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Kotliar M, Kartashov A, Barski A. Accelerating Single-Cell Sequencing Data Analysis with SciDAP: A User-Friendly Approach. bioRxiv 2024:2024.02.28.582604. [PMID: 38464095 PMCID: PMC10925325 DOI: 10.1101/2024.02.28.582604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Single-cell (sc) RNA, ATAC and Multiome sequencing became powerful tools for uncovering biological and disease mechanisms. Unfortunately, manual analysis of sc data presents multiple challenges due to large data volumes and complexity of configuration parameters. This complexity, as well as not being able to reproduce a computational environment, affects the reproducibility of analysis results. The Scientific Data Analysis Platform (https://SciDAP.com) allows biologists without computational expertise to analyze sequencing-based data using portable and reproducible pipelines written in Common Workflow Language (CWL). Our suite of computational pipelines addresses the most common needs in scRNA-Seq, scATAC-Seq and scMultiome data analysis. When executed on SciDAP, it offers a user-friendly alternative to manual data processing, eliminating the need for coding expertise. In this protocol, we describe the use of SciDAP to analyze scMultiome data. Similar approaches can be used for analysis of scRNA-Seq, scATAC-Seq and scVDJ-Seq datasets.
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Affiliation(s)
- Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | | | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
- Datirium, LLC, Cincinnati, OH, USA
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2
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Proper SP, Dwyer AT, Appiagyei A, Felton JM, Ben-Baruch Morgenstern N, Marlman JM, Kotliar M, Barski A, Troutman TD, Rothenberg ME, Mersha TB, Azouz NP. Aryl hydrocarbon receptor and IL-13 signaling crosstalk in human keratinocytes and atopic dermatitis. Front Allergy 2024; 5:1323405. [PMID: 38344408 PMCID: PMC10853333 DOI: 10.3389/falgy.2024.1323405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/10/2024] [Indexed: 02/28/2024] Open
Abstract
Introduction Atopic dermatitis (AD) is an allergic skin disease mediated by skin barrier impairment and IL-13-driven immune response. Activation of the aryl hydrocarbon receptor (AHR) has shown promise in early clinical trials for AD; however, the mechanism by which AHR partially ameliorates AD is not well known. Methods Gene expression data from human biopsies were analyzed, and compared to gene expression from RNA-sequencing in our in-vitro HaCaT cell model system. Western blot, ELISA qRT-PCR were used to further explore the relationship between AHR and IL-13 signaling in HaCaT cells. Results The AHR target gene CYP1A1 was decreased in lesional skin compared with healthy control skin (p = 4.30 × 10-9). Single-cell RNA sequencing (scRNAseq) demonstrated increased AHR expression (p < 1.0 × 10-4) and decreased CYP1A1 expression in lesional AD keratinocytes compared with healthy control keratinocytes (p < 0.001). Activation of AHR by AHR agonists in HaCaT cells reversed IL-13-dependent gene expression of several key genes in AD pathogenesis, most notably the eosinophil chemoattractant CCL26 (eotaxin-3). Differentially expressed genes in keratinocytes of patients with AD substantially overlapped with genes regulated by AHR agonists from HaCaT cells by RNAseq, but in reverse direction. Mechanistically, there was evidence for direct transcriptional effects of AHR; AHR binding motifs were identified in the differentially expressed genes from lesional AD keratinocytes compared to control keratinocytes, and AHR activation did not modify IL-13-dependent signal transducer and activator of transcription 6 (STAT6) translocation to the nucleus. Discussion Together, these data suggest that the AHR pathway is dysregulated in AD and that AHR modulates IL-13 downstream signaling in keratinocytes through genome-wide, transcriptional regulatory effects.
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Affiliation(s)
- Steven P Proper
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Alexander T Dwyer
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Andrews Appiagyei
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Jennifer M Felton
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | | | - Justin M Marlman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Ty D Troutman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Tesfaye B Mersha
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Nurit P Azouz
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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Brown AP, Parameswaran S, Cai L, Elston S, Pham C, Barski A, Weirauch MT, Ji H. TET1 regulates responses to house dust mite by altering chromatin accessibility, DNA methylation, and gene expression in airway epithelial cells. Res Sq 2023:rs.3.rs-3726852. [PMID: 38168374 PMCID: PMC10760239 DOI: 10.21203/rs.3.rs-3726852/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Previous studies have identified TET1 as a potential key regulator of genes linked to asthma. TET1 has been shown to transcriptionally respond to house dust mite extract, an allergen known to directly cause allergic asthma development, and regulate the expression of genes involved in asthma. How TET1 regulates expression of these genes, however, is unknown. TET1 is a DNA demethylase; therefore, most prior research on TET1-based gene regulation has focused on how TET1 affects methylation. However, TET1 can also interact directly with transcription factors and histone modifiers to regulate gene expression. Understanding how TET1 regulates expression to contribute to allergic responses and asthma development thus requires a comprehensive approach. To this end, we measured mRNA expression, DNA methylation, chromatin accessibility and histone modifications in control and TET1 knockdown human bronchial epithelial cells treated or untreated with house dust mite extract. Results Throughout our analyses, we detected strong similarities between the effects of TET1 knockdown alone and the effects of HDM treatment alone. One especially striking pattern was that both TET1 knockdown and HDM treatment generally led to decreased chromatin accessibility at largely the same genomic loci. Transcription factor enrichment analyses indicated that altered chromatin accessibility following the loss of TET1 may affect, or be affected by, CTCF and CEBP binding. TET1 loss also led to changes in DNA methylation, but these changes were generally in regions where accessibility was not changing. Conclusions TET1 regulates gene expression through different mechanisms (DNA methylation and chromatin accessibility) in different parts of the genome in the airway epithelial cells, which mediates inflammatory responses to allergen. Collectively, our data suggest novel molecular mechanisms through which TET1 regulates critical pathways following allergen challenges and contributes to the development of asthma.
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Affiliation(s)
| | | | | | | | | | | | | | - Hong Ji
- University of California Davis
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Rochman Y, Kotliar M, Ben-Baruch Morgenstern N, Barski A, Wen T, Rothenberg ME. TSLP shapes the pathogenic responses of memory CD4 + T cells in eosinophilic esophagitis. Sci Signal 2023; 16:eadg6360. [PMID: 37699081 PMCID: PMC10602003 DOI: 10.1126/scisignal.adg6360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Abstract
The cytokine thymic stromal lymphopoietin (TSLP) mediates type 2 immune responses, and treatments that interfere with TSLP activity are in clinical use for asthma. Here, we investigated whether TSLP contributes to allergic inflammation by directly stimulating human CD4+ T cells and whether this process is operational in eosinophilic esophagitis (EoE), a disease linked to variants in TSLP. We showed that about 10% of esophageal-derived memory CD4+ T cells from individuals with EoE and less than 3% of cells from control individuals expressed the receptor for TSLP and directly responded to TSLP, as determined by measuring the phosphorylation of STAT5, a transcription factor activated downstream of TSLP stimulation. Accordingly, increased numbers of TSLP-responsive memory CD4+ T cells were present in the circulation of individuals with EoE. TSLP increased the proliferation of CD4+ T cells, enhanced type 2 cytokine production, induced the increased abundance of its own receptor, and modified the expression of 212 genes. The epigenetic response to TSLP was associated with an enrichment in BATF and IRF4 chromatin-binding sites, and these transcription factors were induced by TSLP, providing a feed-forward loop. The numbers of circulating and esophageal CD4+ T cells responsive to TSLP correlated with the numbers of esophageal eosinophils, supporting a potential functional role for TSLP in driving the pathogenesis of EoE and providing the basis for a blood-based diagnostic test based on the extent of TSLP-induced STAT5 phosphorylation in circulating CD4+ T cells. These findings highlight the potential therapeutic value of TSLP inhibitors for the treatment of EoE.
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Affiliation(s)
- Yrina Rochman
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Netali Ben-Baruch Morgenstern
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
- Division of Human Genetics, Department of Pediatrics Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Marc E. Rothenberg
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
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5
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Maezawa S, Yukawa M, Hasegawa K, Sugiyama R, Iizuka M, Hu M, Sakashita A, Vidal M, Koseki H, Barski A, DeFalco T, Namekawa SH. PRC1 suppresses a female gene regulatory network to ensure testicular differentiation. Cell Death Dis 2023; 14:501. [PMID: 37542070 PMCID: PMC10403552 DOI: 10.1038/s41419-023-05996-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/27/2023] [Accepted: 07/13/2023] [Indexed: 08/06/2023]
Abstract
Gonadal sex determination and differentiation are controlled by somatic support cells of testes (Sertoli cells) and ovaries (granulosa cells). In testes, the epigenetic mechanism that maintains chromatin states responsible for suppressing female sexual differentiation remains unclear. Here, we show that Polycomb repressive complex 1 (PRC1) suppresses a female gene regulatory network in postnatal Sertoli cells. We genetically disrupted PRC1 function in embryonic Sertoli cells after sex determination, and we found that PRC1-depleted postnatal Sertoli cells exhibited defective proliferation and cell death, leading to the degeneration of adult testes. In adult Sertoli cells, PRC1 suppressed specific genes required for granulosa cells, thereby inactivating the female gene regulatory network. Chromatin regions associated with female-specific genes were marked by Polycomb-mediated repressive modifications: PRC1-mediated H2AK119ub and PRC2-mediated H3K27me3. Taken together, this study identifies a critical Polycomb-based mechanism that suppresses ovarian differentiation and maintains Sertoli cell fate in adult testes.
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Affiliation(s)
- So Maezawa
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, 252-5201, Japan.
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, 278-8510, Japan.
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Sha Tin, New Territories, Hong Kong
| | - Kazuteru Hasegawa
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Ryo Sugiyama
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Mizuho Iizuka
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Mengwen Hu
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA
| | - Akihiko Sakashita
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Department of Molecular Biology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Miguel Vidal
- Centro de Investigaciones Biológicas Margarita Salas, Department of Cellular and Molecular Biology, Madrid, 28040, Spain
| | - Haruhiko Koseki
- Developmental Genetics Laboratory, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tony DeFalco
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Satoshi H Namekawa
- Reproductive Sciences Center, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA, 95616, USA.
