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Lian WS, Wu RW, Lin YH, Chen YS, Jahr H, Wang FS. Tricarboxylic Acid Cycle Regulation of Metabolic Program, Redox System, and Epigenetic Remodeling for Bone Health and Disease. Antioxidants (Basel) 2024; 13:470. [PMID: 38671918 PMCID: PMC11047415 DOI: 10.3390/antiox13040470] [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: 02/26/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Imbalanced osteogenic cell-mediated bone gain and osteoclastic remodeling accelerates the development of osteoporosis, which is the leading risk factor of disability in the elderly. Harmonizing the metabolic actions of bone-making cells and bone resorbing cells to the mineralized matrix network is required to maintain bone mass homeostasis. The tricarboxylic acid (TCA) cycle in mitochondria is a crucial process for cellular energy production and redox homeostasis. The canonical actions of TCA cycle enzymes and intermediates are indispensable in oxidative phosphorylation and adenosine triphosphate (ATP) biosynthesis for osteogenic differentiation and osteoclast formation. Knockout mouse models identify these enzymes' roles in bone mass and microarchitecture. In the noncanonical processes, the metabolites as a co-factor or a substrate involve epigenetic modification, including histone acetyltransferases, DNA demethylases, RNA m6A demethylases, and histone demethylases, which affect genomic stability or chromatin accessibility for cell metabolism and bone formation and resorption. The genetic manipulation of these epigenetic regulators or TCA cycle intermediate supplementation compromises age, estrogen deficiency, or inflammation-induced bone mass loss and microstructure deterioration. This review sheds light on the metabolic functions of the TCA cycle in terms of bone integrity and highlights the crosstalk of the TCA cycle and redox and epigenetic pathways in skeletal tissue metabolism and the intermediates as treatment options for delaying osteoporosis.
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Affiliation(s)
- Wei-Shiung Lian
- Core Laboratory for Phenomics and Diagnostic, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan; (W.-S.L.); (Y.-S.C.)
- Center for Mitochondrial Research and Medicine, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan;
- Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan
| | - Re-Wen Wu
- Department of Orthopedic Surgery, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan;
| | - Yu-Han Lin
- Center for Mitochondrial Research and Medicine, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan;
| | - Yu-Shan Chen
- Core Laboratory for Phenomics and Diagnostic, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan; (W.-S.L.); (Y.-S.C.)
- Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan
| | - Holger Jahr
- Department of Anatomy and Cell Biology, University Hospital RWTH, 52074 Aachen, Germany;
- Department of Orthopedic Surgery, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Feng-Sheng Wang
- Core Laboratory for Phenomics and Diagnostic, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan; (W.-S.L.); (Y.-S.C.)
- Center for Mitochondrial Research and Medicine, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan;
- Department of Medical Research, College of Medicine, Chang Gung University, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833401, Taiwan
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2
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Szoszkiewicz A, Bukowska-Olech E, Jamsheer A. Molecular landscape of congenital vertebral malformations: recent discoveries and future directions. Orphanet J Rare Dis 2024; 19:32. [PMID: 38291488 PMCID: PMC10829358 DOI: 10.1186/s13023-024-03040-0] [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: 07/18/2023] [Accepted: 01/19/2024] [Indexed: 02/01/2024] Open
Abstract
Vertebral malformations (VMs) pose a significant global health problem, causing chronic pain and disability. Vertebral defects occur as isolated conditions or within the spectrum of various congenital disorders, such as Klippel-Feil syndrome, congenital scoliosis, spondylocostal dysostosis, sacral agenesis, and neural tube defects. Although both genetic abnormalities and environmental factors can contribute to abnormal vertebral development, our knowledge on molecular mechanisms of numerous VMs is still limited. Furthermore, there is a lack of resource that consolidates the current knowledge in this field. In this pioneering review, we provide a comprehensive analysis of the latest research on the molecular basis of VMs and the association of the VMs-related causative genes with bone developmental signaling pathways. Our study identifies 118 genes linked to VMs, with 98 genes involved in biological pathways crucial for the formation of the vertebral column. Overall, the review summarizes the current knowledge on VM genetics, and provides new insights into potential involvement of biological pathways in VM pathogenesis. We also present an overview of available data regarding the role of epigenetic and environmental factors in VMs. We identify areas where knowledge is lacking, such as precise molecular mechanisms in which specific genes contribute to the development of VMs. Finally, we propose future research avenues that could address knowledge gaps.
