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Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet 2024; 33:1454-1464. [PMID: 38751339 PMCID: PMC11305685 DOI: 10.1093/hmg/ddae084] [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: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/26/2024] Open
Abstract
Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn's disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.
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Affiliation(s)
- Adam K Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Holly Allen
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
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2
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Peterson P. Novel Insights into the Autoimmunity from the Genetic Approach of the Human Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:3-18. [PMID: 38467969 DOI: 10.1007/978-981-99-9781-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) is a monogenic inborn error of autoimmunity that is caused by damaging germline variants in the AIRE gene and clinically manifests with multiple autoimmune diseases in patients. Studies on the function of the AIRE gene, discovered in 1997, have contributed to fundamental aspects of human immunology as they have been important in understanding the basic mechanism of immune balance between self and non-self. This chapter looks back to the discovery of the AIRE gene, reviews its main properties, and discusses the key findings of its function in the thymus. However, more recent autoantibody profilings in APECED patients have highlighted a gap in our knowledge of the disease pathology and point to the need to revisit the current paradigm of AIRE function. The chapter reviews these new findings in APECED patients, which potentially trigger new thoughts on the mechanism of immune tolerance.
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Affiliation(s)
- Pärt Peterson
- Institute of Biomedical and Translational Medicine, University of Tartu, Tartu, Estonia.
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3
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Duan Y, Du Y, Mu Y, Gu Z, Wang C. Expression, prognostic value and mechanism of SP100 family in pancreatic adenocarcinoma. Aging (Albany NY) 2023; 15:5569-5591. [PMID: 37354211 PMCID: PMC10333092 DOI: 10.18632/aging.204811] [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: 12/14/2022] [Accepted: 05/23/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Pancreatic adenocarcinoma (PAAD) is one of the most aggressive malignancies with a very poor prognosis. Exploring more therapeutic targets and prognostic biomarkers is of great significance to improve the prognosis of PAAD patients. Increasing evidence supports that the speckled protein (SP) 100 family is associated with human cancer and immune disorders. However, the function of the SP100 family members in PAAD is still unclear. METHODS R, Cytoscape, cBioPortal, and other software and online databases were used to comprehensively analyze the expression characteristics, prognostic value, and oncogenic mechanism of the SP100 family in PAAD. RESULTS The high expression of SP100 family members in PAAD was significantly correlated with poor clinicopathological features and poor prognosis of PAAD patients. Mechanistically, TP53 mutations were significantly associated with the expression levels of the SP100 family members, which were significantly coexpressed with M6A methylation regulators and were activated in multiple oncogenic pathways, including the EMT pathways. Moreover, we found that their expression levels were significantly correlated with the sensitivity of multiple traditional chemotherapeutic drugs. CONCLUSION The SP100 family is closely related to the occurrence and development of PAAD and can be used as a new biomarker and therapeutic target for patients with PAAD.
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Affiliation(s)
- Yunjie Duan
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongxing Du
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongrun Mu
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zongting Gu
- Department of Hepatobiliary and Pancreatic Surgery and Minimally Invasive Surgery, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chengfeng Wang
- State Key Lab of Molecular Oncology and Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, China
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4
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Burbelo PD, Ji Y, Iadarola MJ. Advancing Luciferase-Based Antibody Immunoassays to Next-Generation Mix and Read Testing. BIOSENSORS 2023; 13:303. [PMID: 36979515 PMCID: PMC10046223 DOI: 10.3390/bios13030303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Antibody measurements play a central role in the diagnosis of many autoimmune and infectious diseases. One antibody detection technology, Luciferase Immunoprecipitation Systems (LIPS), utilizes genetically encoded recombinant luciferase antigen fusion proteins in an immunoglobulin capture format to generate robust antibody measurement with high diagnostic sensitivity and specificity. The LIPS technology has been highly useful in detecting antibodies for research diagnostics and the discovery of new autoantigens. The methodology of the assay requires immunoglobulin binding reagents such as protein A/G beads and washing steps to process the immune complex before antibody levels are measured by light production with a luminometer. Recently, simplified mix and read immunoassays based on split components of the nanoluciferase enzyme in a complementation format have been developed for antibody measurements without requiring immunoglobulin-capturing beads or washing steps. The mix and read immunoassays utilize two or three nanoluciferase fragments which when reconstituted via antigen-specific antibody binding generate a functional enzyme. At present, these split luciferase tests have been developed mainly for detecting SARS-CoV-2 antibodies. Here, we describe the traditional LIPS technology and compare it to the new split luciferase methodologies focusing on their technical features, strengths, limitations, and future opportunities for diagnostic research, and clinical applications.
