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Yu AQ, Wang J, Jiang ST, Yuan LQ, Ma HY, Hu YM, Han XM, Tan LM, Wang ZX. SIRT7-Induced PHF5A Decrotonylation Regulates Aging Progress Through Alternative Splicing-Mediated Downregulation of CDK2. Front Cell Dev Biol 2021; 9:710479. [PMID: 34604215 PMCID: PMC8484718 DOI: 10.3389/fcell.2021.710479] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022] Open
Abstract
Dysregulation of protein posttranslational modification (PTM) can lead to a variety of pathological processes, such as abnormal sperm development, malignant tumorigenesis, depression, and aging process. SIRT7 is a NAD+-dependent protein deacetylase. Besides known deacetylation, SIRT7 may also have the capacity to remove other acylation. However, the roles of SIRT7-induced other deacylation in aging are still largely unknown. Here, we found that the expression of SIRT7 was significantly increased in senescent fibroblasts and aged tissues. Knockdown or overexpression of SIRT7 can inhibit or promote fibroblast senescence. Knockdown of SIRT7 led to increased pan-lysine crotonylation (Kcr) levels in senescent fibroblasts. Using modern mass spectrometry (MS) technology, we identified 5,149 Kcr sites across 1,541 proteins in senescent fibroblasts, and providing the largest crotonylome dataset to date in senescent cells. Specifically, among the identified proteins, we found SIRT7 decrotonylated PHF5A, an alternative splicing (AS) factor, at K25. Decrotonylation of PHF5A K25 contributed to decreased CDK2 expression by retained intron (RI)-induced abnormal AS, thereby accelerating fibroblast senescence, and supporting a key role of PHF5A K25 decrotonylation in aging. Collectively, our data revealed the molecular mechanism of SIRT7-induced k25 decrotonylation of PHF5A regulating aging and provide new ideas and molecular targets for drug intervention in cellular aging and the treatment of aging-related diseases, and indicating that protein crotonylation has important implications in the regulation of aging progress.
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Affiliation(s)
- Ai Qing Yu
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Jie Wang
- Department of Cardiology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Shi Tao Jiang
- Department of Nuclear Medicine, The First Affiliated Hospital of Zhengzhou University, Zhenzhou, China
| | - Li Qun Yuan
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Hai Yan Ma
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Yi Min Hu
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Xing Min Han
- Department of Nuclear Medicine, The First Affiliated Hospital of Zhengzhou University, Zhenzhou, China
| | - Li Ming Tan
- Department of Clinical Laboratory, Hunan Provincial People's Hospital (The First-Affiliated Hospital of Hunan Normal University), Changsha, China
| | - Zhi Xiao Wang
- Department of Cardiology, The Fifth Affiliated Hospital of Zunyi Medical University, Zhuhai, China
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52
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Zhang KL, Zhou JL, Yang JF, Zhao YZ, Das D, Hao GF, Wu C, Zhang J, Zhu FY, Chen MX, Zhou SM. Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes. Front Mol Biosci 2021; 8:696319. [PMID: 34568424 PMCID: PMC8458698 DOI: 10.3389/fmolb.2021.696319] [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: 04/16/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022] Open
Abstract
As a pivotal regulator of 5’ splice site recognition, U1 small nuclear ribonucleoprotein (U1 snRNP)-specific protein C (U1C) regulates pre-mRNA splicing by interacting with other components of the U1 snRNP complex. Previous studies have shown that U1 snRNP and its components are linked to a variety of diseases, including cancer. However, the phylogenetic relationships and expression profiles of U1C have not been studied systematically. To this end, we identified a total of 110 animal U1C genes and compared them to homologues from yeast and plants. Bioinformatics analysis shows that the structure and function of U1C proteins is relatively conserved and is found in multiple copies in a few members of the U1C gene family. Furthermore, the expression patterns reveal that U1Cs have potential roles in cancer progression and human development. In summary, our study presents a comprehensive overview of the animal U1C gene family, which can provide fundamental data and potential cues for further research in deciphering the molecular function of this splicing regulator.
