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Ma Y, Li X, Zhang J, Zhao X, Lu Y, Shen G, Wang G, Liu H, Hao J. Integrating tertiary lymphoid structure-associated genes into computational models to evaluate prognostication and immune infiltration in pancreatic cancer. J Leukoc Biol 2024; 116:589-600. [PMID: 38484172 DOI: 10.1093/jleuko/qiae067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/03/2024] [Accepted: 02/27/2024] [Indexed: 09/03/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is characterized by poor response to all therapeutic modalities and dismal prognosis. The presence of tertiary lymphoid structures (TLSs) in various solid cancers is of crucial prognostic significance, highlighting the intricate interplay between the tumor microenvironment and immune cells aggregation. However, the extent to which TLSs and immune status affect PDAC prognosis remains incompletely understood. Here, we sought to unveil the unique properties of TLSs in PDAC by leveraging both single-cell and bulk transcriptomics, culminating in a risk model that predicts clinical outcomes. We used TLS scores based on a 12-gene (CCL2, CCL3, CCL4, CCL5, CCL8, CCL18, CCL19, CCL21, CXCL9, CXCL10, CXCL11, and CXCL13) and 9-gene (PTGDS, RBP5, EIF1AY, CETP, SKAP1, LAT, CCR6, CD1D, and CD79B) signature, respectively, and examined their distribution in cell clusters of single-cell data from PDAC samples. The markers involved in these clusters were selected to develop a prognostic model using The Cancer Genome Atlas Program database as the training cohort and Gene Expression Omnibus database as the validation cohort. Further, we compared the immune infiltration, drug sensitivity, and enriched and differentially expressed genes between the high- and low-risk groups in our model. Therefore, we established a risk model that has significant implications for the prognostic assessment of PADC patients with remarkable differences in immune infiltration and chemosensitivity between the low- and high-risk groups. This paradigm established by TLS-related cell marker genes provides a prognostic prediction and a panel of novel therapeutic targets for exploring potential immunotherapy.
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Affiliation(s)
- Ying Ma
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Xuesong Li
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Jin Zhang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Xiangqin Zhao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Yi Lu
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Guangcong Shen
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Guowen Wang
- Department of Bone and Soft Tissue Tumors, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Hong Liu
- Second Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, West Huanhu Road, Hexi District, Tianjin 300060, China
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University, West Huanhu Road, Hexi District, Tianjin 300060, China
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin Medical University, West Huanhu Road, Hexi District, Tianjin 300060, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, West Huanhu Road, Hexi District, Tianjin 300060, China
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2
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Fang S, Cao H, Liu J, Cao G, Li T. Antitumor effects of IOX1 combined with bevacizumab-induced apoptosis and immunity on colorectal cancer cells. Int Immunopharmacol 2024; 141:112896. [PMID: 39146782 DOI: 10.1016/j.intimp.2024.112896] [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: 05/24/2024] [Revised: 07/11/2024] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
Colorectal cancer (CRC), as a fatal cancer, is one of the most common cancers worldwide. Although the standard treatment for colorectal cancer is well researched and established, long-term patient survival remains poor, and mortality remains high. Therefore, more and more effective treatment options are needed. To evaluate the efficacy of bevacizumab, the histone demethylase inhibitor IOX1, or their combination for the treatment of colorectal cancer, we examined the effects of IOX1, bevacizumab, and IOX1 combined with bevacizumab on cell activity, proliferation, and migration of colorectal cancer cell lines HCT116, RKO, and CT26 by CCK8, colony formation assay, wound healing assay, and transwell assay. The effects of the drugs alone as well as in combination on apoptosis in colorectal cancer cell lines were examined by flow cytometry and further validated by Western blotting for apoptosis-related proteins. The antitumor effects of treatment alone or in combination on colorectal cancer cells were examined in animal models. Mice were injected subcutaneously with CT26 cells and the growth and immune infiltration in tumor tissues were detected by IHC after drug treatment. We found that IOX1 could effectively inhibit the activity of CRC cells and had a significant inhibitory effect on the proliferation and migration of CRC cells. The apoptosis rate increased in a dose-dependent manner after IOX1 treatment on colorectal cancer cells, and the expression of apoptosis-related proteins changed accordingly. Further combination with bevacizumab revealed that the combination had a more significant effect on the proliferation, migration, and apoptosis of CRC cells than either IOX1 or bevacizumab alone. In vivo experiments have found that both alone and combination drugs can inhibit the growth of mouse tumors, but the effect of combination inhibition is the most obvious. Combination therapy significantly inhibited the expression of proliferative marker (Ki67) in tumor xenograft models, and increased content of antigen-specific CD4+, CD8+T cell growth, and granzymeB (GZMB), which is associated with T cell cytotoxicity, was detected in combination therapy. Immunoassays suppressed the expression of relevant PD-1 and decreased. The anticancer drug bevacizumab and the histone demethylase inhibitor IOX1 may inhibit colon cancer cell growth by regulating apoptosis. The inhibitory effect of combination therapy on tumor growth may be achieved, in part, through upregulation of infiltration-mediated tumor immunity by T lymphocytes. The combination of IOX1 and bevacizumab produced significant synergistic effects. This study aims to provide a new direction for CRC combination therapy.
