1
|
Alasady MJ, Koeva M, Takagishi SR, Segal D, Amici DR, Smith RS, Ansel DJ, Lindquist S, Whitesell L, Bartom ET, Taipale M, Mendillo ML. An HSF1-JMJD6-HSP feedback circuit promotes cell adaptation to proteotoxic stress. Proc Natl Acad Sci U S A 2024; 121:e2313370121. [PMID: 38985769 PMCID: PMC11260097 DOI: 10.1073/pnas.2313370121] [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: 08/10/2023] [Accepted: 05/10/2024] [Indexed: 07/12/2024] Open
Abstract
Heat Shock Factor 1 (HSF1) is best known as the master transcriptional regulator of the heat-shock response (HSR), a conserved adaptive mechanism critical for protein homeostasis (proteostasis). Combining a genome-wide RNAi library with an HSR reporter, we identified Jumonji domain-containing protein 6 (JMJD6) as an essential mediator of HSF1 activity. In follow-up studies, we found that JMJD6 is itself a noncanonical transcriptional target of HSF1 which acts as a critical regulator of proteostasis. In a positive feedback circuit, HSF1 binds and promotes JMJD6 expression, which in turn reduces heat shock protein 70 (HSP70) R469 monomethylation to disrupt HSP70-HSF1 repressive complexes resulting in enhanced HSF1 activation. Thus, JMJD6 is intricately wired into the proteostasis network where it plays a critical role in cellular adaptation to proteotoxic stress.
Collapse
Affiliation(s)
- Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Martina Koeva
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Cambridge, MA02139
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Dmitri Segal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Daniel J. Ansel
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Cambridge, MA02139
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| |
Collapse
|
2
|
Bhandari K, Ding WQ. Protein Arginine Methyltransferases in Pancreatic Ductal Adenocarcinoma: New Molecular Targets for Therapy. Int J Mol Sci 2024; 25:3958. [PMID: 38612768 PMCID: PMC11011826 DOI: 10.3390/ijms25073958] [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: 02/29/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/14/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignant disease with a low 5-year overall survival rate. It is the third-leading cause of cancer-related deaths in the United States. The lack of robust therapeutics, absence of effective biomarkers for early detection, and aggressive nature of the tumor contribute to the high mortality rate of PDAC. Notably, the outcomes of recent immunotherapy and targeted therapy against PDAC remain unsatisfactory, indicating the need for novel therapeutic strategies. One of the newly described molecular features of PDAC is the altered expression of protein arginine methyltransferases (PRMTs). PRMTs are a group of enzymes known to methylate arginine residues in both histone and non-histone proteins, thereby mediating cellular homeostasis in biological systems. Some of the PRMT enzymes are known to be overexpressed in PDAC that promotes tumor progression and chemo-resistance via regulating gene transcription, cellular metabolic processes, RNA metabolism, and epithelial mesenchymal transition (EMT). Small-molecule inhibitors of PRMTs are currently under clinical trials and can potentially become a new generation of anti-cancer drugs. This review aims to provide an overview of the current understanding of PRMTs in PDAC, focusing on their pathological roles and their potential as new therapeutic targets.
Collapse
Affiliation(s)
| | - Wei-Qun Ding
- Department of Pathology, University of Oklahoma Health Sciences Center, BMSB401A, 940 Stanton L. Young Blvd., Oklahoma City, OK 73104, USA;
| |
Collapse
|
3
|
Tong C, Chang X, Qu F, Bian J, Wang J, Li Z, Xu X. Overview of the development of protein arginine methyltransferase modulators: Achievements and future directions. Eur J Med Chem 2024; 267:116212. [PMID: 38359536 DOI: 10.1016/j.ejmech.2024.116212] [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: 12/04/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
Protein methylation is a post-translational modification (PTM) that organisms undergo. This process is considered a part of epigenetics research. In recent years, there has been an increasing interest in protein methylation, particularly histone methylation, as research has advanced. Methylation of histones is a dynamic process that is subject to fine control by histone methyltransferases and demethylases. In addition, many non-histone proteins also undergo methylation, and these modifications collectively regulate physiological phenomena, including RNA transcription, translation, signal transduction, DNA damage response, and cell cycle. Protein arginine methylation is a crucial aspect of protein methylation, which plays a significant role in regulating the cell cycle and repairing DNA. It is also linked to various diseases. Therefore, protein arginine methyltransferases (PRMTs) that are involved in this process have gained considerable attention as a potential therapeutic target for treating diseases. Several PRMT inhibitors are in phase I/II clinical trials. This paper aims to introduce the structure, biochemical functions, and bioactivity assays of PRMTs. Additionally, we will review the structure-function of currently popular PRMT inhibitors. Through the analysis of various data on known PRMT inhibitors, we hope to provide valuable assistance for future drug design and development.
Collapse
Affiliation(s)
- Chao Tong
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Xiujin Chang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Fangui Qu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China.
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China.
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjin, 211198, China.
| |
Collapse
|
4
|
Buchner J, Alasady MJ, Backe SJ, Blagg BSJ, Carpenter RL, Colombo G, Gelis I, Gewirth DT, Gierasch LM, Houry WA, Johnson JL, Kang BH, Kao AW, LaPointe P, Mattoo S, McClellan AJ, Neckers LM, Prodromou C, Rasola A, Sager RA, Theodoraki MA, Truman AW, Truttman MC, Zachara NE, Bourboulia D, Mollapour M, Woodford MR. Second international symposium on the chaperone code, 2023. Cell Stress Chaperones 2024; 29:88-96. [PMID: 38316354 PMCID: PMC10939070 DOI: 10.1016/j.cstres.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Affiliation(s)
- Johannes Buchner
- Department of Bioscience, Technical University of Munich, D85748, Garching, Germany.
| | - Milad J Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Brian S J Blagg
- Department of Chemistry and Biochemistry, Warren Family Research Center for Drug Discovery and Development, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Richard L Carpenter
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Bloomington, IN, 47405, USA; Medical Sciences, Indiana University School of Medicine, Bloomington, IN, 47405, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN, 47405, USA
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, 27100 Pavia, Italy
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Daniel T Gewirth
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, Amherst, MA, 01003, USA
| | - Lila M Gierasch
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA, 01003, USA; Hauptman-Woodward Medical Research Institute, Buffalo, NY, 14203, USA
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5G 1M1, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Jill L Johnson
- Department of Biological Sciences and the Center for Reproductive Biology, University of Idaho, Moscow, ID, 83844, USA
| | - Byoung Heon Kang
- Department of Biological Sciences, Ulsan National Institutes of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Aimee W Kao
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, 94158, USA
| | - Paul LaPointe
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
| | - Seema Mattoo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN, 47907, USA; Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Amie J McClellan
- Division of Science and Mathematics, Bennington College, Bennington, VT, 05201, USA
| | - Leonard M Neckers
- Center for Cancer Research, National Cancer Institute, Rockville, MD, 20892, USA
| | | | - Andrea Rasola
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy
| | - Rebecca A Sager
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | | | - Andrew W Truman
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Matthias C Truttman
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, 48109, USA; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA; Geriatrics Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Natasha E Zachara
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA; Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Dimitra Bourboulia
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Mark R Woodford
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY, 13210, USA; Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| |
Collapse
|
5
|
Zhu Y, Xia T, Chen DQ, Xiong X, Shi L, Zuo Y, Xiao H, Liu L. Promising role of protein arginine methyltransferases in overcoming anti-cancer drug resistance. Drug Resist Updat 2024; 72:101016. [PMID: 37980859 DOI: 10.1016/j.drup.2023.101016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/21/2023]
Abstract
Drug resistance remains a major challenge in cancer treatment, necessitating the development of novel strategies to overcome it. Protein arginine methyltransferases (PRMTs) are enzymes responsible for epigenetic arginine methylation, which regulates various biological and pathological processes, as a result, they are attractive therapeutic targets for overcoming anti-cancer drug resistance. The ongoing development of small molecules targeting PRMTs has resulted in the generation of chemical probes for modulating most PRMTs and facilitated clinical treatment for the most advanced oncology targets, including PRMT1 and PRMT5. In this review, we summarize various mechanisms underlying protein arginine methylation and the roles of specific PRMTs in driving cancer drug resistance. Furthermore, we highlight the potential clinical implications of PRMT inhibitors in decreasing cancer drug resistance. PRMTs promote the formation and maintenance of drug-tolerant cells via several mechanisms, including altered drug efflux transporters, autophagy, DNA damage repair, cancer stem cell-related function, epithelial-mesenchymal transition, and disordered tumor microenvironment. Multiple preclinical and ongoing clinical trials have demonstrated that PRMT inhibitors, particularly PRMT5 inhibitors, can sensitize cancer cells to various anti-cancer drugs, including chemotherapeutic, targeted therapeutic, and immunotherapeutic agents. Combining PRMT inhibitors with existing anti-cancer strategies will be a promising approach for overcoming anti-cancer drug resistance. Furthermore, enhanced knowledge of the complex functions of arginine methylation and PRMTs in drug resistance will guide the future development of PRMT inhibitors and may help identify new clinical indications.
Collapse
Affiliation(s)
- Yongxia Zhu
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Tong Xia
- Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Da-Qian Chen
- Department of Medicine Oncology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Xia Xiong
- Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Lihong Shi
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Yueqi Zuo
- Shaanxi Key Laboratory of Brain Disorders, Institute of Basic Translational Medicine, Xi'an Medical University, Xi'an 710021, China.
| | - Hongtao Xiao
- Department of Pharmacy, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China.
| | - Li Liu
- Department of Dermatology, The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China.
| |
Collapse
|
6
|
Holtz AG, Lowe TL, Aoki Y, Kubota Y, Hoffman RM, Clarke SG. Asymmetric and symmetric protein arginine methylation in methionine-addicted human cancer cells. PLoS One 2023; 18:e0296291. [PMID: 38134182 PMCID: PMC10745221 DOI: 10.1371/journal.pone.0296291] [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: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The methionine addiction of cancer cells is known as the Hoffman effect. While non-cancer cells in culture can utilize homocysteine in place of methionine for cellular growth, most cancer cells require exogenous methionine for proliferation. It has been suggested that a biochemical basis of this effect is the increased utilization of methionine for S-adenosylmethionine, the major methyl donor for a variety of cellular methyltransferases. Recent studies have pointed to the role of S-adenosylmethionine-dependent protein arginine methyltransferases (PRMTs) in cell proliferation and cancer. To further understand the biochemical basis of the methionine addiction of cancer cells, we compared protein arginine methylation in two previously described isogenic cell lines, a methionine-addicted 143B human osteosarcoma cell line and its less methionine-dependent revertant. Previous work showed that the revertant cells were significantly less malignant than the parental cells. In the present study, we utilized antibodies to detect the asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA) products of PRMTs in polypeptides from cellular extracts and purified histone preparations of these cell lines fractionated by SDS-PAGE. Importantly, we observed little to no differences in the banding patterns of ADMA- and SDMA-containing species between the osteosarcoma parental and revertant cell lines. Furthermore, enzymatic activity assays using S-adenosyl-ʟ-[methyl-3H] methionine, recombinantly purified PRMT enzymes, cell lysates, and specific PRMT inhibitors revealed no major differences in radiolabeled polypeptides on SDS-PAGE gels. Taken together, these results suggest that changes in protein arginine methylation may not be major contributors to the Hoffman effect and that other consequences of methionine addiction may be more important in the metastasis and malignancy of osteosarcoma and potentially other cancers.
