1
|
Boye C, Nirmalan S, Ranjbaran A, Luca F. Genotype × environment interactions in gene regulation and complex traits. Nat Genet 2024; 56:1057-1068. [PMID: 38858456 DOI: 10.1038/s41588-024-01776-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Genotype × environment interactions (GxE) have long been recognized as a key mechanism underlying human phenotypic variation. Technological developments over the past 15 years have dramatically expanded our appreciation of the role of GxE in both gene regulation and complex traits. The richness and complexity of these datasets also required parallel efforts to develop robust and sensitive statistical and computational approaches. Although our understanding of the genetic architecture of molecular and complex traits has been maturing, a large proportion of complex trait heritability remains unexplained. Furthermore, there are increasing efforts to characterize the effect of environmental exposure on human health. We therefore review GxE in human gene regulation and complex traits, advocating for a comprehensive approach that jointly considers genetic and environmental factors in human health and disease.
Collapse
Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Ali Ranjbaran
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, US.
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
| |
Collapse
|
2
|
Randolph HE, Aracena KA, Lin YL, Mu Z, Barreiro LB. Shaping immunity: The influence of natural selection on population immune diversity. Immunol Rev 2024; 323:227-240. [PMID: 38577999 DOI: 10.1111/imr.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.
Collapse
Affiliation(s)
- Haley E Randolph
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Zepeng Mu
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| |
Collapse
|
3
|
Boye C, Kalita CA, Findley AS, Alazizi A, Wei J, Wen X, Pique-Regi R, Luca F. Characterization of caffeine response regulatory variants in vascular endothelial cells. eLife 2024; 13:e85235. [PMID: 38334359 PMCID: PMC10901511 DOI: 10.7554/elife.85235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/08/2024] [Indexed: 02/10/2024] Open
Abstract
Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype-environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 6 variants that regulate the gene expression response to caffeine (GxE, false discovery rate [FDR] < 5%). When overlapping our GxE results with expression quantitative trait loci colocalized with coronary artery disease and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.
Collapse
Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Anthony S Findley
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State UniversityDetroitUnited States
| | - Xiaoquan Wen
- Department of Biostatistics, University of MichiganAnn ArborUnited 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
- Department of Biology, University of Rome Tor VergataRomeItaly
| |
Collapse
|
4
|
Wang Z, Liu T, Li W, Yu G, Mi Z, Wang C, Liao X, Huai P, Chu T, Liu D, Sun L, Fu X, Sun Y, Wang H, Wang N, Liu J, Liu H, Zhang F. Genome-wide meta-analysis and fine-mapping prioritize potential causal variants and genes related to leprosy. MedComm (Beijing) 2023; 4:e415. [PMID: 38020709 PMCID: PMC10674079 DOI: 10.1002/mco2.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/05/2023] [Accepted: 09/22/2023] [Indexed: 12/01/2023] Open
Abstract
To date, genome-wide association studies (GWASs) have discovered 35 susceptible loci of leprosy; however, the cumulative effects of these loci can only partially explain the overall risk of leprosy, and the causal variants and genes within these loci remain unknown. Here, we conducted out new GWASs in two independent cohorts of 5007 cases and 4579 controls and then a meta-analysis in these newly generated and multiple previously published (2277 cases and 3159 controls) datasets were performed. Three novel and 15 previously reported risk loci were identified from these datasets, increasing the known leprosy risk loci of explained genetic heritability from 23.0 to 38.5%. A comprehensive fine-mapping analysis was conducted, and 19 causal variants and 14 causal genes were identified. Specifically, manual checking of epigenomic information from the Epimap database revealed that the causal variants were mainly located within the immune-relevant or immune-specific regulatory elements. Furthermore, by using gene-set, tissue, and cell-type enrichment analyses, we highlighted the key roles of immune-related tissues and cells and implicated the PD-1 signaling pathways in the pathogenetic mechanism of leprosy. Collectively, our study identified candidate causal variants and elucidated the potential regulatory and coding mechanisms for genes associated with leprosy.
Collapse
Affiliation(s)
- Zhenzhen Wang
- Department of BiostatisticsSchool of Public HealthCheeloo College of MedicineShandong UniversityJinanShandongChina
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Tingting Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Wenchao Li
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Gongqi Yu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Zihao Mi
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Chuan Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Xiaojie Liao
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Pengcheng Huai
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Tongsheng Chu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Dianchang Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Lele Sun
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Xi'an Fu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Yonghu Sun
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Honglei Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Na Wang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Jianjun Liu
- Department of Human Genetics, Genome Institute of SingaporeSingaporeSingapore
| | - Hong Liu
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| | - Furen Zhang
- Shandong Provincial Key Lab for Dermatovenereology, Shandong Provincial Hospital for Skin Diseases & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University & Shandong Academy of Medical SciencesJinanShandongChina
| |
Collapse
|
5
|
Resztak JA, Wei J, Zilioli S, Sendler E, Alazizi A, Mair-Meijers HE, Wu P, Wen X, 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. Genome Res 2023; 33:839-856. [PMID: 37442575 PMCID: PMC10519413 DOI: 10.1101/gr.276765.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/08/2023] [Indexed: 07/15/2023]
Abstract
Synthetic glucocorticoids, such as dexamethasone, have been used as a 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 used novel statistical approaches to calculate a mean-independent measure of gene expression variability and a measure of transcriptional response pseudotime. Using these approaches, we showed 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 showed widespread genetic regulation of the transcriptional dynamics of the gene expression response.
