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Sun M, Tong Y, Yuan W, Wang Y, Pu Y, Huang W, Lv B, Xu C, Jiang W, Luo R, Fang R, Tang S, Ren L, Wang J, Feng J, Sun C, Shen K, He F, Hou Y, Ding C. Proteomic Characterization Identifies Clinically Relevant Subgroups of Gastrointestinal Stromal Tumors. Gastroenterology 2024; 166:450-465.e33. [PMID: 37995868 DOI: 10.1053/j.gastro.2023.11.284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND & AIMS Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract, and it has high metastatic and recurrence rates. We aimed to characterize the proteomic features of GIST to understand biological processes and treatment vulnerabilities. METHODS Quantitative proteomics and phosphoproteomics analyses were performed on 193 patients with GIST to reveal the biological characteristics of GIST. Data-driven hypotheses were tested by performing functional experiments using both GIST cell lines and xenograft mouse models. RESULTS Proteomic analysis revealed differences in the molecular features of GISTs from different locations or with different histological grades. MAPK7 was identified and functionally proved to be associated with tumor cell proliferation in GIST. Integrative analysis revealed that increased SQSTM1 expression inhibited the patient response to imatinib mesylate. Proteomics subtyping identified 4 clusters of tumors with different clinical and molecular attributes. Functional experiments confirmed the role of SRSF3 in promoting tumor cell proliferation and leading to poor prognosis. CONCLUSIONS Our study provides a valuable data resource and highlights potential therapeutic approaches for GIST.
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Affiliation(s)
- Mingjun Sun
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yexin Tong
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Yuan
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Pu
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen Huang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Boqiong Lv
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Chen Xu
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Jiang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Rongkui Luo
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Ren
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiachen Wang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jinwen Feng
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Kuntang Shen
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Fuchu He
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, China; Research Unit of Proteomics Driven Cancer Precision Medicine. Chinese Academy of Medical Sciences, Beijing, China.
| | - Yingyong Hou
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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Zhang S, Zheng R, Pan Y, Sun H. Potential Therapeutic Value of the STING Inhibitors. Molecules 2023; 28:3127. [PMID: 37049889 PMCID: PMC10096477 DOI: 10.3390/molecules28073127] [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: 02/17/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The stimulator of interferon genes (STING) is a critical protein in the activation of the immune system in response to DNA. It can participate the inflammatory response process by modulating the inflammation-preferred translation program through the STING-PKR-like endoplasmic reticulum kinase (PERK)-eIF2α pathway or by inducing the secretion of type I interferons (IFNs) and a variety of proinflammatory factors through the recruitment of TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) or the regulation of the nuclear factor kappa-B (NF-κB) pathway. Based on the structure, location, function, genotype, and regulatory mechanism of STING, this review summarizes the potential value of STING inhibitors in the prevention and treatment of infectious diseases, psoriasis, systemic lupus erythematosus, non-alcoholic fatty liver disease, and other inflammatory and autoimmune diseases.
