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Matoba S, Shikata D, Shirai F, Tatebe T, Hirose M, Nakata A, Watanabe N, Hasegawa A, Ito A, Yoshida M, Ogura A. Reduction of H3K9 methylation by G9a inhibitors improves the development of mouse SCNT embryos. Stem Cell Reports 2024; 19:906-921. [PMID: 38729154 DOI: 10.1016/j.stemcr.2024.04.003] [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: 12/01/2023] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
Removal of somatic histone H3 lysine 9 trimethylation (H3K9me3) from the embryonic genome can improve the efficiency of mammalian cloning using somatic cell nuclear transfer (SCNT). However, this strategy involves the injection of histone demethylase mRNA into embryos, which is limiting because of its invasive and labor-consuming nature. Here, we report that treatment with an inhibitor of G9a (G9ai), the major histone methyltransferase that introduces H3K9me1/2 in mammals, greatly improved the development of mouse SCNT embryos. Intriguingly, G9ai caused an immediate reduction of H3K9me1/2, a secondary loss of H3K9me3 in SCNT embryos, and increased the birth rate of cloned pups about 5-fold (up to 3.9%). G9ai combined with the histone deacetylase inhibitor trichostatin A further improved this rate to 14.5%. Mechanistically, G9ai and TSA synergistically enhanced H3K9me3 demethylation and boosted zygotic genome activation. Thus, we established an easy, highly effective SCNT protocol that would enhance future cloning research and applications.
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Affiliation(s)
- Shogo Matoba
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
| | - Daiki Shikata
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Fumiyuki Shirai
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takaki Tatebe
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akiko Nakata
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naomi Watanabe
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akihiro Ito
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Office of University Professors, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; The Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan; Bioresource Engineering Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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Li X, Wang C, Wang Y, Chen X, Li Z, Wang J, Liu Y. Integrated analysis of the role of PR/SET domain 14 in gastric cancer. BMC Cancer 2024; 24:685. [PMID: 38840106 PMCID: PMC11151633 DOI: 10.1186/s12885-024-12424-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/24/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Gastric cancer is one of the most common tumors worldwide, and most patients are deprived of treatment options when diagnosed at advanced stages. PRDM14 has carcinogenic potential in breast and non-small cell lung cancer. however, its role in gastric cancer has not been elucidated. METHODS We aimed to elucidate the expression of PRDM14 using pan-cancer analysis. We monitored the expression of PRDM14 in cells and patients using quantitative polymerase chain reaction, western blotting, and immunohistochemistry. We observed that cell phenotypes and regulatory genes were influenced by PRDM14 by silencing PRDM14. We evaluated and validated the value of the PRDM14-derived prognostic model. Finally, we predicted the relationship between PRDM14 and small-molecule drug responses using the Connectivity Map and The Genomics of Drug Sensitivity in Cancer databases. RESULTS PRDM14 was significantly overexpressed in gastric cancer, which identified in cell lines and patients' tissues. Silencing the expression of PRDM14 resulted in apoptosis promotion, cell cycle arrest, and inhibition of the growth and migration of GC cells. Functional analysis revealed that PRDM14 acts in epigenetic regulation and modulates multiple DNA methyltransferases or transcription factors. The PRDM14-derived differentially expressed gene prognostic model was validated to reliably predict the patient prognosis. Nomograms (age, sex, and PRDM14-risk score) were used to quantify the probability of survival. PRDM14 was positively correlated with sensitivity to small-molecule drugs such as TPCA-1, PF-56,227, mirin, and linsitinib. CONCLUSIONS Collectively, our findings suggest that PRDM14 is a positive regulator of gastric cancer progression. Therefore, it may be a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Xiao Li
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Cong Wang
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Youcai Wang
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xiaobing Chen
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhi Li
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jianwei Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China.
| | - Yingjun Liu
- Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China.
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Pastoors D, Havermans M, Mulet-Lazaro R, Brian D, Noort W, Grasel J, Hoogenboezem R, Smeenk L, Demmers JAA, Milsom MD, Enver T, Groen RWJ, Bindels E, Delwel R. Oncogene EVI1 drives acute myeloid leukemia via a targetable interaction with CTBP2. SCIENCE ADVANCES 2024; 10:eadk9076. [PMID: 38748792 PMCID: PMC11095456 DOI: 10.1126/sciadv.adk9076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/10/2024] [Indexed: 05/19/2024]
Abstract
Acute myeloid leukemia (AML) driven by the activation of EVI1 due to chromosome 3q26/MECOM rearrangements is incurable. Because transcription factors such as EVI1 are notoriously hard to target, insight into the mechanism by which EVI1 drives myeloid transformation could provide alternative avenues for therapy. Applying protein folding predictions combined with proteomics technologies, we demonstrate that interaction of EVI1 with CTBP1 and CTBP2 via a single PLDLS motif is indispensable for leukemic transformation. A 4× PLDLS repeat construct outcompetes binding of EVI1 to CTBP1 and CTBP2 and inhibits proliferation of 3q26/MECOM rearranged AML in vitro and in xenotransplant models. This proof-of-concept study opens the possibility to target one of the most incurable forms of AML with specific EVI1-CTBP inhibitors. This has important implications for other tumor types with aberrant expression of EVI1 and for cancers transformed by different CTBP-dependent oncogenic transcription factors.
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Affiliation(s)
- Dorien Pastoors
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Marije Havermans
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Duncan Brian
- Stem Cell Group, UCL Cancer Institute, University College London, London, UK
| | - Willy Noort
- Department of Hematology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer biology and immunology, Amsterdam, Netherlands
| | - Julius Grasel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
- Division of Experimental Hematology, German Cancer Research Center, DKFZ69120 Heidelberg, Germany
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Leonie Smeenk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Michael D. Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany
- Division of Experimental Hematology, German Cancer Research Center, DKFZ69120 Heidelberg, Germany
| | - Tariq Enver
- Stem Cell Group, UCL Cancer Institute, University College London, London, UK
| | - Richard W. J. Groen
- Department of Hematology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer biology and immunology, Amsterdam, Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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Koryakov DE. Diversity and functional specialization of H3K9-specific histone methyltransferases. Bioessays 2024; 46:e2300163. [PMID: 38058121 DOI: 10.1002/bies.202300163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
Histone modifications play a critical role in the control over activities of the eukaryotic genome; among these chemical alterations, the methylation of lysine K9 in histone H3 (H3K9) is one of the most extensively studied. The number of enzymes capable of methylating H3K9 varies greatly across different organisms: in fission yeast, only one such methyltransferase is present, whereas in mammals, 10 are known. If there are several such enzymes, each of them must have some specific function, and they can interact with one another. Thus arises a complex system of interchangeability, "division of labor," and contacts with each other and with diverse proteins. Histone methyltransferases specialize in the number of methyl groups that they attach and have different intracellular localizations as well as different distributions on chromosomes. Each also shows distinct binding to different types of sequences and has a specific set of nonhistone substrates.
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Affiliation(s)
- Dmitry E Koryakov
- Lab of Molecular Cytogenetics, Institute of Molecular and Cellular Biology, Novosibirsk, Russia
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Suresh V, Bhattacharya B, Tshuva RY, Danan Gotthold M, Olender T, Bose M, Pradhan SJ, Zeev BB, Smith RS, Tole S, Galande S, Harwell CC, Baizabal JM, Reiner O. PRDM16 co-operates with LHX2 to shape the human brain. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae001. [PMID: 38595939 PMCID: PMC10914218 DOI: 10.1093/oons/kvae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/24/2023] [Accepted: 12/15/2023] [Indexed: 04/11/2024]
Abstract
PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a de novo nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.
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Affiliation(s)
- Varun Suresh
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Navy Nagar, Colaba, Mumbai 400005, India
| | - Bidisha Bhattacharya
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
| | - Rami Yair Tshuva
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
| | - Miri Danan Gotthold
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
| | - Mahima Bose
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Navy Nagar, Colaba, Mumbai 400005, India
| | - Saurabh J Pradhan
- Chromatin Biology and Epigenetics Laboratory, Biology Department, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter, 3 Dr. Bohr-Gasse, 1030 Vienna, Austria
| | - Bruria Ben Zeev
- Edmond and Lily Safra Pediatric Hospital, Sheba Medical Center and Tel Aviv School of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Richard Scott Smith
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, 320 E. Superior St., Chicago, IL 60611, USA
| | - Shubha Tole
- Department of Biological Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Navy Nagar, Colaba, Mumbai 400005, India
| | - Sanjeev Galande
- Chromatin Biology and Epigenetics Laboratory, Biology Department, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Department of Life Sciences, Center of Excellence in Epigenetics, Shiv Nadar University, Shiv Nadar IoE, Gautam Buddha Nagar, Uttar Pradesh - 201314, India
| | - Corey C Harwell
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, 35 Medical Center Way, San Francisco, CA 94143, USA
- Weill Institute for Neuroscience, 1651 4th St, San Francisco, CA94158, USA
- Department of Neurology, University of California, San Francisco, 505 Parnassus Ave, San Francisco, CA 94143, USA
| | - José-Manuel Baizabal
- Department of Biology, Indiana University, 1001 E 3rd St., Bloomington, IN 47405, USA
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, 234 Herzl St., Rehovot 7610001, Israel
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Li A, Li M, Wang J, Zhou J, Yang T, Fan M, Zhang K, Gao H, Ren H, Chen M. MECOM: a bioinformatics and experimentally identified marker for the diagnosis and prognosis of lung adenocarcinoma. Biomark Med 2024; 18:79-91. [PMID: 38440890 DOI: 10.2217/bmm-2023-0600] [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] [Indexed: 03/06/2024] Open
Abstract
Objective: We aimed to explore the clinical value of MDS1 and EVI1 complex locus (MECOM) in lung adenocarcinoma (LUAD). Methods: Bioinformatics and experimental validation confirmed MECOM expression levels in LUAD. The value of MECOM was analyzed by receiver operating characteristic (ROC) curve and Cox regression analysis. Results: Serum MECOM levels were lower in LUAD and correlated with gender, TNM stage, tumor size, lymph node metastasis and distant metastasis. The ROC curve showed that the area under the curve of MECOM was 0.804 for LUAD and, of note, could reach 0.889 for advanced LUAD; specificity was up to 90%. Conclusion: MECOM may contribute to independently identifying LUAD patients, particularly in advanced stages.
