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Zhang J, Liu S, Chen X, Xu X, Xu F. Non-immune cell components in tumor microenvironment influencing lung cancer Immunotherapy. Biomed Pharmacother 2023; 166:115336. [PMID: 37591126 DOI: 10.1016/j.biopha.2023.115336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023] Open
Abstract
Lung cancer (LC) is one of the leading causes of cancer-related deaths worldwide, with a significant morbidity and mortality rate, endangering human life and health. The introduction of immunotherapies has significantly altered existing cancer treatment strategies and is expected to improve immune responses, objective response rates, and survival rates. However, a better understanding of the complex immunological networks of LC is required to improve immunotherapy efficacy further. Tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs) are significantly expressed by LC cells, which activate dendritic cells, initiate antigen presentation, and activate lymphocytes to exert antitumor activity. However, as tumor cells combat the immune system, an immunosuppressive microenvironment forms, enabling the enactment of a series of immunological escape mechanisms, including the recruitment of immunosuppressive cells and induction of T cell exhaustion to decrease the antitumor immune response. In addition to the direct effect of LC cells on immune cell function, the secreting various cytokines, chemokines, and exosomes, changes in the intratumoral microbiome and the function of cancer-associated fibroblasts and endothelial cells contribute to LC cell immune escape. Accordingly, combining various immunotherapies with other therapies can elicit synergistic effects based on the complex immune network, improving immunotherapy efficacy through multi-target action on the tumor microenvironment (TME). Hence, this review provides guidance for understanding the complex immune network in the TME and designing novel and effective immunotherapy strategies for LC.
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Affiliation(s)
- Jingtao Zhang
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Shuai Liu
- Central Laboratory, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Xiubao Chen
- Department of Geriatric Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China
| | - Xiangdong Xu
- Central Laboratory, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China.
| | - Fei Xu
- Department of Geriatric Medicine, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250014, China; First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan 250014, China.
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2
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Molecular and Circulating Biomarkers of Gastric Cancer. Int J Mol Sci 2022; 23:ijms23147588. [PMID: 35886934 PMCID: PMC9322632 DOI: 10.3390/ijms23147588] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Gastric cancer (GC)—a common tumor that affects humans worldwide—is highly malignant with a poor prognosis. GC is frequently not diagnosed until a relatively advanced stage. Early detection and efficient monitoring of tumor dynamics are prerequisites for reducing disease burden and mortality. Minimally invasive methods are needed to establish a diagnosis or monitoring the response to treatment of gastric cancer. Blood-based biomarker assays for the detection of early-stage GC could be of great relevance both for the risk group or for population-wide based screening programs, The currently used tumor marker assays for detecting GC are simple and rapid, but their use is limited by their low sensitivity and specificity. In recent years, several markers have been identified and tested for their clinical relevance in the management of gastric cancer. Here we review the available literature on plasma classical tumor markers, circulating free microRNAs (cfmiRNAs), circulating cell-free DNA (cfDNA), circulating tumor cells (CTCs), autoantibodies against tumor associated antigens (TAAs), and circulating extracellular vesicles (EVs) for diagnosis and monitoring of gastric cancer. This review summarizes the present status and approaches for these biomarkers, which could be potentially used for early diagnosis and accurate prediction of therapeutic approaches. We also discuss the future perspective and challenges in the search for new biomarkers of gastric cancer.
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3
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Niloofa R, De Zoysa MI, Seneviratne LS. Autoantibodies in the diagnosis, prognosis, and prediction of colorectal cancer. J Cancer Res Ther 2021; 17:819-833. [PMID: 34528528 DOI: 10.4103/jcrt.jcrt_64_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Colorectal cancer (CRC) is the second-most commonly diagnosed cancer worldwide. Early diagnosis improves prognosis and long-term outcomes. Several studies have found tumor-associated autoantibodies in CRC patients. We aimed to provide an overview on CRC-associated autoantibodies and their reported diagnostic, prognostic, and predictive performance when used singly or in combination. We systematically reviewed studies on CRC-related autoantibodies published till March 2018 and critically analyzed the role of these autoantibodies in CRC. In general, autoantibodies were of low sensitivity when tested individually and the diagnostic characteristics improved when tested in combination. Autoantibodies against CCD83, carcinoembryonic antigen, MAPKAPK3, RPH 3AL, SEC61b, and SPAG9 showed high sensitivity and specificity when tested alone. When tested in combination, autoantibodies against three antigens (PIM1, MAPKAPK3, and ACVR2B) showed high sensitivity and specificity. So far, most CRC-associated autoantibodies have been evaluated in single or in a small number of studies. In contrast, anti-p53 antibodies have been studied in a larger number of CRC studies, but, so far, none of them have high diagnostic characteristics. CRC-associated autoantibodies are detectable from the early stages of malignancy, pointing to their possible use in the early detection of CRC. Some studies suggest that CRC-associated autoantibodies may be a guide to prognosis in CRC.
