1
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Kearly A, Saelee P, Bard J, Sinha S, Satterthwaite A, Garrett-Sinha LA. Sequences within and upstream of the mouse Ets1 gene drive high level expression in B cells, but are not sufficient for consistent expression in T cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606433. [PMID: 39149372 PMCID: PMC11326187 DOI: 10.1101/2024.08.02.606433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The levels of transcription factor Ets1 are high in resting B and T cells, but are downregulated by signaling through antigen receptors and Toll-like receptors (TLRs). Loss of Ets1 in mice leads to excessive immune cell activation and development of an autoimmune syndrome and reduced Ets1 expression has been observed in human PBMCs in the context of autoimmune diseases. In B cells, Ets1 serves to prevent premature activation and differentiation to antibody-secreting cells. Given these important roles for Ets1 in the immune response, stringent control of Ets1 gene expression levels is required for homeostasis. However, the genetic regulatory elements that control expression of the Ets1 gene remain relatively unknown. Here we identify a topologically-associating domain (TAD) in the chromatin of B cells that includes the mouse Ets1 gene locus and describe an interaction hub that extends over 100 kb upstream and into the gene body. Additionally, we compile epigenetic datasets to find several putative regulatory elements within the interaction hub by identifying regions of high DNA accessibility and enrichment of active enhancer histone marks. Using reporter constructs, we determine that DNA sequences within this interaction hub are sufficient to direct reporter gene expression in lymphoid tissues of transgenic mice. Further analysis indicates that the reporter construct drives faithful expression of the reporter gene in mouse B cells, but variegated expression in T cells, suggesting the existence of T cell regulatory elements outside this region. To investigate how the downregulation of Ets1 transcription is associated with alterations in the epigenetic landscape of stimulated B cells, we performed ATAC-seq in resting and BCR-stimulated primary B cells and identified four regions within and upstream of the Ets1 locus that undergo changes in chromatin accessibility that correlate to Ets1 gene expression. Interestingly, functional analysis of several putative Ets1 regulatory elements using luciferase constructs suggested a high level of functional redundancy. Taken together our studies reveal a complex network of regulatory elements and transcription factors that coordinate the B cell-specific expression of Ets1.
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Affiliation(s)
- Alyssa Kearly
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Prontip Saelee
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Jonathan Bard
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Satrajit Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
| | - Anne Satterthwaite
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203
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2
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Castellini-Pérez O, Povedano E, Barturen G, Martínez-Bueno M, Iakovliev A, Kerick M, López-Domínguez R, Marañón C, Martín J, Ballestar E, Borghi MO, Qiu W, Zhu C, Shankara S, Spiliopoulou A, de Rinaldis E, Carnero-Montoro E, Alarcón-Riquelme ME. Molecular subtypes explain lupus epigenomic heterogeneity unveiling new regulatory genetic risk variants. NPJ Genom Med 2024; 9:38. [PMID: 39013887 PMCID: PMC11252280 DOI: 10.1038/s41525-024-00420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/17/2024] [Indexed: 07/18/2024] Open
Abstract
The heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. We performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. In a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel drug targets for SLE. This study reveals possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and novel disease-specific meQTLs. Finally, novel targets for drug development were discovered.
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Affiliation(s)
- Olivia Castellini-Pérez
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
- University of Granada, Granada, Spain
| | - Elena Povedano
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
- Spanish National Research Council (CSIC), Institute of Economy, Geography and Demography, Madrid (IEGD), Madrid, Spain
- Autonomous University of Madrid, Madrid, Spain
| | - Guillermo Barturen
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
- Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain
| | - Manuel Martínez-Bueno
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Andrii Iakovliev
- Usher Institute of Population Health Sciences and Informatics. University of Edinburgh Medical School, EH8 9YL, Edinburgh, UK
| | - Martin Kerick
- IBPLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, 18016, Spain
| | - Raúl López-Domínguez
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Concepción Marañón
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Javier Martín
- IBPLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, Granada, 18016, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | | | - Weiliang Qiu
- Sanofi, Early Development and Research, Cambridge, MA, USA
| | - Cheng Zhu
- Sanofi, Precision Medicine & Computational Biology (PMCB), R&D, Cambridge, MA, USA
| | - Srinivas Shankara
- Sanofi, Precision Medicine & Computational Biology (PMCB), R&D, Cambridge, MA, USA
| | - Athina Spiliopoulou
- Usher Institute of Population Health Sciences and Informatics. University of Edinburgh Medical School, EH8 9YL, Edinburgh, UK
| | - Emanuele de Rinaldis
- Sanofi, Precision Medicine & Computational Biology (PMCB), R&D, Cambridge, MA, USA
| | - Elena Carnero-Montoro
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
- University of Granada, Granada, Spain.
| | - Marta E Alarcón-Riquelme
- GENYO. Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
- Institute for Environmental Medicine, Karolinska Institutet, 171 67, Solna, Sweden.
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3
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Singh MK, Maiti GP, Reddy-Rallabandi H, Fazel-Najafabadi M, Looger LL, Nath SK. A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility. FRONTIERS IN LUPUS 2023; 1:1244670. [PMID: 38317862 PMCID: PMC10843804 DOI: 10.3389/flupu.2023.1244670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4. Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1, and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
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Affiliation(s)
- Manish Kumar Singh
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
| | - Guru Prashad Maiti
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
| | | | - Mehdi Fazel-Najafabadi
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
| | - Loren L. Looger
- Howard Hughes Medical Institute, Department of Neurosciences, University of California San Diego, La Jolla CA, USA
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City OK, USA
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4
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Garrett-Sinha LA. An update on the roles of transcription factor Ets1 in autoimmune diseases. WIREs Mech Dis 2023; 15:e1627. [PMID: 37565573 PMCID: PMC10842644 DOI: 10.1002/wsbm.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Transcription factors are crucial to regulate gene expression in immune cells and in other cell types. In lymphocytes, there are a large number of different transcription factors that are known to contribute to cell differentiation and the balance between quiescence and activation. One such transcription factor is E26 oncogene homolog 1 (Ets1). Ets1 expression is high in quiescent B and T lymphocytes and its levels are decreased upon activation. The human ETS1 gene has been identified as a susceptibility locus for many autoimmune and inflammatory diseases. In accord with this, gene knockout of Ets1 in mice leads to development of a lupus-like autoimmune disease, with enhanced activation and differentiation of both B cells and T cells. Prior reviews have summarized functional roles for Ets1 based on studies of Ets1 knockout mice. In recent years, numerous additional studies have been published that further validate ETS1 as a susceptibility locus for human diseases where immune dysregulation plays a causative role. In this update, new information that further links Ets1 to human autoimmune diseases is organized and collated to serve as a resource. This update also describes recent studies that seek to understand molecularly how Ets1 regulates immune cell activation, either using human cells and tissues or mouse models. This resource is expected to be useful to investigators seeking to understand how Ets1 may regulate the human immune response, particularly in terms of its roles in autoimmunity and inflammation. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA
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5
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Ma S, Feng G, Li L, Li Z, Zhou X, Zhou Y, Zhang R. Downregulation of circETS1 disrupts Th17/Treg homeostasis by inhibiting FOXP3 transcription: A new potential biomarker in systemic lupus erythematosus. Lupus 2023; 32:1430-1439. [PMID: 37852297 DOI: 10.1177/09612033231207545] [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] [Indexed: 10/20/2023]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease associated with an imbalance of T helper 17 (Th17) to regulatory T cells (Tregs). However, the underlying mechanism remains unclear. Increasing evidence suggests that circular RNAs play a crucial role in SLE. Although circETS1 was discovered 30 years ago, detailed exploration of its functions remains limited. In this study, we measured the expression levels of circETS1 in peripheral blood mononuclear cells (PBMCs) and CD4+ T cells of patients with SLE by quantitative polymerase chain reaction. The impact of circETS1 expression on the Th17/Treg balance and underlying mechanism were evaluated using double-luciferase reporter, gain-/loss-of-function, and rescue assays. Receiver operating characteristic (ROC) curve analysis was conducted to assess the diagnostic value of circETS1. Both circETS1 and FOXP3 expression were downregulated in the PBMCs and CD4+ T cells of patients with SLE (n = 28) compared with those in the cells of healthy controls (n = 20). Mechanistically, we found that circETS1 can bind directly to the microRNA miR-1205, acting as a sponge to upregulate the transcription of FOXP3, thereby maintaining the Th17/Treg balance. Notably, ROC analysis showed that the expression level of circETS1 in PBMCs had an area under the curve of 0.873 (95% confidence interval: 0.771-0.976; p < .001) for diagnosing SLE, with a sensitivity of 80.00% and a specificity of 89.29%. Finally, we found negative correlations between the level of circETS1 in PBMCs and disease severity (according to the Systemic Lupus Erythematosus Disease Activity Index) in patients with SLE (r = -0.7712, 95% CI: -0.8910 to -0.5509; p < .001). The imbalance in Th17/Treg cells in SLE may be attributed, in part, to the circETS1/miR-1205/FOXP3 pathway. CircETS1 has potential to serve as a valuable biomarker for the diagnosis and evaluation of SLE.
