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Shin Y. Histone Tail Cleavage as a Mechanism for Epigenetic Regulation. Int J Mol Sci 2024; 25:10789. [PMID: 39409117 PMCID: PMC11477362 DOI: 10.3390/ijms251910789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 09/30/2024] [Indexed: 10/20/2024] Open
Abstract
Histones are essential for DNA packaging and undergo post-translational modifications that significantly influence gene regulation. Among these modifications, histone tail cleavage has recently garnered attention despite being less explored. Cleavage by various proteases impacts processes such as stem cell differentiation, aging, infection, and inflammation, though the mechanisms remain unclear. This review delves into recent insights on histone proteolytic cleavage and its epigenetic significance, highlighting how chromatin, which serves as a dynamic scaffold, responds to signals through histone modification, replacement, and ATP-dependent remodeling. Specifically, histone tail cleavage is linked to critical cellular processes such as granulocyte differentiation, viral infection, aging, yeast sporulation, and cancer development. Although the exact mechanisms connecting histone cleavage to gene expression are still emerging, it is clear that this process represents a novel epigenetic transcriptional mechanism intertwined with chromatin dynamics. This review explores known histone tail cleavage events, the proteolytic enzymes involved, their impact on gene expression, and future research directions in this evolving field.
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Affiliation(s)
- Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
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2
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Gawargi FI, Mishra PK. MMP9 drives ferroptosis by regulating GPX4 and iron signaling. iScience 2024; 27:110622. [PMID: 39252956 PMCID: PMC11382059 DOI: 10.1016/j.isci.2024.110622] [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: 12/12/2023] [Revised: 02/08/2024] [Accepted: 07/26/2024] [Indexed: 09/11/2024] Open
Abstract
Ferroptosis, defined by the suppression of glutathione peroxidase-4 (GPX4) and iron overload, is a distinctive form of regulated cell death. Our in-depth research identifies matrix metalloproteinase-9 (MMP9) as a critical modulator of ferroptosis through its influence on GPX4 and iron homeostasis. Employing an innovative MMP9 construct without collagenase activity, we reveal that active MMP9 interacts with GPX4 and glutathione reductase, reducing GPX4 expression and activity. Furthermore, MMP9 suppresses key transcription factors (SP1, CREB1, NRF2, FOXO3, and ATF4), alongside GPX1 and ferroptosis suppressor protein-1 (FSP1), thereby disrupting the cellular redox balance. MMP9 regulates iron metabolism by modulating iron import, storage, and export via a network of protein interactions. LC-MS/MS has identified 83 proteins that interact with MMP9 at subcellular levels, implicating them in ferroptosis regulation. Integrated pathway analysis (IPA) highlights MMP9's extensive influence on ferroptosis pathways, underscoring its potential as a therapeutic target in conditions with altered redox homeostasis and iron metabolism.
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Affiliation(s)
- Flobater I Gawargi
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Paras K Mishra
- Department of Cellular and Integrative Physiology, University of Nebraska Medical Center, Omaha, NE, USA
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3
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Jo A, Lim HS, Eun KM, Park JA, Hong SN, Kim DW. Neutrophil Extracellular Traps as a Biomarker in Refractory Non-Type 2 CRSwNP. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2024; 16:473-489. [PMID: 39363767 PMCID: PMC11450440 DOI: 10.4168/aair.2024.16.5.473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 06/06/2024] [Accepted: 06/11/2024] [Indexed: 10/05/2024]
Abstract
PURPOSE Chronic rhinosinusitis (CRS) is classified into type 2 (T2) and non-T2 inflammation. T2 CRS presents as a severe form, CRS with nasal polyps (CRSwNP), which often occurs with asthma as a comorbidity worldwide. Some cases of non-T2 CRS show nasal polyposis and refractoriness, mainly in Asian countries. However, its mechanism remains elusive. To investigate a biomarker for the refractoriness of non-T2 CRSwNP via RNA sequencing. METHODS RNA sequencing by using nasal polyps (NPs) and ethmoidal mucosa (EM) from CRS subjects and uncinate tissues from controls was performed, and differentially expressed genes (DEGs) were analyzed (cutoffs: expression change > 2-fold, P < 0.01). Immunofluorescence staining and enzyme-linked immunosorbent assay were performed. RESULTS We identified DEGs among T2-NP, non-T2-NP, T2-EM, non-T2-EM, and controls (NP vs. controls: 1,877 genes, EM vs. controls: 1,124 genes, T2-NP vs. controls: 1,790 genes, non-T2-NP vs. controls: 2,012 genes, T2-EM vs. controls: 740 genes, non-T2-EM vs. controls: 1,553 genes). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that neutrophil extracellular trap (NET) formation, systemic lupus erythematosus, and the phagosome were enriched in non-T2-NP vs. controls and non-T2-EM vs. controls. Immunofluorescence staining confirmed that NETs were elevated in non-T2-NP. Cytokine analysis demonstrated that NETs were significantly related to the refractoriness in non-T2-NPs. CONCLUSIONS This study demonstrated DEGs between T2 and non-T2 inflammation. These results suggest that NETs may contribute to the refractoriness in non-T2-NPs and have a promise as a therapeutic strategy for patients with refractory non-T2-NP.
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Affiliation(s)
- Ara Jo
- Department of Otorhinolaryngology-Head & Neck Surgery, Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
| | - Hee-Suk Lim
- Department of Otorhinolaryngology-Head & Neck Surgery, Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
| | - Kyoung Mi Eun
- Department of Otorhinolaryngology-Head & Neck Surgery, Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
| | - Jin-A Park
- Department of Otorhinolaryngology-Head & Neck Surgery, Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
| | - Seung-No Hong
- Department of Otorhinolaryngology-Head & Neck Surgery, Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea
| | - Dae Woo Kim
- Department of Otorhinolaryngology-Head & Neck Surgery, Boramae Medical Center, Seoul National University College of Medicine, Seoul, Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Korea.
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Zhang J, Liu H, Liu Y, Luo E, Liu S. Unlocking the potential of histone modification in regulating bone metabolism. Biochimie 2024:S0300-9084(24)00181-0. [PMID: 39154977 DOI: 10.1016/j.biochi.2024.08.004] [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: 05/23/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/20/2024]
Abstract
Bone metabolism plays a crucial role in maintaining normal bone tissue homeostasis and function. Imbalances between bone formation and resorption can lead to osteoporosis, osteoarthritis, and other bone diseases. The dynamic and complex process of bone remodeling is driven by various factors, including epigenetics. Histone modification, one of the most important and well-studied components of epigenetic regulation, has emerged as a promising area of research in bone metabolism. Different histone proteins and modification sites exert diverse effects on osteogenesis and osteoclastogenesis. In this review, we summarize recent progress in understanding histone modifications in bone metabolism, including specific modification sites and potential regulatory enzymes. Comprehensive knowledge of histone modifications in bone metabolism could reveal new therapeutic targets and treatment strategies for bone diseases.
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Affiliation(s)
- Jiayuan Zhang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Hanghang Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Yao Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - En Luo
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China
| | - Shibo Liu
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan, China.
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Shin Y, Kim S, Liang G, An W. MMP-9-dependent proteolysis of the histone H3 N-terminal tail: a critical epigenetic step in driving oncogenic transcription and colon tumorigenesis. Mol Oncol 2024; 18:2001-2019. [PMID: 38600695 PMCID: PMC11306514 DOI: 10.1002/1878-0261.13652] [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: 09/19/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024] Open
Abstract
Matrix metalloproteinase 9 (MMP-9) is a member of the MMP family and has been recently identified as a nuclear protease capable of clipping histone H3 N-terminal tails (H3NT). This MMP-9-dependent H3NT proteolysis is critical for establishing an active state of gene transcription during osteoclast differentiation and melanoma development. However, whether H3NT cleavage by MMP-9 plays a similar role in other cellular events has not been explored. Here, we dissect the functional contribution of MMP-9-dependent H3NT clipping to colonic tumorigenesis by using a combination of genome-wide transcriptome data, ChIP/ChIPac-qPCR, CRISPR/dCas9 gene-targeting system, and in vivo xenograft models. We show that MMP-9 is overexpressed in colon cancer cells and catalyzes H3NT proteolysis to drive transcriptional activation of growth stimulatory genes. Our studies using knockdown and inhibition approaches clearly indicate that MMP-9 mediates transcriptional activation and promotes colonic tumorigenesis in a manner dependent on its protease activity toward H3NT. Remarkably, artificial H3NT proteolysis at target gene promoters with dCAS9-MMP-9 is sufficient for establishing their transcriptional competence in colon cancer cells, underscoring the importance of MMP-9-dependent H3NT proteolysis per se in the transactivation process. Our data establish new functions and mechanisms for MMP-9 in driving the oncogenic transcription program in colon cancer through H3NT proteolysis, and demonstrate how this epigenetic pathway can be exploited as a potential therapeutic target for cancer treatment.
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Affiliation(s)
- Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Sungmin Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
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Saeed NM, Ramadan LA, El-Sabbagh WA, Said MA, Abdel-Rahman HM, Mekky RH. Exploring the anti-osteoporosis potential of Petroselinum crispum (Mill.) Fuss extract employing experimentally ovariectomized rat model and network pharmacology approach. Fitoterapia 2024; 175:105971. [PMID: 38663562 DOI: 10.1016/j.fitote.2024.105971] [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: 10/26/2023] [Revised: 03/11/2024] [Accepted: 04/21/2024] [Indexed: 04/30/2024]
Abstract
One of the most prevalent secondary osteoporosis is ovariectomy-induced osteoporosis. Parsley (Petroselinum crispum) has potent estrogenic and antioxidant properties and was used traditionally in the treatment of amenorrhea and dysmenorrhea. The present study aimed to characterize parsley leaf extract (PLE) employing RP-HPLC-MS-MS/MS-based method and possible protective effect in ovariectomized (OVX)-induced osteoporosis in rats was assessed. Rats were randomly assigned into SHAM group, OVX group, PLE + OVX group (150 mg/kg/day, p.o), and estradiol benzoate (E2) + OVX group (30 μg/kg/day, s.c). After eight weeks following ovariectomy, biomarkers of bone strength, bone resorption, oxidative stress and histopathology were carried out. A network pharmacology approach investigated the key targets and potential mechanisms by of PLE metabolites against osteoporosis using databases: PubChem, BindingDB server, DisGeNET, ShinyGO, and KEGG Pathway. Moreover, FunRich 3.1.3, Cytoscape 3.10.0, and MOE 2019.0102 softwares were used for network pharmacology analysis and molecular docking studies. Flavones and hydroxycinnamic acid derivatives were predominant among 38 metabolites in PLE. It significantly restored bone strength and bone resorption biomarkers, osteocalcin (OST), oxidative stress biomarkers and histopathological alterations. The employed network pharmacology approach revealed that 14 primary target genes were associated with decreasing the severity of osteoporosis. Molecular docking revealed that cGMP-PKG signaling pathway has the highest fold enrichment and its downstream PDE5A. Luteolin, diosmetin, and isorhamnetin derivatives affected mostly osteoporosis targets. PLE exhibited protective action against ovariectomy-induced osteoporosis in rats and may be a promising therapy for premenopausal bone loss. cGMP-PKG signaling pathway could be a promising target for PLE in treating osteoporosis.
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Affiliation(s)
- Noha M Saeed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo-Suez Road, 11829 Cairo, Egypt.
| | - Laila A Ramadan
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo-Suez Road, 11829 Cairo, Egypt
| | - Walaa A El-Sabbagh
- Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), 11787 Cairo, Egypt
| | - Mohamed A Said
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo 11829, Egypt
| | - Hanaa M Abdel-Rahman
- Department of Pharmacy Practice, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt; Department of Forensic Medicine and Toxicology, Faculty of Medicine, Ain Shams University, Cairo 11562, Egypt
| | - Reham Hassan Mekky
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Badr City, Cairo-Suez Road, 11829, Cairo, Egypt..
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AlZahrani S, Shinwari Z, Alaiya A, Al-Kahtani A. Impact of Resolvin-E1 and Maresin-1 on Bone Marrow Stem Cell Osteogenesis under Inflammatory Stress. Cells 2024; 13:932. [PMID: 38891064 PMCID: PMC11171860 DOI: 10.3390/cells13110932] [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: 04/19/2024] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Periodontal disease is characterized by inflammation and bone loss. Central to its pathogenesis is the dysregulated inflammatory response, complicating regenerative therapies. Mesenchymal stem cells (MSCs) hold significant promise in tissue repair and regeneration. This study investigated the effects of specialized pro-resolving mediators (SPMs), Resolvin E1 (RvE1) and Maresin 1 (MaR1), on the osteogenic differentiation of human bone marrow-derived MSCs under inflammatory conditions. The stem cells were treated with SPMs in the presence of lipopolysaccharide (LPS) to simulate an inflammatory environment. Osteogenic differentiation was assessed through alkaline phosphatase activity and alizarin red staining. Proteomic analysis was conducted to characterize the protein expression profile changes, focusing on proteins related to osteogenesis and osteoclastogenesis. Treatment with RvE1 and MaR1, both individually and in combination, significantly enhanced calcified deposit formation. Proteomic analysis revealed the differential expression of proteins associated with osteogenesis and osteoclastogenesis, highlighting the modulatory impact of SPMs on bone metabolism. RvE1 and MaR1 promote osteogenic differentiation of hBMMSCs in an inflammatory environment, with their combined application yielding synergistic effects. This study provides insights into the therapeutic potential of SPMs in enhancing bone regeneration, suggesting a promising avenue for developing regenerative therapies for periodontal disease and other conditions characterized by inflammation-induced bone loss.