Collapse
Affiliation(s)
- Ashley G Holtz
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Troy L Lowe
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States of America
| | - Yusuke Aoki
- AntiCancer, Inc, San Diego, CA, United States of America
- Department of Surgery, University of California, San Diego, La Jolla, CA, United States of America
- Department of Orthopedic Surgery, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Yutaro Kubota
- AntiCancer, Inc, San Diego, CA, United States of America
- Department of Surgery, University of California, San Diego, La Jolla, CA, United States of America
| | - Robert M Hoffman
- AntiCancer, Inc, San Diego, CA, United States of America
- Department of Surgery, University of California, San Diego, La Jolla, CA, United States of America
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, United States of America
| |
Collapse
|
7
|
Hu H, Tjaden A, Knapp S, Antolin AA, Müller S. A machine learning and live-cell imaging tool kit uncovers small molecules induced phospholipidosis. Cell Chem Biol 2023; 30:1634-1651.e6. [PMID: 37797617 DOI: 10.1016/j.chembiol.2023.09.003] [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: 05/20/2023] [Revised: 08/09/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
Drug-induced phospholipidosis (DIPL), characterized by excessive accumulation of phospholipids in lysosomes, can lead to clinical adverse effects. It may also alter phenotypic responses in functional studies using chemical probes. Therefore, robust methods are needed to predict and quantify phospholipidosis (PL) early in drug discovery and in chemical probe characterization. Here, we present a versatile high-content live-cell imaging approach, which was used to evaluate a chemogenomic and a lysosomal modulation library. We trained and evaluated several machine learning models using the most comprehensive set of publicly available compounds and interpreted the best model using SHapley Additive exPlanations (SHAP). Analysis of high-quality chemical probes extracted from the Chemical Probes Portal using our algorithm revealed that closely related molecules, such as chemical probes and their matched negative controls can differ in their ability to induce PL, highlighting the importance of identifying PL for robust target validation in chemical biology.
Collapse
Affiliation(s)
- Huabin Hu
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK; Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC, Box 596, SE-751 24 Uppsala, Sweden
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany
| | - Albert A Antolin
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London, UK; ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Catalonia Barcelona, Spain.
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Johann Wolfgang Goethe University, 60438 Frankfurt am Main, Germany.
| |
Collapse
|
8
|
Zhang M, Chen C, Lu Z, Cai Y, Li Y, Zhang F, Liu Y, Chen S, Zhang H, Yang S, Gen H, Jiang Y, Ning C, Huang J, Wang W, Fan L, Zhang Y, Jin M, Han J, Xiong Z, Cai M, Liu J, Huang C, Yang X, Xu B, Li H, Li B, Zhu X, Wei Y, Zhu Y, Tian J, Miao X. Genetic Control of Alternative Splicing and its Distinct Role in Colorectal Cancer Mechanisms. Gastroenterology 2023; 165:1151-1167. [PMID: 37541527 DOI: 10.1053/j.gastro.2023.07.019] [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: 02/18/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND & AIMS Dysregulation of alternative splicing is implicated in many human diseases, and understanding the genetic variation underlying transcript splicing is essential to dissect the molecular mechanisms of cancers. We aimed to provide a comprehensive functional dissection of splicing quantitative trait loci (sQTLs) in cancer and focus on elucidating its distinct role in colorectal cancer (CRC) mechanisms. METHODS We performed a comprehensive sQTL analysis to identify genetic variants that control messenger RNA splicing across 33 cancer types from The Cancer Genome Atlas and independently validated in our 154 CRC tissues. Then, large-scale, multicenter, multi-ethnic case-control studies (34,585 cases and 76,023 controls) were conducted to examine the association of these sQTLs with CRC risk. A series of biological experiments in vitro and in vivo were performed to investigate the potential mechanisms of the candidate sQTLs and target genes. RESULTS The molecular characterization of sQTL revealed its distinct role in cancer susceptibility. Tumor-specific sQTL further showed better response to cancer development. In addition, functionally informed polygenic risk score highlighted the potentiality of sQTLs in the CRC prediction. Complemented by large-scale population studies, we identified that the risk allele (T) of a multi-ancestry-associated sQTL rs61746794 significantly increased the risk of CRC in Chinese (odds ratio, 1.20; 95% CI, 1.12-1.29; P = 8.82 × 10-7) and European (odds ratio, 1.11; 95% CI, 1.07-1.16; P = 1.13 × 10-7) populations. rs61746794-T facilitated PRMT7 exon 16 splicing mediated by the RNA-binding protein PRPF8, thus increasing the level of canonical PRMT7 isoform (PRMT7-V2). Overexpression of PRMT7-V2 significantly enhanced the growth of CRC cells and xenograft tumors compared with PRMT7-V1. Mechanistically, PRMT7-V2 functions as an epigenetic writer that catalyzes the arginine methylation of H4R3 and H3R2, subsequently regulating diverse biological processes, including YAP, AKT, and KRAS pathway. A selective PRMT7 inhibitor, SGC3027, exhibited antitumor effects on human CRC cells. CONCLUSIONS Our study provides an informative sQTLs resource and insights into the regulatory mechanisms linking splicing variants to cancer risk and serving as biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Can Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yanmin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Fuwei Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yizhuo Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuoni Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Heng Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuhui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Hui Gen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yuan Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jinyu Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wenzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Linyun Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yi Zhang
- Department of Hygiene Toxicology, School of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
| | - Meng Jin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jinxin Han
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhen Xiong
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Cai
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiuyang Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chaoqun Huang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Xiaojun Yang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Heng Li
- Department of Urology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University; Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China; Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, China; Jiangsu Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China; Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.
| |
Collapse
|
9
|
Feoli A, Iannelli G, Cipriano A, Milite C, Shen L, Wang Z, Hadjikyriacou A, Lowe TL, Safaeipour C, Viviano M, Sarno G, Morretta E, Monti MC, Yang Y, Clarke SG, Cosconati S, Castellano S, Sbardella G. Identification of a Protein Arginine Methyltransferase 7 (PRMT7)/Protein Arginine Methyltransferase 9 (PRMT9) Inhibitor. J Med Chem 2023; 66:13665-13683. [PMID: 37560786 PMCID: PMC10578352 DOI: 10.1021/acs.jmedchem.3c01030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Indexed: 08/11/2023]
Abstract
Less studied than the other protein arginine methyltransferase isoforms, PRMT7 and PRMT9 have recently been identified as important therapeutic targets. Yet, most of their biological roles and functions are still to be defined, as well as the structural requirements that could drive the identification of selective modulators of their activity. We recently described the structural requirements that led to the identification of potent and selective PRMT4 inhibitors spanning both the substrate and the cosubstrate pockets. The reanalysis of the data suggested a PRMT7 preferential binding for shorter derivatives and prompted us to extend these structural studies to PRMT9. Here, we report the identification of the first potent PRMT7/9 inhibitor and its binding mode to the two PRMT enzymes. Label-free quantification mass spectrometry confirmed significant inhibition of PRMT activity in cells. We also report the setup of an effective AlphaLISA assay to screen small molecule inhibitors of PRMT9.
Collapse
Affiliation(s)
- Alessandra Feoli
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Giulia Iannelli
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
- PhD
Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Alessandra Cipriano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Ciro Milite
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Lei Shen
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Zhihao Wang
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Andrea Hadjikyriacou
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Troy L. Lowe
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Cyrus Safaeipour
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Monica Viviano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Giuliana Sarno
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
- PhD
Program in Drug Discovery and Development, University of Salerno, via Giovanni Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Elva Morretta
- Department
of Pharmacy, ProteoMass Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Maria Chiara Monti
- Department
of Pharmacy, ProteoMass Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Yanzhong Yang
- Department
of Cancer Genetics and Epigenetics, Beckman
Research Institute, City of Hope National Cancer Center, Duarte, California 91010, United States
| | - Steven G. Clarke
- Department
of Chemistry and Biochemistry, and the Molecular Biology Institute, University of California, Los Angeles, California 90095, United States
| | - Sandro Cosconati
- DiSTABiF, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sabrina Castellano
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| | - Gianluca Sbardella
- Department
of Pharmacy, Epigenetic Med Chem Lab, University
of Salerno, via Giovanni
Paolo II 132, Fisciano ,I-84084 SA Italy
| |
Collapse
|
10
|
Chang K, Gao D, Yan J, Lin L, Cui T, Lu S. Critical Roles of Protein Arginine Methylation in the Central Nervous System. Mol Neurobiol 2023; 60:6060-6091. [PMID: 37415067 DOI: 10.1007/s12035-023-03465-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023]
Abstract
A remarkable post-transitional modification of both histones and non-histone proteins is arginine methylation. Methylation of arginine residues is crucial for a wide range of cellular process, including signal transduction, DNA repair, gene expression, mRNA splicing, and protein interaction. Arginine methylation is modulated by arginine methyltransferases and demethylases, like protein arginine methyltransferase (PRMTs) and Jumonji C (JmjC) domain containing (JMJD) proteins. Symmetric dimethylarginine and asymmetric dimethylarginine, metabolic products of the PRMTs and JMJD proteins, can be changed by abnormal expression of these proteins. Many pathologies including cancer, inflammation and immune responses have been closely linked to aberrant arginine methylation. Currently, the majority of the literature discusses the substrate specificity and function of arginine methylation in the pathogenesis and prognosis of cancers. Numerous investigations on the roles of arginine methylation in the central nervous system (CNS) have so far been conducted. In this review, we display the biochemistry of arginine methylation and provide an overview of the regulatory mechanism of arginine methyltransferases and demethylases. We also highlight physiological functions of arginine methylation in the CNS and the significance of arginine methylation in a variety of neurological diseases such as brain cancers, neurodegenerative diseases and neurodevelopmental disorders. Furthermore, we summarize PRMT inhibitors and molecular functions of arginine methylation. Finally, we pose important questions that require further research to comprehend the roles of arginine methylation in the CNS and discover more effective targets for the treatment of neurological diseases.
Collapse
Affiliation(s)
- Kewei Chang
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Dan Gao
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Jidong Yan
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Liyan Lin
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Tingting Cui
- Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Shemin Lu
- Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education of China, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China.
- Department of Biochemistry and Molecular Biology, and Institute of Molecular and Translational Medicine, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, 76 Yanta West Road, Xi'an, 710061, Shaanxi, China.
| |
Collapse
|
11
|
Deng W, Ai J, Zhang W, Zhou Z, Li M, Yan L, Zhang L, Huang Z, Wu Z, Ai J, Jiang H. Arginine methylation of HSPA8 by PRMT9 inhibits ferroptosis to accelerate hepatitis B virus-associated hepatocellular carcinoma progression. J Transl Med 2023; 21:625. [PMID: 37715221 PMCID: PMC10503172 DOI: 10.1186/s12967-023-04408-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND The hepatitis B virus X (HBx) protein is an established cause of hepatitis B virus (HBV)-induced hepatocellular carcinoma (HCC). Whether arginine methylation regulates ferroptosis involved in HBx-induced HCC progression has not been reported. This study aimed to explore whether HBx-regulated protein arginine methyltransferase 9 (PRMT9) mediates the involvement of ferroptosis in the development of HCC. METHODS AND RESULTS HBx inhibited ferroptosis through promoting PRMT9 expression in HCC cells. PRMT9 suppressed ferroptosis to accelerate HCC progression in vivo. PRMT9 targeted HSPA8 and enhanced arginine methylation of HSPA8 at R76 and R100 to regulate ferroptosis in HCC. HSPA8 overexpression altered the transcriptome profile of HepG2 cells, in particular, ferroptosis and immune-related pathways were significantly enriched by differentially expressed genes, including CD44. HSPA8 overexpression up-regulated CD44 expression and knockdown of CD44 significantly reversed the inhibition of ferroptosis caused by PRMT9 overexpression. CONCLUSIONS In conclusion, HBx/PRMT9/HSPA8/CD44 axis is a vital signal pathway regulating ferroptosis in HCC cells. This study provides new opportunities and targets for the treatment of HBV-induced HCC.
