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Immunogenetics of Lupus Erythematosus. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:213-257. [DOI: 10.1007/978-3-030-92616-8_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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52
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Dahlqvist J, Fulco CP, Ray JP, Liechti T, de Boer CG, Lieb DJ, Eisenhaure TM, Engreitz JM, Roederer M, Hacohen N. Systematic identification of genomic elements that regulate FCGR2A expression and harbor variants linked with autoimmune disease. Hum Mol Genet 2021; 31:1946-1961. [PMID: 34970970 PMCID: PMC9239749 DOI: 10.1093/hmg/ddab372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND FCGR2A binds antibody-antigen complexes to regulate the abundance of circulating and deposited complexes along with downstream immune and autoimmune responses. Although the abundance of FCRG2A may be critical in immune-mediated diseases, little is known about whether its surface expression is regulated through cis genomic elements and non-coding variants. In the current study, we aimed to characterize the regulation of FCGR2A expression, the impact of genetic variation and its association with autoimmune disease. METHODS We applied CRISPR-based interference and editing to scrutinize 1.7 Mb of open chromatin surrounding the FCGR2A gene to identify regulatory elements. Relevant transcription factors (TFs) binding to these regions were defined through public databases. Genetic variants affecting regulation were identified using luciferase reporter assays and were verified in a cohort of 1996 genotyped healthy individuals using flow cytometry. RESULTS We identified a complex proximal region and five distal enhancers regulating FCGR2A. The proximal region split into subregions upstream and downstream of the transcription start site, was enriched in binding of inflammation-regulated TFs, and harbored a variant associated with FCGR2A expression in primary myeloid cells. One distal enhancer region was occupied by CCCTC-binding factor (CTCF) whose binding site was disrupted by a rare genetic variant, altering gene expression. CONCLUSIONS The FCGR2A gene is regulated by multiple proximal and distal genomic regions, with links to autoimmune disease. These findings may open up novel therapeutic avenues where fine-tuning of FCGR2A levels may constitute a part of treatment strategies for immune-mediated diseases.
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Affiliation(s)
- Johanna Dahlqvist
- Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA,Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
| | - Charles P Fulco
- Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA,Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA,Bristol Myers Squibb, Cambridge, MA 02142, USA
| | - John P Ray
- Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA,Systems Immunology, Benaroya Research Institute, Seattle, WA 98101, USA
| | - Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20814, USA
| | - Carl G de Boer
- Klarman Cell Observatory, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA,School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David J Lieb
- Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Thomas M Eisenhaure
- Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Jesse M Engreitz
- Center for Cell Circuits, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA,BASE Initiative, Betty Irene Moore Children’s Heart Center, Lucile Packard Children’s Hospital, Stanford University School of Medicine, Stanford, CA, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20814, USA
| | - Nir Hacohen
- To whom correspondence should be addressed at: The Broad Institute of MIT and Harvard University, 415 Main Street, Cambridge, MA 02142, USA. Tel: +1 6177147234, Fax: +1 6177148956;
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Cytosolic Self-DNA—A Potential Source of Chronic Inflammation in Aging. Cells 2021; 10:cells10123544. [PMID: 34944052 PMCID: PMC8700131 DOI: 10.3390/cells10123544] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/28/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
Aging is the consequence of a lifelong accumulation of stochastic damage to tissues and cellular components. Advancing age closely associates with elevated markers of innate immunity and low-grade chronic inflammation, probably reflecting steady increasing incidents of cellular and tissue damage over the life course. The DNA sensing cGAS-STING signaling pathway is activated by misplaced cytosolic self-DNA, which then initiates the innate immune responses. Here, we hypothesize that the stochastic release of various forms of DNA from the nucleus and mitochondria, e.g., because of DNA damage, altered nucleus integrity, and mitochondrial damage, can result in chronic activation of inflammatory responses that characterize the aging process. This cytosolic self-DNA-innate immunity axis may perturb tissue homeostasis and function that characterizes human aging and age-associated pathology. Proper techniques and experimental models are available to investigate this axis to develop therapeutic interventions.
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Murray LM, Thillaiyampalam G, Xi Y, Cristino AS, Upham JW. Whole transcriptome analysis of high and low IFN-α producers reveals differential response patterns following rhinovirus stimulation. Clin Transl Immunology 2021; 10:e1356. [PMID: 34868584 PMCID: PMC8599968 DOI: 10.1002/cti2.1356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives Viral respiratory infections cause considerable morbidity and economic loss. While rhinoviruses (RV) typically cause little more than the common cold, they can produce severe infections and disease exacerbations in susceptible individuals, such as those with asthma. Variations in the regulation of key antiviral cytokines, particularly type I interferon (IFN‐α and IFN‐β), may contribute to RV susceptibility. To understand this variability, we compared the transcriptomes of high and low type I IFN producers. Methods Blood mononuclear cells from 238 individuals with or without asthma were cultured in the presence or absence of RV. Those samples demonstrating high or low RV‐stimulated IFN‐α production (N = 75) underwent RNA‐sequencing. Results Gene expression patterns were similar in samples from healthy participants and those with asthma. At baseline, the high IFN‐α producer group showed higher expression of genes associated with plasmacytoid dendritic cells, the innate immune response and vitamin D activation, but lower expression of oxidative stress pathways than the low IFN‐α producer group. After RV stimulation, the high IFN‐α producer group showed higher expression of genes found in immune response biological pathways and lower expression of genes linked to developmental and catabolic processes when compared to the low IFN‐α producer group. Conclusions These differences suggest that the high IFN‐α group has a higher level of immune system readiness, resulting in a more intense and perhaps more focussed pathogen‐specific immune response. These results contribute to a better understanding of the variability in type I IFN production between individuals.
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Affiliation(s)
- Liisa M Murray
- Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Gayathri Thillaiyampalam
- Diamantina Institute The University of Queensland Brisbane QLD Australia.,Griffith Institute for Drug Discovery Griffith University Brisbane QLD Australia
| | - Yang Xi
- Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Alexandre S Cristino
- Diamantina Institute The University of Queensland Brisbane QLD Australia.,Griffith Institute for Drug Discovery Griffith University Brisbane QLD Australia
| | - John W Upham
- Diamantina Institute The University of Queensland Brisbane QLD Australia.,Respiratory and Sleep Medicine Princess Alexandra Hospital Brisbane QLD Australia
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55
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Randolph HE, Fiege JK, Thielen BK, Mickelson CK, Shiratori M, Barroso-Batista J, Langlois RA, Barreiro LB. Genetic ancestry effects on the response to viral infection are pervasive but cell type specific. Science 2021; 374:1127-1133. [PMID: 34822289 PMCID: PMC8957271 DOI: 10.1126/science.abg0928] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Humans differ in their susceptibility to infectious disease, partly owing to variation in the immune response after infection. We used single-cell RNA sequencing to quantify variation in the response to influenza infection in peripheral blood mononuclear cells from European- and African-ancestry males. Genetic ancestry effects are common but highly cell type specific. Higher levels of European ancestry are associated with increased type I interferon pathway activity in early infection, which predicts reduced viral titers at later time points. Substantial population-associated variation is explained by cis-expression quantitative trait loci that are differentiated by genetic ancestry. Furthermore, genetic ancestry–associated genes are enriched among genes correlated with COVID-19 disease severity, suggesting that the early immune response contributes to ancestry-associated differences for multiple viral infection outcomes.
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Affiliation(s)
- Haley E Randolph
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jessica K Fiege
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Beth K Thielen
- Department of Pediatrics, Division of Pediatric Infectious Diseases and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Clayton K Mickelson
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Mari Shiratori
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - João Barroso-Batista
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ryan A Langlois
- Center for Immunology, University of Minnesota, Minneapolis, MN, USA
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Immunology, University of Chicago, Chicago, IL, USA
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56
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DiMaio D, Emu B, Goodman AL, Mothes W, Justice A. Cancer Microbiology. J Natl Cancer Inst 2021; 114:651-663. [PMID: 34850062 DOI: 10.1093/jnci/djab212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/18/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022] Open
Abstract
Microbes play important roles in cancer from direct carcinogenic effects to their use in treatment. Cancers caused by microorganisms account for approximately 15% of cancers, mostly in low- and middle-income countries. Unique features of infectious carcinogens include their transmissibility, mutability, and specific immune interactions, which provide challenges and opportunities for cancer prevention and treatment. For these agents, infection control through exposure reduction, antivirals, antibiotics, and vaccines is cancer control. In addition, developing evidence suggests that microorganisms including the human microbiome can indirectly modulate cancer formation and influence the effectiveness and toxicity of cancer treatments. Finally, microorganisms themselves can be used to prevent or treat cancer. The convergence of these factors signals the emergence of a new field, Cancer Microbiology. Recognition of Cancer Microbiology will spur research, stimulate cross-disciplinary training, inform drug development, and improve public health.
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Affiliation(s)
- Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, P.O. Box 208005, CT, USA, 06520-8005.,Department of Therapeutic Radiology, Yale School of Medicine, New Haven, P.O. Box 208040, CT, USA, 06520-8040.,Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, P.O. Box 208024, CT, USA, 06520-8024.,Yale Cancer Center, New Haven, P.O. Box 208028, CT, USA, 06520-8028
| | - Brinda Emu
- Yale Cancer Center, New Haven, P.O. Box 208028, CT, USA, 06520-8028.,Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, P.O. Box 208022, CT, 06520-8022
| | - Andrew L Goodman
- Yale Cancer Center, New Haven, P.O. Box 208028, CT, USA, 06520-8028.,Department of Microbial Pathogenesis, Yale University, New Haven, P.O. Box 9812, CT, USA, 06536-0812
| | - Walther Mothes
- Yale Cancer Center, New Haven, P.O. Box 208028, CT, USA, 06520-8028.,Department of Microbial Pathogenesis, Yale University, New Haven, P.O. Box 9812, CT, USA, 06536-0812
| | - Amy Justice
- Yale Cancer Center, New Haven, P.O. Box 208028, CT, USA, 06520-8028.,Department of General Medicine, Yale University, VA Medical Center, New Haven, 06516, CT, USA
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Radojević D, Tomić S, Mihajlović D, Tolinački M, Pavlović B, Vučević D, Bojić S, Golić N, Čolić M, Đokić J. Fecal microbiota composition associates with the capacity of human peripheral blood monocytes to differentiate into immunogenic dendritic cells in vitro. Gut Microbes 2021; 13:1-20. [PMID: 33970783 PMCID: PMC8115579 DOI: 10.1080/19490976.2021.1921927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Although promising for active immunization in cancer patients, dendritic cells (DCs) vaccines generated in vitro display high inter-individual variability in their immunogenicity, which mostly limits their therapeutic efficacy. Gut microbiota composition is a key emerging factor affecting individuals' immune responses, but it is unknown how it affects the variability of donors' precursor cells to differentiate into immunogenic DCs in vitro. By analyzing gut microbiota composition in 14 healthy donors, along with the phenotype and cytokines production by monocyte-derived DCs, we found significant correlations between immunogenic properties of DC and microbiota composition. Namely, donors who had higher α-diversity of gut microbiota and higher abundance of short-chain fatty acid (SCFAs) and SCFA-producing bacteria in feces, displayed lower expression of CD1a on immature (im)DC and higher expression of ILT-3, costimulatory molecules (CD86, CD40) proinflammatory cytokines (TNF-α, IL-6, IL-8) and IL-12p70/IL-10 ratio, all of which correlated with their lower maturation potential and immunogenicity upon stimulation with LPS/IFNγ, a well-known Th1 polarizing cocktail. In contrast, imDCs generated from donors with lower α-diversity and higher abundance of Bifidobacterium and Collinsella in feces displayed higher CD1a expression and higher potential to up-regulate CD86 and CD40, increase TNF-α, IL-6, IL-8 production, and IL-12p70/IL-10 ratio upon stimulation. These results emphasize the important role of gut microbiota on the capacity of donor precursor cells to differentiate into immunogenic DCs suitable for cancer therapy, which could be harnessed for improving the actual and future DC-based cancer therapies.