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Affiliation(s)
- Peter D. Burbelo
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 202892, USA
| | - Youngmi Ji
- Adeno-Associated Virus Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 202892, USA
| | - Michael J. Iadarola
- Department of Perioperative Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 202892, USA
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5
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Matsushita K, Li X, Nakamura Y, Dong D, Mukai K, Tsai M, Montgomery SB, Galli SJ. The role of Sp140 revealed in IgE and mast cell responses in Collaborative Cross mice. JCI Insight 2021; 6:e146572. [PMID: 34156030 PMCID: PMC8262499 DOI: 10.1172/jci.insight.146572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
Mouse IgE and mast cell (MC) functions have been studied primarily using inbred strains. Here, we (a) identified effects of genetic background on mouse IgE and MC phenotypes, (b) defined the suitability of various strains for studying IgE and MC functions, and (c) began to study potentially novel genes involved in such functions. We screened 47 Collaborative Cross (CC) strains, as well as C57BL/6J and BALB/cJ mice, for strength of passive cutaneous anaphylaxis (PCA) and responses to the intestinal parasite Strongyloides venezuelensis (S.v.). CC mice exhibited a diversity in PCA strength and S.v. responses. Among strains tested, C57BL/6J and CC027 mice showed, respectively, moderate and uniquely potent MC activity. Quantitative trait locus analysis and RNA sequencing of BM-derived cultured MCs (BMCMCs) from CC027 mice suggested Sp140 as a candidate gene for MC activation. siRNA-mediated knock-down of Sp140 in BMCMCs decreased IgE-dependent histamine release and cytokine production. Our results demonstrated marked variations in IgE and MC activity in vivo, and in responses to S.v., across CC strains. C57BL/6J and CC027 represent useful models for studying MC functions. Additionally, we identified Sp140 as a gene that contributes to IgE-dependent MC activation.
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Affiliation(s)
- Kazufumi Matsushita
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Immunology, Hyogo College of Medicine, Nishinomiya, Japan
| | - Xin Li
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuki Nakamura
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Danyue Dong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaori Mukai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
| | - Mindy Tsai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen J Galli
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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6
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Huoh YS, Hur S. Death domain fold proteins in immune signaling and transcriptional regulation. FEBS J 2021; 289:4082-4097. [PMID: 33905163 DOI: 10.1111/febs.15901] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/07/2021] [Accepted: 04/23/2021] [Indexed: 01/02/2023]
Abstract
Death domain fold (DDF) superfamily comprises of the death domain (DD), death effector domain (DED), caspase activation recruitment domain (CARD), and pyrin domain (PYD). By utilizing a conserved mode of interaction involving six distinct surfaces, a DDF serves as a building block that can densely pack into homomultimers or filaments. Studies of immune signaling components have revealed that DDF-mediated filament formation plays a central role in mediating signal transduction and amplification. The unique ability of DDFs to self-oligomerize upon external signals and induce oligomerization of partner molecules underlies key processes in many innate immune signaling pathways, as exemplified by RIG-I-like receptor signalosome and inflammasome assembly. Recent studies showed that DDFs are not only limited to immune signaling pathways, but also are involved with transcriptional regulation and other biological processes. Considering that DDF annotation still remains a challenge, the current list of DDFs and their functions may represent just the tip of the iceberg within the full spectrum of DDF biology. In this review, we discuss recent advances in our understanding of DDF functions, structures, and assembly architectures with a focus on CARD- and PYD-containing proteins. We also discuss areas of future research and the potential relationship of DDFs with biomolecular condensates formed by liquid-liquid phase separation (LLPS).
