1
|
Kandel A, Li L, Wang Y, Tuo W, Xiao Z. Differentiation and Regulation of Bovine Th2 Cells In Vitro. Cells 2024; 13:738. [PMID: 38727273 PMCID: PMC11083891 DOI: 10.3390/cells13090738] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Bovine Th2 cells have usually been characterized by IL4 mRNA expression, but it is unclear whether their IL4 protein expression corresponds to transcription. We found that grass-fed healthy beef cattle, which had been regularly exposed to parasites on the grass, had a low frequency of IL4+ Th2 cells during flow cytometry, similar to animals grown in feedlots. To assess the distribution of IL4+ CD4+ T cells across tissues, samples from the blood, spleen, abomasal (draining), and inguinal lymph nodes were examined, which revealed limited IL4 protein detection in the CD4+ T cells across the examined tissues. To determine if bovine CD4+ T cells may develop into Th2 cells, naïve cells were stimulated with anti-bovine CD3 under a Th2 differentiation kit in vitro. The cells produced primarily IFNγ proteins, with only a small fraction (<10%) co-expressing IL4 proteins. Quantitative PCR confirmed elevated IFNγ transcription but no significant change in IL4 transcription. Surprisingly, GATA3, the master regulator of IL4, was highest in naïve CD4+ T cells but was considerably reduced following differentiation. To determine if the differentiated cells were true Th2 cells, an unbiased proteomic assay was carried out. The assay identified 4212 proteins, 422 of which were differently expressed compared to those in naïve cells. Based on these differential proteins, Th2-related upstream components were predicted, including CD3, CD28, IL4, and IL33, demonstrating typical Th2 differentiation. To boost IL4 expression, T cell receptor (TCR) stimulation strength was reduced by lowering anti-CD3 concentrations. Consequently, weak TCR stimulation essentially abolished Th2 expansion and survival. In addition, extra recombinant bovine IL4 (rbIL4) was added during Th2 differentiation, but, despite enhanced expansion, the IL4 level remained unaltered. These findings suggest that, while bovine CD4+ T cells can respond to Th2 differentiation stimuli, the bovine IL4 pathway is not regulated in the same way as in mice and humans. Furthermore, Ostertagia ostertagi (OO) extract, a gastrointestinal nematode in cattle, inhibited signaling via CD3, CD28, IL4, and TLRs/MYD88, indicating that external pathogens can influence bovine Th2 differentiation. In conclusion, though bovine CD4+ T cells can respond to IL4-driven differentiation, IL4 expression is not a defining feature of differentiated bovine Th2 cells.
Collapse
Affiliation(s)
- Anmol Kandel
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.K.); (L.L.)
| | - Lei Li
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.K.); (L.L.)
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
| | - Zhengguo Xiao
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.K.); (L.L.)
| |
Collapse
|
2
|
Marziali F, Song Y, Nguyen XN, Belmudes L, Burlaud-Gaillard J, Roingeard P, Couté Y, Cimarelli A. A Proteomics-Based Approach Identifies the NEDD4 Adaptor NDFIP2 as an Important Regulator of Ifitm3 Levels. Viruses 2023; 15:1993. [PMID: 37896772 PMCID: PMC10611234 DOI: 10.3390/v15101993] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
IFITMs are a family of highly related interferon-induced transmembrane proteins that interfere with the processes of fusion between viral and cellular membranes and are thus endowed with broad antiviral properties. A number of studies have shown how the antiviral potency of IFITMs is highly dependent on their steady-state levels, their intracellular distribution and a complex pattern of post-translational modifications, parameters that are overall tributary of a number of cellular partners. In an effort to identify additional protein partners involved in the biology of IFITMs, we devised a proteomics-based approach based on the piggyback incorporation of IFITM3 partners into extracellular vesicles. MS analysis of the proteome of vesicles bearing or not bearing IFITM3 identified the NDFIP2 protein adaptor protein as an important regulator of IFITM3 levels. NDFIP2 is a membrane-anchored adaptor protein of the E3 ubiquitin ligases of the NEDD4 family that have already been found to be involved in IFITM3 regulation. We show here that NDFIP2 acts as a recruitment factor for both IFITM3 and NEDD4 and mediates their distribution in lysosomal vesicles. The genetic inactivation and overexpression of NDFIP2 drive, respectively, lower and higher levels of IFITM3 accumulation in the cell, overall suggesting that NDFIP2 locally competes with IFITM3 for NEDD4 binding. Given that NDFIP2 is itself tightly regulated and highly responsive to external cues, our study sheds light on a novel and likely dynamic layer of regulation of IFITM3.
Collapse
Affiliation(s)
- Federico Marziali
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69100 Lyon, France (X.-N.N.)
| | - Yuxin Song
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69100 Lyon, France (X.-N.N.)
| | - Xuan-Nhi Nguyen
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69100 Lyon, France (X.-N.N.)
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, 38000 Grenoble, France; (L.B.); (Y.C.)
| | - Julien Burlaud-Gaillard
- Plateforme IBiSA de Microscopie Electronique, Université de Tours et CHU de Tours, 37000 Tours, France; (J.B.-G.); (P.R.)
| | - Philippe Roingeard
- Plateforme IBiSA de Microscopie Electronique, Université de Tours et CHU de Tours, 37000 Tours, France; (J.B.-G.); (P.R.)
- INSERM U1259, Université de Tours et CHU de Tours, 37000 Tours, France
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, 38000 Grenoble, France; (L.B.); (Y.C.)
| | - Andrea Cimarelli
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, 69100 Lyon, France (X.-N.N.)
| |
Collapse
|
3
|
Wilkinson ID, Mahmood T, Yasmin SF, Tomlinson A, Nazari J, Alhaj H, el din SN, Neill J, Pandit C, Ashraf S, Cardno AG, Clapcote SJ, Inglehearn CF, Woodruff PW. In memory of Professor Iain Wilkinson: cognitive and neuroimaging endophenotypes in a consanguineous schizophrenia multiplex family. Psychol Med 2023; 53:3178-3186. [PMID: 35125130 PMCID: PMC10235651 DOI: 10.1017/s0033291721005250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/24/2021] [Accepted: 12/03/2021] [Indexed: 11/05/2022]
Abstract
BACKGROUND Schizophrenia endophenotypes may help elucidate functional effects of genetic risk variants in multiply affected consanguineous families that segregate recessive risk alleles of large effect size. We studied the association between a schizophrenia risk locus involving a 6.1Mb homozygous region on chromosome 13q22-31 in a consanguineous multiplex family and cognitive functioning, haemodynamic response and white matter integrity using neuroimaging. METHODS We performed CANTAB neuropsychological testing on four affected family members (all homozygous for the risk locus), ten unaffected family members (seven homozygous and three heterozygous) and ten healthy volunteers, and tested neuronal responses on fMRI during an n-back working memory task, and white matter integrity on diffusion tensor imaging (DTI) on four affected and six unaffected family members (four homozygous and two heterozygous) and three healthy volunteers. For cognitive comparisons we used a linear mixed model (Kruskal-Wallis) test, followed by posthoc Dunn's pairwise tests with a Bonferroni adjustment. For fMRI analysis, we counted voxels exceeding the p < 0.05 corrected threshold. DTI analysis was observational. RESULTS Family members with schizophrenia and unaffected family members homozygous for the risk haplotype showed attention (p < 0.01) and working memory deficits (p < 0.01) compared with healthy controls; a neural activation laterality bias towards the right prefrontal cortex (voxels reaching p < 0.05, corrected) and observed lower fractional anisotropy in the anterior cingulate cortex and left dorsolateral prefrontal cortex. CONCLUSIONS In this family, homozygosity at the 13q risk locus was associated with impaired cognition, white matter integrity, and altered laterality of neural activation.
Collapse
Affiliation(s)
- Iain D. Wilkinson
- Academic Unit of Radiology, School of Medicine, University of Sheffield, Sheffield, UK
| | - Tariq Mahmood
- Leeds & York Partnership NHS Foundation Trust, Leeds, UK
| | - Sophia Faye Yasmin
- Academic Unit of Radiology, School of Medicine, University of Sheffield, Sheffield, UK
| | | | - Jamshid Nazari
- South West Yorkshire NHS Foundation Trust, Wakefield, UK
| | - Hamid Alhaj
- University of Sharjah, UAE
- Department of Neuroscience, School of Medicine, University of Sheffield, Sheffield, UK
| | | | - Joanna Neill
- Division of Pharmacy and Optometry, University of Manchester, Manchester, UK
| | - Chhaya Pandit
- Leeds & York Partnership NHS Foundation Trust, Leeds, UK
| | - Shahzad Ashraf
- South West Yorkshire NHS Foundation Trust, Wakefield, UK
| | - Alastair G. Cardno
- Psychological & Social Medicine, Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | | | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Peter W. Woodruff
- Department of Neuroscience, School of Medicine, University of Sheffield, Sheffield, UK
| |
Collapse
|
4
|
Shetty A, Tripathi SK, Junttila S, Buchacher T, Biradar R, Bhosale S, Envall T, Laiho A, Moulder R, Rasool O, Galande S, Elo L, Lahesmaa R. A systematic comparison of FOSL1, FOSL2 and BATF-mediated transcriptional regulation during early human Th17 differentiation. Nucleic Acids Res 2022; 50:4938-4958. [PMID: 35511484 PMCID: PMC9122603 DOI: 10.1093/nar/gkac256] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 07/15/2021] [Revised: 03/30/2022] [Accepted: 04/19/2022] [Indexed: 12/21/2022] Open
Abstract
Th17 cells are essential for protection against extracellular pathogens, but their aberrant activity can cause autoimmunity. Molecular mechanisms that dictate Th17 cell-differentiation have been extensively studied using mouse models. However, species-specific differences underscore the need to validate these findings in human. Here, we characterized the human-specific roles of three AP-1 transcription factors, FOSL1, FOSL2 and BATF, during early stages of Th17 differentiation. Our results demonstrate that FOSL1 and FOSL2 co-repress Th17 fate-specification, whereas BATF promotes the Th17 lineage. Strikingly, FOSL1 was found to play different roles in human and mouse. Genome-wide binding analysis indicated that FOSL1, FOSL2 and BATF share occupancy over regulatory regions of genes involved in Th17 lineage commitment. These AP-1 factors also share their protein interacting partners, which suggests mechanisms for their functional interplay. Our study further reveals that the genomic binding sites of FOSL1, FOSL2 and BATF harbour hundreds of autoimmune disease-linked SNPs. We show that many of these SNPs alter the ability of these transcription factors to bind DNA. Our findings thus provide critical insights into AP-1-mediated regulation of human Th17-fate and associated pathologies.
