders variable responses to immune perturbations in human populations. Population studies reveal that, in addition to interindividual heterogeneity, systemic immune signatures display longitudinal stability within individuals, and these signatures may reliably dictate how given individuals respond to immune perturbations. We hypothesize that analyzing relationships among these signatures at the population level may uncover baseline immune phenotypes that correspond with response outcomes to immune stimuli. To test this, we quantified global gene expression in peripheral blood CD4+ cells from healthy individuals at baseline and following CD3/CD28 stimulation at two time points 1 mo apart. Systemic CD4+ cell baseline and poststimulation molecular immune response signatures (MIRS) were defined by identifying genes expressed at levels that were stable between time points within individuals and differential among individuals in each state. Iterative differential gene expression analyses between all possible phenotypic groupings of at least three individuals using the baseline and stimulated MIRS gene sets revealed shared baseline and response phenotypic groupings, indicating the baseline MIRS contained determinants of immune responsiveness. Furthermore, significant numbers of shared phenotype-defining sets of determinants were identified in baseline data across independent healthy cohorts. Combining the cohorts and repeating the analyses resulted in identification of over 6000 baseline immune phenotypic groups, implying that the MIRS concept may be useful in many immune perturbation contexts. These findings demonstrate that patterns in complex gene expression variability can be used to define immune phenotypes and discover determinants of immune responsiveness.
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Affiliation(s)
- Adam D Scheid
- Immunology Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Virginia P Van Keulen
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Sara J Felts
- Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Steven C Neier
- Immunology Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Sumit Middha
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Asha A Nair
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Robert W Techentin
- Special Purpose Processor Development Group, Mayo Clinic, Rochester, MN 55901
| | - Barry K Gilbert
- Special Purpose Processor Development Group, Mayo Clinic, Rochester, MN 55901
| | - Jin Jen
- Medical Genome Facility Gene Expression Core and Department of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN 55905; and
| | - Claudia Neuhauser
- Informatics Institute, University of Minnesota, Minneapolis, MN 55455
| | - Yuji Zhang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
| | - Larry R Pease
- Immunology Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic College of Medicine and Science, Rochester, MN 55905; .,Department of Immunology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905
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24
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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.
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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.
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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.
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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
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Middha S, Zhang L, Nafa K, Jayakumaran G, Wong D, Kim HR, Sadowska J, Berger MF, Delair DF, Shia J, Stadler Z, Klimstra DS, Ladanyi M, Zehir A, Hechtman JF. Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data. JCO Precis Oncol 2017; 2017. [PMID: 30211344 DOI: 10.1200/po.17.00084] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose Microsatellite instability (MSI)/mismatch repair (MMR) status is increasingly important in the management of patients with cancer to predict response to immune checkpoint inhibitors. We determined MSI status from large-panel clinical targeted next-generation sequencing (NGS) data across various solid cancer types. Methods The MSI statuses of 12,288 advanced solid cancers consecutively sequenced with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets clinical NGS assay were inferred by using MSIsensor, a program that reports the percentage of unstable microsatellites as a score. Cutoff score determination and sensitivity/specificity were based on MSI polymerase chain reaction (PCR) and MMR immunohistochemistry. Results By using an MSIsensor score ≥ 10 to define MSI high (MSI-H), 83 (8%) of 996 colorectal cancers (CRCs) and 42 (16%) of 260 uterine endometrioid cancers (UECs) were MSI-H. Validation against MSI PCR and/or MMR immunohistochemistry performed for 138 (24 MSI-H, 114 microsatellite stable [MSS]) CRCs, and 40 (15 MSI-H, 25 MSS) UECs showed a concordance of 99.4%. MSIsensor also identified 68 MSI-H/MMR-deficient (MMR-D) non-CRC/UECs. Of 9,591 non-CRC/UEC tumors with MSS MSIsensor status, 456 (4.8%) had slightly elevated scores(≥3 and <10) of which 96.6% with available material were confirmed to be MSS by MSI PCR. MSI-H was also detected and confirmed in three non-CRC/UECs with low exonic mutation burden (< 20). MSIsensor correctly scored all 15 polymerase ε ultra-mutated cancers as negative for MSI. Conclusion MSI status can be reliably inferred by MSIsensor from large-panel targeted NGS data. Concurrent MSI testing by NGS is resource efficient, is potentially more sensitive for MMR-D than MSI PCR, and allows identification of MSI-H across various cancers not typically screened, as highlighted by the finding that 35% (68 of 193) of all MSI-H tumors were non-CRC/ UEC.
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Affiliation(s)
- Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Donna Wong
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyunjae R Kim
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
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DeLair DF, Burke KA, Selenica P, Lim RS, Scott SN, Middha S, Mohanty AS, Cheng DT, Berger MF, Soslow RA, Weigelt B. The genetic landscape of endometrial clear cell carcinomas. J Pathol 2017; 243:230-241. [PMID: 28718916 DOI: 10.1002/path.4947] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/20/2017] [Accepted: 07/05/2017] [Indexed: 12/18/2022]
Abstract
Clear cell carcinoma of the endometrium is a rare type of endometrial cancer that is generally associated with an aggressive clinical behaviour. Here, we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs), and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs. Eleven (34%), seven (22%) and six (19%) ECCs showed abnormal expression patterns for p53, ARID1A, and at least one DNA mismatch repair (MMR) protein, respectively. Targeted sequencing data were obtained from 30 of the 32 ECCs included in this study, and these revealed that two ECCs (7%) were ultramutated and harboured mutations affecting the exonuclease domain of POLE. In POLE wild-type ECCs, TP53 (46%), PIK3CA (36%), PPP2R1A (36%), FBXW7 (25%), ARID1A (21%), PIK3R1 (18%) and SPOP (18%) were the genes most commonly affected by mutations; 18% and 11% harboured CCNE1 and ERBB2 amplifications, respectively, and 11% showed DAXX homozygous deletions. ECCs less frequently harboured mutations affecting CTNNB1 and PTEN but more frequently harboured PPP2R1A and TP53 mutations than non-POLE endometrioid carcinomas from The Cancer Genome Atlas (TCGA). Compared to endometrial serous carcinomas (TCGA), ECCs less frequently harboured TP53 mutations. When a surrogate model for the molecular-based TCGA classification was used, all molecular subtypes previously identified in endometrial endometrioid and serous carcinomas were present in the ECCs studied, including POLE, MMR-deficient, copy-number high (serous-like)/p53 abnormal, and copy-number low (endometrioid)/p53 wild-type, which were significantly associated with disease-free survival in univariate analysis. These findings demonstrate that ECCs constitute a histologically and genetically heterogeneous group of tumours with varying outcomes. Furthermore, our data suggest that the classification of ECCs as being generally 'high-grade' or 'type II' tumours may not be warranted. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sasinya N Scott
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abhinita S Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert A Soslow
- 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
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DeRycke MS, Gunawardena S, Balcom JR, Pickart AM, Waltman LA, French AJ, McDonnell S, Riska SM, Fogarty ZC, Larson MC, Middha S, Eckloff BW, Asmann YW, Ferber MJ, Haile RW, Gallinger S, Clendenning M, Rosty C, Win AK, Buchanan DD, Hopper JL, Newcomb PA, Le Marchand L, Goode EL, Lindor NM, Thibodeau SN. Targeted sequencing of 36 known or putative colorectal cancer susceptibility genes. Mol Genet Genomic Med 2017; 5:553-569. [PMID: 28944238 PMCID: PMC5606870 DOI: 10.1002/mgg3.317] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 06/02/2017] [Accepted: 06/09/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mutations in several genes predispose to colorectal cancer. Genetic testing for hereditary colorectal cancer syndromes was previously limited to single gene tests; thus, only a very limited number of genes were tested, and rarely those infrequently mutated in colorectal cancer. Next-generation sequencing technologies have made it possible to sequencing panels of genes known and suspected to influence colorectal cancer susceptibility. METHODS Targeted sequencing of 36 known or putative CRC susceptibility genes was conducted for 1231 CRC cases from five subsets: (1) Familial Colorectal Cancer Type X (n = 153); (2) CRC unselected by tumor immunohistochemical or microsatellite stability testing (n = 548); (3) young onset (age <50 years) (n = 333); (4) proficient mismatch repair (MMR) in cases diagnosed at ≥50 years (n = 68); and (5) deficient MMR CRCs with no germline mutations in MLH1, MSH2, MSH6, or PMS2 (n = 129). Ninety-three unaffected controls were also sequenced. RESULTS Overall, 29 nonsense, 43 frame-shift, 13 splice site, six initiator codon variants, one stop codon, 12 exonic deletions, 658 missense, and 17 indels were identified. Missense variants were reviewed by genetic counselors to determine pathogenicity; 13 were pathogenic, 61 were not pathogenic, and 584 were variants of uncertain significance. Overall, we identified 92 cases with pathogenic mutations in APC,MLH1,MSH2,MSH6, or multiple pathogenic MUTYH mutations (7.5%). Four cases with intact MMR protein expression by immunohistochemistry carried pathogenic MMR mutations. CONCLUSIONS Results across case subsets may help prioritize genes for inclusion in clinical gene panel tests and underscore the issue of variants of uncertain significance both in well-characterized genes and those for which limited experience has accumulated.