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Affiliation(s)
- Roshan Niloofa
- Department of Zoology and Environmental Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | - M Ishan De Zoysa
- Department of Surgery, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
| | - L Suranjith Seneviratne
- Department of Zoology and Environmental Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
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4
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Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell 2020; 182:200-225.e35. [PMID: 32649874 PMCID: PMC7373300 DOI: 10.1016/j.cell.2020.06.013] [Citation(s) in RCA: 392] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/06/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, and gender. Proteomic and phosphoproteomic data illuminated biology downstream of copy number aberrations, somatic mutations, and fusions and identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK. Immune subtyping revealed a complex landscape, reinforced the association of STK11 with immune-cold behavior, and underscored a potential immunosuppressive role of neutrophil degranulation. Smoking-associated LUADs showed correlation with other environmental exposure signatures and a field effect in NATs. Matched NATs allowed identification of differentially expressed proteins with potential diagnostic and therapeutic utility. This proteogenomics dataset represents a unique public resource for researchers and clinicians seeking to better understand and treat lung adenocarcinomas.
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Affiliation(s)
- Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, 02115, USA.
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Song Cao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Suhas V Vasaikar
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yize Li
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Wen-Wei Liang
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jiayi Ji
- Department of Population Health Science and Policy; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xiaoyu Song
- Department of Population Health Science and Policy; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wenke Liu
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Runyu Hong
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Lijun Yao
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Lili Blumenberg
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael C Wendl
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lauren C Tang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA; Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Melanie A MacMullan
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA; Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA
| | - Shayan C Avanessian
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | | | - MacIntosh Cornwell
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ramani B Kothadia
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rahul Mannan
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pankaj Vats
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Emily A Kawaler
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tatiana Omelchenko
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Antonio Colaprico
- Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Yosef E Maruvka
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | | | - Maciej Wiznerowicz
- Poznan University of Medical Sciences, Poznań, 61-701, Poland; International Institute for Molecular Oncology, Poznań, 60-203, Poland
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rajwanth R Veluswamy
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Matthew A Wyczalkowski
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Qing Kay Li
- Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins Medical Institutions, Baltimore, MD, 21224, USA
| | - Scott D Jewell
- Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Institute for Systems Genetics and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Marcin P Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Ramaswamy Govindan
- Division of Oncology and Siteman Cancer Center, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
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5
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Jiang L, Chen T, Xiong L, Xu JH, Gong AY, Dai B, Wu G, Zhu K, Lu E, Mathy NW, Chen XM. Knockdown of m6A methyltransferase METTL3 in gastric cancer cells results in suppression of cell proliferation. Oncol Lett 2020; 20:2191-2198. [PMID: 32782536 PMCID: PMC7400027 DOI: 10.3892/ol.2020.11794] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/21/2020] [Indexed: 12/14/2022] Open
Abstract
N6-methyladenosine (m6A) RNA modification regulates multiple biological functions. Methyltransferase like 3 (METTL3), one of the major N6-methyltransferases, is highly expressed in gastric cancer, but its potential role in disease is unclear. The current study knocked out METTL3 (METTL3-KO) in human gastric cancer AGS cells using CRISPR/Cas9. METTL3-KO AGS cells exhibited decreased m6A methylation levels. A significant inhibition of cell proliferation was observed in METTL3-KO AGS cells. Silencing METTL3 in AGS cells altered the expression profile of many effector molecules that were previously demonstrated to serve key roles in AGS cell proliferation, including the suppressor of cytokine signaling (SOCS) family of proteins. The results further demonstrated that SOCS2 upregulation in METTL3-KO AGS cells was associated with a decreased RNA decay rate. Furthermore, SOCS2 KO or SOCS2 overexpression caused a significant increase and decrease in AGS cell proliferation, respectively. The current data suggested that METTL3-KO in gastric cancer cells resulted in the suppression of cell proliferation by inducing SOCS2, suggesting a potential role of elevated METTL3 expression in gastric cancer progression.