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Affiliation(s)
- Shahd AlZahrani
- Department of Restorative Dental Sciences, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11612, Saudi Arabia;
| | - Zakia Shinwari
- Therapeutics & Biomarker Discovery for Clinical Applications, Cell Therapy & Immunobiology Department, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (Z.S.); (A.A.)
| | - Ayodele Alaiya
- Therapeutics & Biomarker Discovery for Clinical Applications, Cell Therapy & Immunobiology Department, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, Riyadh 11211, Saudi Arabia; (Z.S.); (A.A.)
| | - Ahmed Al-Kahtani
- Department of Restorative Dental Sciences, College of Dentistry, King Saud University, P.O. Box 60169, Riyadh 11612, Saudi Arabia;
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Caviness PC, Lazarenko OP, Blackburn ML, Chen JF, Randolph CE, Zabaleta J, Zhan F, Chen JR. Phenolic acids prevent sex-steroid deficiency-induced bone loss and bone marrow adipogenesis in mice. J Nutr Biochem 2024; 127:109601. [PMID: 38367948 DOI: 10.1016/j.jnutbio.2024.109601] [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: 09/20/2023] [Revised: 01/19/2024] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Phenolic acids, such as hippuric acid (HA) and 3-(3-hydroxyphenyl) propionic acid (3-3-PPA), can be produced from microbiome digestion of polyphenols. Previously it was found that HA and 3-3-PPA facilitate bone formation and suppress bone resorption. However, the mechanism of action by which HA and 3-3-PPA protect bone from degeneration is currently unknown. In this report, we present that HA and 3-3-PPA suppression of bone resorption is able to ameliorate bone loss in an ovariectomy (OVX) osteopenic mouse model though not to the extent of Zoledronic acid (ZA). HA and 3-3-PPA treatments were shown to significantly decrease bone marrow adipocyte-like cell formation and inhibited gene expression of key adipogenesis regulator peroxisome proliferator activated receptor gamma (PPARγ) and lipoprotein lipase (Lpl) in bone from OVX mice. In addition, ChIP experiments showed that the association between PPARγ and Lpl promoter region in preadipocyte-like cells was significantly suppressed following HA or 3-3-PPA treatment. Contrasting HA and 3-3-PPA, ZA significantly increased TRAP activity in the area close to growth plate and significantly suppressed bone cell proliferation. These data suggest that phenolics acids such as HA or 3-3-PPA may prevent bone degeneration after OVX through suppression of inflammatory milieu in the bone.
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Affiliation(s)
- Perry C Caviness
- Arkansas Children's Nutrition Center, Little Rock, Arkansas 72205, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Oxana P Lazarenko
- Arkansas Children's Nutrition Center, Little Rock, Arkansas 72205, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Michael L Blackburn
- Arkansas Children's Nutrition Center, Little Rock, Arkansas 72205, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
| | - Jennifer F Chen
- Undergraduate Pre-Medical Program, University of Arkansas at Fayetteville, Fayetteville, Arkansas 72701, USA
| | - Christopher E Randolph
- Center for Translational Pediatric Research, Arkansas Children's Research Institute, Little Rock, Arkansas 72202, USA
| | - Jovanny Zabaleta
- Department of Interdisciplinary Oncology, Louisiana State University Health Sciences Center, New Orleans, Los Angeles 70112, USA
| | - Fenghuang Zhan
- Myeloma Center, Winthrop P. Rockefeller Cancer Institute, Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jin-Ran Chen
- Arkansas Children's Nutrition Center, Little Rock, Arkansas 72205, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA.
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Caloian CS, Ciurea A, Negucioiu M, Roman A, Micu IC, Picoș A, Soancă A. Systemic Impact of Subgingival Infection Control in Periodontitis Patients with Cardiovascular Disease: A Narrative Review. Antibiotics (Basel) 2024; 13:359. [PMID: 38667035 PMCID: PMC11047730 DOI: 10.3390/antibiotics13040359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
INTRODUCTION Periodontitis, an infectious inflammatory condition, is a key contributor to sustained systemic inflammation, intricately linked to atherosclerotic cardiovascular disease (CVD), the leading cause of death in developed nations. Treating periodontitis with subgingival mechanical instrumentation with or without adjunctive antimicrobials reduces the microbial burden and local inflammation, while also potentially bringing systemic benefits for patients with both periodontitis and CVD. This review examines systemic effects of subgingival instrumentation with or without antimicrobial products in individuals with periodontitis and CVD, and explores intricate pathogenetic interactions between periodontitis and CVD. MATERIAL AND METHODS English-language databases (PubMed MEDLINE and Cochrane Library) were searched for studies assessing the effects of nonsurgical periodontal therapies in periodontitis patients with or without CVD. RESULTS While the ability of periodontal therapy to reduce mortality- and morbidity-related outcomes in CVD patients with periodontitis remains uncertain, some studies indicate a decrease in inflammatory markers and blood cell counts. Subgingival mechanical instrumentation delivered over multiple short sessions carries lower risks of adverse effects, particularly systemic inflammation, compared to the full-mouth delivery, making it a preferable option for CVD patients. CONCLUSIONS Subgingival mechanical instrumentation, ideally conducted in a quadrant-based therapeutic approach, to decontaminate periodontal pockets has the potential to reduce both local and systemic inflammation with minimal adverse effects in patients suffering from periodontitis and concurrent CVD.
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Affiliation(s)
- Carmen Silvia Caloian
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hațieganu University of Medicine and Pharmacy Cluj-Napoca, Victor Babeș St., No. 15, 400012 Cluj-Napoca, Romania; (C.S.C.); (A.C.); (I.C.M.); (A.S.)
| | - Andreea Ciurea
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hațieganu University of Medicine and Pharmacy Cluj-Napoca, Victor Babeș St., No. 15, 400012 Cluj-Napoca, Romania; (C.S.C.); (A.C.); (I.C.M.); (A.S.)
| | - Marius Negucioiu
- Department of Prosthodontics, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, Clinicilor St., No. 32, 400006 Cluj-Napoca, Romania;
| | - Alexandra Roman
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hațieganu University of Medicine and Pharmacy Cluj-Napoca, Victor Babeș St., No. 15, 400012 Cluj-Napoca, Romania; (C.S.C.); (A.C.); (I.C.M.); (A.S.)
| | - Iulia Cristina Micu
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hațieganu University of Medicine and Pharmacy Cluj-Napoca, Victor Babeș St., No. 15, 400012 Cluj-Napoca, Romania; (C.S.C.); (A.C.); (I.C.M.); (A.S.)
| | - Andrei Picoș
- Department of Prevention in Dental Medicine, Faculty of Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy Cluj-Napoca, Avram Iancu St., No. 31, 400083 Cluj-Napoca, Romania
| | - Andrada Soancă
- Department of Periodontology, Faculty of Dental Medicine, Iuliu Hațieganu University of Medicine and Pharmacy Cluj-Napoca, Victor Babeș St., No. 15, 400012 Cluj-Napoca, Romania; (C.S.C.); (A.C.); (I.C.M.); (A.S.)
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10
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Yi SJ, Lim J, Kim K. Exploring epigenetic strategies for the treatment of osteoporosis. Mol Biol Rep 2024; 51:398. [PMID: 38453825 DOI: 10.1007/s11033-024-09353-4] [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: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
The worldwide trend toward an aging population has resulted in a higher incidence of chronic conditions, such as osteoporosis. Osteoporosis, a prevalent skeletal disorder characterized by decreased bone mass and increased fracture risk, encompasses primary and secondary forms, each with distinct etiologies. Mechanistically, osteoporosis involves an imbalance between bone resorption by osteoclasts and bone formation by osteoblasts. Current pharmacological interventions for osteoporosis, such as bisphosphonates, denosumab, and teriparatide, aim to modulate bone turnover and preserve bone density. Hormone replacement therapy and lifestyle modifications are also recommended to manage the condition. While current medications offer therapeutic options, they are not devoid of limitations. Recent studies have highlighted the importance of epigenetic mechanisms, including DNA methylation and histone modifications, in regulating gene expression during bone remodeling. The use of epigenetic drugs, or epidrugs, to target these mechanisms offers a promising avenue for therapeutic intervention in osteoporosis. In this review, we comprehensively examine the recent advancements in the application of epidrugs for treating osteoporosis.
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Affiliation(s)
- Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Jaeho Lim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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11
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Purohit JS, Singh M, Raghuvanshi Y, Syeda S, Chaturvedi MM. Evaluation of the Moonlighting Histone H3 Specific Protease (H3ase) Activity and the Dehydrogenase Activity of Glutamate Dehydrogenase (GDH). Cell Biochem Biophys 2024; 82:223-233. [PMID: 38040891 DOI: 10.1007/s12013-023-01201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/19/2023] [Indexed: 12/03/2023]
Abstract
The N-terminus of Histone H3 is proteolytically processed in aged chicken liver. A histone H3 N-terminus specific endopeptidase (named H3ase) has been purified from the nuclear extract of aged chicken liver. By sequencing and a series of biochemical methods including the demonstration of H3ase activity in bacterially expressed GDH, it was established that the H3ase activity was a moonlighting protease activity of glutamate dehydrogenase (GDH). However, the active site for the H3ase in the GDH remains elusive. Here, using cross-linking studies of the homogenously purified H3ase, we show that the GDH and the H3ase remain in the same native state. Further, the H3ase and GDH activities could be uncoupled by partial denaturation of GDH, suggesting strong evidence for the involvement of different active sites for GDH and H3ase activities. Through densitometry of the H3ase clipped H3 products, the H3ase activity was quantified and it was compared with the GDH activity of the chicken liver nuclear GDH. Furthermore, the H3ase mostly remained distributed in the perinuclear area as demonstrated by MNase digestion and immuno-localization of H3ase in chicken liver nuclei, as well as cultured mouse hepatocyte cells, suggesting that H3ase demonstrated regulated access to the chromatin. The present study thus broadly compares the H3ase and GDH activities of the chicken liver GDH.
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Affiliation(s)
- Jogeswar Satchidananda Purohit
- Cluster Innovation Centre, University of Delhi, 110007, Delhi, India.
- Department of Zoology, University of Delhi, 110007, Delhi, India.
| | - Madhulika Singh
- Department of Zoology, University of Delhi, 110007, Delhi, India
| | - Yashankita Raghuvanshi
- Cluster Innovation Centre, University of Delhi, 110007, Delhi, India
- Department of Zoology, University of Delhi, 110007, Delhi, India
| | - Saima Syeda
- Department of Zoology, University of Delhi, 110007, Delhi, India
| | - Madan M Chaturvedi
- Department of Zoology, University of Delhi, 110007, Delhi, India.
- SGT University, Gurugram (Delhi-NCR), Haryana, 122505, India.
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12
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Radzki D, Negri A, Kusiak A, Obuchowski M. Matrix Metalloproteinases in the Periodontium-Vital in Tissue Turnover and Unfortunate in Periodontitis. Int J Mol Sci 2024; 25:2763. [PMID: 38474009 DOI: 10.3390/ijms25052763] [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: 01/12/2024] [Revised: 02/24/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The extracellular matrix (ECM) is a complex non-cellular three-dimensional macromolecular network present within all tissues and organs, forming the foundation on which cells sit, and composed of proteins (such as collagen), glycosaminoglycans, proteoglycans, minerals, and water. The ECM provides a fundamental framework for the cellular constituents of tissue and biochemical support to surrounding cells. The ECM is a highly dynamic structure that is constantly being remodeled. Matrix metalloproteinases (MMPs) are among the most important proteolytic enzymes of the ECM and are capable of degrading all ECM molecules. MMPs play a relevant role in physiological as well as pathological processes; MMPs participate in embryogenesis, morphogenesis, wound healing, and tissue remodeling, and therefore, their impaired activity may result in several problems. MMP activity is also associated with chronic inflammation, tissue breakdown, fibrosis, and cancer invasion and metastasis. The periodontium is a unique anatomical site, composed of a variety of connective tissues, created by the ECM. During periodontitis, a chronic inflammation affecting the periodontium, increased presence and activity of MMPs is observed, resulting in irreversible losses of periodontal tissues. MMP expression and activity may be controlled in various ways, one of which is the inhibition of their activity by an endogenous group of tissue inhibitors of metalloproteinases (TIMPs), as well as reversion-inducing cysteine-rich protein with Kazal motifs (RECK).
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Affiliation(s)
- Dominik Radzki
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdańsk, 80-208 Gdańsk, Poland
- Division of Molecular Bacteriology, Institute of Medical Biotechnology and Experimental Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Alessandro Negri
- Division of Molecular Bacteriology, Institute of Medical Biotechnology and Experimental Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
| | - Aida Kusiak
- Department of Periodontology and Oral Mucosa Diseases, Faculty of Medicine, Medical University of Gdańsk, 80-208 Gdańsk, Poland
| | - Michał Obuchowski
- Division of Molecular Bacteriology, Institute of Medical Biotechnology and Experimental Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdańsk, 80-211 Gdańsk, Poland
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13
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Vo HVT, Nguyen YT, Kim N, Lee HJ. Vitamin A, D, E, and K as Matrix Metalloproteinase-2/9 Regulators That Affect Expression and Enzymatic Activity. Int J Mol Sci 2023; 24:17038. [PMID: 38069361 PMCID: PMC10707015 DOI: 10.3390/ijms242317038] [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: 10/30/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Fat-soluble vitamins (vitamin A, D, E, and K) assume a pivotal role in maintaining human homeostasis by virtue of their enzymatic functions. The daily inclusion of these vitamins is imperative to the upkeep of various physiological processes including vision, bone health, immunity, and protection against oxidative stress. Current research highlights fat-soluble vitamins as potential therapeutics for human diseases, especially cancer. Fat-soluble vitamins exert their therapeutic effects through multiple pathways, including regulation of matrix metalloproteinases' (MMPs) expression and enzymatic activity. As MMPs have been reported to be involved in the pathology of various diseases, such as cancers, cardiovascular diseases, and neurological disorders, regulating the expression and/or activity of MMPs could be considered as a potent therapeutic strategy. Here, we summarize the properties of fat-soluble vitamins and their potential as promising candidates capable of effectively modulating MMPs through multiple pathways to treat human diseases.
