1
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Qin T, Hu Z, Zhang L, Lu F, Xiao R, Liu Y, Fan J, Guo E, Yang B, Fu Y, Zhuang X, Kang X, Wu Z, Fang Z, Cui Y, Hu X, Yin J, Yan M, Li F, Song K, Chen G, Sun C. Genomic profiling of a multi-lineage and multi-passage patient-derived xenograft biobank reflects heterogeneity of ovarian cancer. Cell Rep Med 2024; 5:101631. [PMID: 38986623 PMCID: PMC11293341 DOI: 10.1016/j.xcrm.2024.101631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/16/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024]
Abstract
Ovarian cancer (OC) manifests as a complex disease characterized by inter- and intra-patient heterogeneity. Despite enhanced biological and genetic insights, OC remains a recalcitrant malignancy with minimal survival improvement. Based on multi-site sampling and a multi-lineage patient-derived xenograft (PDX) establishment strategy, we present herein the establishment of a comprehensive PDX biobank from histologically and molecularly heterogeneous OC patients. Comprehensive profiling of matched PDX and patient samples demonstrates that PDXs closely recapitulate parental tumors. By leveraging multi-lineage models, we reveal that the previously reported genomic disparities of PDX could be mainly attributed to intra-patient spatial heterogeneity instead of substantial model-independent genomic evolution. Moreover, DNA damage response pathway inhibitor (DDRi) screening uncovers heterogeneous responses across models. Prolonged iterative drug exposure recapitulates acquired drug resistance in initially sensitive models. Meanwhile, interrogation of induced drug-resistant (IDR) models reveals that suppressed interferon (IFN) response and activated Wnt/β-catenin signaling contribute to acquired DDRi drug resistance.
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Affiliation(s)
- Tianyu Qin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Zhe Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Li Zhang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Funian Lu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Yiting Liu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Junpeng Fan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Ensong Guo
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Bin Yang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Yu Fu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Xucui Zhuang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Xiaoyan Kang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Zimeng Wu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Zixuan Fang
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Yaoyuan Cui
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Xingyuan Hu
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Jingjing Yin
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Miao Yan
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China
| | - Fuxia Li
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Shihezi University School of Medicine, Shihezi, Xinjiang 832008, P.R. China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.
| | - Gang Chen
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China.
| | - Chaoyang Sun
- Department of Gynecological Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China; National Clinical Research Center for Obstetrics and Gynecology, Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430010, P.R. China; Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.
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Deboever N, Jones CM, Yamashita K, Ajani JA, Hofstetter WL. Advances in diagnosis and management of cancer of the esophagus. BMJ 2024; 385:e074962. [PMID: 38830686 DOI: 10.1136/bmj-2023-074962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Esophageal cancer is the seventh most common malignancy worldwide, with over 470 000 new cases diagnosed each year. Two distinct histological subtypes predominate, and should be considered biologically separate disease entities.1 These subtypes are esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC). Outcomes remain poor regardless of subtype, with most patients presenting with late stage disease.2 Novel strategies to improve early detection of the respective precursor lesions, squamous dysplasia, and Barrett's esophagus offer the potential to improve outcomes. The introduction of a limited number of biologic agents, as well as immune checkpoint inhibitors, is resulting in improvements in the systemic treatment of locally advanced and metastatic esophageal cancer. These developments, coupled with improvements in minimally invasive surgical and endoscopic treatment approaches, as well as adaptive and precision radiotherapy technologies, offer the potential to improve outcomes still further. This review summarizes the latest advances in the diagnosis and management of esophageal cancer, and the developments in understanding of the biology of this disease.
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Affiliation(s)
- Nathaniel Deboever
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher M Jones
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
- Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Kohei Yamashita
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Wayne L Hofstetter
- Department of Thoracic and Cardiovascular Surgery, MD Anderson Cancer Center, Houston, TX, USA
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3
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Stachler MD, Jin RU. Molecular Pathology of Gastroesophageal Cancer. Clin Lab Med 2024; 44:239-254. [PMID: 38821643 DOI: 10.1016/j.cll.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Upper gastroesophageal carcinomas consist of cancers arising from the esophagus and stomach. Squamous cell carcinomas and adenocarcinomas are seen in the esophagus and despite arising from the same organ have different biology. Gastric adenocarcinomas are categorized into 4 molecular subtypes: high Epstein-Barr virus load, microsatellite unstable cancers, chromosomal unstable (CIN) cancers, and genomically stable cancers. Genomically stable gastric cancers correlate highly with histologically defined diffuse-type cancers. Esophageal carcinomas and CIN gastric cancers often are driven by high-level amplifications of oncogenes and contain a high degree of intratumoral heterogeneity. Targeted therapeutics is an active area of research for gastroesophageal cancers.
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Affiliation(s)
- Matthew D Stachler
- Department of Pathology, University of California San Francisco, 513 Parnassus Avenue HSW450B, San Francisco, CA 94143, USA.
| | - Ramon U Jin
- Section of Hematology/Oncology, Department of Medicine, Baylor College of Medicine, 7200 Cambridge Street, Suite 7B, MS: BCM904, Houston, TX 77030, USA
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4
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Min Q, Zhang M, Lin D, Zhang W, Li X, Zhao L, Teng H, He T, Sun W, Fan J, Yu X, Chen J, Li J, Gao X, Dong B, Liu R, Liu X, Song Y, Cui Y, Lu SH, Li R, Guo M, Wang Y, Zhan Q. Genomic characterization and risk stratification of esophageal squamous dysplasia. MEDICAL REVIEW (2021) 2024; 4:244-256. [PMID: 38919397 PMCID: PMC11195426 DOI: 10.1515/mr-2024-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Objectives The majority of esophageal squamous dysplasia (ESD) patients progress slowly, while a subset of patients can undergo recurrence rapidly or progress to invasive cancer even after proper treatment. However, the molecular mechanisms underlying these clinical observations are still largely unknown. Methods By sequencing the genomic data of 160 clinical samples from 49 tumor-free ESD patients and 88 esophageal squamous cell carcinoma (ESCC) patients, we demonstrated lower somatic mutation and copy number alteration (CNA) burden in ESD compared with ESCC. Results Cross-species screening and functional assays identified ACSM5 as a novel driver gene for ESD progression. Furthermore, we revealed that miR-4292 promoted ESD progression and could serve as a non-invasive diagnostic marker for ESD. Conclusions These findings largely expanded our understanding of ESD genetics and tumorigenesis, which possessed promising significance for improving early diagnosis, reducing overtreatment, and identifying high-risk ESD patients.
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Affiliation(s)
- Qingjie Min
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | | | - Dongmei Lin
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xianfeng Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Department of Gastroenterology, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Lianmei Zhao
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huajing Teng
- Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Tao He
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
- Department of Pathology, Characteristic Medical Center of Chinese People’s Armed Police Force, Tianjin, China
| | - Wei Sun
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiawen Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiying Yu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xiaohan Gao
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Central Laboratory, Peking University Cancer Hospital & Institute, Beijing, China
| | - Rui Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xuefeng Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongping Cui
- Shenzhen Peking University-The Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Shih-Hsin Lu
- Department of Etiology and Carcinogenesis and State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Beijing, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Peking University International Cancer Institute, Peking University, Beijing, China
- Soochow University Cancer Institute, Suzhou, China
- State Key Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
- Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, China
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5
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Stachler MD, Ain QU. Refining definitions of Barrett's oesophagus to improve clinical resource utilisation. Gut 2024; 73:715-716. [PMID: 38216329 DOI: 10.1136/gutjnl-2023-331458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/07/2024] [Indexed: 01/14/2024]
Affiliation(s)
- Matthew D Stachler
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Qurat Ul Ain
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
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6
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Choi WT, Rabinovitch PS. DNA flow cytometry for detection of genomic instability as a cancer precursor in the gastrointestinal tract. Methods Cell Biol 2024; 186:25-49. [PMID: 38705603 DOI: 10.1016/bs.mcb.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
One of the earliest applications of flow cytometry was the measurement of DNA content in cells. This method is based on the ability to stain DNA in a stoichiometric manner (i.e., the amount of stain is directly proportional to the amount of DNA within the cell). For more than 40years, a number of studies have consistently demonstrated the utility of DNA flow cytometry as a potential diagnostic and/or prognostic tool in patients with most epithelial tumors, including pre-invasive lesions (such as dysplasia) in the gastrointestinal tract. However, its availability as a clinical test has been limited to few medical centers due to the requirement for fresh tissue in earlier studies and perceived technical demands. However, more recent studies have successfully utilized formalin-fixed paraffin-embedded (FFPE) tissue to generate high-quality DNA content histograms, demonstrating the feasibility of this methodology. This review summarizes step-by-step methods on how to perform DNA flow cytometry using FFPE tissue and analyze DNA content histograms based on the published consensus guidelines in order to assist in the diagnosis and/or risk stratification of many different epithelial tumors, with particular emphasis on dysplasia associated with Barrett's esophagus and inflammatory bowel disease.
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Affiliation(s)
- Won-Tak Choi
- Department of Pathology, University of California at San Francisco, San Francisco, CA, United States.
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
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7
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Weh KM, Howard CL, Zhang Y, Tripp BA, Clarke JL, Howell AB, Rubenstein JH, Abrams JA, Westerhoff M, Kresty LA. Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome. JCI Insight 2024; 9:e168112. [PMID: 38329812 PMCID: PMC11063939 DOI: 10.1172/jci.insight.168112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/02/2024] [Indexed: 02/10/2024] Open
Abstract
The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammation-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett's esophagus, and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities and metabolites contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. Sprague-Dawley rats, with or without reflux induction, received water or C-PAC ad libitum (700 μg/rat/day) for 25 or 40 weeks. C-PAC exerted prebiotic activity abrogating reflux-induced dysbiosis and mitigating bile acid metabolism and transport, culminating in significant inhibition of EAC through TLR/NF-κB/TP53 signaling cascades. At the species level, C-PAC mitigated reflux-induced pathogenic bacteria (Streptococcus parasanguinis, Escherichia coli, and Proteus mirabilis). C-PAC specifically reversed reflux-induced bacterial, inflammatory, and immune-implicated proteins and genes, including Ccl4, Cd14, Crp, Cxcl1, Il6, Il1b, Lbp, Lcn2, Myd88, Nfkb1, Tlr2, and Tlr4, aligning with changes in human EAC progression, as confirmed through public databases. C-PAC is a safe, promising dietary constituent that may be utilized alone or potentially as an adjuvant to current therapies to prevent EAC progression through ameliorating reflux-induced dysbiosis, inflammation, and cellular damage.
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Affiliation(s)
- Katherine M. Weh
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Connor L. Howard
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Yun Zhang
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Jennifer L. Clarke
- Department of Statistics, Department of Food Science Technology, Quantitative Life Sciences Initiative, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Amy B. Howell
- Marucci Center for Blueberry and Cranberry Research, Rutgers University, Chatsworth, New Jersey, USA
| | - Joel H. Rubenstein
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- LTC Charles S. Kettles Veterans Affairs Medical Center, Ann Arbor, Michigan, USA
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Maria Westerhoff
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Laura A. Kresty
- Department of Surgery, Section of Thoracic Surgery, and
- Rogel Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
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8
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Martinez-Uribe O, Becker TC, Garman KS. Promises and Limitations of Current Models for Understanding Barrett's Esophagus and Esophageal Adenocarcinoma. Cell Mol Gastroenterol Hepatol 2024; 17:1025-1038. [PMID: 38325549 PMCID: PMC11041847 DOI: 10.1016/j.jcmgh.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND & AIMS This review was developed to provide a thorough and effective update on models relevant to esophageal metaplasia, dysplasia, and carcinogenesis, focusing on the advantages and limitations of different models of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC). METHODS This expert review was written on the basis of a thorough review of the literature combined with expert interpretation of the state of the field. We emphasized advances over the years 2012-2023 and provided detailed information related to the characterization of established human esophageal cell lines. RESULTS New insights have been gained into the pathogenesis of BE and EAC using patient-derived samples and single-cell approaches. Relevant animal models include genetic as well as surgical mouse models and emphasize the development of lesions at the squamocolumnar junction in the mouse stomach. Rat models are generated using surgical approaches that directly connect the small intestine and esophagus. Large animal models have the advantage of including features in human esophagus such as esophageal submucosal glands. Alternatively, cell culture approaches remain important in the field and allow for personalized approaches, and scientific rigor can be ensured by authentication of cell lines. CONCLUSIONS Research in BE and EAC remains highly relevant given the morbidity and mortality associated with cancers of the tubular esophagus and gastroesophageal junction. Careful selection of models and inclusion of human samples whenever possible will ensure relevance to human health and disease.