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Affiliation(s)
- Shangran Zhang
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Runan Zheng
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yanhong Pan
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Department of Pharmacy, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210009, China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing 401135, China
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3
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Zhang R, Hu M, Chen HN, Wang X, Xia Z, Liu Y, Wang R, Xia X, Shu Y, Du D, Meng W, Qi S, Li Y, Xu H, Zhou ZG, Dai L. Phenotypic heterogeneity analysis of APC-mutant colon cancer by proteomics and phosphoproteomics identifies RAI14 as a key prognostic determinant in East Asians and Westerners. Mol Cell Proteomics 2023; 22:100532. [PMID: 36934880 PMCID: PMC10148045 DOI: 10.1016/j.mcpro.2023.100532] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Adenomatous polyposis coli (APC) is an important tumor suppressor and is mostly linked to the regulation of the WNT/β-catenin signaling pathway. APC mutation has been identified as an early event in more than 80% of sporadic colorectal cancers (CRCs). Moreover, prognostic differences are observed in CRC patients with APC mutations. Although previous genomics studies have investigated the roles of concomitant gene mutations in determining the phenotypic heterogeneity of APC-mutant tumors, valuable prognostic determinants for APC-mutant CRC patients are still lacking. Based on the proteome and phosphoproteome data, we classified APC-mutant colon cancer patients and revealed genomic, proteomic and phosphoproteomic heterogeneity in APC-mutant tumors. More importantly, we identified RAI14 as a key prognostic determinant for APC-mutant but not APC-wildtype colon cancer patients. The heterogeneity and the significance of prognostic biomarkers in APC-mutant tumors were further validated in the Clinical Proteomic Tumor Analysis Consortium (CPTAC) colon cancer cohort. In addition, we found that colon cancer patients with high expression of RAI14 were less responsive to chemotherapy. Knockdown of RAI14 in cell lines led to reduced cell migration and changes in epithelial-mesenchymal transition (EMT)-related markers. Mechanistically, knockdown of RAI14 remodeled the phosphoproteome associated with cell adhesion, which might affect EMT marker expression and promote F-actin degradation. Collectively, this work describes the phenotypic heterogeneity of APC-mutant tumors and identifies RAI14 as an important prognostic determinant for APC-mutant colon cancer patients. The prognostic utility of RAI14 in APC-mutant colon cancer will provide early warning and increase the chance of successful treatment.
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Affiliation(s)
- Rou Zhang
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Meng Hu
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hai-Ning Chen
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiuxuan Wang
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhili Xia
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
| | - Yu Liu
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Rui Wang
- West China-Washington Mitochondria and Metabolism Centre, Institutes for Systems Genetics; Advanced Mass Spectrometry Center, Research Core Facility, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xuyang Xia
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Shu
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dan Du
- West China-Washington Mitochondria and Metabolism Centre, Institutes for Systems Genetics; Advanced Mass Spectrometry Center, Research Core Facility, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wenbo Meng
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
| | - Shiqian Qi
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuan Li
- Institute of Digestive Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Heng Xu
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zong-Guang Zhou
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Digestive Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and General Practice Medical Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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Connolly EA, Grimison PS, Horvath LG, Robinson PJ, Reddel RR. Quantitative proteomic studies addressing unmet clinical needs in sarcoma. Front Oncol 2023; 13:1126736. [PMID: 37197427 PMCID: PMC10183589 DOI: 10.3389/fonc.2023.1126736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/31/2023] [Indexed: 05/19/2023] Open
Abstract
Sarcoma is a rare and complex disease comprising over 80 malignant subtypes that is frequently characterized by poor prognosis. Challenges in clinical management include uncertainties in diagnosis and disease classification, limited prognostic and predictive biomarkers, incompletely understood disease heterogeneity among and within subtypes, lack of effective treatment options, and limited progress in identifying new drug targets and novel therapeutics. Proteomics refers to the study of the entire complement of proteins expressed in specific cells or tissues. Advances in proteomics have included the development of quantitative mass spectrometry (MS)-based technologies which enable analysis of large numbers of proteins with relatively high throughput, enabling proteomics to be studied on a scale that has not previously been possible. Cellular function is determined by the levels of various proteins and their interactions, so proteomics offers the possibility of new insights into cancer biology. Sarcoma proteomics therefore has the potential to address some of the key current challenges described above, but it is still in its infancy. This review covers key quantitative proteomic sarcoma studies with findings that pertain to clinical utility. Proteomic methodologies that have been applied to human sarcoma research are briefly described, including recent advances in MS-based proteomic technology. We highlight studies that illustrate how proteomics may aid diagnosis and improve disease classification by distinguishing sarcoma histologies and identify distinct profiles within histological subtypes which may aid understanding of disease heterogeneity. We also review studies where proteomics has been applied to identify prognostic, predictive and therapeutic biomarkers. These studies traverse a range of histological subtypes including chordoma, Ewing sarcoma, gastrointestinal stromal tumors, leiomyosarcoma, liposarcoma, malignant peripheral nerve sheath tumors, myxofibrosarcoma, rhabdomyosarcoma, synovial sarcoma, osteosarcoma, and undifferentiated pleomorphic sarcoma. Critical questions and unmet needs in sarcoma which can potentially be addressed with proteomics are outlined.