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Affiliation(s)
- Li Jiang
- Department of Geriatrics, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, P.R. China.,Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Ting Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA.,National Demonstration Center for Experimental General Medicine Education, College of Clinical Medicine, Hubei University of Science and Technology, Xianning, Hubei 437100, P.R. China
| | - Li Xiong
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA.,National Demonstration Center for Experimental General Medicine Education, College of Clinical Medicine, Hubei University of Science and Technology, Xianning, Hubei 437100, P.R. China
| | - Ji-Hao Xu
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA.,Department of Gastroenterology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Ai-Yu Gong
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Bin Dai
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA.,National Demonstration Center for Experimental General Medicine Education, College of Clinical Medicine, Hubei University of Science and Technology, Xianning, Hubei 437100, P.R. China
| | - Ganlin Wu
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA.,National Demonstration Center for Experimental General Medicine Education, College of Clinical Medicine, Hubei University of Science and Technology, Xianning, Hubei 437100, P.R. China
| | - Kenny Zhu
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Eugene Lu
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Nicholas William Mathy
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
| | - Xian-Ming Chen
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE 68178, USA
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6
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Zhang MY, Wang J, Guo J. Role of Regenerating Islet-Derived Protein 3A in Gastrointestinal Cancer. Front Oncol 2019; 9:1449. [PMID: 31921694 PMCID: PMC6928188 DOI: 10.3389/fonc.2019.01449] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
Regenerating islet-derived protein 3A (Reg3A), a protein mainly expressed in the digestive system, has been found over-expressed in many kinds of gastrointestinal cancer, including hepatocellular carcinoma, pancreatic cancer, gastric cancer, and colorectal cancer, therefore has been considered as a promising tumor marker. In recent years, considerable attention has been focused on the tumorigenesis effects of Reg3A, which were mainly manifested as cell proliferation promotion, cell apoptosis inhibition, the regulation of cancer cell migration and invasion. In particular, based on the significant up-regulation of Reg3A during pancreatic inflammation as well as its tumorigenic potential, Reg3A has been considered to play a key role in inflammation-linked pancreatic carcinogenesis. In addition, we here systematically generalized the reported Reg3A-related signaling molecules, which included JAK2-STAT3- NF-κB, SOCS3, EXTL3-PI3K-Akt, GSK3β, Wnt/β-catenin as well as some invasion and migration-related genes (Snail, MMP-2, MMP-9, E-cadherin, RhoC, and MTA1). And gp130, EGFR, EXTL3, and Fibronectin 1 might act as potential receptors for Reg3A.
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Affiliation(s)
- Meng-Ya Zhang
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, China.,Department of Pharmacy, New Medicine Innovation and Development Institute, College of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Jun Wang
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, China.,Department of Pharmacy, New Medicine Innovation and Development Institute, College of Medicine, Wuhan University of Science and Technology, Wuhan, China
| | - Jie Guo
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, China.,Department of Pharmacy, New Medicine Innovation and Development Institute, College of Medicine, Wuhan University of Science and Technology, Wuhan, China
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7
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Liu S, Tan Q, Song Y, Shi Y, Han X. Anti‐p53 autoantibody in blood as a diagnostic biomarker for colorectal cancer: A meta‐analysis. Scand J Immunol 2019; 91:e12829. [DOI: 10.1111/sji.12829] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 09/15/2019] [Accepted: 09/15/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Shuxia Liu
- Department of Clinical Laboratory National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
- Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs Beijing China
| | - Qiaoyun Tan
- Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs Beijing China
| | - Yuanyuan Song
- Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs Beijing China
| | - Yuankai Shi
- Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs Beijing China
| | - Xiaohong Han
- Department of Clinical Laboratory National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing China
- Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs Beijing China
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8
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Baldauf MC, Gerke JS, Kirschner A, Blaeschke F, Effenberger M, Schober K, Rubio RA, Kanaseki T, Kiran MM, Dallmayer M, Musa J, Akpolat N, Akatli AN, Rosman FC, Özen Ö, Sugita S, Hasegawa T, Sugimura H, Baumhoer D, Knott MML, Sannino G, Marchetto A, Li J, Busch DH, Feuchtinger T, Ohmura S, Orth MF, Thiel U, Kirchner T, Grünewald TGP. Systematic identification of cancer-specific MHC-binding peptides with RAVEN. Oncoimmunology 2018; 7:e1481558. [PMID: 30228952 PMCID: PMC6140548 DOI: 10.1080/2162402x.2018.1481558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/21/2018] [Accepted: 05/21/2018] [Indexed: 02/03/2023] Open
Abstract
Immunotherapy can revolutionize anti-cancer therapy if specific targets are available. Immunogenic peptides encoded by cancer-specific genes (CSGs) may enable targeted immunotherapy, even of oligo-mutated cancers, which lack neo-antigens generated by protein-coding missense mutations. Here, we describe an algorithm and user-friendly software named RAVEN (Rich Analysis of Variable gene Expressions in Numerous tissues) that automatizes the systematic and fast identification of CSG-encoded peptides highly affine to Major Histocompatibility Complexes (MHC) starting from transcriptome data. We applied RAVEN to a dataset assembled from 2,678 simultaneously normalized gene expression microarrays comprising 50 tumor entities, with a focus on oligo-mutated pediatric cancers, and 71 normal tissue types. RAVEN performed a transcriptome-wide scan in each cancer entity for gender-specific CSGs, and identified several established CSGs, but also many novel candidates potentially suitable for targeting multiple cancer types. The specific expression of the most promising CSGs was validated in cancer cell lines and in a comprehensive tissue-microarray. Subsequently, RAVEN identified likely immunogenic CSG-encoded peptides by predicting their affinity to MHCs and excluded sequence identity to abundantly expressed proteins by interrogating the UniProt protein-database. The predicted affinity of selected peptides was validated in T2-cell peptide-binding assays in which many showed binding-kinetics like a very immunogenic influenza control peptide. Collectively, we provide an exquisitely curated catalogue of cancer-specific and highly MHC-affine peptides across 50 cancer types, and a freely available software (https://github.com/JSGerke/RAVENsoftware) to easily apply our algorithm to any gene expression dataset. We anticipate that our peptide libraries and software constitute a rich resource to advance anti-cancer immunotherapy.