Collapse
Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan 48201, USA
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Henriette E Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Peijun Wu
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Richard B Slatcher
- Department of Psychology, University of Georgia, Athens, Georgia 30602, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
- Department of Biology, University of Rome "Tor Vergata," 00133 Rome, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA;
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| |
Collapse
|
6
|
Seah C, Huckins LM, Brennand KJ. Stem Cell Models for Context-Specific Modeling in Psychiatric Disorders. Biol Psychiatry 2023; 93:642-650. [PMID: 36658083 DOI: 10.1016/j.biopsych.2022.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 01/21/2023]
Abstract
Genome-wide association studies reveal the complex polygenic architecture underlying psychiatric disorder risk, but there is an unmet need to validate causal variants, resolve their target genes(s), and explore their functional impacts on disorder-related mechanisms. Disorder-associated loci regulate transcription of target genes in a cell type- and context-specific manner, which can be measured through expression quantitative trait loci. In this review, we discuss methods and insights from context-specific modeling of genetically and environmentally regulated expression. Human induced pluripotent stem cell-derived cell type and organoid models have uncovered context-specific psychiatric disorder associations by investigating tissue-, cell type-, sex-, age-, and stressor-specific genetic regulation of expression. Techniques such as massively parallel reporter assays and pooled CRISPR (clustered regularly interspaced short palindromic repeats) screens make it possible to functionally fine-map genome-wide association study loci and validate their target genes at scale. Integration of disorder-associated contexts with these patient-specific human induced pluripotent stem cell models makes it possible to uncover gene by environment interactions that mediate disorder risk, which will ultimately improve our ability to diagnose and treat psychiatric disorders.
Collapse
Affiliation(s)
- Carina Seah
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York; Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.
| |
Collapse
|
7
|
Das M, David D, Horo I, Van Hooij A, Tió-Coma M, Geluk A, Vedithi SC. Mycobacterium leprae and host immune transcriptomic signatures for reactional states in leprosy. Front Microbiol 2023; 14:1113318. [PMID: 37051521 PMCID: PMC10083373 DOI: 10.3389/fmicb.2023.1113318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
BackgroundMycobacterium leprae transcriptomic and human host immune gene expression signatures that demonstrate a plausible association with type I (T1R) and type II reactions (T2R) aid in early diagnosis, prevention of nerve damage and consequent demyelinating neuropathy in leprosy. The aim of the study is to identify M. leprae and host-associated gene-expression signatures that are associated with reactional states in leprosy.MethodsThe differentially expressed genes from the whole transcriptome of M. leprae were determined using genome-wide hybridization arrays with RNA extracted from skin biopsies of 20 T1R, 20 T2R and 20 non reactional controls (NR). Additionally, human immune gene-expressions were profiled using RT2-PCR profiler arrays and real-time qPCRs.ResultsThe RNA quality was optimal in 16 NR, 18 T1R and 19 T2R samples. Whole transcriptome expression array of these samples revealed significant upregulation of the genes that encode integral and intrinsic membrane proteins, hydrolases and oxidoreductases. In T1R lesional skin biopsy specimens, the top 10 significantly upregulated genes are ML2064, ML1271, ML1960, ML1220, ML2498, ML1996, ML2388, ML0429, ML2030 and ML0224 in comparison to NR. In T2R, genes ML2498, ML1526, ML0394, ML1960, ML2388, ML0429, ML0281, ML1847, ML1618 and ML1271 were significantly upregulated. We noted ML2664 was significantly upregulated in T1R and repressed in T2R. Conversely, we have not noted any genes upregulated in T2R and repressed in T1R. In both T1R and T2R, ML2388 was significantly upregulated. This gene encodes a probable membrane protein and epitope prediction using Bepipred-2.0 revealed a distinct B-cell epitope. Overexpression of ML2388 was noted consistently across the reaction samples. From the host immune gene expression profiles, genes for CXCL9, CXCL10, CXCL2, CD40LG, IL17A and CXCL11 were upregulated in T1R when compared to the NR. In T2R, CXCL10, CXCL11, CXCL9, CXCL2 and CD40LG were upregulated when compared to the NR group.ConclusionA gene set signature involving bacterial genes ML2388, ML2664, and host immune genes CXCL10 and IL-17A can be transcriptomic markers for reactional states in leprosy.
Collapse
Affiliation(s)
- Madhusmita Das
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research and Leprosy Centre, Karigiri, Vellore, Tamil Nadu, India
- *Correspondence: Madhusmita Das,
| | - Diana David
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research and Leprosy Centre, Karigiri, Vellore, Tamil Nadu, India
| | - Ilse Horo
- Molecular Biology and Immunology Division, Schieffelin Institute of Health Research and Leprosy Centre, Karigiri, Vellore, Tamil Nadu, India
| | - Anouk Van Hooij
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | | |
Collapse
|
8
|
Resztak JA, Choe J, Nirmalan S, Wei J, Bruinsma J, Houpt R, Alazizi A, Mair-Meijers HE, Wen X, Slatcher RB, Zilioli S, Pique-Regi R, Luca F. Analysis of transcriptional changes in the immune system associated with pubertal development in a longitudinal cohort of children with asthma. Nat Commun 2023; 14:230. [PMID: 36646693 PMCID: PMC9842661 DOI: 10.1038/s41467-022-35742-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/21/2022] [Indexed: 01/18/2023] Open
Abstract
Puberty is an important developmental period marked by hormonal, metabolic and immune changes. Puberty also marks a shift in sex differences in susceptibility to asthma. Yet, little is known about the gene expression changes in immune cells that occur during pubertal development. Here we assess pubertal development and leukocyte gene expression in a longitudinal cohort of 251 children with asthma. We identify substantial gene expression changes associated with age and pubertal development. Gene expression changes between pre- and post-menarcheal females suggest a shift from predominantly innate to adaptive immunity. We show that genetic effects on gene expression change dynamically during pubertal development. Gene expression changes during puberty are correlated with gene expression changes associated with asthma and may explain sex differences in prevalence. Our results show that molecular data used to study the genetics of early onset diseases should consider pubertal development as an important factor that modifies the transcriptome.