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Affiliation(s)
- Omar Martinez-Uribe
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina
| | - Thomas C Becker
- Division of Endocrinology, Department of Medicine, Duke University, Durham, North Carolina
| | - Katherine S Garman
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, North Carolina.
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9
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Fujii M, Sekine S, Sato T. Decoding the basis of histological variation in human cancer. Nat Rev Cancer 2024; 24:141-158. [PMID: 38135758 DOI: 10.1038/s41568-023-00648-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
Molecular abnormalities that shape human neoplasms dissociate their phenotypic landscape from that of the healthy counterpart. Through the lens of a microscope, tumour pathology optically captures such aberrations projected onto a tissue slide and has categorized human epithelial neoplasms into distinct histological subtypes based on the diverse morphogenetic and molecular programmes that they manifest. Tumour histology often reflects tumour aggressiveness, patient prognosis and therapeutic vulnerability, and thus has been used as a de facto diagnostic tool and for making clinical decisions. However, it remains elusive how the diverse histological subtypes arise and translate into pleiotropic biological phenotypes. Molecular analysis of clinical tumour tissues and their culture, including patient-derived organoids, and add-back genetic reconstruction of tumorigenic pathways using gene engineering in culture models and rodents further elucidated molecular mechanisms that underlie morphological variations. Such mechanisms include genetic mutations and epigenetic alterations in cellular identity codes that erode hard-wired morphological programmes and histologically digress tumours from the native tissues. Interestingly, tumours acquire the ability to grow independently of the niche-driven stem cell ecosystem along with these morphological alterations, providing a biological rationale for histological diversification during tumorigenesis. This Review comprehensively summarizes our current understanding of such plasticity in the histological and lineage commitment fostered cooperatively by molecular alterations and the tumour environment, and describes basic and clinical implications for future cancer therapy.
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Affiliation(s)
- Masayuki Fujii
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
| | - Shigeki Sekine
- Division of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Toshiro Sato
- Department of Integrated Medicine and Biochemistry, Keio University School of Medicine, Tokyo, Japan.
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10
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Wang Y, Douville C, Chien YW, Wang BG, Chen CL, Pinto A, Smith SA, Drapkin R, Chui MH, Numan T, Vang R, Papadopoulos N, Wang TL, Shih IM. Aneuploidy Landscape in Precursors of Ovarian Cancer. Clin Cancer Res 2024; 30:600-615. [PMID: 38048050 DOI: 10.1158/1078-0432.ccr-23-0932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/21/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
PURPOSE Serous tubal intraepithelial carcinoma (STIC) is now recognized as the main precursor of ovarian high-grade serous carcinoma (HGSC). Other potential tubal lesions include p53 signatures and tubal intraepithelial lesions. We aimed to investigate the extent and pattern of aneuploidy in these epithelial lesions and HGSC to define the features that characterize stages of tumor initiation and progression. EXPERIMENTAL DESIGN We applied RealSeqS to compare genome-wide aneuploidy patterns among the precursors, HGSC (cases, n = 85), and histologically unremarkable fallopian tube epithelium (HU-FTE; control, n = 65). On the basis of a discovery set (n = 67), we developed an aneuploidy-based algorithm, REAL-FAST (Repetitive Element AneupLoidy Sequencing Fallopian Tube Aneuploidy in STIC), to correlate the molecular data with pathology diagnoses. We validated the result in an independent validation set (n = 83) to determine its performance. We correlated the molecularly defined precursor subgroups with proliferative activity and histology. RESULTS We found that nearly all p53 signatures lost the entire Chr17, offering a "two-hit" mechanism involving both TP53 and BRCA1 in BRCA1 germline mutation carriers. Proliferatively active STICs harbor gains of 19q12 (CCNE1), 19q13.2, 8q24 (MYC), or 8q arm, whereas proliferatively dormant STICs show 22q loss. REAL-FAST classified HU-FTE and STICs into 5 clusters and identified a STIC subgroup harboring unique aneuploidy that is associated with increased proliferation and discohesive growth. On the basis of a validation set, REAL-FAST showed 95.8% sensitivity and 97.1% specificity in detecting STIC/HGSC. CONCLUSIONS Morphologically similar STICs are molecularly distinct. The REAL-FAST assay identifies a potentially "aggressive" STIC subgroup harboring unique DNA aneuploidy that is associated with increased cellular proliferation and discohesive growth. REAL-FAST offers a highly reproducible adjunct technique to assist the diagnosis of STIC lesions.
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Affiliation(s)
- Yeh Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Yen-Wei Chien
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Brant G Wang
- Department of Pathology, Inova Fairfax Hospital, Falls Church, Virginia
- School of Medicine Inova Campus, University of Virginia, Falls Church, Virginia
- Department of Pathology, Georgetown University Medical Center, Washington, DC
| | - Chi-Long Chen
- Department of Pathology, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Andre Pinto
- University of Miami Sylvester Comprehensive Cancer Center, Miami, Florida
| | - Saron Ann Smith
- Cascade Pathology Services, Legacy Health System, Portland, Oregon
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology and Basser Center for BRCA, University of Pennsylvania, Philadelphia, Pennsylvania
| | - M Herman Chui
- Department of Pathology and Laboratory Medicine, Sloan-Kettering Cancer Center, New York, New York
| | - Tricia Numan
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Pathology, Sibley Memorial Hospital, Washington, DC
| | - Russell Vang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Tian-Li Wang
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, Maryland
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11
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Sun J, Sepulveda JL, Komissarova EV, Hills C, Seckar TD, LeFevre NM, Simonyan H, Young C, Su G, Del Portillo A, Wang TC, Sepulveda AR. CDKN2A-p16 Deletion and Activated KRAS G12D Drive Barrett's-Like Gland Hyperplasia-Metaplasia and Synergize in the Development of Dysplasia Precancer Lesions. Cell Mol Gastroenterol Hepatol 2024; 17:769-784. [PMID: 38296052 PMCID: PMC10966774 DOI: 10.1016/j.jcmgh.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND & AIMS Barrett's esophagus is the precursor of esophageal dysplasia and esophageal adenocarcinoma. CDKN2A-p16 deletions were reported in 34%-74% of patients with Barrett's esophagus who progressed to dysplasia and esophageal adenocarcinoma, suggesting that p16 loss may drive neoplastic progression. KRAS activation frequently occurs in esophageal adenocarcinoma and precancer lesions. LGR5+ stem cells in the squamocolumnar-junction (SCJ) of mouse stomach contribute as Barrett's esophagus progenitors. We aimed to determine the functional effects of p16 loss and KRAS activation in Barrett's-like metaplasia and dysplasia development. METHODS We established mouse models with conditional knockout of CDKN2A-p16 (p16KO) and/or activated KRASG12D expression targeting SCJ LGR5+ cells in interleukin 1b transgenic mice and characterized histologic alterations (mucous-gland hyperplasia/metaplasia, inflammation, and dysplasia) in mouse SCJ. Gene expression was determined by microarray, RNA sequencing, and immunohistochemistry of SCJ tissues and cultured 3-dimensional organoids. RESULTS p16KO mice exhibited increased mucous-gland hyperplasia/metaplasia versus control mice (P = .0051). Combined p16KO+KRASG12D resulted in more frequent dysplasia and higher dysplasia scores (P = .0036), with 82% of p16KO+KRASG12D mice developing high-grade dysplasia. SCJ transcriptome analysis showed several activated pathways in p16KO versus control mice (apoptosis, tumor necrosis factor-α/nuclear factor-kB, proteasome degradation, p53 signaling, MAPK, KRAS, and G1-to-S transition). CONCLUSIONS p16 deletion in LGR5+ cell precursors triggers increased SCJ mucous-gland hyperplasia/metaplasia. KRASG12D synergizes with p16 deletion resulting in higher grades of SCJ glandular dysplasia, mimicking Barrett's high-grade dysplasia. These genetically modified mouse models establish a functional role of p16 and activated KRAS in the progression of Barrett's-like lesions to dysplasia in mice, representing an in vivo model of esophageal adenocarcinoma precancer. Derived 3-dimensional organoid models further provide in vitro modeling opportunities of esophageal precancer stages.
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Affiliation(s)
- Jing Sun
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Jorge L Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Elena V Komissarova
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Caitlin Hills
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Tyler D Seckar
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Narine M LeFevre
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Hayk Simonyan
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Colin Young
- Department of Pharmacology & Physiology, George Washington University, School of Medicine and Health Sciences, Washington, DC
| | - Gloria Su
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Armando Del Portillo
- Department of Pathology and Cell Biology, Columbia University, New York, New York
| | - Timothy C Wang
- Division of Digestive and Liver diseases, Department of Medicine, Columbia University, New York, New York
| | - Antonia R Sepulveda
- Department of Pathology, George Washington University School of Medicine and Health Sciences, Washington, DC.
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12
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Lauricella M, Di Liberto D. Special Issue: "Inflammatory Signaling Pathways Involved in Gastrointestinal Diseases". Int J Mol Sci 2024; 25:1287. [PMID: 38279287 PMCID: PMC10816278 DOI: 10.3390/ijms25021287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Inflammation is a defensive response of the innate and adaptive immune systems against injury and/or harmful microorganisms to restore homeostasis [...].
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Affiliation(s)
- Marianna Lauricella
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
| | - Diana Di Liberto
- Department of Biomedicine, Neurosciences and Advanced Diagnostics (BIND), Institute of Biochemistry, University of Palermo, 90127 Palermo, Italy
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13
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Qurat-ul-Ain, Frei NF, Khoshiwal AM, Stougie P, Odze R, Camilleri-Broet S, Ferri L, Duits LC, Bergman J, Stachler MD. Feasibility Study Utilizing NanoString's Digital Spatial Profiling (DSP) Technology for Characterizing the Immune Microenvironment in Barrett's Esophagus Formalin-Fixed Paraffin-Embedded Tissues. Cancers (Basel) 2023; 15:5895. [PMID: 38136440 PMCID: PMC10742302 DOI: 10.3390/cancers15245895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Characterization of the Barrett's esophagus (BE) microenvironment in patients with a known progression status, to determine how it may influence BE progression to esophageal adenocarcinoma (EAC), has been understudied, hindering both the biological understanding of the progression and the development of novel diagnostics and therapies. This study's aim was to determine if a highly multiplex interrogation of the microenvironment can be performed on endoscopic formalin-fixed, paraffin-embedded (FFPE) samples, utilizing the NanoString GeoMx digital spatial profiling (GeoMx DSP) platform and if it can begin to identify the types of immune cells and pathways that may mediate the progression of BE. We performed a spatial proteomic analysis of 49 proteins expressed in the microenvironment and epithelial cells of FFPE endoscopic biopsies from patients with non-dysplastic BE (NDBE) who later progressed to high-grade dysplasia or EAC (n = 7) or from patients who, after at least 5 years follow-up, did not (n = 8). We then performed an RNA analysis of 1812 cancer-related transcripts on three endoscopic mucosal resections containing regions of BE, dysplasia, and EAC. Profiling with GeoMx DSP showed reasonable quality metrics and detected expected differences between epithelium and stroma. Several proteins were found to have an increased expression within NDBE biopsies from progressors compared to non-progressors, suggesting further studies are warranted.
