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Cheng J, Clayton JS, Acemel RD, Zheng Y, Taylor RL, Keleş S, Franke M, Boackle SA, Harley JB, Quail E, Gómez-Skarmeta JL, Ulgiati D. Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. Front Immunol 2022; 13:901747. [PMID: 35769482 PMCID: PMC9235356 DOI: 10.3389/fimmu.2022.901747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/05/2022] [Indexed: 12/03/2022] Open
Abstract
The Regulators of Complement Activation (RCA) gene cluster comprises several tandemly arranged genes with shared functions within the immune system. RCA members, such as complement receptor 2 (CR2), are well-established susceptibility genes in complex autoimmune diseases. Altered expression of RCA genes has been demonstrated at both the functional and genetic level, but the mechanisms underlying their regulation are not fully characterised. We aimed to investigate the structural organisation of the RCA gene cluster to identify key regulatory elements that influence the expression of CR2 and other genes in this immunomodulatory region. Using 4C, we captured extensive CTCF-mediated chromatin looping across the RCA gene cluster in B cells and showed these were organised into two topologically associated domains (TADs). Interestingly, an inter-TAD boundary was located within the CR1 gene at a well-characterised segmental duplication. Additionally, we mapped numerous gene-gene and gene-enhancer interactions across the region, revealing extensive co-regulation. Importantly, we identified an intergenic enhancer and functionally demonstrated this element upregulates two RCA members (CR2 and CD55) in B cells. We have uncovered novel, long-range mechanisms whereby autoimmune disease susceptibility may be influenced by genetic variants, thus highlighting the important contribution of chromatin topology to gene regulation and complex genetic disease.
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Affiliation(s)
- Jessica Cheng
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Joshua S. Clayton
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Rafael D. Acemel
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States,Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States
| | - Rhonda L. Taylor
- Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia,Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, United States,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| | - Martin Franke
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Susan A. Boackle
- Department of Medicine, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States,Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States,US Department of Veterans Affairs Medical Centre, US Department of Veterans Affairs, Cincinnati, OH, United States
| | - Elizabeth Quail
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Sevilla, Spain
| | - Daniela Ulgiati
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia,*Correspondence: Daniela Ulgiati,
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Heesters BA, van Megesen K, Tomris I, de Vries RP, Magri G, Spits H. Characterization of human FDCs reveals regulation of T cells and antigen presentation to B cells. J Exp Med 2021; 218:e20210790. [PMID: 34424268 PMCID: PMC8404474 DOI: 10.1084/jem.20210790] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/02/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Stromal-derived follicular dendritic cells (FDCs) are essential for germinal centers (GCs), the site where B cells maturate their antibodies. FDCs present native antigen to B cells and maintain a CXCL13 gradient to form the B cell follicle. Yet despite their essential role, the transcriptome of human FDCs remains undefined. Using single-cell RNA sequencing and microarray, we provided the transcriptome of these enigmatic cells as a comprehensive resource. Key genes were validated by flow cytometry and microscopy. Surprisingly, marginal reticular cells (MRCs) rather than FDCs expressed B cell activating factor (BAFF). Furthermore, we found that human FDCs expressed TLR4 and can alter antigen availability in response to pathogen-associated molecular patterns (PAMPs). High expression of PD-L1 and PD-L2 on FDCs activated PD1 on T cells. In addition, we found expression of genes related to T cell regulation, such as HLA-DRA, CD40, and others. These data suggest intimate contact between human FDCs and T cells.
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Affiliation(s)
- Balthasar A. Heesters
- Amsterdam University Medical Centers, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kyah van Megesen
- Amsterdam University Medical Centers, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam, Netherlands
| | - Ilhan Tomris
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Robert P. de Vries
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Giuliana Magri
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d’Investigacions Mèdiques, Barcelona, Spain
| | - Hergen Spits
- Amsterdam University Medical Centers, University of Amsterdam, Department of Experimental Immunology, Amsterdam institute for Infection and Immunity, Amsterdam, Netherlands
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Carpanini SM, Harwood JC, Baker E, Torvell M, Sims R, Williams J, Morgan BP. The Impact of Complement Genes on the Risk of Late-Onset Alzheimer's Disease. Genes (Basel) 2021; 12:443. [PMID: 33804666 PMCID: PMC8003605 DOI: 10.3390/genes12030443] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD), the most common cause of dementia, and a huge global health challenge, is a neurodegenerative disease of uncertain aetiology. To deliver effective diagnostics and therapeutics, understanding the molecular basis of the disease is essential. Contemporary large genome-wide association studies (GWAS) have identified over seventy novel genetic susceptibility loci for LOAD. Most are implicated in microglial or inflammatory pathways, bringing inflammation to the fore as a candidate pathological pathway. Among the most significant GWAS hits are three complement genes: CLU, encoding the fluid-phase complement inhibitor clusterin; CR1 encoding complement receptor 1 (CR1); and recently, C1S encoding the complement enzyme C1s. Complement activation is a critical driver of inflammation; changes in complement genes may impact risk by altering the inflammatory status in the brain. To assess complement gene association with LOAD risk, we manually created a comprehensive complement gene list and tested these in gene-set analysis with LOAD summary statistics. We confirmed associations of CLU and CR1 genes with LOAD but showed no significant associations for the complement gene-set when excluding CLU and CR1. No significant association with other complement genes, including C1S, was seen in the IGAP dataset; however, these may emerge from larger datasets.