Collapse
Affiliation(s)
- Wensheng Deng
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China
| | - Jiaoyu Ai
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, 330000, Jiangxi, China
| | - Wanlin Zhang
- Department of Clinical Laboratory, Ningbo Yinzhou No. 2 Hospital Ningbo Urology and Nephtology Hospital, Ningbo, 315100, Zhejiang, China
| | - Zhenyu Zhou
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Muqi Li
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China
| | - Likun Yan
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China
| | - Lidong Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China
| | - Zongjing Huang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China
| | - Ziyi Wu
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China
| | - Junhua Ai
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China.
| | - Hai Jiang
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, No. 17 Yongwaizheng Street, Donghu District, Nanchang City, 330000, Jiangxi, China.
| |
Collapse
|
12
|
Acosta CH, Clemons GA, Citadin CT, Carr WC, Udo MSB, Tesic V, Sanicola HW, Freelin AH, Toms JB, Jordan JD, Guthikonda B, Rodgers KM, Wu CYC, Lee RHC, Lin HW. PRMT7 can prevent neurovascular uncoupling, blood-brain barrier permeability, and mitochondrial dysfunction in repetitive and mild traumatic brain injury. Exp Neurol 2023; 366:114445. [PMID: 37196697 PMCID: PMC10960645 DOI: 10.1016/j.expneurol.2023.114445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/03/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Mild traumatic brain injury (TBI) comprises the largest percentage of TBI-related injuries, with pathophysiological and functional deficits that persist in a subset of TBI patients. In our three-hit paradigm of repetitive and mild traumatic brain injury (rmTBI), we observed neurovascular uncoupling via decreased red blood cell velocity, microvessel diameter, and leukocyte rolling velocity 3 days post-rmTBI via intra-vital two-photon laser scanning microscopy. Furthermore, our data suggest increased blood-brain barrier (BBB) permeability (leakage), with corresponding decrease in junctional protein expression post-rmTBI. Mitochondrial oxygen consumption rates (measured via Seahorse XFe24) were also altered 3 days post-rmTBI, along with disrupted mitochondrial dynamics of fission and fusion. Overall, these pathophysiological findings correlated with decreased protein arginine methyltransferase 7 (PRMT7) protein levels and activity post-rmTBI. Here, we increased PRMT7 levels in vivo to assess the role of the neurovasculature and mitochondria post-rmTBI. In vivo overexpression of PRMT7 using a neuronal specific AAV vector led to restoration of neurovascular coupling, prevented BBB leakage, and promoted mitochondrial respiration, altogether to suggest a protective and functional role of PRMT7 in rmTBI.
Collapse
Affiliation(s)
- Christina H Acosta
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Garrett A Clemons
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Cristiane T Citadin
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - William C Carr
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Mariana Sayuri Berto Udo
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Vesna Tesic
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Henry W Sanicola
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America; Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Anne H Freelin
- Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Jamie B Toms
- Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - J Dedrick Jordan
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Bharat Guthikonda
- Department of Neurosurgery, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Krista M Rodgers
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Celeste Yin-Chieh Wu
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Reggie Hui-Chao Lee
- Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America
| | - Hung Wen Lin
- Department of Cellular Biology & Anatomy, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America; Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA, United States of America.
| |
Collapse
|
13
|
Kottur J, White KM, Rodriguez ML, Rechkoblit O, Quintana-Feliciano R, Nayar A, García-Sastre A, Aggarwal AK. Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals. PLoS Pathog 2023; 19:e1011546. [PMID: 37523415 PMCID: PMC10414583 DOI: 10.1371/journal.ppat.1011546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/10/2023] [Accepted: 07/06/2023] [Indexed: 08/02/2023] Open
Abstract
The RNA N7-methyltransferase (MTase) activity of SARS-CoV-2's nsp14 protein is essential for viral replication and is a target for the development of new antivirals. Nsp14 uses S-adenosyl methionine (SAM) as the methyl donor to cap the 5' end of the SARS-CoV-2 mRNA and generates S-adenosyl homocysteine (SAH) as the reaction byproduct. Due to the central role of histone MTases in cancer, many SAM/SAH analogs with properties of cell permeability have recently been developed for the inhibition of these MTases. We have succeeded in identifying two such compounds (SGC0946 and SGC8158) that display significant antiviral activity and bind to the SARS-CoV-2 nsp14 N7-MTase core. Unexpectedly, crystal structures of SGC0946 and SGC8158 with the SARS-CoV-2 nsp14 N7-MTase core identify them as bi-substrate inhibitors of the viral MTase, co-occupying both the SAM and RNA binding sites; positing novel features that can be derivatized for increased potency and selectivity for SARS-CoV-2 nsp14. Taken together, the high-resolution structures and the accompanying biophysical and viral replication data provide a new avenue for developing analogs of SGC0946 and SGC8158 as antivirals.
Collapse
Affiliation(s)
- Jithesh Kottur
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Kris M. White
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - M. Luis Rodriguez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Olga Rechkoblit
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Richard Quintana-Feliciano
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Ahana Nayar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- The Tisch Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Aneel K. Aggarwal
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| |
Collapse
|
14
|
Bondoc TJ, Lowe TL, Clarke SG. The exquisite specificity of human protein arginine methyltransferase 7 (PRMT7) toward Arg-X-Arg sites. PLoS One 2023; 18:e0285812. [PMID: 37216364 DOI: 10.1371/journal.pone.0285812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/01/2023] [Indexed: 05/24/2023] Open
Abstract
Mammalian protein arginine methyltransferase 7 (PRMT7) has been shown to target substrates with motifs containing two arginine residues separated by one other residue (RXR motifs). In particular, the repression domain of human histone H2B (29-RKRSR-33) has been a key substrate in determining PRMT7 activity. We show that incubating human PRMT7 and [3H]-AdoMet with full-length Xenopus laevis histone H2B, containing the substitutions K30R and R31K (RKRSR to RRKSR), results in greatly reduced methylation activity. Using synthetic peptides, we have now focused on the enzymology behind this specificity. We show for the human and Xenopus peptide sequences 23-37 the difference in activity results from changes in the Vmax rather than the apparent binding affinity of the enzyme for the substrates. We then characterized six additional peptides containing a single arginine or a pair of arginine residues flanked by glycine and lysine residues. We have corroborated previous findings that peptides with an RXR motif have much higher activity than peptides that contain only one Arg residue. We show that these peptides have similar apparent km values but significant differences in their Vmax values. Finally, we have examined the effect of ionic strength on these peptides. We found the inclusion of salt had little effect on the Vmax value but a considerable increase in the apparent km value, suggesting that the inhibitory effect of ionic strength on PRMT7 activity occurs largely by decreasing apparent substrate-enzyme binding affinity. In summary, we find that even subtle substitutions in the RXR recognition motif can dramatically affect PRMT7 catalysis.
Collapse
Affiliation(s)
- Timothy J Bondoc
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Troy L Lowe
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| |
Collapse
|
15
|
Zhou J, Deng Y, Iyamu ID, Horton JR, Yu D, Hajian T, Vedadi M, Rotili D, Mai A, Blumenthal RM, Zhang X, Huang R, Cheng X. Comparative Study of Adenosine Analogs as Inhibitors of Protein Arginine Methyltransferases and a Clostridioides difficile-Specific DNA Adenine Methyltransferase. ACS Chem Biol 2023; 18:734-745. [PMID: 37082867 PMCID: PMC10127221 DOI: 10.1021/acschembio.3c00035] [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: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/25/2023]
Abstract
S-Adenosyl-l-methionine (SAM) analogs are adaptable tools for studying and therapeutically inhibiting SAM-dependent methyltransferases (MTases). Some MTases play significant roles in host-pathogen interactions, one of which is Clostridioides difficile-specific DNA adenine MTase (CamA). CamA is needed for efficient sporulation and alters persistence in the colon. To discover potent and selective CamA inhibitors, we explored modifications of the solvent-exposed edge of the SAM adenosine moiety. Starting from the two parental compounds (6e and 7), we designed an adenosine analog (11a) carrying a 3-phenylpropyl moiety at the adenine N6-amino group, and a 3-(cyclohexylmethyl guanidine)-ethyl moiety at the sulfur atom off the ribose ring. Compound 11a (IC50 = 0.15 μM) is 10× and 5× more potent against CamA than 6e and 7, respectively. The structure of the CamA-DNA-inhibitor complex revealed that 11a adopts a U-shaped conformation, with the two branches folded toward each other, and the aliphatic and aromatic rings at the two ends interacting with one another. 11a occupies the entire hydrophobic surface (apparently unique to CamA) next to the adenosine binding site. Our work presents a hybrid knowledge-based and fragment-based approach to generating CamA inhibitors that would be chemical agents to examine the mechanism(s) of action and therapeutic potentials of CamA in C. difficile infection.
Collapse
Affiliation(s)
- Jujun Zhou
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Youchao Deng
- Department
of Medicinal Chemistry and Molecular Pharmacology, Institute for Drug
Discovery, Center for Cancer Research, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Iredia D. Iyamu
- Department
of Medicinal Chemistry and Molecular Pharmacology, Institute for Drug
Discovery, Center for Cancer Research, Purdue
University, West Lafayette, Indiana 47907, United States
| | - John R. Horton
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Dan Yu
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Taraneh Hajian
- Drug
Discovery Program, Ontario Institute for
Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Masoud Vedadi
- Department
of Pharmacology and Toxicology, University
of Toronto, Toronto, ON M5S 1A8, Canada
- Drug
Discovery Program, Ontario Institute for
Cancer Research, Toronto, ON M5G 0A3, Canada
| | - Dante Rotili
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department
of Drug Chemistry and Technologies, Sapienza
University of Rome, P.le A. Moro 5, 00185 Rome, Italy
- Pasteur Institute,
Cenci-Bolognetti Foundation, Sapienza University
of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Robert M. Blumenthal
- Department
of Medical Microbiology and Immunology and Program in Bioinformatics, The University of Toledo College of Medicine and Life
Sciences, Toledo, Ohio 43614, United States
| | - Xing Zhang
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Rong Huang
- Department
of Medicinal Chemistry and Molecular Pharmacology, Institute for Drug
Discovery, Center for Cancer Research, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Xiaodong Cheng
- Department
of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| |
Collapse
|
16
|
Grypari IM, Pappa I, Papastergiou T, Zolota V, Bravou V, Melachrinou M, Megalooikonomou V, Tzelepi V. Elucidating the role of PRMTs in prostate cancer using open access databases and a patient cohort dataset. Histol Histopathol 2023; 38:287-302. [PMID: 36082942 DOI: 10.14670/hh-18-513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Protein arginine methylation is an understudied epigenetic mechanism catalyzed by enzymes known as Protein Methyltransferases of Arginine (PRMTs), while the opposite reaction is performed by Jumonji domain- containing protein 6 (JMJD6). There is increasing evidence that PRMTs are deregulated in prostate cancer (PCa). In this study, the expression of two PRMT members, PRMT2 and PRMT7 as well as JMJD6, a demethylase, was analyzed in PCa. Initially, we retrieved data from The Cancer Genome Atlas (TCGA) project and the Gene Expression Omnibus (GEO) database to explore the differential expression of various PRMT family members in patients with PCa and then applied immunohistochemistry in a patient cohort across the spectrum of PCa, including non-neoplastic prostate tissue and lymph node metastatic foci. The results from the TCGA analysis revealed that PRMT7, PRMT6 and PRMT3 expression increased while PRMT2, PRMT9 and JMJD6 levels decreased in the tumor compared to non-neoplastic prostate. Results from the GEO datasets were similar, albeit not identical with the TCGA results, with PRMT7 and PRMT3 being upregulated and PRMT2 and JMJD6 being downregulated in the tumor compared to non-neoplastic tissue in some of them. In addition, PRMT7 levels decreased with stage and grade progression in the TCGA analysis. In the patient cohort, both PRMTs and JMJD6 were overexpressed in PCa compared to non-neoplastic tissue, and nuclear PRMT2 and JMJD6 were upregulated in lymph node metastasis, too. PRMT7 and JMJD6 expression were upregulated with the progression of stage and JMJD6 was also increased with the elevation of grade. After androgen ablation therapy, nuclear expression of PRMT7 and JMJD6 were elevated compared to untreated tumors. PRMT2, PRMT7 and JMD6 were also correlated with markers of EMT and cell cycle regulators. Finally, our findings indicate that PRMTs and JMJD6 are involved in prostate cancer progression and revealed a potential interplay of PRMTs with EMT mediators, underscoring the need for therapeutic targeting of arginine methylation in prostate cancer.