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Affiliation(s)
- Sha Ma
- Department of Rheumatology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Guofu Feng
- Department of Disease Control and Prevention, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Li Li
- School of Public Health, Dali University, Dali, China
| | - Zi Li
- Quality Management Department, Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Xiaoyu Zhou
- Department of Disease Control and Prevention, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Yan Zhou
- Department of Nephrology, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Ruixian Zhang
- Department of Disease Control and Prevention, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
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6
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Jiang P, Wang C, Zhang M, Tian Y, Zhao W, Xin J, Huang Y, Zhao Z, Sun W, Long J, Tang R, Qiu F, Shi X, Zhao Y, Zhu L, Dai N, Liu L, Wu X, Nie J, Jiang B, Shao Y, Gao Y, Yu J, Hu Z, Zang Z, Gong Y, Dai Y, Wang L, Ding N, Xu P, Chen S, Wang L, Xu J, Zhang L, Hong J, Qian R, Li H, Jiang X, Chen C, Tian W, Wu J, Jiang Y, Han C, Zhang K, Qiu H, Li L, Fan H, Chen L, Zhang J, Sun Z, Han X, Dai Z, Li E, Gershwin ME, Lian Z, Ma X, Seldin MF, Chen W, Wang M, Liu X. Differential regulation of JAK1 expression by ETS1 associated with predisposition to primary biliary cholangitis. J Genet Genomics 2023; 50:807-812. [PMID: 37348755 DOI: 10.1016/j.jgg.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Peng Jiang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chan Wang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, Jiangsu 225009, China
| | - Mingming Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ye Tian
- Department of Radiology & Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Weifeng Zhao
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Junyi Xin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Yexi Huang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zhibin Zhao
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Wenjuan Sun
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Jie Long
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Ruqi Tang
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai 200001, China
| | - Fang Qiu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210031, China
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yi Zhao
- Department of Gastrointestinal Endoscopy, Eastern Hepatobiliary Surgery Hospital, Shanghai 201800, China
| | - Li Zhu
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Na Dai
- Department of Gastroenterology, Jiangsu University Affiliated Kunshan Hospital, Kunshan, Jiangsu 215300, China
| | - Lei Liu
- Department of Gastroenterology, Yixing People's Hospital, Yixin, Jiangsu 214200, China
| | - Xudong Wu
- Department of Gastroenterology, Yancheng First People's Hospital, Yancheng, Jiangsu 224005, China
| | - Jinshan Nie
- Department of Gastroenterology, Taicang First People's Hospital, Soochow University, Taicang, Jiangsu 215400, China
| | - Bo Jiang
- Department of Hepatology, Jingjiang Second People's Hospital, Jingjiang, Jiangsu 214500, China
| | - Youlin Shao
- Department of Hepatology, The Third People's Hospital of Changzhou, Changzhou, Jiangsu 213001, China
| | - Yueqiu Gao
- Department of Liver Diseases, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jianjiang Yu
- Department of Laboratory Medicine, Jiangyin People's Hospital, Southeast University, Jiangyin, Jiangsu 214400, China
| | - Zhigang Hu
- Department of Laboratory Medicine, Wuxi Children's Hospital, Wuxi, Jiangsu 214023, China
| | - Zhidong Zang
- Department of Hepatology, The Second Hospital of Nanjing, Southeast University, Nanjing, Jiangsu 210003, China
| | - Yuhua Gong
- Department of Laboratory Medicine, The Third People's Hospital of Zhenjiang, Zhenjiang, Jiangsu 212021, China
| | - Yaping Dai
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu 214000, China
| | - Lan Wang
- Department of Laboratory Medicine, The 81st Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Ningling Ding
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Ping Xu
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Sufang Chen
- The Fifth People's Hospital, Soochow University, Suzhou, Jiangsu 215007, China
| | - Lu Wang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Jing Xu
- Department of Clinical Laboratory, Southeast University ZhongDa Hospital, Nanjing, Jiangsu 210009, China
| | - Luyao Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Junyan Hong
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Ruonan Qian
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hu Li
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xuan Jiang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Congwei Chen
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenyan Tian
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Jian Wu
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Yuzhang Jiang
- Department of Laboratory Medicine, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu 223300, China
| | - Chongxu Han
- Department of Laboratory Medicine, Subei People's Hospital, Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Kui Zhang
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, China
| | - Hong Qiu
- Department of Laboratory Medicine, The 81st Hospital of PLA, Nanjing, Jiangsu 210002, China
| | - Li Li
- Department of Clinical Laboratory, Southeast University ZhongDa Hospital, Nanjing, Jiangsu 210009, China
| | - Hong Fan
- Southeast University Medical College, Nanjing, Jiangsu 210009, China
| | - Liming Chen
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Institute of Cancer, Department of Biochemistry, Nanjing Normal University College of Life Sciences, Nanjing, Jiangsu 210023, China
| | - Jianqiong Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China; Southeast University Medical College, Nanjing, Jiangsu 210009, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Han
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Zhenhua Dai
- Section of Immunology & Joint Immunology Program, The Second Clinical Medical College of Guangzhou University of Chinese Medicine, And Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, Guangdong 510006, China
| | - Erguang Li
- Jiangsu Laboratory of Molecular Medicine, Nanjing University Medical School, Nanjing, Jiangsu 210093, China
| | - M Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Davis, CA, 95616, USA
| | - Zhexiong Lian
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, China
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai 200001, China
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis School of Medicine, Davis, CA, 95616, USA
| | - Weichang Chen
- The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China.
| | - Meilin Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affilated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu 211166, China.