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Affiliation(s)
- Kai-Lu Zhang
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China.,Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.,State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Jian-Li Zhou
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China
| | - Yu-Zhen Zhao
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, China
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Jiangsu, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shao-Ming Zhou
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
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53
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Alternative splicing of mRNA in colorectal cancer: new strategies for tumor diagnosis and treatment. Cell Death Dis 2021; 12:752. [PMID: 34330892 PMCID: PMC8324868 DOI: 10.1038/s41419-021-04031-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) is an important event that contributes to posttranscriptional gene regulation. This process leads to several mature transcript variants with diverse physiological functions. Indeed, disruption of various aspects of this multistep process, such as cis- or trans- factor alteration, promotes the progression of colorectal cancer. Therefore, targeting some specific processes of AS may be an effective therapeutic strategy for treating cancer. Here, we provide an overview of the AS events related to colorectal cancer based on research done in the past 5 years. We focus on the mechanisms and functions of variant products of AS that are relevant to malignant hallmarks, with an emphasis on variants with clinical significance. In addition, novel strategies for exploiting the therapeutic value of AS events are discussed.
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54
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Begum NA, Haque F, Stanlie A, Husain A, Mondal S, Nakata M, Taniguchi T, Taniguchi H, Honjo T. Phf5a regulates DNA repair in class switch recombination via p400 and histone H2A variant deposition. EMBO J 2021; 40:e106393. [PMID: 33938017 PMCID: PMC8204862 DOI: 10.15252/embj.2020106393] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 03/15/2021] [Accepted: 03/22/2021] [Indexed: 11/09/2022] Open
Abstract
Antibody class switch recombination (CSR) is a locus-specific genomic rearrangement mediated by switch (S) region transcription, activation-induced cytidine deaminase (AID)-induced DNA breaks, and their resolution by non-homologous end joining (NHEJ)-mediated DNA repair. Due to the complex nature of the recombination process, numerous cofactors are intimately involved, making it important to identify rate-limiting factors that impact on DNA breaking and/or repair. Using an siRNA-based loss-of-function screen of genes predicted to encode PHD zinc-finger-motif proteins, we identify the splicing factor Phf5a/Sf3b14b as a novel modulator of the DNA repair step of CSR. Loss of Phf5a severely impairs AID-induced recombination, but does not perturb DNA breaks and somatic hypermutation. Phf5a regulates NHEJ-dependent DNA repair by preserving chromatin integrity to elicit optimal DNA damage response and subsequent recruitment of NHEJ factors at the S region. Phf5a stabilizes the p400 histone chaperone complex at the locus, which in turn promotes deposition of H2A variant such as H2AX and H2A.Z that are critical for the early DNA damage response and NHEJ, respectively. Depletion of Phf5a or p400 blocks the repair of both AID- and I-SceI-induced DNA double-strand breaks, supporting an important contribution of this axis to programmed as well as aberrant recombination.
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Affiliation(s)
- Nasim A Begum
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Farazul Haque
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Andre Stanlie
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- BioMedicine DesignPfizer Inc.CambridgeMAUSA
| | - Afzal Husain
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of BiochemistryFaculty of Life SciencesAligarh Muslim UniversityAligarhIndia
| | - Samiran Mondal
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
- Department of ChemistryRammohan CollegeKolkataIndia
| | - Mikiyo Nakata
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
| | - Takako Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Hisaaki Taniguchi
- Division of Disease ProteomicsInstitute for Enzyme ResearchUniversity of TokushimaTokushimaJapan
| | - Tasuku Honjo
- Department of Immunology and Genomic MedicineGraduate School of MedicineKyoto UniversityKyotoJapan
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55
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Wang Y, Wang J, Yang L, Qiu L, Hua Y, Wu S, Zeng S, Yu L, Zheng X. Epigenetic regulation of intestinal peptide transporter PEPT1 as a potential strategy for colorectal cancer sensitization. Cell Death Dis 2021; 12:532. [PMID: 34031358 PMCID: PMC8144210 DOI: 10.1038/s41419-021-03814-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022]
Abstract
Human intestinal peptide transporter PEPT1 is commonly repressed in human colorectal cancer (CRC), yet its relationship with sensitivity to the common CRC treatment ubenimex has not previously been elucidated. In this study, we confirmed PEPT1 suppression in CRC using real-time quantitative polymerase chain reaction and western blotting and then investigated the underlying epigenetic pathways involved using bisulfite sequencing, chromatin immunoprecipitation, siRNA knockdown, and reporter gene assays. We found that PEPT1 transcriptional repression was due to both DNMT1-mediated DNA methylation of the proximal promoter region and HDAC1-mediated histone deacetylation, which blocked P300-mediated H3K18/27Ac at the PEPT1 distal promoter. Finally, the effects of the epigenetic activation of PEPT1 on the CRC response to ubenimex were evaluated using sequential combination therapy of decitabine and ubenimex both in vitro and in xenografts. In conclusion, epigenetic silencing of PEPT1 due to increased DNMT1 and HDAC1 expression plays a vital role in the poor response of CRC to ubenimex.