Collapse
Affiliation(s)
- Ioanna Maria Grypari
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Ioanna Pappa
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Thomas Papastergiou
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Vasiliki Zolota
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Vasiliki Bravou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, Patras, Greece
| | - Maria Melachrinou
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece
| | - Vasileios Megalooikonomou
- Multidimensional Data Analysis and Knowledge Management Laboratory, Computer Engineering and Informatics Department, School of Engineering, University of Patras, Patras, Greece
| | - Vasiliki Tzelepi
- Department of Pathology, School of Medicine, University of Patras, Patras, Greece.
| |
Collapse
|
17
|
Szewczyk MM, Owens DDG, Barsyte-Lovejoy D. Measuring Protein-Protein Interactions in Cells using Nanoluciferase Bioluminescence Resonance Energy Transfer (NanoBRET) Assay. Methods Mol Biol 2023; 2706:137-148. [PMID: 37558946 DOI: 10.1007/978-1-0716-3397-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Protein-protein interactions (PPIs) are increasingly recognized for their roles in functional cellular networks and their importance in disease-targeting contexts. Assessing PPI in the native cellular environment is challenging and requires specific and quantitative methods. Bioluminescence resonance energy transfer (BRET) is a biophysical process that can be used to quantify PPI. With Nanoluciferase bioluminescent protein as a donor and a fluorescent chloroalkane ligand covalently bound to HaloTag protein as an acceptor, NanoBRET provides a versatile and robust system to quantitatively measure PPI in living cells. BRET efficiency is proportional to the distance between the donor and acceptor, allowing for the measurement of PPI in real time. In this paper, we describe the use of NanoBRET to study specific interactions between proteins of interest in living cells that can be perturbed by using small-molecule antagonists and genetic mutations. Here, we provide a detailed protocol for expressing NanoLuc and HaloTag fusion proteins in cell culture and the necessary optimization of NanoBRET assay conditions. Our example results demonstrate the reliability and sensitivity of NanoBRET for measuring interactions between proteins, protein domains, and short peptides and quantitating the PPI antagonist compound activity in living cells.
Collapse
Affiliation(s)
| | - Dominic D G Owens
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
18
|
Ackloo S, Antolin AA, Bartolome JM, Beck H, Bullock A, Betz UAK, Böttcher J, Brown PJ, Chaturvedi M, Crisp A, Daniels D, Dreher J, Edfeldt K, Edwards AM, Egner U, Elkins J, Fischer C, Glendorf T, Goldberg S, Hartung IV, Hillisch A, Homan E, Knapp S, Köster M, Krämer O, Llaveria J, Lessel U, Lindemann S, Linderoth L, Matsui H, Michel M, Montel F, Mueller-Fahrnow A, Müller S, Owen DR, Saikatendu KS, Santhakumar V, Sanderson W, Scholten C, Schapira M, Sharma S, Shireman B, Sundström M, Todd MH, Tredup C, Venable J, Willson TM, Arrowsmith CH. Target 2035 – an update on private sector contributions. RSC Med Chem 2023. [DOI: 10.1039/d2md00441k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Target 2035, an international federation of biomedical scientists from the public and private sectors, is leveraging ‘open’ principles to develop a pharmacological tool for every human protein.
Collapse
Affiliation(s)
- Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Albert A. Antolin
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | | | - Hartmut Beck
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Alex Bullock
- Center for Medicines Discovery, Old Road Campus, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | | | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Peter J. Brown
- Structural Genomics Consortium, University of North Carolina at Chapel Hill, USA
| | - Menorca Chaturvedi
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Alisa Crisp
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Danette Daniels
- Foghorn Therapeutics, 500 Technology Square, Suite 700, Cambridge, MA 02139, USA
| | - Jan Dreher
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Kristina Edfeldt
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Ursula Egner
- Nuvisan Innovation Campus Berlin GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Jon Elkins
- Center for Medicines Discovery, Old Road Campus, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Christian Fischer
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, USA
| | - Tine Glendorf
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Steven Goldberg
- Janssen Research and Development LLC, San Diego, California, USA
| | - Ingo V. Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Alexander Hillisch
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Markus Köster
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Oliver Krämer
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Josep Llaveria
- A Division of Janssen-Cilag S.A., Janssen Research and Development, Toledo, Spain
| | - Uta Lessel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, D-88397 Biberach an der Riss, Germany
| | | | - Lars Linderoth
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Hisanori Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Florian Montel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, D-88397 Biberach an der Riss, Germany
| | | | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Dafydd R. Owen
- Discovery Network Group, Pfizer Medicine Design, Cambridge, MA 02139, USA
| | - Kumar Singh Saikatendu
- Global Research Externalization, Takeda California, Inc., 9625 Towne Center Drive, San Diego, CA 92121, USA
| | | | - Wendy Sanderson
- Janssen Research & Development, Janssen Pharmaceutica N. V, Beerse, Belgium
| | - Cora Scholten
- Research and Development, Bayer AG, Pharmaceuticals, 13353 Berlin, Germany
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sujata Sharma
- Janssen Research and Development LLC, San Diego, California, USA
| | - Brock Shireman
- Janssen Research and Development LLC, San Diego, California, USA
| | - Michael Sundström
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Matthew H. Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Claudia Tredup
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Jennifer Venable
- Janssen Research and Development LLC, San Diego, California, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, M5G 1L7, Canada
| |
Collapse
|
19
|
Rubanov A, Berico P, Hernando E. Epigenetic Mechanisms Underlying Melanoma Resistance to Immune and Targeted Therapies. Cancers (Basel) 2022; 14:cancers14235858. [PMID: 36497341 PMCID: PMC9738385 DOI: 10.3390/cancers14235858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is an aggressive skin cancer reliant on early detection for high likelihood of successful treatment. Solar UV exposure transforms melanocytes into highly mutated tumor cells that metastasize to the liver, lungs, and brain. Even upon resection of the primary tumor, almost thirty percent of patients succumb to melanoma within twenty years. Identification of key melanoma genetic drivers led to the development of pharmacological BRAFV600E and MEK inhibitors, significantly improving metastatic patient outcomes over traditional cytotoxic chemotherapy or pioneering IFN-α and IL-2 immune therapies. Checkpoint blockade inhibitors releasing the immunosuppressive effects of CTLA-4 or PD-1 proved to be even more effective and are the standard first-line treatment. Despite these major improvements, durable responses to immunotherapy and targeted therapy have been hindered by intrinsic or acquired resistance. In addition to gained or selected genetic alterations, cellular plasticity conferred by epigenetic reprogramming is emerging as a driver of therapy resistance. Epigenetic regulation of chromatin accessibility drives gene expression and establishes distinct transcriptional cell states. Here we review how aberrant chromatin, transcriptional, and epigenetic regulation contribute to therapy resistance and discuss how targeting these programs sensitizes melanoma cells to immune and targeted therapies.
Collapse
Affiliation(s)
- Andrey Rubanov
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Pietro Berico
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
| | - Eva Hernando
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
- Interdisciplinary Melanoma Cooperative Group, Perlmutter Cancer Center, NYU Langone Health, New York, NY 10016, USA
- Correspondence:
| |
Collapse
|
20
|
Chen Y, Shi Q, Yang H, Li J, Zhou K, Zhang J, Wang Z, Shi H, Xiong B, Liu J, Huang X, Liu T. Structure-activity Relationship Study of a Series of Nucleoside Derivatives Bearing Sulfonamide Scaffold as Potent and Selective PRMT5 Inhibitors. Bioorg Chem 2022; 130:106228. [DOI: 10.1016/j.bioorg.2022.106228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
|
21
|
Zhao J, Jiang H, Zou G, Lin Q, Wang Q, Liu J, Ma L. CNNArginineMe: A CNN structure for training models for predicting arginine methylation sites based on the One-Hot encoding of peptide sequence. Front Genet 2022; 13:1036862. [PMID: 36324513 PMCID: PMC9618650 DOI: 10.3389/fgene.2022.1036862] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/04/2022] [Indexed: 11/30/2022] Open
Abstract
Protein arginine methylation (PRme), as one post-translational modification, plays a critical role in numerous cellular processes and regulates critical cellular functions. Though several in silico models for predicting PRme sites have been reported, new models may be required to develop due to the significant increase of identified PRme sites. In this study, we constructed multiple machine-learning and deep-learning models. The deep-learning model CNN combined with the One-Hot coding showed the best performance, dubbed CNNArginineMe. CNNArginineMe performed best in AUC scoring metrics in comparisons with several reported predictors. Additionally, we employed CNNArginineMe to predict arginine methylation proteome and performed functional analysis. The arginine methylated proteome is significantly enriched in the amyotrophic lateral sclerosis (ALS) pathway. CNNArginineMe is freely available at https://github.com/guoyangzou/CNNArginineMe.
Collapse
Affiliation(s)
- Jiaojiao Zhao
- Cancer Institute of the Affiliated Hospital of Qingdao University and Qingdao Cancer Institute, Qingdao University, Qingdao, China
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Haoqiang Jiang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Guoyang Zou
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Qian Lin
- Cancer Institute of the Affiliated Hospital of Qingdao University and Qingdao Cancer Institute, Qingdao University, Qingdao, China
| | - Qiang Wang
- Oncology Department, Shandong Second Provincial General Hospital, Jinan, China
| | - Jia Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao, China
| | - Leina Ma
- Cancer Institute of the Affiliated Hospital of Qingdao University and Qingdao Cancer Institute, Qingdao University, Qingdao, China
- *Correspondence: Leina Ma,
| |
Collapse
|
22
|
Jeong A, Cho Y, Cho M, Bae GU, Song DG, Kim SN, Kim YK. PRMT7 Inhibitor SGC8158 Enhances Doxorubicin-Induced DNA Damage and Its Cytotoxicity. Int J Mol Sci 2022; 23:ijms232012323. [PMID: 36293180 PMCID: PMC9604017 DOI: 10.3390/ijms232012323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/09/2022] [Accepted: 10/13/2022] [Indexed: 11/07/2022] Open
Abstract
Protein arginine methyltransferase 7 (PRMT7) regulates various cellular responses, including gene expression, cell migration, stress responses, and stemness. In this study, we investigated the biological role of PRMT7 in cell cycle progression and DNA damage response (DDR) by inhibiting PRMT7 activity with either SGC8158 treatment or its specific siRNA transfection. Suppression of PRMT7 caused cell cycle arrest at the G1 phase, resulting from the stabilization and subsequent accumulation of p21 protein. In addition, PRMT7 activity is closely associated with DNA repair pathways, including both homologous recombination and non-homologous end-joining. Interestingly, SGC8158, in combination with doxorubicin, led to a synergistic increase in both DNA damage and cytotoxicity in MCF7 cells. Taken together, our data demonstrate that PRMT7 is a critical modulator of cell growth and DDR, indicating that it is a promising target for cancer treatment.
Collapse
Affiliation(s)
- Ahyeon Jeong
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Yena Cho
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Minkyeong Cho
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Gyu-Un Bae
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
| | - Dae-Geun Song
- Natural Products Research Institute, KIST Gangneung, Gangneung 25451, Korea
| | - Su-Nam Kim
- Natural Products Research Institute, KIST Gangneung, Gangneung 25451, Korea
- Division of Bio-Medical Science and Technology, University of Science and Technology KIST School, Seoul 02792, Korea
- Correspondence: (S.-N.K.); (Y.K.K.); Tel.: +82-33-650-3503 (S.-N.K.); +82-2-2077-7688 (Y.K.K.)
| | - Yong Kee Kim
- Muscle Physiome Research Center and Drug Information Research Institute, College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Korea
- Correspondence: (S.-N.K.); (Y.K.K.); Tel.: +82-33-650-3503 (S.-N.K.); +82-2-2077-7688 (Y.K.K.)
| |
Collapse
|
23
|
Brobbey C, Liu L, Yin S, Gan W. The Role of Protein Arginine Methyltransferases in DNA Damage Response. Int J Mol Sci 2022; 23:ijms23179780. [PMID: 36077176 PMCID: PMC9456308 DOI: 10.3390/ijms23179780] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/25/2022] [Accepted: 08/27/2022] [Indexed: 11/16/2022] Open
Abstract
In response to DNA damage, cells have developed a sophisticated signaling pathway, consisting of DNA damage sensors, transducers, and effectors, to ensure efficient and proper repair of damaged DNA. During this process, posttranslational modifications (PTMs) are central events that modulate the recruitment, dissociation, and activation of DNA repair proteins at damage sites. Emerging evidence reveals that protein arginine methylation is one of the common PTMs and plays critical roles in DNA damage response. Protein arginine methyltransferases (PRMTs) either directly methylate DNA repair proteins or deposit methylation marks on histones to regulate their transcription, RNA splicing, protein stability, interaction with partners, enzymatic activities, and localization. In this review, we summarize the substrates and roles of each PRMTs in DNA damage response and discuss the synergistic anticancer effects of PRMTs and DNA damage pathway inhibitors, providing insight into the significance of arginine methylation in the maintenance of genome integrity and cancer therapies.
