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Carry PM, Vanderlinden LA, Johnson RK, Buckner T, Steck AK, Kechris K, Yang IV, Fingerlin TE, Fiehn O, Rewers M, Norris JM. Longitudinal changes in DNA methylation during the onset of islet autoimmunity differentiate between reversion versus progression of islet autoimmunity. Front Immunol 2024; 15:1345494. [PMID: 38915393 PMCID: PMC11194352 DOI: 10.3389/fimmu.2024.1345494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 05/21/2024] [Indexed: 06/26/2024] Open
Abstract
Background Type 1 diabetes (T1D) is preceded by a heterogenous pre-clinical phase, islet autoimmunity (IA). We aimed to identify pre vs. post-IA seroconversion (SV) changes in DNAm that differed across three IA progression phenotypes, those who lose autoantibodies (reverters), progress to clinical T1D (progressors), or maintain autoantibody levels (maintainers). Methods This epigenome-wide association study (EWAS) included longitudinal DNAm measurements in blood (Illumina 450K and EPIC) from participants in Diabetes Autoimmunity Study in the Young (DAISY) who developed IA, one or more islet autoantibodies on at least two consecutive visits. We compared reverters - individuals who sero-reverted, negative for all autoantibodies on at least two consecutive visits and did not develop T1D (n=41); maintainers - continued to test positive for autoantibodies but did not develop T1D (n=60); progressors - developed clinical T1D (n=42). DNAm data were measured before (pre-SV visit) and after IA (post-SV visit). Linear mixed models were used to test for differences in pre- vs post-SV changes in DNAm across the three groups. Linear mixed models were also used to test for group differences in average DNAm. Cell proportions, age, and sex were adjusted for in all models. Median follow-up across all participants was 15.5 yrs. (interquartile range (IQR): 10.8-18.7). Results The median age at the pre-SV visit was 2.2 yrs. (IQR: 0.8-5.3) in progressors, compared to 6.0 yrs. (IQR: 1.3-8.4) in reverters, and 5.7 yrs. (IQR: 1.4-9.7) in maintainers. Median time between the visits was similar in reverters 1.4 yrs. (IQR: 1-1.9), maintainers 1.3 yrs. (IQR: 1.0-2.0), and progressors 1.8 yrs. (IQR: 1.0-2.0). Changes in DNAm, pre- vs post-SV, differed across the groups at one site (cg16066195) and 11 regions. Average DNAm (mean of pre- and post-SV) differed across 22 regions. Conclusion Differentially changing DNAm regions were located in genomic areas related to beta cell function, immune cell differentiation, and immune cell function.
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Affiliation(s)
- Patrick M. Carry
- Colorado Program for Musculoskeletal Research, Department of Orthopedics, University of Colorado, Aurora, CO, United States
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
- Department of Biomedical Informatics, School of Medicine, University of Colorado, Aurora, CO, United States
| | | | - Randi K. Johnson
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
- Department of Biomedical Informatics, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Teresa Buckner
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
- Department of Kinesiology, Nutrition, and Dietetics, University of Northern Colorado, Greeley, CO, United States
| | - Andrea K. Steck
- Barbara Davis Center, Department of Pediatrics, University of Colorado, Aurora, CO, United States
| | - Katerina Kechris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
- Department of Biomedical Informatics, School of Medicine, University of Colorado, Aurora, CO, United States
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
| | - Ivana V. Yang
- Department of Biomedical Informatics, School of Medicine, University of Colorado, Aurora, CO, United States
- Department of Medicine, University of Colorado, Aurora, CO, United States
| | - Tasha E. Fingerlin
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO, United States
- Department of Immunology and Genomic Medicine, National Jewish Health, Aurora, CO, United States
| | - Oliver Fiehn
- University of California Davis West Coast Metabolomics Center, Davis, CA, United States
| | - Marian Rewers
- Barbara Davis Center, Department of Pediatrics, University of Colorado, Aurora, CO, United States
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO, United States
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2
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Prosdocimi F, de Farias ST. Life and living beings under the perspective of organic macrocodes. Biosystems 2021; 206:104445. [PMID: 34033908 DOI: 10.1016/j.biosystems.2021.104445] [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: 04/30/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022]
Abstract