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210096, China.
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7
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Singh MK, Maiti GP, Reddy-Rallabandi H, Fazel-Najafabadi M, Looger LL, Nath SK. A Non-Coding Variant in SLC15A4 Modulates Enhancer Activity and Lysosomal Deacidification Linked to Lupus Susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551056. [PMID: 37546883 PMCID: PMC10402135 DOI: 10.1101/2023.07.28.551056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic basis. Despite the identification of several single nucleotide polymorphisms (SNPs) near the SLC15A4 gene that are significantly associated with SLE across multiple populations, specific causal SNP(s) and molecular mechanisms responsible for disease susceptibility are unknown. To address this gap, we employed bioinformatics, expression quantitative trait loci (eQTLs), and 3D chromatin interaction analysis to nominate a likely functional variant, rs35907548, in an active intronic enhancer of SLC15A4 . Through luciferase reporter assays followed by chromatin immunoprecipitation (ChIP)-qPCR, we observed significant allele-specific enhancer effects of rs35907548 in diverse cell lines. The rs35907548 risk allele T is associated with increased regulatory activity and target gene expression, as shown by eQTLs and chromosome conformation capture (3C)-qPCR. The latter revealed long-range chromatin interactions between the rs35907548 enhancer and the promoters of SLC15A4, GLTLD1 , and an uncharacterized lncRNA. The enhancer-promoter interactions and expression effects were validated by CRISPR/Cas9 knock-out (KO) of the locus in HL60 promyeloblast cells. KO cells also displayed dramatically dysregulated endolysosomal pH regulation. Together, our data show that the rs35907548 risk allele affects multiple aspects of cellular physiology and may directly contribute to SLE.
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8
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Battaglia M, Sunshine AC, Luo W, Jin R, Stith A, Lindemann M, Miller LS, Sinha S, Wohlfert E, Garrett-Sinha LA. Ets1 and IL17RA cooperate to regulate autoimmune responses and skin immunity to Staphylococcus aureus. Front Immunol 2023; 14:1208200. [PMID: 37691956 PMCID: PMC10486983 DOI: 10.3389/fimmu.2023.1208200] [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: 04/18/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Ets1 is a lymphoid-enriched transcription factor that regulates B- and Tcell functions in development and disease. Mice that lack Ets1 (Ets1 KO) develop spontaneous autoimmune disease with high levels of autoantibodies. Naïve CD4 + T cells isolated from Ets1 KO mice differentiate more readily to Th17 cells that secrete IL-17, a cytokine implicated in autoimmune disease pathogenesis. To determine if increased IL-17 production contributes to the development of autoimmunity in Ets1 KO mice, we crossed Ets1 KO mice to mice lacking the IL-17 receptor A subunit (IL17RA KO) to generate double knockout (DKO) mice. Methods In this study, the status of the immune system of DKO and control mice was assessed utilizing ELISA, ELISpot, immunofluorescent microscopy, and flow cytometric analysis of the spleen, lymph node, skin. The transcriptome of ventral neck skin was analyzed through RNA sequencing. S. aureus clearance kinetics in in exogenously infected mice was conducted using bioluminescent S. aureus and tracked using an IVIS imaging experimental scheme. Results We found that the absence of IL17RA signaling did not prevent or ameliorate the autoimmune phenotype of Ets1 KO mice but rather that DKO animals exhibited worse symptoms with striking increases in activated B cells and secreted autoantibodies. This was correlated with a prominent increase in the numbers of T follicular helper (Tfh) cells. In addition to the autoimmune phenotype, DKO mice also showed signs of immunodeficiency and developed spontaneous skin lesions colonized by Staphylococcus xylosus. When DKO mice were experimentally infected with Staphylococcus aureus, they were unable to clear the bacteria, suggesting a general immunodeficiency to staphylococcal species. γδ T cells are important for the control of skin staphylococcal infections. We found that mice lacking Ets1 have a complete deficiency of the γδ T-cell subset dendritic epidermal T cells (DETCs), which are involved in skin woundhealing responses, but normal numbers of other skin γδ T cells. To determine if loss of DETC combined with impaired IL-17 signaling might promote susceptibility to staph infection, we depleted DETC from IL17RA KO mice and found that the combined loss of DETC and impaired IL-17 signaling leads to an impaired clearance of the infection. Conclusions Our studies suggest that loss of IL-17 signaling can result in enhanced autoimmunity in Ets1 deficient autoimmune-prone mice. In addition, defects in wound healing, such as that caused by loss of DETC, can cooperate with impaired IL-17 responses to lead to increased susceptibility to skin staph infections.
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Affiliation(s)
- Michael Battaglia
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Alex C. Sunshine
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Wei Luo
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Richard Jin
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY, United States
| | - Alifa Stith
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | | | - Lloyd S. Miller
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Satrajit Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Elizabeth Wohlfert
- Department of Microbiology and Immunology, State University of New York at Buffalo, Buffalo, NY, United States
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY, United States
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9
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ETS-1 facilitates Th1 cell-mediated mucosal inflammation in inflammatory bowel diseases through upregulating CIRBP. J Autoimmun 2022; 132:102872. [DOI: 10.1016/j.jaut.2022.102872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
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10
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Genetic dissection of TLR9 reveals complex regulatory and cryptic proinflammatory roles in mouse lupus. Nat Immunol 2022; 23:1457-1469. [PMID: 36151396 PMCID: PMC9561083 DOI: 10.1038/s41590-022-01310-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 08/08/2022] [Indexed: 02/04/2023]
Abstract
In lupus, Toll-like receptor 7 (TLR7) and TLR9 mediate loss of tolerance to RNA and DNA, respectively. Yet, TLR7 promotes disease, while TLR9 protects from disease, implying differences in signaling. To dissect this 'TLR paradox', we generated two TLR9 point mutants (lacking either ligand (TLR9K51E) or MyD88 (TLR9P915H) binding) in lupus-prone MRL/lpr mice. Ameliorated disease of Tlr9K51E mice compared to Tlr9-/- controls revealed a TLR9 'scaffold' protective function that is ligand and MyD88 independent. Unexpectedly, Tlr9P915H mice were more protected than both Tlr9K51E and Tlr9WT mice, suggesting that TLR9 also possesses ligand-dependent, but MyD88-independent, regulatory signaling and MyD88-mediated proinflammatory signaling. Triple-mixed bone marrow chimeras showed that TLR9-MyD88-independent regulatory roles were B cell intrinsic and restrained differentiation into pathogenic age-associated B cells and plasmablasts. These studies reveal MyD88-independent regulatory roles of TLR9, shedding light on the biology of endosomal TLRs.