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Affiliation(s)
- Anqi Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Li
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jing Wang
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
| | - Jiejun Zhou
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Tian Yang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meng Fan
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kun Zhang
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hengxing Gao
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hui Ren
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mingwei Chen
- Department of Respiratory & Critical Care Medicine, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
- Department of Pulmonary & Critical Care Medicine, Shaanxi Provincial Second People's Hospital, Xi'an, 710005, China
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [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: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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Romanov SE, Shloma VV, Maksimov DA, Koryakov DE. SetDB1 and Su(var)3-9 are essential for late stages of larval development of Drosophila melanogaster. Chromosome Res 2023; 31:35. [PMID: 38099968 DOI: 10.1007/s10577-023-09743-7] [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: 04/19/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Methylation of H3K9 histone residue is a marker of gene silencing in eukaryotes. Three enzymes responsible for adding this modification - G9a, SetDB1/Egg, and Su(var)3-9 - are known in Drosophila. To understand how simultaneous mutations of SetDB1 and Su(var)3-9 may affect the fly development, appropriate combinations were obtained. Double mutants egg; Su(var)3-9 displayed pronounced embryonic lethality, slower larval growth and died before or during metamorphosis. Analysis of transcription in larval salivary glands and wing imaginal disks indicated that the effect of double mutation is tissue-specific. In salivary gland chromosomes, affected genes display low H3K9me2 enrichment and are rarely bound by SetDB1 or Su(var)3-9. We suppose that each of these enzymes directly or indirectly controls its own set of gene targets in different organs, and double mutation results in an imbalanced developmental program. This also indicates that SetDB1 and Su(var)3-9 may affect transcription via H3K9-independent mechanisms. Unexpectedly, in double and triple mutants, amount of di- and tri-methylated H3K9 is drastically reduced, but not completely absent. We hypothesize that this residual methylation implies the existence of additional H3K9-specific methyltransferase in Drosophila.
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Affiliation(s)
- Stanislav E Romanov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
| | - Viktor V Shloma
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
| | - Daniil A Maksimov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia
| | - Dmitry E Koryakov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, 630090, Russia.
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Mehta D, de Boer I, Sutherland HG, Pijpers JA, Bron C, Bainomugisa C, Haupt LM, van den Maagdenberg AMJM, Griffiths LR, Nyholt DR, Terwindt GM. Alterations in DNA methylation associate with reduced migraine and headache days after medication withdrawal treatment in chronic migraine patients: a longitudinal study. Clin Epigenetics 2023; 15:190. [PMID: 38087366 PMCID: PMC10717674 DOI: 10.1186/s13148-023-01604-8] [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: 05/31/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Chronic migraine, a highly disabling migraine subtype, affects nearly 2% of the general population. Understanding migraine chronification is vital for developing better treatment and prevention strategies. An important factor in the chronification of migraine is the overuse of acute headache medication. However, the mechanisms behind the transformation of episodic migraine to chronic migraine and vice versa have not yet been elucidated. We performed a longitudinal epigenome-wide association study to identify DNA methylation (DNAm) changes associated with treatment response in patients with chronic migraine and medication overuse as part of the Chronification and Reversibility of Migraine clinical trial. Blood was taken from patients with chronic migraine (n = 98) at baseline and after a 12-week medication withdrawal period. Treatment responders, patients with ≥ 50% reduction in monthly headache days (MHD), were compared with non-responders to identify DNAm changes associated with treatment response. Similarly, patients with ≥ 50% versus < 50% reduction in monthly migraine days (MMD) were compared. RESULTS At the epigenome-wide significant level (p < 9.42 × 10-8), a longitudinal reduction in DNAm at an intronic CpG site (cg14377273) within the HDAC4 gene was associated with MHD response following the withdrawal of acute medication. HDAC4 is highly expressed in the brain, plays a major role in synaptic plasticity, and modulates the expression and release of several neuroinflammation markers which have been implicated in migraine pathophysiology. Investigating whether baseline DNAm associated with treatment response, we identified lower baseline DNAm at a CpG site (cg15205829) within MARK3 that was significantly associated with MMD response at 12 weeks. CONCLUSIONS Our findings of a longitudinal reduction in HDAC4 DNAm status associated with treatment response and baseline MARK3 DNAm status as an early biomarker for treatment response, provide support for a role of pathways related to chromatin structure and synaptic plasticity in headache chronification and introduce HDAC4 and MARK3 as novel therapeutic targets.
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Affiliation(s)
- Divya Mehta
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- Centre for Data Science, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Irene de Boer
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Heidi G Sutherland
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Judith A Pijpers
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Charlene Bron
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Charlotte Bainomugisa
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- Centre for Data Science, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia
| | - Arn M J M van den Maagdenberg
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia
| | - Dale R Nyholt
- Centre for Genomics and Personalised Health, Queensland University of Technology, 60 Musk Avenue, Brisbane, QLD, 4059, Australia.
- Centre for Data Science, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, 2 George Street, Brisbane, QLD, 4000, Australia.
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Center, Albinusdreef 2, PO Box 9600, 2300 RC, Leiden, The Netherlands.
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10
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Barbachowska M, Arimondo PB. To target or not to target? The role of DNA and histone methylation in bacterial infections. Epigenetics 2023; 18:2242689. [PMID: 37731322 PMCID: PMC10515666 DOI: 10.1080/15592294.2023.2242689] [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: 12/16/2022] [Accepted: 07/25/2023] [Indexed: 09/22/2023] Open
Abstract
Epigenetics describes chemical modifications of the genome that do not alter DNA sequence but participate in the regulation of gene expression and cellular processes such as proliferation, division, and differentiation of eukaryotic cell. Disruption of the epigenome pattern in a human cell is associated with different diseases, including infectious diseases. During infection pathogens induce epigenetic modifications in the host cell. This can occur by controlling expression of genes involved in immune response. That enables bacterial survival and replication within the host and evasion of the immune response. Methylation is an example of epigenetic modification that occurs on DNA and histones. Reasoning that DNA and histone methylation of human host cells plays a crucial role during pathogenesis, these modifications are promising targets for the development of alternative treatment strategies in infectious diseases. Here, we discuss the role of DNA and histone methyltransferases in human host cell upon bacterial infections. We further hypothesize that compounds targeting methyltransferases are tools to study epigenetics in the context of host-pathogen interactions and can open new avenues for the treatment of bacterial infections.
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Affiliation(s)
- Magdalena Barbachowska
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
- Universite Paris Cité, Ecole Doctorale MTCI, Paris, France
- Institut Pasteur, Pasteur- Paris University (PPU)- Oxford International Doctoral Program, Paris, France
| | - Paola B. Arimondo
- Institut Pasteur, Université Paris Cité, CNRS UMR n°3523 Chem4Life, Epigenetic Chemical Biology, Department of Structural Biology and Chemistry, Paris, France
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11
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Mozhui K, Kim H, Villani F, Haghani A, Sen S, Horvath S. Pleiotropic influence of DNA methylation QTLs on physiological and ageing traits. Epigenetics 2023; 18:2252631. [PMID: 37691384 PMCID: PMC10496549 DOI: 10.1080/15592294.2023.2252631] [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: 05/01/2023] [Revised: 07/31/2023] [Accepted: 08/16/2023] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. Trans-modulated CpGs showed age-dependent changes and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and ageing resulted in a more 'aged methylome' for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analyses identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variations in body size and metabolic traits, and influence CpG methylation and epigenetic ageing that could have an impact on lifespan.
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Affiliation(s)
- Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hyeonju Kim
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Saunak Sen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
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12
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Cho HI, Jo S, Kim MS, Kim HB, Liu X, Xuan Y, Cho JW, Jang YK. SETD5 regulates the OGT-catalyzed O-GlcNAcylation of RNA polymerase II, which is involved in the stemness of colorectal cancer cells. Sci Rep 2023; 13:19885. [PMID: 37963940 PMCID: PMC10646014 DOI: 10.1038/s41598-023-46923-1] [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: 06/16/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023] Open
Abstract
The dosage-dependent recruitment of RNA polymerase II (Pol II) at the promoters of genes related to neurodevelopment and stem cell maintenance is required for transcription by the fine-tuned expression of SET-domain-containing protein 5 (SETD5). Pol II O-GlcNAcylation by O-GlcNAc transferase (OGT) is critical for preinitiation complex formation and transcription cycling. SETD5 dysregulation has been linked to stem cell-like properties in some cancer types; however, the role of SETD5 in cancer cell stemness has not yet been determined. We here show that aberrant SETD5 overexpression induces stemness in colorectal cancer (CRC) cells. SETD5 overexpression causes the upregulation of PI3K-AKT pathway-related genes and cancer stem cell (CSC) markers such as CD133, Kruppel-like factor 4 (KLF4), and estrogen-related receptor beta (ESRRB), leading to the gain of stem cell-like phenotypes. Our findings also revealed a functional relationship between SETD5, OGT, and Pol II. OGT-catalyzed Pol II glycosylation depends on SETD5, and the SETD5-Pol II interaction weakens in OGT-depleted cells, suggesting a SETD5-OGT-Pol II interdependence. SETD5 deficiency reduces Pol II occupancy at PI3K-AKT pathway-related genes and CD133 promoters, suggesting a role for SETD5-mediated Pol II recruitment in gene regulation. Moreover, the SETD5 depletion nullified the SETD5-induced stemness of CRC cells and Pol II O-GlcNAcylation. These findings support the hypothesis that SETD5 mediates OGT-catalyzed O-GlcNAcylation of RNA Pol II, which is involved in cancer cell stemness gain via CSC marker gene upregulation.
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Affiliation(s)
- Hye In Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Initiative for Biological Function & Systems, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sora Jo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Initiative for Biological Function & Systems, Yonsei University, Seoul, 03722, Republic of Korea
| | - Min Seong Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Han Byeol Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Department of Neurology, Institute for Cell Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Xingzhe Liu
- Department of Pathology, Yanbian University College of Medicine, No.977, Gongyuan Road, Yanji, 133002, China
| | - Yanhua Xuan
- Department of Pathology, Yanbian University College of Medicine, No.977, Gongyuan Road, Yanji, 133002, China.
| | - Jin Won Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Yeun Kyu Jang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Initiative for Biological Function & Systems, Yonsei University, Seoul, 03722, Republic of Korea.