Collapse
|
24
|
Lazado CC, Strand DA, Breiland MW, Furtado F, Timmerhaus G, Gjessing MC, Hytterød S, Merkin GV, Pedersen LF, Pittman KA, Krasnov A. Mucosal immune and stress responses of Neoparamoeba perurans-infected Atlantic salmon (Salmo salar) treated with peracetic acid shed light on the host-parasite-oxidant interactions. Front Immunol 2022; 13:948897. [PMID: 36090977 PMCID: PMC9454302 DOI: 10.3389/fimmu.2022.948897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/18/2022] [Indexed: 12/05/2022] Open
Abstract
Treatment development for parasitic infestation is often limited to disease resolution as an endpoint response, and physiological and immunological consequences are not thoroughly considered. Here, we report the impact of exposing Atlantic salmon affected with amoebic gill disease (AGD) to peracetic acid (PAA), an oxidative chemotherapeutic. AGD-affected fish were treated with PAA either by exposing them to 5 ppm for 30 min or 10 ppm for 15 min. Unexposed fish from both infected and uninfected groups were also included. Samples for molecular, biochemical, and histological evaluations were collected at 24 h, 2 weeks, and 4 weeks post-treatment. Behavioral changes were observed during PAA exposure, and post-treatment mortality was higher in the infected and PAA treated groups, especially in 10 ppm for 15 min. Plasma indicators showed that liver health was affected by AGD, though PAA treatment did not exacerbate the infection-related changes. Transcriptome profiling in the gills showed significant changes, triggered by AGD and PAA treatments, and the effects of PAA were more notable 24 h after treatment. Genes related to immune pathways of B- and T- cells and protein synthesis and metabolism were downregulated, where the magnitude was more remarkable in 10 ppm for 15 min group. Even though treatment did not fully resolve the pathologies associated with AGD, 5 ppm for 30 min group showed lower parasite load at 4 weeks post-treatment. Mucous cell parameters (i.e., size and density) increased within 24 h post-treatment and were significantly higher at termination, especially in AGD-affected fish, with some treatment effects influenced by the dose of PAA. Infection and treatments resulted in oxidative stress—in the early phase in the gill mucosa, while systemic reactive oxygen species (ROS) dysregulation was evident at the later stage. Infected fish responded to elevated circulating ROS by increasing antioxidant production. Exposing the fish to a crowding stress revealed the interference in the post-stress responses. Lower cortisol response was displayed by AGD-affected groups. Collectively, the study established that PAA, within the evaluated treatment protocols, could not provide a convincing treatment resolution and, thus, requires further optimization. Nonetheless, PAA treatment altered the mucosal immune and stress responses of AGD-affected Atlantic salmon, shedding light on the host-parasite-treatment interactions.
Collapse
Affiliation(s)
- Carlo C. Lazado
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
- *Correspondence: Carlo C. Lazado,
| | | | - Mette W. Breiland
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Tromsø, Norway
| | - Francisco Furtado
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
- Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Gerrit Timmerhaus
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | | | | | | | - Lars-Flemming Pedersen
- DTU Aqua, Section for Aquaculture, The North Sea Research Centre, Technical University of Denmark, Hirtshals, Denmark
| | - Karin A. Pittman
- Quantidoc AS, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Aleksei Krasnov
- Nofima, The Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| |
Collapse
|
25
|
Human Protein Arginine Methyltransferases (PRMTs) Can Be Optimally Active Under Non-Physiological Conditions. J Biol Chem 2022; 298:102290. [PMID: 35868559 PMCID: PMC9418908 DOI: 10.1016/j.jbc.2022.102290] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 11/05/2022] Open
Abstract
Protein arginine methylation is involved in many biological processes and can be enhanced in cancer. In mammals, these reactions are catalyzed on multiple substrates by a family of nine protein arginine methyltransferases (PRMTs). However, conditions that may regulate the activity of each enzyme and that may help us understand the physiological role of PRMTs have not been fully established. Previous studies had suggested unexpected effects of temperature and ionic strength on PRMT7 activity. Here we examine in detail the effects of temperature, pH, and ionic strength on recombinant human PRMT1, PRMT5, and PRMT7. We confirmed the unusual temperature dependence of PRMT7, where optimal activity was observed at 15 °C. On the other hand, we found that PRMT1 and PRMT5 are most active near physiological temperatures of 37 °C. However, we showed all three enzymes still have significant activity at 0 °C. Furthermore, we determined that PRMT1 is most active at a pH of about 7.7, while PRMT5 activity is not dependent on pH in the range of 6.5 to 8.5. Significantly, PRMT7 is most active at an alkaline pH of 8.5 but shows little activity at the physiological intracellular pH of about 7.2. We also detected decreased activity at physiological salt conditions for PRMT1, PRMT5, and PRMT7. We demonstrate that the loss of activity is due to the increasing ionic strength. Taken together, these results open the possibility that PRMTs respond in cells undergoing temperature, salt, or pH stress and demonstrate the potential for in vivo regulation of protein arginine methylation.
Collapse
|
26
|
Massignani E, Giambruno R, Maniaci M, Nicosia L, Yadav A, Cuomo A, Raimondi F, Bonaldi T. ProMetheusDB: An In-Depth Analysis of the High-Quality Human Methyl-proteome. Mol Cell Proteomics 2022; 21:100243. [PMID: 35577067 PMCID: PMC9207298 DOI: 10.1016/j.mcpro.2022.100243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/22/2022] [Accepted: 05/11/2022] [Indexed: 01/01/2023] Open
Abstract
Protein arginine (R) methylation is a post-translational modification involved in various biological processes, such as RNA splicing, DNA repair, immune response, signal transduction, and tumor development. Although several advancements were made in the study of this modification by mass spectrometry, researchers still face the problem of a high false discovery rate. We present a dataset of high-quality methylations obtained from several different heavy methyl stable isotope labeling with amino acids in cell culture experiments analyzed with a machine learning–based tool and show that this model allows for improved high-confidence identification of real methyl-peptides. Overall, our results are consistent with the notion that protein R methylation modulates protein–RNA interactions and suggest a role in rewiring protein–protein interactions, for which we provide experimental evidence for a representative case (i.e., NONO [non-POU domain–containing octamer-binding protein]–paraspeckle component 1 [PSPC1]). Upon intersecting our R-methyl-sites dataset with the PhosphoSitePlus phosphorylation dataset, we observed that R methylation correlates differently with S/T-Y phosphorylation in response to various stimuli. Finally, we explored the application of heavy methyl stable isotope labeling with amino acids in cell culture to identify unconventional methylated residues and successfully identified novel histone methylation marks on serine 28 and threonine 32 of H3. The database generated, named ProMetheusDB, is freely accessible at https://bioserver.ieo.it/shiny/app/prometheusdb. hmSEEKER 2.0 identifies methyl-peptides from hmSILAC data through machine learning. Arginine methylation plays a role in modulating protein–protein interactions. Arginine methylations occur more frequently in proximity of phosphorylation sites. hmSEEKER 2.0 was used to identify methylations occurring on nonstandard amino acids.
Collapse
Affiliation(s)
- Enrico Massignani
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; European School of Molecular Medicine (SEMM), Milan, Italy
| | - Roberto Giambruno
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Center for Genomic Science of Istituto Italiano di Tecnologia at European School of Molecular Medicine, Istituto Italiano di Tecnologia, Milan, Italy; Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Marianna Maniaci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; European School of Molecular Medicine (SEMM), Milan, Italy
| | - Luciano Nicosia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Avinash Yadav
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Francesco Raimondi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Bio@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Haematology-Oncology, University of Milan, Milan, Italy.
| |
Collapse
|
27
|
Srour N, Khan S, Richard S. The Influence of Arginine Methylation in Immunity and Inflammation. J Inflamm Res 2022; 15:2939-2958. [PMID: 35602664 PMCID: PMC9114649 DOI: 10.2147/jir.s364190] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/06/2022] [Indexed: 12/24/2022] Open
Abstract
Exploration in the field of epigenetics has revealed that protein arginine methyltransferases (PRMTs) contribute to disease, and this has given way to the development of specific small molecule compounds that inhibit arginine methylation. Protein arginine methylation is known to regulate fundamental cellular processes, such as transcription; pre-mRNA splicing and other RNA processing mechanisms; signal transduction, including the anti-viral response; and cellular metabolism. PRMTs are also implicated in the regulation of physiological processes, including embryonic development, myogenesis, and the immune system. Finally, the dysregulation of PRMTs is apparent in cancer, neurodegeneration, muscular disorders, and during inflammation. Herein, we review the functions of PRMTs in immunity and inflammation. We also discuss recent progress with PRMTs regarding the modulation of gene expression related to T and B lymphocyte differentiation, germinal center dynamics, and anti-viral signaling responses, as well as the clinical relevance of using PRMT inhibitors alone or in combination with other drugs to treat cancer, immune, and inflammatory-related diseases.
Collapse
Affiliation(s)
- Nivine Srour
- Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, and Departments of Biochemistry, Human Genetics, and Medicine, McGill University, Montréal, Québec, H3T 1E2, Canada
| | - Sarah Khan
- Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, and Departments of Biochemistry, Human Genetics, and Medicine, McGill University, Montréal, Québec, H3T 1E2, Canada
| | - Stephane Richard
- Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, and Departments of Biochemistry, Human Genetics, and Medicine, McGill University, Montréal, Québec, H3T 1E2, Canada
- Correspondence: Stephane Richard, Email
| |
Collapse
|
28
|
Iannelli G, Milite C, Marechal N, Cura V, Bonnefond L, Troffer-Charlier N, Feoli A, Rescigno D, Wang Y, Cipriano A, Viviano M, Bedford MT, Cavarelli J, Castellano S, Sbardella G. Turning Nonselective Inhibitors of Type I Protein Arginine Methyltransferases into Potent and Selective Inhibitors of Protein Arginine Methyltransferase 4 through a Deconstruction-Reconstruction and Fragment-Growing Approach. J Med Chem 2022; 65:11574-11606. [PMID: 35482954 PMCID: PMC9469100 DOI: 10.1021/acs.jmedchem.2c00252] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Protein arginine
methyltransferases (PRMTs) are important therapeutic
targets, playing a crucial role in the regulation of many cellular
processes and being linked to many diseases. Yet, there is still much
to be understood regarding their functions and the biological pathways
in which they are involved, as well as on the structural requirements
that could drive the development of selective modulators of PRMT activity.
Here we report a deconstruction–reconstruction approach that,
starting from a series of type I PRMT inhibitors previously identified
by us, allowed for the identification of potent and selective inhibitors
of PRMT4, which regardless of the low cell permeability show an evident
reduction of arginine methylation levels in MCF7 cells and a marked
reduction of proliferation. We also report crystal structures with
various PRMTs supporting the observed specificity and selectivity.