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Affiliation(s)
- Melissa S. DeRycke
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Shanaka Gunawardena
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Jessica R. Balcom
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Angela M. Pickart
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Lindsey A. Waltman
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Amy J. French
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Shannon McDonnell
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Shaun M. Riska
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Zachary C. Fogarty
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Melissa C. Larson
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | - Sumit Middha
- Department of Biomedical Statistics and InformaticsMayo ClinicRochesterMinnesota
| | | | - Yan W. Asmann
- Department of Health Sciences ResearchMayo ClinicJacksonvilleFlorida
| | - Matthew J. Ferber
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
| | - Robert W. Haile
- Division of OncologyDepartment of MedicineStanford UniversityStanfordCalifornia
| | | | - Mark Clendenning
- Colorectal Oncogenomics GroupGenetic Epidemiology LaboratoryDepartment of PathologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Christophe Rosty
- Colorectal Oncogenomics GroupGenetic Epidemiology LaboratoryDepartment of PathologyThe University of MelbourneParkvilleVictoriaAustralia
- Envoi Specialist PathologistsHerstonQueenslandAustralia
- School of MedicineUniversity of QueenslandHerstonQueenslandAustralia
| | - Aung K. Win
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global HealthThe University of MelbourneParkvilleVictoriaAustralia
- Genetic Medicine and Familial Cancer CentreThe Royal Melbourne HospitalParkvilleVictoriaAustralia
| | - Daniel D. Buchanan
- Colorectal Oncogenomics GroupGenetic Epidemiology LaboratoryDepartment of PathologyThe University of MelbourneParkvilleVictoriaAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global HealthThe University of MelbourneParkvilleVictoriaAustralia
- Genetic Medicine and Familial Cancer CentreThe Royal Melbourne HospitalParkvilleVictoriaAustralia
| | - John L. Hopper
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global HealthThe University of MelbourneParkvilleVictoriaAustralia
| | - Polly A. Newcomb
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWashington
| | - Loic Le Marchand
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHawaii
| | - Ellen L. Goode
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesota
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Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:1004. [PMID: 28777785 DOI: 10.1038/nm0817-1004c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Lipsyc M, Chatila W, Hechtman JF, Sanchez-Vega F, Middha S, Cercek A, Stadler Z, Kundra R, Syed A, Hyman DM, Zehir A, Shahrokni A, Varghese A, Reidy D, Segal NH, Vakiani E, Solit DB, Ladanyi M, Berger MF, Kemeny N, Saltz L, Schultz N, Yaeger R. Abstract 4380: Integrative genomics analysis of metastatic colorectal cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4380] [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 performed an integrated clinical and bioinformatic analysis of colorectal cancers (CRCs) genotyped at our institution from 4/2014-7/2016 to comprehensively characterize genomic alterations in metastatic CRC (mCRC). We analyzed 1008 samples (474 primaries, 534 metastases) from 985 mCRC patients and 128 early stage CRCs sequenced with MSK-IMPACT, a hybridization capture next generation sequencing assay. Metastatic CRCs were divided into 3 groups by mutation burden and MSIsensor algorithm score: microsatellite stable (MSS) (n=939; 95%), microsatellite-high (MSI-H) (n=41; 4%), and ultra-mutated (n=5; 1%). Early stage CRC were enriched for MSI-H due to clinical selection and were 53% MSS, 44% MSI-H, and 4% ultra-mutated. Ultra-mutated tumors exhibited >100 mutations and harbored hotspot mutations in POLE in 8 cases and a potential novel POLE alteration in 1 case.
We evaluated the frequency of oncogenic alterations in MSI-H and MSS mCRCs. The frequency of the resistance biomarkers KRAS and NRAS did not vary between MSI-H and MSS mCRCs (46% v 41%, p=0.6). Potentially actionable alterations were enriched in MSI-H tumors (78% v 33%, p<0.001). Metastases did not have more actionable alterations than primary tumors. We classified clinically relevant targets using the OncoKB classification as level 2B (FDA-approved target in another disease type), 3A (target with compelling early clinical evidence in CRC), and 3B (target with compelling early clinical evidence in another disease type). Twelve percent (109/939) of MSS mCRCs had a level 2B target: BRAF V600E (5%), ERBB2 amplification (AMP) (4%), MET AMP (1%), BRCA1/BRCA2 alteration (1%), TSC1/TSC2 mutation (1%), EGFR mutation (<1%), RET fusion (<1%); there was significant enrichment of BRAF V600E (24%) and BRCA1/BRCA2 alterations (29%) in MSI-H versus MSS mCRC (p<0.001). NTRK fusions, the main 3A alteration identified, occurred in 7% of MSI-H and <1% MSS CRC (p<0.01). Level 3B alterations at ≥ 1% in MSS CRC included PIK3CA (15%), NRAS (3%), AKT1 (1%), MAP2K1 (1%), and ERBB2 (1%) mutations and FGFR1 AMP (2%). PIK3CA and PTCH1 mutations were both enriched in MSI-H versus MSS mCRC (32% v 15%, p<0.01; 27%,v <1%, p<0.001, respectively).
Analysis of mutation frequencies in 3 MSS CRC disease states - early stage resected primary (The Cancer Genome Atlas, TCGA), primary site of mCRC, and metastatic site - found significant depletion of FBXW7 mutations in metastases. We also found significant and progressive enrichment of TP53 alterations (58% TCGA, 73% primaries of mCRC, 79% metastases) and BRAF mutations (4% TCGA, 9% primaries of mCRC, 10% metastases) in advanced disease, suggesting a role of these genes in aggressive disease. One third of the BRAF mutations in our cohorts were not V600 but known to be oncogenic.
In this large dataset, we identified markers of advanced CRC and found that while MSI-H and MSS CRC have a similar frequency of resistance biomarkers, MSI-H CRC more commonly harbor actionable alterations.