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Affiliation(s)
- Dušan Radojević
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia
| | - Sergej Tomić
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | - Dušan Mihajlović
- Faculty of Medicine Foca, University of East Sarajevo, Republic of Srpska, Bosnia and Herzegovina,Medical Faculty of the Military Medical Academy, University of Defence, Belgrade, Serbia
| | - Maja Tolinački
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia
| | | | - Dragana Vučević
- Department for Immunology and Immunoparasitology, Institute for the Application of Nuclear Energy, University of Belgrade, Belgrade, Serbia
| | | | - Nataša Golić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia
| | - Miodrag Čolić
- Faculty of Medicine Foca, University of East Sarajevo, Republic of Srpska, Bosnia and Herzegovina,Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Jelena Đokić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGI), University of Belgrade, Belgrade, Serbia,CONTACT Jelena Đokić Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Vojvode Stepe 444a, Belgrade11042, Serbia
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Genetic variation in NDFIP1 modifies the metabolic patterns in immune cells of multiple sclerosis patients. Sci Rep 2021; 11:21371. [PMID: 34725369 PMCID: PMC8560952 DOI: 10.1038/s41598-021-00528-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/08/2021] [Indexed: 11/29/2022] Open
Abstract
One of the 233 polymorphisms associated with multiple sclerosis (MS) susceptibility lies within the NDFIP1 gene, and it was previously identified as eQTL in healthy controls. NDFIP1 shows interesting immune functions and is involved in the development of the central nervous system. We aimed at studying the NDFIP1 variant on activation and metabolism of immune cells. NDFIP1 mRNA and protein expression were assessed in PBMCs by qPCR and western blot in 87 MS patients and 84 healthy controls genotyped for rs4912622. Immune activation after PHA stimulation was evaluated by CD69 upregulation, and metabolic function of both basal and PHA-activated lymphocytes was studied by Seahorse Xfp-Analyzer. In minor-allele homozygous controls but not in patients, we found higher NDFIP1 expression, significantly reduced protein levels, and CD69 upregulation in B- and T-cells. PBMCs from minor-allele homozygous controls showed significantly higher basal mitochondrial respiration and ATP production compared to major-allele carriers, while minor-allele homozygous patients showed significantly lower metabolic activity than carriers of the major allele. In conclusion, we describe associations in minor-allele homozygous controls with lower levels of NDFIP1 protein, CD69 upregulation, and raised mitochondrial activity, which are not replicated in MS patients, suggesting a NDFIP1 differential effect in health and disease.
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Balliu B, Carcamo-Orive I, Gloudemans MJ, Nachun DC, Durrant MG, Gazal S, Park CY, Knowles DA, Wabitsch M, Quertermous T, Knowles JW, Montgomery SB. An integrated approach to identify environmental modulators of genetic risk factors for complex traits. Am J Hum Genet 2021; 108:1866-1879. [PMID: 34582792 PMCID: PMC8546041 DOI: 10.1016/j.ajhg.2021.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/27/2021] [Indexed: 12/16/2022] Open
Abstract
Complex traits and diseases can be influenced by both genetics and environment. However, given the large number of environmental stimuli and power challenges for gene-by-environment testing, it remains a critical challenge to identify and prioritize specific disease-relevant environmental exposures. We propose a framework for leveraging signals from transcriptional responses to environmental perturbations to identify disease-relevant perturbations that can modulate genetic risk for complex traits and inform the functions of genetic variants associated with complex traits. We perturbed human skeletal-muscle-, fat-, and liver-relevant cell lines with 21 perturbations affecting insulin resistance, glucose homeostasis, and metabolic regulation in humans and identified thousands of environmentally responsive genes. By combining these data with GWASs from 31 distinct polygenic traits, we show that the heritability of multiple traits is enriched in regions surrounding genes responsive to specific perturbations and, further, that environmentally responsive genes are enriched for associations with specific diseases and phenotypes from the GWAS Catalog. Overall, we demonstrate the advantages of large-scale characterization of transcriptional changes in diversely stimulated and pathologically relevant cells to identify disease-relevant perturbations.
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Affiliation(s)
- Brunilda Balliu
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Ivan Carcamo-Orive
- Department of Medicine, Division of Cardiovascular Medicine, Cardiovascular Institute and Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Gloudemans
- Biomedical Informatics Training Program and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew G Durrant
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Gazal
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Chong Y Park
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David A Knowles
- New York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Endocrinology, Ulm University, Ulm 89075, Germany
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua W Knowles
- Department of Medicine, Division of Cardiology and Cardiovascular Institute, Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Stephen B Montgomery
- Department of Pathology and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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60
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Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-meijers HE, Wu P, Slatcher RB, Zhou X, Luca F, Pique-regi R. Genetic control of the dynamic transcriptional response to immune stimuli and glucocorticoids at single cell resolution.. [PMID: 35313584 PMCID: PMC8936121 DOI: 10.1101/2021.09.30.462672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as treatment for many immune conditions, such as asthma and more recently severe COVID-19. Single cell data can capture more fine-grained details on transcriptional variability and dynamics to gain a better understanding of the molecular underpinnings of inter-individual variation in drug response. Here, we used single cell RNA-seq to study the dynamics of the transcriptional response to glucocorticoids in activated Peripheral Blood Mononuclear Cells from 96 African American children. We employed novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we demonstrated that glucocorticoids reverse the effects of immune stimulation on both gene expression mean and variability. Our novel measure of gene expression response dynamics, based on the diagonal linear discriminant analysis, separated individual cells by response status on the basis of their transcriptional profiles and allowed us to identify different dynamic patterns of gene expression along the response pseudotime. We identified genetic variants regulating gene expression mean and variability, including treatment-specific effects, and demonstrated widespread genetic regulation of the transcriptional dynamics of the gene expression response.
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61
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Petukhova L. An Imperative Need for Further Genetic Studies of Alopecia Areata. J Investig Dermatol Symp Proc 2021; 20:S22-S27. [PMID: 33099379 DOI: 10.1016/j.jisp.2020.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human genetic studies of diseases that are multifactorial and prevalent have generated a wealth of knowledge about the genetic architecture of chronic diseases. Generalizable attributes are shaping the development of models to explain how the human genome influences our health and can be leveraged to improve it. Importantly, both rare and common genetic variants contribute to disease risk and provide complementary information. Although initial genetic studies of alopecia areata have yielded insight with high clinical impact, there remains a number of important unanswered questions pertaining to disease biology and patient care that could be addressed by further genetic investigations.
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Affiliation(s)
- Lynn Petukhova
- Department of Dermatology, College of Physicians and Surgeons, Columbia University, New York, New York, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, USA.
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Ullastres A, Merenciano M, González J. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biol 2021; 22:265. [PMID: 34521452 PMCID: PMC8439047 DOI: 10.1186/s13059-021-02471-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
Background Variation in gene expression underlies interindividual variability in relevant traits including immune response. However, the genetic variation responsible for these gene expression changes remains largely unknown. Among the non-coding variants that could be relevant, transposable element insertions are promising candidates as they have been shown to be a rich and diverse source of cis-regulatory elements. Results In this work, we use a population genetics approach to identify transposable element insertions likely to increase the tolerance of Drosophila melanogaster to bacterial infection by affecting the expression of immune-related genes. We identify 12 insertions associated with allele-specific expression changes in immune-related genes. We experimentally validate three of these insertions including one likely to be acting as a silencer, one as an enhancer, and one with a dual role as enhancer and promoter. The direction in the change of gene expression associated with the presence of several of these insertions is consistent with an increased survival to infection. Indeed, for one of the insertions, we show that this is the case by analyzing both natural populations and CRISPR/Cas9 mutants in which the insertion is deleted from its native genomic context. Conclusions We show that transposable elements contribute to gene expression variation in response to infection in D. melanogaster and that this variation is likely to affect their survival capacity. Because the role of transposable elements as regulatory elements is not restricted to Drosophila, transposable elements are likely to play a role in immune response in other organisms as well. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02471-3.
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Affiliation(s)
- Anna Ullastres
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain.
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Van Dyke K, Lutz S, Mekonnen G, Myers CL, Albert FW. Trans-acting genetic variation affects the expression of adjacent genes. Genetics 2021; 217:6126816. [PMID: 33789351 DOI: 10.1093/genetics/iyaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/16/2020] [Indexed: 11/13/2022] Open
Abstract
Gene expression differences among individuals are shaped by trans-acting expression quantitative trait loci (eQTLs). Most trans-eQTLs map to hotspot locations that influence many genes. The molecular mechanisms perturbed by hotspots are often assumed to involve "vertical" cascades of effects in pathways that can ultimately affect the expression of thousands of genes. Here, we report that trans-eQTLs can affect the expression of adjacent genes via "horizontal" mechanisms that extend along a chromosome. Genes affected by trans-eQTL hotspots in the yeast Saccharomyces cerevisiae were more likely to be located next to each other than expected by chance. These paired hotspot effects tended to occur at adjacent genes that also show coexpression in response to genetic and environmental perturbations, suggesting shared mechanisms. Physical proximity and shared chromatin state, in addition to regulation of adjacent genes by similar transcription factors, were independently associated with paired hotspot effects among adjacent genes. Paired effects of trans-eQTLs can occur at neighboring genes even when these genes do not share a common function. This phenomenon could result in unexpected connections between regulatory genetic variation and phenotypes.