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6
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Stefan K, Barski A. Cis-regulatory atlas of primary human CD4+ T cells. BMC Genomics 2023; 24:253. [PMID: 37170195 PMCID: PMC10173520 DOI: 10.1186/s12864-023-09288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome-wide annotation of functional CREs. Despite this, STARR-Seq assays are only employed in cell lines, in part, due to difficulties in delivering reporter constructs. Herein, we implemented and validated a STARR-Seq-based screen in human CD4+ T cells using a non-integrating lentiviral transduction system. Lenti-STARR-Seq is the first example of a genome-wide assay of CRE function in human primary cells, identifying thousands of functional enhancers and negative regulatory elements (NREs) in human CD4+ T cells. We find an unexpected difference in nucleosome organization between enhancers and NRE: enhancers are located between nucleosomes, whereas NRE are occupied by nucleosomes in their endogenous locations. We also describe chromatin modification, eRNA production, and transcription factor binding at both enhancers and NREs. Our findings support the idea of silencer repurposing as enhancers in alternate cell types. Collectively, these data suggest that Lenti-STARR-Seq is a successful approach for CRE screening in primary human cell types, and provides an atlas of functional CREs in human CD4+ T cells.
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Affiliation(s)
- Kurtis Stefan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA
- Medical Scientist Training Program (MSTP), University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3026, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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7
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Brusilovsky M, Rochman M, Shoda T, Kotliar M, Caldwell JM, Mack LE, Besse JA, Chen X, Weirauch MT, Barski A, Rothenberg ME. Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling. Gut 2023; 72:834-845. [PMID: 35918104 PMCID: PMC9892355 DOI: 10.1136/gutjnl-2022-327276] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The contribution of vitamin D (VD) deficiency to the pathogenesis of allergic diseases remains elusive. We aimed to define the impact of VD on oesophageal allergic inflammation. DESIGN We assessed the genomic distribution and function of VD receptor (VDR) and STAT6 using histology, molecular imaging, motif discovery and metagenomic analysis. We examined the role of VD supplementation in oesophageal epithelial cells, in a preclinical model of IL-13-induced oesophageal allergic inflammation and in human subjects with eosinophilic oesophagitis (EoE). RESULTS VDR response elements were enriched in oesophageal epithelium, suggesting enhanced VDR binding to functional gene enhancer and promoter regions. Metagenomic analysis showed that VD supplementation reversed dysregulation of up to 70% of the transcriptome and epigenetic modifications (H3K27Ac) induced by IL-13 in VD-deficient cells, including genes encoding the transcription factors HIF1A and SMAD3, endopeptidases (SERPINB3) and epithelial-mesenchymal transition mediators (TGFBR1, TIAM1, SRC, ROBO1, CDH1). Molecular imaging and chromatin immunoprecipitation showed VDR and STAT6 colocalisation within the regulatory regions of the affected genes, suggesting that VDR and STAT6 interactome governs epithelial tissue responses to IL-13 signalling. Indeed, VD supplementation reversed IL-13-induced epithelial hyperproliferation, reduced dilated intercellular spaces and barrier permeability, and improved differentiation marker expression (filaggrin, involucrin). In a preclinical model of IL-13-mediated oesophageal allergic inflammation and in human EoE, VD levels inversely associated with severity of oesophageal eosinophilia and epithelial histopathology. CONCLUSIONS Collectively, these findings identify VD as a natural IL-13 antagonist with capacity to regulate the oesophageal epithelial barrier functions, providing a novel therapeutic entry point for type 2 immunity-related diseases.
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Affiliation(s)
- Michael Brusilovsky
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Tetsuo Shoda
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Julie M Caldwell
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Lydia E Mack
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - John A Besse
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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8
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Wayman JA, Thomas A, Bejjani A, Katko A, Almanan M, Godarova A, Korinfskaya S, Cazares TA, Yukawa M, Kottyan LC, Barski A, Chougnet CA, Hildeman DA, Miraldi ER. An atlas of gene regulatory networks for memory CD4 + T cells in youth and old age. bioRxiv 2023:2023.03.07.531590. [PMID: 36945549 PMCID: PMC10028906 DOI: 10.1101/2023.03.07.531590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Aging profoundly affects immune-system function, promoting susceptibility to pathogens, cancers and chronic inflammation. We previously identified a population of IL-10-producing, T follicular helper-like cells (" Tfh10 "), linked to suppressed vaccine responses in aged mice. Here, we integrate single-cell ( sc )RNA-seq, scATAC-seq and genome-scale modeling to characterize Tfh10 - and the full CD4 + memory T cell ( CD4 + TM ) compartment - in young and old mice. We identified 13 CD4 + TM populations, which we validated through cross-comparison to prior scRNA-seq studies. We built gene regulatory networks ( GRNs ) that predict transcription-factor control of gene expression in each T-cell population and how these circuits change with age. Through integration with pan-cell aging atlases, we identified intercellular-signaling networks driving age-dependent changes in CD4 + TM. Our atlas of finely resolved CD4 + TM subsets, GRNs and cell-cell communication networks is a comprehensive resource of predicted regulatory mechanisms operative in memory T cells, presenting new opportunities to improve immune responses in the elderly.
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9
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Cazares TA, Rizvi FW, Iyer B, Chen X, Kotliar M, Bejjani AT, Wayman JA, Donmez O, Wronowski B, Parameswaran S, Kottyan LC, Barski A, Weirauch MT, Prasath VBS, Miraldi ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Comput Biol 2023; 19:e1010863. [PMID: 36719906 PMCID: PMC9917285 DOI: 10.1371/journal.pcbi.1010863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/10/2023] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods for TFBS prediction from DNase-seq. However, the more recent Assay-for-Transposase-Accessible-Chromatin (ATAC)-seq has surpassed DNase-seq as the most widely-used chromatin accessibility profiling method. Furthermore, ATAC-seq is the only such technique available at single-cell resolution from standard commercial platforms. While ATAC-seq datasets grow exponentially, suboptimal motif scanning is unfortunately the most common method for TFBS prediction from ATAC-seq. To enable community access to state-of-the-art TFBS prediction from ATAC-seq, we (1) curated an extensive benchmark dataset (127 TFs) for ATAC-seq model training and (2) built "maxATAC", a suite of user-friendly, deep neural network models for genome-wide TFBS prediction from ATAC-seq in any cell type. With models available for 127 human TFs, maxATAC is the largest collection of high-performance TFBS prediction models for ATAC-seq. maxATAC performance extends to primary cells and single-cell ATAC-seq, enabling improved TFBS prediction in vivo. We demonstrate maxATAC's capabilities by identifying TFBS associated with allele-dependent chromatin accessibility at atopic dermatitis genetic risk loci.
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Affiliation(s)
- Tareian A. Cazares
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Faiz W. Rizvi
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Balaji Iyer
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Anthony T. Bejjani
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Joseph A. Wayman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Omer Donmez
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Benjamin Wronowski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sreeja Parameswaran
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Leah C. Kottyan
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Emily R. Miraldi
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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10
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Korinfskaya S, Kotliar M, Katko A, Hildeman D, Miraldi ER, Barski A. Role of transcription factor RUNX1 in the maintenance of T helper cell epigenome and rapid recall response. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.56.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Memory T cells exhibit an accelerated response after a second encounter with the same antigen. In our previous studies, we showed that the ability to produce effector molecules within minutes of the secondary exposure to antigen (“rapid recall response”) is associated with the epigenetic state of the rapid recall genes. This memory epigenome is established during the primary T cell encounter with its cognate antigen. To maintain a “rapid recall response” even when antigen is eliminated, resting memory T cells would have to maintain open chromatin signature for years despite episodic homeostatic T cell proliferation. However, the mechanisms underlying the long-term maintenance of this epigenetic pattern remains unclear. Here, we used 10X Multiome (scRNA-seq and scATAC-seq obtained from the same cells) analysis to show that the association between the chromatin state of memory cells and their cytokine expression upon activation is Th lineage specific.
Bioinformatic analysis showed that open chromatin specific for memory but not naïve CD4 T cells is enriched with motifs of constitutively expressed transcription factors RUNX, SP1, and ETS. Our preliminary Cut&Tag data in total human resting CD4 T cells demonstrates that RUNX1 binds DNA close to T helper cytokines genes (IL3, IL4, IL9, IL10, IL13, IFNG) at “memory-specific” ATAC-seq regions, suggesting the role of RUNX1 in maintaining this “rapid recall” epigenome. Together with the dynamic model of transcriptome and epigenome rearrangements this data could help us to understand how memory T cells establish a platform that enables and maintains their unique ability to respond more rapidly to subsequent encounters with antigen.
Supported by R01AI153442-01A1 from NIAID, NIH
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Affiliation(s)
- Svetlana Korinfskaya
- 1Allergy & Immunology, Cincinnati Children's Hospital Medical Center
- 2MDB Graduate Program, University of Cincinnati College of Medicine
| | - Michael Kotliar
- 1Allergy & Immunology, Cincinnati Children's Hospital Medical Center
| | - Alexander Katko
- 3Immunology, Cincinnati Children's Hospital Medical Center
- 4Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - David Hildeman
- 3Immunology, Cincinnati Children's Hospital Medical Center
| | | | - Artem Barski
- 1Allergy & Immunology, Cincinnati Children's Hospital Medical Center
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11
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Kotliar M, Surumbayeva A, Gabitova L, Peri S, Restifo D, Cai KQ, Barski A, Astsaturov I. Abstract PO-068: Cholesterol auxotrophy promotes the expansion of centroacinar cells giving rise to the basal subtype of pancreatic adenocarcinoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.panca21-po-068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gene expression analyses established at least two molecular subtypes of pancreatic adenocarcinoma (PDAC), the classical (or glandular), and the basal (or mesenchymal), each of which is associated with distinct prognoses and sensitivity to chemotherapy. It remains unclear, however, whether the basal carcinoma cells arise from a separate cell-of-origin, or are emerging from the pre-existing well-differentiated “classical” PDAC cells. To distinguish these alternatives, we conducted single-cell transcriptome analyses and virtual lineage tracing comparing cellular populations at pre-malignant stages in basal versus classical PDAC mouse models. We previously reported that chemical or genetic inhibition of the cholesterol biosynthetic pathway in KrasG12D; Trp53 (KPPC) mice predisposes to basal rather than glandular PDAC development because of the pancreas-specific increased sterol response element-binding protein 1 (SREBP1) activity and TGFβ signaling that induces cancer cell stemness and the EMT (PMID: 32976774). Pancreas-selective knockout of a conditional allele of cholesterol pathway gene, Nsdhl (NAD(P)-dependent steroid dehydrogenase-like), renders pancreatic epithelial cells cholesterol auxotrophs and drives basal PDAC in the majority of animals (KPPCN mice). At 5-6 weeks of age, grossly and microscopically tumor-free pancreatic tissues were selected for single-cell isolation and single-cell RNA sequencing (scRNA seq) using the 10X platform. After standard filtering and sample normalization procedures, downstream analyses included identification of relevant cell clusters using Seurat, lineage tracing algorithms, and in silico modeling of autocrine and paracrine signaling interactions between subsets of PDAC and non-malignant cells. Our key findings are as follows: 1) premalignant KPPCN pancreata exhibit a massive expansion of cancer-associated fibroblasts (CAFs) of predominantly inflammatory differentiation (iCAFs); 2) despite relatively fewer ADM and PanIN pre-malignant lesions in KPPCN compared to KPPC, scRNA seq identifies the significant expansion of epithelial cells with features of centroacinar and stem-like cells (increased expression of Aldh1a2, Nes, Sox9, Ly6a, Cxcl12, and Met); these centroacinar-like cells, while retaining epithelial identity (Epcam, Cdh1), also exhibit features of pluripotency by co-expression of Ins2 and other stem cell markers; 3) alignment with basal PDAC (KPPCN) and classical (KPPC) carcinoma cell populations strongly suggests the continuity of clonal evolution of the centroacinar-like cells towards the basal PDAC. While our genetic model does not recapitulate the multiple alternative pathways leading to basal PDAC development, cholesterol auxotrophy via SREBP1 may be a factor governing the expansion of undifferentiated precursors, which via interactions with cancer-promoting iCAFs, drive basal PDAC development.