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Affiliation(s)
- Ha Vy Thi Vo
- Department of Chemistry Education, Kongju National University, Gongju 32588, Republic of Korea;
| | - Yen Thi Nguyen
- Department of Chemistry, Kongju National University, Gongju 32588, Republic of Korea;
| | - Namdoo Kim
- Department of Chemistry, Kongju National University, Gongju 32588, Republic of Korea;
| | - Hyuck Jin Lee
- Department of Chemistry Education, Kongju National University, Gongju 32588, Republic of Korea;
- Kongju National University Institute of Science Education, Kongju National University, Gongju 32588, Republic of Korea
- Kongju National University’s Physical Fitness for Health Research Lab (KNUPFHR), Kongju National University, Gongju 32588, Republic of Korea
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14
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Oishi T, Hatazawa S, Kujirai T, Kato J, Kobayashi Y, Ogasawara M, Akatsu M, Ehara H, Sekine SI, Hayashi G, Takizawa Y, Kurumizaka H. Contributions of histone tail clipping and acetylation in nucleosome transcription by RNA polymerase II. Nucleic Acids Res 2023; 51:10364-10374. [PMID: 37718728 PMCID: PMC10602921 DOI: 10.1093/nar/gkad754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/19/2023] Open
Abstract
The N-terminal tails of histones protrude from the nucleosome core and are target sites for histone modifications, such as acetylation and methylation. Histone acetylation is considered to enhance transcription in chromatin. However, the contribution of the histone N-terminal tail to the nucleosome transcription by RNA polymerase II (RNAPII) has not been clarified. In the present study, we reconstituted nucleosomes lacking the N-terminal tail of each histone, H2A, H2B, H3 or H4, and performed RNAPII transcription assays. We found that the N-terminal tail of H3, but not H2A, H2B and H4, functions in RNAPII pausing at the SHL(-5) position of the nucleosome. Consistently, the RNAPII transcription assay also revealed that the nucleosome containing N-terminally acetylated H3 drastically alleviates RNAPII pausing at the SHL(-5) position. In addition, the H3 acetylated nucleosome produced increased amounts of the run-off transcript. These results provide important evidence that the H3 N-terminal tail plays a role in RNAPII pausing at the SHL(-5) position of the nucleosome, and its acetylation directly alleviates this nucleosome barrier.
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Affiliation(s)
- Takumi Oishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Junko Kato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuki Kobayashi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mitsuo Ogasawara
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Munetaka Akatsu
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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15
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Yang H, Sui P, Guo Y, Chen S, Maloof ME, Ge G, Nihozeko F, Delma CR, Zhu G, Zhang P, Ye Z, Medina EA, Ayad NG, Mesa R, Nimer SD, Chiang C, Xu M, Chen Y, Yang F. Loss of BRD4 induces cell senescence in HSC/HPCs by deregulating histone H3 clipping. EMBO Rep 2023; 24:e57032. [PMID: 37650863 PMCID: PMC10561362 DOI: 10.15252/embr.202357032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/28/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
Bromodomain-containing protein 4 (BRD4) is overexpressed and functionally implicated in various myeloid malignancies. However, the role of BRD4 in normal hematopoiesis remains largely unknown. Here, utilizing an inducible Brd4 knockout mouse model, we find that deletion of Brd4 (Brd4Δ/Δ ) in the hematopoietic system impairs hematopoietic stem cell (HSC) self-renewal and differentiation, which associates with cell cycle arrest and senescence. ATAC-seq analysis shows increased chromatin accessibility in Brd4Δ/Δ hematopoietic stem/progenitor cells (HSC/HPCs). Genome-wide mapping with cleavage under target and release using nuclease (CUT&RUN) assays demonstrate that increased global enrichment of H3K122ac and H3K4me3 in Brd4Δ/Δ HSC/HPCs is associated with the upregulation of senescence-specific genes. Interestingly, Brd4 deletion increases clipped H3 (cH3) which correlates with the upregulation of senescence-specific genes and results in a higher frequency of senescent HSC/HPCs. Re-expression of BRD4 reduces cH3 levels and rescues the senescence rate in Brd4Δ/Δ HSC/HPCs. This study unveils an important role of BRD4 in HSC/HPC function by preventing H3 clipping and suppressing senescence gene expression.
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Affiliation(s)
- Hui Yang
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Pinpin Sui
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Ying Guo
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Shi Chen
- Department of Molecular MedicineUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Marie E Maloof
- Sylvester Comprehensive Cancer CenterUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Guo Ge
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Francine Nihozeko
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Caroline R Delma
- Department of Pathology and Laboratory Medicine, Division of HematopathologyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Ganqian Zhu
- Department of Molecular MedicineUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Peng Zhang
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Zhenqing Ye
- Department of Population Health SciencesUniversity of Texas Health San AntonioSan AntonioTXUSA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Edward A Medina
- Department of Pathology and Laboratory Medicine, Division of HematopathologyUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Nagi G Ayad
- Department of Oncology, Lombardi Comprehensive Cancer CenterGeorgetown UniversityWashingtonDCUSA
| | - Ruben Mesa
- Mays Cancer CenterUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer CenterUniversity of Miami Miller School of MedicineMiamiFLUSA
| | - Cheng‐Ming Chiang
- Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Mingjiang Xu
- Department of Molecular MedicineUniversity of Texas Health San AntonioSan AntonioTXUSA
- Mays Cancer CenterUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Yidong Chen
- Department of Population Health SciencesUniversity of Texas Health San AntonioSan AntonioTXUSA
- Greehey Children's Cancer Research InstituteUniversity of Texas Health San AntonioSan AntonioTXUSA
| | - Feng‐Chun Yang
- Department of Cell Systems and AnatomyUniversity of Texas Health San AntonioSan AntonioTXUSA
- Mays Cancer CenterUniversity of Texas Health San AntonioSan AntonioTXUSA
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16
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Shin Y, Kim S, Liang G, Ulmer TS, An W. VprBP/DCAF1 Triggers Melanomagenic Gene Silencing through Histone H2A Phosphorylation. Biomedicines 2023; 11:2552. [PMID: 37760992 PMCID: PMC10526264 DOI: 10.3390/biomedicines11092552] [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: 08/02/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Vpr binding protein (VprBP), also known as DDB1- and CUL4-associated factor1 (DCAF1), is a recently identified atypical kinase and plays an important role in downregulating the transcription of tumor suppressor genes as well as increasing the risk for colon and prostate cancers. Melanoma is the most aggressive form of skin cancer arising from pigment-producing melanocytes and is often associated with the dysregulation of epigenetic factors targeting histones. Here, we demonstrate that VprBP is highly expressed and phosphorylates threonine 120 (T120) on histone H2A to drive the transcriptional inactivation of growth-regulatory genes in melanoma cells. As is the case for its epigenetic function in other types of cancers, VprBP acts to induce a gene silencing program dependent on H2AT120 phosphorylation (H2AT120p). The significance of VprBP-mediated H2AT120p is further underscored by the fact that VprBP knockdown- or VprBP inhibitor-induced lockage of H2AT120p mitigates melanoma tumor growth in xenograft models. Collectively, our results establish VprBP-mediated H2AT120p as a key epigenetic signal for melanomagenesis and suggest the therapeutic potential of targeting VprBP kinase activity for effective melanoma treatment.
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Affiliation(s)
- Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; (Y.S.); (S.K.)
| | - Sungmin Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; (Y.S.); (S.K.)
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA;
| | - Tobias S. Ulmer
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA;
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA; (Y.S.); (S.K.)
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17
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Yi SJ, Jang YJ, Lee S, Cho SJ, Kang K, Park JI, Chae HJ, Kim HR, Kim K. TMBIM6 deficiency leads to bone loss by accelerating osteoclastogenesis. Redox Biol 2023; 64:102804. [PMID: 37399733 PMCID: PMC10336580 DOI: 10.1016/j.redox.2023.102804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/15/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023] Open
Abstract
TMBIM6 is an endoplasmic reticulum (ER) protein that modulates various physiological and pathological processes, including metabolism and cancer. However, its involvement in bone remodeling has not been investigated. In this study, we demonstrate that TMBIM6 serves as a crucial negative regulator of osteoclast differentiation, a process essential for bone remodeling. Our investigation of Tmbim6-knockout mice revealed an osteoporotic phenotype, and knockdown of Tmbim6 inhibited the formation of multinucleated tartrate-resistant acid phosphatase-positive cells, which are characteristic of osteoclasts. Transcriptome and immunoblot analyses uncovered that TMBIM6 exerts its inhibitory effect on osteoclastogenesis by scavenging reactive oxygen species and preventing p65 nuclear localization. Additionally, TMBIM6 depletion was found to promote p65 localization to osteoclast-related gene promoters. Notably, treatment with N-acetyl cysteine, an antioxidant, impeded the osteoclastogenesis induced by TMBIM6-depleted cells, supporting the role of TMBIM6 in redox regulation. Furthermore, we discovered that TMBIM6 controls redox regulation via NRF2 signaling pathways. Our findings establish TMBIM6 as a critical regulator of osteoclastogenesis and suggest its potential as a therapeutic target for the treatment of osteoporosis.
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Affiliation(s)
- Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - You-Jee Jang
- Department of Biomedical Laboratory Science, Honam University, Gwangju, Republic of Korea
| | - Seokchan Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sung-Jin Cho
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Kyuho Kang
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Jae-Il Park
- Korea Basic Science Institute, Gwangju Center at Chonnam National University, Gwangju, Republic of Korea
| | - Han-Jung Chae
- School of Pharmacy and New Drug Development Research Institute, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hyung-Ryong Kim
- Department of Pharmacology, College of Dentistry, Jeonbuk National University, Jeonju, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea.
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18
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Shin Y, Kim S, Liang G, Ulmer TS, An W. VprBP/DCAF1 triggers melanomagenic gene silencing through histone H2A phosphorylation. RESEARCH SQUARE 2023:rs.3.rs-3147199. [PMID: 37502858 PMCID: PMC10371079 DOI: 10.21203/rs.3.rs-3147199/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Background Melanoma is the most aggressive form of skin cancer arising from pigment-producing melanocytes and is often associated with dysregulation of epigenetic factors targeting histones. VprBP, also known as DCAF1, is a recently identified kinase and plays an important role in downregulating the transcription of tumor suppressor genes as well as increasing the risk for colon and prostate cancers. However, it remains unknown whether VprBP is also involved in triggering the pathogenesis of other types of cancer. Results We demonstrate that VprBP is highly expressed and phosphorylates threonine 120 (T120) on histone H2A to drive transcriptional inactivation of growth regulatory genes in melanoma cells. As is the case for its epigenetic function in colon and prostate cancers, VprBP acts to induce gene silencing program dependently of H2AT120 phosphorylation (H2AT120p). The significance of VprBP-mediated H2AT120p is further underscored by the fact that VprBP knockdown- or VprBP inhibitor-induced lockage of H2AT120p mitigates melanoma tumor growth in xenograft models. Moreover, artificial tethering of VprBP wild type, but not VprBP kinase-dead mutant, to its responsive genes is sufficient for achieving an inactive transcriptional state in VprBP-depleted cells, indicating that VprBP drives gene silencing program in an H2AT120p-dependent manner. Conclusions Our results establish VprBP-mediated H2AT120p as a key epigenetic signal for melanomagenesis and suggest the therapeutic potential of targeting VprBP kinase activity for effective melanoma treatment.
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Shin Y, Kim S, Liang G, Ulmer TS, An W. VprBP/DCAF1 triggers melanomagenic gene silencing through histone H2A phosphorylation. RESEARCH SQUARE 2023:rs.3.rs-2950076. [PMID: 37293029 PMCID: PMC10246234 DOI: 10.21203/rs.3.rs-2950076/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background Melanoma is the most aggressive form of skin cancer arising from pigment-producing melanocytes and is often associated with dysregulation of epigenetic factors targeting histones. VprBP, also known as DCAF1, is a recently identified kinase and plays an important role in downregulating the transcription of tumor suppressor genes as well as increasing the risk for colon and prostate cancers. However, it remains unknown whether VprBP is also involved in triggering the pathogenesis of other types of cancer. Results We demonstrate that VprBP is highly expressed and phosphorylates threonine 120 (T120) on histone H2A to drive transcriptional inactivation of growth regulatory genes in melanoma cells. As is the case for its epigenetic function in colon and prostate cancers, VprBP acts to induce gene silencing program dependently of H2AT120 phosphorylation (H2AT120p). The significance of VprBP-mediated H2AT120p is further underscored by the fact that VprBP knockdown- or VprBP inhibitor-induced lockage of H2AT120p mitigates melanoma tumor growth in xenograft models. Moreover, artificial tethering of VprBP wild type, but not VprBP kinase-dead mutant, to its responsive genes is sufficient for achieving an inactive transcriptional state in VprBP-depleted cells, indicating that VprBP drives gene silencing program in an H2AT120p-dependent manner. Conclusions Our results establish VprBP-mediated H2AT120p as a key epigenetic signal for melanomagenesis and suggest the therapeutic potential of targeting VprBP kinase activity for effective melanoma treatment.
