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Zhang Z, Chen X, Zhang W, Liu J, Xie Y, Zhang S, Stromberg AJ, Watt DS, Liu X, Wang C, Liu C. Genomic screening methodology not requiring barcoding: Single nucleotide polymorphism-based, mixed-cell screening (SMICS). Genomics 2023; 115:110666. [PMID: 37315874 PMCID: PMC10551848 DOI: 10.1016/j.ygeno.2023.110666] [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: 02/21/2023] [Revised: 05/31/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Although high-throughput, cancer cell-line screening is a time-honored, important tool for anti-cancer drug development, this process involves the testing of each, individual drug in each, individual cell-line. Despite the availability of robotic liquid handling systems, this process remains a time-consuming and costly investment. The Broad Institute developed a new method called Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) to screen a mixture of barcoded, tumor cell-lines. Although this methodology significantly improved the efficiency of screening large numbers of cell-lines, the barcoding process itself was tedious that requires gene transfection and subsequent selection of stable cell-lines. In this study, we developed a new, genomic approach for screening multiple cancer cell-lines using endogenous "tags" that did not require prior barcoding: single nucleotide polymorphism-based, mixed-cell screening (SMICS). The code for SMICS is available at https://github.com/MarkeyBBSRF/SMICS.
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Affiliation(s)
- Zhuwei Zhang
- Department of Statistics, College of Arts and Sciences, University of Kentucky, Lexington, KY 40506, United States of America
| | - Xi Chen
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Center for Drug Innovation and Discovery, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Wen Zhang
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Jinpeng Liu
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America
| | - Yanqi Xie
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Shulin Zhang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Arnold J Stromberg
- Department of Statistics, College of Arts and Sciences, University of Kentucky, Lexington, KY 40506, United States of America
| | - David S Watt
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Xifu Liu
- Center for Drug Innovation and Discovery, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China.
| | - Chi Wang
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY 40506, United States of America.
| | - Chunming Liu
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America.
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Yang PW, Jiao JY, Chen Z, Zhu XY, Cheng CS. Keep a watchful eye on methionine adenosyltransferases, novel therapeutic opportunities for hepatobiliary and pancreatic tumours. Biochim Biophys Acta Rev Cancer 2022; 1877:188793. [PMID: 36089205 DOI: 10.1016/j.bbcan.2022.188793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/31/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022]
Abstract
Methionine adenosyltransferases (MATs) synthesize S-adenosylmethionine (SAM) from methionine, which provides methyl groups for DNA, RNA, protein, and lipid methylation. MATs play a critical role in cellular processes, including growth, proliferation, and differentiation, and have been implicated in tumour development and progression. The expression of MATs is altered in hepatobiliary and pancreatic (HBP) cancers, which serves as a rare biomarker for early diagnosis and prognosis prediction of HBP cancers. Independent of SAM depletion in cells, MATs are often dysregulated at the transcriptional, post-transcriptional, and post-translational levels. Dysregulation of MATs is involved in carcinogenesis, chemotherapy resistance, T cell exhaustion, activation of tumour-associated macrophages, cancer stemness, and activation of tumourigenic pathways. Targeting MATs both directly and indirectly is a potential therapeutic strategy. This review summarizes the dysregulations of MATs, their proposed mechanism, diagnostic and prognostic roles, and potential therapeutic effects in context of HBP cancers.
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Affiliation(s)
- Pei-Wen Yang
- Department of Integrative Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ju-Ying Jiao
- Department of Integrative Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhen Chen
- Department of Integrative Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xiao-Yan Zhu
- Department of Integrative Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Chien-Shan Cheng
- Department of Integrative Oncology, Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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