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13
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Xu H, Tan S, Zhao Y, Zhang L, Cao W, Li X, Tian J, Wang X, Li X, Wang F, Cao J, Zhao T. Lin - PU.1 dim GATA-1 - defines haematopoietic stem cells with long-term multilineage reconstitution activity. Cell Prolif 2023; 56:e13490. [PMID: 37147872 PMCID: PMC10623959 DOI: 10.1111/cpr.13490] [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: 02/10/2023] [Revised: 04/10/2023] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
Despite extensive characterization of the state and function of haematopoietic stem cells (HSCs), the use of transcription factors to define the HSC population is still limited. We show here that the HSC population in mouse bone marrow can be defined by the distinct expression levels of Spi1 and Gata1. By using a double fluorescence knock-in mouse model, PGdKI, in which the expression levels of PU.1 and GATA-1 are indicated by the expression of GFP and mCherry, respectively, we uncover that the HSCs with lymphoid and myeloid repopulating activity are specifically enriched in a Lin- PU.1dim GATA-1- (LPG) cell subset. In vivo competitive repopulation assays demonstrate that bone marrow cells gated by LPG exhibit haematopoietic reconstitution activity which is comparable to that of classical Lin- Sca1+ c-kit+ (LSK). The integrated analysis of single-cell RNA sequence data from LPG and LSK-gated cells reveals that a transcriptional network governed by core TFs contributes to regulation of HSC multipotency. These discoveries provide new clues for HSC characterization and functional study.
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Affiliation(s)
- Haoyu Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaojing Tan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lin Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weiyun Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xing Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jiayi Tian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaojing Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaoyan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fengchao Wang
- National Institute of Biological Sciences (NIBS)BeijingChina
| | - Jiani Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tongbiao Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of ZoologyChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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14
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Canat A, Veillet A, Batrin R, Dubourg C, Lhoumaud P, Arnau-Romero P, Greenberg MVC, Bonhomme F, Arimondo PB, Illingworth R, Fabre E, Therizols P. DAXX safeguards heterochromatin formation in embryonic stem cells. J Cell Sci 2023; 136:jcs261092. [PMID: 37655670 DOI: 10.1242/jcs.261092] [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: 02/24/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023] Open
Abstract
Genomes comprise a large fraction of repetitive sequences folded into constitutive heterochromatin, which protect genome integrity and cell identity. De novo formation of heterochromatin during preimplantation development is an essential step for preserving the ground-state of pluripotency and the self-renewal capacity of embryonic stem cells (ESCs). However, the molecular mechanisms responsible for the remodeling of constitutive heterochromatin are largely unknown. Here, we identify that DAXX, an H3.3 chaperone essential for the maintenance of mouse ESCs in the ground state, accumulates in pericentromeric regions independently of DNA methylation. DAXX recruits PML and SETDB1 to promote the formation of heterochromatin, forming foci that are hallmarks of ground-state ESCs. In the absence of DAXX or PML, the three-dimensional (3D) architecture and physical properties of pericentric and peripheral heterochromatin are disrupted, resulting in de-repression of major satellite DNA, transposable elements and genes associated with the nuclear lamina. Using epigenome editing tools, we observe that H3.3, and specifically H3.3K9 modification, directly contribute to maintaining pericentromeric chromatin conformation. Altogether, our data reveal that DAXX is crucial for the maintenance and 3D organization of the heterochromatin compartment and protects ESC viability.
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Affiliation(s)
- Antoine Canat
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Adeline Veillet
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Renaud Batrin
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Clara Dubourg
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | | | - Pol Arnau-Romero
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | | | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Paola B Arimondo
- Institut Pasteur, Université Paris Cité, CNRS, Epigenetic Chemical Biology, UMR 3523, F-75724 Paris, France
| | - Robert Illingworth
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh BioQuarter, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Emmanuelle Fabre
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
| | - Pierre Therizols
- Université de Paris, Laboratoire Génomes, Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Institut de Recherche St Louis, F-75010 Paris, France
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15
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Suresh V, Bhattacharya B, Tshuva RY, Danan Gotthold M, Olender T, Bose M, Pradhan SJ, Ben Zeev B, Smith RS, Tole S, Galande S, Harwell C, Baizabal JM, Reiner O. PRDM16 co-operates with LHX2 to shape the human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.12.553065. [PMID: 37609127 PMCID: PMC10441425 DOI: 10.1101/2023.08.12.553065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
PRDM16 is a dynamic transcriptional regulator of various stem cell niches, including adipocytic, hematopoietic, cardiac progenitors, and neural stem cells. PRDM16 has been suggested to contribute to 1p36 deletion syndrome, one of the most prevalent subtelomeric microdeletion syndromes. We report a patient with a de novo nonsense mutation in the PRDM16 coding sequence, accompanied by lissencephaly and microcephaly features. Human stem cells were genetically modified to mimic this mutation, generating cortical organoids that exhibited altered cell cycle dynamics. RNA sequencing of cortical organoids at day 32 unveiled changes in cell adhesion and WNT-signaling pathways. ChIP-seq of PRDM16 identified binding sites in postmortem human fetal cortex, indicating the conservation of PRDM16 binding to developmental genes in mice and humans, potentially at enhancer sites. A shared motif between PRDM16 and LHX2 was identified and further examined through comparison with LHX2 ChIP-seq data from mice. These results suggested a collaborative partnership between PRDM16 and LHX2 in regulating a common set of genes and pathways in cortical radial glia cells, possibly via their synergistic involvement in cortical development.
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16
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Zhao F, Guo X, Li X, Liu F, Fu Y, Sun X, Yang Z, Zhang Z, Qin Z. Identification and Expressional Analysis of Putative PRDI-BF1 and RIZ Homology Domain-Containing Transcription Factors in Mulinia lateralis. BIOLOGY 2023; 12:1059. [PMID: 37626944 PMCID: PMC10451705 DOI: 10.3390/biology12081059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
Mollusca represents one of the ancient bilaterian groups with high morphological diversity, while the formation mechanisms of the precursors of all germ cells, primordial germ cells (PGCs), have not yet been clarified in mollusks. PRDI-BF1 and RIZ homology domain-containing proteins (PRDMs) are a group of transcriptional repressors, and PRDM1 (also known as BLIMP1) and PRDM14 have been reported to be essential for the formation of PGCs. In the present study, we performed a genome-wide retrieval in Mulinia lateralis and identified 11 putative PRDMs, all of which possessed an N-terminal PR domain. Expressional profiles revealed that all these prdm genes showed specifically high expression levels in the given stages, implying that all PRDMs played important roles during early development stages. Specifically, Ml-prdm1 was highly expressed at the gastrula stage, the key period when PGCs arise, and was specifically localized in the cytoplasm of two or three cells of blastula, gastrula, or trochophore larvae, matching the typical characteristics of PGCs. These results suggested that Ml-prdm1-positive cells may be PGCs and that Ml-prdm1 could be a candidate marker for tracing the formation of PGCs in M. lateralis. In addition, the expression profiles of Ml-prdm14 hinted that it may not be associated with PGCs of M. lateralis. The present study provides insights into the evolution of the PRDM family in mollusks and offers a better understanding of the formation of PGCs in mollusks.
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Affiliation(s)
- Feng Zhao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaolin Guo
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xixi Li
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Fang Liu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Yifan Fu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Xiaohan Sun
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zujing Yang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
| | - Zhifeng Zhang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Zhenkui Qin
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (F.Z.); (X.G.); (X.L.); (F.L.); (Y.F.); (X.S.); (Z.Y.); (Z.Z.)
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17
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Hu T, Wu Q, Yao Q, Yu J, Jiang K, Wan Y, Tang Q. PRDM16 exerts critical role in myocardial metabolism and energetics in type 2 diabetes induced cardiomyopathy. Metabolism 2023; 146:155658. [PMID: 37433344 DOI: 10.1016/j.metabol.2023.155658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/19/2023] [Accepted: 07/07/2023] [Indexed: 07/13/2023]
Abstract
BACKGROUND The prevalence of type 2 diabetes mellitus (T2DM) has increased over the past decades. Diabetic cardiomyopathy (DCM) is the leading cause of death in T2DM patients, however, the mechanism underlying DCM remains largely unknown. Here, we aimed to investigate the role of cardiac PR-domain containing 16 (PRDM16) in T2DM. METHODS We modeled mice with cardiac-specific deletion of Prdm16 by crossing the floxed Prdm16 mouse model with the cardiomyocyte-specific Cre transgenic mouse. The mice were continuously fed a chow diet or high-fat diet combining with streptozotocin (STZ) for 24 weeks to establish a T2DM model. DB/DB and adequate control mice were given a single intravenous injection of adeno-associated virus 9 (AAV9) carrying cardiac troponin T (cTnT) promoter-driven small hairpin RNA targeting PRDM16 (AAV9-cTnT-shPRDM16) from the retro-orbital venous plexus to knockout Prdm16 in the myocardium. There were at least 12 mice in each group. Mitochondrial morphology and function were detected using transmission electron microscopy, western blot determining the protein level of mitochondrial respiratory chain complex, mitotracker staining and Seahorse XF Cell Mito Stress Test Kit. Untargeted metabolomics analysis and RNA-seq analysis were performed to determine the molecular and metabolic changes associated with Prdm16 deficiency. BODIPY and TUNEL staining were used to detect lipid uptake and apoptosis. Co-immunoprecipitation and ChIP assays were conducted to examine the potential underlying mechanism. RESULTS Prdm16 cardiac-specific deficiency accelerated cardiomyopathy and worsened cardiac dysfunction in mice with T2DM, aggravating mitochondrial dysfunction and apoptosis both in vivo and in vitro, while PRDM16 overexpression the deterioration. Prdm16 deficiency also caused cardiac lipid accumulation resulting in metabolic and molecular alterations in T2DM mouse models. Co-IP and luciferase assays confirmed that PRDM16 targeted and regulated the transcriptional activity, expression and interaction of PPAR-α and PGC-1α, while the overexpression of PPAR-α and PGC-1α reversed Prdm16 deficiency-induced cellular dysfunction in T2DM model. Moreover, PRDM16 regulated PPAR-α and PGC-1α and affected mitochondrial function by mainly depending on epigenetic regulation of H3K4me3. CONCLUSIONS These findings suggest that PRDM16 exerted its protective role in myocardial lipid metabolism and mitochondrial function in T2DM in a histone lysine methyltransferase activity-dependent manner by regulating PPAR-α and PGC-1α.