Collapse
Affiliation(s)
| | | | | | | | - Rahul Biradar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Santosh D Bhosale
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- Department of Biochemistry and Molecular Biology, Protein Research Group, University of Southern Denmark, Campusvej 55, Odense M, DK 5230, Denmark
| | - Tapio Envall
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
- Department of Life Sciences, Shiv Nadar University, Delhi-NCR
| | - Laura L Elo
- Correspondence may also be addressed to Laura Elo. Tel: +358 29 450 2090;
| | - Riitta Lahesmaa
- To whom correspondence should be addressed. Tel: +358 29 450 2415;
| |
Collapse
|
5
|
Choi EH, Hwang D. Association Study of NDFIP2 Genetic Polymorphism with Asthma in the Korean Population. Korean J Clin Lab Sci 2021. [DOI: 10.15324/kjcls.2021.53.3.249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Eun Hye Choi
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
| | - Dahyun Hwang
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Korea
| |
Collapse
|
6
|
Syreeni A, Sandholm N, Sidore C, Cucca F, Haukka J, Harjutsalo V, Groop PH. Genome-wide search for genes affecting the age at diagnosis of type 1 diabetes. J Intern Med 2021; 289:662-674. [PMID: 33179336 PMCID: PMC8247053 DOI: 10.1111/joim.13187] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Type 1 diabetes (T1D) is an autoimmune disease affecting individuals in the early years of life. Although previous studies have identified genetic loci influencing T1D diagnosis age, these studies did not investigate the genome with high resolution. OBJECTIVE AND METHODS We performed a genome-wide meta-analysis for age at diagnosis with cohorts from Finland (Finnish Diabetic Nephropathy Study), the United Kingdom (UK Genetic Resource Investigating Diabetes) and Sardinia. Through SNP associations, transcriptome-wide association analysis linked T1D diagnosis age and gene expression. RESULTS We identified two chromosomal regions associated with T1D diagnosis age: multiple independent variants in the HLA region on chromosome 6 and a locus on chromosome 17q12. We performed gene-level association tests with transcriptome prediction models from two whole blood datasets, lymphocyte cell line, spleen, pancreas and small intestine tissues. Of the non-HLA genes, lower PNMT expression in whole blood, and higher IKZF3 and ZPBP2, and lower ORMDL3 and GSDMB transcription levels in multiple tissues were associated with lower T1D diagnosis age (FDR = 0.05). These genes lie on chr17q12 which is associated with T1D, other autoimmune diseases, and childhood asthma. Additionally, higher expression of PHF20L1, a gene not previously implicated in T1D, was associated with lower diagnosis age in lymphocytes, pancreas, and spleen. Altogether, the non-HLA associations were enriched in open chromatin in various blood cells, blood vessel tissues and foetal thymus tissue. CONCLUSION Multiple genes on chr17q12 and PHF20L1 on chr8 were associated with T1D diagnosis age and only further studies may elucidate the role of these genes for immunity and T1D onset.
Collapse
Affiliation(s)
- A Syreeni
- From the, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - N Sandholm
- From the, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - C Sidore
- Instituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Italy
| | - F Cucca
- Instituto di Ricerca Genetica e Biomedica, CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - J Haukka
- From the, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - V Harjutsalo
- From the, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.,National Institute for Health and Welfare, Helsinki, Finland
| | - P-H Groop
- From the, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.,Abdominal Center, Nephrology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.,Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | | |
Collapse
|
7
|
Renoux F, Stellato M, Haftmann C, Vogetseder A, Huang R, Subramaniam A, Becker MO, Blyszczuk P, Becher B, Distler JHW, Kania G, Boyman O, Distler O. The AP1 Transcription Factor Fosl2 Promotes Systemic Autoimmunity and Inflammation by Repressing Treg Development. Cell Rep 2021; 31:107826. [PMID: 32610127 DOI: 10.1016/j.celrep.2020.107826] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/27/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Regulatory T cells (Tregs) represent a major population in the control of immune homeostasis and autoimmunity. Here we show that Fos-like 2 (Fosl2), a TCR-induced AP1 transcription factor, represses Treg development and controls autoimmunity. Mice overexpressing Fosl2 (Fosl2tg) indeed show a systemic inflammatory phenotype, with immune infiltrates in multiple organs. This phenotype is absent in Fosl2tg × Rag2-/- mice lacking T and B cells, and Fosl2 induces T cell-intrinsic reduction of Treg development that is responsible for the inflammatory phenotype. Fosl2tg T cells can transfer inflammation, which is suppressed by the co-delivery of Tregs, while Fosl2 deficiency in T cells reduces the severity of autoimmunity in the EAE model. We find that Fosl2 could affect expression of FoxP3 and other Treg development genes. Our data highlight the importance of AP1 transcription factors, in particular Fosl2, during T cell development to determine Treg differentiation and control autoimmunity.
Collapse
Affiliation(s)
- Florian Renoux
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Mara Stellato
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Claudia Haftmann
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Riyun Huang
- Sanofi, Immunology and Inflammation Research TA, Cambridge, MA 02139, USA
| | - Arun Subramaniam
- Sanofi, Immunology and Inflammation Research TA, Cambridge, MA 02139, USA
| | - Mike O Becker
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Przemyslaw Blyszczuk
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland; Department of Clinical Immunology, Jagiellonian University Medical College, Cracow, Poland
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Jörg H W Distler
- Department of Internal Medicine 3, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Gabriela Kania
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland; Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland; Faculty of Medicine, University of Zurich, Zurich, Switzerland.
| |
Collapse
|
8
|
Nain Z, Rana HK, Liò P, Islam SMS, Summers MA, Moni MA. Pathogenetic profiling of COVID-19 and SARS-like viruses. Brief Bioinform 2021; 22:1175-1196. [PMID: 32778874 PMCID: PMC7454314 DOI: 10.1093/bib/bbaa173] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/23/2020] [Accepted: 07/08/2020] [Indexed: 12/15/2022] Open
Abstract
The novel coronavirus (2019-nCoV) has recently emerged, causing COVID-19 outbreaks and significant societal/global disruption. Importantly, COVID-19 infection resembles SARS-like complications. However, the lack of knowledge about the underlying genetic mechanisms of COVID-19 warrants the development of prospective control measures. In this study, we employed whole-genome alignment and digital DNA-DNA hybridization analyses to assess genomic linkage between 2019-nCoV and other coronaviruses. To understand the pathogenetic behavior of 2019-nCoV, we compared gene expression datasets of viral infections closest to 2019-nCoV with four COVID-19 clinical presentations followed by functional enrichment of shared dysregulated genes. Potential chemical antagonists were also identified using protein-chemical interaction analysis. Based on phylogram analysis, the 2019-nCoV was found genetically closest to SARS-CoVs. In addition, we identified 562 upregulated and 738 downregulated genes (adj. P ≤ 0.05) with SARS-CoV infection. Among the dysregulated genes, SARS-CoV shared ≤19 upregulated and ≤22 downregulated genes with each of different COVID-19 complications. Notably, upregulation of BCL6 and PFKFB3 genes was common to SARS-CoV, pneumonia and severe acute respiratory syndrome, while they shared CRIP2, NSG1 and TNFRSF21 genes in downregulation. Besides, 14 genes were common to different SARS-CoV comorbidities that might influence COVID-19 disease. We also observed similarities in pathways that can lead to COVID-19 and SARS-CoV diseases. Finally, protein-chemical interactions suggest cyclosporine, resveratrol and quercetin as promising drug candidates against COVID-19 as well as other SARS-like viral infections. The pathogenetic analyses, along with identified biomarkers, signaling pathways and chemical antagonists, could prove useful for novel drug development in the fight against the current global 2019-nCoV pandemic.
Collapse
Affiliation(s)
- Zulkar Nain
- Department of Genetic Engineering and Biotechnology, East West University, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh
| | - Pietro Liò
- Artificial Intelligence Group at the University of Cambridge
| | | | | | | |
Collapse
|
9
|
Wu Y, Zhu J, Liu H, Liu H. Licochalcone A improves the cognitive ability of mice by regulating T- and B-cell proliferation. Aging (Albany NY) 2021; 13:8895-8915. [PMID: 33714945 PMCID: PMC8034954 DOI: 10.18632/aging.202704] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022]
Abstract
Licochalcone A (LA), a flavonoid found in licorice, has anticancer, antioxidant, anti-inflammatory, and neuroprotective properties. Here, we explored the effect of injecting LA into the tail vein of middle-aged C57BL/6 mice on their cognitive ability as measured by the Morris water maze (MWM) test and cerebral blood flow (CBF). The related mechanisms were assessed via RNA-seq, and T (CD3e+) and B (CD45R/B220+) cells in the spleen and whole blood were quantified via flow cytometry. LA improved the cognitive ability, according to the MWM test results, and upregulated the CBF level of treated mice. The RNA-seq results indicate that LA affected the interleukin (IL)-17 signaling pathway, which is related to T- and B-cell proliferation, and the flow cytometry data suggest that LA promoted T- and B-cell proliferation in the spleen and whole blood. We also performed immune reconstruction via a tail vein injection of lymphocytes into B-NDG (NOD-PrkdcscidIl2rgtm1/Bcge) mice before treating them with LA. We tested cognitive ability by subjecting these animals to new object recognition tests and quantified the splenic and whole blood T and B cells. Cognitive ability improved after immune reconstruction and LA treatment, and LA promoted T- and B-cell proliferation in the spleen and whole blood. This study demonstrates that LA, by activating the IL-17 signaling pathway, promotes T- and B-cell proliferation in the spleen and whole blood of mice and improves cognitive ability. Thus, LA may have immune-modulating therapeutic potential for improving cognition.
Collapse
Affiliation(s)
- Yating Wu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Jianbo Zhu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China
| | - Haifeng Liu
- China Colored-Cotton (Group) Co., Ltd., Urumqi 830016, Xinjiang, China
| | - Hailiang Liu
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi 832003, China.,Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, China
| |
Collapse
|
10
|
Patel R, Solatikia F, Zhang H, Wolde A, Kadalayil L, Karmaus W, Ewart S, Arathimos R, Relton C, Ring S, Henderson AJ, Arshad SH, Holloway JW. Sex-specific associations of asthma acquisition with changes in DNA methylation during adolescence. Clin Exp Allergy 2020; 51:318-328. [PMID: 33150670 DOI: 10.1111/cea.13776] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/24/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Underlying biological mechanisms involved in sex differences in asthma status changes from pre- to post-adolescence are unclear. DNA methylation (DNAm) has been shown to be associated with the risk of asthma. OBJECTIVE We hypothesized that asthma acquisition from pre- to post-adolescence was associated with changes in DNAm during this period at asthma-associated cytosine-phosphate-guanine (CpG) sites and such an association was sex-specific. METHODS Subjects from the Isle of Wight birth cohort (IOWBC) with DNAm in blood at ages 10 and 18 years (n = 124 females, 151 males) were studied. Using a training-testing approach, epigenome-wide CpGs associated with asthma were identified. Logistic regression was used to examine sex-specific associations of DNAm changes with asthma acquisition between ages 10 and 18 at asthma-associated CpGs. The ALSPAC birth cohort was used for independent replication. To assess functional relevance of identified CpGs, association of DNAm with gene expression in blood was assessed. RESULTS We identified 535 CpGs potentially associated with asthma. Significant interaction effects of DNAm changes and sex on asthma acquisition in adolescence were found at 13 of the 535 CpGs in IOWBC (P-values <1.0 × 10-3 ). In the replication cohort, consistent interaction effects were observed at 10 of the 13 CpGs. At 7 of these 10 CpGs, opposite DNAm changes across adolescence were observed between sexes in both cohorts. In both cohorts, cg20891917, located on IFRD1 linked to asthma, shows strong sex-specific effects on asthma transition (P-values <.01 in both cohorts). CONCLUSION AND CLINICAL RELEVANCE Gender reversal in asthma acquisition is associated with opposite changes in DNAm (males vs females) from pre- to post-adolescence at asthma-associated CpGs. These CpGs are potential biomarkers of sex-specific asthma acquisition in adolescence.