Collapse
Affiliation(s)
- Justyna A Resztak
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Jane Choe
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | - Julian Bruinsma
- Department of Psychology, Wayne State University, Detroit, MI, USA
| | - Russell Houpt
- Department of Psychology, Wayne State University, Detroit, MI, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA
| | | | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | - Samuele Zilioli
- Department of Psychology, Wayne State University, Detroit, MI, USA
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, USA.
- Department of Biology, University of Rome Tor Vergata, Rome, Italy.
| |
Collapse
|
9
|
Gilchrist JJ, Auckland K, Parks T, Mentzer AJ, Goldblatt L, Naranbhai V, Band G, Rockett KA, Toure OB, Konate S, Sissoko S, Djimdé AA, Thera MA, Doumbo OK, Sow S, Floyd S, Pönnighaus JM, Warndorff DK, Crampin AC, Fine PEM, Fairfax BP, Hill AVS. Genome-wide association study of leprosy in Malawi and Mali. PLoS Pathog 2022; 18:e1010312. [PMID: 36121873 PMCID: PMC9624411 DOI: 10.1371/journal.ppat.1010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/01/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
Collapse
Affiliation(s)
- James J. Gilchrist
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ousmane B. Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibiri Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Samba Sow
- Center for Vaccine Development, Bamako, Mali
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jörg M. Pönnighaus
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - David K. Warndorff
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Amelia C. Crampin
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Paul E. M. Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Benjamin P. Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| |
Collapse
|
10
|
Ferreira H, Leal-Calvo T, Mendes MA, Avanzi C, Busso P, Benjak A, Sales AM, Ferreira CP, de Berrêdo-Pinho M, Cole ST, Sarno EN, Moraes MO, Pinheiro RO. Gene expression patterns associated with multidrug therapy in multibacillary leprosy. Front Cell Infect Microbiol 2022; 12:917282. [PMID: 35937686 PMCID: PMC9354612 DOI: 10.3389/fcimb.2022.917282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Multidrug therapy (MDT) has been successfully used in the treatment of leprosy. However, although patients are cured after the completion of MDT, leprosy reactions, permanent disability, and occasional relapse/reinfection are frequently observed in patients. The immune system of multibacillary patients (MB) is not able to mount an effective cellular immune response against M. leprae. Consequently, clearance of bacilli from the body is a slow process and after 12 doses of MDT not all MB patients reduce bacillary index (BI). In this context, we recruited MB patients at the uptake and after 12-month of MDT. Patients were stratified according to the level of reduction of the BI after 12 doses MDT. A reduction of at least one log in BI was necessary to be considered a responder patient. We evaluated the pattern of host gene expression in skin samples with RNA sequencing before and after MDT and between samples from patients with or without one log reduction in BI. Our results demonstrated that after 12 doses of MDT there was a reduction in genes associated with lipid metabolism, inflammatory response, and cellular immune response among responders (APOBEC3A, LGALS17A, CXCL13, CXCL9, CALHM6, and IFNG). Also, by comparing MB patients with lower BI reduction versus responder patients, we identified high expression of CDH19, TMPRSS4, PAX3, FA2H, HLA-V, FABP7, and SERPINA11 before MDT. From the most differentially expressed genes, we observed that MDT modulates pathways related to immune response and lipid metabolism in skin cells from MB patients after MDT, with higher expression of genes like CYP11A1, that are associated with cholesterol metabolism in the group with the worst response to treatment. Altogether, the data presented contribute to elucidate gene signatures and identify differentially expressed genes associated with MDT outcomes in MB patients.