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Affiliation(s)
- Yu-San Huoh
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA, USA
| | - Sun Hur
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, MA, USA
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7
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Granito A, Muratori L, Tovoli F, Muratori P. Autoantibodies to speckled protein family in primary biliary cholangitis. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2021; 17:35. [PMID: 33789734 PMCID: PMC8011120 DOI: 10.1186/s13223-021-00539-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/17/2021] [Indexed: 02/07/2023]
Abstract
The autoantibody profile of primary biliary cholangitis (PBC) includes antinuclear antibodies (ANA) which are detectable by indirect immunofluorescence in more than 50% of PBC patients. One of the two immunofluorescence patterns which are historically considered "PBC-specific" is the so-called "multiple nuclear dots" (MND) targeting nuclear body proteins such as Sp100, Sp140, Sp140L proteins, promyelocytic leukemia protein (PML) and small ubiquitin-related modifier proteins (SUMO). It has been hypothesized a role of nuclear body protein alterations in immune disorders such as PBC, thus suggesting novel and more refined therapeutic approaches.
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Affiliation(s)
- Alessandro Granito
- Division of Internal Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy.
- Center for the Study, Treatment of Autoimmune Diseases of the Liver, Biliary System, Bologna, Italy.
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Bologna, Italy.
| | - Luigi Muratori
- Division of Internal Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
- Center for the Study, Treatment of Autoimmune Diseases of the Liver, Biliary System, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Francesco Tovoli
- Division of Internal Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
- Center for the Study, Treatment of Autoimmune Diseases of the Liver, Biliary System, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Paolo Muratori
- Division of Internal Medicine, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138, Bologna, Italy
- Center for the Study, Treatment of Autoimmune Diseases of the Liver, Biliary System, Bologna, Italy
- Department for the Science of the Quality of Life (QUVI), Alma Mater Studiorum, University of Bologna, Bologna, Italy
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8
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Collados Rodríguez M. The Fate of Speckled Protein 100 (Sp100) During Herpesviruses Infection. Front Cell Infect Microbiol 2021; 10:607526. [PMID: 33598438 PMCID: PMC7882683 DOI: 10.3389/fcimb.2020.607526] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/14/2020] [Indexed: 12/27/2022] Open
Abstract
The constitutive expression of Speckled-100 (Sp100) is known to restrict the replication of many clinically important DNA viruses. This pre-existing (intrinsic) immune defense to virus infection can be further upregulated upon interferon (IFN) stimulation as a component of the innate immune response. In humans, Sp100 is encoded by a single gene locus, which can produce alternatively spliced isoforms. The widely studied Sp100A, Sp100B, Sp100C and Sp100HMG have functions associated with the transcriptional regulation of viral and cellular chromatin, either directly through their characteristic DNA-binding domains, or indirectly through post-translational modification (PTM) and associated protein interaction networks. Sp100 isoforms are resident component proteins of promyelocytic leukemia-nuclear bodies (PML-NBs), dynamic nuclear sub-structures which regulate host immune defenses against many pathogens. In the case of human herpesviruses, multiple protein antagonists are expressed to relieve viral DNA genome transcriptional silencing imposed by PML-NB and Sp100-derived proteinaceous structures, thereby stimulating viral propagation, pathogenesis, and transmission to new hosts. This review details how different Sp100 isoforms are manipulated during herpesviruses HSV1, VZV, HCMV, EBV, and KSHV infection, identifying gaps in our current knowledge, and highlighting future areas of research.