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Affiliation(s)
- Anna Szoszkiewicz
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
| | - Ewelina Bukowska-Olech
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Rokietnicka 8, 60-806, Poznan, Poland.
- Centers for Medical Genetics GENESIS, Dąbrowskiego 77A, 60-529, Poznan, Poland.
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3
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Trecourt A, Azmani R, Hostein I, Blanchard L, Le Loarer F, Bourdon A, Alame M, Nadaud B, Mayer L, Rebier F, Larmonier C, Moura MS, Soubeyran I, Hartog C, Ray-Coquard I, Treilleux I, Devouassoux-Shisheboran M, Croce S. The KAT6B::KANSL1 Fusion Defines a New Uterine Sarcoma With Hybrid Endometrial Stromal Tumor and Smooth Muscle Tumor Features. Mod Pathol 2023; 36:100243. [PMID: 37307879 DOI: 10.1016/j.modpat.2023.100243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023]
Abstract
Neoplasms harboring a KAT6B/A::KANSL1 fusion were initially reported as benign (leiomyomas) and malignant (leiomyosarcomas, low-grade endometrial stromal sarcomas [LG-ESSs]) uterine neoplasms. However, they may represent an emerging entity characterized by clinical aggressiveness contrasting with a rather reassuring microscopic appearance. Here, we aimed to confirm that this neoplasm is a distinct clinicopathologic and molecular sarcoma and identify criteria that should alert pathologists and lead to KAT6B/A::KANSL1 fusion testing in routine practice. Therefore, we conducted a comprehensive clinical, histopathologic, immunohistochemical, and molecular study, including array comparative genomic hybridization, whole RNA-sequencing, unsupervised clustering, and cDNA mutational profile analyses of 16 tumors with KAT6B::KANSL1 fusion from 12 patients. At presentation, patients were peri-menopausal (median, 47.5 years), and the primary tumors were located in the uterine corpus (12/12, 100%), with an additional prevesical location in 1 (8.3%) of 12 cases. The relapse rate was 33.3% (3/9). All tumors (16/16, 100%) showed morphologic and immunohistochemical features overlapping between leiomyoma and endometrial stromal tumors. A whirling recurrent architecture (resembling fibromyxoid-ESS/fibrosarcoma) was found in 13 (81.3%) of 16 tumors. All tumors (16/16, 100%) exhibited numerous arterioliform vessels, and 13 (81.3%) of 18 had large hyalinized central vessels and collagen deposits. Estrogen and progesterone receptors were expressed in 16 (100%) of 16 and 14 (87.5%) of 16 tumors, respectively. Array comparative genomic hybridization performed on 10 tumors classified these neoplasms as simple genomic sarcomas. Whole RNA-sequencing on 16 samples and clustering analysis on primary tumors found that the KAT6B::KANSL1 fusion always occurred between exons 3 of KAT6B and 11 of KANSL1; no pathogenic variant was identified on cDNA, all neoplasms clustered together, close to LG-ESS, and pathway enrichment analysis showed cell proliferation and immune infiltrate recruitment pathway involvement. These results confirm that the sarcomas harboring a KAT6B/A::KANSL1 fusion represent a distinct clinicopathologic entity, close to LG-ESS but different, with clinical aggressiveness despite a reassuring morphology, for which the KAT6B/A::KANSL1 fusion is the molecular driver alteration.