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Affiliation(s)
- Yanhong Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jiaqi Wang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Lingrong Yang
- Department of Pharmacy, Hangzhou Cancer Hospital, 310002, Hangzhou, China
| | - Liqing Qiu
- Department of Pharmacy, Hangzhou Cancer Hospital, 310002, Hangzhou, China
| | - Yuhui Hua
- Department of Pharmacy, Hangzhou Cancer Hospital, 310002, Hangzhou, China
| | - Shixiu Wu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 518116, Shenzhen, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China.
| | - Xiaoli Zheng
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 518116, Shenzhen, China.
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56
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Sterling J, Menezes SV, Abbassi RH, Munoz L. Histone lysine demethylases and their functions in cancer. Int J Cancer 2021; 148:2375-2388. [PMID: 33128779 DOI: 10.1002/ijc.33375] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022]
Abstract
Histone lysine demethylases (KDMs) are enzymes that remove the methylation marks on lysines in nucleosomes' histone tails. These changes in methylation marks regulate gene transcription during both development and malignant transformation. Depending on which lysine residue is targeted, the effect of a given KDM on gene transcription can be either activating or repressing, and KDMs can regulate the expression of both oncogenes and tumour suppressors. Thus, the functions of KDMs can be regarded as both oncogenic and tumour suppressive, contingent on cell context and the enzyme isoform. Finally, KDMs also demethylate nonhistone proteins and have a variety of demethylase-independent functions. These epigenetic and other mechanisms that KDMs control make them important regulators of malignant tumours. Here, we present an overview of eight KDM subfamilies, their most-studied lysine targets and selected recent data on their roles in cancer stem cells, tumour aggressiveness and drug tolerance.
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Affiliation(s)
- Jayden Sterling
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sharleen V Menezes
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Ramzi H Abbassi
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Lenka Munoz
- School of Medical Sciences and Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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57
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Acetylation of ELF5 suppresses breast cancer progression by promoting its degradation and targeting CCND1. NPJ Precis Oncol 2021; 5:20. [PMID: 33742100 PMCID: PMC7979705 DOI: 10.1038/s41698-021-00158-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
E74-like ETS transcription factor 5 (ELF5) is involved in a wide spectrum of biological processes, e.g., mammogenesis and tumor progression. We have identified a list of p300-interacting proteins in human breast cancer cells. Among these, ELF5 was found to interact with p300 via acetylation, and the potential acetylation sites were identified as K130, K134, K143, K197, K228, and K245. Furthermore, an ELF5-specific deacetylase, SIRT6, was also identified. Acetylation of ELF5 promoted its ubiquitination and degradation, but was also essential for its antiproliferative effect against breast cancer, as overexpression of wild-type ELF5 and sustained acetylation-mimicking ELF5 mutant could inhibit the expression of its target gene CCND1. Taken together, the results demonstrated a novel regulation of ELF5 as well as shedding light on its important role in modulation of breast cancer progression.
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58
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Wang B, Farooq Z, Chu L, Liu J, Wang H, Guo J, Tu J, Ma C, Dai C, Wen J, Shen J, Fu T, Yi B. High-generation near-isogenic lines combined with multi-omics to study the mechanism of polima cytoplasmic male sterility. BMC PLANT BIOLOGY 2021; 21:130. [PMID: 33673810 PMCID: PMC7934456 DOI: 10.1186/s12870-021-02852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/24/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Cytoplasmic male sterility (CMS), which naturally exists in higher plants, is a useful mechanism for analyzing nuclear and mitochondrial genome functions and identifying the role of mitochondrial genes in the plant growth and development. Polima (pol) CMS is the most universally valued male sterility type in oil-seed rape. Previous studies have described the pol CMS restorer gene Rfp and the sterility-inducing gene orf224 in oil-seed rape, located in mitochondria. However, the mechanism of fertility restoration and infertility remains unknown. Moreover, it is still unknown how the fecundity restorer gene interferes with the sterility gene, provokes the sterility gene to lose its function, and leads to fertility restoration. RESULT In this study, we used multi-omics joint analysis to discover candidate genes that interact with the sterility gene orf224 and the restorer gene Rfp of pol CMS to provide theoretical support for the occurrence and restoration mechanisms of sterility. Via multi-omics analysis, we screened 24 differential genes encoding proteins related to RNA editing, respiratory electron transport chain, anther development, energy transport, tapetum development, and oxidative phosphorylation. Using a yeast two-hybrid assay, we obtained a total of seven Rfp interaction proteins, with orf224 protein covering five interaction proteins. CONCLUSIONS We propose that Rfp and its interacting protein cleave the transcript of atp6/orf224, causing the infertility gene to lose its function and restore fertility. When Rfp is not cleaved, orf224 poisons the tapetum cells and anther development-related proteins, resulting in pol CMS mitochondrial dysfunction and male infertility. The data from the joint analysis of multiple omics provided information on pol CMS's potential molecular mechanism and will help breed B. napus hybrids.