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Affiliation(s)
- Shuilong Fang
- Zhengzhou University People's Hospital, Zhengzhou, Henan, China; Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Huicun Cao
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Jian Liu
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Guangshao Cao
- Department of Comprehensive Intervention, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Tianxiao Li
- Zhengzhou University People's Hospital, Zhengzhou, Henan, China; Interventional Center, Henan Provincial People's Hospital, Zhengzhou, Henan, China.
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3
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Ren Z, Tang H, Zhang W, Guo M, Cui J, Wang H, Xie B, Yu J, Chen Y, Zhang M, Han C, Chu T, Liang Q, Zhao S, Huang Y, He X, Liu K, Liu C, Chen C. The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling During Neurodevelopment. Neurosci Bull 2024; 40:1076-1092. [PMID: 38060137 PMCID: PMC11306490 DOI: 10.1007/s12264-023-01161-3] [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: 07/06/2023] [Accepted: 09/13/2023] [Indexed: 12/08/2023] Open
Abstract
Intellectual disability (ID) is a condition characterized by cognitive impairment and difficulties in adaptive functioning. In our research, we identified two de novo mutations (c.955C>T and c.732C>A) at the KDM2A locus in individuals with varying degrees of ID. In addition, by using the Gene4Denovo database, we discovered five additional cases of de novo mutations in KDM2A. The mutations we identified significantly decreased the expression of the KDM2A protein. To investigate the role of KDM2A in neural development, we used both 2D neural stem cell models and 3D cerebral organoids. Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells (NPCs), increases apoptosis, induces premature neuronal differentiation, and affects synapse maturation. Through ChIP-Seq analysis, we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis. In addition, the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes. By integrating ChIP-Seq and RNA-Seq data, we made a significant discovery of the core genes' remarkable enrichment in the MAPK signaling pathway. Importantly, this enrichment was specifically linked to the p38 MAPK pathway. Furthermore, disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID, autism spectrum disorder, and schizophrenia. Overall, our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes, thereby modulating the MAPK signaling pathway and potentially impacting early brain development.
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Affiliation(s)
- Zongyao Ren
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Haiyan Tang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Wendiao Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Minghui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jingjie Cui
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, 410007, China
| | - Bin Xie
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jing Yu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yonghao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Cong Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Tianyao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Qiuman Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Shunan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yingjie Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Xuelian He
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430014, China.
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410011, China.
- Furong Laboratory, Changsha, 410000, China.
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Xie J, Lin H, Zuo A, Shao J, Sun W, Wang S, Song J, Yao W, Luo Y, Sun J, Wang M. The JMJD family of histone demethylase and their intimate links to cardiovascular disease. Cell Signal 2024; 116:111046. [PMID: 38242266 DOI: 10.1016/j.cellsig.2024.111046] [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: 02/23/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
The incidence rate and mortality rate of cardiovascular disease rank first in the world. It is associated with various high-risk factors, and there is no single cause. Epigenetic modifications, such as DNA methylation or histone modification, actively participate in the initiation and development of cardiovascular diseases. Histone lysine methylation is a type of histone post-translational modification. The human Jumonji C domain (JMJD) protein family consists of more than 30 members. JMJD proteins participate in many key nuclear processes and play a key role in the specific regulation of gene expression, DNA damage and repair, and DNA replication. Importantly, increasing evidence shows that JMJD proteins are abnormally expressed in cardiovascular diseases, which may be a potential mechanism for the occurrence and development of these diseases. Here, we discuss the key roles of JMJD proteins in various common cardiovascular diseases. This includes histone lysine demethylase, which has been studied in depth, and less-studied JMJD members. Furthermore, we focus on the epigenetic changes induced by each JMJD member, summarize recent research progress, and evaluate their relationship with cardiovascular diseases and therapeutic potential.