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Affiliation(s)
- Alexis Trecourt
- Multi-Site Department of Pathology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; Claude Bernard University Lyon 1, Faculty of Medicine Lyon-Sud-Charles, UR 3738 CICLY, Lyon, France
| | - Rihab Azmani
- Institute Bergonié, Bioinformatics, Data and Digital Health Department, Comprehensive Cancer Center, Bordeaux, France
| | - Isabelle Hostein
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Larry Blanchard
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - François Le Loarer
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France; INSERM Unit 1312, Bordeaux, France; University of Bordeaux, Talence, France
| | - Aurelien Bourdon
- Institute Bergonié, Bioinformatics, Data and Digital Health Department, Comprehensive Cancer Center, Bordeaux, France
| | - Melissa Alame
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Béatrice Nadaud
- Multi-Site Department of Pathology, Hospices Civils de Lyon, Lyon Est Hospital, Bron, France
| | - Laetitia Mayer
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Flora Rebier
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Claire Larmonier
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Madalena Souto Moura
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
| | - Isabelle Soubeyran
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Cécile Hartog
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France
| | - Isabelle Ray-Coquard
- Claude Bernard University Lyon 1, Faculty of Medicine Lyon-Sud-Charles, UR 3738 CICLY, Lyon, France; Centre Léon Bérard, Department of Medical Oncology, Lyon, France
| | | | - Mojgan Devouassoux-Shisheboran
- Multi-Site Department of Pathology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre-Bénite, France; Claude Bernard University Lyon 1, Faculty of Medicine Lyon-Sud-Charles, UR 3738 CICLY, Lyon, France
| | - Sabrina Croce
- Institute Bergonié, Department of Biopathology, Comprehensive Cancer Center, Bordeaux, France; INSERM Unit 1312, Bordeaux, France.
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Sun D, Ding Z, Hai Y, Cheng Y. Advances in epigenetic research of adolescent idiopathic scoliosis and congenital scoliosis. Front Genet 2023; 14:1211376. [PMID: 37564871 PMCID: PMC10411889 DOI: 10.3389/fgene.2023.1211376] [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: 04/24/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
Scoliosis is a three-dimensional structural deformity of the spine; more than 80% of scoliosis has no specific pathogenesis but is understood to be closely related to genetic, hormonal, and environmental factors. In recent years, the epigenetic alterations observed in scoliosis have been analyzed in numerous studies to determine the pathogenesis and progression of this condition, however, there is currently no comprehensive review of the epigenetic factors to date. We searched PubMed, Embase, and Web of Science databases for relative studies without language and date restrictions in March 2023. Twenty-five studies were included in this review and analyzed from the four main aspects of epigenetic alteration: DNA methylation, non-coding RNAs, histone modifications, and chromatin remodeling. The relationship between DNA methylation, non-coding RNAs, and scoliosis was considerably reported in the literature, and the corresponding related signaling pathways and novel biomarkers observed in scoliosis provide insights into innovative prevention and treatment strategies. However, the role of histone modifications is rarely reported in scoliosis, and few studies have investigated the relationship between scoliosis and chromatin remodeling. Therefore, these related fields need to be further explored to elucidate the overall effects of epigenetics in scoliosis.
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Affiliation(s)
| | | | - Yong Hai
- Department of Orthopedic Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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Zhang H, Xiang G, Li J, He S, Wang Y, Deng A, Wang Y, Guo C. Promotion effect of FGF23 on osteopenia in congenital scoliosis through FGFr3/TNAP/OPN pathway. Chin Med J (Engl) 2023; 136:1468-1477. [PMID: 37192015 PMCID: PMC10278695 DOI: 10.1097/cm9.0000000000002690] [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: 11/09/2022] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Congenital scoliosis (CS) is a complex spinal malformation of unknown etiology with abnormal bone metabolism. Fibroblast growth factor 23 (FGF23), secreted by osteoblasts and osteocytes, can inhibit bone formation and mineralization. This research aims to investigate the relationship between CS and FGF23. METHODS We collected peripheral blood from two pairs of identical twins for methylation sequencing of the target region. FGF23 mRNA levels in the peripheral blood of CS patients and age-matched controls were measured. Receiver operator characteristic (ROC) curve analyses were conducted to evaluate the specificity and sensitivity of FGF23. The expression levels of FGF23 and its downstream factors fibroblast growth factor receptor 3 (FGFr3)/tissue non-specific alkaline phosphatase (TNAP)/osteopontin (OPN) in primary osteoblasts from CS patients (CS-Ob) and controls (CT-Ob) were detected. In addition, the osteogenic abilities of FGF23-knockdown or FGF23-overexpressing Ob were examined. RESULTS DNA methylation of the FGF23 gene in CS patients was decreased compared to that of their identical twins, accompanied by increased mRNA levels. CS patients had increased peripheral blood FGF23 mRNA levels and decreased computed tomography (CT) values compared with controls. The FGF23 mRNA levels were negatively correlated with the CT value of the spine, and ROCs of FGF23 mRNA levels showed high sensitivity and specificity for CS. Additionally, significantly increased levels of FGF23, FGFr3, OPN, impaired osteogenic mineralization and lower TNAP levels were observed in CS-Ob. Moreover, FGF23 overexpression in CT-Ob increased FGFr3 and OPN levels and decreased TNAP levels, while FGF23 knockdown induced downregulation of FGFr3 and OPN but upregulation of TNAP in CS-Ob. Mineralization of CS-Ob was rescued after FGF23 knockdown. CONCLUSIONS Our results suggested increased peripheral blood FGF23 levels, decreased bone mineral density in CS patients, and a good predictive ability of CS by peripheral blood FGF23 levels. FGF23 may contribute to osteopenia in CS patients through FGFr3/TNAP / OPN pathway.