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Affiliation(s)
- Benqi Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Chu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huadong Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jian Guo
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jin Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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Lasconi C, Pahl MC, Cousminer DL, Doege CA, Chesi A, Hodge KM, Leonard ME, Lu S, Johnson ME, Su C, Hammond RK, Pippin JA, Terry NA, Ghanem LR, Leibel RL, Wells AD, Grant SFA. Variant-to-Gene-Mapping Analyses Reveal a Role for the Hypothalamus in Genetic Susceptibility to Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2020; 11:667-682. [PMID: 33069917 PMCID: PMC7843407 DOI: 10.1016/j.jcmgh.2020.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) is a polygenic disorder characterized principally by dysregulated inflammation impacting the gastrointestinal tract. However, there also is increasing evidence for a clinical association with stress and depression. Given the role of the hypothalamus in stress responses and in the pathogenesis of depression, useful insights could be gleaned from understanding its genetic role in IBD. METHODS We conducted genetic correlation analyses on publicly available genome-wide association study summary statistics for depression and IBD traits to identify genetic commonalities. We used partitioned linkage disequilibrium score regression, leveraging our ATAC sequencing and promoter-focused Capture C data, to measure enrichment of IBD single-nucleotide polymorphisms within promoter-interacting open chromatin regions of human embryonic stem cell-derived hypothalamic-like neurons (HNs). Using the same data sets, we performed variant-to-gene mapping to implicate putative IBD effector genes in HNs. To contrast these results, we similarly analyzed 3-dimensional genomic data generated in epithelium-derived colonoids from rectal biopsy specimens from donors without pathologic disease noted at the time of colonoscopy. Finally, we conducted enrichment pathway analyses on the implicated genes to identify putative IBD dysfunctional pathways. RESULTS We found significant genetic correlations (rg) of 0.122 with an adjusted P (Padj) = 1.4 × 10-4 for IBD: rg = 0.122; Padj = 2.5 × 10-3 for ulcerative colitis and genetic correlation (rg) = 0.094; Padj = 2.5 × 10-3 for Crohn's disease, and significant approximately 4-fold (P = .005) and approximately 7-fold (P = .03) enrichment of IBD single-nucleotide polymorphisms in HNs and colonoids, respectively. We implicated 25 associated genes in HNs, among which CREM, CNTF, and RHOA encode key regulators of stress. Seven genes also additionally were implicated in the colonoids. We observed an overall enrichment for immune and hormonal signaling pathways, and a colonoid-specific enrichment for microbiota-relevant terms. CONCLUSIONS Our results suggest that the hypothalamus warrants further study in the context of IBD pathogenesis.