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11
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WhichTF is functionally important in your open chromatin data? PLoS Comput Biol 2022; 18:e1010378. [PMID: 36040971 PMCID: PMC9426921 DOI: 10.1371/journal.pcbi.1010378] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
We present WhichTF, a computational method to identify functionally important transcription factors (TFs) from chromatin accessibility measurements. To rank TFs, WhichTF applies an ontology-guided functional approach to compute novel enrichment by integrating accessibility measurements, high-confidence pre-computed conservation-aware TF binding sites, and putative gene-regulatory models. Comparison with prior sheer abundance-based methods reveals the unique ability of WhichTF to identify context-specific TFs with functional relevance, including NF-κB family members in lymphocytes and GATA factors in cardiac cells. To distinguish the transcriptional regulatory landscape in closely related samples, we apply differential analysis and demonstrate its utility in lymphocyte, mesoderm developmental, and disease cells. We find suggestive, under-characterized TFs, such as RUNX3 in mesoderm development and GLI1 in systemic lupus erythematosus. We also find TFs known for stress response, suggesting routine experimental caveats that warrant careful consideration. WhichTF yields biological insight into known and novel molecular mechanisms of TF-mediated transcriptional regulation in diverse contexts, including human and mouse cell types, cell fate trajectories, and disease-associated cells. Transcription factors (TFs), a class of DNA binding proteins, regulate tissue- and cell-type-specific expression of genes. Identifying the critical TFs in a given cellular context leads to investigating molecular regulatory mechanisms in development, differentiation, and disease. Because there are more than 1,500 human TFs, experimental measurements of genome-wide occupancy across all TFs have been challenging. While computational approaches play pivotal roles, most existing methods rely on statistical enrichment, focusing either on sequence motif similarity recognized by TFs or the similarity of the genomic region of interest with the previously characterized TF occupancy profile. Here we propose WhichTF as an alternative, incorporating curated biomedical knowledge from ontology and integrating it with the high-confidence prediction of conserved TF binding sites in user-provided genomic regions of interest. We develop a new WhichTF score to rank TFs and demonstrate its applicability across human and mouse cell types, cellular differentiation trajectories, and disease-associated cells.
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12
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Lewis EL, Xu R, Beltra JC, Ngiow SF, Cohen J, Telange R, Crane A, Sawinski D, Wherry EJ, Porrett PM. NFAT-dependent and -independent exhaustion circuits program maternal CD8 T cell hypofunction in pregnancy. J Exp Med 2022; 219:e20201599. [PMID: 34882194 PMCID: PMC8666877 DOI: 10.1084/jem.20201599] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/09/2021] [Accepted: 11/18/2021] [Indexed: 11/21/2022] Open
Abstract
Pregnancy is a common immunization event, but the molecular mechanisms and immunological consequences provoked by pregnancy remain largely unknown. We used mouse models and human transplant registry data to reveal that pregnancy induced exhausted CD8 T cells (Preg-TEX), which associated with prolonged allograft survival. Maternal CD8 T cells shared features of exhaustion with CD8 T cells from cancer and chronic infection, including transcriptional down-regulation of ribosomal proteins and up-regulation of TOX and inhibitory receptors. Similar to other models of T cell exhaustion, NFAT-dependent elements of the exhaustion program were induced by fetal antigen in pregnancy, whereas NFAT-independent elements did not require fetal antigen. Despite using conserved molecular circuitry, Preg-TEX cells differed from TEX cells in chronic viral infection with respect to magnitude and dependency of T cell hypofunction on NFAT-independent signals. Altogether, these data reveal the molecular mechanisms and clinical consequences of maternal CD8 T cell hypofunction and identify pregnancy as a previously unappreciated context in which T cell exhaustion may occur.
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Affiliation(s)
- Emma L. Lewis
- Department of Obstetrics and Gynecology, The University of Pennsylvania, Philadelphia, PA
| | - Rong Xu
- Department of Surgery, The University of Pennsylvania, Philadelphia, PA
| | - Jean-Christophe Beltra
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA
| | - Shin Foong Ngiow
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA
| | - Jordana Cohen
- Department of Medicine, The University of Pennsylvania, Philadelphia, PA
| | - Rahul Telange
- Department of Surgery, The University of Alabama at Birmingham, Birmingham, AL
| | - Alexander Crane
- Department of Surgery, The University of Pennsylvania, Philadelphia, PA
| | - Deirdre Sawinski
- Department of Medicine, The University of Pennsylvania, Philadelphia, PA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Parker Institute for Cancer Immunotherapy, University of Pennsylvania, Philadelphia, PA
| | - Paige M. Porrett
- Department of Surgery, The University of Pennsylvania, Philadelphia, PA
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA
- Department of Surgery, The University of Alabama at Birmingham, Birmingham, AL
- Comprehensive Transplant Institute, The University of Alabama at Birmingham, Birmingham, AL
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13
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Wen J, Lagler TM, Sun Q, Yang Y, Chen J, Harigaya Y, Sankaran VG, Hu M, Reiner AP, Raffield LM, Li Y. Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types. PLoS Genet 2022; 18:e1009984. [PMID: 35100265 PMCID: PMC8830683 DOI: 10.1371/journal.pgen.1009984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/10/2022] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Existing studies of chromatin conformation have primarily focused on potential enhancers interacting with gene promoters. By contrast, the interactivity of promoters per se, while equally critical to understanding transcriptional control, has been largely unexplored, particularly in a cell type-specific manner for blood lineage cell types. In this study, we leverage promoter capture Hi-C data across a compendium of blood lineage cell types to identify and characterize cell type-specific super-interactive promoters (SIPs). Notably, promoter-interacting regions (PIRs) of SIPs are more likely to overlap with cell type-specific ATAC-seq peaks and GWAS variants for relevant blood cell traits than PIRs of non-SIPs. Moreover, PIRs of cell-type-specific SIPs show enriched heritability of relevant blood cell trait (s), and are more enriched with GWAS variants associated with blood cell traits compared to PIRs of non-SIPs. Further, SIP genes tend to express at a higher level in the corresponding cell type. Importantly, SIP subnetworks incorporating cell-type-specific SIPs and ATAC-seq peaks help interpret GWAS variants. Examples include GWAS variants associated with platelet count near the megakaryocyte SIP gene EPHB3 and variants associated lymphocyte count near the native CD4 T-Cell SIP gene ETS1. Interestingly, around 25.7% ~ 39.6% blood cell traits GWAS variants residing in SIP PIR regions disrupt transcription factor binding motifs. Importantly, our analysis shows the potential of using promoter-centric analyses of chromatin spatial organization data to identify biologically important genes and their regulatory regions.