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20
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Medina-Gomez C, Mullin BH, Chesi A, Prijatelj V, Kemp JP, Shochat-Carvalho C, Trajanoska K, Wang C, Joro R, Evans TE, Schraut KE, Li-Gao R, Ahluwalia TS, Zillikens MC, Zhu K, Mook-Kanamori DO, Evans DS, Nethander M, Knol MJ, Thorleifsson G, Prokic I, Zemel B, Broer L, McGuigan FE, van Schoor NM, Reppe S, Pawlak MA, Ralston SH, van der Velde N, Lorentzon M, Stefansson K, Adams HHH, Wilson SG, Ikram MA, Walsh JP, Lakka TA, Gautvik KM, Wilson JF, Orwoll ES, van Duijn CM, Bønnelykke K, Uitterlinden AG, Styrkársdóttir U, Akesson KE, Spector TD, Tobias JH, Ohlsson C, Felix JF, Bisgaard H, Grant SFA, Richards JB, Evans DM, van der Eerden B, van de Peppel J, Ackert-Bicknell C, Karasik D, Kague E, Rivadeneira F. Bone mineral density loci specific to the skull portray potential pleiotropic effects on craniosynostosis. Commun Biol 2023; 6:691. [PMID: 37402774 PMCID: PMC10319806 DOI: 10.1038/s42003-023-04869-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 04/25/2023] [Indexed: 07/06/2023] Open
Abstract
Skull bone mineral density (SK-BMD) provides a suitable trait for the discovery of key genes in bone biology, particularly to intramembranous ossification, not captured at other skeletal sites. We perform a genome-wide association meta-analysis (n ~ 43,800) of SK-BMD, identifying 59 loci, collectively explaining 12.5% of the trait variance. Association signals cluster within gene-sets involved in skeletal development and osteoporosis. Among the four novel loci (ZIC1, PRKAR1A, AZIN1/ATP6V1C1, GLRX3), there are factors implicated in intramembranous ossification and as we show, inherent to craniosynostosis processes. Functional follow-up in zebrafish confirms the importance of ZIC1 on cranial suture patterning. Likewise, we observe abnormal cranial bone initiation that culminates in ectopic sutures and reduced BMD in mosaic atp6v1c1 knockouts. Mosaic prkar1a knockouts present asymmetric bone growth and, conversely, elevated BMD. In light of this evidence linking SK-BMD loci to craniofacial abnormalities, our study provides new insight into the pathophysiology, diagnosis and treatment of skeletal diseases.
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Grants
- UL1 TR000128 NCATS NIH HHS
- U01 AG042124 NIA NIH HHS
- U01 AG042145 NIA NIH HHS
- U01 AG042168 NIA NIH HHS
- U01 AG042140 NIA NIH HHS
- U24 AG051129 NIA NIH HHS
- R01 AR051124 NIAMS NIH HHS
- U01 AG027810 NIA NIH HHS
- U01 AR066160 NIAMS NIH HHS
- MC_UU_00007/10 Medical Research Council
- R01 HD058886 NICHD NIH HHS
- RC2 AR058973 NIAMS NIH HHS
- Wellcome Trust
- M01 RR000240 NCRR NIH HHS
- U01 AG042143 NIA NIH HHS
- UL1 RR026314 NCRR NIH HHS
- U01 AG042139 NIA NIH HHS
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- European Cooperation in Science and Technology (COST)
- Wellcome Trust (Wellcome)
- Department of Health | National Health and Medical Research Council (NHMRC)
- U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)
- ZonMw (Netherlands Organisation for Health Research and Development)
- EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))
- Vetenskapsrådet (Swedish Research Council)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)
- Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)
- NCHA (Netherlands Consortium Healthy Ageing) Leiden/ Rotterdam; Dutch Ministry of Economic Affairs, Agriculture and Innovation (project KB-15-004-003); the Research Institute for Diseases in the Elderly [Netherlands] (014-93-015; RIDE2)
- Clinical and Translational Research Center (5-MO1-RR-000240 and UL1 RR-026314); U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) GrantRecipient="Au50"
- European Commission FP6 STRP grant number 018947 (LSHG-CT-2006-01947); Netherlands Organization for Scientific Research and the Russian Foundation for Basic Research (NWO-RFBR 047.017.043); Netherlands Brain Foundation (project number F2013(1)-28) GrantRecipient="Au40"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au28"
- Chief Scientist Office of the Scottish Government (CZB/4/276, CZB/4/710) GrantRecipient="Au38"
- The Pawsey Supercomputing Centre (with Funding from the Australian Government and the Government of Western Australia; PG 16/0162, PG 17/director2025) GrantRecipient="Au45”
- European Commission (EC)
- U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS);NIH Roadmap for Medical Research [USA]: U01 AG027810, U01 AG042124, U01 AG042139, U01 AG042140, U01 AG042143, U01 AG042145, U01 AG042168, U01 AR066160, and UL1 TR000128 GrantRecipient="Au39”
- Versus Arthritis [USA] 21937 GrantRecipient="Au57”
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Affiliation(s)
- Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Benjamin H Mullin
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
| | - Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Vid Prijatelj
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Kemp
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | | | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Carol Wang
- School of Women's and Infants' Health, University of Western Australia, Crawley, WA, 6009, Australia
| | - Raimo Joro
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
| | - Tavia E Evans
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH8 9AG, Scotland
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
- Steno Diabetes Center Copenhagen, Herlev, 2820, Denmark
- The Bioinformatics Center, Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Kun Zhu
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, 2333 ZA, Leiden, The Netherlands
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Maria Nethander
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Maria J Knol
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Ivana Prokic
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Babette Zemel
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Linda Broer
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Fiona E McGuigan
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
| | - Natasja M van Schoor
- Department of Epidemiology and Data Science, Amsterdam UMC, 1081 HV, Amsterdam, The Netherlands
| | - Sjur Reppe
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372, Oslo, Norway
- Department of Medical Biochemistry, Oslo University Hospital, 0372, Oslo, Norway
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - Mikolaj A Pawlak
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Neurology, Poznan University of Medical Sciences, 61-701, Poznan, Poland
| | - Stuart H Ralston
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Nathalie van der Velde
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Geriatric Medicine, Amsterdam Public Health Research Institute, Amsterdam UMC, 1105 AZ, Amsterdam, The Netherlands
| | - Mattias Lorentzon
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC, 3000, Australia
| | | | - Hieab H H Adams
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology & Nuclear Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Latin American Brain Health (BrainLat), Universidad Adolfo Ibáñez, Santiago, Chile
| | - Scott G Wilson
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, 6009, Australia
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, 6009, Australia
- Medical School, University of Western Australia, Perth, WA, 6009, Australia
| | - Timo A Lakka
- Institute of Biomedicine, Physiology, University of Eastern Finland, Kuopio, 70211, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, 70100, Finland
- Department of Clinical Physiology and Nuclear Medicine, University of Eastern Finland, Kuopio, 70210, Finland
| | - Kaare M Gautvik
- Unger-Vetlesen Institute, Lovisenberg Diaconal Hospital, 0456, Oslo, Norway
| | - James F Wilson
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, EH16 4UX, Scotland
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, Scotland
| | - Eric S Orwoll
- Department of Public Health & Preventive Medicine, Oregon Health & Science University, Portland, OR, OR97239, USA
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - Kristina E Akesson
- Clinical and Molecular Osteoporosis Research Unit, Department of Clinical Sciences Malmö, Lund University, 205 02, Malmö, Sweden
- Department of Orthopedics Malmö, Skåne University Hospital, S-21428, Malmö, Sweden
| | - Timothy D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
| | - Jonathan H Tobias
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Bristol, BS10 5NB, UK
| | - Claes Ohlsson
- Center for Bone and Arthritis Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
- Department of Drug Treatment, Sahlgrenska University Hospital, Region Västra Götaland, SE-413 45, Gothenburg, Sweden
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, 2820, Denmark
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Division of Endocrinology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - J Brent Richards
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH, UK
- Lady Davis Institute, Jewish General Hospital, Montreal, H3T 1E2, QC, Canada
| | - David M Evans
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, 4102, Australia
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Bram van der Eerden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | - Jeroen van de Peppel
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands
| | | | - David Karasik
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, 1311502, Israel
- Marcus Institute for Aging Research, Hebrew SeniorLife, Roslindale, MA, 02131, USA
| | - Erika Kague
- The School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Fernando Rivadeneira
- Department of Oral and Maxillofacial Surgery, Erasmus MC, University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands.
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21
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Weekley BH, Rice JC. The MMP-2 histone H3 N-terminal tail protease is selectively targeted to the transcription start sites of active genes. Epigenetics Chromatin 2023; 16:16. [PMID: 37161413 PMCID: PMC10170761 DOI: 10.1186/s13072-023-00491-w] [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: 03/11/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Proteolysis of the histone H3 N-terminal tail (H3NT) is an evolutionarily conserved epigenomic feature of nearly all eukaryotes, generating a cleaved H3 product that is retained in ~ 5-10% of the genome. Although H3NT proteolysis within chromatin was first reported over 60 years ago, the genomic sites targeted for H3NT proteolysis and the impact of this histone modification on chromatin structure and function remain largely unknown. The goal of this study was to identify the specific regions targeted for H3NT proteolysis and investigate the consequence of H3NT "clipping" on local histone post-translational modification (PTM) dynamics. RESULTS Leveraging recent findings that matrix metalloproteinase 2 (MMP-2) functions as the principal nuclear H3NT protease in the human U2OS osteosarcoma cell line, a ChIP-Seq approach was used to map MMP-2 localization genome wide. The results indicate that MMP-2 is selectively targeted to the transcription start sites (TSSs) of protein coding genes, primarily at the + 1 nucleosome. MMP-2 localization was exclusive to highly expressed genes, further supporting a functional role for H3NT proteolysis in transcriptional regulation. MMP-2 dependent H3NT proteolysis at the TSSs of these genes resulted in a > twofold reduction of activation-associated histone H3 PTMs, including H3K4me3, H3K9ac and H3K18ac. One of genes requiring MMP-2 mediated H3NT proteolysis for proficient expression was the lysosomal cathepsin B protease (CTSB), which we discovered functions as a secondary nuclear H3NT protease in U2OS cells. CONCLUSIONS This study revealed that the MMP-2 H3NT protease is selectively targeted to the TSSs of active protein coding genes in U2OS cells. The resulting H3NT proteolysis directly alters local histone H3 PTM patterns at TSSs, which likely functions to regulate transcription. MMP-2 mediated H3NT proteolysis directly activates CTSB, a secondary H3NT protease that generates additional cleaved H3 products within chromatin.
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Affiliation(s)
- Benjamin H Weekley
- Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
| | - Judd C Rice
- Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA.
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22
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Wei F, Pan B, Diao J, Wang Y, Sheng Y, Gao S. The micronuclear histone H3 clipping in the unicellular eukaryote Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:584-594. [PMID: 37078088 PMCID: PMC10077241 DOI: 10.1007/s42995-022-00151-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/07/2022] [Indexed: 05/02/2023]
Abstract
Clipping of the histone H3 N-terminal tail has been implicated in multiple fundamental biological processes for a growing list of eukaryotes. H3 clipping, serving as an irreversible process to permanently remove some post-translational modifications (PTMs), may lead to noticeable changes in chromatin dynamics or gene expression. The eukaryotic model organism Tetrahymena thermophila is among the first few eukaryotes that exhibits H3 clipping activity, wherein the first six amino acids of H3 are cleaved off during vegetative growth. Clipping only occurs in the transcriptionally silent micronucleus of the binucleated T. thermophila, thus offering a unique opportunity to reveal the role of H3 clipping in epigenetic regulation. However, the physiological functions of the truncated H3 and its protease(s) for clipping remain elusive. Here, we review the major findings of H3 clipping in T. thermophila and highlight its association with histone modifications and cell cycle regulation. We also summarize the functions and mechanisms of H3 clipping in other eukaryotes, focusing on the high diversity in terms of protease families and cleavage sites. Finally, we predict several protease candidates in T. thermophila and provide insights for future studies. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00151-0.
