1
|
Wu X, Sun L, Huang L, Huang C, Sun K, Li H. Proteomic alterations associated with the formation of monocyte extracellular trap induced by Candida albicans hyphae. Future Microbiol 2024; 19:307-316. [PMID: 38358357 DOI: 10.2217/fmb-2023-0029] [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: 02/12/2023] [Accepted: 08/03/2023] [Indexed: 02/16/2024] Open
Abstract
Background: The interaction between the host and Candida albicans is dynamic and intricate. We performed proteomic analysis to explore monocyte-C. albicans hyphae interaction. Materials & methods: Primary human monocytes were stimulated by heat-killed C. albicans hyphae and their proteins were profiled by tandem liquid chromatography with mass spectrometry (LC-MS/MS). Results: Based on the protein database of different species for analysis, we found that stimulation of monocytes by hyphae was accompanied by upregulation of histones and activation of extracellular traps (ETs) formation pathway. Meanwhile, monocyte ETs (MoETs) were evoked by synthesis or alteration of C. albicans cell wall proteins expression during the morphological switch to hyphal. Conclusion: MoETs formation is linked to cell wall proteins of C. albicans hyphae.
Collapse
Affiliation(s)
- Xian Wu
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Liying Sun
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Lei Huang
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Chenwei Huang
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Kuixia Sun
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Haixia Li
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| |
Collapse
|
2
|
Vochteloo M, Deelen P, Vink B, Tsai EA, Runz H, Andreu-Sánchez S, Fu J, Zhernakova A, Westra HJ, Franke L. PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs. Genome Biol 2024; 25:29. [PMID: 38254182 PMCID: PMC10802033 DOI: 10.1186/s13059-023-03151-0] [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: 12/22/2022] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICALO, a method for hidden variable inference of eQTL contexts. PICALO identifies and disentangles technical from biological context in heterogeneous blood and brain bulk eQTL datasets. These contexts are biologically informative and reproducible, outperforming cell counts or expression-based principal components. Furthermore, we show that RNA quality and cell type proportions interact with thousands of eQTLs. Knowledge of hidden eQTL contexts may aid in the inference of functional mechanisms underlying disease variants.
Collapse
Affiliation(s)
- Martijn Vochteloo
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Patrick Deelen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Britt Vink
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Institute for Life Science & Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Ellen A Tsai
- Translational Sciences, Research and Development, Biogen, Cambridge, MA, USA
| | - Heiko Runz
- Translational Sciences, Research and Development, Biogen, Cambridge, MA, USA
| | - Sergio Andreu-Sánchez
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|
3
|
Kang JB, Raveane A, Nathan A, Soranzo N, Raychaudhuri S. Methods and Insights from Single-Cell Expression Quantitative Trait Loci. Annu Rev Genomics Hum Genet 2023; 24:277-303. [PMID: 37196361 PMCID: PMC10784788 DOI: 10.1146/annurev-genom-101422-100437] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent advancements in single-cell technologies have enabled expression quantitative trait locus (eQTL) analysis across many individuals at single-cell resolution. Compared with bulk RNA sequencing, which averages gene expression across cell types and cell states, single-cell assays capture the transcriptional states of individual cells, including fine-grained, transient, and difficult-to-isolate populations at unprecedented scale and resolution. Single-cell eQTL (sc-eQTL) mapping can identify context-dependent eQTLs that vary with cell states, including some that colocalize with disease variants identified in genome-wide association studies. By uncovering the precise contexts in which these eQTLs act, single-cell approaches can unveil previously hidden regulatory effects and pinpoint important cell states underlying molecular mechanisms of disease. Here, we present an overview of recently deployed experimental designs in sc-eQTL studies. In the process, we consider the influence of study design choices such as cohort, cell states, and ex vivo perturbations. We then discuss current methodologies, modeling approaches, and technical challenges as well as future opportunities and applications.