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Affiliation(s)
- Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Taylor M. Lagler
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yuchen Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yuriko Harigaya
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Vijay G. Sankaran
- Division of Hematology/Oncology, Boston Children’s Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard Stem Cell Institute, Cambridge, Massachusetts, United States of America
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yun Li
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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14
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Immunogenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:213-257. [DOI: 10.1007/978-3-030-92616-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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15
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Toll-like Receptor Signaling Inhibitory Peptide Improves Inflammation in Animal Model and Human Systemic Lupus Erythematosus. Int J Mol Sci 2021; 22:ijms222312764. [PMID: 34884569 PMCID: PMC8657918 DOI: 10.3390/ijms222312764] [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: 10/28/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/28/2022] Open
Abstract
Toll-like receptors (TLRs) play a major role in the innate immune system. Several studies have shown the regulatory effects of TLR-mediated pathways on immune and inflammatory diseases. Dysregulated functions of TLRs within the endosomal compartment, including TLR7/9 trafficking, may cause systemic lupus erythematosus (SLE). TLR signaling pathways are fine-tuned by Toll/interleukin-1 receptor (TIR) domain-containing adapters, leading to interferon (IFN)-α production. This study describes a TLR inhibitor peptide 1 (TIP1) that primarily suppresses the downstream signaling mediated by TIR domain-containing adapters in an animal model of lupus and patients with SLE. The expression of most downstream proteins of the TLR7/9/myeloid differentiation factor 88 (MyD88)/IFN regulatory factor 7 signaling was downregulated in major tissues such as the kidney, spleen, and lymph nodes of treated mice. Furthermore, the pathological analysis of the kidney tissue confirmed that TIP1 could improve inflammation in MRL/lpr mice. TIP1 treatment downregulated many downstream proteins associated with TLR signaling, such as MyD88, interleukin-1 receptor-associated kinase, tumor necrosis factor receptor-associated factor 6, and IFN-α, in the peripheral blood mononuclear cells of patients with SLE. In conclusion, our data suggest that TIP1 can serve as a potential candidate for the treatment of SLE.
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16
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Association of microRNA-34a rs2666433 (A/G) Variant with Systemic Lupus Erythematosus in Female Patients: A Case-Control Study. J Clin Med 2021; 10:jcm10215095. [PMID: 34768615 PMCID: PMC8584584 DOI: 10.3390/jcm10215095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 01/01/2023] Open
Abstract
Several microRNAs (miRNAs) are associated with autoimmune disease susceptibility and phenotype, including systemic lupus erythematosus (SLE). We aimed to explore for the first time the role of the miRNA-34a gene (MIR34A) rs2666433A > G variant in SLE risk and severity. A total of 163 adult patients with SLE and matched controls were recruited. Real-Time allelic discrimination PCR was applied for genotyping. Correlation with disease activity and clinic-laboratory data was done. The rs2666433 variant conferred protection against SLE development under heterozygous [A/G vs. G/G; OR = 0.57, 95%CI = 0.34-0.95], homozygous [A/A vs. G/G; OR = 0.52, 95%CI = 0.29-0.94], dominant [A/G + A/A vs. GG; OR = 0.55, 95%CI = 0.35-0.88], and log-additive [OR = 0.71, 95%CI = 0.53-0.95] models. Data stratification by sex revealed a significant association with SLE development in female participants under heterozygous/homozygous models (p-interaction = 0.004). There was no clear demarcation between SLE patients carrying different genotypes regarding the disease activity index or patients stratified according to lupus nephritis. Enrichment analysis confirmed the implication of MIR34A in the SLE pathway by targeting several genes related to SLE etiopathology. In conclusion, although the MIR34A rs2666433 variant conferred protection against developing SLE disease in the study population, it showed no association with disease activity. Replication studies in other populations are warranted.
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17
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Neefjes M, van Caam APM, van der Kraan PM. Transcription Factors in Cartilage Homeostasis and Osteoarthritis. BIOLOGY 2020; 9:biology9090290. [PMID: 32937960 PMCID: PMC7563835 DOI: 10.3390/biology9090290] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Osteoarthritis (OA) is the most common degenerative joint disease, and it is characterized by articular cartilage loss. In part, OA is caused by aberrant anabolic and catabolic activities of the chondrocyte, the only cell type present in cartilage. These chondrocyte activities depend on the intra- and extracellular signals that the cell receives and integrates into gene expression. The key proteins for this integration are transcription factors. A large number of transcription factors exist, and a better understanding of the transcription factors activated by the various signaling pathways active during OA can help us to better understand the complex etiology of OA. In addition, establishing such a profile can help to stratify patients in different subtypes, which can be a very useful approach towards personalized therapy. In this review, we discuss crucial transcription factors for extracellular matrix metabolism, chondrocyte hypertrophy, chondrocyte senescence, and autophagy in chondrocytes. In addition, we discuss how insight into these factors can be used for treatment purposes.
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18
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Mirlekar B. Co-expression of master transcription factors determines CD4 + T cell plasticity and functions in auto-inflammatory diseases. Immunol Lett 2020; 222:58-66. [PMID: 32220615 DOI: 10.1016/j.imlet.2020.03.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/05/2020] [Accepted: 03/18/2020] [Indexed: 02/08/2023]
Abstract
Master CD4+ T cell lineage determined transcription factors are found to be dysregulated in pathogenesis of autoimmune and inflammatory diseases. CD4+ T cells categorized into different lineages based on their functions, cell surface markers and master transcription factors those required for expression of lineage specific cytokines. T-bet, GATA3, RORγt and Foxp3 are major transcription regulators of Th1, Th2, Th17 and Treg cells respectively. Significant progress has been made in understanding expression of lineage specific master regulators that drives CD4+ T cell differentiation. It is known that each CD4+ T cell lineage express precise determined transcription factor and due to cross regulation between these factors the CD4+ T cells able to maintain thier specific phenotype. However, recent studies shows that the lineage specifying transcription factors frequently co-expressed. There is an emerging area of research revealing that the co-expression of lineage-specifying transcription factors alters the potential function and flexibility of subsets of CD4+ T cell, this in turn favors the autoimmune pathology. Here, we discuss similarities and differences between mutually co-expressed transcription factors in CD4+ T cell subsets and then recapitulates on cell type specific and dynamic balance between the lineage restricted transcription factors in determining plasticity of CD4+ T cell subsets. Furthermore, we discuss abnormal regulation of such transcription factors that establishes a pathogenic CD4+ T cell phenotype in autoimmune diseases and how this understanding will provide further insight into potential therapeutic development.
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Affiliation(s)
- Bhalchandra Mirlekar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, NC, 27514, USA.
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19
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Weinstein N, Mendoza L, Álvarez-Buylla ER. A Computational Model of the Endothelial to Mesenchymal Transition. Front Genet 2020; 11:40. [PMID: 32226439 PMCID: PMC7080988 DOI: 10.3389/fgene.2020.00040] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/14/2020] [Indexed: 12/13/2022] Open
Abstract
Endothelial cells (ECs) form the lining of lymph and blood vessels. Changes in tissue requirements or wounds may cause ECs to behave as tip or stalk cells. Alternatively, they may differentiate into mesenchymal cells (MCs). These processes are known as EC activation and endothelial-to-mesenchymal transition (EndMT), respectively. EndMT, Tip, and Stalk EC behaviors all require SNAI1, SNAI2, and Matrix metallopeptidase (MMP) function. However, only EndMT inhibits the expression of VE-cadherin, PECAM1, and VEGFR2, and also leads to EC detachment. Physiologically, EndMT is involved in heart valve development, while a defective EndMT regulation is involved in the physiopathology of cardiovascular malformations, congenital heart disease, systemic and organ fibrosis, pulmonary arterial hypertension, and atherosclerosis. Therefore, the control of EndMT has many promising potential applications in regenerative medicine. Despite the fact that many molecular components involved in EC activation and EndMT have been characterized, the system-level molecular mechanisms involved in this process have not been elucidated. Toward this end, hereby we present Boolean network model of the molecular involved in the regulation of EC activation and EndMT. The simulated dynamic behavior of our model reaches fixed and cyclic patterns of activation that correspond to the expected EC and MC cell types and behaviors, recovering most of the specific effects of simple gain and loss-of-function mutations as well as the conditions associated with the progression of several diseases. Therefore, our model constitutes a theoretical framework that can be used to generate hypotheses and guide experimental inquiry to comprehend the regulatory mechanisms behind EndMT. Our main findings include that both the extracellular microevironment and the pattern of molecular activity within the cell regulate EndMT. EndMT requires a lack of VEGFA and sufficient oxygen in the extracellular microenvironment as well as no FLI1 and GATA2 activity within the cell. Additionally Tip cells cannot undergo EndMT directly. Furthermore, the specific conditions that are sufficient to trigger EndMT depend on the specific pattern of molecular activation within the cell.