Citation Format: Michael Kotliar, Aizhan Surumbayeva, Linara Gabitova, Suraj Peri, Diana Restifo, Kathy Q. Cai, Artem Barski, Igor Astsaturov. Cholesterol auxotrophy promotes the expansion of centroacinar cells giving rise to the basal subtype of pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PO-068.
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Affiliation(s)
- Michael Kotliar
- 1Cincinnati Children’s Hospital Medical Center, Cincinnati, OH,
| | - Aizhan Surumbayeva
- 2The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA,
| | - Linara Gabitova
- 2The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA,
| | - Suraj Peri
- 3Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA,
| | - Diana Restifo
- 2The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA,
| | - Kathy Q. Cai
- 4Histopathology Facility, Fox Chase Cancer Center, Philadelphia, PA,
| | - Artem Barski
- 5Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Igor Astsaturov
- 2The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, Philadelphia, PA,
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12
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Felton JM, Bouffi C, Schwartz JT, Schollaert KL, Malik A, Vallabh S, Wronowski B, Magier AZ, Merlin L, Barski A, Weirauch MT, Fulkerson PC, Rothenberg ME. Aiolos regulates eosinophil migration into tissues. Mucosal Immunol 2021; 14:1271-1281. [PMID: 34341502 PMCID: PMC8542574 DOI: 10.1038/s41385-021-00416-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/04/2023]
Abstract
Expression of Ikaros family transcription factor IKZF3 (Aiolos) increases during murine eosinophil lineage commitment and maturation. Herein, we investigated Aiolos expression and function in mature human and murine eosinophils. Murine eosinophils deficient in Aiolos demonstrated gene expression changes in pathways associated with granulocyte-mediated immunity, chemotaxis, degranulation, ERK/MAPK signaling, and extracellular matrix organization; these genes had ATAC peaks within 1 kB of the TSS that were enriched for Aiolos-binding motifs. Global Aiolos deficiency reduced eosinophil frequency within peripheral tissues during homeostasis; a chimeric mouse model demonstrated dependence on intrinsic Aiolos expression by eosinophils. Aiolos deficiency reduced eosinophil CCR3 surface expression, intracellular ERK1/2 signaling, and CCL11-induced actin polymerization, emphasizing an impaired functional response. Aiolos-deficient eosinophils had reduced tissue accumulation in chemokine-, antigen-, and IL-13-driven inflammatory experimental models, all of which at least partially depend on CCR3 signaling. Human Aiolos expression was associated with active chromatin marks enriched for IKZF3, PU.1, and GATA-1-binding motifs within eosinophil-specific histone ChIP-seq peaks. Furthermore, treating the EOL-1 human eosinophilic cell line with lenalidomide yielded a dose-dependent decrease in Aiolos. These collective data indicate that eosinophil homing during homeostatic and inflammatory allergic states is Aiolos-dependent, identifying Aiolos as a potential therapeutic target for eosinophilic disease.
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Affiliation(s)
- Jennifer M Felton
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Carine Bouffi
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Justin T Schwartz
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kaila L Schollaert
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Astha Malik
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Sushmitha Vallabh
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Benjamin Wronowski
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Adam Z Magier
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Li Merlin
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Artem Barski
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics and Division of Developmental Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Patricia C Fulkerson
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marc E Rothenberg
- Division of Allergy and Immunology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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13
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Korinfskaya S, Parameswaran S, Weirauch MT, Barski A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Front Immunol 2021; 12:701924. [PMID: 34421907 PMCID: PMC8377396 DOI: 10.3389/fimmu.2021.701924] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Runx proteins (also known as Runt-domain transcription factors) have been studied for a long time as key regulators of cellular differentiation. RUNX2 has been described as essential for osteogenesis, whereas RUNX1 and RUNX3 are known to control blood cell development during different stages of cell lineage specification. However, recent studies show evidence of complex relationships between RUNX proteins, chromatin-modifying machinery, the cytoskeleton and different transcription factors in various non-embryonic contexts, including mature T cell homeostasis, inflammation and cancer. In this review, we discuss the diversity of Runx functions in mature T helper cells, such as production of cytokines and chemokines by different CD4 T cell populations; apoptosis; and immunologic memory acquisition. We then briefly cover recent findings about the contribution of RUNX1, RUNX2 and RUNX3 to various immunologic diseases. Finally, we discuss areas that require further study to better understand the role that Runx proteins play in inflammation and immunity.
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Affiliation(s)
- Svetlana Korinfskaya
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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14
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Felton JM, Vallabh S, Parameswaran S, Edsall LE, Ernst K, Wronowski B, Malik A, Kotliar M, Weirauch MT, Barski A, Fulkerson PC, Rothenberg ME. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. J Immunol 2021; 207:1044-1054. [PMID: 34330753 DOI: 10.4049/jimmunol.2000207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/07/2021] [Indexed: 12/20/2022]
Abstract
Eosinophils develop in the bone marrow from hematopoietic progenitors into mature cells capable of a plethora of immunomodulatory roles via the choreographed process of eosinophilopoiesis. However, the gene regulatory elements and transcription factors (TFs) orchestrating this process remain largely unknown. The potency and resulting diversity fundamental to an eosinophil's complex immunomodulatory functions and tissue specialization likely result from dynamic epigenetic regulation of the eosinophil genome, a dynamic eosinophil regulome. In this study, we applied a global approach using broad-range, next-generation sequencing to identify a repertoire of eosinophil-specific enhancers. We identified over 8200 active enhancers located within 1-20 kB of expressed eosinophil genes. TF binding motif analysis revealed PU.1 (Spi1) motif enrichment in eosinophil enhancers, and chromatin immunoprecipitation coupled with massively parallel sequencing confirmed PU.1 binding in likely enhancers of genes highly expressed in eosinophils. A substantial proportion (>25%) of these PU.1-bound enhancers were unique to murine, culture-derived eosinophils when compared among enhancers of highly expressed genes of three closely related myeloid cell subsets (macrophages, neutrophils, and immature granulocytes). Gene ontology analysis of eosinophil-specific, PU.1-bound enhancers revealed enrichment for genes involved in migration, proliferation, degranulation, and survival. Furthermore, eosinophil-specific superenhancers were enriched in genes whose homologs are associated with risk loci for eosinophilia and allergic diseases. Our collective data identify eosinophil-specific enhancers regulating key eosinophil genes through epigenetic mechanisms (H3K27 acetylation) and TF binding (PU.1).
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Affiliation(s)
- Jennifer M Felton
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sushmitha Vallabh
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Lee E Edsall
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Kevin Ernst
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Benjamin Wronowski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Astha Malik
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; and
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Patricia C Fulkerson
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
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15
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Chidambaran V, Zhang X, Pilipenko V, Chen X, Wronowski B, Geisler K, Martin LJ, Barski A, Weirauch MT, Ji H. Methylation quantitative trait locus analysis of chronic postsurgical pain uncovers epigenetic mediators of genetic risk. Epigenomics 2021; 13:613-630. [PMID: 33820434 DOI: 10.2217/epi-2020-0424] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Overlap of pathways enriched by single nucleotide polymorphisms and DNA-methylation underlying chronic postsurgical pain (CPSP), prompted pilot study of CPSP-associated methylation quantitative trait loci (meQTL). Materials & methods: Children undergoing spine-fusion were recruited prospectively. Logistic-regression for genome- and epigenome-wide CPSP association and DNA-methylation-single nucleotide polymorphism association/mediation analyses to identify meQTLs were followed by functional genomics analyses. Results: CPSP (n = 20/58) and non-CPSP groups differed in pain-measures. Of 2753 meQTLs, DNA-methylation at 127 cytosine-guanine dinucleotides mediated association of 470 meQTLs with CPSP (p < 0.05). At PARK16 locus, CPSP risk meQTLs were associated with decreased DNA-methylation at RAB7L1 and increased DNA-methylation at PM20D1. Corresponding RAB7L1/PM20D1 blood eQTLs (GTEx) and cytosine-guanine dinucleotide-loci enrichment for histone marks, transcription factor binding sites and ATAC-seq peaks suggest altered transcription factor-binding. Conclusion: CPSP-associated meQTLs indicate epigenetic mechanisms mediate genetic risk. Clinical trial registration: NCT01839461, NCT01731873 (ClinicalTrials.gov).
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Affiliation(s)
- Vidya Chidambaran
- Department of Anesthesiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Valentina Pilipenko
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Benjamin Wronowski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kristie Geisler
- Department of Anesthesiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Artem Barski
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45229, USA
| | - Hong Ji
- Department of Anatomy, Physiology & Cell biology, California National Primate Research Center, University of California, Davis, CA 95616, USA
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16
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Maezawa S, Sakashita A, Yukawa M, Chen X, Takahashi K, Alavattam KG, Nakata I, Weirauch MT, Barski A, Namekawa SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nat Struct Mol Biol 2020; 27:978-988. [PMID: 32895557 PMCID: PMC8690596 DOI: 10.1038/s41594-020-0488-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/10/2020] [Indexed: 01/12/2023]
Abstract
Due to bursts in the expression of thousands of germline-specific genes, the testis has the most diverse and complex transcriptome of all organs. By analyzing the male germline of mice, we demonstrate that the genome-wide reorganization of super-enhancers (SEs) drives bursts in germline gene expression after the mitosis-to-meiosis transition. SE reorganization is regulated by two molecular events: the establishment of meiosis-specific SEs via A-MYB (MYBL1), a key transcription factor for germline genes, and the resolution of SEs in mitotically proliferating cells via SCML2, a germline-specific Polycomb protein required for spermatogenesis-specific gene expression. Prior to entry into meiosis, meiotic SEs are preprogrammed in mitotic spermatogonia to ensure the unidirectional differentiation of spermatogenesis. We identify key regulatory factors for both mitotic and meiotic enhancers, revealing a molecular logic for the concurrent activation of mitotic enhancers and suppression of meiotic enhancers in the somatic and/or mitotic proliferation phases.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan. .,Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda, Chiba, Japan.
