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Yin H, Zhang M, Gu C, Li Z, Hao C, Wang J, Tian L, Xu K, Hu X, Ming L, Zhang M, Wang Z, Yang Y, Zhang D, Dai B. Discovery of Novel 2-Oxoacetamide Derivatives as B3GAT3 Inhibitors for the Treatment of Hepatocellular Carcinoma. J Med Chem 2024; 67:10743-10773. [PMID: 38919032 DOI: 10.1021/acs.jmedchem.4c00242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Beta-1,3-glucuronosyltransferase (B3GAT3), overexpressed in hepatocellular carcinoma (HCC) and negatively correlated to prognosis, is a promising target for cancer therapy. Currently, no studies have reported small molecule inhibitors of B3GAT3. In this study, we designed and synthesized a series of small-molecule inhibitors of B3GAT3 through virtual screening and structure optimization. The lead compound TMLB-C16 exhibited potent B3GAT3 inhibitory activity (KD = 3.962 μM) by effectively suppressing proliferation and migration, and inducing cell cycle arrest and apoptosis in MHCC-97H (IC50= 6.53 ± 0.18 μM) and HCCLM3 (IC50= 6.22 ± 0.23 μM) cells. Furthermore, compound TMLB-C16 demonstrated favorable pharmacokinetic properties with a relatively high bioavailability of 68.37%. It significantly inhibited tumor growth in both MHCC-97H and HCCLM3 xenograft tumor models without causing obvious toxicity. These results indicate that compound TMLB-C16 is an effective small molecule inhibitor of B3GAT3, providing a basis for the future development of B3GAT3-targeted drugs.
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Affiliation(s)
- Hao Yin
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Menghan Zhang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Congying Gu
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Zhenyu Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Chenyan Hao
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Junhui Wang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Lulu Tian
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Kang Xu
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Xiangyu Hu
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Liqin Ming
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Min Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Zhanbo Wang
- Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Yong Yang
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Dayong Zhang
- School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Beiying Dai
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
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Ma M, Wang C, Wu M, Gu S, Yang J, Zhang Y, Cheng S, Xu S, Zhang M, Wu Y, Zhao Y, Tian X, Voon DCC, Takahashi C, Sheng J, Wang Y. CSGALNACT2 restricts ovarian cancer migration and invasion by modulating MAPK/ERK pathway through DUSP1. Cell Oncol (Dordr) 2024; 47:897-915. [PMID: 38082211 PMCID: PMC11219422 DOI: 10.1007/s13402-023-00903-9] [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] [Accepted: 11/23/2023] [Indexed: 07/04/2024] Open
Abstract
PURPOSE Ovarian cancer is one of the leading causes of cancer-related death among women. CSGALNACT2 is a vital Golgi transferase and is related to a variety of human diseases. However, its expression pattern and function in ovarian cancer remain uncertain. METHODS The Cancer Genome Atlas and GEPIA databases were used to assess the expression of CSGALNACT2 in ovarian cancer patients. RNA-seq, qRT-PCR, and IHC were used to verify the expression of CSGALNACT2 in ovarian cancer tissues. Then, in vivo and in vitro experiments were conducted to evaluate the role of CSGALNACT2 in the progression of ovarian cancer. RNA-seq and GSEA were used to reveal the potential biological function and oncogenic pathways of CSGALNACT2. RESULTS We demonstrated that the mRNA expression and protein level of CSGALNACT2 were significantly downregulated in ovarian cancer and ovarian cancer metastatic tissues. CSGALNACT2 can significantly inhibit the migration, invasion, and clonogenic growth of ovarian cancer in vitro and is progressively lost during ovarian cancer progression in vivo. CSGALNACT2 suppresses ovarian cancer migration and invasion via DUSP1 modulation of the MAPK/ERK pathway through RNA-seq, KEGG analysis, and Western blotting. Moreover, CSGALNACT2 expression was correlated with immune cell infiltration and had prognostic value in different immune cell-enriched or decreased ovarian cancer. In addition, patients with CSGALNACT2 downregulation are less likely to benefit from immunotherapy. CONCLUSION As an ovarian cancer suppressor gene, CSGALNACT2 inhibits the development of ovarian cancer, and it might be used as a prognostic biomarker in patients with ovarian cancer.