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Affiliation(s)
- Qurat-ul-Ain
- Department of Pathology, University of California, San Francisco, CA 94143, USA;
| | - Nicola F. Frei
- Amsterdam UMC Locatie AMC, 1105 AZ Amsterdam, The Netherlands
| | | | - Pim Stougie
- Amsterdam UMC Locatie AMC, 1105 AZ Amsterdam, The Netherlands
| | - Robert Odze
- Department of Pathology, School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Sophie Camilleri-Broet
- Division of Thoracic and Upper Gastrointestinal Surgery, Montreal General Hospital, McGill University, Montreal, QC H3G 1A4, Canada
| | - Lorenzo Ferri
- Division of Thoracic and Upper Gastrointestinal Surgery, Montreal General Hospital, McGill University, Montreal, QC H3G 1A4, Canada
| | - Lucas C. Duits
- Amsterdam UMC Locatie AMC, 1105 AZ Amsterdam, The Netherlands
| | - Jacques Bergman
- Amsterdam UMC Locatie AMC, 1105 AZ Amsterdam, The Netherlands
| | - Matthew D. Stachler
- Department of Pathology, University of California, San Francisco, CA 94143, USA;
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14
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Sahgal P, Patil DT, Bala P, Sztupinszki ZM, Tisza V, Spisak S, Luong AG, Huffman B, Prosz A, Singh H, Lazaro JB, Szallasi Z, Cleary JM, Sethi NS. Replicative stress in gastroesophageal cancer is associated with chromosomal instability and sensitivity to DNA damage response inhibitors. iScience 2023; 26:108169. [PMID: 37965133 PMCID: PMC10641495 DOI: 10.1016/j.isci.2023.108169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 11/16/2023] Open
Abstract
Gastroesophageal adenocarcinoma (GEA) is an aggressive malignancy with chromosomal instability (CIN). To understand adaptive responses enabling DNA damage response (DDR) and CIN, we analyzed matched normal, premalignant, and malignant gastric lesions from human specimens and a carcinogen-induced mouse model, observing activation of replication stress, DDR, and p21 in neoplastic progression. In GEA cell lines, expression of DDR markers correlated with ploidy abnormalities, such as number of high-level focal amplifications and whole-genome duplication (WGD). Integrating TP53 status, ploidy abnormalities, and DDR markers into a compositive score helped predict GEA cell lines with enhanced sensitivity to Chk1/2 and Wee1 inhibition, either alone or combined with irinotecan (SN38). We demonstrate that Chk1/2 or Wee1 inhibition combined with SN38/irinotecan shows greater anti-tumor activity in human gastric cancer organoids and an in vivo xenograft mouse model. These findings indicate that specific DDR biomarkers and ploidy abnormalities may predict premalignant progression and response to DDR pathway inhibitors.
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Affiliation(s)
- Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Pratyusha Bala
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
| | - Zsofia M. Sztupinszki
- Danish Cancer Institute, 2100 Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
| | - Anna G. Luong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Brandon Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Aurel Prosz
- Danish Cancer Institute, 2100 Copenhagen, Denmark
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zoltan Szallasi
- Danish Cancer Institute, 2100 Copenhagen, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Bioinformatics and Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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15
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Li S, Hoefnagel SJM, Krishnadath KK. Molecular Biology and Clinical Management of Esophageal Adenocarcinoma. Cancers (Basel) 2023; 15:5410. [PMID: 38001670 PMCID: PMC10670638 DOI: 10.3390/cancers15225410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is a highly lethal malignancy. Due to its rising incidence, EAC has become a severe health challenge in Western countries. Current treatment strategies are mainly chosen based on disease stage and clinical features, whereas the biological background is hardly considered. In this study, we performed a comprehensive review of existing studies and discussed how etiology, genetics and epigenetic characteristics, together with the tumor microenvironment, contribute to the malignant behavior and dismal prognosis of EAC. During the development of EAC, several intestinal-type proteins and signaling cascades are induced. The anti-inflammatory and immunosuppressive microenvironment is associated with poor survival. The accumulation of somatic mutations at the early phase and chromosomal structural rearrangements at relatively later time points contribute to the dynamic and heterogeneous genetic landscape of EAC. EAC is also characterized by frequent DNA methylation and dysregulation of microRNAs. We summarize the findings of dysregulations of specific cytokines, chemokines and immune cells in the tumor microenvironment and conclude that DNA methylation and microRNAs vary with each different phase of BE, LGD, HGD, early EAC and invasive EAC. Furthermore, we discuss the suitability of the currently employed therapies in the clinic and possible new therapies in the future. The development of targeted and immune therapies has been hampered by the heterogeneous genetic characteristics of EAC. In view of this, the up-to-date knowledge revealed by this work is absolutely important for future EAC studies and the discovery of new therapeutics.
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Affiliation(s)
- Shulin Li
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | | | - Kausilia Krishnawatie Krishnadath
- Department of Gastroenterology and Hepatology, Antwerp University Hospital, 2650 Edegem, Belgium
- Laboratory of Experimental Medicine and Pediatrics, University of Antwerp, 2000 Antwerpen, Belgium
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16
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Lee M, Eng G, Handte-Reinecker A, Deshpande VS, Yilmaz OH, Gala MK. Germline Determinants of Esophageal Adenocarcinoma. Gastroenterology 2023; 165:1276-1279.e7. [PMID: 37507074 PMCID: PMC10592248 DOI: 10.1053/j.gastro.2023.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023]
Affiliation(s)
- Minyi Lee
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; MD-PhD Program, Boston University School of Medicine, Boston, Massachusetts
| | - George Eng
- Division of Gastroenterology and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Anna Handte-Reinecker
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Vikram S Deshpande
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Omer H Yilmaz
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Manish K Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts.
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17
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Bao C, Tourdot RW, Brunette GJ, Stewart C, Sun L, Baba H, Watanabe M, Agoston AT, Jajoo K, Davison JM, Nason KS, Getz G, Wang KK, Imamura Y, Odze R, Bass AJ, Stachler MD, Zhang CZ. Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma. Nat Commun 2023; 14:6203. [PMID: 37794034 PMCID: PMC10550953 DOI: 10.1038/s41467-023-41805-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.
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Affiliation(s)
- Chunyang Bao
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Richard W Tourdot
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Gregory J Brunette
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Lili Sun
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 2 Chome-40-1 Kurokami, Chuo Ward, Kumamoto, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kunal Jajoo
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Katie S Nason
- Department of Surgery, Baystate Medical Center, University of Massachusetts Medical School, 759 Chestnut St, Springfield, MA, 01107, USA
| | - Gad Getz
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Department of Pathology and Lab Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Matthew D Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Department of Pathology, University of California, San Francisco. 513 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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18
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Akizue N, Okimoto K, Hirotsu Y, Amemiya K, Kaneko T, Ohta Y, Taida T, Saito K, Matsumura T, Nishimura M, Matsushita K, Mochizuki H, Chiba T, Arai M, Kato J, Omata M, Kato N. Carcinogenic potential in regenerated mucosa after endoscopic resection of esophageal squamous cell carcinoma. J Gastroenterol Hepatol 2023; 38:1546-1551. [PMID: 37194195 DOI: 10.1111/jgh.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/04/2022] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIM Little is known about genetic mutations in the regenerated mucosa (RM) after endoscopic resection (ER) of esophageal carcinoma. Thus, this study investigates the status of genetic variation in RM after ER of esophageal squamous cell carcinoma (ESCC). METHODS The study cohort included 19 patients with ESCC. We used an esophageal carcinoma panel to identify target sequences for squamous cell carcinoma (SCC), background mucosa (BM), and RM after ER of ESCC. We used OncoKB to check whether each mutation was a putative driver. RESULTS We identified 77 mutations of 32 genes in SCC, 133 mutations of 34 genes in BM, and 100 mutations of 29 genes in RM. Putative driver mutations were identified in 20 mutations in 14 cases in SCC, 16 mutations in 10 cases in BM, and 7 mutations in 11 cases in RM. The rate of putative driver mutations to total mutations was significantly lower in RM (26% in SCC vs 12% in BM vs 7% in RM, P = 0.009). Additionally, the rate of cases with TP53 putative driver mutations was significantly lower in RM (63% in SCC vs 37% in BM vs 16% in RM, P = 0.011). The percentage of putative driver mutations and the percentage of cases with a putative driver of TP53 were significantly lower in RM. CONCLUSION Esophageal RM after ER of ESCC could have a lower risk of carcinogenesis.
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Affiliation(s)
- Naoki Akizue
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kenichiro Okimoto
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Japan
| | - Tatsuya Kaneko
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuki Ohta
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takashi Taida
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keiko Saito
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoaki Matsumura
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Motoi Nishimura
- Division of Clinical Genetics and Proteomics, Department of Laboratory Medicine, Chiba University Hospital, Chiba, Japan
| | - Kazuyuki Matsushita
- Division of Clinical Genetics and Proteomics, Department of Laboratory Medicine, Chiba University Hospital, Chiba, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Japan
| | - Tetsuhiro Chiba
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Makoto Arai
- Department of Gastroenterology, Tokyo Women's Medical University Yachiyo Medical Center, Yachiyo, Japan
| | - Jun Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Prefectural Central Hospital, Kofu, Japan
- Tokyo University, Tokyo, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Weh KM, Howard CL, Zhang Y, Tripp BA, Clarke JL, Howell AB, Rubenstein JH, Abrams JA, Westerhoff M, Kresty LA. Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome and esophageal metabolome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554315. [PMID: 37662411 PMCID: PMC10473615 DOI: 10.1101/2023.08.22.554315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammatory-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett's esophagus and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities and metabolites contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. Sprague Dawley rats, with or without reflux-induction received water or C-PAC ad libitum (700 µg/rat/day) for 25 or 40 weeks. C-PAC exerted prebiotic activity abrogating reflux-induced dysbiosis, and mitigating bile acid metabolism and transport, culminating in significant inhibition of EAC through TLR/NF-κB/P53 signaling cascades. At the species level, C-PAC mitigated reflux-induced pathogenic bacteria (Clostridium perfringens, Escherichia coli, and Proteus mirabilis). C-PAC specifically reversed reflux-induced bacterial, inflammatory and immune-implicated proteins and genes including Ccl4, Cd14, Crp, Cxcl1, Il6, Il1β, Lbp, Lcn2, Myd88, Nfkb1, Tlr2 and Tlr4 aligning with changes in human EAC progression, as confirmed through public databases. C-PAC is a safe promising dietary constituent that may be utilized alone or potentially as an adjuvant to current therapies to prevent EAC progression through ameliorating reflux-induced dysbiosis, inflammation and cellular damage.
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20
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Zhang XQ, Miao CW, Liu LP, Wang CL, Chen JZ, Li WH, Hu XD. The prognostic value of 11 th Japanese classification and 8 th AJCC staging systems in Chinese patients with esophageal squamous cell carcinoma. J Cardiothorac Surg 2023; 18:251. [PMID: 37612706 PMCID: PMC10463410 DOI: 10.1186/s13019-023-02350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Two staging systems, the 8th staging system by the American Joint Committee on Cancer (AJCC) and the 11th Japanese classification by Japan Esophageal Society (JES), are currently applied in the clinic for predicting the prognosis of patients with esophageal squamous cell carcinoma (ESCC). The differences between the two staging systems have been widely researched. However, little studies focus on the differences in specific staging between the two systems. Therefore, we aimed to compare the performance of different staging in predicting overall survival (OS) of Chinese patients with ESCC. METHODS This retrospective study included 268 patients who underwent radical esophagectomy and mediastinal lymph node dissection for ESCC between January 2008 and December 2013. Patients were staged by the 8th AJCC and 11th JES staging systems. OS was estimated using the Kaplan-Meier method and compared between N stages and between stage groupings using the log-rank test. Cox proportional hazards regression analysis was performed to identify factors independently related to outcome. Further, we compared the concordance indexes (C-indexes) of the two staging systems. RESULTS The mean age was 61.25 ± 7.056 years, median follow-up was 44.82 months, and 5-year OS rate was 47%. The OS was well predicted by the 8th AJCC N staging (P < 0.001) and the 11th JES N staging (P < 0.001), with a c-index of 0.638 (95% CI: 0.592-0.683) for AJCC N staging and 0.627 (95% CI: 0.583-0.670) for JES N staging (P = 0.13). In addition, the OS was also well predicted by stage groupings of the 8th AJCC (P < 0.001) and the 11th JES systems (P < 0.001), with a c-index of 0.658 (95% CI: 0.616-0.699) for 8th AJCC stage grouping and 0.629 (95% CI: 0.589-0.668) for the11th JES stage grouping (P = 0.211). CONCLUSIONS The prognostic effect of 11th JES staging system is comparable with that of AJCC 8th staging system for patients with ESCC. Therefore, both systems are applicable to clinical practice.