Collapse
Affiliation(s)
| | | | - Nils Marechal
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Vincent Cura
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Luc Bonnefond
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | - Nathalie Troffer-Charlier
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | | | | | - Yalong Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | | | | | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Jean Cavarelli
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258 Illkirch, France.,Université de Strasbourg, 67400 Illkirch, France
| | | | | |
Collapse
|
29
|
Oksa L, Mäkinen A, Nikkilä A, Hyvärinen N, Laukkanen S, Rokka A, Haapaniemi P, Seki M, Takita J, Kauko O, Heinäniemi M, Lohi O. Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia. Cancers (Basel) 2022; 14:2169. [PMID: 35565298 PMCID: PMC9101393 DOI: 10.3390/cancers14092169] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 02/05/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with no well-established prognostic biomarkers. We examined the expression of protein arginine methyltransferases across hematological malignancies and discovered high levels of PRMT7 mRNA in T-ALL, particularly in the mature subtypes of T-ALL. The genetic deletion of PRMT7 by CRISPR-Cas9 reduced the colony formation of T-ALL cells and changed arginine monomethylation patterns in protein complexes associated with the RNA and DNA processing and the T-ALL pathogenesis. Among them was RUNX1, whose target gene expression was consequently deregulated. These results suggest that PRMT7 plays an active role in the pathogenesis of T-ALL.
Collapse
Affiliation(s)
- Laura Oksa
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Artturi Mäkinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, FI-33520 Tampere, Finland
| | - Atte Nikkilä
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Noora Hyvärinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Saara Laukkanen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
| | - Anne Rokka
- Turku Bioscience Center, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland; (A.R.); (P.H.); (O.K.)
| | - Pekka Haapaniemi
- Turku Bioscience Center, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland; (A.R.); (P.H.); (O.K.)
| | - Masafumi Seki
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-17165 Solna, Sweden;
| | - Junko Takita
- Graduate School of Medicine, Kyoto University, Kyoto JP-606-8501, Japan;
| | - Otto Kauko
- Turku Bioscience Center, University of Turku and Åbo Akademi University, FI-20014 Turku, Finland; (A.R.); (P.H.); (O.K.)
| | - Merja Heinäniemi
- The Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland;
| | - Olli Lohi
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, FI-33520 Tampere, Finland; (A.M.); (A.N.); (N.H.); (S.L.); (O.L.)
- Tays Cancer Center, Tampere University Hospital, FI-33520 Tampere, Finland
| |
Collapse
|
30
|
Wang MY, Liow P, Guzman MIT, Qi J. Exploring Methods of Targeting Histone Methyltransferases and Their Applications in Cancer Therapeutics. ACS Chem Biol 2022; 17:744-755. [PMID: 35363464 PMCID: PMC9336197 DOI: 10.1021/acschembio.2c00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone methyltransferases (HMTs) are enzymes that catalyze the methylation of lysine or arginine residues of histone proteins, a key post-translational modification (PTM). Aberrant expression or activity of these enzymes can lead to abnormal histone methylation of cancer-related genes and thus promote tumorigenesis. Histone methyltransferases have been implicated in chemotherapeutic resistance and immune stimulation, making these enzymes potential therapeutic targets of interest, and chemically targeting these proteins provides an avenue for novel drug development in cancer therapy. This Review aims to discuss the evolution of chemical approaches that have emerged in the past five years to design probes targeting these enzymes, including inhibition through noncovalent inhibitors, covalent inhibitors, and targeted protein degradation through proteolysis targeting chimeras (PROTACs). This Review also highlights how these compounds have been used to study the myriad of HMT functions in cancer progression and treatment response. The recent advancement of some of these drugs into human clinical investigation and even to regulatory approval highlights HMTs as a promising class of targets for chemical intervention and novel therapy development.
Collapse
Affiliation(s)
- Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Priscilla Liow
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Maria I. Tarazona Guzman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, United States
| |
Collapse
|
31
|
Vu V, Szewczyk MM, Nie DY, Arrowsmith CH, Barsyte-Lovejoy D. Validating Small Molecule Chemical Probes for Biological Discovery. Annu Rev Biochem 2022; 91:61-87. [PMID: 35363509 DOI: 10.1146/annurev-biochem-032620-105344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Small molecule chemical probes are valuable tools for interrogating protein biological functions and relevance as a therapeutic target. Rigorous validation of chemical probe parameters such as cellular potency and selectivity is critical to unequivocally linking biological and phenotypic data resulting from treatment with a chemical probe to the function of a specific target protein. A variety of modern technologies are available to evaluate cellular potency and selectivity, target engagement, and functional response biomarkers of chemical probe compounds. Here, we review these technologies and the rationales behind using them for the characterization and validation of chemical probes. In addition, large-scale phenotypic characterization of chemical probes through chemical genetic screening is increasingly leading to a wealth of information on the cellular pharmacology and disease involvement of potential therapeutic targets. Extensive compound validation approaches and integration of phenotypic information will lay foundations for further use of chemical probes in biological discovery. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada;
| | - David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
32
|
PRMT7 ablation stimulates anti-tumor immunity and sensitizes melanoma to immune checkpoint blockade. Cell Rep 2022; 38:110582. [PMID: 35354055 PMCID: PMC9838175 DOI: 10.1016/j.celrep.2022.110582] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 01/08/2022] [Accepted: 03/07/2022] [Indexed: 01/17/2023] Open
Abstract
Despite the success of immune checkpoint inhibitor (ICI) therapy for cancer, resistance and relapse are frequent. Combination therapies are expected to enhance response rates and overcome this resistance. Herein, we report that combining PRMT7 inhibition with ICI therapy induces a strong anti-tumor T cell immunity and restrains tumor growth in vivo by increasing immune cell infiltration. PRMT7-deficient B16.F10 melanoma exhibits increased expression of genes in the interferon pathway, antigen presentation, and chemokine signaling. PRMT7 deficiency or inhibition with SGC3027 in B16.F10 melanoma results in reduced DNMT expression, loss of DNA methylation in the regulatory regions of endogenous retroviral elements (ERVs) causing their increased expression. PRMT7-deficient cells increase RIG-I and MDA5 expression with a reduction in the H4R3me2s repressive histone mark at their gene promoters. Our findings identify PRMT7 as a regulatory checkpoint for RIG-I, MDA5, and their ERV-double-stranded RNA (dsRNA) ligands, facilitating immune escape and anti-tumor T cell immunity to restrain tumor growth.
Collapse
|
33
|
Lim Y, Gang DY, Lee WY, Yun SH, Cho YB, Huh JW, Park YA, Kim HC. Proteomic identification of arginine-methylated proteins in colon cancer cells and comparison of messenger RNA expression between colorectal cancer and adjacent normal tissues. Ann Coloproctol 2022:ac.2020.00899.0128. [PMID: 35081685 PMCID: PMC8898628 DOI: 10.3393/ac.2020.00899.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 06/29/2021] [Indexed: 11/12/2022] Open
Abstract
Purpose Identification of type I protein arginine methyltransferase (PRMT) substrates and their functional significance during tumorigenesis is becoming more important. The present study aimed to identify target substrates for type I PRMT using 2-dimensional (2D) gel electrophoresis (GE) and 2D Western blotting (WB). Methods Using immunoblot analysis, we compared the expression of type I PRMTs and endogenous levels of arginine methylation between the primary colorectal cancer (CRC) and adjacent noncancerous tissues paired from the same patient. To identify arginine-methylated proteins in HCT116 cells, we carried out 2D-GE and 2D-WB with a type I PRMT product-specific antibody (anti-dimethyl-arginine antibody, asymmetric [ASYM24]). Arginine-methylated protein spots were identified by mass spectrometry, and messenger RNA (mRNA) levels corresponding to the identified proteins were analyzed using National Center for Biotechnology Information (NCBI) microarray datasets between the primary CRC and noncancerous tissues. Results Type I PRMTs and methylarginine-containing proteins were highly maintained in CRC tissues compared to noncancerous tissues. We matched 142 spots using spot analysis software between a Coomassie blue (CBB)-stained 2D gel and 2D-WB, and we successfully identified 7 proteins that reacted with the ASYM24 antibody: CACYBP, GLOD4, MAPRE1, CCT7, TKT, CK8, and HSPA8. Among these proteins, the levels of 4 mRNAs including MAPRE1, CCT7, TKT, and HSPA8 in CRC tissues showed a statistically significant increase compared to noncancerous tissues from patients using the NCBI microarray datasets. Conclusion Our results indicate that the method shown here is useful in identifying arginine-methylated proteins, and significance of arginine modification in the proteins identified here should be further identified during CRC development.
Collapse
Affiliation(s)
- Yongchul Lim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Da Young Gang
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jung Wook Huh
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoon Ah Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| |
Collapse
|
34
|
Talukdar A, Mukherjee A, Bhattacharya D. Fascinating Transformation of SAM-Competitive Protein Methyltransferase Inhibitors from Nucleoside Analogues to Non-Nucleoside Analogues. J Med Chem 2022; 65:1662-1684. [PMID: 35014841 DOI: 10.1021/acs.jmedchem.1c01208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The abnormal expression of protein methyltransferase (PMT) has been linked with many diseases such as diabetes, neurological disorders, and cancer. S-Adenyl-l-methionine (SAM) is a universal methyl donor and gets converted to S-adenyl-l-homocysteine (SAH), an endogenous competitive inhibitor of SAM. Initially developed SAM/SAH mimetic nucleoside analogues were pan methyltransferase inhibitors. The gradual understanding achieved through ligand-receptor interaction paved the way for various rational approaches of drug design leading to potent and selective nucleoside inhibitors. The present perspective is based on the systematic evolution of selective SAM-competitive heterocyclic non-nucleoside inhibitors from nucleoside inhibitors. This fascinating transition has resolved several issues inherent to nucleoside analogues such as poor pharmacokinetics leading to poor in vivo efficacy. The perspective has brought together various concepts and strategies of drug design that contributed to this rational transition. We firmly believe that the strategies described herein will serve as a template for the future development of drugs in general.
Collapse
Affiliation(s)
- Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
| |
Collapse
|
35
|
Novel PRMT7 mutation in a rare case of dysmorphism and intellectual disability. J Hum Genet 2022; 67:19-26. [PMID: 34244600 DOI: 10.1038/s10038-021-00955-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/05/2021] [Accepted: 06/20/2021] [Indexed: 02/06/2023]
Abstract
Protein arginine N-methyltransferase 7 (PRMT7) encodes an arginine methyltransferase central to a number of fundamental biological processes, mutations in which result in an autosomal recessive developmental disorder characterized by short stature, brachydactyly, intellectual developmental disability and seizures (SBIDDS). To date, fewer than 15 patients with biallelic mutations in PRMT7 have been documented. Here we report brothers from a consanguineous Iraqi family presenting with a developmental disorder characterized by global developmental delay, shortened stature, facial dysmorphisms, brachydactyly, and kidney dysfunction. In both affected brothers, whole genome sequencing (WGS) identified a novel homozygous substitution in PRMT7 (ENST00000339507.5), c.1097 G > A (p.Cys366Tyr), considered to account for the majority of the phenotypic presentation. Rare compound heterozygous mutations in the dysplasia-associated perlecan-encoding HSPG2 gene (ENST00000374695.3) were also found (c.10721-2dupA, p.Ser71Asn and c.212 G > A), potentially accounting for the kidney dysfunction. In addition to expanding the known mutational spectrum of variably expressive PRMT7 mutations alongside potential digenic inheritance with HSPG2, this report underlines the diagnostic utility of a WGS-guided analysis in the detection of rare genetic disorders.
Collapse
|
36
|
Xu J, Richard S. Cellular pathways influenced by protein arginine methylation: Implications for cancer. Mol Cell 2021; 81:4357-4368. [PMID: 34619091 PMCID: PMC8571027 DOI: 10.1016/j.molcel.2021.09.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/24/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023]
Abstract
Arginine methylation is an influential post-translational modification occurring on histones, RNA binding proteins, and many other cellular proteins, affecting their function by altering their protein-protein and protein-nucleic acid interactions. Recently, a wealth of information has been gathered, implicating protein arginine methyltransferases (PRMTs), enzymes that deposit arginine methylation, in transcription, pre-mRNA splicing, DNA damage signaling, and immune signaling with major implications for cancer therapy, especially immunotherapy. This review summarizes this recent progress and the current state of PRMT inhibitors, some in clinical trials, as promising drug targets for cancer.