A powerful and concise concept of life is crucial for studies aiming to understand the characteristics that emerged from an inorganic world. Among biologists, the most accepted argument define life under a top-down strategy by looking into the shared characteristics observed in all cellular organisms. This is often made highlighting (i) autonomy and (ii) evolutionary capacity as fundamental characteristics observed in all cellular organisms. Along the present work, we assume the framework of code biology considering that biology started with the emergence of the first organic code by self-organization. We reinforces that the conceptual structure of life should be reallocated from the ontology class of Matter to its sister class of Process. Along the emergence and early evolution of biological systems, biological codes changed from open systems of "naked" molecules (at the progenote era), to close, encapsulated systems (at the organismic era). Living beings appeared at the very moment when nucleic acids with coding properties became encapsulated. This led to the origin of viruses and, then, to the origin of cells. In this context, we propose that the single character that makes a clear distinction between the abiotic and the biotic world is the capacity to process organic codes. Thus, life appears with the self-assembly of a genetic code and evolves by the emergence of other overlapping codes. Once life has been clearly conceptualized, we go further to conceptualize organisms, parents, lineages, and species in terms of code biology.
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Affiliation(s)
- Francisco Prosdocimi
- Laboratório de Biologia Teórica e de Sistemas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Sávio Torres de Farias
- Laboratório de Genética Evolutiva Paulo Leminski, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Paraíba, Brazil; Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds, LS7 3RB, UK.
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3
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Liu S, Zhong Z, Zhong W, Weng R, Liu J, Gu X, Chen Y. Comprehensive analysis of T-cell receptor repertoire in patients with acute coronary syndrome by high-throughput sequencing. BMC Cardiovasc Disord 2020; 20:253. [PMID: 32460698 PMCID: PMC7254720 DOI: 10.1186/s12872-020-01538-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/18/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND This study aims to investigate the T-cell receptor (TCR) repertoire in patients with acute coronary syndrome (ACS). METHODS The TCR repertoires of 9 unstable angina patients (UA), 14 acute myocardial infarction patients (AMI) and 9 normal coronary artery (NCA) patients were profiled using high-throughput sequencing (HTS). The clonal diversity of the TCR repertoires in different groups was analyzed, as well as the frequencies of variable (V), diversity (D) and joining(J) gene segments. RESULTS ACS patients including UA and AMI, showed reduced TCRβ diversity than NCA patients. ACS patients presented higher levels of clonal expansion. The clonotype overlap of complementarity determining region 3(CDR3) was significantly varied between different groups. A total of 10 V genes and 1 J gene were differently utilized between ACS and NCA patients. We identified some shared CDR3 amino acid sequences that were presented in ACS but not in NCA patients. CONCLUSIONS This study revealed the distinct TCR repertoires in patients with ACS and demonstrated the presence of disease associated T-cell clonotypes. These findings suggested a role of T cells in ACS and provided a new way to explore the mechanisms of ACS.
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Affiliation(s)
- Sudong Liu
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China. .,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, P. R. China.
| | - Zhixiong Zhong
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizho, 514031, P. R. China.,Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, P. R. China
| | - Wei Zhong
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizho, 514031, P. R. China.,Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, P. R. China
| | - Ruiqiang Weng
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, P. R. China
| | - Jing Liu
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, P. R. China
| | - Xiaodong Gu
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, P. R. China
| | - Yongyu Chen
- Clinical Core Laboratory, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No 63 Huangtang Road, Meijiang District, Meizhou, 514031, P. R. China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, P. R. China
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Keenan CR, Iannarella N, Garnham AL, Brown AC, Kim RY, Horvat JC, Hansbro PM, Nutt SL, Allan RS. Polycomb repressive complex 2 is a critical mediator of allergic inflammation. JCI Insight 2019; 4:127745. [PMID: 31092733 DOI: 10.1172/jci.insight.127745] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 04/17/2019] [Indexed: 12/20/2022] Open
Abstract
Strategies that intervene with the development of immune-mediated diseases are urgently needed, as current treatments mostly focus on alleviating symptoms rather than reversing the disease. Targeting enzymes involved in epigenetic modifications to chromatin represents an alternative strategy that has the potential to perturb the function of the lymphocytes that drive the immune response. Here, we report that 2 major epigenetic silencing pathways are increased after T cell activation. By specific inactivation of these molecules in the T cell compartment in vivo, we demonstrate that the polycomb repressive complex 2 (PRC2) is essential for the generation of allergic responses. Furthermore, we show that small-molecule inhibition of the PRC2 methyltransferase, enhancer of zeste homolog 2 (Ezh2), reduces allergic inflammation in mice. Therefore, by systematically surveying the pathways involved in epigenetic gene silencing we have identified Ezh2 as a target for the suppression of allergic disease.