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Affiliation(s)
- Hongqi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Gang Xiang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Jiong Li
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Sihan He
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yunjia Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Ang Deng
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yuxiang Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Chaofeng Guo
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
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Zheng Y, Shen P, Tong M, Li H, Ren C, Wu F, Li H, Yang H, Cai B, Du W, Zhao X, Yao S, Quan R. WISP2 downregulation inhibits the osteogenic differentiation of BMSCs in congenital scoliosis by regulating Wnt/β-catenin pathway. Biochim Biophys Acta Mol Basis Dis 2023:166783. [PMID: 37302424 DOI: 10.1016/j.bbadis.2023.166783] [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: 12/27/2022] [Revised: 05/09/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
OBJECTIVES Bone marrow mesenchymal stem cells (BMSCs) are instrumental in bone development, metabolism, and marrow microenvironment homeostasis. Despite this, the relevant effects and mechanisms of BMSCs on congenital scoliosis (CS) remain undefined. Herein, it becomes our focus to reveal the corresponding effects and mechanisms implicated. METHODS BMSCs from CS patients (hereafter referred as CS-BMSCs) and healthy donors (NC-BMSCs) were observed and identified. Differentially expressed genes in BMSCs were analyzed utilizing scRNA-seq and RNA-seq profiles. The multi-differentiation potential of BMSCs following the transfection or infection was evaluated. The expression levels of factors related to osteogenic differentiation and Wnt/β-catenin pathway were further determined as appropriate. RESULTS A decreased osteogenic differentiation ability was shown in CS-BMSCs. Both the proportion of LEPR+ BMSCs and the expression level of WNT1-inducible-signaling pathway protein 2 (WISP2) were decreased in CS-BMSCs. WISP2 knockdown suppressed the osteogenic differentiation of NC-BMSCs, while WISP2 overexpression facilitated the osteogenesis of CS-BMSCs via acting on the Wnt/β-catenin pathway. CONCLUSIONS Our study collectively indicates WISP2 knockdown blocks the osteogenic differentiation of BMSCs in CS by regulating Wnt/β-catenin signaling, thus providing new insights into the aetiology of CS.
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Affiliation(s)
- Yang Zheng
- Zhejiang Chinese Medical University, Hangzhou, China; Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Panyang Shen
- Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengsha Tong
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Hangchao Li
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Conglin Ren
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Fengqing Wu
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Hanyu Li
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Huan Yang
- Department of Biochemistry, Zhejiang University School of Medicine, Hangzhou, China
| | - Bingbing Cai
- Department of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, China
| | - Weibin Du
- Department of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, China
| | - Xing Zhao
- Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Shasha Yao
- Department of Orthopedics Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Renfu Quan
- Zhejiang Chinese Medical University, Hangzhou, China; Department of Orthopedics, Xiaoshan Traditional Chinese Medical Hospital, Hangzhou, China; Research Institute of Orthopedics, The Affiliated Jiangnan Hospital of Zhejiang Chinese Medical University, Hangzhou, China.