Citation Format: Marla Lipsyc, Walid Chatila, Jaclyn F. Hechtman, Francisco Sanchez-Vega, Sumit Middha, Andrea Cercek, Zsofia Stadler, Ritika Kundra, Aijazuddin Syed, David M. Hyman, Ahmet Zehir, Armin Shahrokni, Anna Varghese, Diane Reidy, Neil H. Segal, Efsevia Vakiani, David B. Solit, Marc Ladanyi, Michael F. Berger, Nancy Kemeny, Leonard Saltz, Nikolaus Schultz, Rona Yaeger. Integrative genomics analysis of metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4380. doi:10.1158/1538-7445.AM2017-4380
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Affiliation(s)
- Marla Lipsyc
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid Chatila
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Anna Varghese
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diane Reidy
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neil H. Segal
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Nancy Kemeny
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Leonard Saltz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
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Ibrahimpasic T, Xu B, Landa I, Dogan S, Middha S, Seshan V, Deraje S, Carlson DL, Migliacci J, Knauf JA, Untch B, Berger MF, Morris L, Tuttle RM, Chan T, Fagin JA, Ghossein R, Ganly I. Genomic Alterations in Fatal Forms of Non-Anaplastic Thyroid Cancer: Identification of MED12 and RBM10 as Novel Thyroid Cancer Genes Associated with Tumor Virulence. Clin Cancer Res 2017. [PMID: 28634282 DOI: 10.1158/1078-0432.ccr-17-1183] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Purpose: Patients with anaplastic thyroid cancer (ATC) have a very high death rate. In contrast, deaths from non-anaplastic thyroid (NAT) cancer are much less common. The genetic alterations in fatal NAT cancers have not been reported.Experimental Design: We performed next-generation sequencing of 410 cancer genes from 57 fatal NAT primary cancers. Results were compared with The Cancer Genome Atlas study (TCGA study) of papillary thyroid cancers (PTCs) and to the genomic changes reported in ATC.Results: There was a very high prevalence of TERT promoter mutations, comparable with that of ATC, and these co-occurred with BRAF and RAS mutations. A high incidence of chromosome 1q gain was seen highlighting its importance in tumor aggressiveness. Two novel fusion genes DLG5-RET and OSBPL1A-BRAF were identified. There was a high frequency of mutations in MED12 and these were mutually exclusive to TERT promoter mutations and also to BRAF and RAS mutations. In addition, a high frequency of mutations in RBM10 was identified and these co-occurred with RAS mutations and PIK3CA mutations. Compared with the PTCs in TCGA, there were higher frequencies of mutations in TP53, POLE, PI3K/AKT/mTOR pathway effectors, SWI/SNF subunits, and histone methyltransferases.Conclusions: These data support a model, whereby fatal NAT cancers arise from well-differentiated tumors through the accumulation of key additional genetic abnormalities. The high rate of TERT promoter mutations, MED12 mutations, RBM10 mutations, and chromosome 1q gain highlight their likely association with tumor virulence. Clin Cancer Res; 23(19); 5970-80. ©2017 AACR.
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Affiliation(s)
- Tihana Ibrahimpasic
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Head and Neck Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Iñigo Landa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shyam Deraje
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diane L Carlson
- Department of Pathology, Cleveland Clinic, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jocelyn Migliacci
- Department of Head and Neck Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey A Knauf
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian Untch
- Human Oncology and Pathogenesis Program, 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.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luc Morris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Head and Neck Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - R Michael Tuttle
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James A Fagin
- 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
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Ian Ganly
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Head and Neck Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
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32
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Iyer G, Audenet F, Middha S, Carlo MI, Regazzi AM, Funt S, Al-Ahmadie H, Solit DB, Rosenberg JE, Bajorin DF. Mismatch repair (MMR) detection in urothelial carcinoma (UC) and correlation with immune checkpoint blockade (ICB) response. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.4511] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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
4511 Background: High mutation burden correlates with response to ICB in UC. Loss of function alterations or epigenetic silencing of MMR genes results in MMR deficient (MMR-D) UC, leading to a microsatellite instability (MSI) mutation signature. We used a CLIA-certified pipeline (MSISensor) to interrogate Next Generation sequencing (NGS) data from UC tumors to identify MMR-D patients (pts). We correlated MMR-D with mutation load and response to ICB. Methods: 447 tumors from 424 UC pts underwent prospective NGS using the MSK-IMPACT exon capture assay and genomic interrogation of microsatellite (MS) sites using MSIsensor, which assesses the number/length of MS within the targeted regions of tumor-normal sample pairs. Loci are considered unstable (somatic) if k-mer distributions are significantly different between tumor and matched normal using a standard multiple testing correction of χ2 p-values. The fraction of unstable sites is reported as an MSIsensor score. MSI high tumors have scores >10 while <3 are denoted MS stable. Scores from 3-10 were categorized as MS intermediate. Results: Thirteen pts (3%) had an MSI score >10 and a median mutation count of 52 (36.5-73.5) vs 8 (5-13) in 410 non-MMR-D pts (p<0.01). Ten pts (71%) had upper tract UC. Of 9 pts with germline sequencing performed, 8 (89%) had heritable loss of function mutations in MMR proteins (Lynch syndrome, LS). One pt had a somatic MSH2 mutation. Fifteen pts had MS scores from 3-10: 3 had LS, one a BRCA1 germline alteration, and 9 did not have germline testing available. Two pts with MSI scores <3 had extremely high mutation loads (213 and 414) and both had POLE mutations. Five pts received ICB therapy for metastatic and all achieved near-complete or complete responses. No MMR-D pt has died at 27 months follow-up vs 125 non-MMR-D pts (p=0.014). Conclusions: The MSI Sensor assay can discriminate MSI high from MMR proficient UC. While rare, MMR-D UC is characterized by a high mutation load, strong association with Lynch syndrome, and durable responses to ICB, similar to data in colon cancer. An MMR-D signature should trigger genetic testing for Lynch syndrome. ICB should be considered early in the treatment course of patients with MMR-D metastatic UC.
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Affiliation(s)
- Gopa Iyer
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sumit Middha
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Samuel Funt
- Memorial Sloan Kettering Cancer Center, New York, NY
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33
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Yaeger R, Chatila W, Lipsyc M, Sanchez-Vega F, Hechtman JF, Cercek A, Stadler ZK, Middha S, Kundra R, Syed A, Zehir A, Varghese AM, Segal NH, Vakiani E, Ladanyi M, Berger MF, Kemeny NE, Shia J, Saltz L, Schultz N. Variability in genomic alterations between right- and left-sided microsatellite stable (MSS) metastatic colorectal cancer and impact on survival. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.3534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
3534 Background: Metastatic colorectal cancers (mCRCs) with a right-sided primary site are associated with shorter survival and insensitivity to EGFR inhibitors compared to those originating in the left side of the colon or rectum. Methods: We performed targeted gene sequencing of 928 consecutive MSS mCRCs. Primary tumor site was divided into right-sided for cecum to distal transverse colon (n = 242), left-sided for splenic flexure to rectum (n = 673), or unknown colonic location (n = 13). Histologic subtypes were conventional (adenocarcinoma not otherwise specified), conventional with mucinous features ( < 50% mucinous), mucinous, signet ring, and poorly differentiated. To evaluate receptor tyrosine kinase (RTK) signaling, we analyzed ligand mRNA expression in TCGA. Results: Overall survival from time of metastasis was shorter for right-sided than left-sided primary site (survival at 5 years: 45% v 67%, p < 0.001). Right-sided tumors had more mutations (5.60 v 4.62 per MB, p < 0.001) but fewer copy-number changes (0.18 v 0.22 fraction genome altered, p = 0.001) compared to left-sided tumors. Alterations of KRAS, BRAF, PIK3CA, PTEN, AKT1, RNF43, and SMAD4 were significantly enriched in right-sided tumors, and of APC and TP53 in left-sided tumors. In a multivariate model, APC (HR = 0.7, p = 0.03), BRAF (HR = 3.7, p < 0.001), and KRAS (HR = 1.7, p < 0.01) alterations predicted for survival, but primary site did not (HR = 0.74, p = 0.07). Amphiregulin, epiregulin, neuregulin, and HGF expression was significantly higher in left-sided tumors. We found a higher proportion of conventional histology (83% v 63%) and moderate differentiation (82% v 69%) for left versus right-sided cases. Conclusions: We find that within MSS mCRC there are significantly more oncogenic mutations in right-sided tumors, and the difference in survival between right- and left-sided mCRC is primarily driven by differences in mutations. Left-sided tumors more commonly exhibit a “simpler” conventional histology that is lower grade and may rely on native RTK signaling, such as EGFR, for growth, providing a potential mechanism for the differential sensitivity to EGFR inhibitors seen by primary tumor site.