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Affiliation(s)
- Xi-Qin Zhang
- Shandong First Medical University, Jinan, 250000, Shandong, China
- Department of Radiotherapy, Xingning People's Hospital, Xingning, 514599, Guangdong, China
| | - Chuan-Wang Miao
- Shandong First Medical University, Jinan, 250000, Shandong, China
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Lan-Pin Liu
- Shandong First Medical University, Jinan, 250000, Shandong, China
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Cun-Liang Wang
- Shandong First Medical University, Jinan, 250000, Shandong, China
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Jia-Zhen Chen
- Shandong First Medical University, Jinan, 250000, Shandong, China
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Wan-Hu Li
- Shandong First Medical University, Jinan, 250000, Shandong, China
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Xu-Dong Hu
- Shandong First Medical University, Jinan, 250000, Shandong, China.
- Department of Radiotherapy, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China.
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21
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Karim F, Amin A, Liu M, Vishnuvardhan N, Amin S, Shabbir R, Swed B, Khan U. Role of Checkpoint Inhibitors in the Management of Gastroesophageal Cancers. Cancers (Basel) 2023; 15:4099. [PMID: 37627127 PMCID: PMC10452271 DOI: 10.3390/cancers15164099] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
PURPOSE This article reviews the essential clinical trials that have led to these immunotherapy approvals and explores the use of predictive biomarkers, such as PD-L1 expression and MSI status, to identify patients who are most likely to benefit from immunotherapies. METHODS This case review series describe findings from different clinical trials and contribute to the evolving understanding of the role of CPIs in managing advanced gastroesophageal cancers and may lead to improved treatment options and patient outcomes. Ongoing clinical trials also hold promise for expanding treatment options and improving patient outcomes in the future. METHODS The systematic review followed the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The protocol has not been registered. A systematic literature review was conducted to identify relevant clinical trials and studies that describe the role of immune checkpoint inhibitors in managing advanced gastroesophageal cancers. Electronic database (PubMed, Clinicaltrials.gov, Society of Immunotherapy of Cancer, Aliment Pharmacology & Therapeutics, BMC cancer, Molecular Cancer Research, Nature Reviews Molecular Cell Biology, American Association for Cancer Research, Science, Nature, Cancer Discovery, Journal of the National Cancer Institute, Advanced Immunology, Oncotarget, Nature Medicine, Nature Genetics, Gut, Pathology and Oncology Research, Journal of Clinical Oncology, The New England Journal of Medicine, Gastrointestinal oncology, JAMA Oncology, Journal of Gastrointestinal Oncology, Current Oncology, Annals of Oncology, The Lancet, JCO Oncology Practice, Future Oncology, Gastric Cancer, CA: A Cancer Journal for Clinicians, American Journal of Gastroenterology, Gastroenterology, Journal of the National Cancer Institute, International Journal of Epidemiology, Helicobacter, Gastroenterology Review) were searched using a combination of relevant keywords and MESH terms. The search encompassed articles published up to 5/2023. Additionally, manual searches of reference lists of selected articles and pertinent review papers were conducted to ensure comprehensive coverage of relevant studies. Studies were included if they provided insights into clinical trials evaluating the efficacy and safety of CPIs in treating advanced gastroesophageal cancers. Relevant case reviews and trials exploring combination therapies involving CPIs were also considered. Articles discussed in the utilization of predictive biomarkers were included to assess their impact on treatment outcomes. Data from selected studies were extracted to inform the narrative review. Key findings were summarized, including clinical trial designs, patient populations, treatment regimens, response rates, progression-free survival (PFS), overall survival (OS), and adverse events. The role of predictive biomarkers, particularly PD-L1 expression and MSI status, in identifying patients likely to benefit from CPIs was critically evaluated based on study results. Ongoing clinical trials investigating novel combination strategies and exploring the broader scope of CPIs in gastroesophageal cancers were also highlighted. The collected data were synthesized to provide a comprehensive overview of the crucial clinical trials that have contributed to the approval of CPIs for advanced gastroesophageal cancers. The role of CPIs in different lines of therapy, including first-line regimens, was discussed. Furthermore, the evolving landscape of predictive biomarkers was examined, emphasizing their potential significance in optimizing patient selection for CPI therapy. Ongoing clinical trials were reviewed to underscore the continuous efforts in expanding treatment options and improving patient outcomes in the future.
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Affiliation(s)
- Frederic Karim
- Internal Medicine, New York-Presbyterian Brooklyn Methodist Hospital, 506 6th Street, Brooklyn, NY 11215, USA; (A.A.); (M.L.); (S.A.); (R.S.)
| | - Adina Amin
- Internal Medicine, New York-Presbyterian Brooklyn Methodist Hospital, 506 6th Street, Brooklyn, NY 11215, USA; (A.A.); (M.L.); (S.A.); (R.S.)
| | - Marie Liu
- Internal Medicine, New York-Presbyterian Brooklyn Methodist Hospital, 506 6th Street, Brooklyn, NY 11215, USA; (A.A.); (M.L.); (S.A.); (R.S.)
| | - Nivetha Vishnuvardhan
- Hematology/Oncology, New York-Presbyterian Brooklyn Methodist Hospital, 506 6th Street, Brooklyn, NY 11215, USA;
| | - Saif Amin
- Internal Medicine, New York-Presbyterian Brooklyn Methodist Hospital, 506 6th Street, Brooklyn, NY 11215, USA; (A.A.); (M.L.); (S.A.); (R.S.)
| | - Raffey Shabbir
- Internal Medicine, New York-Presbyterian Brooklyn Methodist Hospital, 506 6th Street, Brooklyn, NY 11215, USA; (A.A.); (M.L.); (S.A.); (R.S.)
| | - Brandon Swed
- Hematology/Oncology, Weill Cornell Medicine, 515 6th Street, Brooklyn, NY 11215, USA; (B.S.); (U.K.)
| | - Uqba Khan
- Hematology/Oncology, Weill Cornell Medicine, 515 6th Street, Brooklyn, NY 11215, USA; (B.S.); (U.K.)
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22
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Khalsa JK, Cha J, Utro F, Naeem A, Murali I, Kuang Y, Vasquez K, Li L, Tyekucheva S, Fernandes SM, Veronese L, Guieze R, Sasi BK, Wang Z, Machado JH, Bai H, Alasfour M, Rhrissorrakrai K, Levovitz C, Danysh BP, Slowik K, Jacobs RA, Davids MS, Paweletz CP, Leshchiner I, Parida L, Getz G, Brown JR. Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples. Blood 2023; 142:421-433. [PMID: 37146250 PMCID: PMC10447490 DOI: 10.1182/blood.2022016600] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023] Open
Abstract
Although BCL2 mutations are reported as later occurring events leading to venetoclax resistance, many other mechanisms of progression have been reported though remain poorly understood. Here, we analyze longitudinal tumor samples from 11 patients with disease progression while receiving venetoclax to characterize the clonal evolution of resistance. All patients tested showed increased in vitro resistance to venetoclax at the posttreatment time point. We found the previously described acquired BCL2-G101V mutation in only 4 of 11 patients, with 2 patients showing a very low variant allele fraction (0.03%-4.68%). Whole-exome sequencing revealed acquired loss(8p) in 4 of 11 patients, of which 2 patients also had gain (1q21.2-21.3) in the same cells affecting the MCL1 gene. In vitro experiments showed that CLL cells from the 4 patients with loss(8p) were more resistant to venetoclax than cells from those without it, with the cells from 2 patients also carrying gain (1q21.2-21.3) showing increased sensitivity to MCL1 inhibition. Progression samples with gain (1q21.2-21.3) were more susceptible to the combination of MCL1 inhibitor and venetoclax. Differential gene expression analysis comparing bulk RNA sequencing data from pretreatment and progression time points of all patients showed upregulation of proliferation, B-cell receptor (BCR), and NF-κB gene sets including MAPK genes. Cells from progression time points demonstrated upregulation of surface immunoglobulin M and higher pERK levels compared with those from the preprogression time point, suggesting an upregulation of BCR signaling that activates the MAPK pathway. Overall, our data suggest several mechanisms of acquired resistance to venetoclax in CLL that could pave the way for rationally designed combination treatments for patients with venetoclax-resistant CLL.
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MESH Headings
- Humans
- Antineoplastic Agents/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Drug Resistance, Neoplasm/genetics
- Exome Sequencing
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Proto-Oncogene Proteins c-bcl-2
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Affiliation(s)
- Jasneet Kaur Khalsa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Justin Cha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Aishath Naeem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ishwarya Murali
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Kevin Vasquez
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Liang Li
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health, Boston, MA
| | - Stacey M. Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Lauren Veronese
- Service de Cytogénétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
- EA7453 CHELTER, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Romain Guieze
- EA7453 CHELTER, Université Clermont Auvergne, Clermont-Ferrand, France
- Service d’Hématologie clinique et thérapie cellulaire, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Binu Kandathilparambil Sasi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Zixu Wang
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health, Boston, MA
| | - John-Hanson Machado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Harrison Bai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Maryam Alasfour
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - Brian P. Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kara Slowik
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Raquel A. Jacobs
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Cloud P. Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Cancer Center, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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23
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Kumar S, Zhao J, Talluri S, Buon L, Mu S, Potluri LB, Liao C, Shi J, Chakraborty C, Gonzalez GB, Tai YT, Patel J, Pal J, Mashimo H, Samur MK, Munshi NC, Shammas MA. Elevated APE1 Dysregulates Homologous Recombination and Cell Cycle Driving Genomic Evolution, Tumorigenesis, and Chemoresistance in Esophageal Adenocarcinoma. Gastroenterology 2023; 165:357-373. [PMID: 37178737 PMCID: PMC10524563 DOI: 10.1053/j.gastro.2023.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/17/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND & AIMS The purpose of this study was to identify drivers of genomic evolution in esophageal adenocarcinoma (EAC) and other solid tumors. METHODS An integrated genomics strategy was used to identify deoxyribonucleases correlating with genomic instability (as assessed from total copy number events in each patient) in 6 cancers. Apurinic/apyrimidinic nuclease 1 (APE1), identified as the top gene in functional screens, was either suppressed in cancer cell lines or overexpressed in normal esophageal cells and the impact on genome stability and growth was monitored in vitro and in vivo. The impact on DNA and chromosomal instability was monitored using multiple approaches, including investigation of micronuclei, acquisition of single nucleotide polymorphisms, whole genome sequencing, and/or multicolor fluorescence in situ hybridization. RESULTS Expression of 4 deoxyribonucleases correlated with genomic instability in 6 human cancers. Functional screens of these genes identified APE1 as the top candidate for further evaluation. APE1 suppression in EAC, breast, lung, and prostate cancer cell lines caused cell cycle arrest; impaired growth and increased cytotoxicity of cisplatin in all cell lines and types and in a mouse model of EAC; and inhibition of homologous recombination and spontaneous and chemotherapy-induced genomic instability. APE1 overexpression in normal cells caused a massive chromosomal instability, leading to their oncogenic transformation. Evaluation of these cells by means of whole genome sequencing demonstrated the acquisition of changes throughout the genome and identified homologous recombination as the top mutational process. CONCLUSIONS Elevated APE1 dysregulates homologous recombination and cell cycle, contributing to genomic instability, tumorigenesis, and chemoresistance, and its inhibitors have the potential to target these processes in EAC and possibly other cancers.