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Affiliation(s)
- Sarah M. Carpanini
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
- Division of Infection and Immunity, School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - Janet C. Harwood
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK; (J.C.H.); (R.S.)
| | - Emily Baker
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
| | - Megan Torvell
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
- Division of Infection and Immunity, School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | | | - Rebecca Sims
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK; (J.C.H.); (R.S.)
| | - Julie Williams
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
| | - B. Paul Morgan
- UK Dementia Research Institute at Cardiff University, School of Medicine, Cardiff, CF24 4HQ, UK; (S.M.C.); (E.B.); (M.T.); (J.W.)
- Division of Infection and Immunity, School of Medicine, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
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Kullo I, Ding K, Shameer K, McCarty C, Jarvik G, Denny J, Ritchie M, Ye Z, Crosslin D, Chisholm R, Manolio T, Chute C. Complement receptor 1 gene variants are associated with erythrocyte sedimentation rate. Am J Hum Genet 2011; 89:131-8. [PMID: 21700265 DOI: 10.1016/j.ajhg.2011.05.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2011] [Revised: 05/16/2011] [Accepted: 05/23/2011] [Indexed: 10/18/2022] Open
Abstract
The erythrocyte sedimentation rate (ESR), a commonly performed test of the acute phase response, is the rate at which erythrocytes sediment in vitro in 1 hr. The molecular basis of erythrocyte sedimentation is unknown. To identify genetic variants associated with ESR, we carried out a genome-wide association study of 7607 patients in the Electronic Medical Records and Genomics (eMERGE) network. The discovery cohort consisted of 1979 individuals from the Mayo Clinic, and the replication cohort consisted of 5628 individuals from the remaining four eMERGE sites. A nonsynonymous SNP, rs6691117 (Val→IIe), in the complement receptor 1 gene (CR1) was associated with ESR (discovery cohort p = 7 × 10(-12), replication cohort p = 3 × 10(-14), combined cohort p = 9 × 10(-24)). We imputed 61 SNPs in CR1, and a "possibly damaging" SNP (rs2274567, His→Arg) in linkage disequilibrium (r(2) = 0.74) with rs6691117 was also associated with ESR (discovery p = 5 × 10(-11), replication p = 7 × 10(-17), and combined cohort p = 2 × 10(-25)). The two nonsynonymous SNPs in CR1 are near the C3b/C4b binding site, suggesting a possible mechanism by which the variants may influence ESR. In conclusion, genetic variation in CR1, which encodes a protein that clears complement-tagged inflammatory particles from the circulation, influences interindividual variation in ESR, highlighting an association between the innate immunity pathway and erythrocyte interactions.
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McLure CA, Williamson JF, Smyth LA, Agrawal S, Lester S, Millman JA, Keating PJ, Stewart BJ, Dawkins RL. Extensive genomic and functional polymorphism of the complement control proteins. Immunogenetics 2005; 57:805-15. [PMID: 16283405 DOI: 10.1007/s00251-005-0049-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2005] [Accepted: 08/11/2005] [Indexed: 11/25/2022]
Abstract
Using combinations of genomic markers, we describe more than 20 distinct ancestral haplotypes (AH) of complement control proteins (CCPs), located within the regulators of complement activation (RCA) alpha block at 1q32. This extensive polymorphism, including functional sites, is important because CCPs are involved in the regulation of complement activation whilst also serving as self and viral receptors. To identify haplotypes, we used the genomic matching technique (GMT) based on the pragmatic observation that extreme nucleotide polymorphism is packaged with duplicated sequences as polymorphic frozen blocks (PFB). At each PFB, there are many alternative sequences (haplotypes) which are inherited faithfully from very remote ancestors. We have compared frequencies of RCA haplotypes and report differences in recurrent spontaneous abortion (RSA) and psoriasis vulgaris (PV).
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Affiliation(s)
- Craig A McLure
- CY O'Connor ERADE Village, Canning Vale, Western Australia
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Abstract
Clinical and genetic studies in humans and animal models indicate a crucial protective role for the complement system in systemic lupus erythematosus (SLE). This presents a paradox because the complement system is considered to be an important mediator of the inflammation that is observed in patients with SLE. One current view is that complement provides protection by facilitating the rapid removal of apoptotic debris to circumvent an autoimmune response. In this Opinion article, I discuss an alternative model in which complement - together with other components of the innate immune system - participates in the 'presentation' of SLE-inducing self-antigens to developing B cells. In this way, the complement system and innate immunity protect against responses to SLE (self) antigens by enhancing the elimination of self-reactive lymphocytes.
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Affiliation(s)
- Michael C Carroll
- CBR Institute of Biomedical Research, Inc., Harvard Medical School, 800 Huntington Avenue, Boston, Massachusetts 02115, USA.
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