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Affiliation(s)
- Elizabeth A. Connolly
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- *Correspondence: Elizabeth A. Connolly,
| | - Peter S. Grimison
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Lisa G. Horvath
- Department of Medical Oncology, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Phillip J. Robinson
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R. Reddel
- ProCan, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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5
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Sun J, Zhang Q, Sun X, Xue A, Gao X, Shen K. THZ1 targeting CDK7 suppresses c-KIT transcriptional activity in gastrointestinal stromal tumours. Cell Commun Signal 2022; 20:138. [PMID: 36076237 PMCID: PMC9454178 DOI: 10.1186/s12964-022-00928-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Background Gastrointestinal stromal tumours (GISTs) are the most common mesenchymal tumours of the gastrointestinal tract and are characterized by activating mutations of c-KIT or PDGFRa receptor tyrosine kinases (RTKs). Despite the clinical success of tyrosine kinase inhibitors (TKIs), more than half of GIST patients develop resistance due to a second mutation. Cyclin-dependent kinase 7 (CDK7) is the catalytic subunit of CDK-activating kinase (CAK), and it plays an important role in the regulation of cell cycle transitions and gene transcription. THZ1, a CDK7 inhibitor, exhibits a dose-dependent inhibitory effect in various cancers. Methods Data from the public GEO database and tissue microarray were used to analyse the gene expression levels of CDKs in GISTs. The impact of CDK7 knockdown and the CDK7 inhibitor THZ1 on GIST progression was investigated in vitro using CCK-8, colony formation, and flow cytometry assays and in vivo using a xenograft mouse model. RNA sequencing was performed to investigate the mechanism of GIST cell viability impairment mediated by THZ1 treatment. Results Our study demonstrated that CDK7 is relatively overexpressed in high-risk GISTs and predicts a poor outcome. A low concentration of THZ1 exhibited a pronounced antineoplastic effect in GIST cells in vivo and in vitro. Moreover, THZ1 exerted synergistic anticancer effects with imatinib. THZ1 treatment resulted in transcriptional modulation by inhibiting the phosphorylation of Ser2, Ser5, and Ser7 within RNA polymerase II (RNAPII). c-KIT, an oncogene driver of GIST, was transcriptionally repressed by THZ1 treatment or CDK7 knockdown. Transcriptome sequencing analysis showed that OSR1 acts as a downstream target of CDK7 and regulates c-KIT expression. Taken together, our results highlight elevated CDK7 expression as a predictor of poor outcome in GIST and present the combination of CDK7 and RTK inhibitors as a potent therapeutic strategy to improve the efficacy of GIST treatment. Video abstract
Supplementary Information The online version contains supplementary material available at 10.1186/s12964-022-00928-x.
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Affiliation(s)
- Jianyi Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Qiang Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Xiangfei Sun
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Anwei Xue
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China
| | - Xiaodong Gao
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China.
| | - Kuntang Shen
- Department of General Surgery, Zhongshan Hospital, Fudan University School of Medicine, #180 Fenglin Road, Shanghai, 200032, China.