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Affiliation(s)
- Mingjun Ma
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Chao Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Meixuan Wu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Sijia Gu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Jiani Yang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yue Zhang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Shanshan Cheng
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Shilin Xu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Minghai Zhang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yongsong Wu
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yaqian Zhao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xiu Tian
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | | | - Chiaki Takahashi
- Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - Jindan Sheng
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Yu Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, No.2699, Gaoke West Rd, Shanghai, 200092, China.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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Sun Z, Wang H, Xu Y, Liu Y, Wang L, Zhou R, Zhou R, Ma W, Zhang T. High expression of NXPH4 correlates with poor prognosis, metabolic reprogramming, and immune infiltration in colon adenocarcinoma. J Gastrointest Oncol 2024; 15:641-667. [PMID: 38756632 PMCID: PMC11094489 DOI: 10.21037/jgo-23-956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
Background Colon adenocarcinoma (COAD) is a prevalent gastrointestinal malignant disease with high mortality rate, and identification of novel prognostic biomarkers and therapeutic targets is urgently needed. Although neurexophilin 4 (NXPH4) has been investigated in several tumors, its role in COAD remains unclear. The aim of this study was to explore the prognostic value and potential functions of NXPH4 in COAD. Methods The expression of NXPH4 in COAD were analyzed using The Cancer Genome Atlas (TCGA) and datasets from the Gene Expression Omnibus (GEO) database. The prognostic value of NXPH4 was determined using Kaplan-Meier analysis and Cox regression analysis. To investigate the possible mechanism underlying the role of NXPH4 in COAD, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were employed. The correlation between NXPH4 expression and immune cell infiltration levels was examined thorough single-sample gene set enrichment analysis (ssGSEA). Furthermore, the competing endogenous RNA (ceRNA) regulatory network that may be involved in NXPH4 in COAD was predicted and constructed through a variety of databases. Results NXPH4 expression was significantly higher in COAD tissue compared with normal colon tissues. Meanwhile, high expression of NXPH4 was associated with poor prognosis in COAD patients. GO-KEGG and GSEA analyses indicated that NXPH4 was associated with glycolysis and hypoxia pathway, and may promote COAD progression and metastasis by modulating metabolic reprogramming. ssGSEA analysis demonstrated that NXPH4 expression also associated with immune infiltration. Furthermore, we identified various microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) as upstream regulators of NXPH4 in COAD. Conclusions The present study revealed that high expression of NXPH4 is associated with tumor progression, metabolic reprogramming, and immune infiltration. These findings suggest that NXPH4 could serve as a reliable prognostic biomarker and a promising therapeutic target in COAD.
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Affiliation(s)
- Zhe Sun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Haodi Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yao Xu
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yichi Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ruijie Zhou
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Runlong Zhou
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Wenjian Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Qilu Institute of Technology, Jinan, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
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Yun ZY, Wu D, Wang X, Huang P, Li N. MiR-214-3p overexpression-triggered chondroitin polymerizing factor (CHPF) inhibition modulates the ferroptosis and metabolism in colon cancer. Kaohsiung J Med Sci 2024; 40:244-254. [PMID: 38190270 DOI: 10.1002/kjm2.12802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/25/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Colon cancer is a common cancer with high mortality globally. The role of chondroitin polymerizing factor (CHPF) has been elucidated in various cancers. However, its role and mechanism remain unknown in colon cancer. CHPF expression was examined by GEPIA database, reverse transcription-quantitative polymerase chain reaction and western blot. The relationship between CHPF expression and the clinicopathologic characteristics as well as miR-214-3p level was determined in colon cancer patients. The role and mechanism of CHPF in the growth, ferroptosis, and glycolysis of colon cancer cells were evaluated by cell counting kit-8, biochemical detections, luciferase, and western blot experiments. Additionally, the role of CHPF was explored in xenografted mice. CHPF expression was increased and was related to advanced TNM stage, poor differentiation and shorter overall survival in patients with colon cancer. Knockdown of CHPF inhibited colon cancer cell growth, and downregulated the expression of proteins involving in ferroptosis and glycolysis both in vitro and in vivo. Besides, CHPF silencing increased the levels of ferrous iron and ROS, but decreased glucose uptake, lactate product, and ATP level in vitro. Mechanically, miR-214-3p directly targeted CHPF and negatively regulated its expression. Upregulation of miR-214-3p reduced cell viability, glucose uptake, lactate product, and ATP level, but increased the levels of ferrous iron and ROS, which were reversed by the overexpression of CHPF. Upregulation of CHPF predicted poor prognosis, and miR-214-3p/CHPF axis inhibited growth, downregulated the levels of glycolysis-related indexes, and promoted ferroptosis in colon cancer cells.