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Affiliation(s)
- Tongtong Hu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Qingqing Wu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Qi Yao
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Jiabin Yu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Kebing Jiang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Ying Wan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China
| | - Qizhu Tang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, PR China; Cardiovascular Research Institute, Wuhan University, Wuhan 430060, PR China; Hubei Key Laboratory of Metabolic and Chronic Diseases, Wuhan 430060, PR China.
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18
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Haws SA, Miller LJ, La Luz DR, Kuznetsov VI, Trievel RC, Craciun G, Denu JM. Intrinsic catalytic properties of histone H3 lysine-9 methyltransferases preserve monomethylation levels under low S-adenosylmethionine. J Biol Chem 2023; 299:104938. [PMID: 37331600 PMCID: PMC10404681 DOI: 10.1016/j.jbc.2023.104938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023] Open
Abstract
S-adenosylmethionine (SAM) is the methyl donor for site-specific methylation reactions on histone proteins, imparting key epigenetic information. During SAM-depleted conditions that can arise from dietary methionine restriction, lysine di- and tri-methylation are reduced while sites such as Histone-3 lysine-9 (H3K9) are actively maintained, allowing cells to restore higher-state methylation upon metabolic recovery. Here, we investigated if the intrinsic catalytic properties of H3K9 histone methyltransferases (HMTs) contribute to this epigenetic persistence. We employed systematic kinetic analyses and substrate binding assays using four recombinant H3K9 HMTs (i.e., EHMT1, EHMT2, SUV39H1, and SUV39H2). At both high and low (i.e., sub-saturating) SAM, all HMTs displayed the highest catalytic efficiency (kcat/KM) for monomethylation compared to di- and trimethylation on H3 peptide substrates. The favored monomethylation reaction was also reflected in kcat values, apart from SUV39H2 which displayed a similar kcat regardless of substrate methylation state. Using differentially methylated nucleosomes as substrates, kinetic analyses of EHMT1 and EHMT2 revealed similar catalytic preferences. Orthogonal binding assays revealed only small differences in substrate affinity across methylation states, suggesting that catalytic steps dictate the monomethylation preferences of EHMT1, EHMT2, and SUV39H1. To link in vitro catalytic rates with nuclear methylation dynamics, we built a mathematical model incorporating measured kinetic parameters and a time course of mass spectrometry-based H3K9 methylation measurements following cellular SAM depletion. The model revealed that the intrinsic kinetic constants of the catalytic domains could recapitulate in vivo observations. Together, these results suggest catalytic discrimination by H3K9 HMTs maintains nuclear H3K9me1, ensuring epigenetic persistence after metabolic stress.
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Affiliation(s)
- Spencer A Haws
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lillian J Miller
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Diego Rojas La Luz
- Department of Mathematics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Vyacheslav I Kuznetsov
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Gheorghe Craciun
- Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Mathematics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John M Denu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, SMPH, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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19
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Thompson M, Sakabe M, Verba M, Hao J, Meadows SM, Lu QR, Xin M. PRDM16 regulates arterial development and vascular integrity. Front Physiol 2023; 14:1165379. [PMID: 37324380 PMCID: PMC10267475 DOI: 10.3389/fphys.2023.1165379] [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: 02/14/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Proper vascular formation is regulated by multiple signaling pathways. The vascular endothelial growth factor (VEGF) signaling promotes endothelial proliferation. Notch and its downstream targets act to lead endothelial cells toward an arterial fate through regulation of arterial gene expression. However, the mechanisms of how endothelial cells (ECs) in the artery maintain their arterial characteristics remain unclear. Here, we show that PRDM16 (positive regulatory domain-containing protein 16), a zinc finger transcription factor, is expressed in arterial ECs, but not venous ECs in developing embryos and neonatal retinas. Endothelial-specific deletion of Prdm16 induced ectopic venous marker expression in the arterial ECs and reduced vascular smooth muscle cell (vSMC) recruitment around arteries. Whole-genome transcriptome analysis using isolated brain ECs show that the expression of Angpt2 (encoding ANGIOPOIETIN2, which inhibits vSMC recruitment) is upregulated in the Prdm16 knockout ECs. Conversely, forced expression of PRDM16 in venous ECs is sufficient to induce arterial gene expression and repress the ANGPT2 level. Together, these results reveal an arterial cell-autonomous function for PRDM16 in suppressing venous characteristics in arterial ECs.
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Affiliation(s)
- Michael Thompson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Masahide Sakabe
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Mark Verba
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Jiukuan Hao
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX, United States
| | - Stryder M. Meadows
- Cell and Molecular Biology Department, Tulane University, New Orleans, LA, United States
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| | - Q. Richard Lu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
| | - Mei Xin
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, United States
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20
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Carraro M, Hendriks IA, Hammond CM, Solis-Mezarino V, Völker-Albert M, Elsborg JD, Weisser MB, Spanos C, Montoya G, Rappsilber J, Imhof A, Nielsen ML, Groth A. DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Mol Cell 2023; 83:1075-1092.e9. [PMID: 36868228 PMCID: PMC10114496 DOI: 10.1016/j.molcel.2023.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.
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Affiliation(s)
- Massimo Carraro
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin M Hammond
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | | | | | - Jonas D Elsborg
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Melanie B Weisser
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Axel Imhof
- EpiQMAx GmbH, Planegg, Germany; Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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21
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Hurwitz E, Parajuli P, Ozkan S, Prunier C, Nguyen TL, Campbell D, Friend C, Bryan AA, Lu TX, Smith SC, Razzaque MS, Xu K, Atfi A. Antagonism between Prdm16 and Smad4 specifies the trajectory and progression of pancreatic cancer. J Cell Biol 2023; 222:e202203036. [PMID: 36828547 PMCID: PMC9999015 DOI: 10.1083/jcb.202203036] [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: 03/14/2022] [Revised: 11/28/2022] [Accepted: 01/23/2023] [Indexed: 02/26/2023] Open
Abstract
The transcription factor Prdm16 functions as a potent suppressor of transforming growth factor-beta (TGF-β) signaling, whose inactivation is deemed essential to the progression of pancreatic ductal adenocarcinoma (PDAC). Using the KrasG12D-based mouse model of human PDAC, we surprisingly found that ablating Prdm16 did not block but instead accelerated PDAC formation and progression, suggesting that Prdm16 might function as a tumor suppressor in this malignancy. Subsequent genetic experiments showed that ablating Prdm16 along with Smad4 resulted in a shift from a well-differentiated and confined neoplasm to a highly aggressive and metastatic disease, which was associated with a striking deviation in the trajectory of the premalignant lesions. Mechanistically, we found that Smad4 interacted with and recruited Prdm16 to repress its own expression, therefore pinpointing a model in which Prdm16 functions downstream of Smad4 to constrain the PDAC malignant phenotype. Collectively, these findings unveil an unprecedented antagonistic interaction between the tumor suppressors Smad4 and Prdm16 that functions to restrict PDAC progression and metastasis.
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Affiliation(s)
- Eric Hurwitz
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Parash Parajuli
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Seval Ozkan
- Cancer Institute, University of Mississippi Medical Centre, Jackson, MS, USA
| | - Celine Prunier
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Thien Ly Nguyen
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
- Cancer Institute, University of Mississippi Medical Centre, Jackson, MS, USA
| | - Deanna Campbell
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Creighton Friend
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Allyn Austin Bryan
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Ting-Xuan Lu
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | | | | | - Keli Xu
- Cancer Institute, University of Mississippi Medical Centre, Jackson, MS, USA
| | - Azeddine Atfi
- Department of Biochemistry and Molecular Biology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France
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22
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PRDM16, Negatively Regulated by miR-372-3p, Suppresses Cell Proliferation and Invasion in Prostate Cancer. Andrologia 2023. [DOI: 10.1155/2023/9821829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumors. The alternation of microRNA (miRNA) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analyzed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analyzed using western blot. CCK-8, wound healing, and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilized to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
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23
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Li J, Godoy MI, Zhang AJ, Diamante G, Ahn IS, Cebrian-Silla A, Alvarez-Buylla A, Yang X, Novitch BG, Zhang Y. Prdm16 and Vcam1 regulate the postnatal disappearance of embryonic radial glia and the ending of cortical neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528567. [PMID: 36824905 PMCID: PMC9949035 DOI: 10.1101/2023.02.14.528567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Embryonic neural stem cells (NSCs, i.e., radial glia) in the ventricular-subventricular zone (V-SVZ) generate the majority of neurons and glia in the forebrain. Postnatally, embryonic radial glia disappear and a subpopulation of radial glia transition into adult NSCs. As this transition occurs, widespread neurogenesis in brain regions such as the cerebral cortex ends. The mechanisms that regulate the postnatal disappearance of radial glia and the ending of embryonic neurogenesis remain poorly understood. Here, we show that PR domain-containing 16 (Prdm16) promotes the disappearance of radial glia and the ending of neurogenesis in the cerebral cortex. Genetic deletion of Prdm16 from NSCs leads to the persistence of radial glia in the adult V-SVZ and prolonged postnatal cortical neurogenesis. Mechanistically, Prdm16 induces the postnatal reduction in Vascular Cell Adhesion Molecule 1 (Vcam1). The postnatal disappearance of radial glia and the ending of cortical neurogenesis occur normally in Prdm16-Vcam1 double conditional knockout mice. These observations reveal novel molecular regulators of the postnatal disappearance of radial glia and the ending of embryonic neurogenesis, filling a key knowledge gap in NSC biology.