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Affiliation(s)
- Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Walid Chatila
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Marla Lipsyc
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Andrea Cercek
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Sumit Middha
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Neil Howard Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Jinru Shia
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Leonard Saltz
- Memorial Sloan-Kettering Cancer Center, New York, NY
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34
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Ku GY, Sanchez-Vega F, Chatila W, Margolis M, Fein C, Ilson DH, Hechtman JF, Tuvy Y, Bouvier N, Kundra R, Shia J, Heins ZJ, Middha S, Zehir A, Ladanyi M, Berger MF, Tang LH, Solit DB, Schultz N, Janjigian YY. Correlation of benefit from immune checkpoint inhibitors with next gen sequencing (NGS) profiles in esophagogastric cancer (EGC) patients. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.4025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
4025 Background: Immuno-oncology (IO) with anti-PD-1 and –PD-L1 antibodies (Abs) is active in EGC but only benefits a minority of Pts. Biomarkers are needed to identify responders. Methods: We reviewed our experience of Pts treated with anti-PD-1/PD-L1 Abs and correlated their outcomes with PD-L1 and mismatch repair protein (MMR) status by immunohistochemistry (IHC), as well as MSK-IMPACT (≥340-gene) NGS profile. MSIsensor from IMPACT assesses microsatellite instability phenotype, while ≥20 mutations (or 17 mutations/Mb) strongly correlates with MMR-deficiency (dMMR) by IHC (J Clin Oncol 2016;34:2141). Progression-free (PFS) and overall survival (OS) were analyzed from the start of IO. Results: 71 Pts were identified, with 3 Pts receiving 2 IO regimens. 66 had adenoCAs and 5 had squamous CAs. Median age 58, 77% male, 96% had received ≥2 prior chemo regimens. 39 (55%), 18 (25%) and 17 Pts (24%) respectively received anti-PD-1, anti-PD-L1 and anti-CTLA-4 plus anti-PD-1/PD-L1 Abs. 6 Pts (8%) had objective response (2 complete responses or CRs) and the median PFS and OS are 1.6 and 4.7 mos; 2-yr OS is 17%. PD-L1 IHC was performed in 16 Pts (23%; 7 +ve), MMR was tested in 20 Pts (28%; 4 dMMR) and IMPACT was obtained in 44 Pts (62%). All 4 dMMR tumors were also MSI by MSIsensor and had a median of 46 mutations (range, 29-63) or, equivalently, 33 mutations/Mb (range, 21-46); 2 of 2 dMMR tumors tested PD-L1 +ve. 3 of the 4 Pts with dMMR/MSI tumors had a response (including 1 CR) and the median OS of these 4 Pts is not reached with 23+ months of follow-up. Finally, a patient whose tumor is MMR-proficient, not MSI but has 15 mutations (including in POLD1), achieved an ongoing CR at 37+ mos. For the 44 Pts with IMPACT testing, there appeared to be improved OS for tumors with ≥10 vs. <10 mutations/Mb (2-yr OS 80% vs. 12%, p=0.03). Conclusions: Pts with tumors that are MSI or have ≥10 mutations/Mb on MSK-IMPACT appear to derive significant benefit from IO. MSK-IMPACT can offer novel information, identify novel mutations (e.g. POLD1) and may be used to help select Pts for IO. We are seeking to define a mutation no. cut-off that can serve as a biomarker and updated data will be presented.
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Affiliation(s)
| | | | - Walid Chatila
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Carly Fein
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | | | - Yaelle Tuvy
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Nancy Bouvier
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Jinru Shia
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Sumit Middha
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Laura H. Tang
- Memorial Sloan-Kettering Cancer Center, New York, NY
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35
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Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:703-713. [PMID: 28481359 PMCID: PMC5461196 DOI: 10.1038/nm.4333] [Citation(s) in RCA: 2144] [Impact Index Per Article: 306.3] [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: 12/22/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023]
Abstract
Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.
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Affiliation(s)
- Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronak H Shah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hyunjae R Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Barron
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - JinJuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Diana L Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Abhinita S Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mustafa H Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Zhen Y Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ruben Bacares
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iwona J Kiecka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna Razumova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Julie B Son
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lisa Stewart
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tessara Baldi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kerry A Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Adam A Abeshouse
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander V Penson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Philip Jonsson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Niedzica Camacho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew T Chang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Helen H Won
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin E Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zachary J Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hsiao-Wei Chen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sarah Phillips
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jiaojiao Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Wills
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael Eubank
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stacy B Thomas
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stuart M Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dalicia N Reales
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jesse Galle
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert Durany
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Roy Cambria
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - A Ari Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emmet J Jordan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maeve A Lowery
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio M Omuro
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tara E Soumerai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Coleman
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Bernard Bochner
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul J Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jose Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Shia J, Schultz N, Kuk D, Vakiani E, Middha S, Segal NH, Hechtman JF, Berger MF, Stadler ZK, Weiser MR, Wolchok JD, Boland CR, Gönen M, Klimstra DS. Morphological characterization of colorectal cancers in The Cancer Genome Atlas reveals distinct morphology-molecular associations: clinical and biological implications. Mod Pathol 2017; 30:599-609. [PMID: 27982025 PMCID: PMC5380525 DOI: 10.1038/modpathol.2016.198] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/19/2016] [Accepted: 10/19/2016] [Indexed: 12/14/2022]
Abstract
The Cancer Genome Atlas data on colorectal carcinoma have provided a comprehensive view of the tumor's genomic alterations and their tumorigenic roles. Tumor morphology, however, has not been fully integrated into the analysis. The aim of this study was to explore relevant associations between tumor morphology and the newly characterized genomic alterations in colorectal carcinoma. Two hundred and seven colorectal carcinomas that had undergone whole-exome sequencing as part of The Cancer Genome Atlas project and had adequate virtual images in the cBioPortal for Cancer Genomics constituted our study population. Upon analysis, a tight association between 'microsatellite instability-high histology' and microsatellite instability-high (P<0.001) was readily detected and helped validate our image-based histology evaluation. Further, we showed, (1) among all histologies, the not otherwise specified type had the lowest overall mutation count (P<0.001 for entire cohort, P<0.03 for the microsatellite-instable group), and among the microsatellite-instable tumors, this type also correlated with fewer frameshift mutations in coding mononucleotide repeats of a defined set of relevant genes (P<0.01); (2) cytosine phosphate guanine island methylator phenotype-high colorectal cancers with or without microsatellite instability tended to have different histological patterns: the former more often mucinous and the latter more often not otherwise specified; (3) mucinous histology was associated with more frequent alterations in BRAF, PIK3CA, and the transforming growth factor-β pathway when compared with non-mucinous histologies (P<0.001, P=0.01, and P<0.001, respectively); and (4) few colorectal cancers (<9%) exhibited upregulation of immune-inhibitory genes including major immune checkpoints; these tumors were primarily microsatellite-instable (up to 43%, vs <3% in microsatellite-stable group) and had distinctly non-mucinous histologies with a solid growth. These morphology-molecular associations are interesting and propose important clinical implications. The morphological patterns associated with alterations of immune checkpoint genes bear the potential to guide patient selection for clinical trials that target immune checkpoints in colorectal cancer, and provide directions for future studies.
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Affiliation(s)
- Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus Schultz
- Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Deborah Kuk
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neil H. Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K. Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin R. Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jedd D. Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - C. Richard Boland
- GI Cancer Research Laboratory, Baylor University Medical Center; GI Cancer Research Laboratory, Baylor Scott & White Research Institute, Dallas, TX
| | - Mithat Gönen
- Department of Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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Ptashkin RN, Pagan C, Yaeger R, Middha S, Shia J, O'Rourke KP, Berger MF, Wang L, Cimera R, Wang J, Klimstra DS, Saltz L, Ladanyi M, Zehir A, Hechtman JF. Chromosome 20q Amplification Defines a Subtype of Microsatellite Stable, Left-Sided Colon Cancers with Wild-type RAS/RAF and Better Overall Survival. Mol Cancer Res 2017; 15:708-713. [PMID: 28184012 DOI: 10.1158/1541-7786.mcr-16-0352] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 10/13/2016] [Accepted: 01/26/2017] [Indexed: 11/16/2022]
Abstract
Here, comprehensive analysis was performed on the molecular and clinical features of colorectal carcinoma harboring chromosome 20q amplification. Tumor and normal DNA from patients with advanced colorectal carcinoma underwent next-generation sequencing via MSK-IMPACT, and a subset of case samples was subjected to high-resolution microarray (Oncoscan). Relationships between genomic copy number and transcript expression were assessed with The Cancer Genome Atlas (TCGA) colorectal carcinoma data. Of the colorectal carcinoma patients sequenced (n = 401) with MSK-IMPACT, 148 (37%) had 20q gain, and 30 (7%) had 20q amplification. In both the MSK-IMPACT and TCGA datasets, BCL2L1 was the most frequently amplified 20q oncogene. However, SRC was the only recognized 20q oncogene with a significant inverse relationship between mRNA upregulation and RAS/RAF mutation (OR, -0.4 ± 0.2, P = 0.02). In comparison with 20q diploid colorectal carcinoma, 20q gain/amplification was associated with wild-type KRAS (P < 0.001) and BRAF (P = 0.01), microsatellite stability (P < 0.001), distal primary tumors (P < 0.001), and mutant TP53 (P < 0.001), but not stage. On multivariate analysis, longer overall survival from the date of metastasis was observed with chromosome 20q gain (P = 0.02) or amplification (P = 0.04) compared with diploid 20q.Implications: 20q amplification defines a subset of colorectal cancer patients with better overall survival from the date of metastasis, and further studies are warranted to assess whether the inhibition of 20q oncogenes, such as SRC, may benefit this subset of patients. Mol Cancer Res; 15(6); 708-13. ©2017 AACR.