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Affiliation(s)
- Krisna Van Dyke
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sheila Lutz
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gemechu Mekonnen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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Findley AS, Zhang X, Boye C, Lin YL, Kalita CA, Barreiro L, Lohmueller KE, Pique-Regi R, Luca F. A signature of Neanderthal introgression on molecular mechanisms of environmental responses. PLoS Genet 2021; 17:e1009493. [PMID: 34570765 PMCID: PMC8509894 DOI: 10.1371/journal.pgen.1009493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/12/2021] [Accepted: 08/18/2021] [Indexed: 12/17/2022] Open
Abstract
Ancient human migrations led to the settlement of population groups in varied environmental contexts worldwide. The extent to which adaptation to local environments has shaped human genetic diversity is a longstanding question in human evolution. Recent studies have suggested that introgression of archaic alleles in the genome of modern humans may have contributed to adaptation to environmental pressures such as pathogen exposure. Functional genomic studies have demonstrated that variation in gene expression across individuals and in response to environmental perturbations is a main mechanism underlying complex trait variation. We considered gene expression response to in vitro treatments as a molecular phenotype to identify genes and regulatory variants that may have played an important role in adaptations to local environments. We investigated if Neanderthal introgression in the human genome may contribute to the transcriptional response to environmental perturbations. To this end we used eQTLs for genes differentially expressed in a panel of 52 cellular environments, resulting from 5 cell types and 26 treatments, including hormones, vitamins, drugs, and environmental contaminants. We found that SNPs with introgressed Neanderthal alleles (N-SNPs) disrupt binding of transcription factors important for environmental responses, including ionizing radiation and hypoxia, and for glucose metabolism. We identified an enrichment for N-SNPs among eQTLs for genes differentially expressed in response to 8 treatments, including glucocorticoids, caffeine, and vitamin D. Using Massively Parallel Reporter Assays (MPRA) data, we validated the regulatory function of 21 introgressed Neanderthal variants in the human genome, corresponding to 8 eQTLs regulating 15 genes that respond to environmental perturbations. These findings expand the set of environments where archaic introgression may have contributed to adaptations to local environments in modern humans and provide experimental validation for the regulatory function of introgressed variants.
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Affiliation(s)
- Anthony S. Findley
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Xinjun Zhang
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
| | - Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Yen Lung Lin
- Genetics Section, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Cynthia A. Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
| | - Luis Barreiro
- Genetics Section, Department of Medicine, University of Chicago, Chicago, Illinois, United States of America
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, California, United States of America
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, United States of America
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan, United States of America
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Hu W, Jiang C, Kim M, Yang W, Zhu K, Guan D, Lv W, Xiao Y, Wilson JR, Rader DJ, Pui CH, Relling MV, Lazar MA. Individual-specific functional epigenomics reveals genetic determinants of adverse metabolic effects of glucocorticoids. Cell Metab 2021; 33:1592-1609.e7. [PMID: 34233159 PMCID: PMC8340270 DOI: 10.1016/j.cmet.2021.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/26/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023]
Abstract
Glucocorticoids (GCs) are widely used as anti-inflammatory drugs, but their long-term use has severe metabolic side effects. Here, by treating multiple individual adipose stem cell-derived adipocytes and induced pluripotent stem cell-derived hepatocytes with the potent GC dexamethasone (Dex), we uncovered cell-type-specific and individual-specific GC-dependent transcriptomes and glucocorticoid receptor (GR) cistromes. Individual-specific GR binding could be traced to single-nucleotide polymorphisms (SNPs) that altered the binding motifs of GR or its cooperating factors. We also discovered another set of genetic variants that modulated Dex response through affecting chromatin accessibility or chromatin architecture. Several SNPs that altered Dex-regulated GR binding and gene expression controlled Dex-driven metabolic perturbations. Remarkably, these genetic variations were highly associated with increases in serum glucose, lipids, and body mass in subjects on GC therapy. Knowledge of the genetic variants that predispose individuals to metabolic side effects allows for a precision medicine approach to the use of clinically relevant GCs.
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Affiliation(s)
- Wenxiang Hu
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; The Max-Planck Center for Tissue Stem Cell Research and Regenerative Medicine, Bioland Laboratory, Guangzhou, China.
| | - Chunjie Jiang
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mindy Kim
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kun Zhu
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dongyin Guan
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wenjian Lv
- Division of Cardiology and Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yang Xiao
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jessica R Wilson
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Daniel J Rader
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mary V Relling
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mitchell A Lazar
- Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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66
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Brandt M, Kim-Hellmuth S, Ziosi M, Gokden A, Wolman A, Lam N, Recinos Y, Daniloski Z, Morris JA, Hornung V, Schumacher J, Lappalainen T. An autoimmune disease risk variant: A trans master regulatory effect mediated by IRF1 under immune stimulation? PLoS Genet 2021; 17:e1009684. [PMID: 34314424 PMCID: PMC8345867 DOI: 10.1371/journal.pgen.1009684] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/06/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Functional mechanisms remain unknown for most genetic loci associated to complex human traits and diseases. In this study, we first mapped trans-eQTLs in a data set of primary monocytes stimulated with LPS, and discovered that a risk variant for autoimmune disease, rs17622517 in an intron of C5ORF56, affects the expression of the transcription factor IRF1 20 kb away. The cis-regulatory effect specific to IRF1 is active under early immune stimulus, with a large number of trans-eQTL effects across the genome under late LPS response. Using CRISPRi silencing, we showed that perturbation of the SNP locus downregulates IRF1 and causes widespread transcriptional effects. Genome editing by CRISPR had suggestive recapitulation of the LPS-specific trans-eQTL signal and lent support for the rs17622517 site being functional. Our results suggest that this common genetic variant affects inter-individual response to immune stimuli via regulation of IRF1. For this autoimmune GWAS locus, our work provides evidence of the functional variant, demonstrates a condition-specific enhancer effect, identifies IRF1 as the likely causal gene in cis, and indicates that overactivation of the downstream immune-related pathway may be the cellular mechanism increasing disease risk. This work not only provides rare experimental validation of a master-regulatory trans-eQTL, but also demonstrates the power of eQTL mapping to build mechanistic hypotheses amenable for experimental follow-up using the CRISPR toolkit. Although many genetic loci have been associated to disease, understanding how these variants impact molecular and cellular functions to impact disease risk have been challenging. Here, we first used blood cells from a large number of individuals and stimulated them in the laboratory with a proxy for bacterial infection. We identified that a genetic variant associated to autoimmune diseases also affects the expression of the nearby transcription factor IRF1 gene in early immune response, followed by expression change of other genes in late immune response. We then studied this effect in cell lines, using the CRISPR approach to silence the activity of the genomic element of this variant and cause mutations at that position. We found evidence that this autoimmune disease -associated variant is located in a genomic regulatory element that responds to immune stimulus and affects expression of IRF1 and a complex gene regulatory network. Thus, our characterization of genetic regulatory variation in the human population combined with experimental follow-up suggests a plausible, previously uncharacterized molecular mechanism that may underlie this genetic variant’s effect on immune disease risk.
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Affiliation(s)
- Margot Brandt
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America
| | - Sarah Kim-Hellmuth
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany
- Dr. von Hauner Children’s Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Marcello Ziosi
- New York Genome Center, New York, New York, United States of America
| | - Alper Gokden
- New York Genome Center, New York, New York, United States of America
| | - Aaron Wolman
- New York Genome Center, New York, New York, United States of America
| | - Nora Lam
- New York Genome Center, New York, New York, United States of America
- Program of Pathobiology and Mechanisms of Disease, Columbia University, New York, New York, United States of America
| | - Yocelyn Recinos
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, New York, United States of America
| | - Zharko Daniloski
- New York Genome Center, New York, New York, United States of America
- New York University, Department of Biology, New York, New York, United States of America
| | - John A. Morris
- New York Genome Center, New York, New York, United States of America
- New York University, Department of Biology, New York, New York, United States of America
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- * E-mail:
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67
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Yao R, Ianevski A, Kainov D. Safe-in-Man Broad Spectrum Antiviral Agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:313-337. [PMID: 34258746 DOI: 10.1007/978-981-16-0267-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Emerging and re-emerging viral diseases occur with regularity within the human population. The conventional 'one drug, one virus' paradigm for antivirals does not adequately allow for proper preparedness in the face of unknown future epidemics. In addition, drug developers lack the financial incentives to work on antiviral drug discovery, with most pharmaceutical companies choosing to focus on more profitable disease areas. Safe-in-man broad spectrum antiviral agents (BSAAs) can help meet the need for antiviral development by already having passed phase I clinical trials, requiring less time and money to develop, and having the capacity to work against many viruses, allowing for a speedy response when unforeseen epidemics arise. In this chapter, we discuss the benefits of repurposing existing drugs as BSAAs, describe the major steps in safe-in-man BSAA drug development from discovery through clinical trials, and list several database resources that are useful tools for antiviral drug repositioning.
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Affiliation(s)
- Rouan Yao
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Aleksandr Ianevski
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Denis Kainov
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
- Institute of Technology, University of Tartu, Tartu, Estonia.
- Institute for Molecule Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland.
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Abstract
Disease classification, or nosology, was historically driven by careful examination of clinical features of patients. As technologies to measure and understand human phenotypes advanced, so too did classifications of disease, and the advent of genetic data has led to a surge in genetic subtyping in the past decades. Although the fundamental process of refining disease definitions and subtypes is shared across diverse fields, each field is driven by its own goals and technological expertise, leading to inconsistent and conflicting definitions of disease subtypes. Here, we review several classical and recent subtypes and subtyping approaches and provide concrete definitions to delineate subtypes. In particular, we focus on subtypes with distinct causal disease biology, which are of primary interest to scientists, and subtypes with pragmatic medical benefits, which are of primary interest to physicians. We propose genetic heterogeneity as a gold standard for establishing biologically distinct subtypes of complex polygenic disease. We focus especially on methods to find and validate genetic subtypes, emphasizing common pitfalls and how to avoid them.
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Affiliation(s)
- Andy Dahl
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA; .,Department of Neurology, University of California, Los Angeles, California 90024, USA; .,Department of Computational Medicine, University of California, Los Angeles, California 90095, USA
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, California 90024, USA; .,Department of Computational Medicine, University of California, Los Angeles, California 90095, USA
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69
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Resztak JA, Farrell AK, Mair-Meijers H, Alazizi A, Wen X, Wildman DE, Zilioli S, Slatcher RB, Pique-Regi R, Luca F. Psychosocial experiences modulate asthma-associated genes through gene-environment interactions. eLife 2021; 10:e63852. [PMID: 34142656 PMCID: PMC8282343 DOI: 10.7554/elife.63852] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 06/16/2021] [Indexed: 01/04/2023] Open
Abstract
Social interactions and the overall psychosocial environment have a demonstrated impact on health, particularly for people living in disadvantaged urban areas. Here, we investigated the effect of psychosocial experiences on gene expression in peripheral blood immune cells of children with asthma in Metro Detroit. Using RNA-sequencing and a new machine learning approach, we identified transcriptional signatures of 19 variables including psychosocial factors, blood cell composition, and asthma symptoms. Importantly, we found 169 genes associated with asthma or allergic disease that are regulated by psychosocial factors and 344 significant gene-environment interactions for gene expression levels. These results demonstrate that immune gene expression mediates the link between negative psychosocial experiences and asthma risk.