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Affiliation(s)
- Jiwen Li
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
| | - Marlesa I. Godoy
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
| | - Alice J. Zhang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
| | | | - In Sook Ahn
- Department of Integrative Biology and Physiology, UCLA
| | - Arantxa Cebrian-Silla
- Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, Department of Neurological Surgery, University of California, San Francisco, San Francisco, USA
| | - Arturo Alvarez-Buylla
- Eli and Edythe Broad Institute for Stem Cell Research and Regeneration Medicine, Department of Neurological Surgery, University of California, San Francisco, San Francisco, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, UCLA
- Brain Research Institute at UCLA
- Institute for Quantitative and Computational Biosciences at UCLA
- Molecular Biology Institute at UCLA
| | - Bennett G. Novitch
- Brain Research Institute at UCLA
- Molecular Biology Institute at UCLA
- Department of Neurobiology, UCLA
- Intellectual and Developmental Disabilities Research Center at UCLA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA
| | - Ye Zhang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine at the University of California, Los Angeles (UCLA), USA
- Brain Research Institute at UCLA
- Molecular Biology Institute at UCLA
- Intellectual and Developmental Disabilities Research Center at UCLA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA
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24
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Nakagawa T, Hattori S, Hosoi T, Nakayama K. Neurobehavioral characteristics of mice with SETD5 mutations as models of IDD23 and KBG syndromes. Front Genet 2023; 13:1022339. [PMID: 36685966 PMCID: PMC9846138 DOI: 10.3389/fgene.2022.1022339] [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: 08/18/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Genomic analysis has revealed that the genes for various chromatin regulators are mutated in many individuals with neurodevelopmental disorders (NDDs), emphasizing the important role of chromatin regulation in nervous system development and function. Chromatin regulation is mediated by writers, readers, and erasers of histone and DNA modifications, with such proteins being defined by specific domains. One of these domains is the SET domain, which is present in enzymes that catalyze histone methylation. Heterozygous loss-of-function mutations of the SETD5 (SET domain containing 5) gene have been identified in individuals with an NDD designated IDD23 (intellectual developmental disorder, autosomal dominant 23). KBG syndrome (named after the initials of the last names of the first three families identified with the condition) is characterized by features that either overlap with or are distinct from those of IDD23 and was initially thought to be caused only by mutations in the ANKRD11 (ankyrin repeat domain containing 11) gene. However, recent studies have identified SETD5 mutations in some KBG syndrome patients without ANKRD11 mutations. Here we summarize the neurobehavioral characterization of Setd5 +/- mice performed by four independent research groups, compare IDD23 and KBG phenotypes, and address the utility and future development of mouse models for elucidation of the mechanisms underlying NDD pathogenesis, with a focus on SETD5 and its related proteins.
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Affiliation(s)
- Tadashi Nakagawa
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda, Japan,Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan,*Correspondence: Tadashi Nakagawa, ; Keiko Nakayama,
| | - Satoko Hattori
- Research Creation Support Center, Aichi Medical University, Nagakute, Aichi, Japan
| | - Toru Hosoi
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan,*Correspondence: Tadashi Nakagawa, ; Keiko Nakayama,
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25
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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26
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Demond H, Hanna CW, Castillo-Fernandez J, Santos F, Papachristou EK, Segonds-Pichon A, Kishore K, Andrews S, D'Santos CS, Kelsey G. Multi-omics analyses demonstrate a critical role for EHMT1 methyltransferase in transcriptional repression during oogenesis. Genome Res 2023; 33:18-31. [PMID: 36690445 PMCID: PMC9977154 DOI: 10.1101/gr.277046.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
EHMT1 (also known as GLP) is a multifunctional protein, best known for its role as an H3K9me1 and H3K9me2 methyltransferase through its reportedly obligatory dimerization with EHMT2 (also known as G9A). Here, we investigated the role of EHMT1 in the oocyte in comparison to EHMT2 using oocyte-specific conditional knockout mouse models (Ehmt2 cKO, Ehmt1 cKO, Ehmt1/2 cDKO), with ablation from the early phase of oocyte growth. Loss of EHMT1 in Ehmt1 cKO and Ehmt1/2 cDKO oocytes recapitulated meiotic defects observed in the Ehmt2 cKO; however, there was a significant impairment in oocyte maturation and developmental competence in Ehmt1 cKO and Ehmt1/2 cDKO oocytes beyond that observed in the Ehmt2 cKO. Consequently, loss of EHMT1 in oogenesis results, upon fertilization, in mid-gestation embryonic lethality. To identify H3K9 methylation and other meaningful biological changes in each mutant to explore the molecular functions of EHMT1 and EHMT2, we performed immunofluorescence imaging, multi-omics sequencing, and mass spectrometry (MS)-based proteome analyses in cKO oocytes. Although H3K9me1 was depleted only upon loss of EHMT1, H3K9me2 was decreased, and H3K9me2-enriched domains were eliminated equally upon loss of EHMT1 or EHMT2. Furthermore, there were more significant changes in the transcriptome, DNA methylome, and proteome in Ehmt1/2 cDKO than Ehmt2 cKO oocytes, with transcriptional derepression leading to increased protein abundance and local changes in genic DNA methylation in Ehmt1/2 cDKO oocytes. Together, our findings suggest that EHMT1 contributes to local transcriptional repression in the oocyte, partially independent of EHMT2, and is critical for oogenesis and oocyte developmental competence.
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Affiliation(s)
- Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Millennium Institute on Immunology and Immunotherapy, Laboratory of Integrative Biology (LIBi), Centro de Excelencia en Medicina Traslacional (CEMT), Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, 4810296, Temuco, Chile
| | - Courtney W. Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;,Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | | | - Fátima Santos
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Evangelia K. Papachristou
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Anne Segonds-Pichon
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, United Kingdom
| | - Clive S. D'Santos
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;,Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom;,Wellcome-MRC Institute of Metabolic Science–Metabolic Research Laboratories, Cambridge CB2 0QQ, United Kingdom
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27
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CRISPR/Cas9-Induced Inactivation of the Autism-Risk Gene setd5 Leads to Social Impairments in Zebrafish. Int J Mol Sci 2022; 24:ijms24010167. [PMID: 36613611 PMCID: PMC9820161 DOI: 10.3390/ijms24010167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/10/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Haploinsufficiency of the SETD5 gene, encoding a SET domain-containing histone methyltransferase, has been identified as a cause of intellectual disability and Autism Spectrum Disorder (ASD). Recently, the zebrafish has emerged as a valuable model to study neurodevelopmental disorders because of its genetic tractability, robust behavioral traits and amenability to high-throughput drug screening. To model human SETD5 haploinsufficiency, we generated zebrafish setd5 mutants using the CRISPR/Cas9 technology and characterized their morphological, behavioral and molecular phenotypes. According to our observation that setd5 is expressed in adult zebrafish brain, including those areas controlling social behavior, we found that setd5 heterozygous mutants exhibit defective aggregation and coordination abilities required for shoaling interactions, as well as indifference to social stimuli. Interestingly, impairment in social interest is rescued by risperidone, an antipsychotic drug used to treat behavioral traits in ASD individuals. The molecular analysis underscored the downregulation of genes encoding proteins involved in the synaptic structure and function in the adult brain, thus suggesting that brain hypo-connectivity could be responsible for the social impairments of setd5 mutant fishes. The zebrafish setd5 mutants display ASD-like features and are a promising setd5 haploinsufficiency model for drug screening aimed at reversing the behavioral phenotypes.
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28
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Gridina M, Fishman V. Multilevel view on chromatin architecture alterations in cancer. Front Genet 2022; 13:1059617. [PMID: 36468037 PMCID: PMC9715599 DOI: 10.3389/fgene.2022.1059617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 10/31/2022] [Indexed: 12/25/2023] Open
Abstract
Chromosomes inside the nucleus are not located in the form of linear molecules. Instead, there is a complex multilevel genome folding that includes nucleosomes packaging, formation of chromatin loops, domains, compartments, and finally, chromosomal territories. Proper spatial organization play an essential role for the correct functioning of the genome, and is therefore dynamically changed during development or disease. Here we discuss how the organization of the cancer cell genome differs from the healthy genome at various levels. A better understanding of how malignization affects genome organization and long-range gene regulation will help to reveal the molecular mechanisms underlying cancer development and evolution.
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Affiliation(s)
- Maria Gridina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 PMCID: PMC9485127 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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Yin G, Yan C, Hao J, Zhang C, Wang P, Zhao C, Cai S, Meng B, Zhang A, Li L. PRDM16, negatively regulated by miR-372-3p, suppresses cell proliferation and invasion in prostate cancer. Andrologia 2022:e14529. [PMID: 35858224 DOI: 10.1111/and.14529] [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: 03/03/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/26/2022] Open
Abstract
Prostate cancer (PCa) is one of the most prevalent malignant tumours. The alternation of microRNAs (miRNAs) expression is associated with prostate cancer progression, whereas its way to influence progression of prostate cancer remains elusive. The expression levels of PRDM16 mRNA and miR-372-3p in PCa cell lines were analysed using qRT-PCR. The protein expression of PRDM16 in PCa cell lines was also analysed using Western blot. CCK-8, wound healing and Transwell assays were applied to examine cell proliferation, migration, and invasion in prostate cancer cells, respectively. Dual-luciferase reporter assay was utilised to validate the interaction between miR-372-3p and PRDM16. In the present study, markedly decreased PRDM16 mRNA and protein expression levels were observed in prostate cancer cells. PRDM16 overexpression hampered cellular proliferation, migration, and invasion, while silencing PRDM16 had the opposite effect. Moreover, miR-372-3p could target the regulation expression of PRDM16. Rescue experiments demonstrated that upregulating miR-372-3p conspicuously restored the inhibitory effect of increased PRDM16 on cell proliferation, migration, and invasion in PCa. Overall, our study clarifies the biological role of miR-372-3p/PRDM16 axis in prostate cancer progression, which may be effective biomarkers for clinical treatment of prostate cancer.