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Affiliation(s)
- Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carlos Pagan
- Department of Pathology, Columbia University Medical Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kevin P O'Rourke
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Cimera
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jiajing Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- 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
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Ioannidis NM, Rothstein JH, Pejaver V, Middha S, McDonnell SK, Baheti S, Musolf A, Li Q, Holzinger E, Karyadi D, Cannon-Albright LA, Teerlink CC, Stanford JL, Isaacs WB, Xu J, Cooney KA, Lange EM, Schleutker J, Carpten JD, Powell IJ, Cussenot O, Cancel-Tassin G, Giles GG, MacInnis RJ, Maier C, Hsieh CL, Wiklund F, Catalona WJ, Foulkes WD, Mandal D, Eeles RA, Kote-Jarai Z, Bustamante CD, Schaid DJ, Hastie T, Ostrander EA, Bailey-Wilson JE, Radivojac P, Thibodeau SN, Whittemore AS, Sieh W. REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants. Am J Hum Genet 2016; 99:877-885. [PMID: 27666373 DOI: 10.1016/j.ajhg.2016.08.016] [Citation(s) in RCA: 1253] [Impact Index Per Article: 156.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/23/2016] [Indexed: 02/08/2023] Open
Abstract
The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies. We developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons. REVEL was trained with recently discovered pathogenic and rare neutral missense variants, excluding those previously used to train its constituent tools. When applied to two independent test sets, REVEL had the best overall performance (p < 10-12) as compared to any individual tool and seven ensemble methods: MetaSVM, MetaLR, KGGSeq, Condel, CADD, DANN, and Eigen. Importantly, REVEL also had the best performance for distinguishing pathogenic from rare neutral variants with allele frequencies <0.5%. The area under the receiver operating characteristic curve (AUC) for REVEL was 0.046-0.182 higher in an independent test set of 935 recent SwissVar disease variants and 123,935 putatively neutral exome sequencing variants and 0.027-0.143 higher in an independent test set of 1,953 pathogenic and 2,406 benign variants recently reported in ClinVar than the AUCs for other ensemble methods. We provide pre-computed REVEL scores for all possible human missense variants to facilitate the identification of pathogenic variants in the sea of rare variants discovered as sequencing studies expand in scale.
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Tian SK, Killian JK, Rekhtman N, Benayed R, Middha S, Ladanyi M, Lin O, Arcila ME. Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience. Arch Pathol Lab Med 2016; 140:1200-1205. [PMID: 27588332 DOI: 10.5858/arpa.2016-0108-ra] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The value and suitability of cytology specimens for molecular diagnosis has been demonstrated by numerous studies. In practice, however, the success rates vary widely across institutions depending on the disease setting, institutional practices of acquisition, handling/processing, and testing methodologies. As the number of clinically relevant biomarkers continues to increase, more laboratories are turning to next-generation sequencing platforms for testing. Although amplicon-based next-generation sequencing assays, interrogating a limited genomic territory, can be performed with minimal input material, broader-based next-generation sequencing assays have higher DNA input requirements that may not be met if the small tissue samples are not acquired and handled appropriately. We briefly describe some of the process changes we have instituted in our laboratories when handling cytologic material to maximize the tissue available for broad hybrid-capture-based next-generation sequencing assays. Among the key changes established were the consolidation and preservation of previously discarded supernatant material in cytologic samples, the introduction of mineral oil for deparaffinization of cell blocks, and adjustments in the molecular laboratory process and bioinformatics pipelines. We emphasize that even minimal changes can have broad implications for test performance, highlighting the importance of a cohesive group-based approach among clinical, cytopathology, surgical pathology, molecular, and bioinformatics teams.
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Razavi P, Chang MT, Middha S, Ross DS, Zehir A, Proverbs-Singh TA, Kandoth C, Chandarlapaty S, Dickler MN, Reis-Filho JS, Patil S, Seshan V, Smyth L, Iyengar NM, Jhaveri K, Modi S, Dang CT, Robson ME, Norton L, Hudis CA, Ladanyi M, Scaltriti M, Schultz N, Hyman D, Berger MF, Taylor BS, Solit DB, Baselga. J. Abstract 4509: Clinical genomic profiling of 1000 metastatic breast cancer patients: actionable targets, novel alterations, and clinical correlations. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4509] [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
Most large genomic profiling efforts in breast cancer have focused on primary breast tumors. Profiling of metastatic breast cancer (MBC) could more accurately define actionable genomic alterations and reveal novel alterations that arise under the selective pressure and clonal evolution of prior therapy. Utilizing a 410-gene targeted capture-based sequencing platform (MSK-IMPACT), we analyzed 920 tumors (62% metastatic, 38% primary) from 874 MBC patients for somatic mutations, DNA copy number alterations, and structural rearrangements (planned final analysis 1000 patients). Detailed clinical data including treatment outcomes was collected for all patients. The cohort was representative of the well characterized clinical subtypes of breast cancer with 71% ER+ or PR+ and HER2-, 17% HER2+, and 12% triple negative breast cancer (TNBC).
Our analysis revealed recurrent alterations in multiple pathways including PI3K/AKT/mTOR (56%), cell cycle regulation (42%), RTK signaling (40%), epigenetic regulation (33%) and MAPK/ERK (19%) pathways. The most frequent actionable alterations include: PIK3CA mutation (36%), ERBB2 amplification (15%), FGFR1 amplification (12%), ESR1 mutation (11%), PTEN mutation/deletion (10%), AKT1 mutation (6%), and ERBB2 mutation (5%). The genomic landscape was significantly different across breast cancer subtypes. For example, the PI3K/AKT/mTOR pathway was altered in ER+ MBC mainly through activating PIK3CA mutations whereas PTEN deletion/mutations were most common in TNBC. We also identified significant differences in the genomic profiles of metastatic and primary tumor samples. Gene enrichment analyses revealed a subset of genes more frequently altered in metastatic tumors (STK11: 13 vs 2; ROS1: 14 vs 2; FGFR4: 15 vs 1) suggesting that mutations in these genes may play a role in breast tumor metastasis and/or therapy resistance. ESR1 mutations were predominantly present in metastatic tumors (88%) and were significantly associated with duration of prior hormonal therapy (P<0.0001). ESR1 mutations were also associated with a poor response to the ER degrader fulvestrant (median PFS: 4.8 vs 13.7 months, mutated vs wild type; P = 0.01). Analysis for potentially novel hotspot mutations revealed recurrent RHOA G17 mutations in 6 MBC patients, nominating RHOA, a GTPase transducer of membrane receptors, as a candidate driver in a subset of breast cancers. While identified previously in other tumors, RHOA G17 has never been implicated in breast cancer.
In summary, our genomic analyses of this large cohort of MBC patients revealed actionable alterations in over 60% of the patients. 29% of patients with these alterations were enrolled in clinical trials of matched targeted therapies to date (PIK3CA 27%, AKT1 30%, ESR1 23%, ERBB2 39%) suggesting that prospective genomic characterization can accelerate enrollment of patients with MBC onto therapeutic clinical trials.
Citation Format: Pedram Razavi, Matthew T. Chang, Sumit Middha, Dara S. Ross, Ahmet Zehir, Tracy A. Proverbs-Singh, Cyriac Kandoth, Sarat Chandarlapaty, Maura N. Dickler, Jorge S. Reis-Filho, Sujata Patil, Venkatraman Seshan, Lillian Smyth, Neil M. Iyengar, Komal Jhaveri, Shanu Modi, Chau T. Dang, Mark E. Robson, Larry Norton, Clifford A. Hudis, Marc Ladanyi, Maurizio Scaltriti, Nikolaus Schultz, David Hyman, Michael F. Berger, Barry S. Taylor, David B. Solit, José Baselga. Clinical genomic profiling of 1000 metastatic breast cancer patients: actionable targets, novel alterations, and clinical correlations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4509.