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Affiliation(s)
- Zhi-Yuan Yun
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Di Wu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xin Wang
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Peng Huang
- Department of Gastrointestinal Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
| | - Na Li
- Department of Internal Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, Heilongjiang, China
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Zhan J, Zhou L, Zhang H, Zhou J, He Y, Hu T, Le Y, Lin Y, Wang J, Yu H, Liu Y, Xiang X. A comprehensive analysis of the expression, immune infiltration, prognosis and partial experimental validation of CHST family genes in gastric cancer. Transl Oncol 2024; 40:101843. [PMID: 38101175 PMCID: PMC10727950 DOI: 10.1016/j.tranon.2023.101843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/14/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Previous studies have demonstrated that carbohydrate sulfotransferase family proteins (CHSTs) play a crucial role in the extracellular matrix structural constituent and cancer progression, however, the effect of CHSTs on gastric cancer is still superficial. To investigate these, our study seeks to provide a comprehensive understanding of CHSTs' expression, immune infiltration, and prognostic implications in gastric cancer, utilizing data from the TCGA, GEO and GTEx databases. Furthermore, we conducted experimental validation to elucidate the role of CHST14 specifically in gastric cancer. Our findings suggest that most CHSTs were highly expressed in gastric cancer. Gene copy number variations further indicated prevalent CHSTs amplification in gastric cancer, pointing to its potential relevance in disease progression. Intriguingly, we noted strong positive correlations between most CHSTs and immune cell infiltration. Importantly, most members of CHSTs were related to OS and PFI with gastric cancer, with particular emphasis on CHST14 and CHST9. Multifactorial regression analysis indicates that CHST14 is an independent prognostic factor influencing the overall survival of gastric cancer patients. In further experimental validation, our results demonstrate elevated expression of CHST14 in gastric cancer, and knocking down CHST14 inhibits gastric cancer cell proliferation, invasion, migration and EMT. Additionally, CHST14 may exert its function through the regulation of the Wnt pathway. In summary, our study comprehensively analyzes the hitherto undescribed role of CHSTs in gastric cancer through the analysis of multi-omics data. Importantly, we identify CHST14 as a pivotal promoter in the malignant progression of gastric cancer, offering potential targets for gastric cancer therapy.
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Affiliation(s)
- Jinbo Zhan
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Ling Zhou
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Hongjiao Zhang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Juanjuan Zhou
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Yan He
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Tingting Hu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Yi Le
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Yun Lin
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Jingru Wang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Haiming Yu
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China
| | - Yawen Liu
- Department of Oncology, Jiangxi Maternal and Child Health Hospital, 318 Bayi Road, Nanchang 330006, PR China.
| | - Xiaojun Xiang
- Department of Oncology, The First Affiliated Hospital of Nanchang University, 1519 Dongyue Avenue, Nanchang, Jiangxi, PR China; Department of Jiangxi Key Laboratory for Individualized Cancer Therapy, 17 Yongwai Street, Nanchang, Jiangxi 330006, PR China.