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Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | | | | | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - Derek E Wildman
- College of Public Health, University of South FloridaTampaUnited States
| | - Samuele Zilioli
- Department of Psychology, Wayne State UniversityDetroitUnited States
- Department of Family Medicine and Public Health Sciences, Wayne State UniversityDetroitUnited States
| | | | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
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70
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Dabral D, van den Bogaart G. The Roles of Phospholipase A 2 in Phagocytes. Front Cell Dev Biol 2021; 9:673502. [PMID: 34179001 PMCID: PMC8222813 DOI: 10.3389/fcell.2021.673502] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Phagocytic cells, such as macrophages, neutrophils, and dendritic cells, ingest particles larger than about 0.5 μM and thereby clear microbial pathogens and malignant cells from the body. These phagocytic cargoes are proteolytically degraded within the lumen of phagosomes, and peptides derived from them are presented on Major Histocompatibility Complexes (MHC) for the activation of T cells. Mammalian PLA2 isozymes belong to a large family of enzymes that cleave phospholipids at the second position of the glycerol backbone, releasing a free fatty acid and a lysolipid moiety. In human macrophages, at least 15 different PLA2 forms are expressed, and expression of many of these is dependent on pathogenic stimulation. Intriguing questions are why so many PLA2 forms are expressed in macrophages, and what are the functional consequences of their altered gene expression after encountering pathogenic stimuli. In this review, we discuss the evidence of the differential roles of different forms of PLA2 in phagocytic immune cells. These roles include: lipid signaling for immune cell activation, initial phagocytic particle uptake, microbial action for the killing and degradation of ingested microbes, and the repair of membranes induced by oxygen radicals. We also discuss the roles of PLA2 in the subsequent digestion of ingested phagocytic cargoes for antigen presentation to T cells.
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Affiliation(s)
- Deepti Dabral
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Geert van den Bogaart
- Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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71
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Devaprasad A, Radstake TRDJ, Pandit A. Integration of Immunome With Disease-Gene Network Reveals Common Cellular Mechanisms Between IMIDs and Drug Repurposing Strategies. Front Immunol 2021; 12:669400. [PMID: 34108969 PMCID: PMC8181425 DOI: 10.3389/fimmu.2021.669400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/04/2021] [Indexed: 01/25/2023] Open
Abstract
Objective Development and progression of immune-mediated inflammatory diseases (IMIDs) involve intricate dysregulation of the disease-associated genes (DAGs) and their expressing immune cells. Identifying the crucial disease-associated cells (DACs) in IMIDs has been challenging due to the underlying complex molecular mechanism. Methods Using transcriptome profiles of 40 different immune cells, unsupervised machine learning, and disease-gene networks, we constructed the Disease-gene IMmune cell Expression (DIME) network and identified top DACs and DAGs of 12 phenotypically different IMIDs. We compared the DIME networks of IMIDs to identify common pathways between them. We used the common pathways and publicly available drug-gene network to identify promising drug repurposing targets. Results We found CD4+Treg, CD4+Th1, and NK cells as top DACs in inflammatory arthritis such as ankylosing spondylitis (AS), psoriatic arthritis, and rheumatoid arthritis (RA); neutrophils, granulocytes, and BDCA1+CD14+ cells in systemic lupus erythematosus and systemic scleroderma; ILC2, CD4+Th1, CD4+Treg, and NK cells in the inflammatory bowel diseases (IBDs). We identified lymphoid cells (CD4+Th1, CD4+Treg, and NK) and their associated pathways to be important in HLA-B27 type diseases (psoriasis, AS, and IBDs) and in primary-joint-inflammation-based inflammatory arthritis (AS and RA). Based on the common cellular mechanisms, we identified lifitegrast as a potential drug repurposing candidate for Crohn's disease and other IMIDs. Conclusions Existing methods are inadequate in capturing the intricate involvement of the crucial genes and cell types essential to IMIDs. Our approach identified the key DACs, DAGs, common mechanisms between IMIDs, and proposed potential drug repurposing targets using the DIME network. To extend our method to other diseases, we built the DIME tool (https://bitbucket.org/systemsimmunology/dime/) to help scientists uncover the etiology of complex and rare diseases to further drug development by better-determining drug targets, thereby mitigating the risk of failure in late clinical development.
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Affiliation(s)
- Abhinandan Devaprasad
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Timothy R. D. J. Radstake
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Aridaman Pandit
- Division Internal Medicine and Dermatology, University Medical Center Utrecht, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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72
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Findley AS, Monziani A, Richards AL, Rhodes K, Ward MC, Kalita CA, Alazizi A, Pazokitoroudi A, Sankararaman S, Wen X, Lanfear DE, Pique-Regi R, Gilad Y, Luca F. Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. eLife 2021; 10:e67077. [PMID: 33988505 PMCID: PMC8248987 DOI: 10.7554/elife.67077] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022] Open
Abstract
Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type, and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing and were highly variable across contexts. For thousands of genes, we identified variable allelic expression across contexts and characterized different types of gene-environment interactions, many of which are associated with complex traits. Promoter functional and evolutionary features distinguished genes with elevated allelic imbalance mean and variance. On average, half of the genes with dynamic regulatory interactions were missed by large eQTL mapping studies, indicating the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease.
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Affiliation(s)
- Anthony S Findley
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Alan Monziani
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Katherine Rhodes
- Department of Human Genetics, University of ChicagoChicagoUnited States
| | - Michelle C Ward
- Department of Medicine, University of ChicagoChicagoUnited States
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | | | - Sriram Sankararaman
- Department of Computer Science, UCLALos AngelesUnited States
- Department of Human Genetics, UCLALos AngelesUnited States
- Department of Computational Medicine, UCLALos AngelesUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited States
| | - David E Lanfear
- Center for Individualized and Genomic Medicine Research, Henry Ford HospitalDetroitUnited States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
| | - Yoav Gilad
- Department of Human Genetics, University of ChicagoChicagoUnited States
- Department of Medicine, University of ChicagoChicagoUnited States
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
- Department of Obstetrics and Gynecology, Wayne State UniversityDetroitUnited States
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73
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Dannemann M, Gallego Romero I. Harnessing pluripotent stem cells as models to decipher human evolution. FEBS J 2021; 289:2992-3010. [PMID: 33876573 DOI: 10.1111/febs.15885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022]
Abstract
The study of human evolution, long constrained by a lack of experimental model systems, has been transformed by the emergence of the induced pluripotent stem cell (iPSC) field. iPSCs can be readily established from noninvasive tissue sources, from both humans and other primates; they can be maintained in the laboratory indefinitely, and they can be differentiated into other tissue types. These qualities mean that iPSCs are rapidly becoming established as viable and powerful model systems with which it is possible to address questions in human evolution that were until now logistically and ethically intractable, especially in the quest to understand humans' place among the great apes, and the genetic basis of human uniqueness. In this review, we discuss the key lessons and takeaways of this nascent field; from the types of research, iPSCs make possible to lingering challenges and likely future directions. We provide a comprehensive overview of how the seemingly unlikely combination of iPSCs and explicit evolutionary frameworks is transforming what is possible in our understanding of humanity's past and present.
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Affiliation(s)
| | - Irene Gallego Romero
- Institute of Genomics, University of Tartu, Estonia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Australia.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Centre for Stem Cell Systems, The University of Melbourne, Parkville, Australia
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74
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Ollila HM. Narcolepsy type 1: what have we learned from genetics? Sleep 2021; 43:5842137. [PMID: 32442260 PMCID: PMC7658635 DOI: 10.1093/sleep/zsaa099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/22/2020] [Indexed: 01/12/2023] Open
Abstract
Type-1 narcolepsy is a severe neurological disorder with distinct characteristic of loss of hypocretin neurotransmitter. Genetic analysis in type-1 narcolepsy have revealed a unique signal pointing toward autoimmune, rather than psychiatric origin. While type-1 narcolepsy has been intensively studied, the other subtypes of hypersomnolence, narcolepsy, and hypersomnia are less thoroughly understood. This review summarizes the latest breakthroughs in the field in narcolepsy. The goal of this article is to help the reader to understand better the risk from genetic factors and their interplay with immune, genetic, and epidemiological aspects in narcolepsy.
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Affiliation(s)
- Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA.,Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford University, Stanford, CA
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Boahen CK, Joosten LA, Netea MG, Kumar V. Conceptualization of population-specific human functional immune-genomics projects to identify factors that contribute to variability in immune and infectious diseases. Heliyon 2021; 7:e06755. [PMID: 33912719 PMCID: PMC8066384 DOI: 10.1016/j.heliyon.2021.e06755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/23/2021] [Accepted: 04/06/2021] [Indexed: 11/24/2022] Open
Abstract
The human immune system presents remarkable inter-individual variability in response to pathogens or perturbations. Recent high-throughput technologies have enabled the identification of both heritable and non-heritable determinants of immune response variation between individuals. In this review, we summarize the advances made through the Human Functional Genomics Projects (HFGPs), challenges and the need for more refined strategies. Inter-individual variability in stimulation-induced cytokine responses is influenced in part by age, gender, seasonality, and gut microbiome. Host genetic regulators especially single nucleotide polymorphisms in multiple immune gene loci, particularly the TLR1-TLR6-TLR10 locus, have been identified using individuals of predominantly European descent. However, transferability of such findings to other populations is challenging. We are beginning to incorporate diverse population cohorts and leverage multi-omics approaches at single cell level to bridge the current knowledge gap. We believe that such an approach presents the opportunities to comprehensively assess both genetic and environmental factors driving variation seen in immune response phenotype and a better understanding of the molecular and biological mechanisms involved.
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Affiliation(s)
- Collins K. Boahen
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Germany
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, 9700 RB, the Netherlands
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Medical Sciences Complex, Deralakatte, Mangalore, 575018, India
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76
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Bourgeois JS, Smith CM, Ko DC. These Are the Genes You're Looking For: Finding Host Resistance Genes. Trends Microbiol 2021; 29:346-362. [PMID: 33004258 PMCID: PMC7969353 DOI: 10.1016/j.tim.2020.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 12/21/2022]
Abstract
Humanity's ongoing struggle with new, re-emerging and endemic infectious diseases serves as a frequent reminder of the need to understand host-pathogen interactions. Recent advances in genomics have dramatically advanced our understanding of how genetics contributes to host resistance or susceptibility to bacterial infection. Here we discuss current trends in defining host-bacterial interactions at the genome-wide level, including screens that harness CRISPR/Cas9 genome editing, natural genetic variation, proteomics, and transcriptomics. We report on the merits, limitations, and findings of these innovative screens and discuss their complementary nature. Finally, we speculate on future innovation as we continue to progress through the postgenomic era and towards deeper mechanistic insight and clinical applications.