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Affiliation(s)
- Michaela C Baldauf
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Julia S Gerke
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Andreas Kirschner
- Children's Cancer Research Center, Technische Universität München (TUM), Munich, Germany
| | - Franziska Blaeschke
- Department of Pediatrics, Dr. von Hauner'sches Children's Hospital, LMU Munich, Munich, Germany
| | - Manuel Effenberger
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Kilian Schober
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Rebeca Alba Rubio
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | | | - Merve M Kiran
- Department of Pathology, Medical Faculty, Yildirim Beyazit University, Ankara, Turkey
| | - Marlene Dallmayer
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Julian Musa
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Nurset Akpolat
- Department of Pathology, Turgut Ozal Medical Center, Inonu University, Malatya, Turkey
| | - Ayse N Akatli
- Department of Pathology, Turgut Ozal Medical Center, Inonu University, Malatya, Turkey
| | - Fernando C Rosman
- Department for Pathology, Hospital Municipal Jesus, Rio de Janeiro, Brazil
| | - Özlem Özen
- Department of Pathology, Medical Faculty, Başkent University Hospital, Ankara, Turkey
| | - Shintaro Sugita
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Tadashi Hasegawa
- Department of Pathology, Sapporo Medical University, Sapporo, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu School of Medicine, Hamamatsu, Japan
| | - Daniel Baumhoer
- Bone Tumor Reference Center, Institute of Pathology of the University Hospital of Basel, Basel, Switzerland
| | - Maximilian M L Knott
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Giuseppina Sannino
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Aruna Marchetto
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Jing Li
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München (TUM), Munich, Germany
| | - Tobias Feuchtinger
- Department of Pediatrics, Dr. von Hauner'sches Children's Hospital, LMU Munich, Munich, Germany
| | - Shunya Ohmura
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Martin F Orth
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany
| | - Uwe Thiel
- Children's Cancer Research Center, Technische Universität München (TUM), Munich, Germany
| | - Thomas Kirchner
- Faculty of Medicine, Institute of Pathology, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas G P Grünewald
- Faculty of Medicine, Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, LMU Munich, Munich, Germany.,Faculty of Medicine, Institute of Pathology, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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9
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Wang X, Tan Y, Cao X, Kim JA, Chen T, Hu Y, Wexler M, Wang X. Epigenetic activation of HORMAD1 in basal-like breast cancer: role in Rucaparib sensitivity. Oncotarget 2018; 9:30115-30127. [PMID: 30046392 PMCID: PMC6059019 DOI: 10.18632/oncotarget.25728] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 06/22/2018] [Indexed: 12/27/2022] Open
Abstract
Basal-like breast cancer (BLBC) is an aggressive breast cancer subtype with features similar to the basal cells surrounding the mammary ducts. Treatment of patients with BLBC has been challenging due to the lack of well-defined molecular targets. Due to the clinical and pathological similarities of BLBC with BRCA-deficient breast cancers, the effectiveness of Poly (ADP-ribose) polymerase inhibitors (PARPi) has been tested in early phase clinical trials for patients with advanced BLBC, with limited clinical responses. Recently, it was reported that HORMAD1 overexpression sensitizes BLBC to HR-targeting agents by suppressing homologous recombination. Our independent analysis suggests that HORMAD1 is aberrantly overexpressed in about 80% of BLBC, and its expression in normal tissues is restricted to testis. Our experimental data suggests that HORMAD1 overexpression correlates with focal hypomethylation in BLBC. On the other hand, investigation of the Genomics of Drug Sensitivity in Cancer dataset revealed significantly reduced sensitivity of HORMAD1-overexpressing BLBC cell lines to Rucaparib, a commonly used PARPi. To further assess the role of HORMAD1 in PARPi sensitivity, we generated three HORMAD1-overexpressing xenograft models using the HORMAD1-low BLBC cell lines HCC1954, HCC1806, and BT20; we then subjected these xenograft models to Rucaparib treatment. Ectopic expression of HORMAD1 enhances tumor formations in two of these models, and significantly reduces sensitivity to Rucaparib in the HCC1954 model. Taken together, our data suggest that epigenetic activation of HORMAD1 by hypomethylation in BLBC may endow reduced sensitivity to Rucaparib treatment in some tumor models.