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Affiliation(s)
- Fan Wei
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Bo Pan
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Jinghan Diao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yuanyuan Wang
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
| | - Yalan Sheng
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Shan Gao
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237 China
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23
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Zhu G, Chen W, Tang CY, McVicar A, Edwards D, Wang J, McConnell M, Yang S, Li Y, Chang Z, Li YP. Knockout and Double Knockout of Cathepsin K and Mmp9 reveals a novel function of Cathepsin K as a regulator of osteoclast gene expression and bone homeostasis. Int J Biol Sci 2022; 18:5522-5538. [PMID: 36147479 PMCID: PMC9461675 DOI: 10.7150/ijbs.72211] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 08/02/2022] [Indexed: 01/26/2023] Open
Abstract
Cathepsins play a role in regulation of cell function through their presence in the cell nucleus. However, the role of Cathepsin K (Ctsk) as an epigenetic regulator in osteoclasts remains unknown. Our data demonstrated that Ctsk-/-Mmp9-/- mice have a striking phenotype with a 5-fold increase in bone volume compared with WT. RNA-seq analysis of Ctsk-/- , Mmp9-/- and Ctsk-/-/Mmp9-/- osteoclasts revealed their distinct functions in gene expression regulation, including reduced Cebpa expression, increased Nfatc1 expression, and in signaling pathways activity regulation. Western blots and qPCR data validated these changes. ATAC-seq profiling of Ctsk-/- , Mmp9-/-, and Ctsk-/-/Mmp9-/- osteoclasts indicated the changes resulted from reduced chromatin openness in the promoter region of Cebpa and increased chromatin openness in Nfatc1 promoter in Ctsk-/-/Mmp9-/- osteoclasts compared to that in osteoclasts of WT, Ctsk/- and Mmp9-/- . We found co-localization of Ctsk with c-Fos and cleavage of H3K27me3 in wild-type osteoclasts. Remarkably, cleavage of H3K27me3 was blocked in osteoclasts of Ctsk-/- and Ctsk-/-/Mmp9-/- mice, suggesting that Ctsk may epigenetically regulate distinctive groups of genes' expression by regulating proteolysis of H3K27me3. Ctsk-/-/Mmp9-/- double knockout dramatically protects against ovariectomy induced bone loss. We found that Ctsk may function as an essential epigenetic regulator in modulating levels of H3K27me3 in osteoclast activation and maintaining bone homeostasis. Our study revealed complementary and unique functions of Ctsk as epigenetic regulators for maintaining osteoclast activation and bone homeostasis by orchestrating multiple signaling pathways and targeting both Ctsk and Mmp9 is a novel therapeutic approach for osteolytic diseases such as osteoporosis.
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Affiliation(s)
- Guochun Zhu
- State Key Laboratory of Membrane Biology, School of Medicine, Center for Synthetic and Systems Biology, Tsinghua University, 100084 Beijing, China
- Department of Pathology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294-2182, USA
| | - Wei Chen
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, Louisiana, 70112, USA
- Department of Pathology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294-2182, USA
| | - Chen-Yi Tang
- Department of Pathology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294-2182, USA
| | - Abigail McVicar
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, Louisiana, 70112, USA
| | - Diep Edwards
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, Louisiana, 70112, USA
| | - Jinwen Wang
- Department of Pathology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294-2182, USA
| | - Matthew McConnell
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, Louisiana, 70112, USA
| | - Shuying Yang
- Department of Basic & Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yang Li
- Department of Basic & Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhijie Chang
- State Key Laboratory of Membrane Biology, School of Medicine, Center for Synthetic and Systems Biology, Tsinghua University, 100084 Beijing, China
| | - Yi-Ping Li
- Division in Cellular and Molecular Medicine, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, Tulane University, New Orleans, Louisiana, 70112, USA
- Department of Pathology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294-2182, USA
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24
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Su J, Chen T, Liao D, Wang Y, Su Y, Liu S, Chen X, Ruifang Q, Jiang L, Liu Z. Novel peptides extracted from Muraenesox cinereus bone promote calcium transport, osteoblast differentiation, and calcium absorption. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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25
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Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas. Mol Cell 2022; 82:2696-2713.e9. [PMID: 35716669 DOI: 10.1016/j.molcel.2022.05.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 03/28/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022]
Abstract
Cancer cells are highly heterogeneous at the transcriptional level and epigenetic state. Methods to study epigenetic heterogeneity are limited in throughput and information obtained per cell. Here, we adapted cytometry by time-of-flight (CyTOF) to analyze a wide panel of histone modifications in primary tumor-derived lines of diffused intrinsic pontine glioma (DIPG). DIPG is a lethal glioma, driven by a histone H3 lysine 27 mutation (H3-K27M). We identified two epigenetically distinct subpopulations in DIPG, reflecting inherent heterogeneity in expression of the mutant histone. These two subpopulations are robust across tumor lines derived from different patients and show differential proliferation capacity and expression of stem cell and differentiation markers. Moreover, we demonstrate the use of these high-dimensional data to elucidate potential interactions between histone modifications and epigenetic alterations during the cell cycle. Our work establishes new concepts for the analysis of epigenetic heterogeneity in cancer that could be applied to diverse biological systems.
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26
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Augoff K, Hryniewicz-Jankowska A, Tabola R, Stach K. MMP9: A Tough Target for Targeted Therapy for Cancer. Cancers (Basel) 2022; 14:cancers14071847. [PMID: 35406619 PMCID: PMC8998077 DOI: 10.3390/cancers14071847] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/27/2022] [Accepted: 03/31/2022] [Indexed: 02/01/2023] Open
Abstract
Having the capability to proteolyze diverse structural and signaling proteins, matrix metalloproteinase 9 (MMP9), one of the best-studied secretory endopeptidases, has been identified as a crucial mediator of processes closely associated with tumorigenesis, such as the extracellular matrix reorganization, epithelial to mesenchymal transition, cell migration, new blood vessel formation, and immune response. In this review, we present the current state of knowledge on MMP9 and its role in cancer growth in the context of cell adhesion/migration, cancer-related inflammation, and tumor microenvironment formation. We also summarize recent achievements in the development of selective MMP9 inhibitors and the limitations of using them as anticancer drugs.
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Affiliation(s)
- Katarzyna Augoff
- Department of Surgical Education, Wroclaw Medical University, 50-367 Wroclaw, Poland
- Department of Chemistry and Immunochemistry, Wroclaw Medical University, 50-367 Wroclaw, Poland;
- Correspondence:
| | | | - Renata Tabola
- Department of Thoracic Surgery, Wroclaw Medical University, 50-367 Wroclaw, Poland;
| | - Kamilla Stach
- Department of Chemistry and Immunochemistry, Wroclaw Medical University, 50-367 Wroclaw, Poland;
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27
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Wang H, Joshi P, Hong SH, Maye PF, Rowe DW, Shin DG. Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP. BMC Genomics 2022; 23:14. [PMID: 34991467 PMCID: PMC8740472 DOI: 10.1186/s12864-021-08159-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 10/26/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Interferon regulatory factor-8 (IRF8) and nuclear factor-activated T cells c1 (NFATc1) are two transcription factors that have an important role in osteoclast differentiation. Thanks to ChIP-seq technology, scientists can now estimate potential genome-wide target genes of IRF8 and NFATc1. However, finding target genes that are consistently up-regulated or down-regulated across different studies is hard because it requires analysis of a large number of high-throughput expression studies from a comparable context. METHOD We have developed a machine learning based method, called, Cohort-based TF target prediction system (cTAP) to overcome this problem. This method assumes that the pathway involving the transcription factors of interest is featured with multiple "functional groups" of marker genes pertaining to the concerned biological process. It uses two notions, Gene-Present Sufficiently (GP) and Gene-Absent Insufficiently (GA), in addition to log2 fold changes of differentially expressed genes for the prediction. Target prediction is made by applying multiple machine-learning models, which learn the patterns of GP and GA from log2 fold changes and four types of Z scores from the normalized cohort's gene expression data. The learned patterns are then associated with the putative transcription factor targets to identify genes that consistently exhibit Up/Down gene regulation patterns within the cohort. We applied this method to 11 publicly available GEO data sets related to osteoclastgenesis. RESULT Our experiment identified a small number of Up/Down IRF8 and NFATc1 target genes as relevant to osteoclast differentiation. The machine learning models using GP and GA produced NFATc1 and IRF8 target genes different than simply using a log2 fold change alone. Our literature survey revealed that all predicted target genes have known roles in bone remodeling, specifically related to the immune system and osteoclast formation and functions, suggesting confidence and validity in our method. CONCLUSION cTAP was motivated by recognizing that biologists tend to use Z score values present in data sets for the analysis. However, using cTAP effectively presupposes assembling a sizable cohort of gene expression data sets within a comparable context. As public gene expression data repositories grow, the need to use cohort-based analysis method like cTAP will become increasingly important.
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Affiliation(s)
- Honglin Wang
- Computer Science and Engineering Department, University of Connecticut, Storrs, USA
| | - Pujan Joshi
- Computer Science and Engineering Department, University of Connecticut, Storrs, USA
| | - Seung-Hyun Hong
- Computer Science and Engineering Department, University of Connecticut, Storrs, USA
| | - Peter F. Maye
- Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, USA
| | - David W. Rowe
- Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, USA
| | - Dong-Guk Shin
- Computer Science and Engineering Department, University of Connecticut, Storrs, USA
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28
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MMP-9 drives the melanomagenic transcription program through histone H3 tail proteolysis. Oncogene 2022; 41:560-570. [PMID: 34785776 DOI: 10.1038/s41388-021-02109-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 11/08/2022]
Abstract
Melanoma is a type of skin cancer that develops in pigment-producing melanocytes and often spreads to other parts of the body. Aberrant gene expression has been considered as a crucial step for increasing the risk of melanomagenesis, but how chromatin reorganization contributes to this pathogenic process is still not well understood. Here we report that matrix metalloproteinase 9 (MMP-9) localizes to the nucleus of melanoma cells and potentiates gene expression by proteolytically clipping the histone H3 N-terminal tail (H3NT). From genome-wide studies, we discovered that growth-regulatory genes are selectively targeted and activated by MMP-9-dependent H3NT proteolysis in melanoma cells. MMP-9 cooperates functionally with p300/CBP because MMP-9 cleaves H3NT in a manner that is dependent on p300/CBP-mediated acetylation of H3K18. The functional significance of MMP-9-dependent H3NT proteolysis is further underscored by the fact that RNAi knockdown and small-molecule inhibition of MMP-9 and p300/CBP impede melanomagenic gene expression and melanoma tumor growth. Together, our data establish new functions and mechanisms for nuclear MMP-9 in promoting melanomagenesis and demonstrate how MMP-9-dependent H3NT proteolysis can be exploited to prevent and treat melanoma skin cancer.
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29
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Sthanam LK, Roy T, Patwardhan S, Shukla A, Sharma S, Shinde PV, Kale HT, Chandra Shekar P, Kondabagil K, Sen S. MMP modulated differentiation of mouse embryonic stem cells on engineered cell derived matrices. Biomaterials 2021; 280:121268. [PMID: 34871878 DOI: 10.1016/j.biomaterials.2021.121268] [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: 11/15/2019] [Revised: 10/27/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022]
Abstract
Stem cell differentiation is dictated by the dynamic crosstalk between cells and their underlying extracellular matrix. While the importance of matrix degradation mediated by enzymes such as matrix metalloproteinases (MMPs) in the context of cancer invasion is well established, the role of MMPs in stem cell differentiation remains relatively unexplored. Here we address this question by assaying MMP expression and activity during differentiation of mouse embryonic stem cells (mESCs) on mouse embryonic fibroblast (MEF) derived matrices (MEFDMs) of varying stiffness and composition. We show that mESC differentiation into different germ layers is associated with expression of several MMPs including MMP-11, 2, 17, 25 and 9, with MMP-9 detected in cell secreted media. Different extents of softening of the different MEFDMs led to altered integrin expression, activated distinct mechanotransduction and metabolic pathways, and induced expression of germ layer-specific markers. Inhibition of MMP proteolytic activity by the broad spectrum MMP inhibitor GM6001 led to alterations in germ layer commitment of the differentiating mESCs. Together, our results illustrate the effect of MMPs in regulating mESC differentiation on engineered cell derived matrices and establish MEFDMs as suitable substrates for understanding molecular mechanisms regulating stem cell development and for regenerative medicine applications.
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Affiliation(s)
| | - Tanusri Roy
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India
| | - Sejal Patwardhan
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India; Advanced Centre for Treatment, Research and Education in Cancer - Tata Memorial Centre (ACTREC-TMC), Kharghar, Navi Mumbai, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, India
| | - Avi Shukla
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India
| | - Shipra Sharma
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India
| | - Pradip V Shinde
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India
| | | | | | - Kiran Kondabagil
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India
| | - Shamik Sen
- Department. of Biosciences & Bioengineering, IIT Bombay, Mumbai, India.
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30
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Cavalieri V. The Expanding Constellation of Histone Post-Translational Modifications in the Epigenetic Landscape. Genes (Basel) 2021; 12:genes12101596. [PMID: 34680990 PMCID: PMC8535662 DOI: 10.3390/genes12101596] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed.
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Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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31
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Sabry M, Mostafa S, Kamar S, Rashed L, Estaphan S. The cross-talk between matrix metalloproteinase-9, RANKL/OPG system and cardiovascular risk factors in ovariectomized rat model of postmenopausal osteoporosis. PLoS One 2021; 16:e0258254. [PMID: 34610044 PMCID: PMC8491879 DOI: 10.1371/journal.pone.0258254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 09/23/2021] [Indexed: 12/02/2022] Open
Abstract
Epidemiology and pathogenesis of cardiovascular diseases (CVD) and osteoporosis are strikingly overlapping. This study presents matrix metalloproteinase-9 (MMP-9), as a simple molecular link more consistently associated with the pathophysiology of both osteoporosis and CVD risk factors. 40 adult female rats were randomly distributed into 4 groups [control sham-operated, untreated osteoporosis, carvedilol-treated osteoporosis and alendronate-treated osteoporosis]. After 8 weeks, blood samples were collected to estimate Lipid profile (Total cholesterol, HDL, Triglycerides), inflammatory markers (IL-6, TNF alpha, CRP and NO), and Bone turnover markers (BTM) (Alkaline phosphatase, osteocalcin and pyridinoline). The tibias were dissected to estimate MMP-9 and NF-kB gene expression, OPG, RANKL levels and for histological examination. Induction of osteoporosis resulted in a significant elevation in BTM, inflammatory markers and dyslipidemia. MMP-9 was significantly elevated and positively correlated with BTM, inflammation and dyslipidemia markers. Carvedilol and alendronate exerted a bone preservative role and attenuated dyslipidaemia and inflammation in accordance with their respective effect on MMP-9.