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Affiliation(s)
- Christine R Keenan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadia Iannarella
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandra C Brown
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia
| | - Richard Y Kim
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia
| | - Jay C Horvat
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
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5
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Zhong Z, Wu H, Zhang Q, Zhong W, Zhao P. Characteristics of T cell receptor repertoires of patients with acute myocardial infarction through high-throughput sequencing. J Transl Med 2019; 17:21. [PMID: 30634977 PMCID: PMC6330436 DOI: 10.1186/s12967-019-1768-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/02/2019] [Indexed: 01/19/2023] Open
Abstract
Background T cells are key regulators of immunity and one of the cells recruited in atherosclerosis and participated in various stages of the development of atherosclerosis. Characterizing T-cell receptor (TCR) repertoires is a priority of great scientific interest and potential clinical utility for the early diagnosis, risk stratification and prognostic evaluation of acute myocardial infarction (AMI). Methods The TCR repertoires in 21 subjects including 7 patients with non-ST-segment elevation myocardial infarction (NSTEMI), 6 patients with ST-segment elevation myocardial infarction (STEMI) and 8 subjects with normal coronary artery (NCA) as control were characterized by using high-throughput sequencing. Bioinformatics analysis were performed. Results Patients with NSTEMI displayed more diverse TCR sequences than NCA controls, but they had lower percentage of top 200 TCR sequences. However, no significant differences were observed between the patients with STEMI and NCA controls, but STEMI group had lower percentage of top 200 TCR sequences. T cells from patients with AMI and NCA controls showed a differential V and J gene usage, especially, significant difference was observed in frequencies of V gene (TRBV2, TRBV29-1, TRBV30 and TRBV12-3) and J gene (TRBJ2-1) usage. Furthermore, significantly differences in average overlap was observed in groups of AMI and NCA control. The results showed that patients with AMI had distinct TCR repertoires which revealed the association between cardiovascular condition and T-cell clonotypes. Conclusions Our findings revealed the differences of TCR repertoires between patients with AMI and NCA controls, which might be potential biomarkers for evaluating risk stratification or diagnosis of acute coronary syndrome. Electronic supplementary material The online version of this article (10.1186/s12967-019-1768-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhixiong Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Clinical Core Laboratory, Center for Precision Medicine, Guangdong Provincial Engineering and Technology Research Center for Clinical Molecular Diagnostics and Antibody Therapeutics, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou, 514031, People's Republic of China
| | - Heming Wu
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Clinical Core Laboratory, Center for Precision Medicine, Guangdong Provincial Engineering and Technology Research Center for Clinical Molecular Diagnostics and Antibody Therapeutics, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou, 514031, People's Republic of China
| | - Qifeng Zhang
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Clinical Core Laboratory, Center for Precision Medicine, Guangdong Provincial Engineering and Technology Research Center for Clinical Molecular Diagnostics and Antibody Therapeutics, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou, 514031, People's Republic of China
| | - Wei Zhong
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Clinical Core Laboratory, Center for Precision Medicine, Guangdong Provincial Engineering and Technology Research Center for Clinical Molecular Diagnostics and Antibody Therapeutics, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou, 514031, People's Republic of China
| | - Pingsen Zhao
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China. .,Clinical Core Laboratory, Center for Precision Medicine, Guangdong Provincial Engineering and Technology Research Center for Clinical Molecular Diagnostics and Antibody Therapeutics, Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China. .,Guangdong Provincial Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China. .,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China. .,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou, 514031, People's Republic of China.
