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Pandey A, Stawiski EW, Durinck S, Gowda H, Goldstein LD, Barbhuiya MA, Schröder MS, Sreenivasamurthy SK, Kim SW, Phalke S, Suryamohan K, Lee K, Chakraborty P, Kode V, Shi X, Chatterjee A, Datta K, Khan AA, Subbannayya T, Wang J, Chaudhuri S, Gupta S, Shrivastav BR, Jaiswal BS, Poojary SS, Bhunia S, Garcia P, Bizama C, Rosa L, Kwon W, Kim H, Han Y, Yadav TD, Ramprasad VL, Chaudhuri A, Modrusan Z, Roa JC, Tiwari PK, Jang JY, Seshagiri S. Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate. Nat Commun 2020; 11:4225. [PMID: 32839463 PMCID: PMC7445288 DOI: 10.1038/s41467-020-17880-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 07/23/2020] [Indexed: 02/08/2023] Open
Abstract
Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile. In addition, we also sequence samples from 39 GBC high-risk patients and detect evidence of early cancer-related genomic lesions. Among the several significantly mutated genes not previously linked to GBC are ETS domain genes ELF3 and EHF, CTNNB1, APC, NSD1, KAT8, STK11 and NFE2L2. A majority of ELF3 alterations are frame-shift mutations that result in several cancer-specific neoantigens that activate T-cells indicating that they are cancer vaccine candidates. In addition, we identify recurrent alterations in KEAP1/NFE2L2 and WNT pathway in GBC. Taken together, these define multiple targetable therapeutic interventions opportunities for GBC treatment and management.
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Affiliation(s)
- Akhilesh Pandey
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India.
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
- Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Eric W Stawiski
- Bioinformatics and Computational Biology Department, Genentech Inc, South San Francisco, CA, 94080, USA.
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA.
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA.
| | - Steffen Durinck
- Bioinformatics and Computational Biology Department, Genentech Inc, South San Francisco, CA, 94080, USA
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Harsha Gowda
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Leonard D Goldstein
- Bioinformatics and Computational Biology Department, Genentech Inc, South San Francisco, CA, 94080, USA
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Mustafa A Barbhuiya
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
- Department of Pathology and Laboratory Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Markus S Schröder
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
- SciGenom Labs, Cochin, Kerala, 682037, India
| | | | - Sun-Whe Kim
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Sameer Phalke
- Research and Development Department, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka, 560099, India
| | - Kushal Suryamohan
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Kayla Lee
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Papia Chakraborty
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Vasumathi Kode
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Xiaoshan Shi
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Aditi Chatterjee
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
| | - Keshava Datta
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
| | - Aafaque A Khan
- Institute of Bioinformatics, Bangalore, Karnataka, 560066, India
| | | | - Jing Wang
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Sanjiv Gupta
- Department of Pathology, Cancer Hospital and Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Braj Raj Shrivastav
- Department of Surgical Oncology, Cancer Hospital and Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | | | | | - Patricia Garcia
- Department of Pathology, Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carolina Bizama
- Department of Pathology, Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Rosa
- Applied Molecular and Cellular Biology PhD Program Universidad De la Frontera, Temuco, Chile
| | - Wooil Kwon
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Hongbeom Kim
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Youngmin Han
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea
| | - Thakur Deen Yadav
- Department of Surgery, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Vedam L Ramprasad
- Research and Development Department, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka, 560099, India
| | - Amitabha Chaudhuri
- Research and Development Department, MedGenome Inc, Foster City, CA, 94404, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Juan Carlos Roa
- Department of Pathology, Millennium Institute on Immunology and Immunotherapy, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Jin-Young Jang
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, 08826, South Korea.
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA, 94080, USA.
- SciGenom Research Foundation, 3rd Floor, Narayana Nethralaya Building, Narayana Health City, #258/A, Bommasandra, Hosur Road, Bangalore, Karnataka, 560099, India.