Collapse
Affiliation(s)
- Helen Ferreira
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Thyago Leal-Calvo
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Mayara Abud Mendes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Anna Maria Sales
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Cássio Porto Ferreira
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Márcia de Berrêdo-Pinho
- Cellular Microbiology Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Stewart Thomas Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Euzenir Nunes Sarno
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Milton Ozório Moraes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Roberta Olmo Pinheiro
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
- *Correspondence: Roberta Olmo Pinheiro,
| |
Collapse
|
11
|
Yuan YH, Liu J, You YG, Chen XH, Yuan LC, Wen Y, Li HY, Zhang Y. Transcriptomic Analysis of Mycobacterium leprae-Stimulated Response in Peripheral Blood Mononuclear Cells Reveal Potential Biomarkers for Early Diagnosis of Leprosy. Front Cell Infect Microbiol 2022; 11:714396. [PMID: 34993156 PMCID: PMC8724050 DOI: 10.3389/fcimb.2021.714396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify an unique host transcriptional signature in peripheral blood mononuclear cells (PBMCs) in response to Mycobacterium leprae antigens to distinguish between patients with leprosy and non-leprosy controls for early diagnosis of the disease. Sixteen individuals were enrolled in the discovery cohort [eight patients with leprosy, comprising four multibacillary (MB) and four paucibacillary (PB); and eight non-leprosy controls, comprising four healthy house contacts (HHCs) and four endemic controls (ECs)]. The differences in the transcriptome response of PBMCs to M. leprae sonicate antigen were evaluated between leprosy patients and non-leprosy controls, and 12 differentially expressed genes (CCL2/MCP-1, IL-8, JAKM, ATP, ND1, SERP, FLJ10489, LINC00659, LOC34487, LOC101928143, MIR22, and NCF1C) were identified. The accuracy of the 12 differentially expressed genes was further validated for the diagnosis of leprosy using real-time quantitative PCR in 82 individuals (13 MB, 10 PB, 37 HHCs, and 22 ECs) in the validation cohort. We found that a 5 gene signature set IL-8, CCL2/MCP-1, SERP, LINC00659 and FLJ10489 had a suitable performance in discriminating leprosy from ECs. In addition, elevated expression of IL-8, CCL2/MCP-1, SERP and LINC00659 was associated with MB diagnosis compared with ECs, whereas increased expression of IL-8, CCL2/MCP-1, SERP and FLJ10489 was found to be useful biomarkers for PB diagnosis from ECs. Moreover, we found decreased expression of NCF1C among leprosy patients could distinguish leprosy from HHCs, whereas higher expression of CCL2 among MB than PB could distinguish different leprosy patients. In conclusion, among the 12 candidate host genes identified, a three gene signature IL-8, CCL2/MCP-1, and SERP showed the best performance in distinguishing leprosy patients from healthy controls. These findings may have implications for developing a rapid blood-based test for early diagnosis of leprosy.
Collapse
Affiliation(s)
- You-Hua Yuan
- Department of Clinical Microbiology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou, China
| | - Jian Liu
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Yuan-Gang You
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Xiao-Hua Chen
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Lian-Chao Yuan
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Yan Wen
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Huan Ying Li
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
12
|
Alecrin ESD, Oliveira ALGD, Guimarães NS, Lyon S, Martins MAP, Rocha MODC. Factors associated with the development of leprosy in Brazilian contacts: a systematic review. Rev Inst Med Trop Sao Paulo 2022; 64:e55. [PMID: 36197417 PMCID: PMC9528391 DOI: 10.1590/s1678-9946202264055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/13/2022] [Indexed: 12/01/2022] Open
Abstract
People who interact with leprosy patients in their environment, neighborhood, family, or social relationships are at risk to develop the disease. This systematic review investigated the risk and protective factors associated with the development of leprosy in Brazilian contacts. The studies were found in Cochrane Library, PubMed (MEDLINE), Embase, Virtual Health Library, grey literature and hand search until July 2021. The study selection, data extraction and quality assessment were independently performed by two investigators. The quality assessment was performed using the Newcastle-Ottawa Scale (NOS). This review was registered in PROSPERO (CRD42020160680). Seventeen articles fulfilled the inclusion criteria (n=544). The immunological and molecular factors, such as Anti-phenolic Glycolipid Antibodies (Anti-PGL-1) seropositivity, negative Mitsuda test, absence of Bacillus Calmette-Guérin (BCG) scar, positive Polymerase Chain Reaction (PCR) in blood; age and race; conviviality, education, contact time and type of contact, as well as elements related to the index case (bacilloscopic index; genetic conditions, family relationships), and some combined factors were shown to be relevant risk factors associated with the development of the disease in Brazilian leprosy contacts. The protective factors reported were the presence of one or more BCG scars, positive Mitsuda test, and education level. All selected studies were considered of high quality according to NOS. The knowledge of disease-related risk and protective factors provides the scientific basis for decision-making in the management of the disease in leprosy contacts.
Collapse
Affiliation(s)
- Edilamar Silva de Alecrin
- Universidade Federal de Minas Gerais, Brazil; Hospital Eduardo de Menezes, Ambulatório de Dermatologia, Brazil
| | | | | | - Sandra Lyon
- Universidade Federal de Minas Gerais, Brazil; Faculdade de Saúde e Ecologia Humana, Brazil
| | | | | |
Collapse
|
13
|
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.
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Leal-Calvo T, Martins BL, Bertoluci DF, Rosa PS, de Camargo RM, Germano GV, Brito de Souza VN, Pereira Latini AC, Moraes MO. Large-Scale Gene Expression Signatures Reveal a Microbicidal Pattern of Activation in Mycobacterium leprae-Infected Monocyte-Derived Macrophages With Low Multiplicity of Infection. Front Immunol 2021; 12:647832. [PMID: 33936067 PMCID: PMC8085500 DOI: 10.3389/fimmu.2021.647832] [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: 12/30/2020] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
Leprosy is a disease with a clinical spectrum of presentations that is also manifested in diverse histological features. At one pole, lepromatous lesions (L-pole) have phagocytic foamy macrophages heavily parasitized with freely multiplying intracellular Mycobacterium leprae. At the other pole, the presence of epithelioid giant cells and granulomatous formation in tuberculoid lesions (T-pole) lead to the control of M. leprae replication and the containment of its spread. The mechanism that triggers this polarization is unknown, but macrophages are central in this process. Over the past few years, leprosy has been studied using large scale techniques to shed light on the basic pathways that, upon infection, rewire the host cellular metabolism and gene expression. M. leprae is particularly peculiar as it invades Schwann cells in the nerves, reprogramming their gene expression leading to a stem-like cell phenotype. This modulatory behavior exerted by M. leprae is also observed in skin macrophages. Here, we used live M. leprae to infect (10:1 multiplicity of infection) monocyte-derived macrophages (MDMs) for 48 h and analyzed the whole gene expression profile using microarrays. In this model, we observe an intense upregulation of genes consistent with a cellular immune response, with enriched pathways including peptide and protein secretion, leukocyte activation, inflammation, and cellular divalent inorganic cation homeostasis. Among the most differentially expressed genes (DEGs) are CCL5/RANTES and CYP27B1, and several members of the metallothionein and metalloproteinase families. This is consistent with a proinflammatory state that would resemble macrophage rewiring toward granulomatous formation observed at the T-pole. Furthermore, a comparison with a dataset retrieved from the Gene Expression Omnibus of M. leprae-infected Schwann cells (MOI 100:1) showed that the patterns among the DEGs are highly distinct, as the Schwann cells under these conditions had a scavenging and phagocytic gene profile similar to M2-like macrophages, with enriched pathways rearrangements in the cytoskeleton, lipid and cholesterol metabolism and upregulated genes including MVK, MSMO1, and LACC1/FAMIN. In summary, macrophages may have a central role in defining the paradigmatic cellular (T-pole) vs. humoral (L-pole) responses and it is likely that the multiplicity of infection and genetic polymorphisms in key genes are gearing this polarization.