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Affiliation(s)
- Chiara Lasconi
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Matthew C Pahl
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Diana L Cousminer
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Claudia A Doege
- Division of Molecular Genetics (Pediatrics), Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York
| | - Alessandra Chesi
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Kenyaita M Hodge
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Michelle E Leonard
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Sumei Lu
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Matthew E Johnson
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Chun Su
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - Reza K Hammond
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | - James A Pippin
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania
| | | | | | - Rudolph L Leibel
- Division of Molecular Genetics (Pediatrics), Naomi Berrie Diabetes Center, Columbia University Vagelos College of Physicians and Surgeons, New York, New York
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Department of Pathology, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania
| | - Struan F A Grant
- Center for Spatial and Functional Genomics, Philadelphia, Pennsylvania; Division of Human Genetics, Philadelphia, Pennsylvania; Division of Diabetes and Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
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60
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The role of histone methylation in the development of digestive cancers: a potential direction for cancer management. Signal Transduct Target Ther 2020; 5:143. [PMID: 32747629 PMCID: PMC7398912 DOI: 10.1038/s41392-020-00252-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/22/2020] [Accepted: 07/15/2020] [Indexed: 02/08/2023] Open
Abstract
Digestive cancers are the leading cause of cancer-related death worldwide and have high risks of morbidity and mortality. Histone methylation, which is mediated mainly by lysine methyltransferases, lysine demethylases, and protein arginine methyltransferases, has emerged as an essential mechanism regulating pathological processes in digestive cancers. Under certain conditions, aberrant expression of these modifiers leads to abnormal histone methylation or demethylation in the corresponding cancer-related genes, which contributes to different processes and phenotypes, such as carcinogenesis, proliferation, metabolic reprogramming, epithelial–mesenchymal transition, invasion, and migration, during digestive cancer development. In this review, we focus on the association between histone methylation regulation and the development of digestive cancers, including gastric cancer, liver cancer, pancreatic cancer, and colorectal cancer, as well as on its clinical application prospects, aiming to provide a new perspective on the management of digestive cancers.
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61
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Xu S, Fan L, Jeon HY, Zhang F, Cui X, Mickle MB, Peng G, Hussain A, Fazli L, Gleave ME, Dong X, Qi J. p300-Mediated Acetylation of Histone Demethylase JMJD1A Prevents Its Degradation by Ubiquitin Ligase STUB1 and Enhances Its Activity in Prostate Cancer. Cancer Res 2020; 80:3074-3087. [PMID: 32522824 DOI: 10.1158/0008-5472.can-20-0233] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/05/2020] [Accepted: 06/04/2020] [Indexed: 01/24/2023]
Abstract
The androgen receptor (AR) pathway plays a central role in the development of castration-resistant prostate cancer (CRPC). The histone demethylase JMJD1A has been shown to regulate activities of AR and c-Myc transcription factors and promote prostate cancer progression. Here, we report that JMJD1A protein stability is controlled by the ubiquitin ligase STUB1. High levels of JMJD1A were strongly correlated with low STUB1 levels in human CRPC specimens. STUB1 inhibited AR activity, AR-V7 levels, and prostate cancer cell growth partly through degradation of JMJD1A. Furthermore, the acetyltransferase p300 acetylated JMJD1A at lysine (K) 421, a modification that recruits the BET family member BRD4 to block JMJD1A degradation and promote JMJD1A recruitment to AR targets. Increased levels of both total and K421-acetylated JMJD1A were observed in prostate cancer cells as they developed resistance to the AR antagonist enzalutamide. Treatment of prostate cancer cells with either p300 or BET inhibitors destabilized JMJD1A, and enzalutamide-resistant prostate cancer cells were more sensitive than parental cells to these inhibitors. Together, our findings identify a critical role for acetylation of JMJD1A in regulating JMJD1A stability and AR activity in CRPC. These newly identified mechanisms controlling JMJD1A protein stability provide potential druggable targets to encourage the development of additional therapies for advanced prostate cancer. SIGNIFICANCE: Identification of mechanisms regulating JMJD1A protein stability reveals new strategies to destabilize JMJD1A and concomitantly inhibit AR activities as potential prostate cancer therapy.
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Affiliation(s)
- Songhui Xu
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland
| | - Lingling Fan
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland
| | - Hee-Young Jeon
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland
| | - Fengbo Zhang
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland.,Department of Urology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xiaolu Cui
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland.,Department of Urology, First Hospital of China Medical University, Shenyang, China
| | - McKayla B Mickle
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland
| | - Guihong Peng
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland.,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland
| | - Arif Hussain
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland.,Baltimore VA Medical Center, Baltimore, Maryland
| | - Ladan Fazli
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jianfei Qi
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland. .,Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, Maryland
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62
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Yoo J, Jeon YH, Cho HY, Lee SW, Kim GW, Lee DH, Kwon SH. Advances in Histone Demethylase KDM3A as a Cancer Therapeutic Target. Cancers (Basel) 2020; 12:cancers12051098. [PMID: 32354028 PMCID: PMC7280979 DOI: 10.3390/cancers12051098] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Lysine-specific histone demethylase 3 (KDM3) subfamily proteins are H3K9me2/me1 histone demethylases that promote gene expression. The KDM3 subfamily primarily consists of four proteins (KDM3A−D). All four proteins contain the catalytic Jumonji C domain (JmjC) at their C-termini, but whether KDM3C has demethylase activity is under debate. In addition, KDM3 proteins contain a zinc-finger domain for DNA binding and an LXXLL motif for interacting with nuclear receptors. Of the KDM3 proteins, KDM3A is especially deregulated or overexpressed in multiple cancers, making it a potential cancer therapeutic target. However, no KDM3A-selective inhibitors have been identified to date because of the lack of structural information. Uncovering the distinct physiological and pathological functions of KDM3A and their structure will give insight into the development of novel selective inhibitors. In this review, we focus on recent studies highlighting the oncogenic functions of KDM3A in cancer. We also discuss existing KDM3A-related inhibitors and review their potential as therapeutic agents for overcoming cancer.