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Department of Molecular Biology, Keio University School of Medicine, Tokyo, Japan
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kazuki Takahashi
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ippo Nakata
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA.
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17
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Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. J Exp Med 2020; 217:jem.20182009. [PMID: 31653690 PMCID: PMC7037242 DOI: 10.1084/jem.20182009] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/06/2019] [Accepted: 09/23/2019] [Indexed: 12/24/2022] Open
Abstract
Activation of T cells is dependent on the organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naive T cells within 5 h of activation. These newly opened regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at >70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced the expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1-dependent elements with risk loci for multiple immune diseases, including multiple sclerosis, inflammatory bowel disease, and allergic disease. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
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Affiliation(s)
- Masashi Yukawa
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sajjeev Jagannathan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Sushmitha Vallabh
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Andrey V Kartashov
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
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18
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Barski A. Epigenomics of T Cell Activation and Memory. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.78.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
A characteristic feature of adaptive immunity is the rapid recall response of memory T cells, the ability of memory T cells to produce cytokines in response to pathogen much more rapidly than naïve T cells. We have recently found that this rapid recall ability is associated with epigenetic gene poising. Here, we aim to uncover the mechanism that underlie chromatin remodeling during initial activation of T cells and, thus, contribute to the establishment of memory phenotype. Upon encountering an antigen, naïve T helper cells become activated, differentiate into several lineages and contribute to immune response. Activation of T cells is dependent on organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naïve T cells within hours of activation. These newly open regions were strongly enriched for the AP-1 motif, and indeed, ChIP-Seq demonstrated AP-1 binding at more than 70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation, was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1–dependent elements with risk loci for multiple immune diseases, most notably multiple sclerosis, IBD and allergy. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
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Affiliation(s)
- Artem Barski
- 1Cincinnati Children’s Hospital Medical Center
- 2University of Cincinnati College of Medicine
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19
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Lavery WJ, Kotliar M, Chang CF, Brugmann SA, Barski A, Lindsley AW. KMT2D
Haploinsufficiency in Kabuki Syndrome Impairs Differentiation of Neural Crest Cells. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.09189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Pilarowski GO, Cazares T, Zhang L, Benjamin JS, Liu K, Jagannathan S, Mousa N, Kasten J, Barski A, Lindsley AW, Bjornsson HT. Abnormal Peyer patch development and B-cell gut homing drive IgA deficiency in Kabuki syndrome. J Allergy Clin Immunol 2020; 145:982-992. [DOI: 10.1016/j.jaci.2019.11.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/05/2019] [Accepted: 11/14/2019] [Indexed: 01/17/2023]
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21
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Lavery WJ, Barski A, Wiley S, Schorry EK, Lindsley AW. KMT2C/D COMPASS complex-associated diseases [K CDCOM-ADs]: an emerging class of congenital regulopathies. Clin Epigenetics 2020; 12:10. [PMID: 31924266 PMCID: PMC6954584 DOI: 10.1186/s13148-019-0802-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022] Open
Abstract
The type 2 lysine methyltransferases KMT2C and KMT2D are large, enzymatically active scaffold proteins that form the core of nuclear regulatory structures known as KMT2C/D COMPASS complexes (complex of proteins associating with Set1). These evolutionarily conserved proteins regulate DNA promoter and enhancer elements, modulating the activity of diverse cell types critical for embryonic morphogenesis, central nervous system development, and post-natal survival. KMT2C/D COMPASS complexes and their binding partners enhance active gene expression of specific loci via the targeted modification of histone-3 tail residues, in general promoting active euchromatic conformations. Over the last 20 years, mutations in five key COMPASS complex genes have been linked to three human congenital syndromes: Kabuki syndrome (type 1 [KMT2D] and 2 [KDM6A]), Rubinstein-Taybi syndrome (type 1 [CBP] and 2 [EP300]), and Kleefstra syndrome type 2 (KMT2C). Here, we review the composition and biochemical function of the KMT2 complexes. The specific cellular and embryonic roles of the KMT2C/D COMPASS complex are highlight with a focus on clinically relevant mechanisms sensitive to haploinsufficiency. The phenotypic similarities and differences between the members of this new family of disorders are outlined and emerging therapeutic strategies are detailed.
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Affiliation(s)
- William J Lavery
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA
- Division of Human Genetics, CCHMC, Cincinnati, OH, USA
| | - Susan Wiley
- Division of Developmental and Behavioral Pediatrics, CCHMC, Cincinnati, OH, USA
| | | | - Andrew W Lindsley
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center (CCHMC), 3333 Burnet Avenue, Cincinnati, OH, 45229-3026, USA.
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22
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Vanoni S, Zeng C, Marella S, Uddin J, Wu D, Arora K, Ptaschinski C, Que J, Noah T, Waggoner L, Barski A, Kartashov A, Rochman M, Wen T, Martin L, Spence J, Collins M, Mukkada V, Putnam P, Naren A, Chehade M, Rothenberg ME, Hogan SP. Identification of anoctamin 1 (ANO1) as a key driver of esophageal epithelial proliferation in eosinophilic esophagitis. J Allergy Clin Immunol 2020; 145:239-254.e2. [PMID: 31647967 PMCID: PMC7366251 DOI: 10.1016/j.jaci.2019.07.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/13/2019] [Accepted: 07/29/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND The pathology of eosinophilic esophagitis (EoE) is characterized by eosinophil-rich inflammation, basal zone hyperplasia (BZH), and dilated intercellular spaces, and the underlying processes that drive the pathologic manifestations of the disease remain largely unexplored. OBJECTIVE We sought to investigate the involvement of the calcium-activated chloride channel anoctamin 1 (ANO1) in esophageal proliferation and the histopathologic features of EoE. METHODS We examined mRNA and protein expression of ANO1 in esophageal biopsy samples from patients with EoE and in mice with EoE. We performed molecular and cellular analyses and ion transport assays on an in vitro esophageal epithelial 3-dimensional model system (EPC2-ALI) and murine models of EoE to define the relationship between expression and function of ANO1 and esophageal epithelial proliferation in patients with EoE. RESULTS We observed increased ANO1 expression in esophageal biopsy samples from patients with EoE and in mice with EoE. ANO1 was expressed within the esophageal basal zone, and expression correlated positively with disease severity (eosinophils/high-power field) and BZH. Using an in vitro esophageal epithelial 3-dimensional model system revealed that ANO1 undergoes chromatin modification and rapid upregulation of expression after IL-13 stimulation, that ANO1 is the primary apical IL-13-induced Cl- transport mechanism within the esophageal epithelium, and that loss of ANO1-dependent Cl- transport abrogated esophageal epithelial proliferation. Mechanistically, ANO1-dependent regulation of basal cell proliferation was associated with modulation of TP63 expression and phosphorylated cyclin-dependent kinase 2 levels. CONCLUSIONS These data identify a functional role for ANO1 in esophageal cell proliferation and BZH in patients with EoE and provide a rationale for pharmacologic intervention of ANO1 function in patients with EoE.
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Affiliation(s)
- Simone Vanoni
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; PharmGenetix Gmbh, Niederalm-Anif, Austria
| | - Chang Zeng
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sahiti Marella
- Mary H Weiser Food Allergy Center and Department of Pathology, Ann Arbor, Mich
| | - Jazib Uddin
- Mary H Weiser Food Allergy Center and Department of Pathology, Ann Arbor, Mich
| | - David Wu
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Kavisha Arora
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY
| | - Taeko Noah
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Mary H Weiser Food Allergy Center and Department of Pathology, Ann Arbor, Mich
| | - Lisa Waggoner
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Andrey Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mark Rochman
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ting Wen
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lisa Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jason Spence
- Departments of Biomedical Engineering, Internal Medicine and Cell and Developmental Biology, University of Michigan, Ann Arbor, Mich
| | - Margaret Collins
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Vincent Mukkada
- Division of Gastroenterology, Nutrition and Hepatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Phillip Putnam
- Division of Gastroenterology, Nutrition and Hepatology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Anjaparavanda Naren
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Mirna Chehade
- Mount Sinai Center for Eosinophilic Disorders, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Simon P Hogan
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Mary H Weiser Food Allergy Center and Department of Pathology, Ann Arbor, Mich.
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23
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Maezawa S, Yukawa M, Alavattam KG, Barski A, Namekawa SH. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Nucleic Acids Res 2019; 46:593-608. [PMID: 29126117 PMCID: PMC5778473 DOI: 10.1093/nar/gkx1052] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022] Open
Abstract
During spermatogenesis, germ cells undergo massive cellular reconstruction and dynamic chromatin remodeling to facilitate highly diverse transcriptomes, which are required for the production of functional sperm. However, it remains unknown how germline chromatin is organized to promote the dynamic, complex transcriptomes of spermatogenesis. Here, using ATAC-seq, we establish the varied landscape of open chromatin during spermatogenesis. We identify the reorganization of accessible chromatin in intergenic and intronic regions during the mitosis-to-meiosis transition. During the transition, mitotic-type open chromatin is closed while the de novo formation of meiotic-type open chromatin takes place. Contrastingly, differentiation processes such as spermatogonial differentiation and the meiosis-to-postmeiosis transition involve chromatin closure without the de novo formation of accessible chromatin. In spermiogenesis, the germline-specific Polycomb protein SCML2 promotes the closure of open chromatin at autosomes for gene suppression. Paradoxically, we identify the massive de novo formation of accessible chromatin when the sex chromosomes undergo meiotic sex chromosome inactivation, and this is also mediated by SCML2. These results reveal meiotic sex chromosome inactivation as an active process for chromatin organization. Together, our results unravel the genome-wide, dynamic reorganization of open chromatin and reveal mechanisms that underlie diverse transcriptomes during spermatogenesis.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
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24
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Kotliar M, Kartashov AV, Barski A. CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. Gigascience 2019; 8:giz084. [PMID: 31321430 PMCID: PMC6639121 DOI: 10.1093/gigascience/giz084] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/21/2019] [Accepted: 06/21/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Massive growth in the amount of research data and computational analysis has led to increased use of pipeline managers in biomedical computational research. However, each of the >100 such managers uses its own way to describe pipelines, leading to difficulty porting workflows to different environments and therefore poor reproducibility of computational studies. For this reason, the Common Workflow Language (CWL) was recently introduced as a specification for platform-independent workflow description, and work began to transition existing pipelines and workflow managers to CWL. FINDINGS Herein, we present CWL-Airflow, a package that adds support for CWL to the Apache Airflow pipeline manager. CWL-Airflow uses CWL version 1.0 specification and can run workflows on stand-alone MacOS/Linux servers, on clusters, or on a variety of cloud platforms. A sample CWL pipeline for processing of chromatin immunoprecipitation sequencing data is provided. CONCLUSIONS CWL-Airflow will provide users with the features of a fully fledged pipeline manager and the ability to execute CWL workflows anywhere Airflow can run-from a laptop to a cluster or cloud environment. CWL-Airflow is available under Apache License, version 2.0 (Apache-2.0), and can be downloaded from https://barski-lab.github.io/cwl-airflow, https://scicrunch.org/resolver/RRID:SCR_017196.