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Affiliation(s)
- Xian Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ying Tan
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xixi Cao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jin Ah Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tianmeng Chen
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
| | - Yiheng Hu
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
| | - Matthew Wexler
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
| | - Xiaosong Wang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
- Department of Pathology, University of Pittsburgh, PA 15232, USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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10
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Li TT, Liu H, Yu J, Shi GY, Zhao LY, Li GX. Prognostic and predictive blood biomarkers in gastric cancer and the potential application of circulating tumor cells. World J Gastroenterol 2018; 24:2236-2246. [PMID: 29881233 PMCID: PMC5989238 DOI: 10.3748/wjg.v24.i21.2236] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/27/2018] [Accepted: 05/18/2018] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC), with its high incidence and mortality rates, is a highly fatal cancer that is common in East Asia particularly in China. Its recurrence and metastasis are the main causes of its poor prognosis. Circulating tumor cells (CTCs) or other blood biomarkers that are released into the circulating blood stream by tumors are thought to play a crucial role in the recurrence and metastasis of gastric cancer. Therefore, the detection of CTCs and other blood biomarkers has an important clinical significance; in fact, they can help predict the prognosis, assess the staging, monitor the therapeutic effects and determine the drug susceptibility. Recent research has identified many blood biomarkers in GC, such as various serum proteins, autoantibodies against tumor associated antigens, and cell-free DNAs. The analysis of CTCs and circulating cell-free tumor DNA (ctDNA) in the peripheral blood of patients with gastric cancer is called as liquid biopsy. These blood biomarkers provide the disease status for individuals and have clinical meaning. In this review, we focus on the recent scientific advances regarding CTCs and other blood biomarkers, and discuss their origins and clinical meaning.
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Affiliation(s)
- Ting-Ting Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China
| | - Jiang Yu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China
| | - Guang-Yao Shi
- Division of Cardiology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, Guangdong Province, China
| | - Li-Ying Zhao
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China
| | - Guo-Xin Li
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong Province, China
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11
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Zhao W, Lu D, Liu L, Cai J, Zhou Y, Yang Y, Zhang Y, Zhang J. Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) promotes lung tumorigenesis via attenuating p53 stability. Oncotarget 2017; 8:93672-93687. [PMID: 29212181 PMCID: PMC5706827 DOI: 10.18632/oncotarget.21280] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 09/13/2017] [Indexed: 01/10/2023] Open
Abstract
Insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3/IMP3/KOC), initially identified as an RNA-binding protein, is highly expressed in embryonic tissues and a variety of cancers. Previously, our group reported that IGF2BP3 may serve as a potential diagnostic marker for lung cancer. However, little is known about the function of IGF2BP3 in lung cancer development. Here we demonstrate that IGF2BP3 expression was markedly increased in lung cancer tissues compared to normal tissues at both mRNA and protein levels. Overexpression of IGF2BP3 in lung cancer cells promoted cell proliferation, tumor migration and invasion in vitro and in vivo, whereas knockdown of IGF2BP3 exhibited opposite effects. Notably IGF2BP3 was directly associated with a deubiquitinase Ubiquitin specific peptidase 10 (USP10) and attenuated its function in stabilizing p53 protein. Silencing IGF2BP3 expression in lung cancer cells consistently increased the half-life and protein level of p53 and induced G0/G1 arrest. Thus, our data together demonstrate that IGF2BP3 promotes lung tumorigenesis via attenuating p53 protein stability.
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Affiliation(s)
- Wei Zhao
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Beijing, 100191, P.R. China.,Present address: Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing 100029, P.R. China
| | - Dan Lu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Liang Liu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, P.R. China
| | - Juan Cai
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Beijing, 100191, P.R. China
| | - Yu Zhou
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Beijing, 100191, P.R. China
| | - Ying Yang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Beijing, 100191, P.R. China
| | - Yu Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Beijing, 100191, P.R. China
| | - Jun Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Beijing, 100191, P.R. China
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12
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Su YL, Huang HL, Huang BS, Chen PC, Chen CS, Wang HL, Lin PH, Chieh MS, Wu JJ, Yang JC, Chow LP. Combination of OipA, BabA, and SabA as candidate biomarkers for predicting Helicobacter pylori-related gastric cancer. Sci Rep 2016; 6:36442. [PMID: 27819260 PMCID: PMC5098209 DOI: 10.1038/srep36442] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/17/2016] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori ) infection is a major cause of chronic gastritis and is highly related to duodenal ulcer (DU) and gastric cancer (GC). To identify H. pylori-related GC biomarkers with high seropositivity in GC patients, differences in levels of protein expression between H. pylori from GC and DU patients were analyzed by isobaric tag for relative and absolute quantitation (iTRAQ). In total, 99 proteins showed increased expression (>1.5-fold) in GC patients compared to DU patients, and 40 of these proteins were categorized by KEGG pathway. The four human disease-related adhesin identified, AlpA, OipA, BabA, and SabA, were potential GC-related antigens, with a higher seropositivity in GC patients (n = 76) than in non-GC patients (n = 100). Discrimination between GC and non-GC patients was improved using multiple antigens, with an odds ratio of 9.16 (95% CI, 2.99-28.07; p < 0.0001) for three antigens recognized. The optimized combination of OipA, BabA, and SabA gave a 77.3% correct prediction rate. A GC-related protein microarray was further developed using these antigens. The combination of OipA, BabA, and SabA showed significant improvement in the diagnostic accuracy and the protein microarray containing above antigens should provide a rapid and convenient diagnosis of H. pylori-associated GC.