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Wang W, Ou Z, Peng J, Wang N, Zhou Y. Bioinformatics-based analysis of potential candidates chromatin regulators for immune infiltration in osteoarthritis. BMC Musculoskelet Disord 2022; 23:1123. [PMID: 36550476 PMCID: PMC9783407 DOI: 10.1186/s12891-022-06098-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Through the bioinformatics analysis to screen out the potential chromatin regulators (CRs) under the immune infiltration of osteoarthritis (OA), thus providing some theoretical support for future studies of epigenetic mechanisms under OA immune infiltration. METHODS By integrating CRs and the OA gene expression matrix, we performed weighted gene co-expression network analysis (WGCNA), differential analysis, and further screened Hub genes by protein-protein interaction (PPI) analysis. Using the OA gene expression matrix, immune infiltration extraction and quantification were performed to analyze the correlations and differences between immune infiltrating cells and their functions. By virtue of these Hub genes, Hub gene association analysis was completed and their upstream miRNAs were predicted by the FunRich software. Moreover, a risk model was established to analyze the risk probability of associated CRs in OA, and the confidence of the results was validated by the validation dataset. RESULTS This research acquired a total of 32 overlapping genes, and 10 Hub genes were further identified. The strongest positive correlation between dendritic cells and mast cells and the strongest negative correlation between parainflammation and Type I IFN reponse. In the OA group DCs, iDCs, macrophages, MCs, APC co-inhibition, and CCR were significantly increased, whereas B cells, NK cells, Th2 cells, TIL, and T cell co-stimulation were significantly decreased. The risk model results revealed that BRD1 might be an independent risk factor for OA, and the validation dataset results are consistent with it. 60 upstream miRNAs of OA-related CRs were predicted by the FunRich software. CONCLUSION This study identified certain potential CRs and miRNAs that could regulate OA immunity, thus providing certain theoretical supports for future epigenetic mechanism studies on the immune infiltration of OA.
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Affiliation(s)
- Weiwei Wang
- Guilin Hospital of Traditional Chinese Medicine, Guilin, 541002 Guangxi China
| | - Zhixue Ou
- Guilin Hospital of Traditional Chinese Medicine, Guilin, 541002 Guangxi China
| | - Jianlan Peng
- grid.256609.e0000 0001 2254 5798Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine, Nanning, 530001 Guangxi China
| | - Ning Wang
- grid.511973.8The First Affiliated Hospital of Guangxi University of Traditional Chinese Medicine, Nanning, 530001 Guangxi China
| | - Yi Zhou
- grid.256609.e0000 0001 2254 5798Ruikang Hospital Affiliated to Guangxi University of Traditional Chinese Medicine, Nanning, 530001 Guangxi China
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Zhang LQ, Yang H, Liu JJ, Zhang LR, Hao YD, Guo JM, Lin H. Recognition of driver genes with potential prognostic implications in lung adenocarcinoma based on H3K79me2. Comput Struct Biotechnol J 2022; 20:5535-5546. [PMID: 36249560 PMCID: PMC9556929 DOI: 10.1016/j.csbj.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/01/2022] [Accepted: 10/02/2022] [Indexed: 11/21/2022] Open
Abstract
The efficacy of H3K79me2 on gene expression regulation is affirmed in LUAD. An open-source algorithm for identifying LUAD-related driver genes is presented. 12 H3K79me2-targeted driver genes with clinical values are verified by qPCR. The regions with obvious H3K79me2 signals changes on driver genes are pinpointed.