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Affiliation(s)
- Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
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25
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Barski A, Yukawa M, Jagannathan S, Kartashov AV, Chen X, Weirauch MT. Co-Stimulation–Induced AP-1 Activity is Required for Chromatin Opening During T Cell Activation. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.125.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Activation of T cells is dependent on organized and timely opening and closing of chromatin. Herein, we identify AP-1 as the transcription factor that directs most of this remodeling. Chromatin accessibility profiling showed quick opening of closed chromatin in naïve T cells within 5 hours of activation. These newly open regions were strongly enriched for the AP-1 motif, and indeed, ChIP-seq demonstrated AP-1 binding at more than 70% of them. Broad inhibition of AP-1 activity prevented chromatin opening at AP-1 sites and reduced expression of nearby genes. Similarly, induction of anergy in the absence of co-stimulation during activation, was associated with reduced induction of AP-1 and a failure of proper chromatin remodeling. The translational relevance of these findings was highlighted by the substantial overlap of AP-1–dependent elements with risk loci for multiple immune diseases, most notably multiple sclerosis. Our findings define AP-1 as the key link between T cell activation and chromatin remodeling.
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26
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Alavattam KG, Maezawa S, Sakashita A, Khoury H, Barski A, Kaplan N, Namekawa SH. Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. Nat Struct Mol Biol 2019; 26:175-184. [PMID: 30778237 PMCID: PMC6402993 DOI: 10.1038/s41594-019-0189-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/15/2019] [Indexed: 12/17/2022]
Abstract
Germ cells manifest a unique gene expression program and regain totipotency in the zygote. Here, we perform Hi-C analysis to examine 3D chromatin organization in male germ cells during spermatogenesis. We show that the highly compartmentalized 3D chromatin organization characteristic of interphase nuclei is attenuated in meiotic prophase. Meiotic prophase is predominated by short-range intrachromosomal interactions that represent a condensed form akin to that of mitotic chromosomes. However, unlike mitotic chromosomes, meiotic chromosomes display weak genomic compartmentalization, weak topologically associating domains, and localized point interactions in prophase. In postmeiotic round spermatids, genomic compartmentalization increases and gives rise to the strong compartmentalization seen in mature sperm. The X chromosome lacks domain organization during meiotic sex-chromosome inactivation. We propose that male meiosis occurs amid global reprogramming of 3D chromatin organization and that strengthening of chromatin compartmentalization takes place in spermiogenesis to prepare the next generation of life.
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Affiliation(s)
- Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Haia Khoury
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Noam Kaplan
- Department of Physiology, Biophysics & Systems Biology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
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27
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Maezawa S, Alavattam KG, Tatara M, Nagai R, Barski A, Namekawa SH. A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†. Biol Reprod 2019; 100:409-419. [PMID: 30137219 DOI: 10.1093/biolre/ioy181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 07/20/2018] [Accepted: 08/16/2018] [Indexed: 11/14/2022] Open
Abstract
Genes involved in sexual reproduction diverge rapidly as a result of reproductive fitness. Here, we identify a novel protein domain in the germline-specific Polycomb protein SCML2 that is required for the establishment of unique gene expression programs after the mitosis-to-meiosis transition in spermatogenesis. We term this novel domain, which is comprised of rapidly evolved, DNA-binding repeat units of 28 amino acids, the SCML2 DNA-binding (SDB) repeats. These repeats are acquired in a specific subgroup of the rodent lineage, having been subjected to positive selection in the course of evolution. Mouse SCML2 has two DNA-binding domains: one is the SDB repeats and the other is an RNA-binding region, which is conserved in human SCML2. For the recruitment of SCML2 to target loci, the SDB repeats cooperate with the other functional domains of SCML2 to bind chromatin. The cooperative action of these domains enables SCML2 to sense DNA hypomethylation in an in vivo chromatin environment, thereby enabling SCML2 to bind to hypomethylated chromatin. We propose that the rapid evolution of SCML2 is due to reproductive adaptation, which has promoted species-specific gene expression programs in spermatogenesis.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Mayu Tatara
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Rika Nagai
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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28
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Kelly D, Kotliar M, Woo V, Jagannathan S, Whitt J, Moncivaiz J, Aronow BJ, Dubinsky MC, Hyams JS, Markowitz JF, Baldassano RN, Stephens MC, Walters TD, Kugathasan S, Haberman Y, Sundaram N, Rosen MJ, Helmrath M, Karns R, Barski A, Denson LA, Alenghat T. Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. JCI Insight 2018; 3:122104. [PMID: 30232290 PMCID: PMC6237229 DOI: 10.1172/jci.insight.122104] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/07/2018] [Indexed: 12/19/2022] Open
Abstract
Altered response to the intestinal microbiota strongly associates with inflammatory bowel disease (IBD); however, how commensal microbial cues are integrated by the host during the pathogenesis of IBD is not understood. Epigenetics represents a potential mechanism that could enable intestinal microbes to modulate transcriptional output during the development of IBD. Here, we reveal a histone methylation signature of intestinal epithelial cells isolated from the terminal ilea of newly diagnosed pediatric IBD patients. Genes characterized by significant alterations in histone H3-lysine 4 trimethylation (H3K4me3) showed differential enrichment in pathways involving immunoregulation, cell survival and signaling, and metabolism. Interestingly, a large subset of these genes was epigenetically regulated by microbiota in mice and several microbiota-sensitive epigenetic targets demonstrated altered expression in IBD patients. Remarkably though, a substantial proportion of these genes exhibited H3K4me3 levels that correlated with the severity of intestinal inflammation in IBD, despite lacking significant differential expression. Collectively, these data uncover a previously unrecognized epigenetic profile of IBD that can be primed by commensal microbes and indicate sensitive targets in the epithelium that may underlie how microbiota predispose to subsequent intestinal inflammation and disease.
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Affiliation(s)
- Daniel Kelly
- Division of Immunobiology, Center for Inflammation and Tolerance
- Division of Gastroenterology, Hepatology, and Nutrition
| | | | - Vivienne Woo
- Division of Immunobiology, Center for Inflammation and Tolerance
| | | | - Jordan Whitt
- Division of Immunobiology, Center for Inflammation and Tolerance
| | | | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center (CCHMC) and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Marla C. Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey S. Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, Connecticut, USA
| | | | - Robert N. Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael C. Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas D. Walters
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Yael Haberman
- Division of Gastroenterology, Hepatology, and Nutrition
- Sheba Medical Center, Tel Hashomer, affiliated with the Tel-Aviv University, Israel
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, CCHMC and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Michael Helmrath
- Division of Pediatric General and Thoracic Surgery, CCHMC and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Rebekah Karns
- Division of Gastroenterology, Hepatology, and Nutrition
| | - Artem Barski
- Divisions of Allergy and Immunology and Human Genetics, and
| | - Lee A. Denson
- Division of Gastroenterology, Hepatology, and Nutrition
| | - Theresa Alenghat
- Division of Immunobiology, Center for Inflammation and Tolerance
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29
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Maezawa S, Hasegawa K, Alavattam KG, Funakoshi M, Sato T, Barski A, Namekawa SH. SCML2 promotes heterochromatin organization in late spermatogenesis. J Cell Sci 2018; 131:jcs.217125. [PMID: 30097555 DOI: 10.1242/jcs.217125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/31/2018] [Indexed: 12/15/2022] Open
Abstract
Spermatogenesis involves the progressive reorganization of heterochromatin. However, the mechanisms that underlie the dynamic remodeling of heterochromatin remain unknown. Here, we identify SCML2, a germline-specific Polycomb protein, as a critical regulator of heterochromatin organization in spermatogenesis. We show that SCML2 accumulates on pericentromeric heterochromatin (PCH) in male germ cells, where it suppresses PRC1-mediated monoubiquitylation of histone H2A at Lysine 119 (H2AK119ub) and promotes deposition of PRC2-mediated H3K27me3 during meiosis. In postmeiotic spermatids, SCML2 is required for heterochromatin organization, and the loss of SCML2 leads to the formation of ectopic patches of facultative heterochromatin. Our data suggest that, in the absence of SCML2, the ectopic expression of somatic lamins drives this process. Furthermore, the centromere protein CENP-V is a specific marker of PCH in postmeiotic spermatids, and SCML2 is required for CENP-V localization on PCH. Given the essential functions of PRC1 and PRC2 for genome-wide gene expression in spermatogenesis, our data suggest that heterochromatin organization and spermatogenesis-specific gene expression are functionally linked. We propose that SCML2 coordinates the organization of heterochromatin and gene expression through the regulation of Polycomb complexes.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Mayuka Funakoshi
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Taiga Sato
- Department of Animal Science and Biotechnology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
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30
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Grace JO, Malik A, Reichman H, Munitz A, Barski A, Fulkerson PC. Reuse of public, genome-wide, murine eosinophil expression data for hypotheses development. J Leukoc Biol 2018; 104:185-193. [PMID: 29758095 DOI: 10.1002/jlb.1ma1117-444r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/12/2018] [Accepted: 03/18/2018] [Indexed: 12/12/2022] Open
Abstract
The eosinophil (Eos) surface phenotype and activation state is altered after recruitment into tissues and after exposure to pro-inflammatory cytokines. In addition, distinct Eos functional subsets have been described, suggesting that tissue-specific responses for Eos contribute to organ homeostasis. Understanding the mechanisms by which Eos subsets achieve their tissue-specific identity is currently an unmet goal for the eosinophil research community. Publicly archived expression data can be used to answer original questions, test and generate new hypotheses, and serve as a launching point for experimental design. With these goals in mind, we investigated the effect of genetic background, culture methods, and tissue residency on murine Eos gene expression using publicly available, genome-wide expression data. Eos differentiated from cultures have a gene expression profile that is distinct from that of native homeostatic Eos; thus, researchers can repurpose published expression data to aid in selecting the appropriate culture method to study their gene of interest. In addition, we identified Eos lung- and gastrointestinal-specific transcriptomes, highlighting the profound effect of local tissue environment on gene expression in a terminally differentiated granulocyte even at homeostasis. Expanding the "toolbox" of Eos researchers to include public-data reuse can reduce redundancy, increase research efficiency, and lead to new biological insights.