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Wu J, Wang M, Zhang Y, Liu G, Xing Y. Activation of CHPF by transcription factor NFIC promotes NLRP3 activation during the progression of colorectal cancer. Funct Integr Genomics 2024; 24:20. [PMID: 38267731 DOI: 10.1007/s10142-024-01299-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Given the role of chondroitin polymerizing factor (CHPF) in several cancers, we investigated its role in the progression of colorectal cancer (CRC) and its association with NLRP3 inflammasome activation. High expression of CHPF in CRC predicted poor patient prognosis. Using colony formation, EdU staining, wound healing, Transwell invasion, and flow cytometry assays, we revealed that the downregulation of CHPF inhibited the malignant behavior of CRC cells. CHPF promoted NLRP3 inflammasome activation by inducing the MAPK signaling pathway, as evidenced by enhanced expression of Phos-ERK1/2, Phos-MEK1, Phos-MEK2, and NLRP3. Additionally, nuclear factor 1 C-type (NFIC) was revealed as a potential upstream transcription factor of CHPF in the modulation of CRC, and the anti-tumor effects elicited through its knockdown were compromised by CHPF in vitro and in vivo. In summary, we demonstrated that NFIC promoted NLRP3 activation to support CRC development via the CHPF-mediated MAPK signaling.
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Affiliation(s)
- Jiamei Wu
- Department of Basic Medical Science, Baicheng Medical College, Taobei District, No. 27, Mianfang Road, Jilin, 137000, Baicheng, People's Republic of China
| | - Miao Wang
- Department of Clinical Laboratory, Baicheng City Hospital, Jilin, 137000, Baicheng, People's Republic of China
| | - Yuechuan Zhang
- Basic Medical College, Jiamusi University, Heilongjiang, 154007, Jiamusi, People's Republic of China
| | - Guohong Liu
- Department of Basic Medical Science, Baicheng Medical College, Taobei District, No. 27, Mianfang Road, Jilin, 137000, Baicheng, People's Republic of China.
| | - Yutong Xing
- Department of Surgery, Xiamen Fifth Hospital, Xiangan District, No. 101, Minan Road, Fujian, 361100, Xiamen, People's Republic of China.
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Aiba T, Hijiya N, Akagi T, Tsukamoto Y, Hirashita Y, Kinoshita K, Uchida T, Nakada C, Kurogi S, Ueda Y, Shiroshita H, Shiraishi N, Murakami K, Inomata M, Moriyama M. Overexpression of VSNL1 Enhances Cell Proliferation in Colorectal Carcinogenesis. Pathobiology 2023; 91:121-131. [PMID: 37797604 DOI: 10.1159/000533877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
INTRODUCTION We have previously reported that overexpression of visinin-like protein 1 (VSNL1) is frequently observed in advanced colorectal adenocarcinomas and correlates with poorer prognosis. In this study, we determined the levels of VSNL1 expression in the earlier stages of colorectal tumors including adenomas and adenocarcinomas, and attempted to clarify the functional significance of VSNL1 overexpression in colorectal carcinogenesis. METHODS Levels of VSNL expression in colorectal tumor tissues were analyzed using immunohistochemistry. The effects of VSNL1 downregulation and overexpression on cell proliferation, resistance to apoptosis, and invasiveness were determined using two VSNL1-overexpressing colorectal cancer cell lines, CW-2 and HCT-116 and VSNL1 inducibly expressing SNU-C5, respectively. Gene expression signatures in VSNL1-downregulated CW-2 and HCT-116 were identified using transcriptome and gene set enrichment analyses. RESULTS VSNL1 expression was restricted to only a few crypt cells in the non-tumorous epithelium, whereas it became enhanced in adenomas and adenocarcinomas with the progression of tumorigenesis. Downregulation of VSNL1 in CW-2 and HCT-116 cells suppressed their proliferation through induction of apoptosis. Conversely, overexpression of VSNL1 in SNU-C5 cells enhanced resistance to anoikis. Transcriptome and gene set enrichment analyses revealed that downregulation of VSNL1 altered the expression level of the apoptosis-related gene set in CW-2 and HCT-116 cells. CONCLUSION VSNL1 plays a role in both the development and progression of colorectal tumors by enhancing cell viability.
