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Li Z, Gao X, Peng X, May Chen MJ, Li Z, Wei B, Wen X, Wei B, Dong Y, Bu Z, Wu A, Wu Q, Tang L, Li Z, Liu Y, Zhang L, Jia S, Zhang L, Shan F, Zhang J, Wu X, Ji X, Ji K, Wu X, Shi J, Xing X, Wu J, Lv G, Shen L, Ji X, Liang H, Ji J. Multi-omics characterization of molecular features of gastric cancer correlated with response to neoadjuvant chemotherapy. SCIENCE ADVANCES 2020; 6:eaay4211. [PMID: 32133402 PMCID: PMC7043923 DOI: 10.1126/sciadv.aay4211] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 12/06/2019] [Indexed: 05/05/2023]
Abstract
Neoadjuvant chemotherapy is a common treatment for patients with gastric cancer. Although its benefits have been demonstrated, neoadjuvant chemotherapy is underutilized in gastric cancer management, because of the lack of biomarkers for patient selection and a limited understanding of resistance mechanisms. Here, we performed whole-genome, whole-exome, and RNA sequencing on 84 clinical samples (including matched pre- and posttreatment tumors) from 35 patients whose responses to neoadjuvant chemotherapy were rigorously defined. We observed increased microsatellite instability and mutation burden in nonresponse tumors. Through comparisons of response versus nonresponse tumors and pre- versus posttreatment samples, we found that C10orf71 mutations were associated with treatment resistance, which was supported by drug response data and potentially through inhibition of cell cycle, and that MYC amplification correlated with treatment sensitivity, whereas MDM2 amplification showed the opposite pattern. Neoadjuvant chemotherapy also reshapes tumor-immune signaling and microenvironment. Our study provides a critical basis for developing precision neoadjuvant regimens.
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Affiliation(s)
- Ziyu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiangyu Gao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xinxin Peng
- Precision Scientific (Beijing) Ltd., Beijing 100085, China
| | - Mei-Ju May Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhe Li
- Precision Scientific (Beijing) Ltd., Beijing 100085, China
| | - Bin Wei
- Precision Scientific (Beijing) Ltd., Beijing 100085, China
| | - Xianzi Wen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), GI Cancer Translation Research Lab, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Baoye Wei
- Precision Scientific (Beijing) Ltd., Beijing 100085, China
| | - Yu Dong
- Precision Scientific (Beijing) Ltd., Beijing 100085, China
| | - Zhaode Bu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Aiwen Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Qi Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Endoscopy Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Lei Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhongwu Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yiqiang Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Li Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Shuqin Jia
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Molecular Diagnostics, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Fei Shan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Ji Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaojiang Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xin Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Ke Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaolong Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jinyao Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), GI Cancer Translation Research Lab, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaofang Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Molecular Diagnostics, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jianmin Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Guoqing Lv
- Department of Gastrointestinal Surgery, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - Lin Shen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of GI Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xuwo Ji
- Precision Scientific (Beijing) Ltd., Beijing 100085, China
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Corresponding author. (J.J.); (H.L.)
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Gastrointestinal Cancer Center, Peking University Cancer Hospital and Institute, Beijing 100142, China
- Corresponding author. (J.J.); (H.L.)
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Singh RR, Goldberg J, Varghese AM, Yu KH, Park W, O'Reilly EM. Genomic profiling in pancreatic ductal adenocarcinoma and a pathway towards therapy individualization: A scoping review. Cancer Treat Rev 2019; 75:27-38. [PMID: 30927677 PMCID: PMC6504563 DOI: 10.1016/j.ctrv.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/20/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
CONTEXT Pancreatic cancer (PDAC) is one of the most challenging cancers to treat with modest recent improvements in survival from new systemic therapies. There is growing interest in individualized therapy underpinned by somatic and germline genomic alterations. OBJECTIVE A systematic review of data on therapies targeting somatic and germline alterations, and their downstream pathways in PDAC. METHOD A systematic literature search was conducted using PRISMA guidelines to include relevant results published after January 1, 2008. RESULTS A total of 71 relevant studies were included. We identified 36 studies targeting the KRAS-pathway, the most common being with MEK-inhibitor therapy. Twenty-two studies were identified that evaluated platinum-based chemotherapy and PARP inhibitors in patients with deleterious mutations in DNA damage repair genes and have shown encouraging results. Immunotherapy has demonstrated activity in patients with mismatch repair deficiency/microsatellite instability. CONCLUSION Evidence from translational and clinical research presents an exciting platform for genomic targeted therapy in PDAC. Validity for targeting BRCA with platinum and PARP inhibitors and microsatellite instability with immune therapy has been established, nonetheless, evidence for targeting the common driver oncogenes is lacking and much work is needed. Of importance is identifying the subgroup of KRAS -wild type PDAC (approximately 5%) where there is enrichment for targetable opportunities.
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Affiliation(s)
- Ritu R Singh
- Department of Medicine, Icahn School of Medicine at Mount Sinai, Mount Sinai St. Luke's and Mount Sinai West, New York, NY 10019, USA.
| | - Johanna Goldberg
- MSK Library, 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; Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kenneth H Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wungki Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA; David M. Rubenstein Center for Pancreatic Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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