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Affiliation(s)
- Jiarun Xie
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Haoyu Lin
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Anna Zuo
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Junqiao Shao
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Wei Sun
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Shaoting Wang
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jianda Song
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Wang Yao
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Yanyu Luo
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China
| | - Jia Sun
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China.
| | - Ming Wang
- Department of Traditional Chinese Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510515, China.
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5
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You HJ, Ma LH, Wang X, Wang YX, Zhang HY, Bao ES, Zhong YJ, Liu XY, Kong DL, Zheng KY, Kong FY, Tang RX. Hepatitis B virus core protein stabilizes RANGAP1 to upregulate KDM2A and facilitate hepatocarcinogenesis. Cell Oncol (Dordr) 2024; 47:639-655. [PMID: 37845585 DOI: 10.1007/s13402-023-00889-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2023] [Indexed: 10/18/2023] Open
Abstract
PURPOSE As a vital component of the hepatitis B virus (HBV) nucleocapsid, HBV core protein (HBC) contributes to hepatocarcinogenesis. Here, we aimed to assess the effects of RANGAP1 and KDM2A on tumorigenesis induced by HBC. METHODS Co-immunoprecipitation (Co-IP) combined with mass spectrometry were utilized to identify the proteins with the capacity to interact with HBC. The gene and protein levels of RANGAP1 and KDM2A in hepatocellular carcinoma (HCC) and HBV-positive HCC tissues were evaluated using different cohorts. The roles of RANGAP1 and KDM2A in HCC cells mediated by HBC were investigated in vitro and in vivo. Co-IP and western blot were used to estimate the interaction of HBC with RANGAP1 and KDM2A and assess RANGAP1 stabilization regulated by HBC. RESULTS We discovered that HBC could interact with RANGAP1 and KDM2A, the levels of which were markedly elevated in HCC tissues. Relying on RANGAP1 and KDM2A, HBC facilitated HCC cell growth and migration. The increased stabilization of RANGAP1 mediated by HBC was relevant to the disruption of the interaction between RANGAP1 and an E3 ligase SYVN1. RANGAP1 interacted with KDM2A, and it further promoted KDM2A stabilization by disturbing the interaction between KDM2A and SYVN1. HBC enhanced the interaction of KDM2A with RANGAP1 and upregulated the expression of KDM2A via RANGAP1 in HCC cells. CONCLUSIONS These findings demonstrate a novel mechanism by which HBC facilitates hepatocarcinogenesis. RANGAP1 and KDM2A could act as potential molecular targets for treating HBV-associated malignancy.
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Affiliation(s)
- Hong-Juan You
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Li-Hong Ma
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xing Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu-Xin Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Huan-Yang Zhang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - En-Si Bao
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu-Jie Zhong
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiang-Ye Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - De-Long Kong
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Kui-Yang Zheng
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China
- National Demonstration Center for Experimental Basic Medical Sciences Education, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Fan-Yun Kong
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Ren-Xian Tang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu, China.
- National Demonstration Center for Experimental Basic Medical Sciences Education, Xuzhou Medical University, Xuzhou, Jiangsu, China.
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Liu J, Lu Y, Liu Y, Zhang W, Xian S, Wang S, Zheng Z, Lin R, Jin M, Zhang M, Qian W, Tang J, Lu B, Yang Y, Liu Z, Qu M, Ma H, Wu X, Chang Z, Zhang J, Zhang Y. A gene signature linked to fibroblast differentiation for prognostic prediction of mesothelioma. Cell Biosci 2024; 14:33. [PMID: 38462627 PMCID: PMC10926647 DOI: 10.1186/s13578-023-01180-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 12/05/2023] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Malignant mesothelioma is a type of infrequent tumor that is substantially related to asbestos exposure and has a terrible prognosis. We tried to produce a fibroblast differentiation-related gene set for creating a novel classification and prognostic prediction model of MESO. METHOD Three databases, including NCBI-GEO, TCGA, and MET-500, separately provide single-cell RNA sequencing data, bulk RNA sequencing profiles of MESO, and RNA sequencing information on bone metastatic tumors. Dimensionality reduction and clustering analysis were leveraged to acquire fibroblast subtypes in the MESO microenvironment. The fibroblast differentiation-related genes (FDGs), which were associated with survival and subsequently utilized to generate the MESO categorization and prognostic prediction model, were selected in combination with pseudotime analysis and survival information from the TCGA database. Then, regulatory network was constructed for each MESO subtype, and candidate inhibitors were predicted. Clinical specimens were collected for further validation. RESULT A total of six fibroblast subtypes, three differentiation states, and 39 FDGs were identified. Based on the expression level of FDGs, three MESO subtypes were distinguished in the fibroblast differentiation-based classification (FDBC). In the multivariate prognostic prediction model, the risk score that was dependent on the expression level of several important FDGs, was verified to be an independently effective prognostic factor and worked well in internal cohorts. Finally, we predicted 24 potential drugs for the treatment of MESO. Moreover, immunohistochemical staining and statistical analysis provided further validation. CONCLUSION Fibroblast differentiation-related genes (FDGs), especially those in low-differentiation states, might participate in the proliferation and invasion of MESO. Hopefully, the raised clinical subtyping of MESO would provide references for clinical practitioners.