Lung adenocarcinoma is a malignancy with a low overall survival and a poor prognosis. Studies have shown that lung adenocarcinoma progression relates to locus-specific/global changes in histone modifications. To explore the relationship between histone modification and gene expression changes, we focused on 11 histone modifications and quantitatively analyzed their influences on gene expression. We found that, among the studied histone modifications, H3K79me2 displayed the greatest impact on gene expression regulation. Based on the Shannon entropy, 867 genes with differential H3K79me2 levels during tumorigenesis were identified. Enrichment analyses showed that these genes were involved in 16 common cancer pathways and 11 tumors and were target-regulated by trans-regulatory elements, such as Tp53 and WT1. Then, an open-source computational framework was presented (https://github.com/zlq-imu/Identification-of-potential-LUND-driver-genes). Twelve potential driver genes were extracted from the genes with differential H3K79me2 levels during tumorigenesis. The expression levels of these potential driver genes were significantly increased/decreased in tumor cells, as assayed by RT–qPCR. A risk score model comprising these driver genes was further constructed, and this model was strongly negatively associated with the overall survival of patients in different datasets. The proportional hazards assumption and outlier test indicated that this model could robustly distinguish patients with different survival rates. Immune analyses and responses to immunotherapeutic and chemotherapeutic agents showed that patients in the high and low-risk groups may have distinct tendencies for clinical selection. Finally, the regions with clear H3K79me2 signal changes on these driver genes were accurately identified. Our research may offer potential molecular biomarkers for lung adenocarcinoma treatment.
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Affiliation(s)
- Lu-Qiang Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China,Corresponding authors.
| | - Hao Yang
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital and Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot 010020, China
| | - Jun-Jie Liu
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Li-Rong Zhang
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Yu-Duo Hao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
| | - Jun-Mei Guo
- Department of Radiation Oncology, Inner Mongolia Cancer Hospital and Affiliated People's Hospital of Inner Mongolia Medical University, Hohhot 010020, China
| | - Hao Lin
- School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China,Corresponding authors.
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Sun S, Wang X, Ding L, Zhang Q, Li N, Sui X, Li C, Ju L, Zhao Q, Chen H, Ding R, Cao J. Association between preconceptional air pollution exposure and medical purposes for selective termination of pregnancy. ENVIRONMENTAL RESEARCH 2021; 202:111743. [PMID: 34331927 DOI: 10.1016/j.envres.2021.111743] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Exposure to air pollutants is associated with adverse pregnancy outcomes. But evidence on the effects of preconceptional air pollution exposure on the risk of termination of pregnancy (TOP) caused by pregnancy losses and congenital malformations is lacking. METHODS The distributed lag nonlinear model (DLNM) was used to evaluate the impact of short-term air pollutants exposure on the risk of TOP. Stratified analyses by age (<35 years old, ≥ 35 years old) and season (warm season, cold season) were further conducted. Relative risk (RR) and 95 % confidential interval (95 % CI) were calculated for per interquartile range (IQR) increment in air pollutants during the study period. RESULTS PM2.5, PM10, and O3 exposure were significantly associated with elevated risk of TOP. The risk of TOP was associated with PM2.5 exposure from lag11 to lag15 in the single-pollutant model, and the strongest association was observed at lag13 (RR = 1.021, 95%CI:1.002-1.040). PM10 exposure from lag10 to lag15 was associated with increased TOP risk, with the corresponding peak association being at lag13 (RR = 1.020, 95%CI: 1.004-1.037). For O3, the single-day lag association appeared to be statistically significant from lag26 to lag27, with the highest RR of TOP cases being at lag27 (RR = 1.044, 95%CI: 1.005-1.084). Similar results were observed for pregnancy losses (PL). However, no significantly association between air pollution exposure and the risk of congenital malformations (CM) was found in this study. Stratified analyses showed that pregnant women with more advanced ages were more susceptible to PM2.5, PM10, and O3 exposure. The effect of PM2.5 exposure was statistically significant in cold season subgroups. CONCLUSION The findings suggest that exposure to PM2.5, PM10, and O3 before pregnancy are associated with the risk of TOP in Lu'an, China, reflecting the significance of preconceptional environmental exposure in the development of adverse pregnancy outcomes.
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Affiliation(s)
- Shu Sun
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Xiaoyu Wang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China; Department of Obstetrics and Gynecology, Lu'an Hospital Affiliated to Anhui Medical University, 21 West Wanxi Road, Lu'an, China
| | - Liu Ding
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Qi Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Na Li
- Department of Oncology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xinmiao Sui
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Changlian Li
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Liangliang Ju
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China
| | - Qihong Zhao
- Department of Nutrition and Food Hygiene, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, 230032, China
| | - Hongbo Chen
- Department of Obstetrics and Gynecology, Maternal and Child Health Hospital Affiliated to Anhui Medical University, 15 Yimin Road, Hefei, China.
| | - Rui Ding
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.
| | - Jiyu Cao
- Department of Occupational Health and Environmental Health, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China; Department of Teaching Center for Preventive Medicine, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.
