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Lee J, Rosenzweig M, Piper-Vallillo A, Vanderlaan P, Tolba K, Li T, Riess J, Venstrom J, Oxnard G, Schrock A, Costa D, Ou S. MA02.03 MET-Driven Acquired Resistance (AR) in Fusion-Positive Non-Small Cell Lung Cancer (NSCLC). J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.08.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Saori M, Nakamura Y, Sawada K, Horasawa S, Kadowaki S, Kato K, Ueno M, Oki E, Satoh T, Komatsu Y, Tukachinsky H, Lee J, Madison R, Sokol E, Pavlick D, Aiyer A, Fabrizio D, Venstrom J, Oxnard G, Yoshino T. 80P Blood tumor mutational burden (bTMB) and efficacy of immune checkpoint inhibitors (ICIs) in advanced solid tumors: SCRUM-Japan MONSTAR-SCREEN. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Chumsri S, Sammons S, Alder L, Sokol E, Danziger N, Raskina K, Schrock A, Venstrom J, Snow T, Castellanos E, Ochuonyo E, Snider J, Mcgregor K. 237P Real-world outcomes of hormone receptor-positive (HR+) HER2-negative (HER2-) metastatic breast cancer (mBC) with high tumor mutational burden (hTMB) treated with immune checkpoint inhibitors (ICI). Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Ganjoo K, Madison R, Rosenzweig M, Oxnard G, Venstrom J, Ward A, Schrock A. 1532P Fusion and rearrangement (RE) detection using DNA and RNA-based comprehensive genomic profiling (CGP) of sarcomas. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Tejpar S, Tukachinsky H, Zhang L, Schrock A, Decker B, Pavlick D, Venstrom J, Nimeiri H, Oxnard G. 457P Circulating tumor DNA (ctDNA) from patients (pts) with advanced colorectal cancer (CRC) is enriched for EGFR extracellular domain (ECD) mutations. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Necchi A, Grivas P, Spiess P, Jacob J, Schrock A, Madison R, Pavlick D, Sokol E, Danziger N, Ramkissoon S, Severson E, Huang R, Lin D, Mata D, Decker B, Gjoerup O, Mcgregor K, Venstrom J, Alexander B, Ross J, Bratslavsky G. Methylthioadenosine Phosphorylase (MTAP) deletion is more common in Sarcomatoid (srcRCC) than in clear cell Renal Cell Carcinoma (ccRCC). Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01008-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Williams EA, Montesion M, Shah N, Sharaf R, Pavlick DC, Sokol ES, Alexander B, Venstrom J, Elvin JA, Ross JS, Williams KJ, Tse JY, Mochel MC. Melanoma with in-frame deletion of MAP2K1: a distinct molecular subtype of cutaneous melanoma mutually exclusive from BRAF, NRAS, and NF1 mutations. Mod Pathol 2020; 33:2397-2406. [PMID: 32483240 PMCID: PMC7685971 DOI: 10.1038/s41379-020-0581-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 11/12/2022]
Abstract
While the genomics of BRAF, NRAS, and other key genes influencing MAP kinase (MAPK) activity have been thoroughly characterized in melanoma, mutations in MAP2K1 (MEK1) have received significantly less attention and have consisted almost entirely of missense mutations considered secondary oncogenic drivers of melanoma. Here, we investigated melanomas with in-frame deletions of MAP2K1, alterations characterized as MAPK-activating in recent experimental models. Our case archive of clinical melanoma samples with comprehensive genomic profiling by a hybrid capture-based DNA sequencing platform was searched for MAP2K1 genetic alterations. Clinical data, pathology reports, and histopathology were reviewed for each case. From a cohort of 7119 advanced melanomas, 37 unique cases (0.5%) featured small in-frame deletions in MAP2K1. These included E102_I103del (n = 11 cases), P105_A106del (n = 8), Q58_E62del (n = 6), I103_K104del (n = 5), I99_K104del (n = 3), L98_I103del (n = 3), and E41_F53del (n = 1). All 37 were wild type for BRAF, NRAS, and NF1 genomic alterations ("triple wild-type"), representing 2.0% of triple wild-type melanomas overall (37/1882). Median age was 66 years and 49% were male. The majority arose from primary cutaneous sites (35/37; 95%) and demonstrated a UV signature when available (21/25; 84%). Tumor mutational burden was typical for cutaneous melanoma (median = 9.6 mut/Mb, range 0-35.7), and frequently mutated genes included TERTp (63%), CDKN2A (46%), TP53 (11%), PTEN (8%), APC (8%), and CTNNB1 (5%). Histopathology revealed a spectrum of appearances typical of melanoma. For comparison, we evaluated 221 cases with pathogenic missense single nucleotide variants in MAP2K1. The vast majority of melanomas with missense SNVs in MAP2K1 showed co-mutations in BRAF (58%), NF1 (23%), or NRAS (18%). In-frame deletions in MAP2K1, previously shown in experimental models to be strongly MAPK-activating, characterized a significant subset of triple wild-type melanoma (2.0%), suggesting a primary oncogenic role for these mutations. Comprehensive genomic profiling of melanomas enables detection of this alteration, which may have implications for potential therapeutic options.