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Affiliation(s)
- Jun Liu
- Department of Anesthesiology, Shanghai Pulmonary Hospital Affiliated to Tongji University, 507 Zheng Min Road, Shanghai, 200433, China
| | - Yuwei Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yifan Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Department of Urology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, No. 1665 Kongjiang Road, Shanghai, 200092, China
| | - Wei Zhang
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Shuyuan Xian
- Department of Burn Surgery, The First Affiliated Hospital of Naval Medical University, Shanghai, China
- Research Unit of Key Techniques for Treatment of Burns and Combined Burns and Trauma Injury, Chinese Academy of Medical Sciences, Shanghai, China
| | - Siqiao Wang
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Zixuan Zheng
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Ruoyi Lin
- Tongji University School of Medicine, Shanghai, 200092, China
| | - Minghao Jin
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mengyi Zhang
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Weijin Qian
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jieling Tang
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Bingnan Lu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yiting Yang
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zichang Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mingyu Qu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Haonan Ma
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinru Wu
- Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhengyan Chang
- Department of Pathology, School of Medicine, Shanghai Tenth People's Hospital, Tongji University, 301 Yanchang Road, Shanghai, 200072, China.
| | - Jie Zhang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, 2699 Gaoke West Road, Shanghai, 201204, China.
| | - Yuan Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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7
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Li Q, Qin K, Tian Y, Chen B, Zhao G, Xu S, Wu L. Inhibition of demethylase by IOX1 modulates chromatin accessibility to enhance NSCLC radiation sensitivity through attenuated PIF1. Cell Death Dis 2023; 14:817. [PMID: 38086789 PMCID: PMC10716120 DOI: 10.1038/s41419-023-06346-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Chromatin accessibility is a critical determinant of gene transcriptional expression and regulated by histones modification. However, the potential for manipulating chromatin accessibility to regulate radiation sensitivity remains unclear. Our findings demonstrated that the histone demethylase inhibitor, 5-carboxy-8-hydroxyquinoline (IOX1), could enhance the radiosensitivity of non-small cell lung cancer (NSCLC) in vitro and in vivo. Mechanistically, IOX1 treatment reduced chromatin accessibility in the promoter region of DNA damage repair genes, leading to decreased DNA repair efficiency and elevated DNA damage induced by γ irradiation. Notably, IOX1 treatment significantly reduced both chromatin accessibility and the transcription of phytochrome interacting factor 1 (PIF1), a key player in telomere maintenance. Inhibition of PIF1 delayed radiation-induced DNA and telomeric DNA damage repair, as well as increased radiosensitivity of NSCLC in vitro and in vivo. Further study indicated that the above process was regulated by a reduction of transcription factor myc-associated zinc finger protein (MAZ) binding to the distal intergenic region of the PIF1. Taken together, IOX1-mediated demethylase inactivation reduced chromatin accessibility, leading to elevated telomere damage which is partly due to PIF1 inhibition, thereby enhancing NSCLC radiosensitivity.
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Affiliation(s)
- Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Kexin Qin
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Yushan Tian
- China National Tobacco Quality Supervision and Test Center, Zhengzhou, Henan, 450001, PR China
| | - Biao Chen
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China
| | - Guoping Zhao
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China
| | - Shengmin Xu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
| | - Lijun Wu
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui, 230026, PR China.
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, PR China.
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8
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Qu L, Yin T, Zhao Y, Lv W, Liu Z, Chen C, Liu K, Shan S, Zhou R, Li X, Dong H. Histone demethylases in the regulation of immunity and inflammation. Cell Death Discov 2023; 9:188. [PMID: 37353521 DOI: 10.1038/s41420-023-01489-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Pathogens or danger signals trigger the immune response. Moderate immune response activation removes pathogens and avoids excessive inflammation and tissue damage. Histone demethylases (KDMs) regulate gene expression and play essential roles in numerous physiological processes by removing methyl groups from lysine residues on target proteins. Abnormal expression of KDMs is closely associated with the pathogenesis of various inflammatory diseases such as liver fibrosis, lung injury, and autoimmune diseases. Despite becoming exciting targets for diagnosing and treating these diseases, the role of these enzymes in the regulation of immune and inflammatory response is still unclear. Here, we review the underlying mechanisms through which KDMs regulate immune-related pathways and inflammatory responses. In addition, we also discuss the future applications of KDMs inhibitors in immune and inflammatory diseases.