Collapse
Affiliation(s)
- Rutu Patel
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Farnaz Solatikia
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA.,Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Alemayehu Wolde
- Department of Mathematical Sciences, University of Memphis, Memphis, TN, USA
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK.,Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry Psychology and Neuroscience, King's College London, London, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,National Institute for Health Research Bristol Biomedical Research Centre, University of Bristol, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | | | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,David Hide Asthma and Allergy Research Centre, Isle of Wight, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| |
Collapse
|
11
|
Mahmood T, El-Asrag ME, Poulter JA, Cardno AG, Tomlinson A, Ahmed S, Al-Amri A, Nazari J, Neill J, Chamali RS, Kiwan N, Ghuloum S, Alhaj HA, Randerson Moor J, Khan S, Al-Amin H, Johnson CA, Woodruff P, Wilkinson ID, Ali M, Clapcote SJ, Inglehearn CF. A Recessively Inherited Risk Locus on Chromosome 13q22-31 Conferring Susceptibility to Schizophrenia. Schizophr Bull 2020; 47:796-802. [PMID: 33159203 PMCID: PMC8084434 DOI: 10.1093/schbul/sbaa161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report a consanguineous family in which schizophrenia segregates in a manner consistent with recessive inheritance of a rare, partial-penetrance susceptibility allele. From 4 marriages between 2 sets of siblings who are half first cousins, 6 offspring have diagnoses of psychotic disorder. Homozygosity mapping revealed a 6.1-Mb homozygous region on chromosome 13q22.2-31.1 shared by all affected individuals, containing 13 protein-coding genes. Microsatellite analysis confirmed homozygosity for the affected haplotype in 12 further apparently unaffected members of the family. Psychiatric reports suggested an endophenotype of milder psychiatric illness in 4 of these individuals. Exome and genome sequencing revealed no potentially pathogenic coding or structural variants within the risk haplotype. Filtering for noncoding variants with a minor allele frequency of <0.05 identified 17 variants predicted to have significant effects, the 2 most significant being within or adjacent to the SCEL gene. RNA sequencing of blood from an affected homozygote showed the upregulation of transcription from NDFIP2 and SCEL. NDFIP2 is highly expressed in brain, unlike SCEL, and is involved in determining T helper (Th) cell type 1 and Th2 phenotypes, which have previously been implicated with schizophrenia.
Collapse
Affiliation(s)
- Tariq Mahmood
- Becklin Centre, Leeds and York Partnership NHS Foundation Trust, Leeds, UK
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
- Division of Cardiovascular Sciences, School of Medicine, University of Manchester, Manchester, UK
| | - James A Poulter
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | | | - Anneka Tomlinson
- Becklin Centre, Leeds and York Partnership NHS Foundation Trust, Leeds, UK
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Sophia Ahmed
- NIHR-Sheffield Biomedical Research Centre, University of Sheffield, Sheffield, UK
| | - Ahmed Al-Amri
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- National Genetic Centre, Royal Hospital, Muscat, Oman
| | - Jamshid Nazari
- Becklin Centre, Leeds and York Partnership NHS Foundation Trust, Leeds, UK
| | - Joanna Neill
- Division of Pharmacy and Optometry, University of Manchester, Manchester, UK
| | - Rifka S Chamali
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Nancy Kiwan
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Suhaila Ghuloum
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
- Psychiatry Department, Hamad Medical Corporation, Doha, Qatar
| | - Hamid A Alhaj
- Sheffield Health and Social Care NHS Foundation Trust, Sheffield, UK
| | | | - Shabana Khan
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Hassen Al-Amin
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
| | - Colin A Johnson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Peter Woodruff
- NIHR-Sheffield Biomedical Research Centre, University of Sheffield, Sheffield, UK
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, Doha, Qatar
- Psychiatry Department, Hamad Medical Corporation, Doha, Qatar
- Sheffield Health and Social Care NHS Foundation Trust, Sheffield, UK
| | - Iain D Wilkinson
- NIHR-Sheffield Biomedical Research Centre, University of Sheffield, Sheffield, UK
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | | | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- To whom correspondence should be addressed; Beckett Street, Leeds, LS9 7TF, UK; tel: 44-(0)113-343-8646, e-mail:
| |
Collapse
|
12
|
Abstract
The immune system plays a critical role in protecting hosts from the invasion of organisms. CD4 T cells, as a key component of the immune system, are central in orchestrating adaptive immune responses. After decades of investigation, five major CD4 T helper cell (Th) subsets have been identified: Th1, Th2, Th17, Treg (T regulatory), and Tfh (follicular T helper) cells. Th1 cells, defined by the expression of lineage cytokine interferon (IFN)-γ and the master transcription factor T-bet, participate in type 1 immune responses to intracellular pathogens such as mycobacterial species and viruses; Th2 cells, defined by the expression of lineage cytokines interleukin (IL)-4/IL-5/IL-13 and the master transcription factor GAΤA3, participate in type 2 immune responses to larger extracellular pathogens such as helminths; Th17 cells, defined by the expression of lineage cytokines IL-17/IL-22 and the master transcription factor RORγt, participate in type 3 immune responses to extracellular pathogens including some bacteria and fungi; Tfh cells, by producing IL-21 and expressing Bcl6, help B cells produce corresponding antibodies; whereas Foxp3-expressing Treg cells, unlike Th1/Th2/Th17/Tfh exerting their effector functions, regulate immune responses to maintain immune cell homeostasis and prevent immunopathology. Interestingly, innate lymphoid cells (ILCs) have been found to mimic the functions of three major effector CD4 T helper subsets (Th1, Th2, and Th17) and thus can also be divided into three major subsets: ILC1s, ILC2s, and ILC3s. In this review, we will discuss the differentiation and functions of each CD4 T helper cell subset in the context of ILCs and human diseases associated with the dysregulation of these lymphocyte subsets particularly caused by monogenic mutations.
Collapse
Affiliation(s)
- Xiaoliang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| |
Collapse
|
13
|
Radens CM, Blake D, Jewell P, Barash Y, Lynch KW. Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing. RNA 2020; 26:1320-1333. [PMID: 32554554 PMCID: PMC7491319 DOI: 10.1261/rna.075929.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Human CD4+ T cells are often subdivided into distinct subtypes, including Th1, Th2, Th17, and Treg cells, that are thought to carry out distinct functions in the body. Typically, these T-cell subpopulations are defined by the expression of distinct gene repertoires; however, there is variability between studies regarding the methods used for isolation and the markers used to define each T-cell subtype. Therefore, how reliably studies can be compared to one another remains an open question. Moreover, previous analysis of gene expression in CD4+ T-cell subsets has largely focused on gene expression rather than alternative splicing. Here we take a meta-analysis approach, comparing eleven independent RNA-seq studies of human Th1, Th2, Th17, and/or Treg cells to determine the consistency in gene expression and splicing within each subtype across studies. We find that known master-regulators are consistently enriched in the appropriate subtype; however, cytokines and other genes often used as markers are more variable. Importantly, we also identify previously unknown transcriptomic markers that appear to consistently differentiate between subsets, including a few Treg-specific splicing patterns. Together this work highlights the heterogeneity in gene expression between samples designated as the same subtype, but also suggests additional markers that can be used to define functional groupings.
Collapse
Affiliation(s)
- Caleb M Radens
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Davia Blake
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Paul Jewell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yoseph Barash
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
14
|
Kowsar R, Keshtegar B, Miyamoto A. Understanding the hidden relations between pro- and anti-inflammatory cytokine genes in bovine oviduct epithelium using a multilayer response surface method. Sci Rep 2019; 9:3189. [PMID: 30816156 DOI: 10.1038/s41598-019-39081-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 01/18/2019] [Indexed: 02/06/2023] Open
Abstract
An understanding gene-gene interaction helps users to design the next experiments efficiently and (if applicable) to make a better decision of drugs application based on the different biological conditions of the patients. This study aimed to identify changes in the hidden relationships between pro- and anti-inflammatory cytokine genes in the bovine oviduct epithelial cells (BOECs) under various experimental conditions using a multilayer response surface method. It was noted that under physiological conditions (BOECs with sperm or sex hormones, such as ovarian sex steroids and LH), the mRNA expressions of IL10, IL1B, TNFA, TLR4, and TNFA were associated with IL1B, TNFA, TLR4, IL4, and IL10, respectively. Under pathophysiological + physiological conditions (BOECs with lipopolysaccharide + hormones, alpha-1-acid glycoprotein + hormones, zearalenone + hormones, or urea + hormones), the relationship among genes was changed. For example, the expression of IL10 and TNFA was associated with (IL1B, TNFA, or IL4) and TLR4 expression, respectively. Furthermore, under physiological conditions, the co-expression of IL10 + TNFA, TLR4 + IL4, TNFA + IL4, TNFA + IL4, or IL10 + IL1B and under pathophysiological + physiological conditions, the co-expression of IL10 + IL4, IL4 + IL10, TNFA + IL10, TNFA + TLR4, or IL10 + IL1B were associated with IL1B, TNFA, TLR4, IL10, or IL4 expression, respectively. Collectively, the relationships between pro- and anti-inflammatory cytokine genes can be changed with respect to the presence/absence of toxins, sex hormones, sperm, and co-expression of other gene pairs in BOECs, suggesting that considerable cautions are needed in interpreting the results obtained from such narrowly focused in vitro studies.
Collapse
|
15
|
Sumida T, Lincoln MR, Ukeje CM, Rodriguez DM, Akazawa H, Noda T, Naito AT, Komuro I, Dominguez-Villar M, Hafler DA. Activated β-catenin in Foxp3 + regulatory T cells links inflammatory environments to autoimmunity. Nat Immunol 2018; 19:1391-1402. [PMID: 30374130 PMCID: PMC6240373 DOI: 10.1038/s41590-018-0236-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [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: 11/22/2017] [Accepted: 09/11/2018] [Indexed: 12/18/2022]
Abstract
Foxp3+ regulatory T cells (Treg cells) are the central component of peripheral immune tolerance. While dysregulated Treg cytokine signature has been observed in autoimmune diseases, the regulatory mechanisms underlying pro- and anti-inflammatory cytokine production are elusive. Here, we identify imbalance between IFN-γ and IL-10 as a shared Treg signature, present in patients with multiple sclerosis (MS) and under high salt conditions. RNA-sequencing analysis on human Treg subpopulations reveals β-catenin as a key regulator of IFN-γ and IL-10 expression. The activated β-catenin signature is enriched in human IFN-γ+ Treg cells, which is confirmed in vivo with Treg specific β-catenin-stabilized mice exhibiting lethal autoimmunity with a dysfunctional Treg phenotype. Moreover, we identify prostaglandin E receptor 2 (PTGER2) as a regulator for IFN-γ and IL-10 production under high salt environment, with skewed activation of the β-catenin-SGK1-Foxo axis. Our findings reveal a novel PTGER2-β-catenin loop in Treg cells linking environmental high salt conditions to autoimmunity. Further information on experimental design is available in the Nature Research Reporting Summary linked to this article.