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6
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Prieto-Torres L, Rodriguez-Pinilla SM, Onaindia A, Ara M, Requena L, Piris MÁ. CD30-positive primary cutaneous lymphoproliferative disorders: molecular alterations and targeted therapies. Haematologica 2019; 104:226-235. [PMID: 30630983 PMCID: PMC6355473 DOI: 10.3324/haematol.2018.197152] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/07/2018] [Indexed: 01/06/2023] Open
Abstract
Primary cutaneous CD30-positive T-cell lymphoproliferative disorders are the second most common subgroup of cutaneous T-cell lymphomas. They include two clinically different entities with some overlapping features and borderline cases: lymphomatoid papulosis and primary cutaneous anaplastic large cell lymphoma. Molecular studies of primary cutaneous anaplastic large cell lymphoma reveal an increasing level of heterogeneity that is associated with histological and immunophenotypic features of the cases and their response to specific therapies. Here, we review the most significant genetic, epigenetic and molecular alterations described to date in primary cutaneous CD30-positive T-cell lymphoproliferative disorders, and their potential as therapeutic targets.
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Affiliation(s)
| | - Socorro M Rodriguez-Pinilla
- Department of Pathology, Hospital Universitario Fundación Jiménez Díaz, Madrid.,Hospital Universitario Fundación Jiménez Díaz, Madrid, CIBERONC, Madrid
| | - Arantza Onaindia
- Pathology, Hospital Universitario Marques de Valdecilla, Santander
| | - Mariano Ara
- Dermatology Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
| | | | - Miguel Á Piris
- Department of Pathology, Hospital Universitario Fundación Jiménez Díaz, Madrid.,Hospital Universitario Fundación Jiménez Díaz, Madrid, CIBERONC, Madrid
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7
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Human γδ T cells: From a neglected lymphocyte population to cellular immunotherapy: A personal reflection of 30years of γδ T cell research. Clin Immunol 2016; 172:90-97. [DOI: 10.1016/j.clim.2016.07.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/10/2016] [Indexed: 01/06/2023]
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8
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Shao Y, Chernaya V, Johnson C, Yang WY, Cueto R, Sha X, Zhang Y, Qin X, Sun J, Choi ET, Wang H, Yang XF. Metabolic Diseases Downregulate the Majority of Histone Modification Enzymes, Making a Few Upregulated Enzymes Novel Therapeutic Targets--"Sand Out and Gold Stays". J Cardiovasc Transl Res 2016; 9:49-66. [PMID: 26746407 DOI: 10.1007/s12265-015-9664-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 12/01/2015] [Indexed: 12/17/2022]
Abstract
To determine whether the expression of histone modification enzymes is regulated in physiological and pathological conditions, we took an experimental database mining approach pioneered in our labs to determine a panoramic expression profile of 164 enzymes in 19 human and 17 murine tissues. We have made the following significant findings: (1) Histone enzymes are differentially expressed in cardiovascular, immune, and other tissues; (2) our new pyramid model showed that heart and T cells are among a few tissues in which histone acetylation/deacetylation, and histone methylation/demethylation are in the highest varieties; and (3) histone enzymes are more downregulated than upregulated in metabolic diseases and regulatory T cell (Treg) polarization/ differentiation, but not in tumors. These results have demonstrated a new working model of "Sand out and Gold stays," where more downregulation than upregulation of histone enzymes in metabolic diseases makes a few upregulated enzymes the potential novel therapeutic targets in metabolic diseases and Treg activity.