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Affiliation(s)
- Takayuki Aiba
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Naoki Hijiya
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Tomonori Akagi
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Yoshiyuki Tsukamoto
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yuka Hirashita
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Keisuke Kinoshita
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Advanced Medical Sciences, Faculty of Medicine, Oita University, Oita, Japan
| | - Chisato Nakada
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
- Department of Urology, Faculty of Medicine, Oita University, Oita, Japan
| | - Shusaku Kurogi
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
| | - Yoshitake Ueda
- Department of Comprehensive Surgery for Community Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Hidefumi Shiroshita
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Norio Shiraishi
- Department of Comprehensive Surgery for Community Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Faculty of Medicine, Oita University, Oita, Japan
| | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Faculty of Medicine, Oita University, Oita, Japan
| | - Masatsugu Moriyama
- Department of Molecular Pathology, Faculty of Medicine, Oita University, Oita, Japan
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Sun G, Zhao S, Fan Z, Wang Y, Liu H, Cao H, Sun G, Huang T, Cai H, Pan H, Rong D, Gao Y, Tang W. CHSY1 promotes CD8 + T cell exhaustion through activation of succinate metabolism pathway leading to colorectal cancer liver metastasis based on CRISPR/Cas9 screening. J Exp Clin Cancer Res 2023; 42:248. [PMID: 37749638 PMCID: PMC10519095 DOI: 10.1186/s13046-023-02803-0] [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: 01/07/2023] [Accepted: 08/19/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND The most common site of metastasis in colorectal cancer (CRC) is the liver and liver metastases occur in more than 50% of patients during diagnosis or treatment. The occurrence of metastasis depends on a series of events known as the invasive-metastasis cascade. Currently, the underlying genes and pathways regulating metastasis initiation in the liver microenvironment are unknown. METHODS We performed systematic CRISPR/Cas9 screening using an in vivo mouse model of CRC liver metastasis to identify key regulators of CRC metastasis. We present the full results of this screen,which included a list of genes that promote or repress CRC liver colonization. By silencing these genes individually, we found that chondroitin sulfate synthase 1 (CHSY1) may be involved in CRC metastasis. We verified the function of CHSY1 and its involvement in liver metastasis of CRC through in vivo and in vitro experiments. RESULT The results of TCGA and CRISPR/Cas9 showed that CHSY1 was overexpressed in CRC primary and liver metastasis tissues and indicated a worse clinical prognosis. In vitro and in vivo experiments confirmed that CHSY1 facilitated the liver metastasis of CRC and CHSY1 induced CD8+ T cell exhaustion and upregulated PD-L1 expression. The metabolomic analysis indicated that CHSY1 promoted CD8+ T cell exhaustion by activating the succinate metabolism pathway leading to liver metastasis of CRC. Artemisinin as a CHSY1 inhibitor reduced liver metastasis and enhanced the effect of anti-PD1 in CRC. PLGA-loaded Artemisinin and ICG probe reduced liver metastasis and increased the efficiency of anti-PD1 treatment in CRC. CONCLUSION CHSY1 could promote CD8+ T cell exhaustion through activation of the succinate metabolic and PI3K/AKT/HIF1A pathway, leading to CRC liver metastasis. The combination of CHSY1 knockdown and anti-PD1 contributes to synergistic resistance to CRC liver metastasis. Artemisinin significantly inhibits CHSY1 activity and in combination with anti-PD1 could synergistically treat CRC liver metastases. This study provides new targets and specific strategies for the treatment of CRC liver metastases, bringing new hope and benefits to patients.
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Affiliation(s)
- Guangshun Sun
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
- Department of Breast Surgery, the First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Siqi Zhao
- Department of Surgery, the Second Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Zhongguo Fan
- Department of Cardiology Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Yuliang Wang
- School of Basic Medicine, Nanjing Medical University, Nanjing, China
| | - Hanyuan Liu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hengsong Cao
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Guoqiang Sun
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Tian Huang
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China
| | - Hongzhou Cai
- Department of Urology, Jiangsu Cancer Hospital &The Affiliated Cancer Hospital of Nanjing Medical University& Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Hong Pan
- Department of Breast Surgery, the First Affiliated Hospital With Nanjing Medical University, Nanjing, China.
| | - Dawei Rong
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Yun Gao
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, the First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, China.