Collapse
Affiliation(s)
- Tomokazu Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA. .,Department of Cardiovascular Medicine, University of Tokyo Graduate School of Medicine, Tokyo, Japan.
| | - Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Chinonso M Ukeje
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Donald M Rodriguez
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.,University of Chicago, Chicago, IL, USA
| | - Hiroshi Akazawa
- Department of Cardiovascular Medicine, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Tetsuo Noda
- Department of Cell Biology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Atsuhiko T Naito
- Department of Pharmacology, Faculty of Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Issei Komuro
- Department of Cardiovascular Medicine, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Margarita Dominguez-Villar
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Department of Medicine, Immunology, Imperial College London, London, UK
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
16
|
Pasandideh M, Rahimi-mianji G, Gholizadeh M. A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep. J Genet 2018; 97:493-503. [DOI: 10.1007/s12041-018-0941-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
17
|
Schmidt A, Marabita F, Kiani NA, Gross CC, Johansson HJ, Éliás S, Rautio S, Eriksson M, Fernandes SJ, Silberberg G, Ullah U, Bhatia U, Lähdesmäki H, Lehtiö J, Gomez-Cabrero D, Wiendl H, Lahesmaa R, Tegnér J. Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3. BMC Biol 2018; 16:47. [PMID: 29730990 DOI: 10.1186/s12915-018-0518-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 04/10/2018] [Indexed: 02/08/2023] Open
Abstract
Background Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first-in-man trials of Treg transfer have achieved promising outcomes. Yet, the mechanisms governing induced Treg (iTreg) differentiation and the regulation of FOXP3 are incompletely understood. Results To gain a comprehensive and unbiased molecular understanding of FOXP3 induction, we performed time-series RNA sequencing (RNA-Seq) and proteomics profiling on the same samples during human iTreg differentiation. To enable the broad analysis of universal FOXP3-inducing pathways, we used five differentiation protocols in parallel. Integrative analysis of the transcriptome and proteome confirmed involvement of specific molecular processes, as well as overlap of a novel iTreg subnetwork with known Treg regulators and autoimmunity-associated genes. Importantly, we propose 37 novel molecules putatively involved in iTreg differentiation. Their relevance was validated by a targeted shRNA screen confirming a functional role in FOXP3 induction, discriminant analyses classifying iTregs accordingly, and comparable expression in an independent novel iTreg RNA-Seq dataset. Conclusion The data generated by this novel approach facilitates understanding of the molecular mechanisms underlying iTreg generation as well as of the concomitant changes in the transcriptome and proteome. Our results provide a reference map exploitable for future discovery of markers and drug candidates governing control of Tregs, which has important implications for the treatment of cancer, autoimmune, and inflammatory diseases. Electronic supplementary material The online version of this article (10.1186/s12915-018-0518-3) contains supplementary material, which is available to authorized users.
Collapse
|
18
|
O'Hagan KL, Miller SD, Phee H. Pak2 is essential for the function of Foxp3+ regulatory T cells through maintaining a suppressive Treg phenotype. Sci Rep 2017; 7:17097. [PMID: 29213081 DOI: 10.1038/s41598-017-17078-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
Foxp3, a key transcription factor that drives lineage differentiation of regulatory T cells (Tregs), was thought to imprint a unique and irreversible genetic signature within Tregs. Recent evidence, however, suggests that loss or attenuation of Foxp3 expression can cause Tregs to de-differentiate into effector T cells capable of producing proinflammatory cytokines. Herein, we report that the signaling kinase, p21-activated kinase 2 (Pak2), is essential for maintaining Treg stability and suppressive function. Loss of Pak2, specifically in Tregs, resulted in reduced expression of multiple Treg functional molecules, including Foxp3, CD25, Nrp-1 and CTLA-4, coupled with a loss of Treg suppressive function in vitro and in vivo. Interestingly, Pak2-deficient Tregs gained expression of Th2-associated cytokines and the transcription factor, Gata3, becoming Th2-like cells, explaining their inability to regulate immune responses. Collectively, these findings suggest Pak2 as an important signaling molecule for guarding against aberrant immune responses through regulating the stability of Foxp3+ Tregs and maintaining a suppressive Treg phenotype.
Collapse
|
19
|
Li Z, Khan MM, Kuja-Panula J, Wang H, Chen Y, Guo D, Chen ZJ, Lahesmaa R, Rauvala H, Tian L. AMIGO2 modulates T cell functions and its deficiency in mice ameliorates experimental autoimmune encephalomyelitis. Brain Behav Immun 2017; 62:110-123. [PMID: 28119027 DOI: 10.1016/j.bbi.2017.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 12/26/2016] [Accepted: 01/10/2017] [Indexed: 01/10/2023] Open
Abstract
The immune function of AMIGO2 is currently unknown. Here, we revealed novel roles of AMIGO2 in modulating T-cell functions and EAE using Amigo2-knockout (AMG2KO) mice. Amigo2 was abundantly expressed by murine T helper (Th) cells. Its deficiency impaired transplanted T-cell infiltration into the secondary lymphoid organs and dampened Th-cell activation, but promoted splenic Th-cell proliferation and abundancy therein. AMG2KO Th cells had respectively elevated T-bet in Th1- and GATA-3 in Th2-lineage during early Th-cell differentiation, accompanied with increased IFN-γ and IL-10 but decreased IL-17A production. AMG2KO mice exhibited ameliorated EAE, dampened spinal T-cell accumulation, decreased serum IL-17A levels and enhanced splenic IL-10 production. Adoptive transfer of encephalitogenic AMG2KO T cells induced milder EAE and dampened spinal Th-cell accumulation and Tnf expression. Mechanistically, Amigo2-overexpression in 293T cells dampened NF-kB transcriptional activity, while Amigo2-deficiency enhanced Akt but suppressed GSK-3β phosphorylation and promoted nuclear translocations of NF-kB and NFAT1 in Th-cells. Collectively, our data demonstrate that AMIGO2 is important in regulating T-cell functions and EAE, and may be harnessed as a potential therapeutic target for multiple sclerosis.
Collapse
Affiliation(s)
- Zhilin Li
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Mohd Moin Khan
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Juha Kuja-Panula
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Hongyun Wang
- College of Life Sciences, Wuhan University, Wuhan, China.
| | - Yu Chen
- College of Life Sciences, Wuhan University, Wuhan, China.
| | - Deyin Guo
- College of Life Sciences, Wuhan University, Wuhan, China; School of Basic Medical Sciences, Wuhan University, Wuhan, China.
| | - Zhi Jane Chen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Heikki Rauvala
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.
| | - Li Tian
- Neuroscience Center, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland; Psychiatry Research Center, Beijing Huilongguan Hospital, Peking University, Beijing, China.
| |
Collapse
|
20
|
Rafiq S, Purdon TJ, Daniyan AF, Koneru M, Dao T, Liu C, Scheinberg DA, Brentjens RJ. Optimized T-cell receptor-mimic chimeric antigen receptor T cells directed toward the intracellular Wilms Tumor 1 antigen. Leukemia 2017; 31:1788-97. [PMID: 27924074 DOI: 10.1038/leu.2016.373] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/09/2016] [Accepted: 11/14/2016] [Indexed: 12/16/2022]
Abstract
CD19-directed chimeric antigen receptor (CAR) T cells are clinically effective in a limited set of leukemia patients. However, CAR T-cell therapy thus far has been largely restricted to targeting extracellular tumor-associated antigens (TAA). Herein, we report a T-cell receptor-mimic (TCRm) CAR, termed WT1-28z, that is reactive to a peptide portion of the intracellular onco-protein Wilms Tumor 1(WT1), as it is expressed on the surface of the tumor cell in the context of HLA-A*02:01. T cells modified to express WT1-28z specifically targeted and lysed HLA-A*02:01+ WT1+ tumors and enhanced survival of mice engrafted with HLA-A*02:01+, WT1+ leukemia or ovarian tumors. This in vivo functional validation of TCRm CAR T cells provides the proof-of-concept necessary to expand the range of TAA that can be effectively targeted for immunotherapy to include attractive intracellular targets, and may hold great potential to expand on the success of CAR T-cell therapy.
Collapse
|
21
|
Rattazzi L, Piras G, Brod S, Smith K, Ono M, D'Acquisto F. Impact of Enriched Environment on Murine T Cell Differentiation and Gene Expression Profile. Front Immunol 2016; 7:381. [PMID: 27746779 PMCID: PMC5042968 DOI: 10.3389/fimmu.2016.00381] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
T cells are known to be plastic and to change their phenotype according to the cellular and biochemical milieu they are embedded in. In this study, we transposed this concept at a macroscopic level assessing whether changes in the environmental housing conditions of C57/BL6 mice would influence the phenotype and function of T cells. Our study shows that exposure to 2 weeks in an enriched environment (EE) does not impact the T cell repertoire in vivo and causes no changes in the early TCR-driven activation events of these cells. Surprisingly, however, T cells from enriched mice showed a unique T helper effector cell phenotype upon differentiation in vitro. This was featured by a significant reduction in their ability to produce IFN-γ and by an increased release of IL-10 and IL-17. Microarray analysis of these cells also revealed a unique gene fingerprint with key signaling pathways involved in autoimmunity being modulated. Together, our results provide first evidence for a specific effect of EE on T cell differentiation and its associated changes in gene expression profile. In addition, our study sheds new light on the possible mechanisms by which changes in environmental factors can significantly influence the immune response of the host and favor the resolution of the inflammatory response.