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10
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Liu G, Zhao H, Yan Z, Zhao S, Niu Y, Li X, Wang S, Yang Y, Liu S, Zhang TJ, Wu Z, Wu N. Whole-genome methylation analysis reveals novel epigenetic perturbations of congenital scoliosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:1281-1287. [PMID: 33717649 PMCID: PMC7907230 DOI: 10.1016/j.omtn.2021.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 02/05/2021] [Indexed: 11/24/2022]
Abstract
Congenital scoliosis (CS) is a congenital disease caused by malformations of vertebrae. Recent studies demonstrated that DNA modification could contribute to the pathogenesis of disease. This study aims to identify epigenetic perturbations that may contribute to the pathogenesis of CS. Four CS patients with hemivertebra were enrolled and underwent spine correction operations. DNA was extracted from the hemivertebrae and spinal process collected from the specimen during the hemivertebra resection. Genome-wide DNA methylation profiling was examined at base-pair resolution using whole-genome bisulfite sequencing (WGBS). We identified 343 genes with hyper-differentially methylated regions (DMRs) and 222 genes with hypo-DMRs, respectively. These genes were enriched in the mitogen-activated protein kinase (MAPK) signaling pathway, calcium signaling pathway, and axon guidance in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and were enriched in positive regulation of cell morphogenesis involved in differentiation, regulation of cell morphogenesis involved in differentiation, and regulation of neuron projection development in Biological Process of Gene Ontology (GO-BP) terms. Hyper-DMR-related genes, including IGHG1, IGHM, IGHG3, RNF213, and GSE1, and hypo DMR-related genes, including SORCS2, COL5A1, GRID1, RGS3, and ROBO2, may contribute to the pathogenesis of hemivertebra. The aberrant DNA methylation may be associated with the formation of hemivertebra and congenital scoliosis.
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Affiliation(s)
- Gang Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zihui Yan
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Sen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Key Laboratory of Big Data for Spinal Deformities, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China.,Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
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11
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Wiesel-Motiuk N, Assaraf YG. The key roles of the lysine acetyltransferases KAT6A and KAT6B in physiology and pathology. Drug Resist Updat 2020; 53:100729. [PMID: 33130515 DOI: 10.1016/j.drup.2020.100729] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Histone modifications and more specifically ε-lysine acylations are key epigenetic regulators that control chromatin structure and gene transcription, thereby impacting on various important cellular processes and phenotypes. Furthermore, lysine acetylation of many non-histone proteins is involved in key cellular processes including transcription, DNA damage repair, metabolism, cellular proliferation, mitosis, signal transduction, protein folding, and autophagy. Acetylation affects protein functions through multiple mechanisms including regulation of protein stability, enzymatic activity, subcellular localization, crosstalk with other post-translational modifications as well as regulation of protein-protein and protein-DNA interactions. The paralogous lysine acetyltransferases KAT6A and KAT6B which belong to the MYST family of acetyltransferases, were first discovered approximately 25 years ago. KAT6 acetyltransferases acylate both histone H3 and non-histone proteins. In this respect, KAT6 acetyltransferases play key roles in regulation of transcription, various developmental processes, maintenance of hematopoietic and neural stem cells, regulation of hematopoietic cell differentiation, cell cycle progression as well as mitosis. In the current review, we discuss the physiological functions of the acetyltransferases KAT6A and KAT6B as well as their functions under pathological conditions of aberrant expression, leading to several developmental syndromes and cancer. Importantly, both upregulation and downregulation of KAT6 proteins was shown to play a role in cancer formation, progression, and therapy resistance, suggesting that they can act as oncogenes or tumor suppressors. We also describe reciprocal regulation of expression between KAT6 proteins and several microRNAs as well as their involvement in cancer formation, progression and resistance to therapy.
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Affiliation(s)
- Naama Wiesel-Motiuk
- The Fred Wyszkowski Cancer Research Laboratory, Dept. of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Dept. of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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