Collapse
Affiliation(s)
- Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Bruna Leticia Martins
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Daniele Ferreira Bertoluci
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | | | - Rodrigo Mendes de Camargo
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Giovanna Vale Germano
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Vania Nieto Brito de Souza
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Ana Carla Pereira Latini
- Divisão de Pesquisa e Ensino, Instituto Lauro de Souza Lima, Bauru, Brazil.,Departamento de Doenças Tropicais, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista, Botucatu, Brazil
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| |
Collapse
|
17
|
Zhang DF, Li HL, Zheng Q, Bi R, Xu M, Wang D, Zhu GP, Li YY, Yao YG. Mapping leprosy-associated coding variants of interleukin genes by targeted sequencing. Clin Genet 2021; 99:802-811. [PMID: 33646620 DOI: 10.1111/cge.13945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/25/2021] [Accepted: 02/16/2021] [Indexed: 12/30/2022]
Abstract
Previous genotyping-based assays have identified non-coding variants of several interleukins (ILs) being associated with genetic susceptibility to leprosy. However, understanding of the involvement of coding variants within all IL family genes in leprosy was still limited. To obtain the full mutation spectrum of all ILs in leprosy, we performed a targeted deep sequencing of coding regions of 58 ILs genes in 798 leprosy patients (age 56.2 ± 14.4; female 31.5%) and 990 healthy controls (age 38.1 ± 14.0; female 44.3%) from Yunnan, Southwest China. mRNA expression alterations of ILs in leprosy skin lesions or in response to M. leprae treatment were estimated by using publicly available expression datasets. Two coding variants in IL27 (rs17855750, p.S59A, p = 4.02 × 10-8 , odds ratio [OR] = 1.748) and IL1RN (rs45507693, p.A106T, p = 1.45 × 10-5 , OR = 3.629) were significantly associated with leprosy risk. mRNA levels of IL27 and IL1RN were upregulated in whole blood cells after M. leprae stimulation. These data showed that IL27 and IL1RN are leprosy risk genes. Further functional study is required for characterizing the exact role of ILs in leprosy.
Collapse
Affiliation(s)
- Deng-Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Hui-Long Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Quanzhen Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Dong Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guo-Ping Zhu
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yu-Ye Li
- Department of Dermatology, the First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| |
Collapse
|
18
|
Ward MC, Banovich NE, Sarkar A, Stephens M, Gilad Y. Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes. eLife 2021; 10:57345. [PMID: 33554857 PMCID: PMC7906610 DOI: 10.7554/elife.57345] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
One life-threatening outcome of cardiovascular disease is myocardial infarction, where cardiomyocytes are deprived of oxygen. To study inter-individual differences in response to hypoxia, we established an in vitro model of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We measured gene expression levels, chromatin accessibility, and methylation levels in four culturing conditions that correspond to normoxia, hypoxia, and short- or long-term re-oxygenation. We characterized thousands of gene regulatory changes as the cells transition between conditions. Using available genotypes, we identified 1,573 genes with a cis expression quantitative locus (eQTL) in at least one condition, as well as 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of genes with dynamic eQTLs is associated with complex traits and disease. Our data demonstrate how dynamic genetic effects on gene expression, which are likely relevant for disease, can be uncovered under stress.