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Huang X, Liu Y, Qian C, Shen Q, Wu M, Zhu B, Feng Y. CHSY3 promotes proliferation and migration in gastric cancer and is associated with immune infiltration. J Transl Med 2023; 21:474. [PMID: 37461041 PMCID: PMC10351153 DOI: 10.1186/s12967-023-04333-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/09/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND The glycosyltransferase CHSY3 is a CHSY family member, yet its importance in the context of gastric cancer development remains incompletely understood. The present study was thus developed to explore the mechanistic importance of CHSY3 as a regulator of gastric cancer. METHODS Expression of CHSY3 was verified by TCGA, GEO and HPA databases. Kaplan-Meier curve, ROC, univariate cox, multivariate cox, and nomogram models were used to verify the prognostic impact and predictive value of CHSY3. KEGG and GO methods were used to identify signaling pathways associated with CHSY3. TIDE and IPS scores were used to assess the immunotherapeutic value of CHSY3. WGCNA, Cytoscape constructs PPI networks and random forest models to identify key Hub genes. Finally, qRT-PCR and immunohistochemical staining were performed to verify CHSY3 expression in clinical specimens. The ability of CHSY3 to regulate tumor was further assessed by CCK-8 assay and cloning assay, EDU assay, migration assay, invasion assay, and xenograft tumor model analysis. RESULTS The expression of CHSY3 was discovered to be abnormally upregulated in GC tissues through TCGA, GEO, and HPA databases, and the expression of CHSY3 was associated with poor prognosis in GC patients. Correlation analysis and Cox regression analysis revealed higher CHSY3 expression in higher T staging, an independent prognostic factor for GC. Moreover, elevated expression of CHSY3 was found to reduce the benefit of immunotherapy as assessed by the TIDE score and IPS score. Then, utilizing WGCNA, the PPI network constructed by Cytoscape, and random forest model, the Hub genes of COL5A2, POSTN, COL1A1, and FN1 associated with immunity were screened. Finally, the expression of CHSY3 in GC tissues was verified by qRT-PCR and immunohistochemical staining. Moreover, the expression of CHSY3 was further demonstrated by in vivo and in vitro experiments to promote the proliferation, migration, and invasive ability of GC. CONCLUSIONS The results of this study suggest that CHSY3 is an important regulator of gastric cancer progression, highlighting its promise as a therapeutic target for gastric cancer.
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Affiliation(s)
- Xinkun Huang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Graduate School, Dalian Medical University, Dalian, 116000, Liaoning, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong, 226001, Jiangsu, China
| | - Yonghui Liu
- Department of Laboratory Medicine, Nanjing Zhongda Hospital, School of Medicine, Southeast University, Nanjing, 210009, People's Republic of China
| | - Chenyu Qian
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Medical school, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong, 226001, Jiangsu, China
| | - Qicheng Shen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Medical school, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong, 226001, Jiangsu, China
| | - Menglong Wu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China
- Graduate School, Dalian Medical University, Dalian, 116000, Liaoning, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong, 226001, Jiangsu, China
| | - Bin Zhu
- Department of General Surgery, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, Yancheng, China.
- Department of Central Laboratory, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, Yancheng, China.
| | - Ying Feng
- Department of Gastrointestinal Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, China.
- Medical school, Nantong University, 19 Qixiu Road, Nantong, 226001, Jiangsu, China.
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 Xisi Street, Nantong, 226001, Jiangsu, China.
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Plaas AHK, Moran MM, Sandy JD, Hascall VC. Aggrecan and Hyaluronan: The Infamous Cartilage Polyelectrolytes - Then and Now. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1402:3-29. [PMID: 37052843 DOI: 10.1007/978-3-031-25588-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Cartilages are unique in the family of connective tissues in that they contain a high concentration of the glycosaminoglycans, chondroitin sulfate and keratan sulfate attached to the core protein of the proteoglycan, aggrecan. Multiple aggrecan molecules are organized in the extracellular matrix via a domain-specific molecular interaction with hyaluronan and a link protein, and these high molecular weight aggregates are immobilized within the collagen and glycoprotein network. The high negative charge density of glycosaminoglycans provides hydrophilicity, high osmotic swelling pressure and conformational flexibility, which together function to absorb fluctuations in biomechanical stresses on cartilage during movement of an articular joint. We have summarized information on the history and current knowledge obtained by biochemical and genetic approaches, on cell-mediated regulation of aggrecan metabolism and its role in skeletal development, growth as well as during the development of joint disease. In addition, we describe the pathways for hyaluronan metabolism, with particular focus on the role as a "metabolic rheostat" during chondrocyte responses in cartilage remodeling in growth and disease.Future advances in effective therapeutic targeting of cartilage loss during osteoarthritic diseases of the joint as an organ as well as in cartilage tissue engineering would benefit from 'big data' approaches and bioinformatics, to uncover novel feed-forward and feed-back mechanisms for regulating transcription and translation of genes and their integration into cell-specific pathways.