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Affiliation(s)
- Jillian O Grace
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Astha Malik
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hadar Reichman
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Ariel Munitz
- Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Patricia C Fulkerson
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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31
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Barski A, Yukawa M, Jagannathan S, Kartashov A, Chen X, Weirauch M. AP-1 transcription factor remodels chromatin during T cell activation. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.110.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Upon encountering an antigen, naïve T helper cells activate, differentiate into several lineages and contribute to immune response. Epigenetic changes at cytokine and other effector genes during activation have been described, but the underlying mechanism is not understood. We profiled open chromatin during human T cell activation using ATAC-Seq and identified regions of epigenetic changes genome-wide. Open chromatin correlated with expression at nearby genes, which were enriched for functions related to T cell activation and immune response. As AP-1 and NFAT motifs were enriched in these newly open chromatin regions, we profiled their binding using ChIP-Seq. AP-1 was present at the majority of activation-specific open chromatin regions, which were often co-bound by both transcription factors. Notably, super enhancer formation was associated with AP-1 binding and chromatin opening during T cell activation. We also found that autoimmune disease-associated SNPs were significantly enriched in the newly open chromatin regions. Our data suggest that AP-1 activity contributes to the formation of the activated T cell epigenome and that mutations at the activation-specific open chromatin regions may contribute to autoimmune diseases.
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32
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Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nat Genet 2018; 50:699-707. [PMID: 29662164 PMCID: PMC6022759 DOI: 10.1038/s41588-018-0102-3] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 01/31/2018] [Indexed: 01/10/2023]
Abstract
Explaining the genetics of many diseases is challenging because most associations localize to incompletely characterized regulatory regions. We show that transcription factors (TFs) occupy multiple loci of individual complex genetic disorders using novel computational methods. Application to 213 phenotypes and 1,544 TF binding datasets identifies 2,264 relationships between hundreds of TFs and 94 phenotypes, including AR in prostate cancer and GATA3 in breast cancer. Strikingly, nearly half of the systemic lupus erythematosus risk loci are occupied by the Epstein-Barr virus EBNA2 protein and many co-clustering human TFs, revealing gene-environment interaction. Similar EBNA2-anchored associations exist in multiple sclerosis, rheumatoid arthritis, inflammatory bowel disease, type 1 diabetes, juvenile idiopathic arthritis, and celiac disease. Instances of allele-dependent DNA binding and downstream effects on gene expression at plausibly causal variants support genetic mechanisms dependent upon EBNA2. Our results nominate mechanisms that operate across risk loci within disease phenotypes, suggesting new paradigms for disease origins.
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Affiliation(s)
- John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA.
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mario Pujato
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Avery Maddox
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Carmy Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Albert F Magnusen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Arthur Lynch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kashish Chetal
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Masashi Yukawa
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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33
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Rochman Y, Dienger-Stambaugh K, Richgels PK, Lewkowich IP, Kartashov AV, Barski A, Khurana Hershey GK, Leonard WJ, Singh H. TSLP signaling in CD4 + T cells programs a pathogenic T helper 2 cell state. Sci Signal 2018. [PMID: 29535264 DOI: 10.1126/scisignal.aam8858] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pathogenic T helper 2 (TH2) cells, which produce increased amounts of the cytokines interleukin-5 (IL-5) and IL-13, promote allergic disorders, including asthma. Thymic stromal lymphopoietin (TSLP), a cytokine secreted by epithelial and innate immune cells, stimulates such pathogenic TH2 cell responses. We found that TSLP signaling in mouse CD4+ T cells initiated transcriptional changes associated with TH2 cell programming. IL-4 signaling amplified and stabilized the genomic response of T cells to TSLP, which increased the frequency of T cells producing IL-4, IL-5, and IL-13. Furthermore, the TSLP- and IL-4-programmed TH2 cells had a pathogenic phenotype, producing greater amounts of IL-5 and IL-13 and other proinflammatory cytokines than did TH2 cells stimulated with IL-4 alone. TSLP-mediated TH2 cell induction involved distinct molecular pathways, including activation of the transcription factor STAT5 through the kinase JAK2 and repression of the transcription factor BCL6. Mice that received wild-type CD4+ T cells had exacerbated pathogenic TH2 cell responses upon exposure to house dust mites compared to mice that received TSLP receptor-deficient CD4+ T cells. Transient TSLP signaling stably programmed pathogenic potential in memory TH2 cells. In human CD4+ T cells, TSLP and IL-4 promoted the generation of TH2 cells that produced greater amounts of IL-5 and IL-13. Compared to healthy controls, asthmatic children showed enhancement of such T cell responses in peripheral blood. Our data support a sequential cytokine model for pathogenic TH2 cell differentiation and provide a mechanistic basis for the therapeutic targeting of TSLP signaling in human allergic diseases.
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Affiliation(s)
- Yrina Rochman
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA. .,Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Krista Dienger-Stambaugh
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Phoebe K Richgels
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ian P Lewkowich
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and Immunology Center, National Heart, Lung, and Blood Institute, Bethesda, MD 20892, USA
| | - Harinder Singh
- Division of Immunobiology and the Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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34
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Adams SR, Maezawa S, Alavattam KG, Abe H, Sakashita A, Shroder M, Broering TJ, Sroga Rios J, Thomas MA, Lin X, Price CM, Barski A, Andreassen PR, Namekawa SH. RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes. PLoS Genet 2018; 14:e1007233. [PMID: 29462142 PMCID: PMC5834201 DOI: 10.1371/journal.pgen.1007233] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 03/02/2018] [Accepted: 01/31/2018] [Indexed: 11/18/2022] Open
Abstract
The sex chromosomes are enriched with germline genes that are activated during the late stages of spermatogenesis. Due to meiotic sex chromosome inactivation (MSCI), these sex chromosome-linked genes must escape silencing for activation in spermatids, thereby ensuring their functions for male reproduction. RNF8, a DNA damage response protein, and SCML2, a germline-specific Polycomb protein, are two major, known regulators of this process. Here, we show that RNF8 and SCML2 cooperate to regulate ubiquitination during meiosis, an early step to establish active histone modifications for subsequent gene activation. Double mutants of Rnf8 and Scml2 revealed that RNF8-dependent monoubiquitination of histone H2A at Lysine 119 (H2AK119ub) is deubiquitinated by SCML2, demonstrating interplay between RNF8 and SCML2 in ubiquitin regulation. Additionally, we identify distinct functions of RNF8 and SCML2 in the regulation of ubiquitination: SCML2 deubiquitinates RNF8-independent H2AK119ub but does not deubiquitinate RNF8-dependent polyubiquitination. RNF8-dependent polyubiquitination is required for the establishment of H3K27 acetylation, a marker of active enhancers, while persistent H2AK119ub inhibits establishment of H3K27 acetylation. Following the deposition of H3K27 acetylation, H3K4 dimethylation is established as an active mark on poised promoters. Together, we propose a model whereby regulation of ubiquitin leads to the organization of poised enhancers and promoters during meiosis, which induce subsequent gene activation from the otherwise silent sex chromosomes in postmeiotic spermatids.
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Affiliation(s)
- Shannel R. Adams
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Department of Obstetrics and Gynecology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Kris G. Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Hironori Abe
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Megan Shroder
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Tyler J. Broering
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Julie Sroga Rios
- Department of Obstetrics and Gynecology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Michael A. Thomas
- Department of Obstetrics and Gynecology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Xinhua Lin
- State Key Laboratory of Genetic Engineering, Institute of Genetics, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Carolyn M. Price
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Paul R. Andreassen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Satoshi H. Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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35
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Maezawa S, Hasegawa K, Yukawa M, Sakashita A, Alavattam KG, Andreassen PR, Vidal M, Koseki H, Barski A, Namekawa SH. Polycomb directs timely activation of germline genes in spermatogenesis. Genes Dev 2017; 31:1693-1703. [PMID: 28924034 PMCID: PMC5647939 DOI: 10.1101/gad.302000.117] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/21/2017] [Indexed: 01/08/2023]
Abstract
Maezawa et al. show that Polycomb-repressive complex 1 (PRC1) directs timely activation of germline genes during spermatogenesis. During spermatogenesis, a large number of germline genes essential for male fertility are coordinately activated. However, it remains unknown how timely activation of this group of germline genes is accomplished. Here we show that Polycomb-repressive complex 1 (PRC1) directs timely activation of germline genes during spermatogenesis. Inactivation of PRC1 in male germ cells results in the gradual loss of a stem cell population and severe differentiation defects, leading to male infertility. In the stem cell population, RNF2, the dominant catalytic subunit of PRC1, activates transcription of Sall4, which codes for a transcription factor essential for subsequent spermatogenic differentiation. Furthermore, RNF2 and SALL4 together occupy transcription start sites of germline genes in the stem cell population. Once differentiation commences, these germline genes are activated to enable the progression of spermatogenesis. Our study identifies a novel mechanism by which Polycomb directs the developmental process by activating a group of lineage-specific genes.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Kazuteru Hasegawa
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Akihiko Sakashita
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
| | - Paul R Andreassen
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA.,Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, 28040 Madrid, Spain
| | - Haruhiko Koseki
- Developmental Genetics Laboratory, RIKEN Center for Allergy and Immunology, Yokohama, Kanagawa 230-0045, Japan
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 49229, USA
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36
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Yue M, Ogawa A, Yamada N, Charles Richard JL, Barski A, Ogawa Y. Xist RNA repeat E is essential for ASH2L recruitment to the inactive X and regulates histone modifications and escape gene expression. PLoS Genet 2017; 13:e1006890. [PMID: 28686623 PMCID: PMC5521851 DOI: 10.1371/journal.pgen.1006890] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 07/21/2017] [Accepted: 06/22/2017] [Indexed: 12/21/2022] Open
Abstract
Long non-coding RNA Xist plays a crucial role in establishing and maintaining X-chromosome inactivation (XCI) which is a paradigm of long non-coding RNA-mediated gene regulation. Xist has Xist-specific repeat elements A-F which are conserved among eutherian mammals, underscoring their functional importance. Here we report that Xist RNA repeat E, a conserved Xist repeat element in the Xist exon 7, interacts with ASH2L and contributes to maintenance of escape gene expression level on the inactive X-chromosome (Xi) during XCI. The Xist repeat E-deletion mutant female ES cells show the depletion of ASH2L from the Xi upon differentiation. Furthermore, a subset of escape genes exhibits unexpectedly higher expression in the repeat E mutant cells than the cells expressing wildtype Xist during X-inactivation, whereas the silencing of X-linked non-escape genes is not affected. We discuss the implications of these results to understand the role of ASH2L and Xist repeat E for histone modifications and escape gene regulation during random X-chromosome inactivation.