Collapse
Affiliation(s)
- Michelle C Ward
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, United States
| | - Nicholas E Banovich
- Department of Human Genetics, University of Chicago, Chicago, United States.,Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, United States
| | - Abhishek Sarkar
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Matthew Stephens
- Department of Human Genetics, University of Chicago, Chicago, United States.,Department of Statistics, University of Chicago, Chicago, United States
| | - Yoav Gilad
- Department of Medicine, University of Chicago, Chicago, United States.,Department of Human Genetics, University of Chicago, Chicago, United States
| |
Collapse
|
19
|
Polymorphisms in mitochondrial ribosomal protein S5 (MRPS5) are associated with leprosy risk in Chinese. PLoS Negl Trop Dis 2020; 14:e0008883. [PMID: 33362202 PMCID: PMC7757804 DOI: 10.1371/journal.pntd.0008883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/13/2020] [Indexed: 01/15/2023] Open
Abstract
Leprosy is an infectious disease caused by Mycobacterium leprae (M. leprae), with about 210,000 new cases per year worldwide. Although numerous risk loci have been uncovered by genome-wide association studies, the effects of common genetic variants are relatively modest. To identify possible new genetic locus involved in susceptibility to leprosy, whole exome sequencing was performed for 28 subjects including 14 patients and 12 unaffected members from 8 leprosy-affected families as well as another case and an unrelated control, and then the follow-up SNP genotyping of the candidate variants was studied in case-control sample sets. A rare missense variant in mitochondrial ribosomal protein S5 (MRPS5), rs200730619 (c. 95108402T>C [p. Tyr137Cys]) was identified and validated in 369 cases and 270 controls of Chinese descent (Padjusted = 0.006, odds ratio [OR] = 2.74) as a contributing factor to leprosy risk. Moreover, the mRNA level of MRPS5 was downregulated in M. leprae sonicate-stimulated peripheral blood mononuclear cells. Our results indicated that MRPS5 may be involved in leprosy pathogenesis. Further studies are needed to determine if defective MRPS5 could lead to impairment of energy metabolism of host immune cells, which could further cause defect in clearing M. leprae and increase susceptibility to infection.
Collapse
|
20
|
Foulon M, Robbe-Saule M, Manry J, Esnault L, Boucaud Y, Alcaïs A, Malloci M, Fanton d’Andon M, Beauvais T, Labarriere N, Jeannin P, Abel L, Saint-André JP, Croué A, Delneste Y, Boneca IG, Marsollier L, Marion E. Mycolactone toxin induces an inflammatory response by targeting the IL-1β pathway: Mechanistic insight into Buruli ulcer pathophysiology. PLoS Pathog 2020; 16:e1009107. [PMID: 33338061 PMCID: PMC7748131 DOI: 10.1371/journal.ppat.1009107] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Mycolactone, a lipid-like toxin, is the major virulence factor of Mycobacterium ulcerans, the etiological agent of Buruli ulcer. Its involvement in lesion development has been widely described in early stages of the disease, through its cytotoxic and immunosuppressive activities, but less is known about later stages. Here, we revisit the role of mycolactone in disease outcome and provide the first demonstration of the pro-inflammatory potential of this toxin. We found that the mycolactone-containing mycobacterial extracellular vesicles produced by M. ulcerans induced the production of IL-1β, a potent pro-inflammatory cytokine, in a TLR2-dependent manner, targeting NLRP3/1 inflammasomes. We show our data to be relevant in a physiological context. The in vivo injection of these mycolactone-containing vesicles induced a strong local inflammatory response and tissue damage, which were prevented by corticosteroids. Finally, several soluble pro-inflammatory factors, including IL-1β, were detected in infected tissues from mice and Buruli ulcer patients. Our results revisit Buruli ulcer pathophysiology by providing new insight, thus paving the way for the development of new therapeutic strategies taking the pro-inflammatory potential of mycolactone into account. Buruli ulcer is a neglected tropical disease occurring mainly in poor rural areas of West and Central Africa. This cutaneous disease is caused by Mycobacterium ulcerans, a bacterium belonging to the same family as M. tuberculosis and M. leprae. The skin lesions are caused by a cytotoxic toxin named mycolactone, also known to act as an immunosuppressor and an anti-inflammatory molecule. However, Buruli ulcer lesions are characterized by a chronic cutaneous inflammation with a recruitment of cellular immune cells trying to counteract M. ulcerans. Our work allows for a reconcilitation of previous observations. We found by in vitro experiment on macrophages that the mycolactone-containing mycobacterial extracellular vesicles produced by M. ulcerans induced the production of IL-1β, a potent pro-inflammatory molecule, while other pro-inflammatory soluble factors are inhibited. We also detected IL-1β protein in a mouse model of M. ulcerans infection as well as in biopsies of Buruli ulcer patients. The pro-inflammatory potential of mycolacone has to be taken into account to understand the full pathophysiology of Buruli ulcer.