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Affiliation(s)
- Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Duke Human Vaccine Institute, School of Medicine, Duke University Durham, NC, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA; University Program in Genetics and Genomics, Duke University, Durham, NC, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, USA.
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77
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Yankovitz G, Cohn O, Bacharach E, Peshes-Yaloz N, Steuerman Y, Iraqi FA, Gat-Viks I. Leveraging the cell lineage to predict cell-type specificity of regulatory variation from bulk genomics. Genetics 2021; 217:6126814. [PMID: 33734353 DOI: 10.1093/genetics/iyab016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/12/2021] [Indexed: 11/12/2022] Open
Abstract
Recent computational methods have enabled the inference of the cell-type-specificity of eQTLs based on bulk transcriptomes from highly heterogeneous tissues. However, these methods are limited in their scalability to highly heterogeneous tissues and limited in their broad applicability to any cell-type specificity of eQTLs. Here we present and demonstrate Cell Lineage Genetics (CeL-Gen), a novel computational approach that allows inference of eQTLs together with the subsets of cell types in which they have an effect, from bulk transcriptome data. To obtain improved scalability and broader applicability, CeL-Gen takes as input the known cell lineage tree and relies on the observation that dynamic changes in genetic effects occur relatively infrequently during cell differentiation. CeL-Gen can therefore be used not only to tease apart genetic effects derived from different cell types but also to infer the particular differentiation steps in which genetic effects are altered.
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Affiliation(s)
- Gal Yankovitz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ofir Cohn
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Eran Bacharach
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Naama Peshes-Yaloz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Steuerman
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Fuad A Iraqi
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Irit Gat-Viks
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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78
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Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun 2021; 12:1611. [PMID: 33712590 PMCID: PMC7955039 DOI: 10.1038/s41467-021-21854-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE. Thousands of genetic variants have been associated with lupus, but causal variants and mechanisms are unknown. Here, the authors combine a massively parallel reporter assay with genome-wide ChIP experiments to identify risk variants with allelic enhancer activity mediated through transcription factor binding.
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79
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Swanzey E, O'Connor C, Reinholdt LG. Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics. Trends Genet 2021; 37:251-265. [PMID: 33010949 PMCID: PMC7889615 DOI: 10.1016/j.tig.2020.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/07/2023]
Abstract
Interrogation of disease-relevant cellular and molecular traits exhibited by genetically diverse cell populations enables in vitro systems genetics approaches for uncovering the basic properties of cellular function and identity. Primary cells, stem cells, and organoids derived from genetically diverse mouse strains, such as Collaborative Cross and Diversity Outbred populations, offer the opportunity for parallel in vitro/in vivo screening. These panels provide genetic resolution for variant discovery and functional characterization, as well as disease modeling and in vivo validation capabilities. Here we review mouse cellular systems genetics approaches for characterizing the influence of genetic variation on signaling networks and phenotypic diversity, and we discuss approaches for data integration and cross-species validation.
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Affiliation(s)
| | - Callan O'Connor
- The Jackson Laboratory, Bar Harbor, ME, USA; Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
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80
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Nancy Z, Yan L, Hui S, Paul B, Liye C. From the Genetics of Ankylosing Spondylitis to New Biology and Drug Target Discovery. Front Immunol 2021; 12:624632. [PMID: 33679768 PMCID: PMC7925991 DOI: 10.3389/fimmu.2021.624632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/22/2021] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified 113 single nucleotide polymorphisms (SNPs) affecting the risk of developing ankylosing spondylitis (AS), and an on-going GWAS study will likely identify 100+ new risk loci. The translation of genetic findings to novel disease biology and treatments has been difficult due to the following challenges: (1) difficulties in determining the causal genes regulated by disease-associated SNPs, (2) difficulties in determining the relevant cell-type(s) that causal genes exhibit their function(s), (3) difficulties in determining appropriate cellular contexts to interrogate the functional role of causal genes in disease biology. This review will discuss recent progress and unanswered questions with a focus on these challenges. Additionally, we will review the investigation of biology and the development of drugs related to the IL-23/IL-17 pathway, which has been partially driven by the AS genetics, and discuss what can be learned from these studies for the future functional and translational study of AS-associated genes.
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Affiliation(s)
- Zaarour Nancy
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Li Yan
- Department of Rheumatology, The First Affiliated Hospital of Xiamen University, Medical College of Xiamen University, Xiamen, China
| | - Shi Hui
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Bowness Paul
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Chen Liye
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
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81
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Quintana-Murci L. Dangerous liaisons: human genetic adaptation to infectious agents. C R Biol 2021; 343:297-309. [PMID: 33621457 DOI: 10.5802/crbiol.30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 11/24/2022]
Abstract
The study of the demographic and adaptive history of Homo sapiens has entered its golden age with the advent of genome-wide approaches. The analyses of genome diversity across different human populations have allowed us to better understand the ways in which our species rapidly dispersed around the world, how our ancestors admixed with archaic, now-extinct hominins, and the effects of natural selection on the diversity of the human genome. This work has, in turn, made it possible to increase our understanding of the genetic mechanisms by which humans have adapted to the wide range of environments they have encountered. These studies, combined with functional genomics approaches, have helped to identify genes and biological functions of key importance for host survival against pathogens and involved in the phenotypic variability of our species, including the risk to develop infectious, autoimmune and inflammatory diseases.
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Affiliation(s)
- Lluis Quintana-Murci
- Chaire Génomique Humaine et Évolution, Collège de France, Paris 75005, France.,Unité de Génétique Évolutive Humaine, CNRS UMR 2000, Institut Pasteur, Paris 75015, France
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82
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Umans BD, Battle A, Gilad Y. Where Are the Disease-Associated eQTLs? Trends Genet 2021; 37:109-124. [PMID: 32912663 PMCID: PMC8162831 DOI: 10.1016/j.tig.2020.08.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/07/2020] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Most disease-associated variants, although located in putatively regulatory regions, do not have detectable effects on gene expression. One explanation could be that we have not examined gene expression in the cell types or conditions that are most relevant for disease. Even large-scale efforts to study gene expression across tissues are limited to human samples obtained opportunistically or postmortem, mostly from adults. In this review we evaluate recent findings and suggest an alternative strategy, drawing on the dynamic and highly context-specific nature of gene regulation. We discuss new technologies that can extend the standard regulatory mapping framework to more diverse, disease-relevant cell types and states.
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Affiliation(s)
- Benjamin D Umans
- Department of Medicine, University of Chicago, Chicago, IL, USA.
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, IL, USA; Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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83
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Yang F, Yang Y, Chen Y, Li G, Zhang G, Chen L, Zhang Z, Mai Q, Zeng G. MiR-21 Is Remotely Governed by the Commensal Bacteria and Impairs Anti-TB Immunity by Down-Regulating IFN-γ. Front Microbiol 2021; 11:512581. [PMID: 33552001 PMCID: PMC7859650 DOI: 10.3389/fmicb.2020.512581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 11/30/2020] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB), which is a frequent and important infectious disease caused by Mycobacterium tuberculosis, has resulted in an extremely high burden of morbidity and mortality. The importance of intestinal dysbacteriosis in regulating host immunity has been implicated in TB, and accumulating evidence suggests that microRNAs (miRNAs) might act as a key mediator in maintaining intestinal homeostasis through signaling networks. However, the involvement of miRNA in gut microbiota, TB and the host immune system remains unknown. Here we showed that intestinal dysbacteriosis increases the susceptibility to TB and remotely increased the expression of miR-21 in lung. Systemic antagonism of miR-21 enhanced IFN-γ production and further conferred immune protection against TB. Molecular experiments further indicated that miR-21a-3p could specifically target IFN-γ mRNA. These findings revealed regulatory pathways implicating intestinal dysbacteriosis induced-susceptibility to TB: intestinal dysbiosis→lung miRNA→targeting IFN-γ→impaired anti-TB immunity. This study also suggested that deregulated miRNAs by commensal bacteria could become promising targets as TB therapeutics.
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Affiliation(s)
- Fang Yang
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
| | - Yi Yang
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
| | - Yiwei Chen
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
| | - Guobao Li
- Department of Tuberculosis, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Guoliang Zhang
- National Clinical Research Center for Tuberculosis, Guangdong Key Laboratory for Emerging Infectious Diseases, Shenzhen Third People’s Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Lingming Chen
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
| | - Zhiyi Zhang
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
| | - Qiongdan Mai
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
| | - Gucheng Zeng
- Department of Microbiology, Zhongshan School of Medicine, Key Laboratory for Tropical Diseases Control of the Ministryof Education, Sun Yat-sen University, Guangzhou, China
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84
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Kim MS, Lozano R, Kim JH, Bae DN, Kim ST, Park JH, Choi MS, Kim J, Ok HC, Park SK, Gore MA, Moon JK, Jeong SC. The patterns of deleterious mutations during the domestication of soybean. Nat Commun 2021; 12:97. [PMID: 33397978 PMCID: PMC7782591 DOI: 10.1038/s41467-020-20337-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
Globally, soybean is a major protein and oil crop. Enhancing our understanding of the soybean domestication and improvement process helps boost genomics-assisted breeding efforts. Here we present a genome-wide variation map of 10.6 million single-nucleotide polymorphisms and 1.4 million indels for 781 soybean individuals which includes 418 domesticated (Glycine max), 345 wild (Glycine soja), and 18 natural hybrid (G. max/G. soja) accessions. We describe the enhanced detection of 183 domestication-selective sweeps and the patterns of putative deleterious mutations during domestication and improvement. This predominantly selfing species shows 7.1% reduction of overall deleterious mutations in domesticated soybean relative to wild soybean and a further 1.4% reduction from landrace to improved accessions. The detected domestication-selective sweeps also show reduced levels of deleterious alleles. Importantly, genotype imputation with this resource increases the mapping resolution of genome-wide association studies for seed protein and oil traits in a soybean diversity panel.
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Affiliation(s)
- Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
- Plant Immunity Research Center, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Ji Hong Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Dong Nyuk Bae
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Sang-Tae Kim
- Department of Life Science, The Catholic University of Korea, Bucheon, 14662, Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Jaehyun Kim
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Hyun-Choong Ok
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea.
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, Jeonbuk, 55365, Korea.