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Affiliation(s)
- Guangwei Yin
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chengquan Yan
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Jing Hao
- Office of Academic Affairs, North China University of Science and Technology, Tangshan, Hebei Province, China
| | - Chunying Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Pengfei Wang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Chaofei Zhao
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Shengyong Cai
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Bin Meng
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Aili Zhang
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
| | - Lin Li
- The Third Department of Urology, Tangshan Gongren Hospital, Tangshan, Hebei Province, China
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El-Meligui YM, Hassan NM, Kassem AB, Gouda NA, Mohanad M, Hamouda MA, Salahuddin A. Impact of HOXB4 and PRDM16 Gene Expressions on Prognosis and Treatment Response in Acute Myeloid Leukemia Patients. Pharmgenomics Pers Med 2022; 15:663-674. [PMID: 35782688 PMCID: PMC9241994 DOI: 10.2147/pgpm.s368640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/14/2022] [Indexed: 12/08/2022] Open
Abstract
Introduction Acute myeloid leukemia (AML) is the most common type of leukemia among adults and is characterized by various genetic abnormalities. HOXB4 and PRDM16 are promising markers of AML. Our objective is to assess the potential roles of HOXB4 and PRDM16 as prognostic and predictive markers in newly diagnosed AML patients and determine the correlation between their expressions and other prognostic markers as FLT3-ITD, NPM1 exon 12 mutations, response to treatment, and patient’s survival. Methods This study included 83 de novo AML adult patients. All patients were subjected to clinical, morphological, cytochemical, and molecular analysis to detect HOXB4 and PRDM16 gene expressions and FLT3-ITD, NPM1 exon 12 mutations. Results The results showed that a low expression of HOXB4 was found in 31.3% of AML patients, whereas a high expression of PRDM16 was evident in 33.8% of AML patients. FLT3-ITD mutations were detected in 6 patients (7.2%), while NPM1 exon 12 mutations were detected in 7 patients (19.4%) out of 36 patients with intermediate genetic risk. Out of the 50 patients who achieved complete remission (CR), relapse occurred in 16% of the cases. Low expression of HOXB4 and high expression of PRDM16 were associated with CR of 32% and 28%, respectively, and a short overall survival (OS) and disease-free survival (DFS). Conclusion Further larger study should be conducted to verify that high PRDM16 and low HOXB4 gene expressions could be used as a poor prognostic predictor for AML. The correlation between PRDM16 and HOXB4 gene expressions and FLT3-ITD and NPM1 exon 12 mutations might have a role on CR, relapse, OS, and, however, this should be clarified in analysis with a larger number of samples.
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Affiliation(s)
- Yomna M El-Meligui
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Naglaa M Hassan
- Clinical Pathology Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Amira B Kassem
- Clinical Pharmacy and Pharmacy Practice Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
- Correspondence: Amira B Kassem, Email
| | - Nora A Gouda
- Cancer Epidemiology and Biostatistics Department, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Marwa Mohanad
- Biochemistry Department, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, Giza, Egypt
| | - Manal A Hamouda
- Clinical Pharmacy Department, Faculty of Pharmacy, Menoufia University, Shibin El Kom, Egypt
| | - Ahmad Salahuddin
- Biochemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, Egypt
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Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat Rev Mol Cell Biol 2022; 23:623-640. [PMID: 35562425 PMCID: PMC9099300 DOI: 10.1038/s41580-022-00483-w] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/14/2022]
Abstract
Heterochromatin is characterized by dimethylated or trimethylated histone H3 Lys9 (H3K9me2 or H3K9me3, respectively) and is found at transposable elements, satellite repeats and genes, where it ensures their transcriptional silencing. The histone methyltransferases (HMTs) that methylate H3K9 — in mammals Suppressor of variegation 3–9 homologue 1 (SUV39H1), SUV39H2, SET domain bifurcated 1 (SETDB1), SETDB2, G9A and G9A-like protein (GLP) — and the ‘readers’ of H3K9me2 or H3K9me3 are highly conserved and show considerable redundancy. Despite their redundancy, genetic ablation or mistargeting of an individual H3K9 methyltransferase can correlate with impaired cell differentiation, loss of tissue identity, premature aging and/or cancer. In this Review, we discuss recent advances in understanding the roles of the known H3K9-specific HMTs in ensuring transcriptional homeostasis during tissue differentiation in mammals. We examine the effects of H3K9-methylation-dependent gene repression in haematopoiesis, muscle differentiation and neurogenesis in mammals, and compare them with mechanistic insights obtained from the study of model organisms, notably Caenorhabditis elegans and Drosophila melanogaster. In all these organisms, H3K9-specific HMTs have both unique and redundant roles that ensure the maintenance of tissue integrity by restricting the binding of transcription factors to lineage-specific promoters and enhancer elements. Histone H3 Lys9 (H3K9)-methylated heterochromatin ensures transcriptional silencing of repetitive elements and genes, and its deregulation leads to impaired cell and tissue identity, premature aging and cancer. Recent studies in mammals clarified the roles H3K9-specific histone methyltransferases in ensuring transcriptional homeostasis during tissue differentiation.
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Jiang N, Yang M, Han Y, Zhao H, Sun L. PRDM16 Regulating Adipocyte Transformation and Thermogenesis: A Promising Therapeutic Target for Obesity and Diabetes. Front Pharmacol 2022; 13:870250. [PMID: 35462933 PMCID: PMC9024053 DOI: 10.3389/fphar.2022.870250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Given that obesity and diabetes have been major public health concerns and that disease morbidities have been rising continuously, effective treatment for these diseases is urgently needed. Because adipose tissue metabolism is involved in the progression of obesity and diabetes, it might be efficient to target adipocyte metabolic pathways. Positive regulatory domain zinc finger region protein 16 (PRDM16), a transcription factor that is highly expressed in adipocytes, plays a key role in adipose tissue metabolism, such as the browning and thermogenesis of adipocytes, the beigeing of adipocytes, the adipogenic differentiation of myoblasts, and the conversion of visceral adipocytes to subcutaneous adipocytes. Furthermore, clinical and basic studies have shown that the expression of PRDM16 is associated with obesity and diabetes and that PRDM16 signaling participates in the treatment of the two diseases. For example, metformin promotes thermogenesis and alleviates obesity by activating the AMPK/αKG/PRDM16 signaling pathway; rosiglitazone alleviates obesity under the synergistic effect of PRDM16; resveratrol plays an antiobesity role by inducing the expression of PRDM16; liraglupeptide improves insulin resistance by inducing the expression of PRDM16; and mulberry leaves play an anti-inflammatory and antidiabetes role by activating the expression of brown fat cell marker genes (including PRDM16). In this review, we summarize the evidence of PRDM16 involvement in the progression of obesity and diabetes and that PRDM16 may be a promising therapy for obesity and diabetes.
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Maeda R, Tachibana M. HP1 maintains protein stability of H3K9 methyltransferases and demethylases. EMBO Rep 2022; 23:e53581. [PMID: 35166421 PMCID: PMC8982598 DOI: 10.15252/embr.202153581] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 11/09/2022] Open
Abstract
Di- or tri-methylated H3K9 (H3K9me2/3) is an epigenetic mark of heterochromatin. Heterochromatin protein 1 (HP1) specifically recognizes H3K9me2/3, contributing to transcriptional suppression and spread of H3K9me2/3. Here, we demonstrate another role of HP1 in heterochromatin organization: regulation of protein stability of H3K9 methyltransferases (H3K9 MTs) and demethylases (H3K9 DMs). We show that HP1 interaction-defective mutants of H3K9 MTs, Suv39h1 and Setdb1, undergo protein degradation. We further establish mouse embryonic stem cell lines lacking all three HP1 paralogs. In the HP1-deficient cells, Suv39h1, Suv39h2, Setdb1, and G9a/GLP complex decrease at the protein level, and the enzymes are released from chromatin. HP1 mutants that cannot recognize H3K9me2/3 or form dimers cannot stabilize these enzymes, indicating that the tethering of H3K9 MTs to chromatin is critical for their protein stability. We show that HP1 also stabilizes H3K9 DMs, Jmjd1a and Jmjd1b. Our study indicates that mammalian HP1 forms a heterochromatin hub that governs protein stability of H3K9 MTs and H3K9 DMs.
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Affiliation(s)
- Ryo Maeda
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan,Institute of Advanced Medical SciencesTokushima UniversityTokushimaJapan
| | - Makoto Tachibana
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan,Institute of Advanced Medical SciencesTokushima UniversityTokushimaJapan
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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Bang ML, Bogomolovas J, Chen J. Understanding the molecular basis of cardiomyopathy. Am J Physiol Heart Circ Physiol 2022; 322:H181-H233. [PMID: 34797172 PMCID: PMC8759964 DOI: 10.1152/ajpheart.00562.2021] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/16/2021] [Accepted: 11/16/2021] [Indexed: 02/03/2023]
Abstract
Inherited cardiomyopathies are a major cause of mortality and morbidity worldwide and can be caused by mutations in a wide range of proteins located in different cellular compartments. The present review is based on Dr. Ju Chen's 2021 Robert M. Berne Distinguished Lectureship of the American Physiological Society Cardiovascular Section, in which he provided an overview of the current knowledge on the cardiomyopathy-associated proteins that have been studied in his laboratory. The review provides a general summary of the proteins in different compartments of cardiomyocytes associated with cardiomyopathies, with specific focus on the proteins that have been studied in Dr. Chen's laboratory.
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Affiliation(s)
- Marie-Louise Bang
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Milan Unit, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano (Milan), Italy
| | - Julius Bogomolovas
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
| | - Ju Chen
- Division of Cardiovascular Medicine, Department of Medicine Cardiology, University of California, San Diego, La Jolla, California
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Li M, Ren H, Zhang Y, Liu N, Fan M, Wang K, Yang T, Chen M, Shi P. MECOM/PRDM3 and PRDM16 Serve as Prognostic-Related Biomarkers and Are Correlated With Immune Cell Infiltration in Lung Adenocarcinoma. Front Oncol 2022; 12:772686. [PMID: 35174083 PMCID: PMC8841357 DOI: 10.3389/fonc.2022.772686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/03/2022] [Indexed: 12/24/2022] Open
Abstract
Background The MDS1 and EVI1 complex locus (MECOM, also called PRDM3) and PR domain containing 16 (PRDM16) are two highly related zinc finger transcription factors associated with many malignancies. However, the mechanisms of MECOM and PRDM16 in prognosis and tumor immune infiltration in lung adenocarcinoma (LUAD) remain uncertain. Methods The Cancer Genome Atlas (TCGA), Oncomine, UALCAN, GEPIA, and TIMER databases were searched to determine the relationship between the expression of MECOM and PRDM16, clinicopathological features, immune infiltration, and prognosis in LUAD. Coexpressed genes of the two genes were investigated by CBioPortal, and the potential mechanism of MECOM- and PRDM16-related genes was elucidated by GO and KEGG analyses. STRING database was utilized to further construct the protein-protein interaction network of the coexpressed genes, and the hub genes were identified by Cytoscape. Finally, qRT-PCR was performed to identify the mRNA levels of the target genes in LUAD. Results mRNA levels of MECOM and PRDM16 were downregulated in LUAD (p < 0.05), and the low expression of the two genes was associated with the age, gender, smoking duration, tissue subtype, poor stage, nodal metastasis status, TP53 mutation, and prognosis in LUAD (p < 0.05). MECOM and PRDM16 were also found to be correlated with the expression of a variety of immune cell subsets and their markers. KEGG analysis showed that both of them were mainly enriched in the cell cycle, cellular senescence, DNA replication, and p53 signaling pathway. Importantly, the mRNA levels of the two genes were also found to be decreased in the clinical samples of LUAD by qRT-PCR. Conclusion MECOM and PRDM16 may serve as potential prognostic biomarkers which govern immune cell recruitment to LUAD.