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9
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The Speckled Protein (SP) Family: Immunity's Chromatin Readers. Trends Immunol 2020; 41:572-585. [PMID: 32386862 DOI: 10.1016/j.it.2020.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/25/2020] [Accepted: 04/04/2020] [Indexed: 01/25/2023]
Abstract
Chromatin 'readers' are central interpreters of the epigenome that facilitate cell-specific transcriptional programs and are therapeutic targets in cancer and inflammation. The Speckled Protein (SP) family of chromatin 'readers' in humans consists of SP100, SP110, SP140, and SP140L. SPs possess functional domains (SAND, PHD, bromodomain) that dock to DNA or post-translationally modified histones and a caspase activation and recruitment domain (CARD) to promote multimerization. Mutations within immune expressed SPs associate with numerous immunological diseases including Crohn's disease, multiple sclerosis, chronic lymphocytic leukemia, veno-occlusive disease with immunodeficiency, as well as Mycobacterium tuberculosis infection, underscoring their importance in immune regulation. In this review, we posit that SPs are central chromatin regulators of gene silencing that establish immune cell identity and function.
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10
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Jain K, Fraser CS, Marunde MR, Parker MM, Sagum C, Burg JM, Hall N, Popova IK, Rodriguez KL, Vaidya A, Krajewski K, Keogh MC, Bedford MT, Strahl BD. Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions. Epigenetics Chromatin 2020; 13:3. [PMID: 31980037 PMCID: PMC6979384 DOI: 10.1186/s13072-020-0328-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 01/13/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Plant homeodomain (PHD) fingers are central "readers" of histone post-translational modifications (PTMs) with > 100 PHD finger-containing proteins encoded by the human genome. Many of the PHDs studied to date bind to unmodified or methylated states of histone H3 lysine 4 (H3K4). Additionally, many of these domains, and the proteins they are contained in, have crucial roles in the regulation of gene expression and cancer development. Despite this, the majority of PHD fingers have gone uncharacterized; thus, our understanding of how these domains contribute to chromatin biology remains incomplete. RESULTS We expressed and screened 123 of the annotated human PHD fingers for their histone binding preferences using reader domain microarrays. A subset (31) of these domains showed strong preference for the H3 N-terminal tail either unmodified or methylated at H3K4. These H3 readers were further characterized by histone peptide microarrays and/or AlphaScreen to comprehensively define their H3 preferences and PTM cross-talk. CONCLUSIONS The high-throughput approaches utilized in this study establish a compendium of binding information for the PHD reader family with regard to how they engage histone PTMs and uncover several novel reader domain-histone PTM interactions (i.e., PHRF1 and TRIM66). This study highlights the usefulness of high-throughput analyses of histone reader proteins as a means of understanding how chromatin engagement occurs biochemically.
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Affiliation(s)
- Kanishk Jain
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Caroline S Fraser
- Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA.,Curriculum in Genetics and Molecular Biology, The University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Madison M Parker
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | | | | | | | | | | | - Krzysztof Krajewski
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA
| | | | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA.
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina, Chapel Hill, NC, 27599, USA. .,Lineberger Comprehensive Cancer Center, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA. .,Curriculum in Genetics and Molecular Biology, The University of North Carolina, Chapel Hill, NC, 27599, USA.
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11
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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12
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Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets. Genes (Basel) 2017; 8:genes8080196. [PMID: 28783137 PMCID: PMC5575660 DOI: 10.3390/genes8080196] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 12/19/2022] Open
Abstract
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation. This genetic modification machinery involves various writers, readers, and erasers that have unique structures, functions, and modes of action. Regarding human disease, studies have mainly focused on the genetic mechanisms; however, alteration in the balance of epigenetic networks can result in major pathologies including mental retardation, chromosome instability syndromes, and various types of cancers. Owing to its critical influence, great potential lies in developing epigenetic therapies. In this regard, this review has highlighted mechanistic and structural interactions of the main epigenetic families with their targets, which will help to identify more efficient and safe drugs against several diseases.