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Wang B, Zhao L, Gao Z, Luo J, Zhang H, Gan L, Jiang K, Wang S, Ye Y, Shen Z. Quantitative proteomic analysis of aberrant expressed lysine acetylation in gastrointestinal stromal tumors. Clin Proteomics 2021; 18:16. [PMID: 34022816 PMCID: PMC8141230 DOI: 10.1186/s12014-021-09322-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Gastrointestinal stromal tumor (GIST) is a common digestive tract tumor with high rate of metastasis and recurrence. Currently, we understand the genome, transcriptome and proteome in GIST. However, posttranscriptional modification features in GIST remain unclear. In the present study, we aimed to construct a complete profile of acetylome in GIST. METHODS Five common protein modifications, including acetylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, and malonylation were tested among GIST subgroups and significantly differentially- expressed lysine acetylation was found. The acetylated peptides labeled with Tandem Mass Tag (TMT)under high sensitive mass spectrometry, and some proteins with acetylation sites were identified. Subsequently, these proteins and peptides were classified into high/moderate (H/M) risk and low (L) risk groups according to the modified NIH classification standard. Furthermore, cell components, molecular function, biological processes, KEGG pathways and protein interaction networks were analyzed. RESULTS A total of 2904 acetylation sites from 1319 proteins were identified, of which quantitative information of 2548 sites from 1169 proteins was obtained. Finally, the differentially-expressed lysine acetylation sites were assessed and we found that 42 acetylated sites of 38 proteins were upregulated in the H/M risk group compared with the L risk group, while 48 acetylated sites of 44 proteins were downregulated, of which Ki67 K1063Ac and FCHSD2 K24Ac were the two acetylated proteins that were most changed. CONCLUSIONS Our novel findings provide further understanding of acetylome in GIST and might demonstrate the possibility in the acetylation targeted diagnosis and therapy of GIST.
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Affiliation(s)
- Bo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China.,Laboratory of Surgical Oncology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China.,Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, People's Republic of China
| | - Zhidong Gao
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China
| | - Jianyuan Luo
- Department of Medical Genetics, Peking University Health Science Center, Beijing, People's Republic of China
| | - Haoran Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China
| | - Lin Gan
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China
| | - Kewei Jiang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China
| | - Shan Wang
- Laboratory of Surgical Oncology, Peking University People's Hospital, Beijing, People's Republic of China.,Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, People's Republic of China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, People's Republic of China
| | - Zhanlong Shen
- Laboratory of Surgical Oncology, Peking University People's Hospital, Beijing, People's Republic of China. .,Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Beijing, People's Republic of China.
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7
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Milighetti M, Krasny L, Lee ATJ, Morani G, Szecsei C, Chen Y, Guljar N, McCarthy F, Wilding CP, Arthur A, Fisher C, Judson I, Thway K, Cheang MCU, Jones RL, Huang PH. Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry. J Proteomics 2021; 241:104236. [PMID: 33895336 PMCID: PMC8135130 DOI: 10.1016/j.jprot.2021.104236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 04/02/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic and epigenomic profiling of STS have been undertaken, proteomic analysis has thus far been limited. Here we utilise sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for proteomic profiling of formalin fixed paraffin embedded (FFPE) specimens from a cohort of STS patients (n = 36) across four histological subtypes (leiomyosarcoma, synovial sarcoma, undifferentiated pleomorphic sarcoma and dedifferentiated liposarcoma). We quantified 2951 proteins across all cases and show that there is a significant enrichment of gene sets associated with smooth muscle contraction in leiomyosarcoma, RNA splicing regulation in synovial sarcoma and leukocyte activation in undifferentiated pleomorphic sarcoma. We further identified a subgroup of STS cases that have a distinct expression profile in a panel of proteins, with worse survival outcomes when compared to the rest of the cohort. Our study highlights the value of comprehensive proteomic characterisation as a means to identify histotype-specific STS profiles that describe key biological pathways of clinical and therapeutic relevance; as well as for discovering new prognostic biomarkers in this group of rare and difficult-to-treat diseases. Proteomic analysis of FFPE specimens from four soft tissue sarcoma histological subtypes was performed by SWATH MS. Subtype-specific biological pathways and protein-protein interaction networks were identified. A panel of proteins associated with sarcoma patient survival outcome was defined. A subset of proteins identified by SWATH MS was validated by orthogonal immunohistochemical analysis.