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Affiliation(s)
- Subodh Kumar
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Jiangning Zhao
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Srikanth Talluri
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Leutz Buon
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Shidai Mu
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Lakshmi B Potluri
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Chengcheng Liao
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts
| | - Jialan Shi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts; Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Gabriel B Gonzalez
- Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts; Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Yu-Tzu Tai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Jaymin Patel
- Department of Medicine, Harvard Medical School, Boston, Massachusetts; Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Jagannath Pal
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Pt. Jawahar Lal Nehru Memorial Medical College, Raipur, Chhattisgarh, India
| | - Hiroshi Mashimo
- Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts; Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Mehmet K Samur
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts; Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Masood A Shammas
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts; Hematology and Oncology, Veterans Affairs Boston Healthcare System, West Roxbury, Massachusetts.
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24
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Strasser MK, Gibbs DL, Gascard P, Bons J, Hickey JW, Schürch CM, Tan Y, Black S, Chu P, Ozkan A, Basisty N, Sangwan V, Rose J, Shah S, Camilleri-Broet S, Fiset PO, Bertos N, Berube J, Djambazian H, Li R, Oikonomopoulos S, Fels-Elliott DR, Vernovsky S, Shimshoni E, Collyar D, Russell A, Ragoussis I, Stachler M, Goldenring JR, McDonald S, Ingber DE, Schilling B, Nolan GP, Tlsty TD, Huang S, Ferri LE. Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.08.544265. [PMID: 37333362 PMCID: PMC10274886 DOI: 10.1101/2023.06.08.544265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Esophageal adenocarcinoma arises from Barrett's esophagus, a precancerous metaplastic replacement of squamous by columnar epithelium in response to chronic inflammation. Multi-omics profiling, integrating single-cell transcriptomics, extracellular matrix proteomics, tissue-mechanics and spatial proteomics of 64 samples from 12 patients' paths of progression from squamous epithelium through metaplasia, dysplasia to adenocarcinoma, revealed shared and patient-specific progression characteristics. The classic metaplastic replacement of epithelial cells was paralleled by metaplastic changes in stromal cells, ECM and tissue stiffness. Strikingly, this change in tissue state at metaplasia was already accompanied by appearance of fibroblasts with characteristics of carcinoma-associated fibroblasts and of an NK cell-associated immunosuppressive microenvironment. Thus, Barrett's esophagus progresses as a coordinated multi-component system, supporting treatment paradigms that go beyond targeting cancerous cells to incorporating stromal reprogramming.
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25
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Lipsyc-Sharf M, Jain E, Collins LC, Rosenberg SM, Ruddy KJ, Tamimi RM, Schapira L, Come SE, Peppercorn JM, Borges VF, Warner E, Snow C, Krop IE, Kim D, Weiss J, Zanudo JGT, Partridge AH, Wagle N, Waks AG. Genomics of ERBB2-Positive Breast Cancer in Young Women Before and After Exposure to Chemotherapy Plus Trastuzumab. JCO Precis Oncol 2023; 7:e2300076. [PMID: 37364233 DOI: 10.1200/po.23.00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
PURPOSE Erb-B2 receptor tyrosine kinase 2 (ERBB2)-positive breast cancer (BC) is particularly common in young women. Genomic features of ERBB2-positive tumors before and after chemotherapy and trastuzumab (chemo + H) have not been described in young women and are important for guiding study of therapeutic resistance in this population. METHODS From a large prospective cohort of women age 40 years or younger with BC, we identified patients with ERBB2-positive BC and tumor tissue available before and after chemo + H. Whole-exome sequencing (WES) was performed on each tumor and on germline DNA from blood. Tumor-normal pairs were analyzed for mutations and copy number (CN) changes. RESULTS Twenty-two women had successful WES on samples from at least one time point; 12 of these had paired sequencing results from before and after chemo + H and 10 had successful sequencing from either time point. TP53 was the only significantly recurrently mutated gene in both pre- and post-treatment samples. MYC gene amplification was observed in four post-treatment tumors. Seven of 12 patients with paired samples showed acquired and/or clonally enriched alterations in cancer-related genes. One patient had an increased clonality putative activating mutation in ERBB2. Another patient acquired a clonal hotspot mutation in TP53. Other genomic changes acquired in post-treatment specimens included alterations in NOTCH2, STIL, PIK3CA, and GATA3. There was no significant change in median ERBB2 CN (20.3 v 22.6; Wilcoxon P = .79) between paired samples. CONCLUSION ERBB2-positive BCs in young women displayed substantial genomic evolution after treatment with chemo + H. Approximately half of patients with paired samples demonstrated acquired and/or clonally enriched genomic changes in cancer genes. ERBB2 CN changes were uncommon. We identified several genes warranting exploration as potential mechanisms of resistance to therapy in this population.
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Affiliation(s)
- Marla Lipsyc-Sharf
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Esha Jain
- Dana-Farber Cancer Institute, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
- Repare Therapeutics, Cambridge, MA
| | - Laura C Collins
- Harvard Medical School, Boston, MA
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | - Rulla M Tamimi
- Weill Cornell Medicine, New York, NY
- Brigham and Women's Hospital, Boston, MA
| | | | - Steven E Come
- Harvard Medical School, Boston, MA
- Breast Medical Oncology Program, Beth Israel Deaconess Medical Center and Dana-Farber/Harvard Cancer Center, Boston, MA
| | | | | | - Ellen Warner
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Craig Snow
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
| | - Ian E Krop
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Yale Cancer Center, New Haven, CT
| | - Dewey Kim
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jakob Weiss
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jorge Gomez Tejeda Zanudo
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Nikhil Wagle
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Adrienne G Waks
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA
- Harvard Medical School, Boston, MA
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26
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M Naeini M, Newell F, Aoude LG, Bonazzi VF, Patel K, Lampe G, Koufariotis LT, Lakis V, Addala V, Kondrashova O, Johnston RL, Sharma S, Brosda S, Holmes O, Leonard C, Wood S, Xu Q, Thomas J, Walpole E, Tao Mai G, Ackland SP, Martin J, Burge M, Finch R, Karapetis CS, Shannon J, Nott L, Bohmer R, Wilson K, Barnes E, Zalcberg JR, Mark Smithers B, Simes J, Price T, Gebski V, Nones K, Watson DI, Pearson JV, Barbour AP, Waddell N. Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy. Nat Commun 2023; 14:3155. [PMID: 37258531 DOI: 10.1038/s41467-023-38891-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Oesophageal adenocarcinoma is a poor prognosis cancer and the molecular features underpinning response to treatment remain unclear. We investigate whole genome, transcriptomic and methylation data from 115 oesophageal adenocarcinoma patients mostly from the DOCTOR phase II clinical trial (Australian New Zealand Clinical Trials Registry-ACTRN12609000665235), with exploratory analysis pre-specified in the study protocol of the trial. We report genomic features associated with poorer overall survival, such as the APOBEC mutational and RS3-like rearrangement signatures. We also show that positron emission tomography non-responders have more sub-clonal genomic copy number alterations. Transcriptomic analysis categorises patients into four immune clusters correlated with survival. The immune suppressed cluster is associated with worse survival, enriched with myeloid-derived cells, and an epithelial-mesenchymal transition signature. The immune hot cluster is associated with better survival, enriched with lymphocytes, myeloid-derived cells, and an immune signature including CCL5, CD8A, and NKG7. The immune clusters highlight patients who may respond to immunotherapy and thus may guide future clinical trials.
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Affiliation(s)
- Marjan M Naeini
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Lauren G Aoude
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Vanessa F Bonazzi
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Kalpana Patel
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Guy Lampe
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | | | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Venkateswar Addala
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Rebecca L Johnston
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, 4006, Australia
- Anatomical Pathology, Australian Clinical Labs, 2153, Sydney, Australia
| | - Sandra Brosda
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Janine Thomas
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
- Mater Research Institute, Mater Misericordiae, South Brisbane, QLD, 4101, Australia
| | - Euan Walpole
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - G Tao Mai
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
| | - Stephen P Ackland
- Department of Medical Oncology, Calvary Mater Newcastle, Waratah, NSW, 2298, Australia
| | - Jarad Martin
- Department of Radiation Oncology, Calvary Mater Newcastle, Waratah, NSW, 2298, Australia
| | - Matthew Burge
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Robert Finch
- Royal Brisbane and Women's Hospital, Herston, QLD, 4029, Australia
| | - Christos S Karapetis
- Flinders University Department of Medical Oncology, Flinders Medical Centre, Adelaide, SA, 5042, Australia
| | - Jenny Shannon
- Nepean Cancer Care Centre, Nepean Hospital, Sydney, NSW, 2747, Australia
| | - Louise Nott
- Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Robert Bohmer
- Department of General Surgery, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Kate Wilson
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Elizabeth Barnes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - John R Zalcberg
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - B Mark Smithers
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, 4006, Australia
| | - John Simes
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Timothy Price
- Medical Oncology Unit, The Queen Elizabeth Hospital and University of Adelaide, Adelaide, SA, 5011, Australia
| | - Val Gebski
- NHMRC Clinical Trials Centre, University of Sydney, Sydney, NSW, 2006, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - David I Watson
- Flinders University Discipline of Surgery, Flinders Medical Centre, Adelaide, SA, 5042, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Andrew P Barbour
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia.
- Princess Alexandra Hospital, Woolloongabba, QLD, 4102, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
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27
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Maslenkina K, Mikhaleva L, Naumenko M, Vandysheva R, Gushchin M, Atiakshin D, Buchwalow I, Tiemann M. Signaling Pathways in the Pathogenesis of Barrett's Esophagus and Esophageal Adenocarcinoma. Int J Mol Sci 2023; 24:ijms24119304. [PMID: 37298253 DOI: 10.3390/ijms24119304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Barrett's esophagus (BE) is a premalignant lesion that can develop into esophageal adenocarcinoma (EAC). The development of Barrett's esophagus is caused by biliary reflux, which causes extensive mutagenesis in the stem cells of the epithelium in the distal esophagus and gastro-esophageal junction. Other possible cellular origins of BE include the stem cells of the mucosal esophageal glands and their ducts, the stem cells of the stomach, residual embryonic cells and circulating bone marrow stem cells. The classical concept of healing a caustic lesion has been replaced by the concept of a cytokine storm, which forms an inflammatory microenvironment eliciting a phenotypic shift toward intestinal metaplasia of the distal esophagus. This review describes the roles of the NOTCH, hedgehog, NF-κB and IL6/STAT3 molecular pathways in the pathogenesis of BE and EAC.
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Affiliation(s)
- Ksenia Maslenkina
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Liudmila Mikhaleva
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Maxim Naumenko
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Rositsa Vandysheva
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Michail Gushchin
- A.P. Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119991 Moscow, Russia
| | - Dmitri Atiakshin
- Research and Educational Resource Centre for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples' Friendship University of Russia Named after Patrice Lumumba, 117198 Moscow, Russia
| | - Igor Buchwalow
- Research and Educational Resource Centre for Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis Innovative Technologies, Peoples' Friendship University of Russia Named after Patrice Lumumba, 117198 Moscow, Russia
- Institute for Hematopathology, Fangdieckstr. 75a, 22547 Hamburg, Germany
| | - Markus Tiemann
- Institute for Hematopathology, Fangdieckstr. 75a, 22547 Hamburg, Germany
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28
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:biology12050671. [PMID: 37237485 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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29
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Shah MA, Altorki N, Patel P, Harrison S, Bass A, Abrams JA. Improving outcomes in patients with oesophageal cancer. Nat Rev Clin Oncol 2023; 20:390-407. [PMID: 37085570 DOI: 10.1038/s41571-023-00757-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2023] [Indexed: 04/23/2023]
Abstract
The care of patients with oesophageal cancer or of individuals who have an elevated risk of oesophageal cancer has changed dramatically. The epidemiology of squamous cell and adenocarcinoma of the oesophagus has diverged over the past several decades, with a marked increase in incidence only for oesophageal adenocarcinoma. Only in the past decade, however, have molecular features that distinguish these two forms of the disease been identified. This advance has the potential to improve screening for oesophageal cancers through the development of novel minimally invasive diagnostic technologies predicated on cancer-specific genomic or epigenetic alterations. Surgical techniques have also evolved towards less invasive approaches associated with less morbidity, without compromising oncological outcomes. With improvements in multidisciplinary care, advances in radiotherapy and new tools to detect minimal residual disease, certain patients may no longer even require surgical tumour resection. However, perhaps the most anticipated advance in the treatment of patients with oesophageal cancer is the advent of immune-checkpoint inhibitors, which harness and enhance the host immune response against cancer. In this Review, we discuss all these advances in the management of oesophageal cancer, representing only the beginning of a transformation in our quest to improve patient outcomes.