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Affiliation(s)
- Nathan Weinstein
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis Mendoza
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Elena R Álvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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20
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Xu C, Liu Q, Zhou J, Xie M, Feng J, Jiang T. Quantifying functional impact of non-coding variants with multi-task Bayesian neural network. Bioinformatics 2020; 36:1397-1404. [PMID: 31693090 DOI: 10.1093/bioinformatics/btz767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Advances in high-throughput genotyping and sequencing technologies during recent years have revealed essential roles of non-coding regions in gene regulation. Genome-wide association studies (GWAS) suggested that a large proportion of risk variants are located in non-coding regions and remain unexplained by current expression quantitative trait loci catalogs. Interpreting the causal effects of these genetic modifications is crucial but difficult owing to our limited knowledge of how regulatory elements function. Although several computational methods have been designed to prioritize regulatory variants that substantially impact human phenotypes, few of them achieve consistently high performance even when large-scale multi-omic data are integrated. RESULTS We propose a novel multi-task framework based on Bayesian deep neural networks, MtBNN, to quantify the deleterious impact of single nucleotide polymorphisms in non-coding genomic regions. With the high-efficiency provided by the multi-task Bayesian framework to integrate information from different sources, MtBNN is capable of extracting features from genomic sequences of large-scale chromatin-profiling data, such as chromatin accessibility and transcript factor binding affinities, and calculating the distribution of the probability that a non-coding variant disrupts regulatory activities. A series of comprehensive experiments show that MtBNN quantifies the functional impact of cis-regulatory variations with high accuracy, including expression quantitative trait locus, DNase I sensitivity quantitative trait locus and functional genetic variants located within ATAC-peaks that affect the accessibility of the corresponding peak and achieves significantly better performance than the existing methods. Moreover, MtBNN has applications in the discovery of potentially causal disease-associated single-nucleotide polymorphisms (SNPs), thus helping fine-map the GWAS SNPs. AVAILABILITY AND IMPLEMENTATION Code can be downloaded from https://github.com/Zoesgithub/MtBNN. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chencheng Xu
- Bioinformatics Division, BNRIST.,Department of Computer Science and Technology
| | - Qiao Liu
- Bioinformatics Division, BNRIST.,Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jianyu Zhou
- Bioinformatics Division, BNRIST.,Department of Computer Science and Technology
| | - Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, Changsha 410081, China
| | | | - Tao Jiang
- Bioinformatics Division, BNRIST.,Department of Computer Science and Technology.,Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
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21
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Cho J, Lahiri M, Teoh LK, Dhanasekaran P, Cheung PP, Lateef A. Predicting flares in patients with stable systemic lupus erythematosus. Semin Arthritis Rheum 2019; 49:91-97. [PMID: 30660381 DOI: 10.1016/j.semarthrit.2019.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/12/2018] [Accepted: 01/02/2019] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Data on flares in Asian patients with systemic lupus erythematosus (SLE) are scarce. Here, we aim to identify the baseline predictors of flares in a cohort of Southeast Asian patients with SLE. METHODS Consecutive adult patients with prevalent SLE according to the 1997 ACR or 2012 SLICC criteria were enrolled and followed three-monthly. Clinical and laboratory data were collected at every visit using a standardised protocol. Flares were defined using the SELENA-SLEDAI Flare Index (SFI). Baseline predictors of flare in patients with stable disease (SLE Disease Activity Index-2K (SLEDAI-2K) of ≤ 4) were determined using Cox proportional hazards. RESULTS Of the 210 patients recruited, 148 (70.5%) were Chinese. The median (IQR) SLEDAI-2K at entry was 2 (0-4) and the median (IQR) disease duration was 10 (4.4-16.4) years. At baseline, 152 (72.4%) patients had stable disease. After a median (IQR) follow-up of 31.5 (24.1-36.3) months, 109 (51.9%) flared. Stable patients who flared tended to be in the lowest tertile of age (HR 3.08, 95% CI 1.72-5.48, p < 0.01), had thrombocytopenia (HR 5.01, 95% CI 1.32-18.99, p = 0.02), hypocomplementemia (HR 3.35, 95% CI 1.54-7.30, p < 0.01) and had the highest baseline prednisolone doses (HR 2.39, 95% CI 1.28-4.46, p = 0.01). Conversely, patients in the lowest tertile of disease duration tended not to flare (HR 0.41, 95% CI 0.21-0.80, p = 0.01). CONCLUSION Flares are common in Asian SLE patients with initial stable disease. Close monitoring is needed for patients who are younger, with longer disease duration, thrombocytopenia, hypocomplementemia, or who required a higher baseline prednisolone dose.
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Affiliation(s)
- Jiacai Cho
- Division of Rheumatology, Department of Medicine, National University Hospital of Singapore, Level 10, NUHS Tower Block, 1E Kent Ridge Road, 119228, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Manjari Lahiri
- Division of Rheumatology, Department of Medicine, National University Hospital of Singapore, Level 10, NUHS Tower Block, 1E Kent Ridge Road, 119228, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lay Kheng Teoh
- Division of Rheumatology, Department of Medicine, National University Hospital of Singapore, Level 10, NUHS Tower Block, 1E Kent Ridge Road, 119228, Singapore
| | - Preeti Dhanasekaran
- Division of Rheumatology, Department of Medicine, National University Hospital of Singapore, Level 10, NUHS Tower Block, 1E Kent Ridge Road, 119228, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Peter P Cheung
- Division of Rheumatology, Department of Medicine, National University Hospital of Singapore, Level 10, NUHS Tower Block, 1E Kent Ridge Road, 119228, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Aisha Lateef
- Division of Rheumatology, Department of Medicine, National University Hospital of Singapore, Level 10, NUHS Tower Block, 1E Kent Ridge Road, 119228, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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22
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Sunshine A, Goich D, Stith A, Sortino K, Dalton J, Metcalfe S, Svensson EC, Garrett-Sinha LA. Ets1 Controls the Development of B Cell Autoimmune Responses in a Cell-Intrinsic Manner. Immunohorizons 2019; 3:331-340. [PMID: 31356162 PMCID: PMC7008956 DOI: 10.4049/immunohorizons.1900033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/27/2019] [Indexed: 12/18/2022] Open
Abstract
Ets1 is emerging as a key transcription factor that is required to prevent autoimmunity in mice and humans. Ets1 is expressed in both B and T cells, and mice lacking Ets1 are characterized by excess B and T cell activation, leading to enhanced formation of Ab-secreting cells and high titers of autoantibodies. In humans, genome-wide association studies have detected associations of single nucleotide polymorphisms in the human ETS1 gene with autoimmune diseases, including lupus. An increased fraction of CD4+ T cells from Ets1−/− mice have an activated effector-memory phenotype, and there are aberrations in differentiation that contribute to the autoimmune phenotype. In vitro studies of B cells suggest that Ets1 may have B cell–intrinsic effects as well. To confirm B cell–intrinsic roles for Ets1, we crossed CD19-Cre mice to mice with a floxed allele of Ets1. Mice with a B cell–specific deletion of Ets1 show increases in B cell activation, numbers of Ab-secreting cells, and levels of autoantibodies, despite the fact that T cells are normal. However, when compared with conventional Ets1 knockout mice, mice with B cell–specific loss of Ets1 have a significantly milder phenotype. These results demonstrate that Ets1 is required in B cells to prevent autoimmune responses but that loss of Ets1 activity in other cell types is required for maximal autoimmune phenotypes.