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Affiliation(s)
- Maha Sabry
- Faculty of Medicine, Physiology Department, Cairo University, Giza, Egypt
| | - Seham Mostafa
- Faculty of Medicine, Physiology Department, Cairo University, Giza, Egypt
| | - Samaa Kamar
- Faculty of Medicine, Histology and Cell Biology Department, Cairo University, Giza, Egypt
- Histology Department, Armed Forces College of Medicine, Cairo, Egypt
| | - Laila Rashed
- Faculty of Medicine, Biochemistry Department, Cairo University, Giza, Egypt
| | - Suzanne Estaphan
- Faculty of Medicine, Physiology Department, Cairo University, Giza, Egypt
- ANU Medical School, Australian National University, Canberra, Australian Capital Territory, Australia
- * E-mail: ,
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32
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Ghate NB, Kim S, Spiller E, Kim S, Shin Y, Rhie SK, Smbatyan G, Lenz HJ, Mumenthaler SM, An W. VprBP directs epigenetic gene silencing through histone H2A phosphorylation in colon cancer. Mol Oncol 2021; 15:2801-2817. [PMID: 34312968 PMCID: PMC8486565 DOI: 10.1002/1878-0261.13068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/30/2022] Open
Abstract
Histone modification is aberrantly regulated in cancer and generates an unbalanced state of gene transcription. VprBP, a recently identified kinase, phosphorylates histone H2A on threonine 120 (T120) and is involved in oncogenic transcriptional dysregulation; however, its specific role in colon cancer is undefined. Here, we show that VprBP is overexpressed in colon cancer and directly contributes to epigenetic gene silencing and cancer pathogenesis. Mechanistically, the observed function of VprBP is mediated through H2AT120 phosphorylation (H2AT120p)‐driven transcriptional repression of growth regulatory genes, resulting in a significantly higher proliferative capacity of colon cancer cells. Our preclinical studies using organoid and xenograft models demonstrate that treatment with the VprBP inhibitor B32B3 impairs colonic tumor growth by blocking H2AT120p and reactivating a transcriptional program resembling that of normal cells. Collectively, our work describes VprBP as a master kinase contributing to the development and progression of colon cancer, making it a new molecular target for novel therapeutic strategies.
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Affiliation(s)
- Nikhil Baban Ghate
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Sangnam Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Erin Spiller
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sungmin Kim
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Yonghwan Shin
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Goar Smbatyan
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
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33
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Marruecos L, Bertran J, Álvarez-Villanueva D, Mulero MC, Guillén Y, Palma LG, Floor M, Vert A, Arce-Gallego S, Pecharroman I, Batlle L, Villà-Freixa J, Ghosh G, Bigas A, Espinosa L. Dynamic chromatin association of IκBα is regulated by acetylation and cleavage of histone H4. EMBO Rep 2021; 22:e52649. [PMID: 34224210 DOI: 10.15252/embr.202152649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/27/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022] Open
Abstract
IκBs exert principal functions as cytoplasmic inhibitors of NF-kB transcription factors. Additional roles for IκB homologues have been described, including chromatin association and transcriptional regulation. Phosphorylated and SUMOylated IκBα (pS-IκBα) binds to histones H2A and H4 in the stem cell and progenitor cell compartment of skin and intestine, but the mechanisms controlling its recruitment to chromatin are largely unknown. Here, we show that serine 32-36 phosphorylation of IκBα favors its binding to nucleosomes and demonstrate that p-IκBα association with H4 depends on the acetylation of specific H4 lysine residues. The N-terminal tail of H4 is removed during intestinal cell differentiation by proteolytic cleavage by trypsin or chymotrypsin at residues 17-19, which reduces p-IκBα binding. Inhibition of trypsin and chymotrypsin activity in HT29 cells increases p-IκBα chromatin binding but, paradoxically, impaired goblet cell differentiation, comparable to IκBα deletion. Taken together, our results indicate that dynamic binding of IκBα to chromatin is a requirement for intestinal cell differentiation and provide a molecular basis for the understanding of the restricted nuclear distribution of p-IκBα in specific stem cell compartments.
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Affiliation(s)
- Laura Marruecos
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Joan Bertran
- Faculty of Science and Technology, Bioinformatics and Medical Statistics Group, University of Vic - Central University of Catalonia, Barcelona, Spain
| | - Daniel Álvarez-Villanueva
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - María Carmen Mulero
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain.,Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Yolanda Guillén
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Luis G Palma
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Martin Floor
- Faculty of Science and Technology, Bioinformatics and Medical Statistics Group, University of Vic - Central University of Catalonia, Barcelona, Spain.,Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Anna Vert
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Sara Arce-Gallego
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Irene Pecharroman
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Laura Batlle
- Tissue Engineering Unit. Center for Genomic Regulation (CRG), Barcelona, Spain
| | - Jordi Villà-Freixa
- Faculty of Science and Technology, Bioinformatics and Medical Statistics Group, University of Vic - Central University of Catalonia, Barcelona, Spain.,Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, Spain
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Anna Bigas
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
| | - Lluís Espinosa
- Cancer Research Program, Institut Mar d'Investigacions Mèdiques, CIBERONC, Hospital del Mar, Barcelona, Spain
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34
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Zhu L, Tang Y, Li XY, Keller ET, Yang J, Cho JS, Feinberg TY, Weiss SJ. Osteoclast-mediated bone resorption is controlled by a compensatory network of secreted and membrane-tethered metalloproteinases. Sci Transl Med 2021; 12:12/529/eaaw6143. [PMID: 32024800 DOI: 10.1126/scitranslmed.aaw6143] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 10/03/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022]
Abstract
Osteoclasts actively remodel both the mineral and proteinaceous components of bone during normal growth and development as well as pathologic states ranging from osteoporosis to bone metastasis. The cysteine proteinase cathepsin K confers osteoclasts with potent type I collagenolytic activity; however, cathepsin K-null mice, as well as cathepsin K-mutant humans, continue to remodel bone and degrade collagen by as-yet-undefined effectors. Here, we identify a cathepsin K-independent collagenolytic system in osteoclasts that is composed of a functionally redundant network of the secreted matrix metalloproteinase MMP9 and the membrane-anchored matrix metalloproteinase MMP14. Unexpectedly, whereas deleting either of the proteinases individually leaves bone resorption intact, dual targeting of Mmp9 and Mmp14 inhibited the resorptive activity of mouse osteoclasts in vitro and in vivo and human osteoclasts in vitro. In vivo, Mmp9/Mmp14 conditional double-knockout mice exhibited marked increases in bone density and displayed a highly protected status against either parathyroid hormone- or ovariectomy-induced pathologic bone loss. Together, these studies characterize a collagenolytic system operative in mouse and human osteoclasts and identify the MMP9/MMP14 axis as a potential target for therapeutic interventions for bone-wasting disease states.
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Affiliation(s)
- Lingxin Zhu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China. .,Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi Tang
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiao-Yan Li
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Evan T Keller
- Department of Pathology, Department of Urology and the Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jingwen Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan 430079, China.,School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jung-Sun Cho
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamar Y Feinberg
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA.,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stephen J Weiss
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA. .,Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
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35
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Ali MAM, Garcia-Vilas JA, Cromwell CR, Hubbard BP, Hendzel MJ, Schulz R. Matrix metalloproteinase-2 mediates ribosomal RNA transcription by cleaving nucleolar histones. FEBS J 2021; 288:6736-6751. [PMID: 34101354 DOI: 10.1111/febs.16061] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/09/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Cell proliferation and survival require continuous ribosome biogenesis and protein synthesis. Genes encoding ribosomal RNA are physically located in a specialized substructure within the nucleus known as the nucleolus, which has a central role in the biogenesis of ribosomes. Matrix metalloproteinase-2 was previously detected in the nucleus, however, its role there is elusive. Herein we report that matrix metalloproteinase-2 resides within the nucleolus to regulate ribosomal RNA transcription. Matrix metalloproteinase-2 is enriched at the promoter region of ribosomal RNA gene repeats, and its inhibition downregulates preribosomal RNA transcription. The N-terminal tail of histone H3 is clipped by matrix metalloproteinase-2 in the nucleolus, which is associated with increased ribosomal RNA transcription. Knocking down/out matrix metalloproteinase-2, or inhibiting its activity, prevents histone H3 cleavage and reduces both ribosomal RNA transcription and cell proliferation. In addition to the known extracellular roles of matrix metalloproteinase-2 in tumor growth, our data reveal an epigenetic mechanism whereby intranucleolar matrix metalloproteinase-2 regulates cell proliferation through histone clipping and facilitation of ribosomal RNA transcription.
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Affiliation(s)
- Mohammad A M Ali
- Department of Pediatrics, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.,Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, State University of New York, Binghamton, NY, USA
| | - Javier A Garcia-Vilas
- Department of Pediatrics, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.,Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Christopher R Cromwell
- Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Michael J Hendzel
- Department of Oncology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Richard Schulz
- Department of Pediatrics, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.,Department of Pharmacology, Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
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36
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Daura E, Tegelberg S, Yoshihara M, Jackson C, Simonetti F, Aksentjeff K, Ezer S, Hakala P, Katayama S, Kere J, Lehesjoki AE, Joensuu T. Cystatin B-deficiency triggers ectopic histone H3 tail cleavage during neurogenesis. Neurobiol Dis 2021; 156:105418. [PMID: 34102276 DOI: 10.1016/j.nbd.2021.105418] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/30/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022] Open
Abstract
Cystatin B (CSTB) acts as an inhibitor of cysteine proteases of the cathepsin family and loss-of-function mutations result in human brain diseases with a genotype-phenotype correlation. In the most severe case, CSTB-deficiency disrupts brain development, and yet the molecular basis of this mechanism is missing. Here, we establish CSTB as a regulator of chromatin structure during neural stem cell renewal and differentiation. Murine neural precursor cells (NPCs) undergo transient proteolytic cleavage of the N-terminal histone H3 tail by cathepsins B and L upon induction of differentiation into neurons and glia. In contrast, CSTB-deficiency triggers premature H3 tail cleavage in undifferentiated self-renewing NPCs and sustained H3 tail proteolysis in differentiating neural cells. This leads to significant transcriptional changes in NPCs, particularly of nuclear-encoded mitochondrial genes. In turn, these transcriptional alterations impair the enhanced mitochondrial respiration that is induced upon neural stem cell differentiation. Collectively, our findings reveal the basis of epigenetic regulation in the molecular pathogenesis of CSTB deficiency.
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Affiliation(s)
- Eduard Daura
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Saara Tegelberg
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Stockholm, Sweden
| | - Christopher Jackson
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Francesca Simonetti
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Katri Aksentjeff
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Sini Ezer
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Paula Hakala
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Shintaro Katayama
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Stockholm, Sweden
| | - Juha Kere
- Folkhälsan Research Center, 00290 Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Stockholm, Sweden; Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Anna-Elina Lehesjoki
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
| | - Tarja Joensuu
- Folkhälsan Research Center, 00290 Helsinki, Finland; Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
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37
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Cheung P, Schaffert S, Chang SE, Dvorak M, Donato M, Macaubas C, Foecke MH, Li TM, Zhang L, Coan JP, Schulert GS, Grom AA, Henderson LA, Nigrovic PA, Elias JE, Gozani O, Mellins ED, Khatri P, Utz PJ, Kuo AJ. Repression of CTSG, ELANE and PRTN3-mediated histone H3 proteolytic cleavage promotes monocyte-to-macrophage differentiation. Nat Immunol 2021; 22:711-722. [PMID: 34017121 PMCID: PMC8159908 DOI: 10.1038/s41590-021-00928-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/05/2021] [Indexed: 12/31/2022]
Abstract
Chromatin undergoes extensive reprogramming during immune cell differentiation. Here we report the repression of controlled histone H3 amino terminus proteolytic cleavage (H3ΔN) during monocyte-to-macrophage development. This abundant histone mark in human peripheral blood monocytes is catalyzed by neutrophil serine proteases (NSPs) cathepsin G, neutrophil elastase and proteinase 3. NSPs are repressed as monocytes mature into macrophages. Integrative epigenomic analysis reveals widespread H3ΔN distribution across the genome in a monocytic cell line and primary monocytes, which becomes largely undetectable in fully differentiated macrophages. H3ΔN is enriched at permissive chromatin and actively transcribed genes. Simultaneous NSP depletion in monocytic cells results in H3ΔN loss and further increase in chromatin accessibility, which likely primes the chromatin for gene expression reprogramming. Importantly, H3ΔN is reduced in monocytes from patients with systemic juvenile idiopathic arthritis, an autoinflammatory disease with prominent macrophage involvement. Overall, we uncover an epigenetic mechanism that primes the chromatin to facilitate macrophage development.