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Affiliation(s)
- Ying Shao
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Valeria Chernaya
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Candice Johnson
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - William Y Yang
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Ramon Cueto
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Xiaojin Sha
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Yi Zhang
- Fels Institute for Cancer Research & Molecular Biology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Xuebin Qin
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Jianxin Sun
- Department of Medicine, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Eric T Choi
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA.,Department of Surgery, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Hong Wang
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA
| | - Xiao-feng Yang
- Centers for Metabolic Disease Research, Cardiovascular Research & Thrombosis Research, Department of Pharmacology, Temple University School of Medicine, Philadelphia, PA, 19140, USA. .,Centers for Metabolic Disease Research and Cardiovascular Research, Temple University School of Medicine, 3500 North Broad Street, MERB 1059, Philadelphia, PA, 19140, USA.
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9
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Epigenetic dynamics in immunity and autoimmunity. Int J Biochem Cell Biol 2015; 67:65-74. [DOI: 10.1016/j.biocel.2015.05.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 02/01/2023]
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10
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Liu M, Gao W, van Velkinburgh JC, Wu Y, Ni B, Tian Y. Role of Ets Proteins in Development, Differentiation, and Function of T-Cell Subsets. Med Res Rev 2015; 36:193-220. [PMID: 26301869 DOI: 10.1002/med.21361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 07/12/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022]
Abstract
Through positive selection, double-positive cells in the thymus differentiate into CD4(+) or CD8(+) T single-positive cells that subsequently develop into different types of effective T cells, such as T-helper and cytotoxic T lymphocyte cells, that play distinctive roles in the immune system. Development, differentiation, and function of thymocytes and CD4(+) and CD8(+) T cells are controlled by a multitude of secreted and intracellular factors, ranging from cytokine signaling modules to transcription factors and epigenetic modifiers. Members of the E26 transformation specific (Ets) family of transcription factors, in particular, are potent regulators of these CD4(+) or CD8(+) T-cell processes. In this review, we summarize and discuss the functions and underlying mechanisms of the Ets family members that have been characterized as involved in these processes. Ongoing research of these factors is expected to identify practical applications for the Ets family members as novel therapeutic targets for inflammation-related diseases.
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Affiliation(s)
- Mian Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China.,Battalion 10 of Cadet Brigade, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Weiwu Gao
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | | | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Bing Ni
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
| | - Yi Tian
- Institute of Immunology, PLA, Third Military Medical University, Chongqing, 400038, P.R. China
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Singh H. Transcriptional and epigenetic networks orchestrating immune cell development and function. Immunol Rev 2015; 261:5-8. [PMID: 25123273 DOI: 10.1111/imr.12210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Harinder Singh
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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12
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MicroRNA Expression Profiling and DNA Methylation Signature for Deregulated MicroRNA in Cutaneous T-Cell Lymphoma. J Invest Dermatol 2015; 135:1128-1137. [DOI: 10.1038/jid.2014.487] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 10/07/2014] [Accepted: 10/25/2014] [Indexed: 02/07/2023]
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13
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MacDonald IA, Hathaway NA. Epigenetic roots of immunologic disease and new methods for examining chromatin regulatory pathways. Immunol Cell Biol 2014; 93:261-70. [PMID: 25533290 DOI: 10.1038/icb.2014.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/31/2014] [Indexed: 12/19/2022]
Abstract
The ability to accurately quantitate and experimentally examine epigenetic modifications across the human genome has exploded in the past decade. This has given rise to a wealth of new information concerning the contributions of epigenetic regulatory networks to the pathogenesis of human disease. In particular, immunological disorders have strong developmental roots in chromatin regulatory pathways. In this review, we focus on the epigenetic signatures and new discoveries revealing the epigenetic compositions of specific immunological cancers and autoimmune diseases. We also comment on the conserved epigenetic roots among diverse immunological disorders and suggest inhibition strategies that may be relevant for future treatment. Finally, we highlight emerging experimental tools with the capability to examine the mechanisms of chromatin regulatory enzymes with a high level of temporal control. The knowledge of genetic and epigenetic defects in immunological disease combined with new experimental approaches will elucidate the contribution of individual enzymes in complex epigenetic regulatory networks. This could lead to new diagnostic and therapeutic approaches for some very diverse and difficult to treat human diseases.
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Affiliation(s)
- Ian A MacDonald
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Nathaniel A Hathaway
- 1] Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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