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3
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Deng S, Zhang X, Qin Y, Chen W, Fan H, Feng X, Wang J, Yan R, Zhao Y, Cheng Y, Wei Y, Fan X, Ashktorab H, Smoot D, Meltzer SJ, Li S, Li K, Peng Y, Jin Z. miRNA-192 and -215 activate Wnt/β-catenin signaling pathway in gastric cancer via APC. J Cell Physiol 2020; 235:6218-6229. [PMID: 32091625 DOI: 10.1002/jcp.29550] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022]
Abstract
Although great progress has been made in surgical techniques, traditional radiotherapy, and chemotherapy, gastric cancer (GC) is still the most common malignant tumor and has a high mortality, which highlights the importance of novel diagnostic markers. Emerging studies suggest that different microRNAs (miRNAs) are involved in tumorigenesis of GC. In this study, we found that miRNA-192 and -215 are significantly upregulated in GC and promote cell proliferation and migration. Adenomatous polyposis coli (APC), a well-known negative regulator in Wnt signaling, has been proved to be a target of miRNA-192 and -215. Inhibition of miRNA-192 or -215 reduced the Topflash activities and repressed the expression of Wnt signaling pathway proteins, while APC small interfering RNAs reversed the inhibitory effects, suggesting that miRNA-192 and -215 activate Wnt signaling via APC. In addition, APC mediates the cell proliferation and migration regulated by miRNA-192 and -215. Furthermore, APC is downregulated in GC tissues and negatively correlated with the expression of miRNA-192 and -215. In summary, miRNA-192 and -215 target APC and function as oncogenic miRNAs by activating Wnt signaling in GC, revealing to be potential therapeutic targets.
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Affiliation(s)
- Shiqi Deng
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xiaojing Zhang
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Health Science Center, Shenzhen University, Shenzhen, China.,Department of Pathology, Guangdong Province Key Laboratory of Molecular Oncologic Pathology, Guangdong, China
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Wangchun Chen
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Hu Fan
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xianling Feng
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jian Wang
- Department of Pathology and Pathophysiology, The Guangzhou Medical University, Guangzhou, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Yulan Cheng
- Department of Medicine/GI Division, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong, China
| | - Xinmin Fan
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, College of Medicine, Howard University, Washington DC
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, Tennessee
| | - Stephen J Meltzer
- Department of Medicine/GI Division, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Song Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Kuan Li
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yin Peng
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhe Jin
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Health Science Center, Shenzhen University, Shenzhen, China
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4
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Mishra SK, Kumari N, Krishnani N. Molecular pathogenesis of gallbladder cancer: An update. Mutat Res 2019; 816-818:111674. [PMID: 31330366 DOI: 10.1016/j.mrfmmm.2019.111674] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 01/17/2023]
Abstract
Gallbladder carcinoma (GBC) is the most aggressive gastrointestinal malignancy throughout the world, with wide geographical variance. It is the subtype of biliary tract malignancy that has the poorest prognosis and lower survival among all biliary tract malignancies. Various factors are associated with GBC pathogenesis such as environmental, microbial, metabolic and molecular. Chronic inflammation of gallbladder due to presence of gallstone or microbial infection (eg. Salmonella or H. pylori) results in sustained production of inflammatory mediators in the tissue microenvironment, which can cause genomic changes linked to carcinogenesis. Genetic alterations are one of the major factors, associated with aggressiveness and prognosis. Researches have been done to explore suitable biomarker for early diagnosis and identify altered molecular pathways to develop appropriate biomarkers for early diagnosis, therapy and predicting prognosis. Different agents for targeted therapy against actionable mutations of molecules like EGFR, VEGF, mTOR, HER2, PDL-1, PD-1, MET, PI3K, N-cadherin, VEGFR, MEK1 and MEK2 are being tried. Despite these advancements, there is dismal improvement in the survival of GBC patients. Genetic aberrations other than actionable mutations and epigenetic modification including aberrant expressions of micro-RNAs, are also being studied both as diagnostic biomarker and therapeutic targets. Complex pathogenesis of GBC still needs to be unfolded. In this review we focus on the molecular pathogenesis of GBC elucidated till date along with future directions that can be explored to achieve better management of GBC patients.
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Affiliation(s)
- Shravan Kumar Mishra
- Department of Pathology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
| | - Niraj Kumari
- Department of Pathology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
| | - Narendra Krishnani
- Department of Pathology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, 226014, India.
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