Collapse
Affiliation(s)
- Joyce B Kang
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | | | - Aparna Nathan
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
| | - Nicole Soranzo
- Human Technopole, Milan, Italy; ,
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- British Heart Foundation Centre of Research Excellence and Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Soumya Raychaudhuri
- Center for Data Sciences and Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; ,
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA;
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
4
|
Pan J, Zhang X, Xu J, Chang Z, Xin Z, Wang G. Landscape of Exhausted T Cells in Tuberculosis Revealed by Single-Cell Sequencing. Microbiol Spectr 2023; 11:e0283922. [PMID: 36916943 PMCID: PMC10100881 DOI: 10.1128/spectrum.02839-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 02/13/2023] [Indexed: 03/16/2023] Open
Abstract
Tuberculosis, a contagious bacterial infection caused by Mycobacterium tuberculosis, is a substantial global health problem, impacting millions of lives annually. Exhausted T-cell signatures are critical for predicting clinical responses to tuberculosis infection. To obtain a panoramic transcriptional profile of T cells, we performed single-cell RNA-sequencing analysis of CD4+ T and CD8+ T cells isolated from peripheral blood mononuclear cells of healthy individuals and patients with tuberculosis. We identified seven subsets in CD8+ T cells and eight subsets in CD4+ T cells and elucidated the transcriptomic landscape changes and characteristics of each subset. We further investigated the cell-to-cell relationship of each subgroup of the two cell types. Different signature genes and pathways of exhausted CD4+ and CD8+ T cells were examined. We identified 12 genes with potential associations of T-cell exhaustion after tuberculosis infection. We also identified five genes as potential exhaustion marker genes. The CD8-EX3 subcluster in CD8+ T-exhausted cells was identified as an exhaustion-specific subcluster. The identified gene module further clarified the key factors influencing CD8+ T cell exhaustion. These data provide new insights into T-cell signatures in tuberculosis-exhausted populations. IMPORTANCE Identifying the changes in immune cells in response to infection can provide a better understanding of the effects of Mycobacterium tuberculosis on the host immune system. We performed single-cell RNA-sequencing analysis of CD4+ T and CD8+ T cells isolated from peripheral blood mononuclear cells of healthy individuals and patients with tuberculosis to reveal the cellular characteristics. Different signature genes and pathways of exhausted CD4+ and CD8+ T cells were examined. These will facilitate a more comprehensive understanding of the onset and underlying mechanism of T-cell exhaustion during active Mtb infection.
Collapse
Affiliation(s)
- Jiahui Pan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Xinyue Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Jianting Xu
- The First Hospital of Jilin University, Changchun, China
| | - Zecheng Chang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Zhuoyuan Xin
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Guoqing Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| |
Collapse
|
5
|
Gago S, Mandarano M, Floridi C, Zelante T. Host, pathogenic fungi and the microbiome: A genetic triangle in infection. Front Immunol 2023; 13:1078014. [PMID: 36733397 PMCID: PMC9887327 DOI: 10.3389/fimmu.2022.1078014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Sara Gago
- Manchester Fungal Infection Group, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Martina Mandarano
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Claudia Floridi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Teresa Zelante
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy,*Correspondence: Teresa Zelante,
| |
Collapse
|
6
|
Naik S, Mohammed A. Coexpression network analysis of human candida infection reveals key modules and hub genes responsible for host-pathogen interactions. Front Genet 2022; 13:917636. [PMID: 36482897 PMCID: PMC9722774 DOI: 10.3389/fgene.2022.917636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 11/08/2022] [Indexed: 07/30/2023] Open
Abstract
Invasive fungal infections are a significant reason for morbidity and mortality among organ transplant recipients. Therefore, it is critical to investigate the host and candida niches to understand the epidemiology of fungal infections in transplantation. Candida albicans is an opportunistic fungal pathogen that causes fatal invasive mucosal infections, particularly in solid organ transplant patients. Therefore, identifying and characterizing these genes would play a vital role in understanding the complex regulation of host-pathogen interactions. Using 32 RNA-sequencing samples of human cells infected with C. albicans, we developed WGCNA coexpression networks and performed DESeq2 differential gene expression analysis to identify the genes that positively correlate with human candida infection. Using hierarchical clustering, we identified 5 distinct modules. We studied the inter- and intramodular gene network properties in the context of sample status traits and identified the highly enriched genes in the correlated modules. We identified 52 genes that were common in the most significant WGCNA turquoise module and differentially expressed genes in human endothelial cells (HUVEC) infection vs. control samples. As a validation step, we identified the differentially expressed genes from the independent Candida-infected human oral keratinocytes (OKF6) samples and validated 30 of the 52 common genes. We then performed the functional enrichment analysis using KEGG and GO. Finally, we performed protein-protein interaction (PPI) analysis using STRING and CytoHubba from 30 validated genes. We identified 8 hub genes (JUN, ATF3, VEGFA, SLC2A1, HK2, PTGS2, PFKFB3, and KLF6) that were enriched in response to hypoxia, angiogenesis, vasculogenesis, hypoxia-induced signaling, cancer, diabetes, and transplant-related disease pathways. The discovery of genes and functional pathways related to the immune system and gene coexpression and differential gene expression analyses may serve as novel diagnostic markers and potential therapeutic targets.