Collapse
Affiliation(s)
- Lorenza Rattazzi
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London , London , UK
| | - Giuseppa Piras
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London , London , UK
| | - Samuel Brod
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London , London , UK
| | - Koval Smith
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London , London , UK
| | - Masahiro Ono
- Department of Life Science, Faculty of Natural Science, Imperial College of Science, Technology and Medicine , London , UK
| | - Fulvio D'Acquisto
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London , London , UK
| |
Collapse
|
22
|
Livanos AE, Greiner TU, Vangay P, Pathmasiri W, Stewart D, McRitchie S, Li H, Chung J, Sohn J, Kim S, Gao Z, Barber C, Kim J, Ng S, Rogers AB, Sumner S, Zhang XS, Cadwell K, Knights D, Alekseyenko A, Bäckhed F, Blaser MJ. Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice. Nat Microbiol 2016; 1:16140. [PMID: 27782139 PMCID: PMC5808443 DOI: 10.1038/nmicrobiol.2016.140] [Citation(s) in RCA: 234] [Impact Index Per Article: 29.3] [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: 01/05/2016] [Accepted: 07/12/2016] [Indexed: 12/15/2022]
Abstract
The early life microbiome plays important roles in host immunological and metabolic development. Because the incidence of type 1 diabetes (T1D) has been increasing substantially in recent decades, we hypothesized that early-life antibiotic use alters gut microbiota, which predisposes to disease. Using non-obese diabetic mice that are genetically susceptible to T1D, we examined the effects of exposure to either continuous low-dose antibiotics or pulsed therapeutic antibiotics (PAT) early in life, mimicking childhood exposures. We found that in mice receiving PAT, T1D incidence was significantly higher, and microbial community composition and structure differed compared with controls. In pre-diabetic male PAT mice, the intestinal lamina propria had lower Th17 and Treg proportions and intestinal SAA expression than in controls, suggesting key roles in transducing the altered microbiota signals. PAT affected microbial lipid metabolism and host cholesterol biosynthetic gene expression. These findings show that early-life antibiotic treatments alter the gut microbiota and its metabolic capacities, intestinal gene expression and T-cell populations, accelerating T1D onset in non-obese diabetic mice.
Collapse
Affiliation(s)
- Alexandra E. Livanos
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Thomas U. Greiner
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Pajau Vangay
- Biomedical Informatics and Computational Biology Program, University of Minnesota, Minneapolis, Minneapolis 55455, USA
| | - Wimal Pathmasiri
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Delisha Stewart
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Susan McRitchie
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Huilin Li
- Departments of Population Health, New York University Langone Medical Center, New York, New York 10016, USA
| | - Jennifer Chung
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Jiho Sohn
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Sara Kim
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Zhan Gao
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Cecily Barber
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Joanne Kim
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Sandy Ng
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Arlin B. Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts 01536, USA
| | - Susan Sumner
- Systems and Translational Sciences, RTI International, Research Triangle Park, North Carolina 27709, USA
| | - Xue-Song Zhang
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
| | - Ken Cadwell
- Department of Microbiology, New York University Langone Medical Center, New York, New York 10016, USA
- Skirball Institute, New York University Langone Medical Center, New York, New York 10016, USA
| | - Dan Knights
- Computer Science and Engineering, University of Minnesota, Minneapolis, Minneapolis 55455, USA
- Biotechnology Institute, University of Minnesota, Saint Paul, Minneapolis 55108, USA
| | - Alexander Alekseyenko
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
- CHIBI, New York University Langone Medical Center, New York, New York 10016, USA
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, University of Gothenburg, 40530 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Martin J. Blaser
- Departments of Medicine and Microbiology, Human Microbiome Program, New York University Langone Medical Center, Medical Service, New York, New York 10016, USA
- New York Harbor Veterans Affairs Medical Center, New York, New York 10010, USA
| |
Collapse
|
23
|
Hong X, Ladd-Acosta C, Hao K, Sherwood B, Ji H, Keet CA, Kumar R, Caruso D, Liu X, Wang G, Chen Z, Ji Y, Mao G, Walker SO, Bartell TR, Ji Z, Sun Y, Tsai HJ, Pongracic JA, Weeks DE, Wang X. Epigenome-wide association study links site-specific DNA methylation changes with cow's milk allergy. J Allergy Clin Immunol 2016; 138:908-911.e9. [PMID: 27236499 DOI: 10.1016/j.jaci.2016.01.056] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/08/2015] [Accepted: 01/29/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ben Sherwood
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Corinne A Keet
- Division of Pediatric Allergy and Immunology, Johns Hopkins University School of Medicine, Baltimore, Md
| | - Rajesh Kumar
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Deanna Caruso
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Xin Liu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Ill
| | - Guoying Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Zhu Chen
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Yuelong Ji
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Guanyun Mao
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md; Department of Preventive Medicine, School of Environmental Science & Public Health, Wenzhou Medical University, Wenzhou, China
| | - Sheila Ohlsson Walker
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md; Institute for Interdisciplinary Salivary Bioscience Research, Arizona State University, Tempe, Ariz; The Johns Hopkins School of Education, Baltimore, Md
| | - Tami R Bartell
- Mary Ann & J. Milburn Smith Child Health Research Program, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Zhicheng Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Yifei Sun
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md
| | - Hui-Ju Tsai
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Ill; Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Jacqueline A Pongracic
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Ill
| | - Daniel E Weeks
- Departments of Human Genetics and Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pa
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Md; Division of General Pediatrics & Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Md.
| |
Collapse
|
24
|
Troy NM, Hollams EM, Holt PG, Bosco A. Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses. BMC Med Genomics 2016; 9:9. [PMID: 26922672 PMCID: PMC4769846 DOI: 10.1186/s12920-016-0171-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/22/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Asthma is strongly associated with allergic sensitization, but the mechanisms that determine why only a subset of atopics develop asthma are not well understood. The aim of this study was to test the hypothesis that variations in allergen-driven CD4 T cell responses are associated with susceptibility to expression of asthma symptoms. METHODS The study population consisted of house dust mite (HDM) sensitized atopics with current asthma (n = 22), HDM-sensitized atopics without current asthma (n = 26), and HDM-nonsensitized controls (n = 24). Peripheral blood mononuclear cells from these groups were cultured in the presence or absence of HDM extract for 24 h. CD4 T cells were then isolated by immunomagnetic separation, and gene expression patterns were profiled on microarrays. RESULTS Differential network analysis of HDM-induced CD4 T cell responses in sensitized atopics with or without asthma unveiled a cohort of asthma-associated genes that escaped detection by more conventional data analysis techniques. These asthma-associated genes were enriched for targets of STAT6 signaling, and they were nested within a larger coexpression module comprising 406 genes. Upstream regulator analysis suggested that this module was driven primarily by IL-2, IL-4, and TNF signaling; reconstruction of the wiring diagram of the module revealed a series of hub genes involved in inflammation (IL-1B, NFkB, STAT1, STAT3), apoptosis (BCL2, MYC), and regulatory T cells (IL-2Ra, FoxP3). Finally, we identified several negative regulators of asthmatic CD4 T cell responses to allergens (e.g. IL-10, type I interferons, microRNAs, drugs, metabolites), and these represent logical candidates for therapeutic intervention. CONCLUSION Differential network analysis of allergen-induced CD4 T cell responses can unmask covert disease-associated genes and pin point novel therapeutic targets.
Collapse
Affiliation(s)
- Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia.
| | - Elysia M Hollams
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia.
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia. .,Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia.
| |
Collapse
|
25
|
Kanduri K, Tripathi S, Larjo A, Mannerström H, Ullah U, Lund R, Hawkins RD, Ren B, Lähdesmäki H, Lahesmaa R. Identification of global regulators of T-helper cell lineage specification. Genome Med 2015; 7:122. [PMID: 26589177 PMCID: PMC4654807 DOI: 10.1186/s13073-015-0237-0] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 11/15/2022] Open
Abstract
Background Activation and differentiation of T-helper (Th) cells into Th1 and Th2 types is a complex process orchestrated by distinct gene activation programs engaging a number of genes. This process is crucial for a robust immune response and an imbalance might lead to disease states such as autoimmune diseases or allergy. Therefore, identification of genes involved in this process is paramount to further understand the pathogenesis of, and design interventions for, immune-mediated diseases. Methods We aimed at identifying protein-coding genes and long non-coding RNAs (lncRNAs) involved in early differentiation of T-helper cells by transcriptome analysis of cord blood-derived naïve precursor, primary and polarized cells. Results Here, we identified lineage-specific genes involved in early differentiation of Th1 and Th2 subsets by integrating transcriptional profiling data from multiple platforms. We have obtained a high confidence list of genes as well as a list of novel genes by employing more than one profiling platform. We show that the density of lineage-specific epigenetic marks is higher around lineage-specific genes than anywhere else in the genome. Based on next-generation sequencing data we identified lineage-specific lncRNAs involved in early Th1 and Th2 differentiation and predicted their expected functions through Gene Ontology analysis. We show that there is a positive trend in the expression of the closest lineage-specific lncRNA and gene pairs. We also found out that there is an enrichment of disease SNPs around a number of lncRNAs identified, suggesting that these lncRNAs might play a role in the etiology of autoimmune diseases. Conclusion The results presented here show the involvement of several new actors in the early differentiation of T-helper cells and will be a valuable resource for better understanding of autoimmune processes. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0237-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kartiek Kanduri
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland. .,Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Subhash Tripathi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Antti Larjo
- Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Henrik Mannerström
- Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - Riikka Lund
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| | - R David Hawkins
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland. .,Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA, 98195, USA. .,Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA. .,Department of Cellular and Molecular Medicine, Institute of Genomic Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University School of Science, Espoo, Finland.
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.
| |
Collapse
|
26
|
Meenu S, Thiagarajan S, Ramalingam S, Michael A, Ramalingam S. Modulation of host ubiquitin system genes in human endometrial cell line infected with Mycobacterium tuberculosis. Med Microbiol Immunol 2015; 205:163-71. [PMID: 26403675 DOI: 10.1007/s00430-015-0432-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 08/14/2015] [Indexed: 12/18/2022]
Abstract
Endometrium is one of the most commonly affected sites in genital tuberculosis. The understanding of its interaction with the tubercle bacilli is of paramount importance for studying the pathogenesis of this disease. The main objective of this work was to study the interplay between Mycobacterium tuberculosis and host endometrial epithelial cell lines (Ishikawa cell lines), and to identify the differentially expressed genes upon tuberculosis infection. To study this, suppression subtractive hybridization library was constructed using M. tuberculosis H37Rv-infected Ishikawa cell line harvested 24 h post-infection. The subtracted cDNA library was screened, and 105 differentially expressed genes were identified and grouped based on their functions. Since ubiquitination process has gained importance in targeting M. tuberculosis to xenophagy, ubiquitin system genes obtained in the library were selected, and time course analysis of their gene expression was performed. We observed an upregulation of mkrn1 and cops5 and downregulation of zfp91, ndfip2, ube2f, rnft1, psmb6, and psmd13 at 24 h post-infection. From the results obtained, we surmise that ubiquitination pathway genes may have roles in combating tuberculosis which are yet uncharted.