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Affiliation(s)
- Anna H K Plaas
- Department of Internal Medicine (Rheumatology), Rush University Medical Center, Chicago, IL, USA
| | - Meghan M Moran
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, USA
| | - John D Sandy
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Vincent C Hascall
- Department of Biomedical Engineering, The Cleveland Clinic Foundation, Cleveland, OH, USA
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Li CH, Chan MH, Chang YC, Hsiao M. The CHST11 gene is linked to lung cancer and pulmonary fibrosis. J Gene Med 2022; 24:e3451. [PMID: 36181245 DOI: 10.1002/jgm.3451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/18/2022] [Accepted: 09/25/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The abnormal modification of chondroitin sulfate is one of the leading causes of disease, including cancer progression. During chondroitin sulfate biosynthesis, the CHST11 enzyme plays a vital role in its modification, but its role in cancer is not fully understood. Therefore, understanding the relationship between CHST11 and pulmonary-related diseases through clinically relevant information may be useful for diagnosis or treatment. METHODS A variety of pulmonary fibrosis clinical gene expression omnibus (GEO) datasets were used to assess the association between CHST11-related manifestations and fibrosis. Multiple lung cancer-related databases, including The Cancer Genome Atlas, GEO datasets, UCSC Xena, GEPIA2, Cbioportal and ingenuity pathway analysis were used to evaluate the clinical correlation between CHST11 and lung cancer and potential molecular mechanisms. For drug repurposing prediction, the molecules that correlated with CHST11 were subjected to the LINCS L1000 algorithm. A variety of in vitro assays were performed to evaluate the in-silico models, including RNA and protein expression, proliferation, migration and invasion. RESULTS Clinical analyses indicate that the levels of CHST11 are significantly elevated in cases of pulmonary-related diseases, including fibrosis and lung cancer. According to multiple lung cancer cohorts, CHST11 is the only member of the carbohydrate sulfotransferase family associated with overall survival for lung adenocarcinomas, and it is highly related to smoking-induced lung cancer patients. Based on the results of in vitro experiments, CHST11 expression contributes to tumor malignancy and promotes multiple fibrotic activators. Correlation-based ingenuity pathway analysis indicated that CHST11-related molecules contributed to pulmonary fibrosis or lung adenocarcinomas via similar upstream stimulators. Based on known molecular regulatory relationships, CHST11 has been associated with the regulation of TGF-β and INFγ as important molecules contributing to fibrosis and cancer progression. Interestingly, WordCloud analysis revealed that CHST11-related molecules are involved in regulation primarily by integrin signaling, and these relationships were consistently reflected in the analysis of cell lines and the clinical correlation. A CHST11 signature-based drug repurposing analysis demonstrated that the CHST11/integrin axis could be targeted by AG-1478 (Tyrphostin AG 1478), brefeldin A, geldanamycin and importazole. CONCLUSIONS This study provides the first demonstration that CHST11 may be used as a biomarker for pulmonary fibrosis or lung cancer, and the levels of CHST11 were increased by TGF-β and INFγ. The molecular simulation analyses demonstrate that the CHST11/integrin axis is a potential therapeutic target for treating lung cancer.