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea.
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85
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Mair F, Liechti T. Comprehensive Phenotyping of Human Dendritic Cells and Monocytes. Cytometry A 2020; 99:231-242. [PMID: 33200508 DOI: 10.1002/cyto.a.24269] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/02/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022]
Abstract
Professional antigen-presenting cells (APCs), which include dendritic cells (DCs) and monocytes are essential for inducing and steering adaptive T-cell responses. Recent technological developments in single-cell analysis have significantly advanced our understanding of APC subset heterogeneity. To accurately resolve this functional diversity and to account for tissue-specific adaptation, novel phenotyping markers have been described more recently. While some of these largely overlap with traditionally used markers, more fine-grained phenotyping might be essential during inflammatory settings, where the traditional distinction between monocytes and dendritic cells has become blurred. Within this phenotype report, we provide a concise overview of traditional and recently described markers for the phenotyping of DCs and monocytes in the human system.
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Affiliation(s)
- Florian Mair
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, USA
| | - Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, Maryland, USA
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86
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Host genetics and infectious disease: new tools, insights and translational opportunities. Nat Rev Genet 2020; 22:137-153. [PMID: 33277640 PMCID: PMC7716795 DOI: 10.1038/s41576-020-00297-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Understanding how human genetics influence infectious disease susceptibility offers the opportunity for new insights into pathogenesis, potential drug targets, risk stratification, response to therapy and vaccination. As new infectious diseases continue to emerge, together with growing levels of antimicrobial resistance and an increasing awareness of substantial differences between populations in genetic associations, the need for such work is expanding. In this Review, we illustrate how our understanding of the host–pathogen relationship is advancing through holistic approaches, describing current strategies to investigate the role of host genetic variation in established and emerging infections, including COVID-19, the need for wider application to diverse global populations mirroring the burden of disease, the impact of pathogen and vector genetic diversity and a broad array of immune and inflammation phenotypes that can be mapped as traits in health and disease. Insights from study of inborn errors of immunity and multi-omics profiling together with developments in analytical methods are further advancing our knowledge of this important area. Infectious diseases are an ever-present global threat. In this Review, Kwok, Mentzer and Knight discuss our latest understanding of how human genetics influence susceptibility to disease. Furthermore, they discuss emerging progress in the interplay between host and pathogen genetics, molecular responses to infection and vaccination, and opportunities to bring these aspects together for rapid responses to emerging diseases such as COVID-19.
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87
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Uddin MI, Kilburn TC, Duvall CL, Penn JS. Visualizing HIF-1α mRNA in a Subpopulation of Bone Marrow-Derived Cells to Predict Retinal Neovascularization. ACS Chem Biol 2020; 15:3004-3012. [PMID: 33080135 DOI: 10.1021/acschembio.0c00662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Bone marrow-derived progenitor cells and macrophages are known to migrate into the retina in response to inflammation and neovascularization. These migratory cells might play important regulatory roles in the pathogenesis of neovascularization, a common complication observed in diabetic retinopathy, retinopathy of prematurity, and retinal vein occlusion. Hypoxia-inducible factor 1α (HIF-1α) has been shown to contribute to the pathogenesis of retinal inflammation and neovascularization. However, contributions of monocyte-derived macrophages to neovascularization are largely unknown. We hypothesized that selective visualization of these microglia/macrophages could be a powerful method for predicting the onset of neovascularization and its progression at the molecular level. In this report, we describe the synthesis of a new hybrid nanoparticle to visualize HIF-1α mRNA selectively in microglia/macrophages in a mouse model of neovascularization. HIF-1α expression was confirmed in MRC-1 positive monocytes/macrophages as well as in CD4 positive T-cells and CD19 positive B-cells using single-cell RNA sequencing data analysis. The imaging probes (AS- or NS-shRNA-lipid) were synthesized by conjugating diacyl-lipids to short hairpin RNA with an antisense sequence complementary to HIF-1α mRNA and a fluorophore that is quenched by a black hole quencher. We believe that imaging mRNA selectively in tissue specific microglia/macrophages could be a powerful method for predicting the onset of neovascularization, its progression, and its response to therapy.
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Affiliation(s)
- Md. Imam Uddin
- Department of Ophthalmology and Visual Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Tyler C. Kilburn
- Department of Ophthalmology and Visual Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Craig L. Duvall
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John S. Penn
- Department of Ophthalmology and Visual Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, United States
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, United States
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88
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Brion C, Lutz SM, Albert FW. Simultaneous quantification of mRNA and protein in single cells reveals post-transcriptional effects of genetic variation. eLife 2020; 9:60645. [PMID: 33191917 PMCID: PMC7707838 DOI: 10.7554/elife.60645] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 11/14/2020] [Indexed: 01/27/2023] Open
Abstract
Trans-acting DNA variants may specifically affect mRNA or protein levels of genes located throughout the genome. However, prior work compared trans-acting loci mapped in separate studies, many of which had limited statistical power. Here, we developed a CRISPR-based system for simultaneous quantification of mRNA and protein of a given gene via dual fluorescent reporters in single, live cells of the yeast Saccharomyces cerevisiae. In large populations of recombinant cells from a cross between two genetically divergent strains, we mapped 86 trans-acting loci affecting the expression of ten genes. Less than 20% of these loci had concordant effects on mRNA and protein of the same gene. Most loci influenced protein but not mRNA of a given gene. One locus harbored a premature stop variant in the YAK1 kinase gene that had specific effects on protein or mRNA of dozens of genes. These results demonstrate complex, post-transcriptional genetic effects on gene expression.
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Affiliation(s)
- Christian Brion
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Sheila M Lutz
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
| | - Frank Wolfgang Albert
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, United States
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89
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Huang W, Carbone MA, Lyman RF, Anholt RRH, Mackay TFC. Genotype by environment interaction for gene expression in Drosophila melanogaster. Nat Commun 2020; 11:5451. [PMID: 33116142 PMCID: PMC7595129 DOI: 10.1038/s41467-020-19131-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/22/2020] [Indexed: 01/17/2023] Open
Abstract
The genetics of phenotypic responses to changing environments remains elusive. Using whole-genome quantitative gene expression as a model, here we study how the genetic architecture of regulatory variation in gene expression changed in a population of fully sequenced inbred Drosophila melanogaster strains when flies developed in different environments (25 °C and 18 °C). We find a substantial fraction of the transcriptome exhibited genotype by environment interaction, implicating environmentally plastic genetic architecture of gene expression. Genetic variance in expression increases at 18 °C relative to 25 °C for most genes that have a change in genetic variance. Although the majority of expression quantitative trait loci (eQTLs) for the gene expression traits in the two environments are shared and have similar effects, analysis of the environment-specific eQTLs reveals enrichment of binding sites for two transcription factors. Finally, although genotype by environment interaction in gene expression could potentially disrupt genetic networks, the co-expression networks are highly conserved across environments. Genes with higher network connectivity are under stronger stabilizing selection, suggesting that stabilizing selection on expression plays an important role in promoting network robustness.
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Affiliation(s)
- Wen Huang
- Program in Genetics, Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695-7614, USA.
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
| | - Mary Anna Carbone
- Program in Genetics, Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695-7614, USA
- Center for Integrated Fungal Research and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7244, USA
| | - Richard F Lyman
- Program in Genetics, Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695-7614, USA
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC, 29646, USA
| | - Robert R H Anholt
- Program in Genetics, Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695-7614, USA
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC, 29646, USA
| | - Trudy F C Mackay
- Program in Genetics, Department of Biological Sciences, W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC, 27695-7614, USA.
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC, 29646, USA.
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90
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Schott BH, Antonia AL, Wang L, Pittman KJ, Sixt BS, Barnes AB, Valdivia RH, Ko DC. Modeling of variables in cellular infection reveals CXCL10 levels are regulated by human genetic variation and the Chlamydia-encoded CPAF protease. Sci Rep 2020; 10:18269. [PMID: 33106516 PMCID: PMC7588472 DOI: 10.1038/s41598-020-75129-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
Susceptibility to infectious diseases is determined by a complex interaction between host and pathogen. For infections with the obligate intracellular bacterium Chlamydia trachomatis, variation in immune activation and disease presentation are regulated by both host genetic diversity and pathogen immune evasion. Previously, we discovered a single nucleotide polymorphism (rs2869462) associated with absolute abundance of CXCL10, a pro-inflammatory T-cell chemokine. Here, we report that levels of CXCL10 change during C. trachomatis infection of cultured cells in a manner dependent on both host and pathogen. Linear modeling of cellular traits associated with CXCL10 levels identified a strong, negative correlation with bacterial burden, suggesting that C. trachomatis actively suppresses CXCL10. We identified the pathogen-encoded factor responsible for this suppression as the chlamydial protease- or proteasome-like activity factor, CPAF. Further, we applied our modeling approach to other host cytokines in response to C. trachomatis and found evidence that RANTES, another T-cell chemoattractant, is actively suppressed by Chlamydia. However, this observed suppression of RANTES is not mediated by CPAF. Overall, our results demonstrate that CPAF suppresses CXCL10 to evade the host cytokine response and that modeling of cellular infection parameters can reveal previously unrecognized facets of host-pathogen interactions.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC, 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Barbara S Sixt
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Alyson B Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA.
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC, 27710, USA.
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC, 27710, USA.
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91
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Lundtoft C, Pucholt P, Imgenberg-Kreuz J, Carlsson-Almlöf J, Eloranta ML, Syvänen AC, Nordmark G, Sandling JK, Kockum I, Olsson T, Rönnblom L, Hagberg N. Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling. PLoS Genet 2020; 16:e1009199. [PMID: 33104735 PMCID: PMC7644105 DOI: 10.1371/journal.pgen.1009199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/05/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
Interferons (IFNs) are cytokines that are central to the host defence against viruses and other microorganisms. If not properly regulated, IFNs may contribute to the pathogenesis of inflammatory autoimmune, or infectious diseases. To identify genetic polymorphisms regulating the IFN system we performed an unbiased genome-wide protein-quantitative trait loci (pQTL) mapping of cell-type specific type I and type II IFN receptor levels and their responses in immune cells from 303 healthy individuals. Seven genome-wide significant (p < 5.0E-8) pQTLs were identified. Two independent SNPs that tagged the multiple sclerosis (MS)-protective HLA class I alleles A*02/A*68 and B*44, respectively, were associated with increased levels of IFNAR2 in B and T cells, with the most prominent effect in IgD–CD27+ memory B cells. The increased IFNAR2 levels in B cells were replicated in cells from an independent set of healthy individuals and in MS patients. Despite increased IFNAR2 levels, B and T cells carrying the MS-protective alleles displayed a reduced response to type I IFN stimulation. Expression and methylation-QTL analysis demonstrated increased mRNA expression of the pseudogene HLA-J in B cells carrying the MS-protective class I alleles, possibly driven via methylation-dependent transcriptional regulation. Together these data suggest that the MS-protective effects of HLA class I alleles are unrelated to their antigen-presenting function, and propose a previously unappreciated function of type I IFN signalling in B and T cells in MS immune-pathogenesis. Genetic association studies have been very successful in identifying disease-associated single nucleotide polymorphisms (SNPs), but it has been challenging to define the molecular mechanisms underlying these associations. As interferons (IFNs) have a central role in the immune system, we hypothesized that some of the SNPs associated to immune-mediated diseases would affect the IFN system. By combining genetic data with characterization of interferon receptor levels and their responses on the protein level in immune cells from 303 genotyped healthy individuals, we show that two SNPs tagging the HLA class I alleles A*02/A*68 and B*44 are associated with a decreased response to type I IFN stimulation in B cells and T cells. Notably, both HLA-A*02 and HLA-B*44 confer protection from developing multiple sclerosis (MS), which is a chronic inflammatory neurologic disease. In addition to suggesting a pathogenic role of enhanced type I interferon signalling in B cells and T cells in MS, our data emphasize the fact that genetic associations in the HLA locus can affect functions not directly associated to antigen presentation, which conceptually may be important for other diseases genetically associated to the HLA locus.