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Affiliation(s)
- Lihua Qu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Tong Yin
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Yijin Zhao
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Wenting Lv
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Ziqi Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Chao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Kejun Liu
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Shigang Shan
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Xiaoqing Li
- Biological Targeted Therapy Key Laboratory in Hubei, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Center for Stem Cell Research and Application, Union Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Huifen Dong
- Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China.
- Department of Pathogenic Biology, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei, China.
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9
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Burlibasa L, Nicu AT, Chifiriuc MC, Medar C, Petrescu A, Jinga V, Stoica I. H3 histone methylation landscape in male urogenital cancers: from molecular mechanisms to epigenetic biomarkers and therapeutic targets. Front Cell Dev Biol 2023; 11:1181764. [PMID: 37228649 PMCID: PMC10203431 DOI: 10.3389/fcell.2023.1181764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
During the last decades, male urogenital cancers (including prostate, renal, bladder and testicular cancers) have become one of the most frequently encountered malignancies affecting all ages. While their great variety has promoted the development of various diagnosis, treatment and monitoring strategies, some aspects such as the common involvement of epigenetic mechanisms are still not elucidated. Epigenetic processes have come into the spotlight in the past years as important players in the initiation and progression of tumors, leading to a plethora of studies highlighting their potential as biomarkers for diagnosis, staging, prognosis, and even as therapeutic targets. Thus, fostering research on the various epigenetic mechanisms and their roles in cancer remains a priority for the scientific community. This review focuses on one of the main epigenetic mechanisms, namely, the methylation of the histone H3 at various sites and its involvement in male urogenital cancers. This histone modification presents a great interest due to its modulatory effect on gene expression, leading either to activation (e.g., H3K4me3, H3K36me3) or repression (e.g., H3K27me3, H3K9me3). In the last few years, growing evidence has demonstrated the aberrant expression of enzymes that methylate/demethylate histone H3 in cancer and inflammatory diseases, that might contribute to the initiation and progression of such disorders. We highlight how these particular epigenetic modifications are emerging as potential diagnostic and prognostic biomarkers or targets for the treatment of urogenital cancers.
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Affiliation(s)
| | | | - Mariana Carmen Chifiriuc
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Romanian Academy, Bucharest, Romania
| | - Cosmin Medar
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Clinical Hospital “Prof. dr Theodor Burghele”, Bucharest, Romania
| | - Amelia Petrescu
- Clinical Hospital “Prof. dr Theodor Burghele”, Bucharest, Romania
| | - Viorel Jinga
- Academy of Romanian Scientists, Bucharest, Romania
- University of Medicine and Pharmacy “Carol Davila”, Bucharest, Romania
- Clinical Hospital “Prof. dr Theodor Burghele”, Bucharest, Romania
| | - Ileana Stoica
- Faculty of Biology, University of Bucharest, Bucharest, Romania
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Ershov P, Yablokov E, Mezentsev Y, Ivanov A. Interactomics of CXXC proteins involved in epigenetic regulation of gene expression. BIOMEDITSINSKAYA KHIMIYA 2022; 68:339-351. [DOI: 10.18097/pbmc20226805339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Regulation of gene expression is an extremely complex and multicomponent biological phenomenon. Proteins containing the CXXC-domain “zinc fingers” (CXXC-proteins) are master regulators of expression of many genes and have conserved functions of methylation of DNA bases and histone proteins. CXXC proteins function as a part of multiprotein complexes, which indicates the fundamental importance of studying post-translational regulation through modulation of the protein-protein interaction spectrum (PPI) in both normal and pathological conditions. In this paper we discuss general aspects of the involvement of CXXC proteins and their protein partners in neoplastic processes, both from the literature data and our own studies. Special attention is paid to recent data on the particular interactomics of the CFP1 protein encoded by the CXXC1 gene located on the human chromosome 18. CFP1 is devoid of enzymatic activity and implements epigenetic regulation of expression through binding to chromatin and a certain spectrum of PPIs.
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Affiliation(s)
- P.V. Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - A.S. Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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