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Affiliation(s)
- Jung Yoo
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Yu Hyun Jeon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Ha Young Cho
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Sang Wu Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - Dong Hoon Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, Korea; (J.Y.); (Y.H.J.); (H.Y.C.); (S.W.L.); (G.W.K.); (D.H.L.)
- Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-32-749-4513
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63
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Sun C. The SF3b complex: splicing and beyond. Cell Mol Life Sci 2020; 77:3583-3595. [PMID: 32140746 PMCID: PMC7452928 DOI: 10.1007/s00018-020-03493-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022]
Abstract
The SF3b complex is an intrinsic component of the functional U2 small nuclear ribonucleoprotein (snRNP). As U2 snRNP enters nuclear pre-mRNA splicing, SF3b plays key roles in recognizing the branch point sequence (BPS) and facilitating spliceosome assembly and activation. Since the discovery of SF3b, substantial progress has been made in elucidating its molecular mechanism during splicing. In addition, numerous recent studies indicate that SF3b and its components are engaged in various molecular and cellular events that are beyond the canonical role in splicing. This review summarizes the current knowledge on the SF3b complex and highlights its multiple roles in splicing and beyond.
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Affiliation(s)
- Chengfu Sun
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500, China.
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64
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Tang DE, Dai Y, Fan LL, Geng XY, Fu DX, Jiang HW, Xu SH. Histone Demethylase JMJD1A Promotes Tumor Progression via Activating Snail in Prostate Cancer. Mol Cancer Res 2020; 18:698-708. [PMID: 32019811 DOI: 10.1158/1541-7786.mcr-19-0889] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/27/2019] [Accepted: 01/31/2020] [Indexed: 11/16/2022]
Abstract
The histone demethylase JMJD1A plays a key functional role in spermatogenesis, sex determination, stem cell renewal, and cancer via removing mono- and di-methyl groups from H3K9 to epigenetically control gene expression. However, its role in prostate cancer progression remains unclear. Here, we found JMJD1A was significantly elevated in prostate cancer tissue compared with matched normal tissue. Ectopic JMJD1A expression in prostate cancer cells promoted proliferation, migration, and invasion in vitro, and tumorigenesis in vivo; JMJD1A knockdown exhibited the opposite effects. Mechanically, we revealed that JMJD1A directly interacted with the Snail gene promoter and regulated its transcriptional activity, promoting prostate cancer progression both in vitro and in vivo. Furthermore, we found that JMJD1A transcriptionally activated Snail expression via H3K9me1 and H3K9me2 demethylation at its special promoter region. In summary, our studies reveal JMJD1A plays an important role in regulating proliferation and progression of prostate cancer cells though Snail, and thus highlight JMJD1A as potential therapeutic target for advanced prostate cancer. IMPLICATIONS: Our studies identify that JMJD1A promotes the proliferation and progression of prostate cancer cells through enabling Snail transcriptional activation, and thus highlight JMJD1A as potential therapeutic target for advanced prostate cancer.
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Affiliation(s)
- Dong-E Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong, P.R. China
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong, P.R. China
| | - Ling-Ling Fan
- Department of Biochemistry, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Xin-Yan Geng
- Department of Biochemistry, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - De-Xue Fu
- Department of Surgery, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
| | - Hao-Wu Jiang
- Department of Anesthesiology and Center for the Study of Itch, Washington University School of Medicine, St. Louis, Missouri
| | - Song-Hui Xu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People's Hospital, Shenzhen, Guangdong, P.R. China. .,Department of Biochemistry, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland
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