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Affiliation(s)
- Manish A Shah
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Nasser Altorki
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Pretish Patel
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Sebron Harrison
- Department of Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Adam Bass
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Julian A Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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30
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Iyer PG, Chak A. Surveillance in Barrett's Esophagus: Challenges, Progress, and Possibilities. Gastroenterology 2023; 164:707-718. [PMID: 36746210 PMCID: PMC10079619 DOI: 10.1053/j.gastro.2023.01.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/08/2023]
Abstract
Endoscopic surveillance of Barrett's esophagus, aiming to detect prevalent dysplasia and adenocarcinoma, followed by effective endoscopic treatment, is an integral part of the esophageal adenocarcinoma prevention paradigm. However, several limitations, such as the subtle appearance of dysplasia, sampling error (inherent in current surveillance protocols), and noncompliance with surveillance recommendations, lead to missed dysplasia and neoplasia, reducing the effectiveness of surveillance as currently practiced. Careful endoscopic assessment with high-resolution white-light endoscopy, dye-based or electronic chromoendoscopy, and comprehensive sampling of the BE mucosa, remains the cornerstone of endoscopic surveillance. Emerging innovations in this area span the gamut of more efficient sampling methods, advanced imaging tools, artificial intelligence, and molecular marker-powered approaches as adjuncts, to identify prevalent and predict incident dysplasia or adenocarcinoma. Development and implementation of validated quality indicators will allow additional advancement of this critical field. These approaches will hopefully enable efficient and effective cancer prevention and treatment.
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Affiliation(s)
- Prasad G Iyer
- Barrett's Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
| | - Amitabh Chak
- Division of Gastroenterology and Hepatology, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, Ohio
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31
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Luebeck J, Ng AWT, Galipeau PC, Li X, Sanchez CA, Katz-Summercorn AC, Kim H, Jammula S, He Y, Lippman SM, Verhaak RGW, Maley CC, Alexandrov LB, Reid BJ, Fitzgerald RC, Paulson TG, Chang HY, Wu S, Bafna V, Mischel PS. Extrachromosomal DNA in the cancerous transformation of Barrett's oesophagus. Nature 2023; 616:798-805. [PMID: 37046089 PMCID: PMC10132967 DOI: 10.1038/s41586-023-05937-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/09/2023] [Indexed: 04/14/2023]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) drives the evolution of tumours and their resistance to treatment, and is associated with poor outcomes for patients with cancer1-6. At present, it is unclear whether ecDNA is a later manifestation of genomic instability, or whether it can be an early event in the transition from dysplasia to cancer. Here, to better understand the development of ecDNA, we analysed whole-genome sequencing (WGS) data from patients with oesophageal adenocarcinoma (EAC) or Barrett's oesophagus. These data included 206 biopsies in Barrett's oesophagus surveillance and EAC cohorts from Cambridge University. We also analysed WGS and histology data from biopsies that were collected across multiple regions at 2 time points from 80 patients in a case-control study at the Fred Hutchinson Cancer Center. In the Cambridge cohorts, the frequency of ecDNA increased between Barrett's-oesophagus-associated early-stage (24%) and late-stage (43%) EAC, suggesting that ecDNA is formed during cancer progression. In the cohort from the Fred Hutchinson Cancer Center, 33% of patients who developed EAC had at least one oesophageal biopsy with ecDNA before or at the diagnosis of EAC. In biopsies that were collected before cancer diagnosis, higher levels of ecDNA were present in samples from patients who later developed EAC than in samples from those who did not. We found that ecDNAs contained diverse collections of oncogenes and immunomodulatory genes. Furthermore, ecDNAs showed increases in copy number and structural complexity at more advanced stages of disease. Our findings show that ecDNA can develop early in the transition from high-grade dysplasia to cancer, and that ecDNAs progressively form and evolve under positive selection.
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Affiliation(s)
- Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Alvin Wei Tian Ng
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Patricia C Galipeau
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Xiaohong Li
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Carissa A Sanchez
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Hoon Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Biohealth Regulatory Science, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sriganesh Jammula
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK
| | - Yudou He
- Moores Cancer Center, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Scott M Lippman
- Moores Cancer Center, UC San Diego Health, La Jolla, CA, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Carlo C Maley
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Ludmil B Alexandrov
- Moores Cancer Center, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Rebecca C Fitzgerald
- Early Cancer Institute, Hutchison Research Centre, University of Cambridge, Cambridge, UK.
| | - Thomas G Paulson
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
- Halıcıoğlu Data Science Institute, University of California at San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA.
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32
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Wang DH. Extrachromosomal DNA appears before cancer forms. Nature 2023; 616:664-665. [PMID: 37045953 DOI: 10.1038/d41586-023-00982-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
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33
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Sahgal P, Patil DT, Sztupinszki ZM, Tisza V, Spisak S, Huffman B, Prosz A, Singh H, Lazaro JB, Szallasi Z, Cleary JM, Sethi NS. Replicative stress in gastroesophageal adenocarcinoma is associated with chromosomal instability and sensitivity to DNA damage response inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.27.534412. [PMID: 37034740 PMCID: PMC10081209 DOI: 10.1101/2023.03.27.534412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Gastroesophageal adenocarcinoma (GEA) is an aggressive, often lethal, malignancy that displays marked chromosomal instability (CIN). To understand adaptive responses that enable CIN, we analyzed paired normal, premalignant, and malignant gastric lesions from human specimens and a carcinogen-induced mouse model, observing activation of replication stress, DNA damage response (DDR), and cell cycle regulator p21 in neoplastic progression. In GEA cell lines, expression of DDR markers correlated with ploidy abnormalities, including high-level focal amplifications and whole-genome duplication (WGD). Moreover, high expression of DNA damage marker H2AX correlated with CIN, WGD, and inferior patient survival. By developing and implementing a composite diagnostic score that incorporates TP53 mutation status, ploidy abnormalities, and H2AX expression, among other genomic information, we can identify GEA cell lines with enhanced sensitivity to DDR pathway inhibitors targeting Chk1/2 and Wee1. Anti-tumor properties were further augmented in combination with irinotecan (SN38) but not gemcitabine chemotherapy. These results implicate specific DDR biomarkers and ploidy abnormalities as diagnostic proxy that may predict premalignant progression and response to DDR pathway inhibitors.
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Affiliation(s)
- Pranshu Sahgal
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, 02142, USA
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - Deepa T. Patil
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | | | - Viktoria Tisza
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Sandor Spisak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Brandon Huffman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aurel Prosz
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
| | - Harshabad Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jean-Bernard Lazaro
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for DNA Damage and Repair (CDDR), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Zoltan Szallasi
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Danish Cancer Society Research Center, Copenhagen, 2100, Denmark
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, 02115, USA
| | - James M. Cleary
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nilay S. Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA, 02142, USA
- Division of Gastrointestinal Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Lead Contact
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34
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Sun L, Kang X, Wang C, Wang R, Yang G, Jiang W, Wu Q, Wang Y, Wu Y, Gao J, Chen L, Zhang J, Tian Z, Zhu G, Sun S. Single-cell and spatial dissection of precancerous lesions underlying the initiation process of oral squamous cell carcinoma. Cell Discov 2023; 9:28. [PMID: 36914617 PMCID: PMC10011538 DOI: 10.1038/s41421-023-00532-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023] Open
Abstract
Precancerous lesions of the oral mucosa, especially those accompanied by moderate to severe dysplasia, contribute to the initiation of oral squamous cell carcinoma (OSCC). However, the cellular compositions and spatial organization of the precancerous stage and how these factors promote human OSCC initiation remain unclear. Here, we built a single-cell transcriptome atlas and a spatial transcriptome map after obtaining data from pairwise human oral mucosal biopsies of 9 individuals consisting of very early-stage OSCC, adjacent precancerous lesions with moderate to severe dysplasia, as well as a matched normal region. An altered epithelial gene-expression profile was identified which favored OSCC initiation. This observation was coupled with distinct fibroblast, monocytic, and regulatory T-cell subclusters involved in reshaping the microenvironment. In particular, a unique immune-inhibitory monocyte subtype and spatial-switching regulation of VEGF signaling were observed surrounding precancerous lesions, concertedly strengthening activities in promoting cancer initiation. Collectively, our work elucidated the cellular landscapes and roles of precancerous lesions underlying OSCC initiation, which is essential for understanding the entire OSCC initiation process and helps inform therapeutic strategies for cancer intervention.
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Affiliation(s)
- Lulu Sun
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Xindan Kang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Chong Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Rui Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Guizhu Yang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Wen Jiang
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China.,Department of Oral and Maxillofacial-Head Neck Oncology, Division of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Wu
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yujue Wang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Yaping Wu
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiamin Gao
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Lan Chen
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jie Zhang
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China
| | - Zhen Tian
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China.,Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guopei Zhu
- College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China.,Department of Oral and Maxillofacial-Head Neck Oncology, Division of Radiation Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuyang Sun
- Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,College of Stomatology, Shanghai Jiao Tong University, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of Stomatology, Shanghai, China.
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35
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Mejza M, Małecka-Wojciesko E. Diagnosis and Management of Barrett's Esophagus. J Clin Med 2023; 12:jcm12062141. [PMID: 36983142 PMCID: PMC10057256 DOI: 10.3390/jcm12062141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Barrett's esophagus is a metaplastic change of esophageal mucosa, which can be characterized by its salmon-colored lining and the presence of columnar epithelium with goblet cells. It is a well-established precancerous state of esophageal adenocarcinoma, a tumor with very poor survival rates, which incidence is rapidly growing. Despite numerous research, the debate about its diagnosis and management is still ongoing. This article aims to provide an overview of the current recommendations and new discoveries regarding the subject.
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Affiliation(s)
- Maja Mejza
- Department of Digestive Tract Diseases, Medical University, 90-153 Lodz, Poland
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36
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Lambuta RA, Nanni L, Liu Y, Diaz-Miyar J, Iyer A, Tavernari D, Katanayeva N, Ciriello G, Oricchio E. Whole-genome doubling drives oncogenic loss of chromatin segregation. Nature 2023; 615:925-933. [PMID: 36922594 PMCID: PMC10060163 DOI: 10.1038/s41586-023-05794-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies1-8. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here we show that in p53-deficient cells, WGD induces loss of chromatin segregation (LCS). This event is characterized by reduced segregation between short and long chromosomes, A and B subcompartments and adjacent chromatin domains. LCS is driven by the downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primes genomic regions for subcompartment repositioning in WGD cells. This results in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Notably, subcompartment repositioning events were largely independent of chromosomal alterations, which indicates that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, which suggests that chromatin evolution is a hallmark of WGD-driven cancer.
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Affiliation(s)
- Ruxandra A Lambuta
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Luca Nanni
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yuanlong Liu
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Juan Diaz-Miyar
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Arvind Iyer
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Daniele Tavernari
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland.
- Swiss Cancer Center Leman, Lausanne, Switzerland.