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Affiliation(s)
- Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dara S. Ross
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Sujata Patil
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Lillian Smyth
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Komal Jhaveri
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shanu Modi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chau T. Dang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - David Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - José Baselga.
- Memorial Sloan Kettering Cancer Center, New York, NY
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Coombs C, Zehir A, Devlin S, Middha S, Cheng D, Kishtagari A, Hyman D, Solit D, Robson M, Baselga J, Arcila M, Tallman M, Levine R, Berger M. Abstract 2640: Clonal hematopoiesis identified by matched-normal blood sequencing of solid tumor patients without hematologic malignancy is common and is associated with decreased overall survival. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2640] [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: Recent genomic studies have identified somatic mutations in leukemia genes in asymptomatic individuals without hematologic malignancy. A subset of patients (pts) with clonal hematopoiesis (CH) subsequently develops hematologic malignancies. However, the incidence of CH in pts with solid tumors has not been extensively studied. We sought to assess for CH and its associated clinical impact in pts with solid tumors who were profiled using paired tumor/blood sequencing.
Methods: This study included pts who were consented on protocol NCT01775072. All had tumor and blood genomic profiling using the MSK-IMPACT hybridization capture-based next-generation sequencing assay, encompassing all protein-coding exons of 410 cancer-associated genes. In matched blood, we investigated for hotspot mutations from COSMIC database (v71) and non-hotspot mutations in leukemia-associated genes and genes reported in prior CH studies. Mutations were scored as present if variant allele frequency (VAF) in blood was greater than 2% and at least twice the VAF seen in tumor. For cases where at least one mutation exceeded these thresholds, we reduced the VAF threshold in blood to 1% to detect subsequent events. Mutations with VAF >35% in both blood and tumor were excluded as likely germline events.
Results: We analyzed 2,146 pts, including 239 pts (11%) with CH. Most commonly identified mutations were in DNMT3A, TET2, and TP53, seen in 167, 52, and 18 pts, respectively. The mean age at time of testing was 62.6 years in pts with CH and 55.4 years in pts without CH (p< 0.001). When comparing baseline blood parameters, there were no statistically significant differences except for higher MCV in CH vs. non-CH pts (91 vs. 90, p = 0.047). 51% of pts with CH had previous radiation therapy compared to 45% of pts without clonal mutations in their blood (p = 0.057). There was no statistically significant difference in the proportion of pts who had received previous chemotherapy (71% of pts in each group). On prospective follow up of pts with CH, no pts have progressed to develop overt hematologic malignancy, with limited follow up (median 13.1 months). Overall survival (OS) was estimated for pts without CH (n = 1907; 1-yr OS: 0.70), CH with 1 mutation (n = 184; 1-yr OS: 0.64), and CH with >1 mutation (n = 55; 1-yr OS: 0.59). The univariate hazard ratios were 1.16 (p = 0.269) and 1.63 (p = 0.015) for 1 mutation and >1 mutation, respectively, when compared to pts without CH. After adjusting for age and sex, a marginal OS association persisted for >1 mutation compared to no CH (HR: 1.46, p = 0.060)
Conclusions: CH is common among solid tumor pts without known hematologic malignancy, occurring in 11% of pts, and appears to be associated with decreased OS. Analyses will be replicated in a larger cohort with longer follow up to determine the clinical impact of these mutations in cancer pts.
Citation Format: Catherine Coombs, Ahmet Zehir, Sean Devlin, Sumit Middha, Donavan Cheng, Ashwin Kishtagari, David Hyman, David Solit, Mark Robson, Jose Baselga, Maria Arcila, Martin Tallman, Ross Levine, Michael Berger. Clonal hematopoiesis identified by matched-normal blood sequencing of solid tumor patients without hematologic malignancy is common and is associated with decreased overall survival. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2640.
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Affiliation(s)
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean Devlin
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donavan Cheng
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - David Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Solit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jose Baselga
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ross Levine
- Memorial Sloan Kettering Cancer Center, New York, NY
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Stadler ZK, Battaglin F, Middha S, Hechtman JF, Tran C, Cercek A, Yaeger R, Segal NH, Varghese AM, Reidy-Lagunes DL, Kemeny NE, Salo-Mullen EE, Ashraf A, Weiser MR, Garcia-Aguilar J, Robson ME, Offit K, Arcila ME, Berger MF, Shia J, Solit DB, Saltz LB. Reliable Detection of Mismatch Repair Deficiency in Colorectal Cancers Using Mutational Load in Next-Generation Sequencing Panels. J Clin Oncol 2016; 34:2141-7. [PMID: 27022117 PMCID: PMC4962706 DOI: 10.1200/jco.2015.65.1067] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [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: 01/08/2023] Open
Abstract
PURPOSE Tumor screening for Lynch syndrome is recommended in all or most patients with colorectal cancer (CRC). In metastatic CRC, sequencing of RAS/BRAF is necessary to guide clinical management. We hypothesized that a next-generation sequencing (NGS) panel that identifies RAS/BRAF and other actionable mutations could also reliably identify tumors with DNA mismatch repair protein deficiency (MMR-D) on the basis of increased mutational load. METHODS We identified all CRCs that underwent genomic mutation profiling with a custom NGS assay (MSK-IMPACT) between March 2014 and July 2015. Tumor mutational load, with exclusion of copy number changes, was determined for each case and compared with MMR status as determined by routine immunohistochemistry. RESULTS Tumors from 224 patients with unique CRC analyzed for MMR status also underwent MSK-IMPACT. Thirteen percent (n = 28) exhibited MMR-D by immunohistochemistry. Using the 341-gene assay, 100% of the 193 tumors with < 20 mutations were MMR-proficient. Of 31 tumors with ≥ 20 mutations, 28 (90%) were MMR-D. The three remaining tumors were easily identified as being distinct from the MMR-D tumors with > 150 mutations each. Each of these tumors harbored the P286R hotspot POLE mutation consistent with the ultramutator phenotype. Among MMR-D tumors, the median number of mutations was 50 (range, 20 to 90) compared with six (range, 0 to 17) in MMR-proficient/POLE wild-type tumors (P < .001). With a mutational load cutoff of ≥ 20 and < 150 for MMR-D detection, sensitivity and specificity were both 1.0 (95% CI, 0.93 to 1.0). CONCLUSION A cutoff for mutational load can be identified via multigene NGS tumor profiling, which provides a highly accurate means of screening for MMR-D in the same assay that is used for tumor genotyping.
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Affiliation(s)
- Zsofia K Stadler
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Francesca Battaglin
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Sumit Middha
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Jaclyn F Hechtman
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Christina Tran
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Andrea Cercek
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Rona Yaeger
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Neil H Segal
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Anna M Varghese
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Diane L Reidy-Lagunes
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Nancy E Kemeny
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Erin E Salo-Mullen
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Asad Ashraf
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Martin R Weiser
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Julio Garcia-Aguilar
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Mark E Robson
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Kenneth Offit
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Maria E Arcila
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Michael F Berger
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Jinru Shia
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - David B Solit
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy
| | - Leonard B Saltz
- Zsofia K. Stadler, Francesca Battaglin, Sumit Middha, Jaclyn F. Hechtman, Christina Tran, Andrea Cercek, Rona Yaeger, Neil H. Segal, Anna M. Varghese, Diane L. Reidy-Lagunes, Nancy E. Kemeny, Erin E. Salo-Mullen, Asad Ashraf, Martin R. Weiser, Julio Garcia-Aguilar, Mark E. Robson, Kenneth Offit, Maria E. Arcila, Michael F. Berger, Jinru Shia, David B. Solit, and Leonard B. Saltz, Memorial Sloan Kettering Cancer Center, New York, NY; and Francesca Battaglin, Veneto Institute of Oncology, Padua, Italy.