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Affiliation(s)
- Christian Lundtoft
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Juliana Imgenberg-Kreuz
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jonas Carlsson-Almlöf
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johanna K. Sandling
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Ingrid Kockum
- Centre for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Centre for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lars Rönnblom
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Niklas Hagberg
- Rheumatology and Science for Life Laboratories, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- * E-mail:
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92
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Hagberg N, Lundtoft C, Rönnblom L. Immunogenetics in systemic lupus erythematosus: Transitioning from genetic associations to cellular effects. Scand J Immunol 2020; 92:e12894. [DOI: 10.1111/sji.12894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Niklas Hagberg
- Rheumatology and Science for Life Laboratories Department of Medical Sciences Uppsala University Uppsala Sweden
| | - Christian Lundtoft
- Rheumatology and Science for Life Laboratories Department of Medical Sciences Uppsala University Uppsala Sweden
| | - Lars Rönnblom
- Rheumatology and Science for Life Laboratories Department of Medical Sciences Uppsala University Uppsala Sweden
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93
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Malik U, Zafar S, Younas N, Zerr I, Javed A. Unveiling the Physical and Functional Niches of FAM26F by Analyzing Its Subcellular Localization and Novel Interacting Partners. ACS OMEGA 2020; 5:22008-22020. [PMID: 32923759 PMCID: PMC7482079 DOI: 10.1021/acsomega.0c01249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The knowledge of a protein's subcellular localization and interacting partners are crucial for elucidating its cellular function and associated regulatory networks. Although FAM26F (family with sequence similarity 26, member F) has been recognized as a vital player in various infections, stimulation studies, cancer, and immune pathogenesis, the precise location and function of FAM26F are not well understood. The current study is the first to focus on functional characterization of FAM26F by analyzing its subcellular localization and identifying its novel interacting partners using advanced proteome approaches. The immunofluorescence and confocal microscopy results revealed FAM26F to be largely localized within the Golgi apparatus of the cell. However, its minor presence in endoplasmic reticulum (ER) pointed toward the probable retrograde transfer of FAM26F from Golgi to ER during adverse conditions. Moreover, co-immunoprecipitation and MS/MS results demonstrated a total of 85 proteins, 44 of which significantly copurified with FAM26F. Interestingly, out of these 44 MS/MS identified proteins, almost 52% were involved in innate immunity, 38.6% in neutrophil degranulation, and remaining 10% were either involved in phosphorylation, degradation, or regulation of apoptosis. Further characterization through Ingenuity Pathway Analysis showed that majority of these proteins was involved in maintaining calcium homeostasis of cell. Consequently, the validation of selected proteins uncovered the key interaction of FAM26F with Thioredoxin, which essentially paved the way for depicting its mechanism of action under stress or disease conditions. It is proposed that activation and inhibition of the cellular immune response is essentially dependent on whether FAM26F or Thioredoxin considerably interact with CD30R.
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Affiliation(s)
- Uzma Malik
- Department
of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences
(ASAB), National University of Sciences
and Technology (NUST), H-12 Campus, 44000 Islamabad, Pakistan
- Department
of Neurology, University Medical Centre Göttingen (UMG), Georg-August-Universität Göttingen, 37075 Göttingen, Germany
| | - Saima Zafar
- Department
of Neurology, University Medical Centre Göttingen (UMG), Georg-August-Universität Göttingen, 37075 Göttingen, Germany
- Department
of Biomedical Engineering & Sciences, School of Mechanical &
Manufacturing Engineering (SMME), National
University of Sciences and Technology (NUST), H-12
Campus, 44000 Islamabad, Pakistan
| | - Neelam Younas
- Department
of Neurology, University Medical Centre Göttingen (UMG), Georg-August-Universität Göttingen, 37075 Göttingen, Germany
| | - Inga Zerr
- Department
of Neurology, University Medical Centre Göttingen (UMG), Georg-August-Universität Göttingen, 37075 Göttingen, Germany
| | - Aneela Javed
- Department
of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences
(ASAB), National University of Sciences
and Technology (NUST), H-12 Campus, 44000 Islamabad, Pakistan
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94
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Zhang Z, Luo K, Zou Z, Qiu M, Tian J, Sieh L, Shi H, Zou Y, Wang G, Morrison J, Zhu AC, Qiao M, Li Z, Stephens M, He X, He C. Genetic analyses support the contribution of mRNA N 6-methyladenosine (m 6A) modification to human disease heritability. Nat Genet 2020; 52:939-949. [PMID: 32601472 PMCID: PMC7483307 DOI: 10.1038/s41588-020-0644-z] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/11/2020] [Indexed: 12/18/2022]
Abstract
N6-methyladenosine (m6A) plays important roles in regulating messenger RNA processing. Despite rapid progress in this field, little is known about the genetic determinants of m6A modification and their role in common diseases. In this study, we mapped the quantitative trait loci (QTLs) of m6A peaks in 60 Yoruba (YRI) lymphoblastoid cell lines. We found that m6A QTLs are largely independent of expression and splicing QTLs and are enriched with binding sites of RNA-binding proteins, RNA structure-changing variants and transcriptional features. Joint analysis of the QTLs of m6A and related molecular traits suggests that the downstream effects of m6A are heterogeneous and context dependent. We identified proteins that mediate m6A effects on translation. Through integration with data from genome-wide association studies, we show that m6A QTLs contribute to the heritability of various immune and blood-related traits at levels comparable to splicing QTLs and roughly half of expression QTLs. By leveraging m6A QTLs in a transcriptome-wide association study framework, we identified putative risk genes of these traits.
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Affiliation(s)
- Zijie Zhang
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Kaixuan Luo
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Zhongyu Zou
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Maguanyun Qiu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiakun Tian
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Laura Sieh
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Hailing Shi
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuxin Zou
- Department of Statistics, The University of Chicago, Chicago, IL, USA
| | - Gao Wang
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Jean Morrison
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Allen C Zhu
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA
| | - Min Qiao
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongshan Li
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Matthew Stephens
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
- Department of Statistics, The University of Chicago, Chicago, IL, USA.
| | - Xin He
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA.
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
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95
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Theusch E, Chen YDI, Rotter JI, Krauss RM, Medina MW. Genetic variants modulate gene expression statin response in human lymphoblastoid cell lines. BMC Genomics 2020; 21:555. [PMID: 32787775 PMCID: PMC7430882 DOI: 10.1186/s12864-020-06966-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 08/03/2020] [Indexed: 01/10/2023] Open
Abstract
Background Statins are widely prescribed to lower plasma low-density lipoprotein cholesterol levels. Though statins reduce cardiovascular disease risk overall, statin efficacy varies, and some people experience adverse side effects while on statin treatment. Statins also have pleiotropic effects not directly related to their cholesterol-lowering properties, but the mechanisms are not well understood. To identify potential genetic modulators of clinical statin response, we looked for genetic variants associated with statin-induced changes in gene expression (differential eQTLs or deQTLs) in lymphoblastoid cell lines (LCLs) derived from participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial. We exposed CAP LCLs to 2 μM simvastatin or control buffer for 24 h and performed polyA-selected, strand-specific RNA-seq. Statin-induced changes in gene expression from 259 European ancestry or 153 African American ancestry LCLs were adjusted for potential confounders prior to association with genotyped and imputed genetic variants within 1 Mb of each gene’s transcription start site. Results From the deQTL meta-analysis of the two ancestral populations, we identified significant cis-deQTLs for 15 genes (TBC1D4, MDGA1, CHI3L2, OAS1, GATM, ASNSD1, GLUL, TDRD12, PPIP5K2, OAS3, SERPINB1, ANKDD1A, DTD1, CYFIP2, and GSDME), eight of which were significant in at least one of the ancestry subsets alone. We also conducted eQTL analyses of the endogenous (control-treated), statin-treated, and average of endogenous and statin-treated LCL gene expression levels. We identified eQTLs for approximately 6000 genes in each of the three (endogenous, statin-treated, and average) eQTL meta-analyses, with smaller numbers identified in the ancestral subsets alone. Conclusions Several of the genes in which we identified deQTLs have functions in human health and disease, such as defense from viruses, glucose regulation, and response to chemotherapy drugs. This suggests that DNA variation may play a role in statin effects on various health outcomes. These findings could prove useful to future studies aiming to assess benefit versus risk of statin treatment using individual genetic profiles.
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Affiliation(s)
- Elizabeth Theusch
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA
| | - Yii-Der I Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- Departments of Pediatrics and Medicine, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ronald M Krauss
- Departments of Pediatrics and Medicine, University of California San Francisco, Oakland, CA, USA
| | - Marisa W Medina
- Department of Pediatrics, University of California San Francisco, Oakland, CA, USA.