Collapse
Affiliation(s)
- S Meenu
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India
- PSG College of Arts and Science, Coimbatore, Tamil Nadu, 641 004, India
| | - S Thiagarajan
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India
| | - Sudha Ramalingam
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India
| | - A Michael
- PSG College of Arts and Science, Coimbatore, Tamil Nadu, 641 004, India
| | - Sankaran Ramalingam
- PSG Center for Molecular Medicine and Therapeutics, PSG Institute of Medical Sciences and Research, Coimbatore, Tamil Nadu, 641 004, India.
| |
Collapse
|
27
|
Albert R, Thakar J. Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions. Wiley Interdiscip Rev Syst Biol Med 2015; 6:353-69. [PMID: 25269159 DOI: 10.1002/wsbm.1273] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The biomolecules inside or near cells form a complex interacting system. Cellular phenotypes and behaviors arise from the totality of interactions among the components of this system. A fruitful way of modeling interacting biomolecular systems is by network-based dynamic models that characterize each component by a state variable, and describe the change in the state variables due to the interactions in the system. Dynamic models can capture the stable state patterns of this interacting system and can connect them to different cell fates or behaviors. A Boolean or logic model characterizes each biomolecule by a binary state variable that relates the abundance of that molecule to a threshold abundance necessary for downstream processes. The regulation of this state variable is described in a parameter free manner, making Boolean modeling a practical choice for systems whose kinetic parameters have not been determined. Boolean models integrate the body of knowledge regarding the components and interactions of biomolecular systems, and capture the system's dynamic repertoire, for example the existence of multiple cell fates. These models were used for a variety of systems and led to important insights and predictions. Boolean models serve as an efficient exploratory model, a guide for follow-up experiments, and as a foundation for more quantitative models.
Collapse
|
28
|
Abstract
Pathogenic Leptospira has the capacity to infect a broad range of mammalian hosts. Leptospirosis may appear as an acute, potentially fatal infection in accidental hosts, or progress into a chronic, largely asymptomatic infection in natural maintenance hosts. The course that Leptospira infection follows is dependent upon poorly understood factors, but is heavily influenced by both the host species and bacterial serovar involved in infection. Recognition of pathogen-associated molecular patterns (PAMPs) by a variety of host pattern recognition receptors (PRRs) activates the host immune system. The outcome of this response may result in bacterial clearance, limited bacterial colonization of a few target organs, principally the kidney, or induction of sepsis as the host succumbs to infection and dies. This chapter describes current knowledge of how the host recognizes Leptospira and responds to infection using innate and acquired immune responses. Aspects of immune-mediated pathology and pathogen strategies to evade the host immune response are also addressed.
Collapse
Affiliation(s)
- Richard L Zuerner
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University for Agricultural Sciences, 75007, Uppsala, Sweden,
| |
Collapse
|
29
|
Blackwell J, Harries LW, Pilling LC, Ferrucci L, Jones A, Melzer D. Changes in CEBPB expression in circulating leukocytes following eccentric elbow-flexion exercise. J Physiol Sci 2014; 65:145-50. [PMID: 25391587 PMCID: PMC4276809 DOI: 10.1007/s12576-014-0350-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 06/05/2014] [Accepted: 10/31/2014] [Indexed: 01/03/2023]
Abstract
In mouse models, CCAAT enhancer-binding protein beta (CEBPB) is necessary for M2 macrophage-mediated regeneration after muscle injury. In humans, CEBPB expression in blood was strongly associated with muscle strength. In this study we aimed to test whether CEBPB expression in blood in people is increased 2 days after exercise designed to induce muscle damage and subsequent repair. Sixteen healthy male volunteers undertook elbow flexor exercises designed to induce acute muscle micro-damage. Peripheral blood samples were collected at baseline and days 1, 2, 4 and 7 following exercise. Expression of CEBPB and related genes were analysed by qRT-PCR. Extent of muscle damage was determined by decline in maximal voluntary isometric torque and by plasma creatine kinase activity. Nine subjects had peak (day 4) creatine kinase activity exceeding 10,000 U/l. In this subgroup, CEBPB expression was elevated from baseline to 2 days post exercise (paired-samples t(1,8) = 3.72, p = 0.006). Related expression and selected cytokine changes after exercise did not reach significance. Muscle-damaging exercise in humans can be followed by induction of CEBPB transcript expression in peripheral blood. Associations between CEBPB expression in blood and muscle strength may be consistent with the CEBPB-dependent muscle repair process.
Collapse
Affiliation(s)
- Jamie Blackwell
- Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, St. Luke's Campus, Exeter, UK
| | | | | | | | | | | |
Collapse
|
30
|
Abstract
Combined with TCR stimuli, extracellular cytokine signals initiate the differentiation of naive CD4(+) T cells into specialized effector T-helper (Th) and regulatory T (Treg) cell subsets. The lineage specification and commitment process occurs through the combinatorial action of multiple transcription factors (TFs) and epigenetic mechanisms that drive lineage-specific gene expression programs. In this article, we review recent studies on the transcriptional and epigenetic regulation of distinct Th cell lineages. Moreover, we review current study linking immune disease-associated single-nucleotide polymorphisms with distal regulatory elements and their potential role in the disease etiology.
Collapse
Affiliation(s)
- Subhash K Tripathi
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
- National Doctoral Programme in Informational and
Structural BiologyTurku, Finland
- Turku Doctoral Programme of Molecular Medicine (TuDMM),
University of TurkuTurku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and
Åbo Akademi UniversityTurku, Finland
| |
Collapse
|
31
|
Abstract
Signal transducers and activators of transcription 5(STAT5) are cytokine induced signaling proteins, which regulate key immunological processes, such as tolerance induction, maintenance of homeostasis, and CD4 T-effector cell differentiation. In this study, transcriptional targets of STAT5 in CD4 T cells were studied by Chromatin Immunoprecipitation (ChIP). Genomic mapping of the sites cloned and identified in this study revealed the striking observation that the majority of STAT5-binding sites mapped to intergenic (>50 kb upstream) or intronic, rather than promoter proximal regions. Of the 105 STAT5 responsive binding sites identified, 94% contained the canonical (IFN-γ activation site) GAS motifs. A number of putative target genes identified here are associated with tumor biology. Here, we identified Fos-related antigen 2 (FRA2) as a transcriptional target of IL-2 regulated STAT5. FRA2 is a basic -leucine zipper (bZIP) motif ‘Fos’ family transcription factor that is part of the AP-1 transcription factor complex and is also known to play a critical role in the progression of human tumours and more recently as a determinant of T cell plasticity. The binding site mapped to an internal intron within the FRA2 gene. The epigenetic architecture of FRA2, characterizes a transcriptionally active promoter as indicated by enrichment for histone methylation marks H3K4me1, H3K4me2, H3K4me3, and transcription/elongation associated marks H2BK5me1 and H4K20me1. FRA2 is regulated by IL-2 in activated CD4 T cells. Consistently, STAT5 bound to GAS sequence in the internal intron of FRA2 and reporter gene assays confirmed IL-2 induced STAT5 binding and transcriptional activation. Furthermore, addition of JAK3 inhibitor (R333) or Daclizumab inhibited the induction in TCR stimulated cells. Taken together, our data suggest that FRA2 is a novel STAT5 target gene, regulated by IL-2 in activated CD4 T cells.
Collapse
Affiliation(s)
- Aradhana Rani
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
| | - Roseanna Greenlaw
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
| | - Manohursingh Runglall
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
| | - Stipo Jurcevic
- Division of Transplantation Immunology and Mucosal Biology, King's College London, London, United Kingdom
- * E-mail: (SJurcevic); (SJohn)
| | - Susan John
- Department of Immunobiology, King's College London, London, United Kingdom
- * E-mail: (SJurcevic); (SJohn)
| |
Collapse
|
32
|
Abstract
As members of the basic helix-loop-helix (bHLH) family of transcription factors, E proteins function in the immune system by directing and maintaining a vast transcriptional network that regulates cell survival, proliferation, differentiation, and function. Proper activity of this network is essential to the functionality of the immune system. Aberrations in E protein expression or function can cause numerous defects, ranging from impaired lymphocyte development and immunodeficiency to aberrant function, cancer, and autoimmunity. Additionally, disruption of inhibitor of DNA-binding (Id) proteins, natural inhibitors of E proteins, can induce additional defects in development and function. Although E proteins have been investigated for several decades, their study continues to yield novel and exciting insights into the workings of the immune system. The goal of this chapter is to discuss the various classical roles of E proteins in lymphocyte development and highlight new and ongoing research into how these roles, if compromised, can lead to disease.
Collapse
Affiliation(s)
- Ian Belle
- Department of Immunology, Duke University Medical Center, Durham North Carolina, USA.
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham North Carolina, USA
| |
Collapse
|
33
|
Riley JP, Kulkarni A, Mehrotra P, Koh B, Perumal NB, Kaplan MH, Goenka S. PARP-14 binds specific DNA sequences to promote Th2 cell gene expression. PLoS One 2013; 8:e83127. [PMID: 24376650 PMCID: PMC3869773 DOI: 10.1371/journal.pone.0083127] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 05/16/2013] [Accepted: 10/31/2013] [Indexed: 12/24/2022] Open
Abstract
PARP-14, a member of the poly ADP-ribose polymerase super family, promotes T helper cell 2 (Th2) differentiation by regulating interleukin-4 (IL-4) and STAT6-dependent transcription. Yet, whether PARP-14 globally impacts gene regulation has not been determined. In this report, using an RNA pol II ChIP-seq approach, we identify genes in Th2 cells that are regulated by PARP-14, and either dependent or independent of ADP-ribosyltransferase catalytic activity. Our data demonstrate that PARP-14 enhances the expression of Th2 genes as it represses the expression of Th1-associated genes. Among the relevant targets are Signal Transducer and Activator of Transcription genes required for polarizing Th1 and Th2 cells. To define a mechanism for PARP-14 function, we use an informatics approach to identify putative PARP-14 DNA binding sites. Two putative PARP-14 binding motifs are identified in multiple Th2 cytokine genes, and we demonstrate that PARP-14 interacts with each motif using in vitro binding assays. Taken together our results indicate that PARP-14 is an important factor for T helper cell differentiation and it binds to specific DNA sequences to mediate its function.
Collapse
Affiliation(s)
- Jonathan P. Riley
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Aishwarya Kulkarni
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- School of Informatics, Indiana University-Purdue University, Indianapolis, Indianapolis, Indiana, United States of America
| | - Purvi Mehrotra
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Byunghee Koh
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Narayanan B. Perumal
- School of Informatics, Indiana University-Purdue University, Indianapolis, Indianapolis, Indiana, United States of America
| | - Mark H. Kaplan
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
| | - Shreevrat Goenka
- Department of Pediatrics, HB Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| |
Collapse
|
34
|
Abstract
Molecular mechanisms guiding naïve T helper cell differentiation into functionally specified effector cells are intensively studied. The rapidly growing knowledge is mainly achieved by using mouse cells or disease models. Comparatively exiguous data is gathered from human primary cells although they provide the "ultimate model" for immunology in man, have been exploited in many original studies paving the way for the field, and can be analyzed more easily than ever with the help of modern technology and methods. As usage of mouse models is unavoidable in translational research, parallel human and mouse studies should be performed to assure the relevancy of the hypothesis created during the basic research. In this review, we give an overview on the status of the studies conducted with human primary cells aiming at elucidating the mechanisms instructing the priming of T helper cell subtypes. The special emphasis is given to the recent high-throughput studies. In addition, by comparing the human and mouse studies we intend to point out the regulatory mechanisms and questions which are lacking examination with human primary cells.