Collapse
Affiliation(s)
- M. Foulon
- Université d’Angers, INSERM, CRCINA, Angers, France
| | | | - J. Manry
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Paris, France
- Université de Paris, Imagine Institute, France
| | - L. Esnault
- Université d’Angers, INSERM, CRCINA, Angers, France
| | - Y. Boucaud
- Université d’Angers, INSERM, CRCINA, Angers, France
| | - A. Alcaïs
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Paris, France
- Université de Paris, Imagine Institute, France
| | - M. Malloci
- Plateforme MicroPiCell, SFR santé François Bonamy, Nantes, France
| | - M. Fanton d’Andon
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France; CNRS, INSERM, Équipe Avenir, Paris, France
| | - T. Beauvais
- Université de Nantes, INSERM, CRCINA, Nantes
| | | | - P. Jeannin
- Université d’Angers, INSERM, CRCINA, Angers, France
- Laboratoire d’Immunologie et Allergologie, CHU Angers, Angers, France
| | - L. Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Paris, France
- Université de Paris, Imagine Institute, France
| | - J. P. Saint-André
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France
| | - A. Croué
- Département de Pathologie Cellulaire et Tissulaire, CHU Angers, Angers, France
| | - Y. Delneste
- Université d’Angers, INSERM, CRCINA, Angers, France
- Laboratoire d’Immunologie et Allergologie, CHU Angers, Angers, France
| | - I. G. Boneca
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France; CNRS, INSERM, Équipe Avenir, Paris, France
| | | | - E. Marion
- Université d’Angers, INSERM, CRCINA, Angers, France
- * E-mail:
| |
Collapse
|
21
|
Reanalysis and integration of public microarray datasets reveals novel host genes modulated in leprosy. Mol Genet Genomics 2020; 295:1355-1368. [PMID: 32661593 DOI: 10.1007/s00438-020-01705-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/01/2020] [Indexed: 01/24/2023]
Abstract
Due to multiple hypothesis testing with often limited sample size, microarrays and other-omics technologies can sometimes produce irreproducible findings. Complementary to better experimental design, reanalysis and integration of gene expression datasets may help overcome reproducibility issues by identifying consistent differentially expressed genes from independent studies. In this work, after a systematic search, nine microarray datasets evaluating host gene expression in leprosy were reanalyzed and the information was integrated to strengthen evidence of differential expression for several genes. Our results are relevant in prioritizing genes and pathways for further investigation, whether in functional studies or in biomarker discovery. Reanalysis of individual datasets revealed several differentially expressed genes (DEGs) in accordance with original reports. Then, five integration methods (P value and effect size based) were tested. In the end, random-effects model and ratio association were selected as the main methods to pinpoint DEGs. Overall, classic pathways were found corroborating previous findings and validating this approach. Also, we identified some novel DEG involved especially with skin development processes (AQP3, AKR1C3, CYP27B1, LTB, VDR) and keratinocyte biology (CSTA, DSG1, KRT14, KRT5, PKP1, IVL), both still poorly understood in leprosy context. In addition, here we provide aggregated evidence towards some gene candidates that should be prioritized in further leprosy research, as they are likely important in immunopathogenesis. Altogether, these data are useful in better understanding host responses to the disease and, at the same time, provide a list of potential host biomarkers that could be useful in complementing leprosy diagnosis based on transcriptional levels.
Collapse
|
22
|
Sarfraz I, Asif M, Hijazi K. MiCA: An extended tool for microarray gene expression analysis. Comput Biol Med 2019; 116:103561. [PMID: 31785415 DOI: 10.1016/j.compbiomed.2019.103561] [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: 07/27/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
Gene expression microarrays capture a complete image of all the transcriptional activity in a biological sample. Microarrays produce a large amount of data, which becomes a challenge when it comes to exploring and interpreting using modern computational and statistical tools. We propose the Microarray Analysis (MiCA) tool that outperforms other similar tools both in terms of ease of use and statistical features requiring minimal input to conduct an analysis. MiCA is an integrated, interactive, and streamlined desktop software for the analysis of microarray gene expression data. MiCA consists of a complete microarray analysis pipeline including but not limited to fetching data directly from GEO, normalization, interactive quality control, batch-effect correction, regression analysis, surrogate variable analysis and functional annotation methods such as GSVA using known existing R packages. We compare the features offered by MiCA and other similar tools while performing differential expression analysis using previously published datasets. MiCA offers additional statistical and visualization methods to conduct a microarray data analysis compared to other available microarray analysis tools. MiCA minimizes the need for technical knowledge by providing a very intuitive and versatile interface that integrates all necessary tasks and features required for basic microarray data analysis. We analyzed multiple published datasets and showed that the features offered by MiCA not only simplify the analysis pipeline but also provide additional interpretation to the data.
Collapse
Affiliation(s)
- Irzam Sarfraz
- Department of Computer Science, National Textile University, Faisalabad, Pakistan.
| | - Muhammad Asif
- Department of Computer Science, National Textile University, Faisalabad, Pakistan.
| | - Kahkeshan Hijazi
- Department of Biology, SBASSE, Lahore University of Management Sciences, Lahore, Pakistan; Section of Computational Biomedicine (CBM), Boston University Medical Center, Boston, MA, United States.
| |
Collapse
|
23
|
Abstract
Leprosy is a chronic infectious disease of the skin and peripheral nerves that presents a strong link with the host genetic background. Different approaches in genetic studies have been applied to leprosy and today leprosy is among the infectious diseases with the greatest number of genetic risk variants identified. Several leprosy genes have been implicated in host immune response to pathogens and point to specific pathways that are relevant for host defense to infection. In addition, host genetic factors are also involved in the heterogeneity of leprosy clinical manifestations and in excessive inflammatory responses that occur in some leprosy patients. Finally, genetic studies in leprosy have provided strong evidence of pleiotropic effects between leprosy and other complex diseases, such as immune-mediated or neurodegenerative diseases. These findings not only impact on the field of leprosy and infectious diseases but also make leprosy a good model for the study of complex immune-mediated diseases. Here, we summarize recent genetic findings in leprosy susceptibility and discuss the overlap of the genetic control in leprosy with Parkinson's disease and inflammatory bowel disease. Moreover, some limitations, challenges, and potential new avenues for future genetics studies of leprosy are also discussed in this review.
Collapse
|
24
|
Dallmann-Sauer M, Correa-Macedo W, Schurr E. Human genetics of mycobacterial disease. Mamm Genome 2018; 29:523-538. [PMID: 30116885 PMCID: PMC6132723 DOI: 10.1007/s00335-018-9765-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022]
Abstract
Mycobacterial diseases are caused by members of the genus Mycobacterium, acid-fast bacteria characterized by the presence of mycolic acids within their cell walls. Claiming almost 2 million lives every year, tuberculosis (TB) is the most common mycobacterial disease and is caused by infection with M. tuberculosis and, in rare cases, by M. bovis or M. africanum. The second and third most common mycobacterial diseases are leprosy and buruli ulcer (BU), respectively. Both diseases affect the skin and can lead to permanent sequelae and deformities. Leprosy is caused by the uncultivable M. leprae while the etiological agent of BU is the environmental bacterium M. ulcerans. After exposure to these mycobacterial species, a majority of individuals will not progress to clinical disease and, among those who do, inter-individual variability in disease manifestation and outcome can be observed. Susceptibility to mycobacterial diseases carries a human genetic component and intense efforts have been applied over the past decades to decipher the exact nature of the genetic factors controlling disease susceptibility. While for BU this search was mostly conducted on the basis of candidate genes association studies, genome-wide approaches have been widely applied for TB and leprosy. In this review, we summarize some of the findings achieved by genome-wide linkage, association and transcriptome analyses in TB disease and leprosy and the recent genetic findings for BU susceptibility.