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37
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Ahmed I, Yang SH, Ogden S, Zhang W, Li Y, Sharrocks AD. eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways. eLife 2023; 12:e80840. [PMID: 36803948 PMCID: PMC9998086 DOI: 10.7554/elife.80840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/20/2023] [Indexed: 02/22/2023] Open
Abstract
Cancer is driven by both genetic and epigenetic changes that impact on gene expression profiles and the resulting tumourigenic phenotype. Enhancers are transcriptional regulatory elements that are key to our understanding of how this rewiring of gene expression is achieved in cancer cells. Here, we have harnessed the power of RNA-seq data from hundreds of patients with oesophageal adenocarcinoma (OAC) or its precursor state Barrett's oesophagus coupled with open chromatin maps to identify potential enhancer RNAs and their associated enhancer regions in this cancer. We identify ~1000 OAC-specific enhancers and use these data to uncover new cellular pathways that are operational in OAC. Among these are enhancers for JUP, MYBL2, and CCNE1, and we show that their activity is required for cancer cell viability. We also demonstrate the clinical utility of our dataset for identifying disease stage and patient prognosis. Our data therefore identify an important set of regulatory elements that enhance our molecular understanding of OAC and point to potential new therapeutic directions.
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Affiliation(s)
- Ibrahim Ahmed
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Shen-Hsi Yang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Samuel Ogden
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Wei Zhang
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | - Yaoyong Li
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
| | | | - Andrew D Sharrocks
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of ManchesterManchesterUnited Kingdom
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38
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Cui S, McGranahan N, Gao J, Chen P, Jiang W, Yang L, Ma L, Liao J, Xie T, Xie C, Enver T, Wu S. Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing. Nat Commun 2023; 14:892. [PMID: 36807354 PMCID: PMC9938262 DOI: 10.1038/s41467-023-36558-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Intratumoral heterogeneity (ITH) has been linked to decreased efficacy of clinical treatments. However, although genomic ITH has been characterized in genetic, transcriptomic and epigenetic alterations are hallmarks of esophageal squamous cell carcinoma (ESCC), the extent to which these are heterogeneous in ESCC has not been explored in a unified framework. Further, the extent to which tumor-infiltrated T lymphocytes are directed against cancer cells, but how the immune infiltration acts as a selective force to shape the clonal evolution of ESCC is unclear. In this study, we perform multi-omic sequencing on 186 samples from 36 primary ESCC patients. Through multi-omics analyses, it is discovered that genomic, epigenomic, and transcriptomic ITH are underpinned by ongoing chromosomal instability. Based on the RNA-seq data, we observe diverse levels of immune infiltrate across different tumor sites from the same tumor. We reveal genetic mechanisms of neoantigen evasion under distinct selection pressure from the diverse immune microenvironment. Overall, our work offers an avenue of dissecting the complex contribution of the multi-omics level to the ITH in ESCC and thereby enhances the development of clinical therapy.
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Affiliation(s)
- Sijia Cui
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | | | - Jing Gao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Peng Chen
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Jiang
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Lingrong Yang
- Hangzhou Cancer Institution, Hangzhou Cancer Hospital, Hangzhou, China
| | - Li Ma
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Junfang Liao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Tian Xie
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Congying Xie
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.
| | - Tariq Enver
- Cancer Institute, University College London, London, UK.
| | - Shixiu Wu
- Department of Radiation and Medical Oncology, Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China. .,National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.
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39
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Gier RA, Hueros RAR, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM. Clonal cell states link Barrett's esophagus and esophageal adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525564. [PMID: 36747708 PMCID: PMC9900873 DOI: 10.1101/2023.01.26.525564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett's esophagus have not been resolved in humans. To address this, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis revealed discrete lineages in Barrett's esophagus, normal esophagus, and gastric cardia. Transitional basal progenitor cells of the gastroesophageal junction were unexpectedly related to both esophagus and gastric cardia cells. Barrett's esophagus was polyclonal, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic foci were initiated by the expansion of a single molecularly aberrant Barrett's esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the full disease trajectory, from its origin to cancer.
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Affiliation(s)
- Rodrigo A. Gier
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Raúl A. Reyes Hueros
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jiazhen Rong
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maureen DeMarshall
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tatiana A. Karakasheva
- Gastrointestinal Epithelium Modeling Program, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Amanda B. Muir
- Gastrointestinal Epithelium Modeling Program, Division of Gastroenterology, Hepatology and Nutrition, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Gary W. Falk
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nancy R. Zhang
- Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, USA
| | - Sydney M. Shaffer
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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40
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Chatila WK, Walch H, Hechtman JF, Moyer SM, Sgambati V, Faleck DM, Srivastava A, Tang L, Benhamida J, Ismailgeci D, Campos C, Wu F, Chang Q, Vakiani E, de Stanchina E, Weiser MR, Widmar M, Yantiss RK, Shah MA, Bass AJ, Stadler ZK, Katz LH, Mellinghoff IK, Sethi NS, Schultz N, Ganesh K, Kelsen D, Yaeger R. Integrated clinical and genomic analysis identifies driver events and molecular evolution of colitis-associated cancers. Nat Commun 2023; 14:110. [PMID: 36611031 PMCID: PMC9825391 DOI: 10.1038/s41467-022-35592-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/13/2022] [Indexed: 01/08/2023] Open
Abstract
Inflammation has long been recognized to contribute to cancer development, particularly across the gastrointestinal tract. Patients with inflammatory bowel disease have an increased risk for bowel cancers, and it has been posited that a field of genetic changes may underlie this risk. Here, we define the clinical features, genomic landscape, and germline alterations in 174 patients with colitis-associated cancers and sequenced 29 synchronous or isolated dysplasia. TP53 alterations, an early and highly recurrent event in colitis-associated cancers, occur in half of dysplasia, largely as convergent evolution of independent events. Wnt pathway alterations are infrequent, and our data suggest transcriptional rewiring away from Wnt. Sequencing of multiple dysplasia/cancer lesions from mouse models and patients demonstrates rare shared alterations between lesions. These findings suggest neoplastic bowel lesions developing in a background of inflammation experience lineage plasticity away from Wnt activation early during tumorigenesis and largely occur as genetically independent events.
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Affiliation(s)
- Walid K Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sydney M Moyer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Valeria Sgambati
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Faleck
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amitabh Srivastava
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dorina Ismailgeci
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carl Campos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fan Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qing Chang
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin R Weiser
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Widmar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rhonda K Yantiss
- Department of Pathology, Weill Cornell Medicine, New York, NY, USA
| | - Manish A Shah
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Adam J Bass
- Herbert Irving Comprehensive Cancer Research Center, Columbia University Irving Medical Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lior H Katz
- Gastroenterology Institute, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Ingo K Mellinghoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nilay S Sethi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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41
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Ooki A, Osumi H, Chin K, Watanabe M, Yamaguchi K. Potent molecular-targeted therapies for advanced esophageal squamous cell carcinoma. Ther Adv Med Oncol 2023; 15:17588359221138377. [PMID: 36872946 PMCID: PMC9978325 DOI: 10.1177/17588359221138377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 10/21/2022] [Indexed: 01/15/2023] Open
Abstract
Esophageal cancer (EC) remains a public health concern with a high mortality and disease burden worldwide. Esophageal squamous cell carcinoma (ESCC) is a predominant histological subtype of EC that has unique etiology, molecular profiles, and clinicopathological features. Although systemic chemotherapy, including cytotoxic agents and immune checkpoint inhibitors, is the main therapeutic option for recurrent or metastatic ESCC patients, the clinical benefits are limited with poor prognosis. Personalized molecular-targeted therapies have been hampered due to the lack of robust treatment efficacy in clinical trials. Therefore, there is an urgent need to develop effective therapeutic strategies. In this review, we summarize the molecular profiles of ESCC based on the findings of pivotal comprehensive molecular analyses, highlighting potent therapeutic targets for establishing future precision medicine for ESCC patients, with the most recent results of clinical trials.
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Affiliation(s)
- Akira Ooki
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Hiroki Osumi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Keisho Chin
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterological Chemotherapy, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
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42
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Seferbekova Z, Lomakin A, Yates LR, Gerstung M. Spatial biology of cancer evolution. Nat Rev Genet 2022; 24:295-313. [PMID: 36494509 DOI: 10.1038/s41576-022-00553-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2022] [Indexed: 12/13/2022]
Abstract
The natural history of cancers can be understood through the lens of evolution given that the driving forces of cancer development are mutation and selection of fitter clones. Cancer growth and progression are spatial processes that involve the breakdown of normal tissue organization, invasion and metastasis. For these reasons, spatial patterns are an integral part of histological tumour grading and staging as they measure the progression from normal to malignant disease. Furthermore, tumour cells are part of an ecosystem of tumour cells and their surrounding tumour microenvironment. A range of new spatial genomic, transcriptomic and proteomic technologies offers new avenues for the study of cancer evolution with great molecular and spatial detail. These methods enable precise characterizations of the tumour microenvironment, cellular interactions therein and micro-anatomical structures. In conjunction with spatial genomics, it emerges that tumours and microenvironments co-evolve, which helps explain observable patterns of heterogeneity and offers new routes for therapeutic interventions.
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Zhao H, Cheng Y, Kalra A, Ma K, Zheng Y, Ziman B, Tressler C, Glunde K, Shin EJ, Ngamruengphong S, Khashab M, Singh V, Anders RA, Jit S, Wyhs N, Chen W, Li X, Lin DC, Meltzer SJ. Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model. Sci Transl Med 2022; 14:eabq6146. [PMID: 36449602 PMCID: PMC10026384 DOI: 10.1126/scitranslmed.abq6146] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Inactivation of the tumor suppressor genes tumor protein p53 (TP53) and cyclin-dependent kinase inhibitor 2A (CDKN2A) occurs early during gastroesophageal junction (GEJ) tumorigenesis. However, because of a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have not been characterized. Here, we report the development of a wild-type primary human GEJ organoid model and a CRISPR-edited transformed GEJ organoid model. CRISPR-Cas9-mediated TP53 and CDKN2A knockout (TP53/CDKN2AKO) in GEJ organoids induced morphologic dysplasia and proneoplastic features in vitro and tumor formation in vivo. Lipidomic profiling identified several platelet-activating factors (PTAFs) among the most up-regulated lipids in CRISPR-edited organoids. PTAF/PTAF receptor (PTAFR) abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) reduced proliferation and other proneoplastic features of TP53/CDKN2AKO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts of Eso26, an established human esophageal adenocarcinoma cell line, were suppressed by WEB2086. Mechanistically, TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly forkhead box M1 (FOXM1). FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying the PTAF-PTAFR pathway. Together, these studies established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and revealed a potential cancer therapeutic strategy. This work provides insights into proneoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia, which may facilitate early diagnosis and prevention of GEJ neoplasms.
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Affiliation(s)
- Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an 710061, Shaanxi, China
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Einstein Healthcare Network, Philadelphia, PA 19136, USA
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Benjamin Ziman
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Caitlin Tressler
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eun Ji Shin
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Saowanee Ngamruengphong
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mouen Khashab
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vikesh Singh
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert A. Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Simran Jit
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nicolas Wyhs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an 710061, Shaanxi, China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Jajosky A, Fels Elliott DR. Esophageal Cancer Genetics and Clinical Translation. Thorac Surg Clin 2022; 32:425-435. [DOI: 10.1016/j.thorsurg.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Zhao H, Collet C, Peng D, Sinha UK, Lin DC. Investigation of early neoplastic transformation and premalignant biology using genetically engineered organoid models. Comput Struct Biotechnol J 2022; 20:5309-5315. [PMID: 36212534 PMCID: PMC9513696 DOI: 10.1016/j.csbj.2022.09.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Organoid modeling is a powerful, robust and efficient technology faithfully preserving physiological and pathological characteristics of tissues of origin. Recently, substantial advances have been made in applying genetically engineered organoid models to study early tumorigenesis and premalignant biology. These efforts promise to identify novel avenues for early cancer detection, intervention and prevention. Here, we highlight significant advancements in the functional characterization of early genomic and epigenomic events during neoplastic evolution using organoid modeling, discuss the application of the lineage-tracing methodology in organoids to study cancer cells-of-origin, and review future opportunities for further development and improvement of organoid modeling of cancer precursors.