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Affiliation(s)
- Peggie Cheung
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Steven Schaffert
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah E Chang
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mai Dvorak
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Michele Donato
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Claudia Macaubas
- Program in Immunology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mariko H Foecke
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Tie-Mei Li
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - John P Coan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Grant S Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Alexei A Grom
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Lauren A Henderson
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter A Nigrovic
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Elizabeth D Mellins
- Program in Immunology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
| | - Alex J Kuo
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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Yi SJ, Jang YJ, Kim HJ, Lee K, Lee H, Kim Y, Kim J, Hwang SY, Song JS, Okada H, Park JI, Kang K, Kim K. The KDM4B-CCAR1-MED1 axis is a critical regulator of osteoclast differentiation and bone homeostasis. Bone Res 2021; 9:27. [PMID: 34031372 PMCID: PMC8144413 DOI: 10.1038/s41413-021-00145-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Bone undergoes a constant and continuous remodeling process that is tightly regulated by the coordinated and sequential actions of bone-resorbing osteoclasts and bone-forming osteoblasts. Recent studies have shown that histone demethylases are implicated in osteoblastogenesis; however, little is known about the role of histone demethylases in osteoclast formation. Here, we identified KDM4B as an epigenetic regulator of osteoclast differentiation. Knockdown of KDM4B significantly blocked the formation of tartrate-resistant acid phosphatase-positive multinucleated cells. Mice with myeloid-specific conditional knockout of KDM4B showed an osteopetrotic phenotype due to osteoclast deficiency. Biochemical analysis revealed that KDM4B physically and functionally associates with CCAR1 and MED1 in a complex. Using genome-wide chromatin immunoprecipitation (ChIP)-sequencing, we revealed that the KDM4B–CCAR1–MED1 complex is localized to the promoters of several osteoclast-related genes upon receptor activator of NF-κB ligand stimulation. We demonstrated that the KDM4B–CCAR1–MED1 signaling axis induces changes in chromatin structure (euchromatinization) near the promoters of osteoclast-related genes through H3K9 demethylation, leading to NF-κB p65 recruitment via a direct interaction between KDM4B and p65. Finally, small molecule inhibition of KDM4B activity impeded bone loss in an ovariectomized mouse model. Taken together, our findings establish KDM4B as a critical regulator of osteoclastogenesis, providing a potential therapeutic target for osteoporosis.
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Affiliation(s)
- Sun-Ju Yi
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - You-Jee Jang
- Korea Basic Science Institute, Gwangju Center at Chonnam National University, Gwangju, Republic of Korea
| | - Hye-Jung Kim
- New Drug Development Center, KBIO Osong Medical Innovation Foundation, Cheongju, Chungbuk, Republic of Korea
| | - Kyubin Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Hyerim Lee
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Yeojin Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Junil Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Seon Young Hwang
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Jin Sook Song
- Data Convergence Drug Research Center, Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hitoshi Okada
- Department of Biochemistry, Kindai University Faculty of Medicine, Osakasayama, Osaka, Japan
| | - Jae-Il Park
- Korea Basic Science Institute, Gwangju Center at Chonnam National University, Gwangju, Republic of Korea
| | - Kyuho Kang
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| | - Kyunghwan Kim
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea.
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Rice JC, Weekley BH, Kanholm T, Chen Z, Lee S, Fernandez DJ, Abrahamson R, Castaldi A, Borok Z, Dynlacht BD, An W. MMP-2 is a novel histone H3 N-terminal protease necessary for myogenic gene activation. Epigenetics Chromatin 2021; 14:23. [PMID: 34001241 PMCID: PMC8130154 DOI: 10.1186/s13072-021-00398-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/06/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Selective proteolysis of the histone H3 N-terminal tail (H3NT) is frequently observed during eukaryotic development, generating a cleaved histone H3 (H3cl) product within a small, but significant, portion of the genome. Although increasing evidence supports a regulatory role for H3NT proteolysis in gene activation, the nuclear H3NT proteases and the biological significance of H3NT proteolysis remain largely unknown. RESULTS In this study, established cell models of skeletal myogenesis were leveraged to investigate H3NT proteolysis. These cells displayed a rapid and progressive accumulation of a single H3cl product within chromatin during myoblast differentiation. Using conventional approaches, we discovered that the canonical extracellular matrix (ECM) protease, matrix metalloproteinase 2 (MMP-2), is the principal H3NT protease of myoblast differentiation that cleaves H3 between K18-Q19. Gelatin zymography demonstrated progressive increases in nuclear MMP-2 activity, concomitant with H3cl accumulation, during myoblast differentiation. RNAi-mediated depletion of MMP-2 impaired H3NT proteolysis and resulted in defective myogenic gene activation and myoblast differentiation. Supplementation of MMP-2 ECM activity in MMP-2-depleted cells was insufficient to rescue defective H3NT proteolysis and myogenic gene activation. CONCLUSIONS This study revealed that MMP-2 is a novel H3NT protease and the principal H3NT protease of myoblast differentiation. The results indicate that myogenic signaling induces MMP-2-dependent H3NT proteolysis at early stages of myoblast differentiation. Importantly, the results support the necessity of nuclear MMP-2 H3NT protease activity, independent of MMP-2 activity in the ECM, for myogenic gene activation and proficient myoblast differentiation.
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Affiliation(s)
- Judd C Rice
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA.
| | - Benjamin H Weekley
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
| | - Tomas Kanholm
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
| | - Zhihui Chen
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
| | - Sunyoung Lee
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
| | - Daniel J Fernandez
- Department of Molecular Microbiology and Immunology, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, Los Angeles, CA, 90033, USA
| | - Rachel Abrahamson
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
| | - Alessandra Castaldi
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Zea Borok
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Brian D Dynlacht
- Department of Pathology and Cancer Institute, NYU School of Medicine,, New York, NY, 10016, USA
| | - Woojin An
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1450 Biggy Street, HNRT 6506, Los Angeles, CA, 90033, USA
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Knapinska AM, Singh C, Drotleff G, Blanco D, Chai C, Schwab J, Herd A, Fields GB. Matrix Metalloproteinase 13 Inhibitors for Modulation of Osteoclastogenesis: Enhancement of Solubility and Stability. ChemMedChem 2021; 16:1133-1142. [PMID: 33331147 PMCID: PMC8035250 DOI: 10.1002/cmdc.202000911] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/14/2020] [Indexed: 11/08/2022]
Abstract
Matrix metalloproteinase 13 (MMP-13) activity has been correlated to breast cancer bone metastasis. It has been proposed that MMP-13 contributes to bone metastasis through the promotion of osteoclastogenesis. To explore the mechanisms of MMP-13 action, we previously described a highly efficacious and selective MMP-13 inhibitor, RF036. Unfortunately, further pursuit of RF036 as a probe of MMP-13 in vitro and in vivo activities was not practical due to the limited solubility and stability of the inhibitor. Our new study has explored replacing the RF036 backbone sulfur atom and terminal methyl group to create inhibitors with more favorable pharmacokinetic properties. One compound, designated inhibitor 3, in which the backbone sulfur and terminal methyl group of RF036 were replaced by nitrogen and oxetane, respectively, had comparable activity, selectivity, and membrane permeability to RF036, while exhibiting greatly enhanced solubility and stability. Inhibitor 3 effectively inhibited MMP-13-mediated osteoclastogenesis but spared collagenolysis, and thus represents a next-generation MMP-13 probe applicable for in vivo studies of breast cancer metastasis.
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Affiliation(s)
- Anna M Knapinska
- Department of Chemistry & Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Chandani Singh
- Department of Chemistry & Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Gary Drotleff
- Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA
| | - Daniela Blanco
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Cedric Chai
- Department of Biological Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431, USA
| | - Jason Schwab
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Anu Herd
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
| | - Gregg B Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
- Institute for Human Health & Disease Intervention (I-HEALTH), Florida Atlantic University, 5353 Parkside Drive, Jupiter, FL 33458, USA
- Department of Chemistry, The Scripps Research Institute/Scripps Florida, 120 Scripps Way, Jupiter, FL 33458, USA
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Peng Y, Li S, Landsman D, Panchenko AR. Histone tails as signaling antennas of chromatin. Curr Opin Struct Biol 2021; 67:153-160. [PMID: 33279866 PMCID: PMC8096652 DOI: 10.1016/j.sbi.2020.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/07/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022]
Abstract
Histone tails, representing the N-terminal or C-terminal regions flanking the histone core, play essential roles in chromatin signaling networks. Intrinsic disorder of histone tails and their propensity for post-translational modifications allow them to serve as hubs in coordination of epigenetic processes within the nucleosomal context. Deposition of histone variants with distinct histone tail properties further enriches histone tails' repertoire in epigenetic signaling. Given the advances in experimental techniques and in silico modelling, we review the most recent data on histone tails' effects on nucleosome stability and dynamics, their function in regulating chromatin accessibility and folding. Finally, we discuss different molecular mechanisms to understand how histone tails are involved in nucleosome recognition by binding partners and formation of higher-order chromatin structures.
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Affiliation(s)
- Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada.
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42
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Matrix metalloproteinase 9 a potential major player connecting atherosclerosis and osteoporosis in high fat diet fed rats. PLoS One 2021; 16:e0244650. [PMID: 33571214 PMCID: PMC7877768 DOI: 10.1371/journal.pone.0244650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 12/14/2020] [Indexed: 01/19/2023] Open
Abstract
Background Cardiovascular diseases (CVD) represent one of the major sequelae of obesity. On the other hand, the relationship between bone diseases and obesity remains unclear. An increasing number of biological and epidemiological studies suggest the presence of a link between atherosclerosis and osteoporosis, however, the precise molecular pathways underlying this close association remain poorly understood. The present work thus aimed to study Matrix Metalloproteinase 9 (MMP-9), as a proposed link between atherosclerosis and osteoporosis in high fat diet fed rats. Methods and findings 40 rats were randomly divided into 4 groups: control, untreated atherosclerosis group, atherosclerotic rats treated with carvedilol (10mg/kg/d) and atherosclerotic rats treated with alendronate sodium (10mg/kg/d). After 8 weeks, blood samples were collected for estimation of Lipid profile (Total cholesterol, HDL, TGs), inflammatory markers (IL-6, TNF-α, CRP and NO) and Bone turnover markers (BTMs) (Alkaline phosphatase, osteocalcin and pyridinoline). Rats were then euthanized and the aortas and tibias were dissected for histological examination and estimation of MMP-9, N-terminal propeptide of type I procollagen (PINP), C-terminal telopeptide of type I collagen (CTX) and NF-kB expression. Induction of atherosclerosis via high fat diet and chronic stress induced a significant increase in BTMs, inflammatory markers and resulted in a state of dyslipidaemia. MMP-9 has also shown to be significantly increased in the untreated atherosclerosis rats and showed a significant correlation with all measured parameters. Interestingly, Carvedilol and bisphosphonate had almost equal effects restoring the measured parameters back to normal, partially or completely. Conclusion MMP-9 is a pivotal molecule that impact the atherogenic environment of the vessel wall. A strong cross talk exists between MMP-9, cytokine production and macrophage function. It also plays an important regulatory role in osteoclastogenesis. So, it may be a key molecule in charge for coupling CVD and bone diseases in high fat diet fed rats. Therefore, we suggest MMP-9 as a worthy molecule to be targeted pharmacologically in order to control both conditions simultaneously. Further studies are needed to support, to invest and to translate this hypothesis into clinical studies and guidelines.
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43
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Ferrari KJ, Amato S, Noberini R, Toscani C, Fernández-Pérez D, Rossi A, Conforti P, Zanotti M, Bonaldi T, Tamburri S, Pasini D. Intestinal differentiation involves cleavage of histone H3 N-terminal tails by multiple proteases. Nucleic Acids Res 2021; 49:791-804. [PMID: 33398338 PMCID: PMC7826276 DOI: 10.1093/nar/gkaa1228] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/14/2022] Open
Abstract
The proteolytic cleavage of histone tails, also termed histone clipping, has been described as a mechanism for permanent removal of post-translational modifications (PTMs) from histone proteins. Such activity has been ascribed to ensure regulatory function in key cellular processes such as differentiation, senescence and transcriptional control, for which different histone-specific proteases have been described. However, all these studies were exclusively performed using cell lines cultured in vitro and no clear evidence that histone clipping is regulated in vivo has been reported. Here we show that histone H3 N-terminal tails undergo extensive cleavage in the differentiated cells of the villi in mouse intestinal epithelium. Combining biochemical methods, 3D organoid cultures and in vivo approaches, we demonstrate that intestinal H3 clipping is the result of multiple proteolytic activities. We identified Trypsins and Cathepsin L as specific H3 tail proteases active in small intestinal differentiated cells and showed that their proteolytic activity is differentially affected by the PTM pattern of histone H3 tails. Together, our findings provide in vivo evidence of H3 tail proteolysis in mammalian tissues, directly linking H3 clipping to cell differentiation.