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Affiliation(s)
- Meng Li
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Hui Ren
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Yanpeng Zhang
- Department of Talent Highland, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Thoracic Surgery, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Department of Center for Translational Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Na Liu
- Department of Medical Oncology, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Meng Fan
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Ke Wang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Tian Yang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mingwei Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
| | - Puyu Shi
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Puyu Shi, ; ; Mingwei Chen, ;
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Histone Chaperone Nrp1 Mutation Affects the Acetylation of H3K56 in Tetrahymena thermophila. Cells 2022; 11:cells11030408. [PMID: 35159218 PMCID: PMC8833950 DOI: 10.3390/cells11030408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 02/04/2023] Open
Abstract
Histone modification and nucleosome assembly are mainly regulated by various histone-modifying enzymes and chaperones. The roles of histone-modification enzymes have been well analyzed, but the molecular mechanism of histone chaperones in histone modification and nucleosome assembly is incompletely understood. We previously found that the histone chaperone Nrp1 is localized in the micronucleus (MIC) and the macronucleus (MAC) and involved in the chromatin stability and nuclear division of Tetrahymena thermophila. In the present work, we found that truncated C-terminal mutant HA-Nrp1TrC abnormally localizes in the cytoplasm. The truncated-signal-peptide mutants HA-Nrp1TrNLS1 and HA-Nrp1TrNLS2 are localized in the MIC and MAC. Overexpression of Nrp1TrNLS1 inhibited cellular proliferation and disrupted micronuclear mitosis during the vegetative growth stage. During sexual development, Nrp1TrNLS1 overexpression led to abnormal bouquet structures and meiosis arrest. Furthermore, Histone H3 was not transported into the nucleus; instead, it formed an abnormal speckled cytoplastic distribution in the Nrp1TrNLS1 mutants. The acetylation level of H3K56 in the mutants also decreased, leading to significant changes in the transcription of the genome of the Nrp1TrNLS1 mutants. The histone chaperone Nrp1 regulates the H3 nuclear import and acetylation modification of H3K56 and affects chromatin stability and genome transcription in Tetrahymena.
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Lin GN, Song W, Wang W, Wang P, Yu H, Cai W, Jiang X, Huang W, Qian W, Chen Y, Chen M, Yu S, Xu T, Jiao Y, Liu Q, Zhang C, Yi Z, Fan Q, Chen J, Wang Z. De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder. SCIENCE ADVANCES 2022; 8:eabi6180. [PMID: 35020433 PMCID: PMC8754407 DOI: 10.1126/sciadv.abi6180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a chronic anxiety disorder with a substantial genetic basis and a broadly undiscovered etiology. Recent studies of de novo mutation (DNM) exome-sequencing studies for OCD have reinforced the hypothesis that rare variation contributes to the risk. We performed, to our knowledge, the first whole-genome sequencing on 53 parent-offspring families with offspring affected with OCD to investigate all rare de novo variants and insertions/deletions. We observed higher mutation rates in promoter-anchored chromatin loops (empirical P = 0.0015) and regions with high frequencies of histone marks (empirical P = 0.0001). Mutations affecting coding regions were significantly enriched within coexpression modules of genes involved in chromatin modification during human brain development. Four genes—SETD5, KDM3B, ASXL3, and FBL—had strong aggregated evidence and functionally converged on transcription’s epigenetic regulation, suggesting an important OCD risk mechanism. Our data characterized different genome-wide DNMs and highlighted the contribution of chromatin modification in the etiology of OCD.
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Affiliation(s)
- Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Corresponding author. (G.N.L.); (Z.W.)
| | - Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Weidi Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Pei Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Psychological and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Yu
- Novogene Bioinformatics Institute, Beijing, China
| | - Wenxiang Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Xue Jiang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wu Huang
- Novogene Bioinformatics Institute, Beijing, China
| | - Wei Qian
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yucan Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miao Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Tingting Xu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Institute of Psychological and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yumei Jiao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Liu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Zhang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenghui Yi
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Fan
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Jue Chen
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
- Institute of Psychological and Behavioral Science, Shanghai Jiao Tong University, Shanghai, China
- Corresponding author. (G.N.L.); (Z.W.)
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Genome-wide DNA Methylation Analysis in Pediatric Acute Myeloid Leukemia. Blood Adv 2022; 6:3207-3219. [PMID: 35008106 PMCID: PMC9198913 DOI: 10.1182/bloodadvances.2021005381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/20/2021] [Indexed: 12/03/2022] Open
Abstract
FLT3-ITD and high PRDM16 expression induced methylation changes at STAT5 and AP-1 binding sites in pediatric AML. Hypomethylated regions in PRDM16-highly expressed AMLs were correlated with enhanced chromatin accessibilities at multiple genomic regions.
We investigated genome-wide DNA methylation patterns in 64 pediatric patients with acute myeloid leukemia (AML). Based on unsupervised clustering with the 567 most variably methylated cytosine guanine dinucleotide (CpG) sites, patients were categorized into 4 clusters associated with genetic alterations. Clusters 1 and 3 were characterized by the presence of known favorable prognostic factors, such as RUNX1-RUNX1T1 fusion and KMT2A rearrangement with low MECOM expression, and biallelic CEBPA mutations (all 8 patients), respectively. Clusters 2 and 4 comprised patients exhibiting molecular features associated with adverse outcomes, namely internal tandem duplication of FLT3 (FLT3-ITD), partial tandem duplication of KMT2A, and high PRDM16 expression. Depending on the methylation values of the 1243 CpG sites that were significantly different between FLT3-ITD+ and FLT3-ITD− AML, patients were categorized into 3 clusters: A, B, and C. The STAT5-binding motif was most frequently found close to the 1243 CpG sites. All 8 patients with FLT3-ITD in cluster A harbored high PRDM16 expression and experienced adverse events, whereas only 1 of 7 patients with FLT3-ITD in the other clusters experienced adverse events. PRDM16 expression levels were also related to DNA methylation patterns, which were drastically changed at the cutoff value of PRDM16/ABL1 = 0.10. The assay for transposase-accessible chromatin sequencing of AMLs supported enhanced chromatin accessibility around genomic regions, such as HOXB cluster genes, SCHIP1, and PRDM16, which were associated with DNA methylation changes in AMLs with FLT3-ITD and high PRDM16 expression. Our results suggest that DNA methylation levels at specific CpG sites are useful to support genetic alterations and gene expression patterns of patients with pediatric AML.
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Paredes R, Doleschall N, Connors K, Geary B, Meyer S. EVI1 protein interaction dynamics: targetable for therapeutic intervention? Exp Hematol 2021; 107:1-8. [PMID: 34958895 DOI: 10.1016/j.exphem.2021.12.398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/04/2022]
Abstract
High expression of the transcriptional regulator EVI1 encoded at the MECOM locus at 3q26 is one of the most aggressive oncogenic drivers in acute myeloid leukaemia (AML) and carries a very poor prognosis. How EVI1 confers leukaemic transformation and chemotherapy resistance in AML is subject to important ongoing clinical and experimental studies. Recent discoveries have revealed critical details about genetic mechanisms of the activation of EVI1 overexpression and downstream events of aberrantly high EVI1 expression. Here we review and discuss aspects concerning the protein interactions of EVI1 and the related proteins MDS-EVI1 and ΔEVI1 from the perspective of their potential for therapeutic intervention.
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Affiliation(s)
- Roberto Paredes
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Academic Health Science Centre, National Institute for Health Research Biomedical Research Centre, Manchester
| | - Nora Doleschall
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Academic Health Science Centre, National Institute for Health Research Biomedical Research Centre, Manchester
| | - Kathleen Connors
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Academic Health Science Centre, National Institute for Health Research Biomedical Research Centre, Manchester
| | - Bethany Geary
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Academic Health Science Centre, National Institute for Health Research Biomedical Research Centre, Manchester
| | - Stefan Meyer
- Stem Cell and Leukaemia Proteomics Laboratory, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Academic Health Science Centre, National Institute for Health Research Biomedical Research Centre, Manchester; Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital; Young Oncology Unit, The Christie NHS Foundation Trust.
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Rienzo M, Di Zazzo E, Casamassimi A, Gazzerro P, Perini G, Bifulco M, Abbondanza C. PRDM12 in Health and Diseases. Int J Mol Sci 2021; 22:ijms222112030. [PMID: 34769459 PMCID: PMC8585061 DOI: 10.3390/ijms222112030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
PRDM12 is a member of the PRDI-BF1 (positive regulatory domain I-binding factor 1) homologous domain (PRDM)-containing protein family, a subfamily of Kruppel-like zinc finger proteins, controlling key processes in the development of cancer. PRDM12 is expressed in a spatio-temporal manner in neuronal systems where it exerts multiple functions. PRDM12 is essential for the neurogenesis initiation and activation of a cascade of downstream pro-neuronal transcription factors in the nociceptive lineage. PRDM12 inactivation, indeed, results in a complete absence of the nociceptive lineage, which is essential for pain perception. Additionally, PRDM12 contributes to the early establishment of anorexigenic neuron identity and the maintenance of high expression levels of pro-opiomelanocortin, which impacts on the program bodyweight homeostasis. PRDMs are commonly involved in cancer, where they act as oncogenes/tumor suppressors in a “Yin and Yang” manner. PRDM12 is not usually expressed in adult normal tissues but its expression is re-activated in several cancer types. However, little information is currently available on PRDM12 expression in cancers and its mechanism of action has not been thoroughly described. In this review, we summarize the recent findings regarding PRDM12 by focusing on four main biological processes: neurogenesis, pain perception, oncogenesis and cell metabolism. Moreover, we wish to highlight the importance of future studies focusing on the PRDM12 signaling pathway(s) and its role in cancer onset and progression.