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Affiliation(s)
- Chien-Hsiu Li
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yu-Chan Chang
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
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12
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Kazakova AN, Anufrieva KS, Ivanova OM, Shnaider PV, Malyants IK, Aleshikova OI, Slonov AV, Ashrafyan LA, Babaeva NA, Eremeev AV, Boichenko VS, Lukina MM, Lagarkova MA, Govorun VM, Shender VO, Arapidi GP. Deeper insights into transcriptional features of cancer-associated fibroblasts: An integrated meta-analysis of single-cell and bulk RNA-sequencing data. Front Cell Dev Biol 2022; 10:825014. [PMID: 36263012 PMCID: PMC9574913 DOI: 10.3389/fcell.2022.825014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) have long been known as one of the most important players in tumor initiation and progression. Even so, there is an incomplete understanding of the identification of CAFs among tumor microenvironment cells as the list of CAF marker genes varies greatly in the literature, therefore it is imperative to find a better way to identify reliable markers of CAFs. To this end, we summarized a large number of single-cell RNA-sequencing data of multiple tumor types and corresponding normal tissues. As a result, for 9 different types of cancer, we identified CAF-specific gene expression signatures and found 10 protein markers that showed strongly positive staining of tumor stroma according to the analysis of IHC images from the Human Protein Atlas database. Our results give an insight into selecting the most appropriate combination of cancer-associated fibroblast markers. Furthermore, comparison of different approaches for studying differences between cancer-associated and normal fibroblasts (NFs) illustrates the superiority of transcriptome analysis of fibroblasts obtained from fresh tissue samples. Using single-cell RNA sequencing data, we identified common differences in gene expression patterns between normal and cancer-associated fibroblasts, which do not depend on the type of tumor.
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Affiliation(s)
- Anastasia N. Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- *Correspondence: Anastasia N. Kazakova, ; Ksenia S. Anufrieva,
| | - Ksenia S. Anufrieva
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- *Correspondence: Anastasia N. Kazakova, ; Ksenia S. Anufrieva,
| | - Olga M. Ivanova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Polina V. Shnaider
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of biology, Lomonosov Moscow State University, Moscow, Russia
| | - Irina K. Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - Olga I. Aleshikova
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Andrey V. Slonov
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Lev A. Ashrafyan
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Nataliya A. Babaeva
- National Medical Scientific Centre of Obstetrics, Gynecology and Perinatal Medicine named after V.I. Kulakov, Moscow, Russia
| | - Artem V. Eremeev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Veronika S. Boichenko
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Faculty of biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria M. Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Maria A. Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Vadim M. Govorun
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Scientific Research Institute for Systems Biology and Medicine, Moscow, Russia
| | - Victoria O. Shender
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - Georgij P. Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
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Stewart N, Wisnovsky S. Bridging Glycomics and Genomics: New Uses of Functional Genetics in the Study of Cellular Glycosylation. Front Mol Biosci 2022; 9:934584. [PMID: 35782863 PMCID: PMC9243437 DOI: 10.3389/fmolb.2022.934584] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
All living cells are coated with a diverse collection of carbohydrate molecules called glycans. Glycans are key regulators of cell behavior and important therapeutic targets for human disease. Unlike proteins, glycans are not directly templated by discrete genes. Instead, they are produced through multi-gene pathways that generate a heterogenous array of glycoprotein and glycolipid antigens on the cell surface. This genetic complexity has sometimes made it challenging to understand how glycosylation is regulated and how it becomes altered in disease. Recent years, however, have seen the emergence of powerful new functional genomics technologies that allow high-throughput characterization of genetically complex cellular phenotypes. In this review, we discuss how these techniques are now being applied to achieve a deeper understanding of glyco-genomic regulation. We highlight specifically how methods like ChIP-seq, RNA-seq, CRISPR genomic screening and scRNA-seq are being used to map the genomic basis for various cell-surface glycosylation states in normal and diseased cell types. We also offer a perspective on how emerging functional genomics technologies are likely to create further opportunities for studying cellular glycobiology in the future. Taken together, we hope this review serves as a primer to recent developments at the glycomics-genomics interface.
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Affiliation(s)
- Natalie Stewart
- Biochemistry and Microbiology Dept, University of Victoria, Victoria, BC, Canada
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Simon Wisnovsky
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Simon Wisnovsky,
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