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Affiliation(s)
- Yu-Lin Su
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiang-Ling Huang
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bo-Shih Huang
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Chung Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Taoyuan, Taiwan
| | - Hong-Long Wang
- Department of Statistics, National Taipei University, New Taipei City, Taiwan
| | - Pin-Hsin Lin
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Shu Chieh
- First Core Laboratory, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Jiunn-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jyh-Chin Yang
- Department of Internal Medicine, Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Lu-Ping Chow
- Graduate Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
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13
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Aouida M, Eid A, Mahfouz MM. CRISPR/Cas9-mediated target validation of the splicing inhibitor Pladienolide B. BIOCHIMIE OPEN 2016; 3:72-75. [PMID: 29450134 PMCID: PMC5801905 DOI: 10.1016/j.biopen.2016.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/11/2016] [Indexed: 12/31/2022]
Abstract
CRISPR/Cas9 system confers molecular immunity in archeal and bacterial species against invading foreign nucleic acids. CRISPR/Cas9 system is used for genome engineering applications across diverse eukaryotic species. In this study, we demonstrate the utility of the CRISPR/Cas9 genome engineering system for drug target validation in human cells. Pladienolide B is a natural macrolide with antitumor activities mediated through the inhibition of pre-mRNA splicing. To validate the spliceosomal target of Pladienolide B, we employed the CRSIPR/Cas9 system to introduce targeted mutations in the subunits of the SF3B complex in the HEK293T cells. Our data reveal that targeted mutagenesis of the SF3b1 subunit exhibited higher levels of resistance to Pladienolide B. Therefore, our data validate the spliceosomal target of Pladienolide B and provide a proof of concept on using the CRISPR/Cas9 system for drug target identification and validation. CRISPR/Cas9 system serves as an excellent tool for drug target validation. Pladienolide B an antitumor macrolide known to bind to the SF3b complex and inhibit pre-mRNA splicing. Use of CRISPR/Cas9 system to confirm and validate the Pladienolide B spliceosomal target. Our data confirm that the SF3b1 is a specific target for Pladienolide B.
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Key Words
- AB, Alamar Blue
- CRIPSR/Cas9
- CRISPR, Clustered Regulatory Interspaced Short Palindromic Repeats
- Cas9, CRISPR associated protein
- DSB, double strand break
- Drug discovery
- Drug target validation
- HR, Homologous Recombination
- NHJE, Non-Homologous End-Joining
- PB, Pladienolide B
- Pladienolide B
- Pre-mRNA splicing
- SSNs, Site Specific Nucleases
- Spliceosome
- T7EI, T7 Endonuclease I
- TALENs, Transcription Like Effector Nucleases
- ZFN, Zing Finger Nucleases
- sgRNA, Guide RNA
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Affiliation(s)
- Mustapha Aouida
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences & Center for Desert Agriculture, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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14
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Kalniņa Z, Meistere I, Kikuste I, Tolmanis I, Zayakin P, Linē A. Emerging blood-based biomarkers for detection of gastric cancer. World J Gastroenterol 2015; 21:11636-11653. [PMID: 26556992 PMCID: PMC4631966 DOI: 10.3748/wjg.v21.i41.11636] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/08/2015] [Accepted: 09/30/2015] [Indexed: 02/06/2023] Open
Abstract
Early detection and efficient monitoring of tumor dynamics are prerequisites for reducing disease burden and mortality, and for improving the management of patients with gastric cancer (GC). Blood-based biomarker assays for the detection of early-stage GC could be of great relevance both for population-wide or risk group-based screening programs, while circulating biomarkers that reflect the genetic make-up and dynamics of the tumor would allow monitoring of treatment efficacy, predict recurrences and assess the genetic heterogeneity of the tumor. Recent research to identify blood-based biomarkers of GC has resulted in the identification of a wide variety of cancer-associated molecules, including various proteins, autoantibodies against tumor associated antigens, cell-free DNA fragments, mRNAs and various non-coding RNAs, circulating tumor cells and cancer-derived extracellular vesicles. Each type of these biomarkers provides different information on the disease status, has different advantages and disadvantages, and distinct clinical usefulness. In the current review, we summarize the recent developments in blood-based GC biomarker discovery, discuss the origin of various types of biomarkers and their clinical usefulness and the technological challenges in the development of biomarker assays for clinical use.