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Affiliation(s)
- Minghui Yue
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Akiyo Ogawa
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Norishige Yamada
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - John Lalith Charles Richard
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Allergy & Immunology and Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Yuya Ogawa
- Division of Reproductive Sciences, Perinatal Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail:
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37
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Barski A. AP-1 transcription factor reprograms T cell epigenome during activation. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.124.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Upon encountering an antigen, naïve T helper (Th) cells are activated, differentiate into several lineages and contribute to immune response. Epigenetic changes at several cytokine and other effector genes during activation has been described previously, but the mechanism behind these changes is not understood. Here, we have profiled open chromatin during human T cell activation using ATAC-Seq approach and identified the regions where epigenetic changes take place. T cell activation requires antigen signaling via T cell receptor and co-stimulation via CD28 which in turn result in nuclear translocation of NFAT and AP-1 transcription factors. For this reason, we profiled genome-wide distribution of these proteins during activation by ChIP-Seq. Our results show that 73% of activation-induced open chromatin loci contain binding sites for AP-1, whereas 39% of them bind NFAT. Over 90 % of the binding sites for NFAT were shared with AP-1. We and others have previously shown that the lack of co-stimulation results in reduction or delay of AP-1 translocation into the nucleus. In order to confirm the role of AP-1 in establishment of the open chromatin structure during activation we mapped open chromatin in the cells that were activated without co-stimulation. Our data showed that ATAC signal was reduced at the open chromatin sites bound by AP-1 in the absence of co-stimulation, suggesting that CD28 signaling and AP-1 transcription factor are involved in open chromatin formation during T cell activation.
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Affiliation(s)
- Artem Barski
- 1Cincinnati Children’s Hosp. Med. Ctr
- 2Univ. of Cincinnati
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38
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Stevens ML, Chaturvedi P, Rankin SA, Macdonald M, Jagannathan S, Yukawa M, Barski A, Zorn AM. Genomic integration of Wnt/β-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional programs. Development 2017; 144:1283-1295. [PMID: 28219948 DOI: 10.1242/dev.145789] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/03/2017] [Indexed: 12/16/2022]
Abstract
Digestive system development is orchestrated by combinatorial signaling interactions between endoderm and mesoderm, but how these signals are interpreted in the genome is poorly understood. Here we identified the transcriptomes of Xenopus foregut and hindgut progenitors, which are conserved with mammals. Using RNA-seq and ChIP-seq we show that BMP/Smad1 regulates dorsal-ventral gene expression in both the endoderm and mesoderm, whereas Wnt/β-catenin acts as a genome-wide toggle between foregut and hindgut programs. Unexpectedly, β-catenin and Smad1 binding were associated with both transcriptional activation and repression, with Wnt-repressed genes often lacking canonical Tcf DNA binding motifs, suggesting a novel mode of direct repression. Combinatorial Wnt and BMP signaling was mediated by Smad1 and β-catenin co-occupying hundreds of cis-regulatory DNA elements, and by a crosstalk whereby Wnt negatively regulates BMP ligand expression in the foregut. These results extend our understanding of gastrointestinal organogenesis and of how Wnt and BMP might coordinate genomic responses in other contexts.
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Affiliation(s)
- Mariana L Stevens
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Scott A Rankin
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Melissa Macdonald
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Sajjeev Jagannathan
- Division of Allergy & Immunology and Human Genetics, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Masashi Yukawa
- Division of Allergy & Immunology and Human Genetics, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Artem Barski
- Division of Allergy & Immunology and Human Genetics, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Research Foundation and Department of Pediatrics College of Medicine, University of Cincinnati, Cincinnati, OH 45229, USA
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Zeng C, Wu D, Vanoni S, Noah T, Aihara E, Barski A, Kartashov A, Rochman M, Sherrill J, Rothenberg ME, Hogan SP. The Effect Of SLC9A3 On Esophageal Epithelium In Eosinophilic Esophagitis (EoE). J Allergy Clin Immunol 2017. [DOI: 10.1016/j.jaci.2016.12.235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Barski A, Cuddapah S, Kartashov AV, Liu C, Imamichi H, Yang W, Peng W, Lane HC, Zhao K. Rapid Recall Ability of Memory T cells is Encoded in their Epigenome. Sci Rep 2017; 7:39785. [PMID: 28054639 PMCID: PMC5215294 DOI: 10.1038/srep39785] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022] Open
Abstract
Even though T-cell receptor (TCR) stimulation together with co-stimulation is sufficient for the activation of both naïve and memory T cells, the memory cells are capable of producing lineage specific cytokines much more rapidly than the naïve cells. The mechanisms behind this rapid recall response of the memory cells are still not completely understood. Here, we performed epigenetic profiling of human resting naïve, central and effector memory T cells using ChIP-Seq and found that unlike the naïve cells, the regulatory elements of the cytokine genes in the memory T cells are marked by activating histone modifications even in the resting state. Therefore, the ability to induce expression of rapid recall genes upon activation is associated with the deposition of positive histone modifications during memory T cell differentiation. We propose a model of T cell memory, in which immunological memory state is encoded epigenetically, through poising and transcriptional memory.
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Affiliation(s)
- Artem Barski
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, NY, 10987, USA
| | - Andrey V Kartashov
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Chong Liu
- Divisions of Allergy &Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA
| | - Hiromi Imamichi
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wenjing Yang
- Department of Physics, The George Washington University, D.C., 20052, USA
| | - Weiqun Peng
- Department of Physics, The George Washington University, D.C., 20052, USA
| | - H Clifford Lane
- Clinical and Molecular Retrovirology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Bian F, Gao F, Kartashov AV, Jegga AG, Barski A, Das SK. Polycomb repressive complex 1 controls uterine decidualization. Sci Rep 2016; 6:26061. [PMID: 27181215 PMCID: PMC4867636 DOI: 10.1038/srep26061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/27/2016] [Indexed: 01/21/2023] Open
Abstract
Uterine stromal cell decidualization is an essential part of the reproductive process. Decidual tissue development requires a highly regulated control of the extracellular tissue remodeling; however the mechanism of this regulation remains unknown. Through systematic expression studies, we detected that Cbx4/2, Rybp, and Ring1B [components of polycomb repressive complex 1 (PRC1)] are predominantly utilized in antimesometrial decidualization with polyploidy. Immunofluorescence analyses revealed that PRC1 members are co-localized with its functional histone modifier H2AK119ub1 (mono ubiquitination of histone-H2A at lysine-119) in polyploid cell. A potent small-molecule inhibitor of Ring1A/B E3-ubiquitin ligase or siRNA-mediated suppression of Cbx4 caused inhibition of H2AK119ub1, in conjunction with perturbation of decidualization and polyploidy development, suggesting a role for Cbx4/Ring1B-containing PRC1 in these processes. Analyses of genetic signatures by RNA-seq studies showed that the inhibition of PRC1 function affects 238 genes (154 up and 84 down) during decidualization. Functional enrichment analyses identified that about 38% genes primarily involved in extracellular processes are specifically targeted by PRC1. Furthermore, ~15% of upregulated genes exhibited a significant overlap with the upregulated Bmp2 null-induced genes in mice. Overall, Cbx4/Ring1B-containing PRC1 controls decidualization via regulation of extracellular gene remodeling functions and sheds new insights into underlying molecular mechanism(s) through transcriptional repression regulation.
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Affiliation(s)
- Fenghua Bian
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Fei Gao
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrey V Kartashov
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anil G Jegga
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sanjoy K Das
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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Barski A, Kartashov A. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.209.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Development of next generation sequencing (NGS) has revolutionized molecular biology by enhancing our ability to perform genome-wide studies. However, due to the need for bioinformatics expertise and the sheer size of resulting datasets, use of these technologies is still beyond the capabilities of many laboratories. Here we present BioWardrobe, a platform that allows storing, visualizing and analyzing epigenomics and transcriptomics NGS data using a biologist friendly web-based graphical user interface without the need for programming expertize. BioWardrobe can be installed on consumer class hardware within an institutional local network. Analysis capabilities include predefined pipelines that allow the user to download data from either institutional core facility or public databases, perform quality control, map reads, and visualize data on a built-in mirror of the UCSC genome browser. Reads Per Kilobase per Million mapped (RPKMs) are calculated for RNA-Seq, and islands of enrichment are identified for ChIP-Seq and similar datasets. Advanced analysis capabilities include differential gene expression and binding analysis, and creation of average tag density profiles and heatmaps. BioWardrobe package and documentation is available at http://biowardrobe.com.
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Yukawa M, Jagannathan S, Kartashov A, Barski A. CD28 co-stimulatory signaling and AP-1 transcription factor are involved in the establishment of open chromatin during T cell activation. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.133.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Upon encountering an antigen, naïve T helper (Th) cells are activated, differentiate into several lineages and contribute to immune response. Epigenetic changes at several cytokine and other effector genes during activation has been described previously, but the mechanism behind these changes is not understood. Here, we have profiled open chromatin during human T cell activation using ATAC-Seq approach and identified the regions where epigenetic changes take place genome-wide. Open chromatin formation correlated with induction of gene expression at nearby genes. This gene set was also enriched for functions related to T cell activation and immune response in GO analysis. T cell activation requires antigen signaling via T cell receptor and co-stimulation via CD28 which in turn result in nuclear translocation of NFAT and AP-1 transcription factors. For this reason, we profiled genome-wide distribution of these proteins during activation by ChIP-Seq. Our results show that 73% of activation-induced open chromatin loci contain binding sites for AP-1, whereas 39% of them bind NFAT. Over 90 % of the binding sites for NFAT were shared with AP-1 binding sites. We and others have previously shown that the lack of co-stimulation results in reduction or delay of AP-1 translocation into the nucleus. In order to confirm the role of AP-1 in establishment of the open chromatin structure during activation we mapped open chromatin in the cells that were activated without co-stimulation. Our data showed that ATAC signal was reduced at the open chromatin sites bound by AP-1 in the absence of co-stimulation, suggesting that CD28 signaling and AP-1 transcription factor are involved in open chromatin formation during T cell activation.