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13
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Huang YQ. Recent advances in the diagnosis and treatment of primary biliary cholangitis. World J Hepatol 2016; 8:1419-1441. [PMID: 27957241 PMCID: PMC5124714 DOI: 10.4254/wjh.v8.i33.1419] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/26/2016] [Accepted: 08/29/2016] [Indexed: 02/06/2023] Open
Abstract
Primary biliary cholangitis (PBC), formerly referred to as primary biliary cirrhosis, is an infrequent progressive intrahepatic cholestatic autoimmune illness that can evolve into hepatic fibrosis, hepatic cirrhosis, hepatic failure, and, in some cases, hepatocellular carcinoma. The disease itself is characterized by T-lymphocyte-mediated chronic non-suppurative destructive cholangitis and elevated serum levels of extremely specific anti-mitochondrial autoantibodies (AMAs). In this article, we will not only review epidemiology, risk factors, natural history, predictive scores, radiologic approaches (e.g., acoustic radiation force impulse imaging, vibration controlled transient elastography, and magnetic resonance elastography), clinical features, serological characteristics covering biochemical markers, immunoglobulins, infections markers, biomarkers, predictive fibrosis marker, specific antibodies (including AMAs such as AMA-M2), anti-nuclear autoantibodies [such as anti-multiple nuclear dot autoantibodies (anti-sp100, PML, NDP52, anti-sp140), anti-rim-like/membranous anti-nuclear autoantibodies (anti-gp210, anti-p62), anti-centromere autoantibodies, and some of the novel autoantibodies], histopathological characteristics of PBC, diagnostic advances, and anti-diastole of PBC. Furthermore, this review emphasizes the recent advances in research of PBC in terms of therapies, including ursodeoxycholic acid, budesonide, methotrexate, obeticholic acid, cyclosporine A, fibrates such as bezafibrate and fenofibrate, rituximab, mesenchymal stem cells transplant, and hepatic transplant. Currently, hepatic transplant remains the only optimal choice with acknowledged treatment efficiency for end-stage PBC patients.
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14
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Zhang X, Zhao D, Xiong X, He Z, Li H. Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C. J Biol Chem 2016; 291:12786-12798. [PMID: 27129259 PMCID: PMC4933467 DOI: 10.1074/jbc.m116.721159] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/06/2016] [Indexed: 02/05/2023] Open
Abstract
The decoding of histone post-translational modifications by chromatin-binding modules ("readers") constitutes one major mechanism of epigenetic regulation. Nuclear antigen Sp100 (SPECKLED, 100 kDa), a constitutive component of the promyelocytic leukemia nuclear bodies, plays key roles in intrinsic immunity and transcriptional repression. Sp100C, a splicing isoform specifically up-regulated upon interferon stimulation, harbors a unique tandem plant homeodomain (PHD) finger and bromodomain at its C terminus. Combining structural, quantitative binding, and cellular co-localization studies, we characterized Sp100C PHD finger as an unmethylated histone H3 Lys(4) (H3K4me0) reader that tolerates histone H3 Thr(3) phosphorylation (H3T3ph), histone H3 Lys(9) trimethylation (H3K9me3), and histone H3 Ser(10) phosphorylation (H3S10ph), hallmarks associated with the mitotic chromosome. In contrast, whereas H3K4me0 reader activity is conserved in Sp140, an Sp100C paralog, the multivalent tolerance of H3T3ph, H3K9me3, and H3S10ph was lost for Sp140. The complex structure determined at 2.1 Å revealed a highly coordinated lysine ϵ-amine recognition sphere formed by an extended N-terminal motif for H3K4me0 readout. Interestingly, reader pocket rigidification by disulfide bond formation enhanced H3K4me0 binding by Sp100C. An additional complex structure solved at 2.7 Å revealed that H3T3ph is recognized by the arginine residue, Arg(713), that is unique to the PHD finger of Sp100C. Consistent with a restrictive cellular role of Sp100C, these results establish a direct chromatin targeting function of Sp100C that may regulate transcriptional gene silencing and promyelocytic leukemia nuclear body-mediated intrinsic immunity in response to interferon stimulation.
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Affiliation(s)
- Xiaojie Zhang
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Dan Zhao
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Xiaozhe Xiong
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Zhimin He
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Haitao Li
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and; the Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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