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Razavi P, Cecchi F, Ross DS, Middha S, Zehir A, Arcila ME, Hembrough TA, Berger MF, Scaltriti M. Use of next generation sequencing and quantitative mass spectrometry to determine HER2 status. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23237] [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)
- Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Dara S. Ross
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
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Ganesh K, Middha S, Hechtman JF, Ashraf A, Tran C, Villano D, Yaeger RD, Segal NH, Cercek A, Varghese AM, Reidy DL, Kemeny NE, Vijai J, Robson ME, Offit K, Solit DB, Saltz L, Berger MF, Shia J, Stadler ZK. Somatic tumor profiling of DNA mismatch repair deficient (MMR-D) colorectal cancers (CRC). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.1528] [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)
- Karuna Ganesh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Asad Ashraf
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Andrea Cercek
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Leonard Saltz
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Kinga Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Cropp CD, McDonnell SK, Middha S, DeRycke M, Karyadi DM, Schaid D, Thibodeau SN, Isaacs WB, Ostrander EA, Stanford J, Cooney KA, Bailey-Wilson JE, Carpten JD. Abstract B40: Rare variant discovery in known cancer genes from whole-exome sequencingof African American hereditary prostate cancer families. Cancer Epidemiol Biomarkers Prev 2016. [DOI: 10.1158/1538-7755.disp15-b40] [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
African American Hereditary Prostate Cancer Study (AAHPC) was developed as a national collaboration to explore the role of genetics in the causation of hereditary prostate cancer (HPC) in African American (AA) men. AAHPC is in partnership with the International Consortium for Prostate Cancer Genetics (ICPCG), which conducts collaborative studies of HPC genetics in multiplex families. As part of an ICPCG sequencing study of 539 affected individuals from 366 HPC pedigrees, we performed whole exome sequencing in 21 ICPCG AA families, of which there were 14 AAHPC affected men from 11 pedigrees. The combined ICPCG AA cohort consisted of N=26 affected members. Post-variant calling quality control (QC) was implemented using Golden Helix SVS 8 software with filters set for removal of variants with Read Depth < 10, Quality Score < 20, Quality Score: Read Depth Ratio < 0.5, Call Rate < 0.75. Variants were additionally filtered by MAF based on the NHLBI ESP650051-V2 exomes variant frequencies for the AA population using a MAF threshold of 5%. Following QC, 176/299 SNVs and 20/39 INDELs remained for further analysis. In these analyses, we focused on 13 known cancer genes (MSR1, AR, BRCA1, BRCA2, BTNL2, EPHB2, CDH1, RNASEL, ELAC2, HOXB13, CHEK2, TP53 and NBN). Three sequenced families had > 1 affected members sequenced (2 or 3 per family) and the remaining 18 families had one member sequenced. Under the dominant model, our preliminary results show that no rare variants in the 13 candidate genes were found in 3/3 affecteds in two families. Rare SNVs in seven candidate genes (AR, CDH1, ELAC2, HOXB13, RNASEL, BRCA2 and EPHB2) were found in 2/3 affecteds for two families and 2/2 affecteds in one family. Several of the remaining 18 affected men (1 sequenced per pedigree) shared the same rare SNV in these candidate genes. For INDELs, rare variants in three candidate genes were found in pedigrees with ≥ 2 affecteds. Several of the remaining 18 affected men (one sequenced per pedigree) shared the same rare INDEL. Additional QC is underway to validate these variants and bioinformatic analyses are being used to predict effects of the variants in an effort to unravel the complex genetic heterogeneity of HPC in AA.
Citation Format: Cheryl D. Cropp, Shannon K. McDonnell, Sumit Middha, Melissa DeRycke, Danielle M. Karyadi, Daniel Schaid, Stephen N. Thibodeau, William B. Isaacs, Elaine A. Ostrander, Janet Stanford, Kathleen A. Cooney, Joan E. Bailey-Wilson, John D. Carpten. Rare variant discovery in known cancer genes from whole-exome sequencingof African American hereditary prostate cancer families. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr B40.
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Affiliation(s)
- Cheryl D. Cropp
- 1Translational Genomics Research Institute (TGen), Phoenix, AZ,
| | | | | | | | - Danielle M. Karyadi
- 3Cancer Genetics Branch, National Human Genome Research institute, Bethesda, MD,
| | | | | | | | - Elaine A. Ostrander
- 3Cancer Genetics Branch, National Human Genome Research institute, Bethesda, MD,
| | | | | | - Joan E. Bailey-Wilson
- 7Computational and Statistical Genomics Branch, National Human Genome Research Institute, Baltimore, MD
| | - John D. Carpten
- 1Translational Genomics Research Institute (TGen), Phoenix, AZ,
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Hechtman JF, Zehir A, Yaeger R, Wang L, Middha S, Zheng T, Hyman DM, Solit D, Arcila ME, Borsu L, Shia J, Vakiani E, Saltz L, Ladanyi M. Identification of Targetable Kinase Alterations in Patients with Colorectal Carcinoma That are Preferentially Associated with Wild-Type RAS/RAF. Mol Cancer Res 2015; 14:296-301. [PMID: 26660078 DOI: 10.1158/1541-7786.mcr-15-0392-t] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/29/2015] [Indexed: 01/13/2023]
Abstract
UNLABELLED Targeted therapy for metastatic colorectal carcinoma consists of anti-EGFR therapy for patients with RAS/RAF wild-type tumors. However, the response rate remains low, suggesting the presence of alternative drivers possibly also representing potential therapeutic targets. We investigated receptor tyrosine kinase (RTK) alterations and MAP2K1 (MEK1) mutations in a large cohort of colorectal carcinoma patients studied by Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets and The Cancer Genome Atlas, focusing on amplifications, fusions, and hotspot mutations in RTK genes and MAP2K1. RTK gene amplifications were confirmed with FISH and immunohistochemical (IHC) staining. Among 751 colorectal carcinoma cases with next-generation sequencing data, 7% and 1% of colorectal carcinoma harbored RTK alterations and MAP2K1 hotspot mutations (n = 7), respectively. RTK-altered cases had fewer concurrent RAS/RAF mutations (P = 0.003) than RTK/MAP2K1 wild-type colorectal carcinoma. MAP2K1-mutated colorectal carcinoma showed no RAS/RAF mutations. ERBB2 (n = 32) and EGFR (n = 13) were the most frequently altered RTKs, both activated by amplification and/or hotspot mutations. Three RTK fusions were identified: NCOA4-RET, ERBB2-GRB7, and ETV6-NTRK3. Only 1 of 6 patients with an RTK or MAP2K1 alteration who received anti-EGFR and/or anti-ERBB2 therapy demonstrated stable disease; the rest progressed immediately. Overall, RTK alterations and MAP2K1 mutations occur in approximately 8% of colorectal carcinoma. In spite of the usual absence of RAS/RAF mutations, response to anti-EGFR and/or anti-ERBB2 therapy was poor in this limited group. Larger studies are warranted to further define these kinase alterations as novel therapeutic targets in colorectal carcinoma and as negative predictors of response to anti-EGFR therapy. IMPLICATIONS Targetable kinase alterations were identified in a subset of advanced colorectal carcinoma patients, preferentially associated with wild-type RAS/RAF, and may predict poor response to standard anti-EGFR therapy.
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Affiliation(s)
- Jaclyn F Hechtman
- 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
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tao Zheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leonard Saltz
- Department of Pathology, 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 & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
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Thibodeau SN, French AJ, McDonnell SK, Cheville J, Middha S, Tillmans L, Riska S, Baheti S, Larson MC, Fogarty Z, Zhang Y, Larson N, Nair A, O'Brien D, Wang L, Schaid DJ. Identification of candidate genes for prostate cancer-risk SNPs utilizing a normal prostate tissue eQTL data set. Nat Commun 2015; 6:8653. [PMID: 26611117 PMCID: PMC4663677 DOI: 10.1038/ncomms9653] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [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: 03/26/2015] [Accepted: 09/17/2015] [Indexed: 01/23/2023] Open
Abstract
Multiple studies have identified loci associated with the risk of developing prostate cancer but the associated genes are not well studied. Here we create a normal prostate tissue-specific eQTL data set and apply this data set to previously identified prostate cancer (PrCa)-risk SNPs in an effort to identify candidate target genes. The eQTL data set is constructed by the genotyping and RNA sequencing of 471 samples. We focus on 146 PrCa-risk SNPs, including all SNPs in linkage disequilibrium with each risk SNP, resulting in 100 unique risk intervals. We analyse cis-acting associations where the transcript is located within 2 Mb (±1 Mb) of the risk SNP interval. Of all SNP–gene combinations tested, 41.7% of SNPs demonstrate a significant eQTL signal after adjustment for sample histology and 14 expression principal component covariates. Of the 100 PrCa-risk intervals, 51 have a significant eQTL signal and these are associated with 88 genes. This study provides a rich resource to study biological mechanisms underlying genetic risk to PrCa. Single nucleotide polymorphisms—SNPs—have been identified for prostate cancer but whether these SNPs alter the expression of genes is largely unknown. In this study, the authors search for genes located within 2 Mb of the SNPs and identify SNPs that influence gene expression, so called expression quantitative trait loci.