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15
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Binder DC, Engels B, Arina A, Yu P, Slauch JM, Fu YX, Karrison T, Burnette B, Idel C, Zhao M, Hoffman RM, Munn DH, Rowley DA, Schreiber H. Antigen-specific bacterial vaccine combined with anti-PD-L1 rescues dysfunctional endogenous T cells to reject long-established cancer. Cancer Immunol Res 2015; 1:123-33. [PMID: 24455752 DOI: 10.1158/2326-6066.cir-13-0058] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Immunogenic tumors grow progressively even when heavily infiltrated by CD8(+) T cells. We investigated how to rescue CD8(+) T cell function in long-established immunogenic melanomas that contained a high percentage of endogenous PD-1(+) tumor-specific CD8(+) T cells that were dysfunctional. Treatment with αPD-L1 and αCTLA-4 blocking antibodies did not prevent tumors from progressing rapidly. We then tested exogenous tumor-specific antigen delivery into tumors using Salmonella Typhimurium A1-R to increase antigen levels and generate a proinflammatory tumor microenvironment. Antigen-producing A1-R rescued the endogenous tumor-specific CD8(+) T cell response: proliferation was induced in the lymphoid organs and effector function was recovered in the tumor. Treatment with antigen-producing A1-R led to improved mouse survival and resulted in 32% rejection of long-established immunogenic melanomas. Following treatment with antigen-producing A1-R, the majority of tumor-specific CD8(+) T cells still expressed a high level of PD-1 in the tumor. Combining antigen-producing A1-R with αPD-L1 blocking antibody enhanced the expansion of tumor-specific CD8(+) T cells and resulted in 80% tumor rejection. Collectively, these data demonstrate a powerful new therapeutic approach to rescue dysfunctional endogenous tumor-specific CD8(+) T cells and eradicate advanced immunogenic tumors.
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Affiliation(s)
- David C Binder
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637 ; Department of Pathology, The University of Chicago, Chicago, IL 60637
| | - Boris Engels
- Department of Pathology, The University of Chicago, Chicago, IL 60637 ; Committee on Immunology, The University of Chicago, Chicago, IL 60637
| | - Ainhoa Arina
- Department of Pathology, The University of Chicago, Chicago, IL 60637 ; Committee on Immunology, The University of Chicago, Chicago, IL 60637
| | - Ping Yu
- Committee on Immunology, The University of Chicago, Chicago, IL 60637 ; Department of Medicine, The University of Chicago, Chicago, IL 60637
| | - James M Slauch
- Department of Microbiology and College of Medicine, University of Illinois, Urbana, IL 61801
| | - Yang-Xin Fu
- Department of Pathology, The University of Chicago, Chicago, IL 60637 ; Committee on Immunology, The University of Chicago, Chicago, IL 60637
| | - Theodore Karrison
- Department of Health Sciences, The University of Chicago, Chicago, IL 60637
| | - Byron Burnette
- Department of Radiation Oncology, The University of Chicago, Chicago, IL 60637
| | - Christian Idel
- Department of Pathology, The University of Chicago, Chicago, IL 60637 ; Committee on Immunology, The University of Chicago, Chicago, IL 60637 ; Department of Otorhinolaryngology, University of Lübeck, Lübeck, Germany
| | - Ming Zhao
- AntiCancer, Inc., San Diego, CA 92111
| | - Robert M Hoffman
- AntiCancer, Inc., San Diego, CA 92111 ; Dept. of Surgery, University of California San Diego, San Diego, CA 92103-8220
| | - David H Munn
- Georgia Health Sciences University Cancer Center, Augusta, GA 30912
| | - Donald A Rowley
- Department of Pathology, The University of Chicago, Chicago, IL 60637
| | - Hans Schreiber
- Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637 ; Department of Pathology, The University of Chicago, Chicago, IL 60637 ; Committee on Immunology, The University of Chicago, Chicago, IL 60637
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16
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Xu QW, Zhang Y, Wang XS. HEPA and PARSE: Systematic discovery of clinically relevant tumor-specific antigens. Oncoimmunology 2014; 2:e23249. [PMID: 23802073 PMCID: PMC3661158 DOI: 10.4161/onci.23249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 12/13/2012] [Indexed: 01/10/2023] Open
Abstract
The effective discovery of tumor-specific antigens (TSAs) holds the key for the development of new diagnostic assays and immunotherapeutic approaches against cancer. Here, we discuss our recently developed technologies, HEPA and PARSE, which allow for the systematic identification of TSAs, generating a reservoir of immunologically and clinically relevant targets.
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Affiliation(s)
- Qing-Wen Xu
- Department of Immunology; Peking University Health Science Center; Beijing, China
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17
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Yang Y, Zhao W, Xu QW, Wang XS, Zhang Y, Zhang J. IQGAP3 promotes EGFR-ERK signaling and the growth and metastasis of lung cancer cells. PLoS One 2014; 9:e97578. [PMID: 24849319 PMCID: PMC4029748 DOI: 10.1371/journal.pone.0097578] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 04/21/2014] [Indexed: 12/23/2022] Open
Abstract
Proteins of the IQGAP family display complicated and often contradictory activities in tumorigenesis. IQGAP1 has well documented oncogenic potential and IQGAP2 has putative tumor-suppressive function. IQGAP3 is the latest addition to this family and its role in cancer development remains to be defined. Here we demonstrate IQGAP3 expression is markedly increased in lung cancer tissues at both mRNA and protein levels. Overexpression of IQGAP3 promoted tumor cell growth, and migration and invasion, whereas knockdown of IQGAP3 exhibited opposite effects. Moreover, suppression of IQGAP3 in a lung cancer cell line caused a reduction in the tumorigenicity of these cells in lung tissue after intravenous injection. Furthermore, we showed that IQGAP3 is able to interact with ERK1 and enhance its phosphorylation following treatment with EGF. These data suggest that IQGAP3 may contribute to the pathogenesis of lung cancer by modulating EGFR-ERK signaling.