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Affiliation(s)
- Alex Sunshine
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
| | - David Goich
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
| | - Alifa Stith
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
| | - Katherine Sortino
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
| | - Justin Dalton
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
| | - Sarah Metcalfe
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
| | - Eric C Svensson
- Division of Cardiology, Department of Medicine, University of Chicago, Chicago, IL 60637
| | - Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203; and
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23
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Zhang R, Pan B, Li Y, Li X. SNP rs4937333 in the miRNA-5003-Binding Site of the ETS1 3'-UTR Decreases ETS1 Expression. Front Genet 2019; 10:581. [PMID: 31275358 PMCID: PMC6593064 DOI: 10.3389/fgene.2019.00581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in and reduced expression of the ETS1 gene may be associated with systemic lupus erythematosus (SLE). Here, we report a replication study to investigate associations of eight ETS1 single-nucleotide polymorphisms in the 3′-untranslated region (3′-UTR) with SLE and their regulation of ETS1 expression in a study population. We found that the rs4937333 T allele was associated with a significantly increased risk of SLE (odds ratio: 1.800, 95% confidence interval: 1.02–3.157, P = 0.040) and with dramatically reduced levels of ETS1 in B cells from SLE subjects. Functionally, the rs4937333 T allele alters the binding affinity between miR-5003 and its ETS1 3′-UTR target, thus enhancing suppression of ETS1 expression. Furthermore, immunoglobulin M-secreting plasmacytes were significantly reduced among B cells with the rs4937333 C allele versus the T allele according to FACS and ELISA. Additionally, miR-5003 expression was higher in B cells than in T cells from SLE patients, and a negative correlation between miR-5003 and ETS1 was found, especially in B cells with the T allele. These findings suggest that the rs4937333 T allele is a risk factor for susceptibility to SLE in the studied population. The rs4937333 T allele may enhance the binding of miR-5003 to ETS1, which probably promotes the involvement of ETS1 in the differentiation of B cells into plasmacytes.
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Affiliation(s)
- Ruixian Zhang
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Bangpin Pan
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yi Li
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolan Li
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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24
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Jenks SA, Cashman KS, Woodruff MC, Lee FEH, Sanz I. Extrafollicular responses in humans and SLE. Immunol Rev 2019; 288:136-148. [PMID: 30874345 PMCID: PMC6422038 DOI: 10.1111/imr.12741] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022]
Abstract
Chronic autoimmune diseases, and in particular Systemic Lupus Erythematosus (SLE), are endowed with a long-standing autoreactive B-cell compartment that is presumed to reactivate periodically leading to the generation of new bursts of pathogenic antibody-secreting cells (ASC). Moreover, pathogenic autoantibodies are typically characterized by a high load of somatic hypermutation and in some cases are highly stable even in the context of prolonged B-cell depletion. Long-lived, highly mutated antibodies are typically generated through T-cell-dependent germinal center (GC) reactions. Accordingly, an important role for GC reactions in the generation of pathogenic autoreactivity has been postulated in SLE. Nevertheless, pathogenic autoantibodies and autoimmune disease can be generated through B-cell extrafollicular (EF) reactions in multiple mouse models and human SLE flares are characterized by the expansion of naive-derived activated effector B cells of extrafollicular phenotype. In this review, we will discuss the properties of the EF B-cell pathway, its relationship to other effector B-cell populations, its role in autoimmune diseases, and its contribution to human SLE. Furthermore, we discuss the relationship of EF B cells with Age-Associated B cells (ABCs), a TLR-7-driven B-cell population that mediates murine autoimmune and antiviral responses.
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Affiliation(s)
- Scott A. Jenks
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Kevin S. Cashman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Matthew C. Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - F. Eun-Hyung Lee
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care, Emory University, Atlanta, Georgia, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
- Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
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25
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Weeding E, Coit P, Yalavarthi S, Kaplan MJ, Knight JS, Sawalha AH. Genome-wide DNA methylation analysis in primary antiphospholipid syndrome neutrophils. Clin Immunol 2018; 196:110-116. [PMID: 30471352 DOI: 10.1016/j.clim.2018.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023]
Abstract
Antiphospholipid syndrome (APS) is a systemic autoimmune disease characterized by thromboembolic events and pregnancy loss. We sought to characterize the DNA methylation profile of primary APS in comparison to healthy controls and individuals with SLE. In primary APS neutrophils compared to controls, 17 hypomethylated and 25 hypermethylated CpG sites were identified. Notable hypomethylated genes included ETS1, a genetic risk locus for SLE, and PTPN2, a genetic risk locus for other autoimmune diseases. Gene ontology analysis of hypomethylated genes revealed enrichment of genes involved in pregnancy. None of the differentially methylated sites in primary APS were differentially methylated in SLE neutrophils, and there was no demethylation of interferon signature genes in primary APS as is seen in SLE. Hypomethylation within a single probe in the IFI44L promoter (cg06872964) was able to distinguish SLE from primary APS with a sensitivity of 93.3% and specificity of 80.0% at a methylation fraction of 0.329.