Collapse
Affiliation(s)
- Soile Tuomela
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, 20520 Turku, Finland
| | | |
Collapse
|
35
|
Abstract
Proper differentiation of naïve T helper cells into functionally distinct subsets is of critical importance to human health. Consequently, the process is tightly controlled by a complex intracellular signalling network. To dissect the regulatory principles of this network, immunologists have early on embraced system-wide transcriptomics tools, leading to identification of large panels of potential regulatory factors. In contrast, the use of proteomics approaches in T helper cell research has been notably rare, and to this date relatively few high-throughput datasets have been reported. Here, we discuss the importance of such research and envision the possibilities afforded by mass spectrometry-based proteomics in the near future.
Collapse
Affiliation(s)
- Tapio Lönnberg
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
| | | | | |
Collapse
|
36
|
Lehtimäki S, Lahesmaa R. Regulatory T Cells Control Immune Responses through Their Non-Redundant Tissue Specific Features. Front Immunol 2013; 4:294. [PMID: 24069022 PMCID: PMC3780303 DOI: 10.3389/fimmu.2013.00294] [Citation(s) in RCA: 28] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 09/07/2013] [Indexed: 01/11/2023] Open
Abstract
Regulatory T cells (Treg) are needed in the control of immune responses and to maintain immune homeostasis. Of this subtype of regulatory lymphocytes, the most potent are Foxp3 expressing CD4+ T cells, which can be roughly divided into two main groups; natural Treg cells (nTreg), developing in the thymus, and induced or adaptive Treg cells (iTreg), developing in the periphery from naïve, conventional T cells. Both nTreg cells and iTreg cells have their own, non-redundant roles in the immune system, with nTreg cells mainly maintaining tolerance toward self-structures, and iTreg developing in response to externally delivered antigens or commensal microbes. In addition, Treg cells acquire tissue specific features and are adapted to function in the tissue they reside. This review will focus on some specific features of Treg cells in different compartments of the body.
Collapse
Affiliation(s)
- Sari Lehtimäki
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University , Turku , Finland
| | | |
Collapse
|
37
|
Chen Z, Lönnberg T, Lahesmaa R. Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets. Scand J Immunol 2013; 78:172-80. [PMID: 23679154 DOI: 10.1111/sji.12071] [Citation(s) in RCA: 3] [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] [Received: 05/03/2013] [Accepted: 05/11/2013] [Indexed: 01/22/2023]
Abstract
Current knowledge of helper T cell differentiation largely relies on data generated from mouse studies. To develop therapeutical strategies combating human diseases, understanding the molecular mechanisms how human naïve T cells differentiate to functionally distinct T helper (Th) subsets as well as studies on human differentiated Th cell subsets is particularly valuable. Systems biology approaches provide a holistic view of the processes of T helper differentiation, enable discovery of new factors and pathways involved and generation of new hypotheses to be tested to improve our understanding of human Th cell differentiation and immune-mediated diseases. Here, we summarize studies where high-throughput systems biology approaches have been exploited to human primary T cells. These studies reveal new factors and signalling pathways influencing T cell differentiation towards distinct subsets, important for immune regulation. Such information provides new insights into T cell biology and into targeting immune system for therapeutic interventions.
Collapse
Affiliation(s)
- Z Chen
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | | | | |
Collapse
|
38
|
Abstract
The differentiation of CD4 helper T cells into specialized effector lineages has provided a powerful model for understanding immune cell differentiation. Distinct lineages have been defined by differential expression of signature cytokines and the lineage-specifying transcription factors necessary and sufficient for their production. The traditional paradigm of differentiation towards Th1 and Th2 subtypes driven by T-bet and GATA3, respectively, has been extended to incorporate additional T cell lineages and transcriptional regulators. Technological advances have expanded our view of these lineage-specifying transcription factors to the whole genome and revealed unexpected interplay between them. From these data, it is becoming clear that lineage specification is more complex and plastic than previous models might have suggested. Here, we present an overview of the different forms of transcription factor interplay that have been identified and how T cell phenotypes arise as a product of this interplay within complex regulatory networks. We also suggest experimental strategies that will provide further insight into the mechanisms that underlie T cell lineage specification and plasticity.
Collapse
Affiliation(s)
- Catherine M Evans
- Division of Infection and Immunity and UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6BT, UK.
| | | |
Collapse
|
39
|
Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R. Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization. Immunity 2013; 38:1271-84. [PMID: 23791644 DOI: 10.1016/j.immuni.2013.05.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 03/14/2013] [Indexed: 12/22/2022]
Abstract
Naive CD4⁺ T cells can differentiate into specific helper and regulatory T cell lineages in order to combat infection and disease. The correct response to cytokines and a controlled balance of these populations is critical for the immune system and the avoidance of autoimmune disorders. To investigate how early cell-fate commitment is regulated, we generated the first human genome-wide maps of histone modifications that reveal enhancer elements after 72 hr of in vitro polarization toward T helper 1 (Th1) and T helper 2 (Th2) cell lineages. Our analysis indicated that even at this very early time point, cell-specific gene regulation and enhancers were at work directing lineage commitment. Further examination of lineage-specific enhancers identified transcription factors (TFs) with known and unknown T cell roles as putative drivers of lineage-specific gene expression. Lastly, an integrative analysis of immunopathogenic-associated SNPs suggests a role for distal regulatory elements in disease etiology.
Collapse
|
40
|
van den Ham HJ, de Waal L, Zaaraoui-Boutahar F, Bijl M, van Ijcken WFJ, Osterhaus ADME, de Boer RJ, Andeweg AC. Early divergence of Th1 and Th2 transcriptomes involves a small core response and sets of transiently expressed genes. Eur J Immunol 2013; 43:1074-84. [PMID: 23436590 DOI: 10.1002/eji.201242979] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/03/2012] [Accepted: 01/28/2013] [Indexed: 12/24/2022]
Abstract
Th cells can adopt a number of different phenotypes. We performed microarray-assisted mRNA profiling on antigen-stimulated, TCR transgenic murine splenocytes that were cultured in the presence of cytokines. Transcriptome snapshots of Th cells differentiating into Th1 and Th2 phenotypes were obtained at various time points. Principal component analysis shows that time since activation and Th skewing are the largest sources of variance (i.e. the largest contributing factors) in our profiling experiments. Divergence between the Th1 and Th2 phenotypes is established early and does not increase in terms of number of differential genes from day 1 to day 4 after stimulation. Notwithstanding the lack of further divergence between the Th1 and Th2 lineages, we show that gene expression is best described by a 'turnover' rather than a 'core response' model, although we find evidence for both. We identify clusters of skewed genes associated with early persistent ('core response') and late ('turnover') Th1 and Th2 gene expression. In addition to the classical Th genes, members of the Batf transcription factor family are differentially expressed in particular helper phenotypes, suggesting an important role for this family in Th-cell phenotype differentiation.
Collapse
Affiliation(s)
- Henk-Jan van den Ham
- Department of Virology, Erasmus MC, Rotterdam, The Netherlands; Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, The Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Abstract
Given the complexity and interactive nature of biological systems, constructing informative and coherent network models of these systems and subsequently developing efficient approaches to analyze the assembled networks is of immense importance. The integration of network analysis and dynamic modeling enables one to investigate the behavior of the underlying system as a whole and to make experimentally testable predictions about less-understood aspects of the processes involved. In this paper, we present a tutorial on the fundamental steps of Boolean modeling of biological regulatory networks. We demonstrate how to infer a Boolean network model from the available experimental data, analyze the network using graph-theoretical measures, and convert it into a predictive dynamic model. For each step, the pitfalls one may encounter and possible ways to circumvent them are also discussed. We illustrate these steps on a toy network as well as in the context of the Drosophila melanogaster segment polarity gene network.
Collapse
Affiliation(s)
- Assieh Saadatpour
- Department of Mathematics, The Pennsylvania State University, University Park, PA 16802, USA
| | | |
Collapse
|
42
|
Baynam G, Walters M, Claes P, Kung S, LeSouef P, Dawkins H, Gillett D, Goldblatt J. The facial evolution: looking backward and moving forward. Hum Mutat 2012; 34:14-22. [PMID: 23033261 DOI: 10.1002/humu.22219] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/30/2012] [Indexed: 01/16/2023]
Abstract
Three-dimensional (3D) facial analysis is ideal for high-resolution, nonionizing, noninvasive objective, high-throughput phenotypic, and phenomic studies. It is a natural complement to (epi)genetic technologies to facilitate advances in the understanding of rare and common diseases. The face is uniquely reflective of the primordial tissues, and there is evidence supporting the application of 3D facial analysis to the investigation of variation and disease including studies showing that the face can reflect systemic health, provides diagnostic clues to disorders, and that facial variation reflects biological pathways. In addition, facial variation has been related to evolutionary factors. The purpose of this review is to look backward to suggest that knowledge of human evolution supports, and may instruct, the application and interpretation of studies of facial morphology for documentation of human variation and investigation of its relationships with health and disease. Furthermore, in the context of advances of deep phenotyping and data integration, to look forward to suggest approaches to scalable implementation of facial analysis, and to suggest avenues for future research and clinical application of this technology.
Collapse
Affiliation(s)
- Gareth Baynam
- Genetic Services of Western Australia, Princess Margaret and King Edward Memorial Hospitals, Perth, Australia
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Aijö T, Edelman SM, Lönnberg T, Larjo A, Kallionpää H, Tuomela S, Engström E, Lahesmaa R, Lähdesmäki H. An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. BMC Genomics 2012; 13:572. [PMID: 23110343 PMCID: PMC3526425 DOI: 10.1186/1471-2164-13-572] [Citation(s) in RCA: 21] [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: 01/09/2012] [Accepted: 10/02/2012] [Indexed: 01/19/2023] Open
Abstract
Background A proper balance between different T helper (Th) cell subsets is necessary for normal functioning of the adaptive immune system. Revealing key genes and pathways driving the differentiation to distinct Th cell lineages provides important insight into underlying molecular mechanisms and new opportunities for modulating the immune response. Previous computational methods to quantify and visualize kinetic differential expression data of three or more lineages to identify reciprocally regulated genes have relied on clustering approaches and regression methods which have time as a factor, but have lacked methods which explicitly model temporal behavior. Results We studied transcriptional dynamics of human umbilical cord blood T helper cells cultured in absence and presence of cytokines promoting Th1 or Th2 differentiation. To identify genes that exhibit distinct lineage commitment dynamics and are specific for initiating differentiation to different Th cell subsets, we developed a novel computational methodology (LIGAP) allowing integrative analysis and visualization of multiple lineages over whole time-course profiles. Applying LIGAP to time-course data from multiple Th cell lineages, we identified and experimentally validated several differentially regulated Th cell subset specific genes as well as reciprocally regulated genes. Combining differentially regulated transcriptional profiles with transcription factor binding site and pathway information, we identified previously known and new putative transcriptional mechanisms involved in Th cell subset differentiation. All differentially regulated genes among the lineages together with an implementation of LIGAP are provided as an open-source resource. Conclusions The LIGAP method is widely applicable to quantify differential time-course dynamics of many types of datasets and generalizes to any number of conditions. It summarizes all the time-course measurements together with the associated uncertainty for visualization and manual assessment purposes. Here we identified novel human Th subset specific transcripts as well as regulatory mechanisms important for the initiation of the Th cell subset differentiation.