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Affiliation(s)
- Karin Johanna Ferrari
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Roberta Noberini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Cecilia Toscani
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Daniel Fernández-Pérez
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alessandra Rossi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Pasquale Conforti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Marika Zanotti
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simone Tamburri
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
| | - Diego Pasini
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy.,University of Milan, Department of Health Sciences, Via A. di Rudinì, 8, 20142 Milan, Italy
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44
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Caffrey PJ, Delaney S. Nucleosome Core Particles Lacking H2B or H3 Tails Are Altered Structurally and Have Differential Base Excision Repair Fingerprints. Biochemistry 2021; 60:210-218. [PMID: 33426868 DOI: 10.1021/acs.biochem.0c00877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A recently discovered post-translational modification of histone proteins is the irreversible proteolytic clipping of the histone N-terminal tail domains. This modification is involved in the regulation of various biological processes, including the DNA damage response. In this work, we used chemical footprinting to characterize the structural alterations to nucleosome core particles (NCPs) that result from a lack of a histone H2B or H3 tail. We also examine the influence of these histone tails on excision of the mutagenic lesion 1,N6-ethenoadenine (εA) by the repair enzyme alkyladenine DNA glycosylase. We found that the absence of the H2B or H3 tail results in altered DNA periodicity relative to that of native NCPs. We correlated these structural alterations to εA excision by utilizing a global analysis of 21 εA sites in NCPs and unincorporated duplex DNA. In comparison to native NCPs, there is enhanced excision of εA in tailless H2B NCPs in regions that undergo DNA unwrapping. This enhanced excision is not observed for tailless H3 NCPs; rather, excision is inhibited in more static areas of the NCP not prone to unwrapping. Our results support in vivo observations of alkylation damage profiles and the potential role of tail clipping as a mechanism for overcoming physical obstructions caused by packaging in NCPs but also reveal the potential inhibition of repair by tail clipping in some locations. Taken together, these results further our understanding of how base excision repair can be facilitated or diminished by histone tail removal and contribute to our understanding of the underlying mechanism that leads to mutational hot spots.
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Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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45
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Bassiouni W, Ali MAM, Schulz R. Multifunctional intracellular matrix metalloproteinases: implications in disease. FEBS J 2021; 288:7162-7182. [PMID: 33405316 DOI: 10.1111/febs.15701] [Citation(s) in RCA: 137] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that were first discovered as proteases, which target and cleave extracellular proteins. During the past 20 years, however, intracellular roles of MMPs were uncovered and research on this new aspect of their biology expanded. MMP-2 is the first of this protease family to be reported to play a crucial intracellular role where it cleaves several sarcomeric proteins inside cardiac myocytes during oxidative stress-induced injury. Beyond MMP-2, currently at least eleven other MMPs are known to function intracellularly including MMP-1, MMP-3, MMP-7, MMP-8, MMP-9, MMP-10, MMP-11, MMP-12, MMP-14, MMP-23 and MMP-26. These intracellular MMPs are localized to different compartments inside the cell including the cytosol, sarcomere, mitochondria, and the nucleus. Intracellular MMPs contribute to the pathogenesis of various diseases. Cardiovascular renal disorders, inflammation, and malignancy are some examples. They also exert antiviral and bactericidal effects. Interestingly, MMPs can act intracellularly through both protease-dependent and protease-independent mechanisms. In this review, we will highlight the intracellular mechanisms of MMPs activation, their numerous subcellular locales, substrates, and roles in different pathological conditions. We will also discuss the future direction of MMP research and the necessity to exploit the knowledge of their intracellular targets and actions for the design of targeted inhibitors.
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Affiliation(s)
- Wesam Bassiouni
- Department of Pharmacology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Mohammad A M Ali
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, State University of New York-Binghamton, NY, USA
| | - Richard Schulz
- Department of Pharmacology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada.,Department of Pediatrics, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
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46
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Frolova AS, Petushkova AI, Makarov VA, Soond SM, Zamyatnin AA. Unravelling the Network of Nuclear Matrix Metalloproteinases for Targeted Drug Design. BIOLOGY 2020; 9:E480. [PMID: 33352765 PMCID: PMC7765953 DOI: 10.3390/biology9120480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
Matrix metalloproteinases (MMPs) are zinc-dependent endopeptidases that are responsible for the degradation of a wide range of extracellular matrix proteins, which are involved in many cellular processes to ensure the normal development of tissues and organs. Overexpression of MMPs has been observed to facilitate cellular growth, migration, and metastasis of tumor cells during cancer progression. A growing number of these proteins are being found to exist in the nuclei of both healthy and tumor cells, thus highlighting their localization as having a genuine purpose in cellular homeostasis. The mechanism underlying nuclear transport and the effects of MMP nuclear translocation have not yet been fully elucidated. To date, nuclear MMPs appear to have a unique impact on cellular apoptosis and gene regulation, which can have effects on immune response and tumor progression, and thus present themselves as potential therapeutic targets in certain types of cancer or disease. Herein, we highlight and evaluate what progress has been made in this area of research, which clearly has some value as a specific and unique way of targeting the activity of nuclear matrix metalloproteinases within various cell types.
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Affiliation(s)
- Anastasia S. Frolova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.S.F.); (A.I.P.); (V.A.M.); (S.M.S.)
| | - Anastasiia I. Petushkova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.S.F.); (A.I.P.); (V.A.M.); (S.M.S.)
| | - Vladimir A. Makarov
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.S.F.); (A.I.P.); (V.A.M.); (S.M.S.)
| | - Surinder M. Soond
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.S.F.); (A.I.P.); (V.A.M.); (S.M.S.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, 119991 Moscow, Russia; (A.S.F.); (A.I.P.); (V.A.M.); (S.M.S.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biotechnology, Sirius University of Science and Technology, 1 Olympic Ave., 354340 Sochi, Russia
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Nagakannan P, Islam MI, Conrad M, Eftekharpour E. Cathepsin B is an executioner of ferroptosis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118928. [PMID: 33340545 DOI: 10.1016/j.bbamcr.2020.118928] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/21/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022]
Abstract
Ferroptosis is a necrotic form of cell death caused by inactivation of the glutathione system and uncontrolled iron-mediated lipid peroxidation. Increasing evidence implicates ferroptosis in a wide range of diseases from neurotrauma to cancer, highlighting the importance of identifying an executioner system that can be exploited for clinical applications. In this study, using pharmacological and genetic models of ferroptosis, we observed that lysosomal membrane permeabilization and cytoplasmic leakage of cathepsin B unleashes structural and functional changes in mitochondria and promotes a not previously reported cleavage of histone H3. Inhibition of cathepsin-B robustly rescued cellular membrane integrity and chromatin degradation. We show that these protective effects are independent of glutathione peroxidase-4 and are mediated by preventing lysosomal membrane damage. This was further confirmed when cathepsin B knockout primary fibroblasts remained unaffected in response to various ferroptosis inducers. Our work identifies new and yet-unrecognized aspects of ferroptosis and identifies cathepsin B as a mediator of ferroptotic cell death.
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Affiliation(s)
- Pandian Nagakannan
- Department of Physiology and Pathophysiology, Regenerative Medicine Program and Spinal Cord Research Centre, University of Manitoba, Winnipeg, Canada
| | - Md Imamul Islam
- Department of Physiology and Pathophysiology, Regenerative Medicine Program and Spinal Cord Research Centre, University of Manitoba, Winnipeg, Canada
| | - Marcus Conrad
- Institute for Metabolism and Cell Death, Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Eftekhar Eftekharpour
- Department of Physiology and Pathophysiology, Regenerative Medicine Program and Spinal Cord Research Centre, University of Manitoba, Winnipeg, Canada.
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Tsukasaki M, Huynh NCN, Okamoto K, Muro R, Terashima A, Kurikawa Y, Komatsu N, Pluemsakunthai W, Nitta T, Abe T, Kiyonari H, Okamura T, Sakai M, Matsukawa T, Matsumoto M, Kobayashi Y, Penninger JM, Takayanagi H. Stepwise cell fate decision pathways during osteoclastogenesis at single-cell resolution. Nat Metab 2020; 2:1382-1390. [PMID: 33288951 DOI: 10.1038/s42255-020-00318-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 11/04/2020] [Indexed: 12/16/2022]
Abstract
Osteoclasts are the exclusive bone-resorbing cells, playing a central role in bone metabolism, as well as the bone damage that occurs under pathological conditions1,2. In postnatal life, haematopoietic stem-cell-derived precursors give rise to osteoclasts in response to stimulation with macrophage colony-stimulating factor and receptor activator of nuclear factor-κB ligand, both of which are produced by osteoclastogenesis-supporting cells such as osteoblasts and osteocytes1-3. However, the precise mechanisms underlying cell fate specification during osteoclast differentiation remain unclear. Here, we report the transcriptional profiling of 7,228 murine cells undergoing in vitro osteoclastogenesis, describing the stepwise events that take place during the osteoclast fate decision process. Based on our single-cell transcriptomic dataset, we find that osteoclast precursor cells transiently express CD11c, and deletion of receptor activator of nuclear factor-κB specifically in CD11c-expressing cells inhibited osteoclast formation in vivo and in vitro. Furthermore, we identify Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 2 (Cited2) as the molecular switch triggering terminal differentiation of osteoclasts, and deletion of Cited2 in osteoclast precursors in vivo resulted in a failure to commit to osteoclast fate. Together, the results of this study provide a detailed molecular road map of the osteoclast differentiation process, refining and expanding our understanding of the molecular mechanisms underlying osteoclastogenesis.
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Affiliation(s)
- Masayuki Tsukasaki
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nam Cong-Nhat Huynh
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuo Okamoto
- Department of Osteoimmunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryunosuke Muro
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Asuka Terashima
- Department of Osteoimmunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshitaka Kurikawa
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Komatsu
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Warunee Pluemsakunthai
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nitta
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Mashito Sakai
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Toshiya Matsukawa
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Michihiro Matsumoto
- Department of Molecular Metabolic Regulation, Diabetes Research Center, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yasuhiro Kobayashi
- Division of Hard Tissue Research, Institute for Oral Science, Matsumoto Dental University, Shiojiri, Japan
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Science, Vienna, Austria
- Life Science Institute, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Hiroshi Takayanagi
- Department of Immunology, Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
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Poe AJ, Kulkarni M, Leszczynska A, Tang J, Shah R, Jami-Alahmadi Y, Wang J, Kramerov AA, Wohlschlegel J, Punj V, Ljubimov AV, Saghizadeh M. Integrated Transcriptome and Proteome Analyses Reveal the Regulatory Role of miR-146a in Human Limbal Epithelium via Notch Signaling. Cells 2020; 9:cells9102175. [PMID: 32993109 PMCID: PMC7650592 DOI: 10.3390/cells9102175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
MiR-146a is upregulated in the stem cell-enriched limbal region vs. central human cornea and can mediate corneal epithelial wound healing. The aim of this study was to identify miR-146a targets in human primary limbal epithelial cells (LECs) using genomic and proteomic analyses. RNA-seq combined with quantitative proteomics based on multiplexed isobaric tandem mass tag labeling was performed in LECs transfected with miR-146a mimic vs. mimic control. Western blot and immunostaining were used to confirm the expression of some targeted genes/proteins. A total of 251 differentially expressed mRNAs and 163 proteins were identified. We found that miR-146a regulates the expression of multiple genes in different pathways, such as the Notch system. In LECs and organ-cultured corneas, miR-146a increased Notch-1 expression possibly by downregulating its inhibitor Numb, but decreased Notch-2. Integrated transcriptome and proteome analyses revealed the regulatory role of miR-146a in several other processes, including anchoring junctions, TNF-α, Hedgehog signaling, adherens junctions, TGF-β, mTORC2, and epidermal growth factor receptor (EGFR) signaling, which mediate wound healing, inflammation, and stem cell maintenance and differentiation. Our results provide insights into the regulatory network of miR-146a and its role in fine-tuning of Notch-1 and Notch-2 expressions in limbal epithelium, which could be a balancing factor in stem cell maintenance and differentiation.
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Affiliation(s)
- Adam J. Poe
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Mangesh Kulkarni
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Aleksandra Leszczynska
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA;
| | - Ruchi Shah
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; (Y.J.-A.); (J.W.)
| | - Jason Wang
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Andrei A. Kramerov
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA; (Y.J.-A.); (J.W.)
| | - Vasu Punj
- Department of Medicine, University of Southern California, Los Angeles, CA 90089, USA;
| | - Alexander V. Ljubimov
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Mehrnoosh Saghizadeh
- Board of Governors Regenerative Medicine Institute, Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; (A.J.P.); (M.K.); (A.L.); (R.S.); (J.W.); (A.A.K.); (A.V.L.)
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Correspondence: ; Tel.: +1-310-248-8696
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50
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Kurotaki D, Yoshida H, Tamura T. Epigenetic and transcriptional regulation of osteoclast differentiation. Bone 2020; 138:115471. [PMID: 32526404 DOI: 10.1016/j.bone.2020.115471] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 01/28/2023]
Abstract
Osteoclasts are derived from mononuclear phagocyte lineage cells and are indispensable for bone resorption. Recent findings suggest that fetal yolk sac macrophage progenitors give rise to neonatal osteoclasts, while hematopoietic stem cell-derived cells, such as monocytes, contribute to maintaining osteoclast syncytia in vivo. Osteoclast differentiation is dependent on macrophage colony-stimulating factor (M-CSF) and receptor activator of nuclear factor-κB ligand (RANKL) signaling that mediates global epigenetic and transcriptional changes. PU.1 is a transcription factor that establishes cell type-specific enhancer landscapes in osteoclast precursors and mature osteoclasts by collaborating with interferon regulatory factor-8 (IRF8) and nuclear factor of activated T-cells (NFATc1), respectively. Irf8 and Nfatc1 genes are tightly controlled by epigenetic mechanisms such as DNA methylation and histone modifications during osteoclastogenesis. Thus, key transcription factors orchestrate osteoclast-specific transcription regulatory networks through epigenetic modifications. In this review, we discuss recent advances in our understanding of the molecular mechanisms involved in osteoclast development.
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Affiliation(s)
- Daisuke Kurotaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
| | - Haruka Yoshida
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
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