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Affiliation(s)
- Ying Yang
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Public Health, Peking University Health Science Center, Beijing, P. R. China
| | - Wei Zhao
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Public Health, Peking University Health Science Center, Beijing, P. R. China
| | - Qing-Wen Xu
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Public Health, Peking University Health Science Center, Beijing, P. R. China
| | - Xiao-Song Wang
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Public Health, Peking University Health Science Center, Beijing, P. R. China
| | - Yu Zhang
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Public Health, Peking University Health Science Center, Beijing, P. R. China
- * E-mail: (YZ); (JZ)
| | - Jun Zhang
- Department of Immunology, School of Basic Medical Sciences, Key Laboratory of Medical Immunology of Ministry of Public Health, Peking University Health Science Center, Beijing, P. R. China
- * E-mail: (YZ); (JZ)
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18
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Blood autoantibodies against tumor-associated antigens as biomarkers in early detection of colorectal cancer. Cancer Lett 2014; 346:178-87. [DOI: 10.1016/j.canlet.2014.01.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/07/2014] [Accepted: 01/15/2014] [Indexed: 02/07/2023]
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19
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Werner S, Chen H, Tao S, Brenner H. Systematic review: serum autoantibodies in the early detection of gastric cancer. Int J Cancer 2014; 136:2243-52. [PMID: 24615018 DOI: 10.1002/ijc.28807] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 02/18/2014] [Indexed: 12/15/2022]
Abstract
Antibodies against tumor-associated antigens have been found in serum of patients with various types of cancers and may serve as biomarkers for early detection of gastric cancer as well. This systematic review aims to give an overview about known autoantibodies and their diagnostic value in gastric cancer. We conducted a systematic literature search in two databases to identify studies which performed serological testing for autoantibodies in gastric cancer patients and controls. Data on study characteristics and results were extracted independently by two reviewers. Overall, 39 articles reporting the detection of 34 different autoantibodies met the inclusion criteria for this review. The most common antibody detection method was enzyme-linked immunosorbent assay and the most frequently assessed autoantibody was anti-p53, which was tested in 13 studies. Most antibodies were assessed in only one study and only few authors have evaluated the diagnostic value of combinations of multiple autoantibodies. For single autoantibodies, specificity was generally very high (median: 99.15%), but sensitivity was mostly rather low (median: 12.35%). For some autoantibody combinations, substantially higher sensitivity at reasonably high levels of specificity could be achieved. Development of extended and optimized multimarker panels of autoantibodies might be a promising approach for gastric cancer early detection.
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Affiliation(s)
- Simone Werner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
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GuhaThakurta D, Sheikh NA, Meagher TC, Letarte S, Trager JB. Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome. Expert Rev Clin Pharmacol 2014; 6:387-401. [DOI: 10.1586/17512433.2013.811814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Liu R, Wang X, Aihara K, Chen L. Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers. Med Res Rev 2013; 34:455-78. [PMID: 23775602 DOI: 10.1002/med.21293] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Many studies have been carried out for early diagnosis of complex diseases by finding accurate and robust biomarkers specific to respective diseases. In particular, recent rapid advance of high-throughput technologies provides unprecedented rich information to characterize various disease genotypes and phenotypes in a global and also dynamical manner, which significantly accelerates the study of biomarkers from both theoretical and clinical perspectives. Traditionally, molecular biomarkers that distinguish disease samples from normal samples are widely adopted in clinical practices due to their ease of data measurement. However, many of them suffer from low coverage and high false-positive rates or high false-negative rates, which seriously limit their further clinical applications. To overcome those difficulties, network biomarkers (or module biomarkers) attract much attention and also achieve better performance because a network (or subnetwork) is considered to be a more robust form to characterize diseases than individual molecules. But, both molecular biomarkers and network biomarkers mainly distinguish disease samples from normal samples, and they generally cannot ensure to identify predisease samples due to their static nature, thereby lacking ability to early diagnosis. Based on nonlinear dynamical theory and complex network theory, a new concept of dynamical network biomarkers (DNBs, or a dynamical network of biomarkers) has been developed, which is different from traditional static approaches, and the DNB is able to distinguish a predisease state from normal and disease states by even a small number of samples, and therefore has great potential to achieve "real" early diagnosis of complex diseases. In this paper, we comprehensively review the recent advances and developments on molecular biomarkers, network biomarkers, and DNBs in particular, focusing on the biomarkers for early diagnosis of complex diseases considering a small number of samples and high-throughput data (or big data). Detailed comparisons of various types of biomarkers as well as their applications are also discussed.
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Affiliation(s)
- Rui Liu
- Department of Mathematics, South China University of Technology, Guangzhou, 510640, China
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