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Affiliation(s)
- Erik A Williams
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA.
| | - Meagan Montesion
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Nikunj Shah
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Radwa Sharaf
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Dean C Pavlick
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Ethan S Sokol
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Brian Alexander
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeff Venstrom
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Julia A Elvin
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology, State University of New York Upstate Medical University, 766 Irving Avenue, Syracuse, NY, 13210, USA
| | - Kevin Jon Williams
- Department of Physiology, Department of Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, 19140, USA
| | - Julie Y Tse
- Foundation Medicine, Inc., 150 Second Street, Cambridge, MA, 02141, USA
- Department of Pathology & Laboratory Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Mark C Mochel
- Departments of Pathology and Dermatology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
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Lee J, Chung J, Venstrom J, Alexander B, Schrock A, Ou SH. 99P Pan-tumor characterization of KRAS mutations (KRASm) detected in circulating tumor DNA (ctDNA) and concordance with paired tissue. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Elvin J, Danziger N, Corines J, Vergilio JA, Killian J, Lin D, Williams E, Tse J, Ramkissoon S, Severson E, Hemmerich A, Edgerly C, Duncan D, Huang R, Schrock A, Alexander B, Venstrom J, Reddy P, McGregor K, Ross J. 2001P Adenoid cystic carcinomas (ACC) of the trachea, salivary gland, breast: A comparative comprehensive genomic profiling (CGP) study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Alexander B, Sokol E, Danziger N, Pavlick D, Elvin J, Killian J, Lin D, Williams E, Ramkissoon S, Severson E, Hemmerich A, Duncan D, Edgerly C, Huang R, Hiemenz M, Reddy P, McGregor K, Venstrom J, Schrock A, Ross J. 107P Immune Checkpoint Inhibitor (ICPI) resistance genes STK11 and KEAP1: A comparative Comprehensive Genomic Profiling (CGP) study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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McGregor K, Ross J, Danziger N, Sokol E, Venstrom J, Chung J, Lee J, Alexander B, Schrock A, Tukachinsky H. 305P Patterns of acquired mutations in estrogen receptor-positive metastatic breast cancer (MBC) patients identified by comprehensive genomic profiling (CGP). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Reddy P, Danziger N, Elvin J, Vergilio JA, Killian J, Lin D, Williams E, Ramkissoon S, Severson E, Hemmerich A, Duncan D, Edgerly C, Huang R, Hiemenz M, Chung J, McGregor K, Venstrom J, Schrock A, Alexander B, Ross J. 957P Ameloblastoma of the head and neck (HNAMB): A comprehensive profiling (CGP) study. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Xu PP, Sun C, Cao X, Zhao X, Dai HJ, Lu S, Guo JJ, Fu SJ, Liu YX, Li SC, Chen M, McCord R, Venstrom J, Szafer-Glusman E, Punnoose E, Kiermaier A, Cheng G, Zhao WL. Immune Characteristics of Chinese Diffuse Large B-Cell Lymphoma Patients: Implications for Cancer Immunotherapies. EBioMedicine 2018; 33:94-104. [PMID: 29936139 PMCID: PMC6085499 DOI: 10.1016/j.ebiom.2018.06.010] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Immunotherapeutic agents have demonstrated encouraging signs of clinical utility in non-Hodgkin lymphoma. The goal of this study is to analyze the immune characteristics of Chinese patients with diffuse large B-cell lymphoma (DLBCL) to inform the development of immunotherapies in this patient population. Tumor samples from 211 DLBCL patients were analyzed for cell of origin (COO) and immune characteristics using the NanoString platform as well as MYC protein expression through immunohistochemistry. Lower incidence of the germinal center B-cell (GCB) subtype (93/211, 44.1%) was observed in this cohort. Compared to the GCB subtype, the activated B-cell (ABC) subtype was associated with significantly increased expression of multiple pro-inflammatory gene signatures and decreased expression of anti-inflammatory gene signatures. Instead of affecting the pro-inflammatory genes, MYC protein overexpression showed a negative correlation with the expression of T-cell receptor (TCR) and T regulatory genes as well as the OX40 gene. Regardless of COO, higher PD-L1 or IDO1 gene expression correlated with increased expression of T effector and Interferon-γ gene signatures while the expression of multiple oncogenes including ACTR3B, ERBB2, AKT2 and SMARCD1 was down-regulated. Our findings may thus be helpful in guiding further development of immunotherapies for the different subsets of Chinese DLBCL patients.
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Affiliation(s)
- Peng-Peng Xu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chun Sun
- Oncology Biomarker Development, Genentech Inc., Shanghai, China
| | - Xu Cao
- Oncology Biomarker Development, Genentech Inc., Shanghai, China
| | - Xia Zhao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hang-Jun Dai
- Roche Product Development in Asia Pacific, Roche (China) Holding, Ltd., Shanghai, China
| | - Shan Lu
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Jian-Jun Guo
- Oncology Biomarker Development, Genentech Inc., Shanghai, China
| | - Shi-Jing Fu
- Oncology Biomarker Development, Genentech Inc., Shanghai, China
| | - Yu-Xia Liu
- Oncology Biomarker Development, Genentech Inc., Shanghai, China
| | - Su-Chun Li
- Roche Product Development in Asia Pacific, Roche (China) Holding, Ltd., Shanghai, China
| | - Meng Chen
- Roche Product Development in Asia Pacific, Roche (China) Holding, Ltd., Shanghai, China
| | - Ron McCord
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Jeff Venstrom
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | | | - Elizabeth Punnoose
- Oncology Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Astrid Kiermaier
- Oncology Biomarker Development, Genentech Inc., Basel, Switzerland
| | - Gang Cheng
- Oncology Biomarker Development, Genentech Inc., Shanghai, China.
| | - Wei-Li Zhao
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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