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Affiliation(s)
- Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy;
- Correspondence:
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano, Salerno, Italy;
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy;
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MECOM promotes supporting cell proliferation and differentiation in cochlea. J Otol 2021; 17:59-66. [PMID: 35949554 PMCID: PMC9349018 DOI: 10.1016/j.joto.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/18/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
Permanent damage to hair cells (HCs) is the leading cause of sensory deafness. Supporting cells (SCs) are essential in the restoration of hearing in mammals because they can proliferate and differentiate to HCs. MDS1 and EVI1 complex locus (MECOM) is vital in early development and cell differentiation and regulates the TGF-β signaling pathway to adapt to pathophysiological events, such as hematopoietic proliferation, differentiation and cells death. In addition, MECOM plays an essential role in neurogenesis and craniofacial development. However, the role of MECOM in the development of cochlea and its way to regulate related signaling are not fully understood. To address this problem, this study examined the expression of MECOM during the development of cochlea and observed a significant increase of MECOM at the key point of auditory epithelial morphogenesis, indicating that MECOM may have a vital function in the formation of cochlea and regeneration of HCs. Meanwhile, we tried to explore the possible effect and potential mechanism of MECOM in SC proliferation and HC regeneration. Findings from this study indicate that overexpression of MECOM markedly increases the proliferation of SCs in the inner ear, and the expression of Smad3 and Cdkn2b related to TGF signaling is significantly down-regulated, corresponding to the overexpression of MECOM. Collectively, these data may provide an explanation of the vital function of MECOM in SC proliferation and trans-differentiation into HCs, as well as its regulation. The interaction between MECOM, Wnt, Notch and the TGF-β signaling may provide a feasible approach to induce the regeneration of HCs.
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [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: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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Grabowicz IE, Wilczyński B, Kamińska B, Roura AJ, Wojtaś B, Dąbrowski MJ. The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes. Sci Rep 2021; 11:15668. [PMID: 34341417 PMCID: PMC8329071 DOI: 10.1038/s41598-021-95009-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-wide studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different glioma types. We have recently created a unique atlas encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we intersected genome-wide atlas data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in WHO low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found the set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing specific glioma-related genes. Moreover, many genes associated with the cell-matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by long-range contacts with enhancers. Presented results demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy.
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Affiliation(s)
- Ilona E Grabowicz
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
| | - Bartek Wilczyński
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Bożena Kamińska
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Adria-Jaume Roura
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtaś
- Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Michał J Dąbrowski
- Institute of Computer Science of the Polish Academy of Sciences, Warsaw, Poland.
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Trager MH, Sah B, Chen Z, Liu L. Control of Breast Cancer Pathogenesis by Histone Methylation and the Hairless Histone Demethylase. Endocrinology 2021; 162:6259332. [PMID: 33928351 PMCID: PMC8237996 DOI: 10.1210/endocr/bqab088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 12/19/2022]
Abstract
Breast cancer is a highly heterogeneous disease, encompassing many subtypes that have distinct origins, behaviors, and prognoses. Although traditionally seen as a genetic disease, breast cancer is now also known to involve epigenetic abnormalities. Epigenetic regulators, such as DNA methyltransferases and histone-modifying enzymes, play essential roles in gene regulation and cancer development. Dysregulation of epigenetic regulator activity has been causally linked with breast cancer pathogenesis. Hairless (HR) encodes a 130-kDa transcription factor that is essential for development and tissue homeostasis. Its role in transcription regulation is partly mediated by its interaction with multiple nuclear receptors, including thyroid hormone receptor, retinoic acid receptor-related orphan receptors, and vitamin D receptor. HR has been studied primarily in epidermal development and homeostasis. Hr-mutant mice are highly susceptible to ultraviolet- or carcinogen-induced skin tumors. Besides its putative tumor suppressor function in skin, loss of HR function has also been implicated in increased leukemia susceptibility and promotes the growth of melanoma and brain cancer cells. HR has also been demonstrated to function as a histone H3 lysine 9 demethylase. Recent genomics studies have identified HR mutations in a variety of human cancers, including breast cancer. The anticancer function and mechanism of action by HR in mammary tissue remains to be investigated. Here, we review the emerging role of HR, its histone demethylase activity and histone methylation in breast cancer development, and potential for epigenetic therapy.
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Affiliation(s)
- Megan H Trager
- Columbia University Vagelos College of Physicians and Surgeons, New York, New York 10032, USA
| | - Bindeshwar Sah
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
| | - Zhongming Chen
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55912, USA
| | - Liang Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55912, USA
- Correspondence: Liang Liu, PhD, The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
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Complete loss of H3K9 methylation dissolves mouse heterochromatin organization. Nat Commun 2021; 12:4359. [PMID: 34272378 PMCID: PMC8285382 DOI: 10.1038/s41467-021-24532-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/17/2021] [Indexed: 12/26/2022] Open
Abstract
Histone H3 lysine 9 (H3K9) methylation is a central epigenetic modification that defines heterochromatin from unicellular to multicellular organisms. In mammalian cells, H3K9 methylation can be catalyzed by at least six distinct SET domain enzymes: Suv39h1/Suv39h2, Eset1/Eset2 and G9a/Glp. We used mouse embryonic fibroblasts (MEFs) with a conditional mutation for Eset1 and introduced progressive deletions for the other SET domain genes by CRISPR/Cas9 technology. Compound mutant MEFs for all six SET domain lysine methyltransferase (KMT) genes lack all H3K9 methylation states, derepress nearly all families of repeat elements and display genomic instabilities. Strikingly, the 6KO H3K9 KMT MEF cells no longer maintain heterochromatin organization and have lost electron-dense heterochromatin. This is a compelling analysis of H3K9 methylation-deficient mammalian chromatin and reveals a definitive function for H3K9 methylation in protecting heterochromatin organization and genome integrity.
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48
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Abstract
Membrane-bound organelles provide physical and functional compartmentalization of biological processes in eukaryotic cells. The characteristic shape and internal organization of these organelles is determined by a combination of multiple internal and external factors. The maintenance of the shape of nucleus, which houses the genetic material within a double membrane bilayer, is crucial for a seamless spatio-temporal control over nuclear and cellular functions. Dynamic morphological changes in the shape of nucleus facilitate various biological processes. Chromatin packaging, nuclear and cytosolic protein organization, and nuclear membrane lipid homeostasis are critical determinants of overall nuclear morphology. As such, a multitude of molecular players and pathways act together to regulate the nuclear shape. Here, we review the known mechanisms governing nuclear shape in various unicellular and multicellular organisms, including the non-spherical nuclei and non-lamin-related structural determinants. The review also touches upon cellular consequences of aberrant nuclear morphologies.
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Affiliation(s)
- Pallavi Deolal
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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49
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Biferali B, Bianconi V, Perez DF, Kronawitter SP, Marullo F, Maggio R, Santini T, Polverino F, Biagioni S, Summa V, Toniatti C, Pasini D, Stricker S, Di Fabio R, Chiacchiera F, Peruzzi G, Mozzetta C. Prdm16-mediated H3K9 methylation controls fibro-adipogenic progenitors identity during skeletal muscle repair. SCIENCE ADVANCES 2021; 7:7/23/eabd9371. [PMID: 34078594 PMCID: PMC8172132 DOI: 10.1126/sciadv.abd9371] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 04/06/2021] [Indexed: 05/15/2023]
Abstract
H3K9 methylation maintains cell identity orchestrating stable silencing and anchoring of alternate fate genes within the heterochromatic compartment underneath the nuclear lamina (NL). However, how cell type-specific genomic regions are specifically targeted to the NL is still elusive. Using fibro-adipogenic progenitors (FAPs) as a model, we identified Prdm16 as a nuclear envelope protein that anchors H3K9-methylated chromatin in a cell-specific manner. We show that Prdm16 mediates FAP developmental capacities by orchestrating lamina-associated domain organization and heterochromatin sequestration at the nuclear periphery. We found that Prdm16 localizes at the NL where it cooperates with the H3K9 methyltransferases G9a/GLP to mediate tethering and silencing of myogenic genes, thus repressing an alternative myogenic fate in FAPs. Genetic and pharmacological disruption of this repressive pathway confers to FAP myogenic competence, preventing fibro-adipogenic degeneration of dystrophic muscles. In summary, we reveal a druggable mechanism of heterochromatin perinuclear sequestration exploitable to reprogram FAPs in vivo.
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Affiliation(s)
- Beatrice Biferali
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Valeria Bianconi
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Daniel Fernandez Perez
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | | | - Fabrizia Marullo
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Roberta Maggio
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Federica Polverino
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Stefano Biagioni
- Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy
| | - Vincenzo Summa
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
| | - Carlo Toniatti
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
| | - Diego Pasini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
- Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Sigmar Stricker
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Romano Di Fabio
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Italy
- Promidis, Via Olgettina 60, 20132 Milano, Italy
| | - Fulvio Chiacchiera
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Chiara Mozzetta
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy c/o Department of Biology and Biotechnology "C. Darwin," Sapienza University, 00185 Rome, Italy.
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50
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Dissecting Murine Muscle Stem Cell Aging through Regeneration Using Integrative Genomic Analysis. Cell Rep 2021; 32:107964. [PMID: 32726628 PMCID: PMC8025697 DOI: 10.1016/j.celrep.2020.107964] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 04/12/2020] [Accepted: 07/03/2020] [Indexed: 12/19/2022] Open
Abstract
During aging, there is a progressive loss of volume and function in skeletal muscle that impacts mobility and quality of life. The repair of skeletal muscle is regulated by tissue-resident stem cells called satellite cells (or muscle stem cells [MuSCs]), but in aging, MuSCs decrease in numbers and regenerative capacity. The transcriptional networks and epigenetic changes that confer diminished regenerative function in MuSCs as a result of natural aging are only partially understood. Herein, we use an integrative genomics approach to profile MuSCs from young and aged animals before and after injury. Integration of these datasets reveals aging impacts multiple regulatory changes through significant differences in gene expression, metabolic flux, chromatin accessibility, and patterns of transcription factor (TF) binding activities. Collectively, these datasets facilitate a deeper understanding of the regulation tissue-resident stem cells use during aging and healing.
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