Collapse
Affiliation(s)
- Tarmo Aijö
- Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Wu X, Chen Y, Sun R, Wei H, Tian Z. Impairment of hepatic NK cell development in IFN-γ deficient mice. Cytokine 2012; 60:616-25. [PMID: 22921904 DOI: 10.1016/j.cyto.2012.07.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 07/07/2012] [Accepted: 07/10/2012] [Indexed: 12/12/2022]
Abstract
It is already clearly demonstrated that IFN-γ plays important roles in differentiation and maturation of T cells, B cells and macrophages; however, it is not clear whether NK cell development is regulated by IFN-γ. In our study by using IFN-γ-deficient mice (GKO), we observed that the percentage and number of NK1.1(+)CD3(-) cells were declined significantly in the liver, but not in the spleen, bone marrow and lymph node, of adult IFN-γ(-/-) mice. However, Lin(-)CD122(+) NK progenitor cells developed normally both in liver and bone marrow in IFN-γ(-/-) mice. Moreover, more mature CD27(-)CD11b(+) NK cells accumulated in the liver of IFN-γ(-/-) mice. Deficiency of IFN-γ resulted in the lower expression of CD69, GranzymeB and TRAIL by hepatic NK1.1(+)CD3(-) cells and the phenotypes of IFN-γ(-/-) hepatic NK1.1(+)CD3(-) cells were altered from WT hepatic NK cells. When stimulated with Poly (I:C) in vivo, attenuated accumulating in the liver and weaker expression of GranzymeB, TRAIL and FasL of NK1.1(+)CD3(-) cells were observed of IFN-γ(-/-) mice. Accordingly, these results demonstrate that IFN-γ plays important role in mounting liver environment for development of hepatic NK cells.
Collapse
Affiliation(s)
- Xian Wu
- Institute of Immunology, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | | | | | | | | |
Collapse
|
45
|
Imbeault M, Giguère K, Ouellet M, Tremblay MJ. Exon level transcriptomic profiling of HIV-1-infected CD4(+) T cells reveals virus-induced genes and host environment favorable for viral replication. PLoS Pathog 2012; 8:e1002861. [PMID: 22876188 PMCID: PMC3410884 DOI: 10.1371/journal.ppat.1002861] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 06/30/2012] [Indexed: 01/01/2023] Open
Abstract
HIV-1 is extremely specialized since, even amongst CD4+ T lymphocytes (its major natural reservoir in peripheral blood), the virus productively infects only a small proportion of cells under an activated state. As the percentage of HIV-1-infected cells is very low, most studies have so far failed to capture the precise transcriptomic profile at the whole-genome scale of cells highly susceptible to virus infection. Using Affymetrix Exon array technology and a reporter virus allowing the magnetic isolation of HIV-1-infected cells, we describe the host cell factors most favorable for virus establishment and replication along with an overview of virus-induced changes in host gene expression occurring exclusively in target cells productively infected with HIV-1. We also establish that within a population of activated CD4+ T cells, HIV-1 has no detectable effect on the transcriptome of uninfected bystander cells at early time points following infection. The data gathered in this study provides unique insights into the biology of HIV-1-infected CD4+ T cells and identifies genes thought to play a determinant role in the interplay between the virus and its host. Furthermore, it provides the first catalogue of alternative splicing events found in primary human CD4+ T cells productively infected with HIV-1. Some previous studies have monitored HIV-1-induced gene expression in various host cell targets and tissues but the discrimination between productively infected cells and uninfected bystander cells represents a technical challenge yet to be solved. Consequently, data interpretation has always been biased towards the transcriptional response of a majority of uninfected bystander cells that were exposed to soluble factors released by virus-infected cells. Following the design of a unique and innovative molecular tool to identify cells productively infected with HIV-1 and the description of an efficient magnetic beads-based technique to separate them from uninfected bystander cells, we undertake this challenge and perform the first comparative whole-genome transcriptomic and large-scale proteomic profiling of both HIV-1-infected and uninfected bystander CD4+ T cells. We demonstrate herein that HIV-1- infected and uninfected bystander cells display distinctive transcriptomic signatures which might permit to identify new susceptibility and resistance factors.
Collapse
Affiliation(s)
- Michaël Imbeault
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec - CHUL, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Katia Giguère
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec - CHUL, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Michel Ouellet
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec - CHUL, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
| | - Michel J. Tremblay
- Centre de Recherche en Infectiologie, Centre Hospitalier Universitaire de Québec - CHUL, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
- Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec City, Québec, Canada
- * E-mail:
| |
Collapse
|
46
|
Ullah U, Tripathi P, Lahesmaa R, Rao KV. Gene set enrichment analysis identifies LIF as a negative regulator of human Th2 cell differentiation. Sci Rep 2012; 2:464. [PMID: 22712053 DOI: 10.1038/srep00464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/01/2012] [Indexed: 02/07/2023] Open
Abstract
In this study we show that IL-4 is crucial during reinforcement window of human Th2 differentiation for optimal Th2 development. We have also shown here that during this stage, IL-4 helps in cellular decision-making process of differentiation versus proliferation. We have combined computational and experimental methods to analyze Th2 transcription network to name novel players of the process of Th2 differentiation. Here we report that LIF through STAT3 negatively regulates Th2 differentiation. This approach can be generalized to analyze “omics” data to identify key regulatory modules.
Collapse
|
47
|
Baynam G, Walters M, Claes P, Le Souef P. 3D facial analysis can investigate vaccine responses. Med Hypotheses 2012; 78:497-501. [DOI: 10.1016/j.mehy.2012.01.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 01/09/2012] [Indexed: 02/01/2023]
|
48
|
Baynam G, Claes P, Craig JM, Goldblatt J, Kung S, Le Souef P, Walters M. Intersections of Epigenetics, Twinning and Developmental Asymmetries: Insights Into Monogenic and Complex Diseases and a Role for 3D Facial Analysis. Twin Res Hum Genet 2012; 14:305-15. [DOI: 10.1375/twin.14.4.305] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
For decades the relationships of twinning and alterations in body patterning, such as laterality and asymmetry, have been investigated. However, the tools to define and quantify these relationships have been limited and the majority of these studies have relied on associations with subjectively defined phenotypes. The emerging technologies of 3-dimensional (3D) facial scanning and geometric morphometrics are providing the means to establish objective criteria, including measures of asymmetry, which can be used for phenotypic classification and investigations. Additionally, advances in molecular epigenetics provide new opportunities for novel investigations of mechanisms central to early developmental processes, twinning and related phenotypes. We review the evidence for overlapping etiologies of twinning, asymmetry and selected monogenic and complex diseases, and we suggest that the combination of epigenetic investigations with detailed and objective phenotyping, utilizing 3D facial analysis tools, can reveal insights into the genesis of these phenomena.
Collapse
|
49
|
Bruhn S, Barrenäs F, Mobini R, Andersson BA, Chavali S, Egan BS, Hovig E, Sandve GK, Langston MA, Rogers G, Wang H, Benson M. Increased expression of IRF4 and ETS1 in CD4+ cells from patients with intermittent allergic rhinitis. Allergy 2012; 67:33-40. [PMID: 21919915 DOI: 10.1111/j.1398-9995.2011.02707.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [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] [Indexed: 11/28/2022]
Abstract
BACKGROUND The transcription factor (TF) IRF4 is involved in the regulation of Th1, Th2, Th9, and Th17 cells, and animal studies have indicated an important role in allergy. However, IRF4 and its target genes have not been examined in human allergy. METHODS IRF4 and its target genes were examined in allergen-challenged CD4(+) cells from patients with IAR, using combined gene expression microarrays and chromatin immunoprecipitation chips (ChIP-chips), computational target prediction, and RNAi knockdowns. RESULTS IRF4 increased in allergen-challenged CD4(+) cells from patients with IAR, and functional studies supported its role in Th2 cell activation. IRF4 ChIP-chip showed that IRF4 regulated a large number of genes relevant to Th cell differentiation. However, neither Th1 nor Th2 cytokines were the direct targets of IRF4. To examine whether IRF4 induced Th2 cytokines via one or more downstream TFs, we combined gene expression microarrays, ChIP-chips, and computational target prediction and found a putative intermediary TF, namely ETS1 in allergen-challenged CD4(+) cells from allergic patients. ETS1 increased significantly in allergen-challenged CD4(+) cells from patients compared to controls. Gene expression microarrays before and after ETS1 RNAi knockdown showed that ETS1 induced Th2 cytokines as well as disease-related pathways. CONCLUSIONS Increased expression of IRF4 in allergen-challenged CD4(+) cells from patients with intermittent allergic rhinitis leads to activation of a complex transcriptional program, including Th2 cytokines.
Collapse
Affiliation(s)
- S Bruhn
- The Centre for Individualized Medication, Linköping University Hospital, Linköping, Sweden
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Horiuchi S, Onodera A, Hosokawa H, Watanabe Y, Tanaka T, Sugano S, Suzuki Y, Nakayama T. Genome-wide analysis reveals unique regulation of transcription of Th2-specific genes by GATA3. J Immunol 2011; 186:6378-89. [PMID: 21536806 DOI: 10.4049/jimmunol.1100179] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Differentiation of naive CD4 T cells into Th2 cells is accompanied by chromatin remodeling and increased expression of a set of Th2-specific genes, including those encoding Th2 cytokines. IL-4-mediated STAT6 activation induces high levels of transcription of GATA3, a master regulator of Th2 cell differentiation, and enforced expression of GATA3 induces Th2 cytokine expression. However, it remains unclear whether the expression of other Th2-specific genes is induced directly by GATA3. A genome-wide unbiased chromatin immunoprecipitation assay coupled with massive parallel sequencing analysis revealed that GATA3 bound to 1279 genes selectively in Th2 cells, and 101 genes in both Th1 and Th2 cells. Simultaneously, we identified 26 highly Th2-specific STAT6-dependent inducible genes by DNA microarray analysis-based three-step selection processes, and among them 17 genes showed GATA3 binding. We assessed dependency on GATA3 for the transcription of these 26 Th2-specific genes, and 10 genes showed increased transcription in a GATA3-dependent manner, whereas 16 genes showed no significant responses. The transcription of the 16 GATA3-nonresponding genes was clearly increased by the introduction of an active form of STAT6, STAT6VT. Therefore, although GATA3 has been recognized as a master regulator of Th2 cell differentiation, many Th2-specific genes are not regulated by GATA3 itself, but in collaboration with STAT6.
Collapse
Affiliation(s)
- Shu Horiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
| | | | | | | | | | | | | | | |
Collapse
|