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Affiliation(s)
- Emma Weeding
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Srilakshmi Yalavarthi
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Jason S Knight
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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26
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De Smit E, Lukowski SW, Anderson L, Senabouth A, Dauyey K, Song S, Wyse B, Wheeler L, Chen CY, Cao K, Wong Ten Yuen A, Shuey N, Clarke L, Lopez Sanchez I, Hung SSC, Pébay A, Mackey DA, Brown MA, Hewitt AW, Powell JE. Longitudinal expression profiling of CD4+ and CD8+ cells in patients with active to quiescent giant cell arteritis. BMC Med Genomics 2018; 11:61. [PMID: 30037347 PMCID: PMC6057030 DOI: 10.1186/s12920-018-0376-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022] Open
Abstract
Background Giant cell arteritis (GCA) is the most common form of vasculitis affecting elderly people. It is one of the few true ophthalmic emergencies but symptoms and signs are variable thereby making it a challenging disease to diagnose. A temporal artery biopsy is the gold standard to confirm GCA, but there are currently no specific biochemical markers to aid diagnosis. We aimed to identify a less invasive method to confirm the diagnosis of GCA, as well as to ascertain clinically relevant predictive biomarkers by studying the transcriptome of purified peripheral CD4+ and CD8+ T lymphocytes in patients with GCA. Methods We recruited 16 patients with histological evidence of GCA at the Royal Victorian Eye and Ear Hospital, Melbourne, Australia, and aimed to collect blood samples at six time points: acute phase, 2–3 weeks, 6–8 weeks, 3 months, 6 months and 12 months after clinical diagnosis. CD4+ and CD8+ T-cells were positively selected at each time point through magnetic-assisted cell sorting. RNA was extracted from all 195 collected samples for subsequent RNA sequencing. The expression profiles of patients were compared to those of 16 age-matched controls. Results Over the 12-month study period, polynomial modelling analyses identified 179 and 4 statistically significant transcripts with altered expression profiles (FDR < 0.05) between cases and controls in CD4+ and CD8+ populations, respectively. In CD8+ cells, two transcripts remained differentially expressed after 12 months; SGTB, associated with neuronal apoptosis, and FCGR3A, associatied with Takayasu arteritis. We detected genes that correlate with both symptoms and biochemical markers used for predicting long-term prognosis. 15 genes were shared across 3 phenotypes in CD4 and 16 across CD8 cells. In CD8, IL32 was common to 5 phenotypes including Polymyalgia Rheumatica, bilateral blindness and death within 12 months. Conclusions This is the first longitudinal gene expression study undertaken to identify robust transcriptomic biomarkers of GCA. Our results show cell type-specific transcript expression profiles, novel gene-phenotype associations, and uncover important biological pathways for this disease. In the acute phase, the gene-phenotype relationships we have identified could provide insight to potential disease severity and as such guide in initiating appropriate patient management. Electronic supplementary material The online version of this article (10.1186/s12920-018-0376-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisabeth De Smit
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia.
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Lisa Anderson
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Anne Senabouth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Kaisar Dauyey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
| | - Sharon Song
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Bruce Wyse
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Lawrie Wheeler
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Christine Y Chen
- Ophthalmology Department at Monash Health, Department of Surgery, School of Clinical Sciences at Monash Health, Melbourne, 3168, Victoria, Australia
| | - Khoa Cao
- Ophthalmology Department at Monash Health, Department of Surgery, School of Clinical Sciences at Monash Health, Melbourne, 3168, Victoria, Australia
| | - Amy Wong Ten Yuen
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Neil Shuey
- Department of Neuro-Ophthalmology, Royal Victorian Eye and Ear Hospital, Melbourne, 3002, Victoria, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Isabel Lopez Sanchez
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Sandy S C Hung
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Lions Eye Institute, Perth, 6009, Western Australia, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, 4102, Queensland, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, The University of Melbourne, Royal Victorian Eye & Ear Hospital, 32 Gisborne Street, East Melbourne, 3002, Australia.,School of Medicine, Menzies Research Institute Tasmania, University of Tasmania, Hobart, 7000, Tasmania, Australia
| | - Joseph E Powell
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4072, Queensland, Australia
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27
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Zhang Z, Shi L, Song L, Maurer K, Petri MA, Sullivan KE. Overall Downregulation of mRNAs and Enrichment of H3K4me3 Change Near Genome-Wide Association Study Signals in Systemic Lupus Erythematosus: Cell-Specific Effects. Front Immunol 2018; 9:497. [PMID: 29593737 PMCID: PMC5859352 DOI: 10.3389/fimmu.2018.00497] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/26/2018] [Indexed: 01/09/2023] Open
Abstract
This study was designed to define gene expression and H3K4me3 histone modifications in T cells, B cells, and monocytes in systemic lupus erythematosus (SLE). Array studies of total peripheral blood mononuclear cells have demonstrated gene expression signatures related to neutrophils, interferon, and other inflammatory pathways. It is not clear how consistent these effects are across different cell types. In this study, RNA-seq and chromatin immunoprecipitation-seq were utilized to identify gene expression patterns and H3K4me3 histone modifications related to promoter activation in SLE. Across the three cell types, there was 55% concordance for gene expression changes related to SLE. Key conserved pathways were ribosome biogenesis among upregulated genes and heat shock response among downregulated genes. ETS family transcription factors (TFs) and STAT1 were revealed as common regulators by position weight matrices. When epigenetic changes were leveraged with gene expression, the pivotal TFs ATF3 and FOS were defined with ATF3 also cross-referencing with gene expression-identified TFs. Genome-wide association study (GWAS) single nucleotide polymorphisms associated with SLE were cross-referenced with both mRNA and H3K4me3 changes in SLE. Baseline mRNA expression and H3K4me3 peak height was higher at sites that cross-referenced with GWAS signals, however, all three cell types exhibited an overall decrease in expression of GWAS-associated RNAs differentially expressed in SLE. H3K4me3 changes in SLE were also enriched in GWAS-associated sites. In summary, the SLE disease process is associated with both shared and cell-specific changes in gene expression and epigenetics. Surprisingly, GWAS-associated RNAs were overall markedly decreased across all three cell types. TF analysis identified ATF3, FOS, STAT1, and ETS family members as critical, all pathways with a recognized relationship to the SLE disease process. GWAS signals clearly mark both cell-type specific changes in SLE as well as concordant changes across all three cell types. Interpretation of single nucleotide polymorphism effects in SLE will require tissue-specific mechanistic studies and therapeutics will require mechanistic studies in multiple cell types.
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Affiliation(s)
- Zhe Zhang
- The Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Lihua Shi
- The Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Li Song
- The Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Kelly Maurer
- The Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Michele A Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kathleen E Sullivan
- The Division of Allergy Immunology, The Children's Hospital of Philadelphia, Philadelphia, PA, United States
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28
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Satterthwaite AB. Bruton's Tyrosine Kinase, a Component of B Cell Signaling Pathways, Has Multiple Roles in the Pathogenesis of Lupus. Front Immunol 2018; 8:1986. [PMID: 29403475 PMCID: PMC5786522 DOI: 10.3389/fimmu.2017.01986] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/21/2017] [Indexed: 01/08/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by the loss of adaptive immune tolerance to nucleic acid-containing antigens. The resulting autoantibodies form immune complexes that promote inflammation and tissue damage. Defining the signals that drive pathogenic autoantibody production is an important step in the development of more targeted therapeutic approaches for lupus, which is currently treated primarily with non-specific immunosuppression. Here, we review the contribution of Bruton’s tyrosine kinase (Btk), a component of B and myeloid cell signaling pathways, to disease in murine lupus models. Both gain- and loss-of-function genetic studies have revealed that Btk plays multiple roles in the production of autoantibodies. These include promoting the activation, plasma cell differentiation, and class switching of autoreactive B cells. Small molecule inhibitors of Btk are effective at reducing autoantibody levels, B cell activation, and kidney damage in several lupus models. These studies suggest that Btk may promote end-organ damage both by facilitating the production of autoantibodies and by mediating the inflammatory response of myeloid cells to these immune complexes. While Btk has not been associated with SLE in GWAS studies, SLE B cells display signaling defects in components both upstream and downstream of Btk consistent with enhanced activation of Btk signaling pathways. Taken together, these observations indicate that limiting Btk activity is critical for maintaining B cell tolerance and preventing the development of autoimmune disease. Btk inhibitors, generally well-tolerated and approved to treat B cell malignancy, may thus be a useful therapeutic approach for SLE.
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Affiliation(s)
- Anne B Satterthwaite
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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