Collapse
Affiliation(s)
- Jian Xu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA; Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, and Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research, Gerald Bronfman Department of Oncology, and Departments of Medicine, Human Genetics, and Biochemistry, McGill University, Montréal, QC H3T 1E2, Canada.
| |
Collapse
|
37
|
PRMT7: A Pivotal Arginine Methyltransferase in Stem Cells and Development. Stem Cells Int 2021; 2021:6241600. [PMID: 34712331 PMCID: PMC8548130 DOI: 10.1155/2021/6241600] [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: 06/07/2021] [Accepted: 09/30/2021] [Indexed: 12/11/2022] Open
Abstract
Protein arginine methylation is a posttranslational modification catalyzed by protein arginine methyltransferases (PRMTs), which play critical roles in many biological processes. To date, nine PRMT family members, namely, PRMT1, 2, 3, 4, 5, 6, 7, 8, and 9, have been identified in mammals. Among them, PRMT7 is a type III PRMT that can only catalyze the formation of monomethylarginine and plays pivotal roles in several kinds of stem cells. It has been reported that PRMT7 is closely associated with embryonic stem cells, induced pluripotent stem cells, muscle stem cells, and human cancer stem cells. PRMT7 deficiency or mutation led to severe developmental delay in mice and humans, which is possibly due to its crucial functions in stem cells. Here, we surveyed and summarized the studies on PRMT7 in stem cells and development in mice and humans and herein provide a discussion of the underlying molecular mechanisms. Furthermore, we also discuss the roles of PRMT7 in cancer, adipogenesis, male reproduction, cellular stress, and cellular senescence, as well as the future perspectives of PRMT7-related studies. Overall, PRMT7 mediates the proliferation and differentiation of stem cells. Deficiency or mutation of PRMT7 causes developmental delay, including defects in skeletal muscle, bone, adipose tissues, neuron, and male reproduction. A better understanding of the roles of PRMT7 in stem cells and development as well as the underlying mechanisms will provide information for the development of strategies for in-depth research of PRMT7 and stem cells as well as their applications in life sciences and medicine.
Collapse
|
38
|
Maniaci M, Boffo FL, Massignani E, Bonaldi T. Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach. Front Mol Biosci 2021; 8:688973. [PMID: 34557518 PMCID: PMC8454774 DOI: 10.3389/fmolb.2021.688973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/11/2021] [Indexed: 12/03/2022] Open
Abstract
RNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization, and interactions with other proteins or RNAs. Recent proteome-wide experiments showed that RBPs are the most representative group within the class of arginine (R)-methylated proteins. Moreover, emerging evidence suggests that this modification plays a role in the regulation of RBP-RNA interactions. Nevertheless, a systematic analysis of how changes in protein-R-methylation can affect globally RBPs-RNA interactions is still missing. We describe here a quantitative proteomics approach to profile global changes of RBP-RNA interactions upon the modulation of type I and II protein arginine methyltransferases (PRMTs). By coupling the recently described Orthogonal Organic Phase Separation (OOPS) strategy with the Stable Isotope Labelling with Amino acids in Cell culture (SILAC) and pharmacological modulation of PRMTs, we profiled RNA-protein interaction dynamics in dependence of protein-R-methylation. Data are available via ProteomeXchange with identifier PXD024601.
Collapse
Affiliation(s)
- Marianna Maniaci
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy.,European School of Molecular Medicine (SEMM), Milan, Italy
| | - Francesca Ludovica Boffo
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy
| | - Enrico Massignani
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy.,European School of Molecular Medicine (SEMM), Milan, Italy
| | - Tiziana Bonaldi
- Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, Italy
| |
Collapse
|
39
|
Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. Repurposing epigenetic inhibitors to target the Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics 2021; 17:970-981. [PMID: 34523387 PMCID: PMC9487755 DOI: 10.1080/15592294.2021.1976910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Epigenetically targeted therapeutic development, particularly for SAM-dependent methylations of DNA, mRNA and histones has been proceeding rapidly for cancer treatments over the past few years. However, this approach has barely begun to be exploited for developing new antibiotics, despite an overwhelming global need to counter antimicrobial resistance. Here, we explore whether SAM analogues, some of which are in (pre)clinical studies as inhibitors of human epigenetic enzymes, can also inhibit Clostridioides difficile-specific DNA adenine methyltransferase (CamA), a sporulation regulator present in all C. difficile genomes sequenced to date, but found in almost no other bacteria. We found that SGC0946 (an inhibitor of DOT1L), JNJ-64619178 (an inhibitor of PRMT5) and SGC8158 (an inhibitor of PRMT7) inhibit CamA enzymatic activity in vitro at low micromolar concentrations. Structural investigation of the ternary complexes of CamA-DNA in the presence of SGC0946 or SGC8158 revealed conformational rearrangements of the N-terminal arm, with no apparent disturbance of the active site. This N-terminal arm and its modulation of exchanges between SAM (the methyl donor) and SAH (the reaction product) during catalysis of methyl transfer are, to date, unique to CamA. Our work presents a substantial first step in generating potent and selective inhibitors of CamA that would serve in the near term as chemical probes to investigate the cellular mechanism(s) of CamA in controlling spore formation and colonization, and eventually as therapeutic antivirulence agents useful in treating C. difficile infection.
Collapse
Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Yu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
40
|
Fulton MD, Cao M, Ho MC, Zhao X, Zheng YG. The macromolecular complexes of histones affect protein arginine methyltransferase activities. J Biol Chem 2021; 297:101123. [PMID: 34492270 PMCID: PMC8511957 DOI: 10.1016/j.jbc.2021.101123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/14/2021] [Accepted: 08/24/2021] [Indexed: 11/29/2022] Open
Abstract
Histone arginine methylation is a key post-translational modification that mediates epigenetic events that activate or repress gene transcription. Protein arginine methyltransferases (PRMTs) are the driving force for the process of arginine methylation, and the core histone proteins have been shown to be substrates for most PRMT family members. However, previous reports of the enzymatic activities of PRMTs on histones in the context of nucleosomes seem contradictory. Moreover, what governs nucleosomal substrate recognition of different PRMT members is not understood. We sought to address this key biological question by examining how different macromolecular contexts where the core histones reside may regulate arginine methylation catalyzed by individual PRMT members (i.e., PRMT1, PRMT3, PRMT4, PRMT5, PRMT6, PRMT7, and PRMT8). Our results demonstrated that the substrate context exhibits a huge impact on the histone arginine methylation activity of PRMTs. Although all the tested PRMTs methylate multiple free histones individually, they show a preference for one particular histone substrate in the context of the histone octamer. We found that PRMT1, PRMT3, PRMT5, PRMT6, PRMT7, and PRMT8 preferentially methylate histone H4, whereas PRMT4/coactivator-associated arginine methyltransferase 1 prefers histone H3. Importantly, neither reconstituted nor cell-extracted mononucleosomes could be methylated by any PRMTs tested. Structural analysis suggested that the electrostatic interaction may play a mechanistic role in priming the substrates for methylation by PRMT enzymes. Taken together, this work expands our knowledge on the molecular mechanisms of PRMT substrate recognition and has important implications for understanding cellular dynamics and kinetics of histone arginine methylation in regulating gene transcription and other chromatin-templated processes.
Collapse
Affiliation(s)
- Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia, USA
| | - Mengtong Cao
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei, Taiwan
| | - Xinyang Zhao
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Y George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia, USA.
| |
Collapse
|
41
|
Zhu J, Li X, Cai X, Zha H, Zhou Z, Sun X, Rong F, Tang J, Zhu C, Liu X, Fan S, Wang J, Liao Q, Ouyang G, Xiao W. Arginine monomethylation by PRMT7 controls MAVS-mediated antiviral innate immunity. Mol Cell 2021; 81:3171-3186.e8. [PMID: 34171297 DOI: 10.1016/j.molcel.2021.06.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/10/2021] [Accepted: 06/02/2021] [Indexed: 12/14/2022]
Abstract
Accurate control of innate immune responses is required to eliminate invading pathogens and simultaneously avoid autoinflammation and autoimmune diseases. Here, we demonstrate that arginine monomethylation precisely regulates the mitochondrial antiviral-signaling protein (MAVS)-mediated antiviral response. Protein arginine methyltransferase 7 (PRMT7) forms aggregates to catalyze MAVS monomethylation at arginine residue 52 (R52), attenuating its binding to TRIM31 and RIG-I, which leads to the suppression of MAVS aggregation and subsequent activation. Upon virus infection, aggregated PRMT7 is disabled in a timely manner due to automethylation at arginine residue 32 (R32), and SMURF1 is recruited to PRMT7 by MAVS to induce proteasomal degradation of PRMT7, resulting in the relief of PRMT7 suppression of MAVS activation. Therefore, we not only reveal that arginine monomethylation by PRMT7 negatively regulates MAVS-mediated antiviral signaling in vitro and in vivo but also uncover a mechanism by which PRMT7 is tightly controlled to ensure the timely activation of antiviral defense.
Collapse
Affiliation(s)
- Junji Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiong Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaolian Cai
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Huangyuan Zha
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Ziwen Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xueyi Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Fangjing Rong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jinghua Tang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Chunchun Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xing Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; The Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, P.R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Sijia Fan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; The Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, P.R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Qian Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Gang Ouyang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; The Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, P.R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P.R. China
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, P.R. China; The Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Wuhan 430072, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430072, P.R. China; Hubei Hongshan Laboratory, Wuhan 430070, P.R. China.
| |
Collapse
|
42
|
Halabelian L, Barsyte-Lovejoy D. Structure and Function of Protein Arginine Methyltransferase PRMT7. Life (Basel) 2021; 11:768. [PMID: 34440512 PMCID: PMC8399567 DOI: 10.3390/life11080768] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 01/06/2023] Open
Abstract
PRMT7 is a member of the protein arginine methyltransferase (PRMT) family, which methylates a diverse set of substrates. Arginine methylation as a posttranslational modification regulates protein-protein and protein-nucleic acid interactions, and as such, has been implicated in various biological functions. PRMT7 is a unique, evolutionarily conserved PRMT family member that catalyzes the mono-methylation of arginine. The structural features, functional aspects, and compounds that inhibit PRMT7 are discussed here. Several studies have identified physiological substrates of PRMT7 and investigated the substrate methylation outcomes which link PRMT7 activity to the stress response and RNA biology. PRMT7-driven substrate methylation further leads to the biological outcomes of gene expression regulation, cell stemness, stress response, and cancer-associated phenotypes such as cell migration. Furthermore, organismal level phenotypes of PRMT7 deficiency have uncovered roles in muscle cell physiology, B cell biology, immunity, and brain function. This rapidly growing information on PRMT7 function indicates the critical nature of context-dependent functions of PRMT7 and necessitates further investigation of the PRMT7 interaction partners and factors that control PRMT7 expression and levels. Thus, PRMT7 is an important cellular regulator of arginine methylation in health and disease.
Collapse
Affiliation(s)
- Levon Halabelian
- Structural Genomics Consortium, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, Temerty Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| |
Collapse
|
43
|
Zhang W, Li S, Li K, Li LI, Yin P, Tong G. The role of protein arginine methyltransferase 7 in human developmentally arrested embryos cultured in vitro. Acta Biochim Biophys Sin (Shanghai) 2021; 53:925-932. [PMID: 34041522 DOI: 10.1093/abbs/gmab068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
Human embryos of in vitro fertilization (IVF) are often susceptible to developmental arrest, which greatly reduces the efficiency of IVF treatment. In recent years, it has been found that protein arginine methyltransferase 7 (PRMT7) plays an important role in the process of early embryonic development. However, not much is known about the relationship between PRMT7 and developmentally arrested embryos. The role of PRMT7 in developmentally arrested embryos was thus investigated in this study. Discarded human embryos from IVF were collected for experimental materials. Quantitative real-time polymerase chain reaction (qRT-PCR) and confocal analyses were used to identify PRMT7 mRNA and protein levels in early embryos at different developmental stages, as well as changes in the methylation levels of H4R3me2s. Additionally, PRMT7 was knocked down in the developmentally arrested embryos to observe the further development of these embryos. Our results demonstrated that PRMT7 mRNA and protein levels in arrested embryos were significantly increased compared with those in control embryos; meanwhile, the methylation levels of H4R3me2s in arrested embryos were also increased significantly. Knockdown of PRMT7 could rescue partially developmentally arrested embryos, and even individual developmentally arrested embryos could develop into blastocysts. In conclusion, over-expression of PRMT7 disrupts the early embryo development process, leading to early embryos developmental arrest, but these developmentally arrested defects could be partially rescued by knockdown of the PRMT7 protein.