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Affiliation(s)
- S N Thibodeau
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - A J French
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S K McDonnell
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - J Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S Middha
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - L Tillmans
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S Riska
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - S Baheti
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - M C Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Z Fogarty
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - Y Zhang
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, 660W Redwood Street, Baltimore, Maryland 21201, USA
| | - N Larson
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - A Nair
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - D O'Brien
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
| | - L Wang
- Department of Pathology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, USA
| | - D J Schaid
- Department of Health Sciences Research, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, Minnesota 55905, USA
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Jour G, Wang L, Middha S, Zehir A, Chen W, Sadowska J, Healey J, Agaram NP, Choi L, Nafa K, Hameed M. The molecular landscape of extraskeletal osteosarcoma: A clinicopathological and molecular biomarker study. J Pathol Clin Res 2015; 2:9-20. [PMID: 27499911 PMCID: PMC4858130 DOI: 10.1002/cjp2.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/29/2015] [Indexed: 12/12/2022]
Abstract
Extraskeletal osteosarcoma (ESOSA) is a rare soft tissue neoplasm representing <5% of osteosarcomas and <1% of all soft-tissue sarcomas. Herein, we investigate the clinicopathological and molecular features of ESOSA and explore potential parameters that may affect outcome. Thirty-two cases were retrieved and histomorphology was reviewed. Clinical history and follow-up were obtained through electronic record review. DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted and processed from 27 cases. Genome-wide DNA copy number (CN) alterations and allelic imbalances were analyzed by single nucleotide polymorphism array using Affymetrix OncoScan FFPE Assay. Massive high-throughput deep parallel sequencing was performed using a customized panel targeting 410 cancer genes. Log rank, Fisher's exact test and Cox proportional hazards were used for statistical analysis. In this series of 32 patients (male n = 12, female n = 20), the average age was 66 years (19-93) and median follow up was 24 months (range 6-120 months). Frequent genomic alterations included CN losses in tumour suppressor genes including CDKN2A (70%), TP53 (56%) and RB1 (49%). Mutations affecting methylation/demethylation, chromatin remodeling and WNT/SHH pathways were identified in 40%, 27%, and 27%, respectively. PIK3CA and TERT promoter variant mutations were identified in 11% of the cases. Cases harbouring simultaneous TP53 and RB1 biallelic CN losses were associated with worse overall survival and local recurrence (p = 0.04, p = 0.02, respectively). CDKN2A losses and positive margins were also associated with worse overall survival (p = 0.002; p = 0.03, respectively). Our findings suggest that age above 60, positive margin status, simultaneous biallelic TP53 and RB1 losses and CDKN2A loss are associated with a worse outcome in ESOSA. Comparison between conventional paediatric osteosarcoma and ESOSA shows that, while both share genetic similarities, there are notable dissimilarities and mechanistic differences in the molecular pathways involved in ESOSA.
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Affiliation(s)
- George Jour
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Lu Wang
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Sumit Middha
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Ahmet Zehir
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Wen Chen
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Justyna Sadowska
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - John Healey
- Department of Orthopedic Surgery Memorial Sloan Kettering Cancer Center New York NY USA
| | - Narasimhan P Agaram
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Lisa Choi
- Department of Orthopedic Surgery Memorial Sloan Kettering Cancer Center New York NY USA
| | - Khedoudja Nafa
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Meera Hameed
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
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Kisiel JB, Raimondo M, Taylor WR, Yab TC, Mahoney DW, Sun Z, Middha S, Baheti S, Zou H, Smyrk TC, Boardman LA, Petersen GM, Ahlquist DA. New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice. Clin Cancer Res 2015; 21:4473-81. [PMID: 26023084 PMCID: PMC4592385 DOI: 10.1158/1078-0432.ccr-14-2469] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [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: 09/23/2014] [Accepted: 05/12/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE Discriminant markers for pancreatic cancer detection are needed. We sought to identify and validate methylated DNA markers for pancreatic cancer using next-generation sequencing unbiased by known targets. EXPERIMENTAL DESIGN At a referral center, we conducted four sequential case-control studies: discovery, technical validation, biologic validation, and clinical piloting. Candidate markers were identified using variance-inflated logistic regression on reduced-representation bisulfite DNA sequencing results from matched pancreatic cancers, benign pancreas, and normal colon tissues. Markers were validated technically on replicate discovery study DNA and biologically on independent, matched, blinded tissues by methylation-specific PCR. Clinical testing of six methylation candidates and mutant KRAS was performed on secretin-stimulated pancreatic juice samples from 61 patients with pancreatic cancer, 22 with chronic pancreatitis, and 19 with normal pancreas on endoscopic ultrasound. Areas under receiver-operating characteristics curves (AUC) for markers were calculated. RESULTS Sequencing identified >500 differentially hyper-methylated regions. On independent tissues, AUC on 19 selected markers ranged between 0.73 and 0.97. Pancreatic juice AUC values for CD1D, KCNK12, CLEC11A, NDRG4, IKZF1, PKRCB, and KRAS were 0.92*, 0.88, 0.85, 0.85, 0.84, 0.83, and 0.75, respectively, for pancreatic cancer compared with normal pancreas and 0.92*, 0.73, 0.76, 0.85*, 0.73, 0.77, and 0.62 for pancreatic cancer compared with chronic pancreatitis (*, P = 0.001 vs. KRAS). CONCLUSIONS We identified and validated novel DNA methylation markers strongly associated with pancreatic cancer. On pilot testing in pancreatic juice, best markers (especially CD1D) highly discriminated pancreatic cases from controls.
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Affiliation(s)
- John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Massimo Raimondo
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida
| | - William R Taylor
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Tracy C Yab
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Zhifu Sun
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Sumit Middha
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Saurabh Baheti
- Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Hongzhi Zou
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - David A Ahlquist
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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50
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Hebert SL, Marquet-de Rougé P, Lanza IR, McCrady-Spitzer SK, Levine JA, Middha S, Carter RE, Klaus KA, Therneau TM, Highsmith EW, Nair KS. Mitochondrial Aging and Physical Decline: Insights From Three Generations of Women. J Gerontol A Biol Sci Med Sci 2015; 70:1409-17. [PMID: 26297939 DOI: 10.1093/gerona/glv086] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 05/22/2015] [Indexed: 02/07/2023] Open
Abstract
Decline in mitochondrial DNA (mtDNA) copy number, function, and accumulation of mutations and deletions have been proposed to contribute to age-related physical decline, based on cross sectional studies in genetically unrelated individuals. There is wide variability of mtDNA and functional measurements in many population studies and therefore we assessed mitochondrial function and physical function in 18 families of grandmothers, mothers, and daughters who share the same maternally inherited mtDNA sequence. A significant age-related decline in mtDNA copy number, mitochondrial protein expression, citrate synthase activity, cytochrome c oxidase content, and VO2 peak were observed. Also, a lower abundance of SIRT3, accompanied by an increase in acetylated skeletal muscle proteins, was observed in grandmothers. Muscle tissue-based full sequencing of mtDNA showed greater than 5% change in minor allele frequency over a lifetime in two locations, position 189 and 408 in the noncoding D-loop region but no changes were noted in blood cells mtDNA. The decline in oxidative capacity and muscle function with age in three generations of women who share the same mtDNA sequence are associated with a decline in muscle mtDNA copy number and reduced protein deacetylase activity of SIRT3.
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Affiliation(s)
| | | | | | | | | | - Sumit Middha
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, 200 First Street SW, Joseph 5-194, Rochester, Minnesota 55905
| | - Rickey E Carter
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, 200 First Street SW, Joseph 5-194, Rochester, Minnesota 55905
| | | | - Terry M Therneau
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, 200 First Street SW, Joseph 5-194, Rochester, Minnesota 55905
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