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Affiliation(s)
- Martina Milighetti
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Lukas Krasny
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Alex T J Lee
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK; Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Gabriele Morani
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK; Clinical Trials and Statistics Unit, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Cornelia Szecsei
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Yingtong Chen
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK; Clinical Trials and Statistics Unit, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Nafia Guljar
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Frank McCarthy
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK
| | - Cyril Fisher
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK
| | - Ian Judson
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK
| | - Maggie C U Cheang
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK; Clinical Trials and Statistics Unit, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Robin L Jones
- Sarcoma Unit, The Royal Marsden NHS Foundation Trust, 203 Fulham Road, SW3 6JJ London, UK; Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, SM2 5NG Sutton, London, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, 237 Fulham Road, SW3 6JB London, UK.
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Liu J, Ma T, Gao M, Liu Y, Liu J, Wang S, Xie Y, Wang L, Cheng J, Liu S, Zou J, Wu J, Li W, Xie H. Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment. Sci Rep 2020; 10:14921. [PMID: 32913333 PMCID: PMC7483447 DOI: 10.1038/s41598-020-71154-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/07/2020] [Indexed: 02/05/2023] Open
Abstract
As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment affecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the effect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and differentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable difference between the two laboratories, whereby γ ray dose rate was significantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g. ribosome, RNA transport and oxidative phosphorylation) were significantly enriched. These data suggest that proliferation of V79 cells was inhibited in the DUGL, likely because cells were exposed to reduced background radiation. The apparent changes in the proteome profile may have induced cellular changes that delayed proliferation but enhanced survival, rendering V79 cells adaptable to the changing environment.
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Affiliation(s)
- Jifeng Liu
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu, China
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Tengfei Ma
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu, China
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mingzhong Gao
- College of Water Resources & Hydropower, Sichuan University, Chengdu, China
| | - Yilin Liu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Liu
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu, China
| | - Shichao Wang
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yike Xie
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Wang
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Juan Cheng
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shixi Liu
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu, China.
| | - Jian Zou
- Department of Otolaryngology Head and Neck Surgery, West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu, China.
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Jiang Wu
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
| | - Heping Xie
- Deep Underground Space Medical Center, West China Hospital, Sichuan University, Chengdu, China
- College of Water Resources & Hydropower, Sichuan University, Chengdu, China
- Institute of Deep Earth Science and Green Energy, Shenzhen University, Shenzhen, China
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Burns J, Wilding CP, L Jones R, H Huang P. Proteomic research in sarcomas - current status and future opportunities. Semin Cancer Biol 2019; 61:56-70. [PMID: 31722230 PMCID: PMC7083238 DOI: 10.1016/j.semcancer.2019.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023]
Abstract
Sarcomas are a rare group of mesenchymal cancers comprising over 70 different histological subtypes. For the majority of these diseases, the molecular understanding of the basis of their initiation and progression remains unclear. As such, limited clinical progress in prognosis or therapeutic regimens have been made over the past few decades. Proteomics techniques are being increasingly utilised in the field of sarcoma research. Proteomic research efforts have thus far focused on histological subtype characterisation for the improvement of biological understanding, as well as for the identification of candidate diagnostic, predictive, and prognostic biomarkers for use in clinic. However, the field itself is in its infancy, and none of these proteomic research findings have been translated into the clinic. In this review, we provide a brief overview of the proteomic strategies that have been employed in sarcoma research. We evaluate key proteomic studies concerning several rare and ultra-rare sarcoma subtypes including, gastrointestinal stromal tumours, osteosarcoma, liposarcoma, leiomyosarcoma, malignant rhabdoid tumours, Ewing sarcoma, myxofibrosarcoma, and alveolar soft part sarcoma. Consequently, we illustrate how routine implementation of proteomics within sarcoma research, integration of proteomics with other molecular profiling data, and incorporation of proteomics into clinical trial studies has the potential to propel the biological and clinical understanding of this group of complex rare cancers moving forward.
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Affiliation(s)
- Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Robin L Jones
- Division of Clinical Studies, The Institute of Cancer Research, London SW3 6JB, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK.
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