Collapse
Affiliation(s)
- Monica Dallmann-Sauer
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Wilian Correa-Macedo
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada.,The McGill International TB Centre, McGill University, Montreal, QC, Canada.,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Erwin Schurr
- Program in Infectious Diseases and Immunity in Global Health, Research Institute, McGill University Health Centre, Montreal, QC, Canada. .,The McGill International TB Centre, McGill University, Montreal, QC, Canada. .,Departments of Human Genetics and Medicine, Faculty of Medicine, McGill University, Montreal, QC, Canada. .,Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada.
| |
Collapse
|
25
|
Papp AC, Azad AK, Pietrzak M, Williams A, Handelman SK, Igo RP, Stein CM, Hartmann K, Schlesinger LS, Sadee W. AmpliSeq transcriptome analysis of human alveolar and monocyte-derived macrophages over time in response to Mycobacterium tuberculosis infection. PLoS One 2018; 13:e0198221. [PMID: 29847580 PMCID: PMC5976201 DOI: 10.1371/journal.pone.0198221] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/15/2018] [Indexed: 12/19/2022] Open
Abstract
Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. AmpliSeqTM yields highly precise and reproducible gene expression profiles (R2 >0.99). Taking advantage of AmpliSeq's reproducibility, we establish well-defined quantitative RNA expression patterns of HAM versus MDM, including significant M.tb-inducible genes, in networks and pathways that differ in part between MDM and HAM. A similar number of expressed genes are detected at all time-points between uninfected MDM and HAM, in common pathways including inflammatory and immune functions, but canonical pathway differences also exist. In particular, at 2 h, multiple genes relevant to the immune response are preferentially expressed in either uninfected HAM or MDM, while the HAM RNA profiles approximate MDM profiles over time in culture, highlighting the unique RNA expression profile of freshly obtained HAM. MDM demonstrate a greater transcriptional response than HAM upon M.tb infection, with 2 to >10 times more genes up- or down-regulated. The results identify key genes involved in cellular responses to M.tb in two different human macrophage types. Follow-up bioinformatics analysis indicates that approximately 30% of response genes have expression quantitative trait loci (eQTLs in GTEx), common DNA variants that can influence host gene expression susceptibility or resistance to M.tb, illustrated with the TREM1 gene cluster and IL-10.
Collapse
Affiliation(s)
- Audrey C. Papp
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Abul K. Azad
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Maciej Pietrzak
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Williams
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Samuel K. Handelman
- Division of Gastroenterology, Department of Internal Medicine, School of Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Robert P. Igo
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Catherine M. Stein
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
- Center for Proteomics & Bioinformatics, Tuberculosis Research Unit, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Katherine Hartmann
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- European Organization for the Research and Treatment of Cancer, Brussels, Belgium
| | - Larry S. Schlesinger
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- * E-mail: (LSS); (WS)
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (LSS); (WS)
| |
Collapse
|
26
|
Wang D, Fan Y, Malhi M, Bi R, Wu Y, Xu M, Yu XF, Long H, Li YY, Zhang DF, Yao YG. Missense Variants in HIF1A and LACC1 Contribute to Leprosy Risk in Han Chinese. Am J Hum Genet 2018; 102:794-805. [PMID: 29706348 DOI: 10.1016/j.ajhg.2018.03.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/01/2018] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWASs) and genome-wide linkage studies (GWLSs) have identified numerous risk genes affecting the susceptibility to leprosy. However, most of the reported GWAS hits are noncoding variants and account for only part of the estimated heritability for this disease. In order to identify additional risk genes and map the potentially functional variants within the GWAS loci, we performed a three-stage study combining whole-exome sequencing (WES; discovery stage), targeted next-generation sequencing (NGS; screening stage), and refined validation of risk missense variants in 1,433 individuals with leprosy and 1,625 healthy control individuals from Yunnan Province, Southwest China. We identified and validated a rare damaging variant, rs142179458 (c.1045G>A [p.Asp349Asn]) in HIF1A, as contributing to leprosy risk (p = 4.95 × 10-9, odds ratio [OR] = 2.266). We were able to show that affected individuals harboring the risk allele presented with multibacillary leprosy at an earlier age (p = 0.025). We also confirmed the association between missense variant rs3764147 (c.760A>G [p.Ile254Val]) in the GWAS hit LACC1 (formerly C13orf31) and leprosy (p = 6.11 × 10-18, OR = 1.605). By using the population attributable fraction, we have shown that HIF1A and LACC1 are the major genes with missense variants contributing to leprosy risk in our study groups. Consistently, mRNA expression levels of both HIF1A and LACC1 were upregulated in the skin lesions of individuals with leprosy and in Mycobacterium leprae-stimulated cells, indicating an active role of HIF1A and LACC1 in leprosy pathogenesis.
Collapse
|