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96
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Frangieh M, McHenry A, Phillips R, Ye C, Bernier A, Laffel L, Elyaman W, Bradshaw EM. IL-27: An endogenous constitutive repressor of human monocytes. Clin Immunol 2020; 217:108498. [PMID: 32531345 PMCID: PMC8984538 DOI: 10.1016/j.clim.2020.108498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/21/2020] [Accepted: 06/07/2020] [Indexed: 12/23/2022]
Abstract
Interleukin (IL)-27 is a pleiotropic cytokine that initially was described as being pro-inflammatory and an inducer of T helper (Th)1 cells. In contrast, it has also been described as an anti-inflammatory cytokine in that it suppresses pro-inflammatory Th17 cells and induces anti-inflammatory IL-10 producing T regulatory (Tr)1 cells. While the majority of studies have been focused on the effects of IL-27 on T cells, human antigen-presenting cells express high levels of the IL-27 receptor ex vivo, in addition to being the major producer of IL-27. We report here that human monocytes are repressed by endogenous IL-27, in that the addition of an anti-IL-27 neutralizing antibody increases the production of pro-inflammatory cytokines ex vivo. We observed that neutralizing monocyte-derived IL-27 leads to increased IL-17A production by CD4+ T cells and a down-regulation of the IL-17 modulating ectonucleotidase CD39 on monocytes. The locus that contains the IL27 gene has been linked to susceptibility for type 1 diabetes (T1D). Interestingly, ex vivo monocytes from subjects with T1D produce more IL-27 suggesting this upregulation of IL-27 acts as a negative feedback loop to attempt to counterbalance the pro-inflammatory immune response in the disease state. In summary, we provide evidence that IL-27 is an endogenous regulator of human monocytes and has consequences on CD4+ T cell phenotype, particularly Th17 cells.
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Affiliation(s)
- Michael Frangieh
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Allison McHenry
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Roxanne Phillips
- Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Chun Ye
- Institute for Human Genetics, University of California San Francisco, CA 94143, USA; Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA; Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA; Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Angelina Bernier
- Department of Pediatrics, University of Florida, Gainesville, FL 32611, USA
| | - Lori Laffel
- Joslin Diabetes Center, Harvard Medical School, Boston, MA 02215, USA
| | - Wassim Elyaman
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Elizabeth M Bradshaw
- Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA.
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97
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Huang QQ, Tang HHF, Teo SM, Mok D, Ritchie SC, Nath AP, Brozynska M, Salim A, Bakshi A, Holt BJ, Khor CC, Sly PD, Holt PG, Holt KE, Inouye M. Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. Nat Commun 2020; 11:3761. [PMID: 32724101 PMCID: PMC7387553 DOI: 10.1038/s41467-020-17477-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic immune-mediated diseases of adulthood often originate in early childhood. To investigate genetic associations between neonatal immunity and disease, we map expression quantitative trait loci (eQTLs) in resting myeloid cells and CD4+ T cells from cord blood samples, as well as in response to lipopolysaccharide (LPS) or phytohemagglutinin (PHA) stimulation, respectively. Cis-eQTLs are largely specific to cell type or stimulation, and 31% and 52% of genes with cis-eQTLs have response eQTLs (reQTLs) in myeloid cells and T cells, respectively. We identified cis regulatory factors acting as mediators of trans effects. There is extensive colocalisation between condition-specific neonatal cis-eQTLs and variants associated with immune-mediated diseases, in particular CTSH had widespread colocalisation across diseases. Mendelian randomisation shows causal neonatal gene expression effects on disease risk for BTN3A2, HLA-C and others. Our study elucidates the genetics of gene expression in neonatal immune cells, and aetiological origins of autoimmune and allergic diseases. Some immune-mediated diseases may originate in early childhood. The authors mapped eQTLs and response eQTLs to various stimuli in neonatal myeloid cells and T cells, and revealed their potential role in immune-mediated diseases using colocalisation and Mendelian randomisation.
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Affiliation(s)
- Qin Qin Huang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shu Mei Teo
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Danny Mok
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Scott C Ritchie
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
| | - Artika P Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marta Brozynska
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Agus Salim
- Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, 3010, Australia.,Melbourne School of Population and Global Health, Carlton, VIC, 3053, Australia
| | - Andrew Bakshi
- Monash Biomedicine Discovery Institute, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
| | - Barbara J Holt
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Chiea Chuen Khor
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138672, Singapore.,Singapore Eye Research Institute, Singapore, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Peter D Sly
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, 4101, Australia
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Perth, WA, 6009, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, QLD, 4101, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,The London School of Hygiene and Tropical Medicine, London, WC1E 7TH, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia. .,Cambridge Baker Systems Genomics Initiative, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK. .,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK. .,National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK. .,The Alan Turing Institute, London, UK. .,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK. .,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK.
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98
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Tong O, Fairfax BP. Dissecting genetic determinants of variation in human immune responses. Curr Opin Immunol 2020; 65:74-78. [PMID: 32634755 DOI: 10.1016/j.coi.2020.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 10/23/2022]
Abstract
The immune system is paradigmatic for a complex arrangement of heterogenous cells performing distinct, frequently temporally and anatomically dissociated, functions. Immune dysfunction is a common characteristic across most diseases and human genetic approaches have revealed that many disease risk loci are associated with expression profiles and counts of specific immune subsets. Furthermore, genetic regulators of immune function may only demonstrate activity in specific disease-linked contexts. Here we explore steps taken to dissect the genetic determinants of variation in immune response across cell counts and function, and the insights these have provided into human immunity.
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Affiliation(s)
- Orion Tong
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom
| | - Benjamin P Fairfax
- Department of Oncology, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom.
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99
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Diedisheim M, Carcarino E, Vandiedonck C, Roussel R, Gautier JF, Venteclef N. Regulation of inflammation in diabetes: From genetics to epigenomics evidence. Mol Metab 2020; 41:101041. [PMID: 32603690 PMCID: PMC7394913 DOI: 10.1016/j.molmet.2020.101041] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
Background Diabetes is one of the greatest public health challenges worldwide, and we still lack complementary approaches to significantly enhance the efficacy of preventive and therapeutic approaches. Genetic and environmental factors are the culprits involved in diabetes risk. Evidence from the last decade has highlighted that deregulation in the immune and inflammatory responses increase susceptibility to type 1 and type 2 diabetes. Spatiotemporal patterns of gene expression involved in immune cell polarisation depend on genomic enhancer elements in response to inflammatory and metabolic cues. Several studies have reported that most regulatory genetic variants are located in the non-protein coding regions of the genome and particularly in enhancer regions. The progress of high-throughput technologies has permitted the characterisation of enhancer chromatin properties. These advances support the concept that genetic alteration of enhancers may influence the immune and inflammatory responses in relation to diabetes. Scope of review Results from genome-wide association studies (GWAS) combined with functional and integrative analyses have elucidated the impacts of some diabetes risk-associated variants that are involved in the regulation of the immune system. Additionally, genetic variant mapping to enhancer regions may alter enhancer status, which in turn leads to aberrant expression of inflammatory genes associated with diabetes susceptibility. The focus of this review was to provide an overview of the current indications that inflammatory processes are regulated at the genetic and epigenomic levels in diabetes, along with perspectives on future research avenues that may improve understanding of the disease. Major conclusions In this review, we provide genetic evidence in support of a deregulated immune response as a risk factor in diabetes. We also argue about the importance of enhancer regions in the regulation of immune cell polarisation and how the recent advances using genome-wide methods for enhancer identification have enabled the determination of the impact of enhancer genetic variation on diabetes onset and phenotype. This could eventually lead to better management plans and improved treatment responses in human diabetes.
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Affiliation(s)
- Marc Diedisheim
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, IMMEDIAB Laboratory, F-75006, Paris, France
| | - Elena Carcarino
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, IMMEDIAB Laboratory, F-75006, Paris, France
| | - Claire Vandiedonck
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, IMMEDIAB Laboratory, F-75006, Paris, France
| | - Ronan Roussel
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, IMMEDIAB Laboratory, F-75006, Paris, France; Bichat-Claude Bernard, Hospital, AP-HP, Diabetology Department, Université de Paris, Paris, France
| | - Jean-François Gautier
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, IMMEDIAB Laboratory, F-75006, Paris, France; Lariboisière Hospital, AP-HP, Diabetology Department, Université de Paris, Paris, France
| | - Nicolas Venteclef
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, IMMEDIAB Laboratory, F-75006, Paris, France.
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100
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Gresle MM, Jordan MA, Stankovich J, Spelman T, Johnson LJ, Laverick L, Hamlett A, Smith LD, Jokubaitis VG, Baker J, Haartsen J, Taylor B, Charlesworth J, Bahlo M, Speed TP, Brown MA, Field J, Baxter AG, Butzkueven H. Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells. Life Sci Alliance 2020; 3:3/7/e202000650. [PMID: 32518073 PMCID: PMC7283543 DOI: 10.26508/lsa.202000650] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/20/2022] Open
Abstract
At least 200 single-nucleotide polymorphisms (SNPs) are associated with multiple sclerosis (MS) risk. A key function that could mediate SNP-encoded MS risk is their regulatory effects on gene expression. We performed microarrays using RNA extracted from purified immune cell types from 73 untreated MS cases and 97 healthy controls and then performed Cis expression quantitative trait loci mapping studies using additive linear models. We describe MS risk expression quantitative trait loci associations for 129 distinct genes. By extending these models to include an interaction term between genotype and phenotype, we identify MS risk SNPs with opposing effects on gene expression in cases compared with controls, namely, rs2256814 MYT1 in CD4 cells (q = 0.05) and rs12087340 RF00136 in monocyte cells (q = 0.04). The rs703842 SNP was also associated with a differential effect size on the expression of the METTL21B gene in CD8 cells of MS cases relative to controls (q = 0.03). Our study provides a detailed map of MS risk loci that function by regulating gene expression in cell types relevant to MS.
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Affiliation(s)
- Melissa M Gresle
- Department of Medicine, University of Melbourne, Parkville, Australia.,Melbourne Brain Centre, Royal Melbourne Hospital, University of Melbourne, Parkville, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Margaret A Jordan
- Molecular & Cell Biology, James Cook University, Townsville, Australia
| | - Jim Stankovich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Tim Spelman
- Department of Medicine, University of Melbourne, Parkville, Australia.,Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - Laura J Johnson
- Florey Institutes of Neuroscience and Mental Health, Parkville, Australia
| | - Louise Laverick
- Department of Medicine, University of Melbourne, Parkville, Australia
| | - Alison Hamlett
- Florey Institutes of Neuroscience and Mental Health, Parkville, Australia
| | - Letitia D Smith
- Molecular & Cell Biology, James Cook University, Townsville, Australia
| | - Vilija G Jokubaitis
- Department of Medicine, University of Melbourne, Parkville, Australia.,Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Josephine Baker
- Multiple Sclerosis Clinical & Research Unit, Melbourne Health, Royal Melbourne Hospital, Parkville, Australia
| | - Jodi Haartsen
- Eastern Clinical Research Unit, Eastern Health, Box Hill, Australia
| | - Bruce Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Jac Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Terence P Speed
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Woolloongabba, Australia.,Guy's and St Thomas' NHS Foundation Trust and King's College London NIHR Biomedical Research Centre, London, England
| | - Judith Field
- Florey Institutes of Neuroscience and Mental Health, Parkville, Australia
| | - Alan G Baxter
- Molecular & Cell Biology, James Cook University, Townsville, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
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