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Affiliation(s)
- Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Casey Collet
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Dongzi Peng
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Department of Gastroenterology, The Second Xiangya Hospital of Central South University, Changsha 410011, China
| | - Uttam K. Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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46
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Zhang Y, Weh KM, Howard CL, Riethoven JJ, Clarke JL, Lagisetty KH, Lin J, Reddy RM, Chang AC, Beer DG, Kresty LA. Characterizing isoform switching events in esophageal adenocarcinoma. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 29:749-768. [PMID: 36090744 PMCID: PMC9437810 DOI: 10.1016/j.omtn.2022.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/14/2022] [Indexed: 12/14/2022]
Abstract
Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment-naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification based on TP53 status increased the number of significant isoform switches to 135, suggesting switching events affect cellular functions based on TP53 mutation and tissue histopathology. Analysis of isoforms agnostic, exclusive, and shared with mutant TP53 revealed unique signatures including demethylation, lipid and retinoic acid metabolism, and glucuronidation, respectively. Nearly half of isoform switching events were identified without significant gene-level expression changes. Importantly, two TP53-interacting isoforms, RNF128 and WRAP53, were significantly linked to patient survival. Thus, analysis of isoform switching events may provide new insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC.
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Affiliation(s)
- Yun Zhang
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Katherine M. Weh
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Connor L. Howard
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jean-Jack Riethoven
- Nebraska Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Jennifer L. Clarke
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Kiran H. Lagisetty
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jules Lin
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rishindra M. Reddy
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew C. Chang
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - David G. Beer
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laura A. Kresty
- Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Corresponding author Laura A. Kresty, PhD, Department of Surgery, Thoracic Surgery Section, University of Michigan, Ann Arbor, MI 48109, USA.
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A patient-driven clinicogenomic partnership for metastatic prostate cancer. CELL GENOMICS 2022; 2. [PMID: 36177448 PMCID: PMC9518748 DOI: 10.1016/j.xgen.2022.100169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Molecular profiling studies have enabled discoveries for metastatic prostate cancer (MPC) but have predominantly occurred in academic medical institutions and involved non-representative patient populations. We established the Metastatic Prostate Cancer Project (MPCproject, mpcproject.org), a patient-partnered initiative to involve patients with MPC living anywhere in the US and Canada in molecular research. Here, we present results from our partnership with the first 706 MPCproject participants. While 41% of patient partners live in rural, physician-shortage, or medically underserved areas, the MPCproject has not yet achieved racial diversity, a disparity that demands new initiatives detailed herein. Among molecular data from 333 patient partners (572 samples), exome sequencing of 63 tumor and 19 cell-free DNA (cfDNA) samples recapitulated known findings in MPC, while inexpensive ultra-low-coverage sequencing of 318 cfDNA samples revealed clinically relevant AR amplifications. This study illustrates the power of a growing, longitudinal partnership with patients to generate a more representative understanding of MPC. Crowdis et al. describe the MPCproject (mpcproject.org), a decentralized initiative to partner with patients with metastatic prostate cancer in the US and Canada to accelerate molecular research. The authors describe clinicogenomic results from the first 706 geographically diverse patient partners and lay the foundation for sustained and inclusive partnership in this disease.
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Fujino T, Asada S, Goyama S, Kitamura T. Mechanisms involved in hematopoietic stem cell aging. Cell Mol Life Sci 2022; 79:473. [PMID: 35941268 PMCID: PMC11072869 DOI: 10.1007/s00018-022-04356-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Hematopoietic stem cells (HSCs) undergo progressive functional decline over time due to both internal and external stressors, leading to aging of the hematopoietic system. A comprehensive understanding of the molecular mechanisms underlying HSC aging will be valuable in developing novel therapies for HSC rejuvenation and to prevent the onset of several age-associated diseases and hematological malignancies. This review considers the general causes of HSC aging that range from cell-intrinsic factors to cell-extrinsic factors. In particular, epigenetics and inflammation have been implicated in the linkage of HSC aging, clonality, and oncogenesis. The challenges in clarifying mechanisms of HSC aging have accelerated the development of therapeutic interventions to rejuvenate HSCs, the major goal of aging research; these details are also discussed in this review.
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Affiliation(s)
- Takeshi Fujino
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Shuhei Asada
- The Institute of Laboratory Animals, Tokyo Women's Medical University, Tokyo, 1628666, Japan
| | - Susumu Goyama
- Division of Molecular Oncology Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 1088639, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
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Sugano K, Spechler SJ, El-Omar EM, McColl KEL, Takubo K, Gotoda T, Fujishiro M, Iijima K, Inoue H, Kawai T, Kinoshita Y, Miwa H, Mukaisho KI, Murakami K, Seto Y, Tajiri H, Bhatia S, Choi MG, Fitzgerald RC, Fock KM, Goh KL, Ho KY, Mahachai V, O'Donovan M, Odze R, Peek R, Rugge M, Sharma P, Sollano JD, Vieth M, Wu J, Wu MS, Zou D, Kaminishi M, Malfertheiner P. Kyoto international consensus report on anatomy, pathophysiology and clinical significance of the gastro-oesophageal junction. Gut 2022; 71:1488-1514. [PMID: 35725291 PMCID: PMC9279854 DOI: 10.1136/gutjnl-2022-327281] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/03/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVE An international meeting was organised to develop consensus on (1) the landmarks to define the gastro-oesophageal junction (GOJ), (2) the occurrence and pathophysiological significance of the cardiac gland, (3) the definition of the gastro-oesophageal junctional zone (GOJZ) and (4) the causes of inflammation, metaplasia and neoplasia occurring in the GOJZ. DESIGN Clinical questions relevant to the afore-mentioned major issues were drafted for which expert panels formulated relevant statements and textural explanations.A Delphi method using an anonymous system was employed to develop the consensus, the level of which was predefined as ≥80% of agreement. Two rounds of voting and amendments were completed before the meeting at which clinical questions and consensus were finalised. RESULTS Twenty eight clinical questions and statements were finalised after extensive amendments. Critical consensus was achieved: (1) definition for the GOJ, (2) definition of the GOJZ spanning 1 cm proximal and distal to the GOJ as defined by the end of palisade vessels was accepted based on the anatomical distribution of cardiac type gland, (3) chemical and bacterial (Helicobacter pylori) factors as the primary causes of inflammation, metaplasia and neoplasia occurring in the GOJZ, (4) a new definition of Barrett's oesophagus (BO). CONCLUSIONS This international consensus on the new definitions of BO, GOJ and the GOJZ will be instrumental in future studies aiming to resolve many issues on this important anatomic area and hopefully will lead to better classification and management of the diseases surrounding the GOJ.
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Affiliation(s)
- Kentaro Sugano
- Division of Gastroenterology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Stuart Jon Spechler
- Division of Gastroenterology, Center for Esophageal Diseases, Baylor University Medical Center, Dallas, Texas, USA
| | - Emad M El-Omar
- Microbiome Research Centre, St George & Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine & Health, Sydney, New South Wales, Australia
| | - Kenneth E L McColl
- Division of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Kaiyo Takubo
- Research Team for Geriatric Pathology, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Takuji Gotoda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsunori Iijima
- Department of Gastroenterology, Akita University Graduate School of Medicine, Akita, Japan
| | - Haruhiro Inoue
- Digestive Disease Center, Showa University Koto Toyosu Hospital, Tokyo, Japan
| | - Takashi Kawai
- Department of Gastroenterological Endoscopy, Tokyo Medical University, Tokyo, Japan
| | | | - Hiroto Miwa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Hyogo College of Medicine, Kobe, Japan
| | - Ken-ichi Mukaisho
- Education Center for Medicine and Nursing, Shiga University of Medical Science, Otsu, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Faculty of Medicine, Yuhu, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hisao Tajiri
- Jikei University School of Medicine, Minato-ku, Tokyo, Japan
| | | | - Myung-Gyu Choi
- Gastroenterology, Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, The Republic of Korea
| | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
| | - Kwong Ming Fock
- Department of Gastroenterology and Hepatology, Duke NUS School of Medicine, National University of Singapore, Singapore
| | | | - Khek Yu Ho
- Department of Medicine, National University of Singapore, Singapore
| | - Varocha Mahachai
- Center of Excellence in Digestive Diseases, Thammasat University and Science Resarch and Innovation, Bangkok, Thailand
| | - Maria O'Donovan
- Department of Histopathology, Cambridge University Hospital NHS Trust UK, Cambridge, UK
| | - Robert Odze
- Department of Pathology, Tuft University School of Medicine, Boston, Massachusetts, USA
| | - Richard Peek
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Massimo Rugge
- Department of Medicine DIMED, Surgical Pathology and Cytopathology Unit, University of Padova, Padova, Italy
| | - Prateek Sharma
- Department of Gastroenterology and Hepatology, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Jose D Sollano
- Department of Medicine, University of Santo Tomas, Manila, Philippines
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth, Friedrich-Alexander University Erlangen, Nurenberg, Germany
| | - Justin Wu
- Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Ming-Shiang Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Duowu Zou
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Peter Malfertheiner
- Medizinixhe Klinik und Poliklinik II, Ludwig Maximillian University Klinikum, Munich, Germany,Klinik und Poliklinik für Radiologie, Ludwig Maximillian University Klinikum, Munich, Germany
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50
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Pinto R, Hauge T, Jeanmougin M, Pharo HD, Kresse SH, Honne H, Winge SB, Five MB, Kumar T, Mala T, Hauge T, Johnson E, Lind GE. Targeted genetic and epigenetic profiling of esophageal adenocarcinomas and non-dysplastic Barrett's esophagus. Clin Epigenetics 2022; 14:77. [PMID: 35701814 PMCID: PMC9195284 DOI: 10.1186/s13148-022-01287-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 05/10/2022] [Indexed: 11/22/2022] Open
Abstract
Background Despite the efforts to describe the molecular landscape of esophageal adenocarcinoma (EAC) and its precursor lesion Barrett’s esophagus (BE), discrepant findings are reported. Here, we investigated the prevalence of selected genetic (TP53 mutations and microsatellite instability (MSI) status) and epigenetic (DNA promoter hypermethylation of APC, CDKN2A, MGMT, TIMP3 and MLH1) modifications in a series of 19 non-dysplastic BE and 145 EAC samples. Additional biopsies from adjacent normal tissue were also evaluated. State-of-the-art methodologies and well-defined scoring criteria were applied in all molecular analyses. Results Overall, we confirmed frequent TP53 mutations among EAC (28%) in contrast to BE, which harbored no mutations. We demonstrated that MSI and MLH1 promoter hypermethylation are rare events, both in EAC and in BE. Our findings further support that APC, CDKN2A, MGMT and TIMP3 promoter hypermethylation is frequently seen in both lesions (21–89%), as well as in a subset of adjacent normal samples (up to 12%). Conclusions Our study further enlightens the molecular background of BE and EAC. To the best of our knowledge, this is one of the largest studies addressing a targeted analysis of genetic and epigenetic modifications simultaneously across a combined series of non-dysplastic BE and EAC samples. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01287-7.
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Affiliation(s)
- Rita Pinto
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Tobias Hauge
- Department of Pediatric and Gastrointestinal Surgery, Oslo University Hospital, Ullevål, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Heidi D Pharo
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Stine H Kresse
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Hilde Honne
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Sara B Winge
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - May-Britt Five
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway.,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway
| | - Theresa Kumar
- Department of Pathology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Tom Mala
- Department of Pediatric and Gastrointestinal Surgery, Oslo University Hospital, Ullevål, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Truls Hauge
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Gastroenterology, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Egil Johnson
- Department of Pediatric and Gastrointestinal Surgery, Oslo University Hospital, Ullevål, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Montebello, 0379, Oslo, Norway. .,K.G. Jebsen Colorectal Cancer Research Centre, Division for Cancer Medicine, Oslo University Hospital, Oslo, Norway. .,Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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