Collapse
Affiliation(s)
- Wuwen Zhang
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Shifeng Li
- Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kai Li
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - L i Li
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ping Yin
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Guoqing Tong
- Reproductive Medicine Center, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| |
Collapse
|
44
|
Protein arginine methylation: from enigmatic functions to therapeutic targeting. Nat Rev Drug Discov 2021; 20:509-530. [PMID: 33742187 DOI: 10.1038/s41573-021-00159-8] [Citation(s) in RCA: 177] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2021] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) are emerging as attractive therapeutic targets. PRMTs regulate transcription, splicing, RNA biology, the DNA damage response and cell metabolism; these fundamental processes are altered in many diseases. Mechanistically understanding how these enzymes fuel and sustain cancer cells, especially in specific metabolic contexts or in the presence of certain mutations, has provided the rationale for targeting them in oncology. Ongoing inhibitor development, facilitated by structural biology, has generated tool compounds for the majority of PRMTs and enabled clinical programmes for the most advanced oncology targets, PRMT1 and PRMT5. In-depth mechanistic investigations using genetic and chemical tools continue to delineate the roles of PRMTs in regulating immune cells and cancer cells, and cardiovascular and neuronal function, and determine which pathways involving PRMTs could be synergistically targeted in combination therapies for cancer. This research is enhancing our knowledge of the complex functions of arginine methylation, will guide future clinical development and could identify new clinical indications.
Collapse
|
45
|
Cai T, Yu Z, Wang Z, Liang C, Richard S. Arginine methylation of SARS-Cov-2 nucleocapsid protein regulates RNA binding, its ability to suppress stress granule formation, and viral replication. J Biol Chem 2021; 297:100821. [PMID: 34029587 PMCID: PMC8141346 DOI: 10.1016/j.jbc.2021.100821] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/13/2021] [Accepted: 05/20/2021] [Indexed: 12/18/2022] Open
Abstract
Viral proteins are known to be methylated by host protein arginine methyltransferases (PRMTs) necessary for the viral life cycle, but it remains unknown whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins are methylated. Herein, we show that PRMT1 methylates SARS-CoV-2 nucleocapsid (N) protein at residues R95 and R177 within RGG/RG motifs, preferred PRMT target sequences. We confirmed arginine methylation of N protein by immunoblotting viral proteins extracted from SARS-CoV-2 virions isolated from cell culture. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5'-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging. We also defined the N protein interactome in HEK293 cells, which identified PRMT1 and many of its RGG/RG substrates, including the known interacting protein G3BP1 as well as other components of stress granules (SGs), which are part of the host antiviral response. Methylation of R95 regulated the ability of N protein to suppress the formation of SGs, as R95K substitution or MS023 treatment blocked N-mediated suppression of SGs. Also, the coexpression of methylarginine reader Tudor domain-containing protein 3 quenched N protein-mediated suppression of SGs in a dose-dependent manner. Finally, pretreatment of VeroE6 cells with MS023 significantly reduced SARS-CoV-2 replication. Because type I PRMT inhibitors are already undergoing clinical trials for cancer treatment, inhibiting arginine methylation to target the later stages of the viral life cycle such as viral genome packaging and assembly of virions may represent an additional therapeutic application of these drugs.
Collapse
Affiliation(s)
- Ting Cai
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada
| | - Zhen Wang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Chen Liang
- McGill Centre for Viral Diseases, Lady Davis Institute for Medical Research and Department of Medicine, Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, Québec, Canada.
| |
Collapse
|
46
|
Guccione E, Schwarz M, Di Tullio F, Mzoughi S. Cancer synthetic vulnerabilities to protein arginine methyltransferase inhibitors. Curr Opin Pharmacol 2021; 59:33-42. [PMID: 34052526 DOI: 10.1016/j.coph.2021.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022]
Abstract
Protein arginine methylation is an abundant post-translational modification involved in the modulation of essential cellular processes ranging from transcription, post-transcriptional RNA metabolism, and propagation of signaling cascades to the regulation of the DNA damage response. Excitingly for the field, in the past few years there have been remarkable advances in the development of molecular tools and clinical compounds able to selectively and potently inhibit protein arginine methyltransferase (PRMT) functions. In this review, we first discuss how the somatic mutations that confer advantages to cancer cells are often associated with vulnerabilities that can be exploited by PRMTs' inhibition. In a second part, we discuss strategies to uncover synthetic lethal combinations between existing therapies and PRMT inhibitors.
Collapse
Affiliation(s)
- Ernesto Guccione
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Megan Schwarz
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Federico Di Tullio
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Slim Mzoughi
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mount Sinai Center for Therapeutics Discovery, Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
47
|
Kapell S, Jakobsson ME. Large-scale identification of protein histidine methylation in human cells. NAR Genom Bioinform 2021; 3:lqab045. [PMID: 34046594 PMCID: PMC8140740 DOI: 10.1093/nargab/lqab045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 12/14/2022] Open
Abstract
Methylation can occur on histidine, lysine and arginine residues in proteins and often serves a regulatory function. Histidine methylation has recently attracted attention through the discovery of the human histidine methyltransferase enzymes SETD3 and METTL9. There are currently no methods to enrich histidine methylated peptides for mass spectrometry analysis and large-scale studies of the modification are hitherto absent. Here, we query ultra-comprehensive human proteome datasets to generate a resource of histidine methylation sites. In HeLa cells alone, we report 299 histidine methylation sites as well as 895 lysine methylation events. We use this resource to explore the frequency, localization, targeted domains, protein types and sequence requirements of histidine methylation and benchmark all analyses to methylation events on lysine and arginine. Our results demonstrate that histidine methylation is widespread in human cells and tissues and that the modification is over-represented in regions of mono-spaced histidine repeats. We also report colocalization of the modification with functionally important phosphorylation sites and disease associated mutations to identify regions of likely regulatory and functional importance. Taken together, we here report a system level analysis of human histidine methylation and our results represent a comprehensive resource enabling targeted studies of individual histidine methylation events.
Collapse
Affiliation(s)
- Sebastian Kapell
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | | |
Collapse
|
48
|
Hwang JW, Cho Y, Bae GU, Kim SN, Kim YK. Protein arginine methyltransferases: promising targets for cancer therapy. Exp Mol Med 2021; 53:788-808. [PMID: 34006904 PMCID: PMC8178397 DOI: 10.1038/s12276-021-00613-y] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 02/08/2023] Open
Abstract
Protein methylation, a post-translational modification (PTM), is observed in a wide variety of cell types from prokaryotes to eukaryotes. With recent and rapid advancements in epigenetic research, the importance of protein methylation has been highlighted. The methylation of histone proteins that contributes to the epigenetic histone code is not only dynamic but is also finely controlled by histone methyltransferases and demethylases, which are essential for the transcriptional regulation of genes. In addition, many nonhistone proteins are methylated, and these modifications govern a variety of cellular functions, including RNA processing, translation, signal transduction, DNA damage response, and the cell cycle. Recently, the importance of protein arginine methylation, especially in cell cycle regulation and DNA repair processes, has been noted. Since the dysregulation of protein arginine methylation is closely associated with cancer development, protein arginine methyltransferases (PRMTs) have garnered significant interest as novel targets for anticancer drug development. Indeed, several PRMT inhibitors are in phase 1/2 clinical trials. In this review, we discuss the biological functions of PRMTs in cancer and the current development status of PRMT inhibitors in cancer therapy.
Collapse
Affiliation(s)
- Jee Won Hwang
- grid.412670.60000 0001 0729 3748Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Yena Cho
- grid.412670.60000 0001 0729 3748Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Gyu-Un Bae
- grid.412670.60000 0001 0729 3748Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| | - Su-Nam Kim
- grid.35541.360000000121053345Natural Product Research Institute, Korea Institute of Science and Technology, Gangneung, 25451 Republic of Korea
| | - Yong Kee Kim
- grid.412670.60000 0001 0729 3748Research Institute of Pharmaceutical Sciences, College of Pharmacy, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| |
Collapse
|
49
|
Samuel SF, Barry A, Greenman J, Beltran-Alvarez P. Arginine methylation: the promise of a 'silver bullet' for brain tumours? Amino Acids 2021; 53:489-506. [PMID: 33404912 PMCID: PMC8107164 DOI: 10.1007/s00726-020-02937-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
Despite intense research efforts, our pharmaceutical repertoire against high-grade brain tumours has not been able to increase patient survival for a decade and life expectancy remains at less than 16 months after diagnosis, on average. Inhibitors of protein arginine methyltransferases (PRMTs) have been developed and investigated over the past 15 years and have now entered oncology clinical trials, including for brain tumours. This review collates recent advances in the understanding of the role of PRMTs and arginine methylation in brain tumours. We provide an up-to-date literature review on the mechanisms for PRMT regulation. These include endogenous modulators such as alternative splicing, miRNA, post-translational modifications and PRMT-protein interactions, and synthetic inhibitors. We discuss the relevance of PRMTs in brain tumours with a particular focus on PRMT1, -2, -5 and -8. Finally, we include a future perspective where we discuss possible routes for further research on arginine methylation and on the use of PRMT inhibitors in the context of brain tumours.
Collapse
Affiliation(s)
| | - Antonia Barry
- Department of Biomedical Sciences, University of Hull, Hull, UK
| | - John Greenman
- Department of Biomedical Sciences, University of Hull, Hull, UK
| | | |
Collapse
|
50
|
Li WJ, He YH, Yang JJ, Hu GS, Lin YA, Ran T, Peng BL, Xie BL, Huang MF, Gao X, Huang HH, Zhu HH, Ye F, Liu W. Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth. Nat Commun 2021; 12:1946. [PMID: 33782401 PMCID: PMC8007824 DOI: 10.1038/s41467-021-21963-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 02/12/2021] [Indexed: 02/05/2023] Open
Abstract
Numerous substrates have been identified for Type I and II arginine methyltransferases (PRMTs). However, the full substrate spectrum of the only type III PRMT, PRMT7, and its connection to type I and II PRMT substrates remains unknown. Here, we use mass spectrometry to reveal features of PRMT7-regulated methylation. We find that PRMT7 predominantly methylates a glycine and arginine motif; multiple PRMT7-regulated arginine methylation sites are close to phosphorylations sites; methylation sites and proximal sequences are vulnerable to cancer mutations; and methylation is enriched in proteins associated with spliceosome and RNA-related pathways. We show that PRMT4/5/7-mediated arginine methylation regulates hnRNPA1 binding to RNA and several alternative splicing events. In breast, colorectal and prostate cancer cells, PRMT4/5/7 are upregulated and associated with high levels of hnRNPA1 arginine methylation and aberrant alternative splicing. Pharmacological inhibition of PRMT4/5/7 suppresses cancer cell growth and their co-inhibition shows synergistic effects, suggesting them as targets for cancer therapy. Arginine methyltransferases (PRMTs) are involved in the regulation of various physiological and pathological conditions. Using proteomics, the authors here profile the methylation substrates of PRMTs 4, 5 and 7 and characterize the roles of these enzymes in cancer-associated splicing regulation.
Collapse
Affiliation(s)
- Wen-Juan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yao-Hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jing-Jing Yang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yi-An Lin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ting Ran
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Bing-Ling Peng
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Bing-Lan Xie
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Ming-Feng Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xiang Gao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China
| | - Hai-Hua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Helen He Zhu
- Department of Urology, Ren Ji Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Ye
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Fujian, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China. .,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Pharmaceutical Sciences, Xiamen University, Xiamen, Fujian, China.
| |
Collapse
|