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Jagannathan L, Jose CC, Arita A, Kluz T, Sun H, Zhang X, Yao Y, Kartashov AV, Barski A, Costa M, Cuddapah S. Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. J Cell Physiol 2015; 231:1611-20. [PMID: 26588041 DOI: 10.1002/jcp.25262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/04/2023]
Abstract
Oxygen levels range from 2% to 9% in vivo. Atmospheric O2 levels (21%) are known to induce cell proliferation defects and cellular senescence in primary cell cultures. However, the mechanistic basis of the deleterious effects of higher O2 levels is not fully understood. On the other hand, immortalized cells including cancer cell lines, which evade cellular senescence are normally cultured at 21% O2 and the effects of higher O2 on these cells are understudied. Here, we addressed this problem by culturing immortalized human bronchial epithelial (BEAS-2B) cells at ambient atmospheric, 21% O2 and lower, 10% O2. Our results show increased inflammatory response at 21% O2 but not at 10% O2. We found higher RelA binding at the NF-κB1/RelA target gene promoters as well as upregulation of several pro-inflammatory cytokines in cells cultured at 21% O2. RelA knockdown prevented the upregulation of the pro-inflammatory cytokines at 21% O2, suggesting NF-κB1/RelA as a major mediator of inflammatory response in cells cultured at 21% O2. Interestingly, unlike the 21% O2 cultured cells, exposure of 10% O2 cultured cells to H2O2 did not elicit inflammatory response, suggesting increased ability to tolerate oxidative stress in cells cultured at lower O2 levels.
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Affiliation(s)
- Lakshmanan Jagannathan
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Cynthia C Jose
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Adriana Arita
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Thomas Kluz
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Yixin Yao
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Andrey V Kartashov
- Division of Allergy and Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Artem Barski
- Division of Allergy and Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
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Bouffi C, Kartashov AV, Schollaert KL, Chen X, Bacon WC, Weirauch MT, Barski A, Fulkerson PC. Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. J Immunol 2015; 195:2683-95. [PMID: 26268651 DOI: 10.4049/jimmunol.1500510] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/14/2015] [Indexed: 12/13/2022]
Abstract
The production of mature eosinophils (Eos) is a tightly orchestrated process with the aim to sustain normal Eos levels in tissues while also maintaining low numbers of these complex and sensitive cells in the blood. To identify regulators of homeostatic eosinophilopoiesis in mice, we took a global approach to identify genome-wide transcriptome and epigenome changes that occur during homeostasis at critical developmental stages, including Eos-lineage commitment and lineage maturation. Our analyses revealed a markedly greater number of transcriptome alterations associated with Eos maturation (1199 genes) than with Eos-lineage commitment (490 genes), highlighting the greater transcriptional investment necessary for differentiation. Eos-lineage-committed progenitors (EoPs) were noted to express high levels of granule proteins and contain granules with an ultrastructure distinct from that of mature resting Eos. Our analyses also delineated a 976-gene Eos-lineage transcriptome that included a repertoire of 56 transcription factors, many of which have never previously been associated with Eos. EoPs and Eos, but not granulocyte-monocyte progenitors or neutrophils, expressed Helios and Aiolos, members of the Ikaros family of transcription factors, which regulate gene expression via modulation of chromatin structure and DNA accessibility. Epigenetic studies revealed a distinct distribution of active chromatin marks between genes induced with lineage commitment and genes induced with cell maturation during Eos development. In addition, Aiolos and Helios binding sites were significantly enriched in genes expressed by EoPs and Eos with active chromatin, highlighting a potential novel role for Helios and Aiolos in regulating gene expression during Eos development.
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Affiliation(s)
- Carine Bouffi
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Kaila L Schollaert
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Xiaoting Chen
- School of Electronic and Computing Systems, University of Cincinnati, Cincinnati, OH 45221
| | - W Clark Bacon
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229; Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229; and
| | - Artem Barski
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229; Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229
| | - Patricia C Fulkerson
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH 45229;
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Kartashov AV, Barski A. BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data. Genome Biol 2015; 16:158. [PMID: 26248465 PMCID: PMC4531538 DOI: 10.1186/s13059-015-0720-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/07/2015] [Indexed: 01/24/2023] Open
Abstract
High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps. BioWardrobe can be found at http://biowardrobe.com.
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Affiliation(s)
- Andrey V Kartashov
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA. .,Division of Human Genetics, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA.
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Abstract
Background The male germline transcriptome changes dramatically during the mitosis-to-meiosis transition to activate late spermatogenesis genes and to transiently suppress genes commonly expressed in somatic lineages and spermatogenesis progenitor cells, termed somatic/progenitor genes. Results These changes reflect epigenetic regulation. Induction of late spermatogenesis genes during spermatogenesis is facilitated by poised chromatin established in the stem cell phases of spermatogonia, whereas silencing of somatic/progenitor genes during meiosis and postmeiosis is associated with formation of bivalent domains which also allows the recovery of the somatic/progenitor program after fertilization. Importantly, during spermatogenesis mechanisms of epigenetic regulation on sex chromosomes are different from autosomes: X-linked somatic/progenitor genes are suppressed by meiotic sex chromosome inactivation without deposition of H3K27me3. Conclusions Our results suggest that bivalent H3K27me3 and H3K4me2/3 domains are not limited to developmental promoters (which maintain bivalent domains that are silent throughout the reproductive cycle), but also underlie reversible silencing of somatic/progenitor genes during the mitosis-to-meiosis transition in late spermatogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0159-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ho-Su Sin
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.,Present address: Department of Developmental Biology, Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA
| | - Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.,Present address: Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Artem Barski
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 49229, USA.
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Rochman M, Kartashov A, Caldwell J, Collins M, Stucke E, Kc K, Sherrill J, Herren J, Barski A, Rothenberg M. Neurotrophic tyrosine kinase receptor 1 is a direct transcriptional and epigenetic target of IL-13 involved in allergic inflammation. Mucosal Immunol 2015; 8:785-98. [PMID: 25389033 PMCID: PMC4429043 DOI: 10.1038/mi.2014.109] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 10/09/2014] [Indexed: 02/04/2023]
Abstract
Although interleukin (IL)-13 and neurotrophins are functionally important for the pathogenesis of immune responses, the interaction of these pathways has not been explored. Herein, by interrogating IL-13-induced responses in human epithelial cells we show that neurotrophic tyrosine kinase receptor, type 1 (NTRK1), a cognate, high-affinity receptor for nerve growth factor (NGF), is an early transcriptional IL-13 target. Induction of NTRK1 was accompanied by accumulation of activating epigenetic marks in the promoter; transcriptional and epigenetic changes were signal transducer and activator of transcription 6 dependent. Using eosinophilic esophagitis as a model for human allergic inflammation, we found that NTRK1 was increased in inflamed tissue and dynamically expressed as a function of disease activity and that the downstream mediator of NTRK1 signaling early growth response 1 protein was elevated in allergic inflammatory tissue compared with control tissue. Unlike NTRK1, its ligand NGF was constitutively expressed in control and disease states, indicating that IL-13-stimulated NTRK1 induction is a limiting factor in pathway activation. In epithelial cells, NGF and IL-13 synergistically induced several target genes, including chemokine (C-C motif) ligand 26 (eotaxin-3). In summary, we have demonstrated that IL-13 confers epithelial cell responsiveness to NGF by regulating NTRK1 levels by a transcriptional and epigenetic mechanism and that this process likely contributes to allergic inflammation.
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Affiliation(s)
- M. Rochman
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - A.V. Kartashov
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - J.M. Caldwell
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - M.H. Collins
- Divisions of Pathology and Laboratory Medicine, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - E.M. Stucke
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - K. Kc
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - J.D. Sherrill
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - J. Herren
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - A. Barski
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
| | - M.E. Rothenberg
- Divisions of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229-3026, USA
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Rochman Y, Yukawa M, Kartashov AV, Barski A. Functional characterization of human T cell hyporesponsiveness induced by CTLA4-Ig. PLoS One 2015; 10:e0122198. [PMID: 25860138 PMCID: PMC4393265 DOI: 10.1371/journal.pone.0122198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/08/2015] [Indexed: 01/08/2023] Open
Abstract
During activation, T cells integrate multiple signals from APCs and cytokine milieu. The blockade of these signals can have clinical benefits as exemplified by CTLA4-Ig, which blocks interaction of B7 co-stimulatory molecules on APCs with CD28 on T cells. Variants of CTLA4-Ig, abatacept and belatacept are FDA approved as immunosuppressive agents in arthritis and transplantation, yet murine studies suggested that CTLA4-Ig could be beneficial in a number of other diseases. However, detailed analysis of human CD4 cell hyporesponsivness induced by CTLA4-Ig has not been performed. Herein, we established a model to study the effect of CTLA4-Ig on the activation of human naïve T cells in a human mixed lymphocytes system. Comparison of human CD4 cells activated in the presence or absence of CTLA4-Ig showed that co-stimulation blockade during TCR activation does not affect NFAT signaling but results in decreased activation of NF-κB and AP-1 transcription factors followed by a profound decrease in proliferation and cytokine production. The resulting T cells become hyporesponsive to secondary activation and, although capable of receiving TCR signals, fail to proliferate or produce cytokines, demonstrating properties of anergic cells. However, unlike some models of T cell anergy, these cells did not possess increased levels of the TCR signaling inhibitor CBLB. Rather, the CTLA4-Ig-induced hyporesponsiveness was associated with an elevated level of p27kip1 cyclin-dependent kinase inhibitor.
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Affiliation(s)
- Yrina Rochman
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Masashi Yukawa
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Andrey V. Kartashov
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
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Hasegawa K, Sin HS, Maezawa S, Broering TJ, Kartashov AV, Alavattam KG, Ichijima Y, Zhang F, Bacon WC, Greis KD, Andreassen PR, Barski A, Namekawa SH. SCML2 establishes the male germline epigenome through regulation of histone H2A ubiquitination. Dev Cell 2015; 32:574-88. [PMID: 25703348 PMCID: PMC4391279 DOI: 10.1016/j.devcel.2015.01.014] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 12/23/2014] [Accepted: 01/16/2015] [Indexed: 01/03/2023]
Abstract
Gametogenesis is dependent on the expression of germline-specific genes. However, it remains unknown how the germline epigenome is distinctly established from that of somatic lineages. Here we show that genes commonly expressed in somatic lineages and spermatogenesis-progenitor cells undergo repression in a genome-wide manner in late stages of the male germline and identify underlying mechanisms. SCML2, a germline-specific subunit of a Polycomb repressive complex 1 (PRC1), establishes the unique epigenome of the male germline through two distinct antithetical mechanisms. SCML2 works with PRC1 and promotes RNF2-dependent ubiquitination of H2A, thereby marking somatic/progenitor genes on autosomes for repression. Paradoxically, SCML2 also prevents RNF2-dependent ubiquitination of H2A on sex chromosomes during meiosis, thereby enabling unique epigenetic programming of sex chromosomes for male reproduction. Our results reveal divergent mechanisms involving a shared regulator by which the male germline epigenome is distinguished from that of the soma and progenitor cells.
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Affiliation(s)
- Kazuteru Hasegawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Ho-Su Sin
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Tyler J Broering
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Andrey V Kartashov
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Yosuke Ichijima
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - W Clark Bacon
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Artem Barski
- Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.
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