Collapse
Affiliation(s)
- Surabhi Naik
- Department of Surgery, James D. Eason Transplant Institute, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Akram Mohammed
- Center for Biomedical Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| |
Collapse
|
7
|
Oelen R, de Vries DH, Brugge H, Gordon MG, Vochteloo M, Ye CJ, Westra HJ, Franke L, van der Wijst MGP. Single-cell RNA-sequencing of peripheral blood mononuclear cells reveals widespread, context-specific gene expression regulation upon pathogenic exposure. Nat Commun 2022; 13:3267. [PMID: 35672358 PMCID: PMC9174272 DOI: 10.1038/s41467-022-30893-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/24/2022] [Indexed: 12/15/2022] Open
Abstract
The host's gene expression and gene regulatory response to pathogen exposure can be influenced by a combination of the host's genetic background, the type of and exposure time to pathogens. Here we provide a detailed dissection of this using single-cell RNA-sequencing of 1.3M peripheral blood mononuclear cells from 120 individuals, longitudinally exposed to three different pathogens. These analyses indicate that cell-type-specificity is a more prominent factor than pathogen-specificity regarding contexts that affect how genetics influences gene expression (i.e., eQTL) and co-expression (i.e., co-expression QTL). In monocytes, the strongest responder to pathogen stimulations, 71.4% of the genetic variants whose effect on gene expression is influenced by pathogen exposure (i.e., response QTL) also affect the co-expression between genes. This indicates widespread, context-specific changes in gene expression level and its regulation that are driven by genetics. Pathway analysis on the CLEC12A gene that exemplifies cell-type-, exposure-time- and genetic-background-dependent co-expression interactions, shows enrichment of the interferon (IFN) pathway specifically at 3-h post-exposure in monocytes. Similar genetic background-dependent association between IFN activity and CLEC12A co-expression patterns is confirmed in systemic lupus erythematosus by in silico analysis, which implies that CLEC12A might be an IFN-regulated gene. Altogether, this study highlights the importance of context for gaining a better understanding of the mechanisms of gene regulation in health and disease.
Collapse
Affiliation(s)
- Roy Oelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Dylan H de Vries
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Harm Brugge
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - M Grace Gordon
- Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- UCSF Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Martijn Vochteloo
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Chun J Ye
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- UCSF Division of Rheumatology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, 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
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| |
Collapse
|
8
|
Gonçalves SM, Cunha C, Carvalho A. Understanding the genetic basis of immune responses to fungal infection. Expert Rev Anti Infect Ther 2022; 20:987-996. [PMID: 35385368 DOI: 10.1080/14787210.2022.2063839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Fungal infections represent a global public health problem that affect millions of people. Despite remarkable advances achieved over the last decades, available diagnostic and therapeutic tools remain insufficient for the optimal management of these diseases. The clinical course of fungal infection is highly variable, and evidence accumulated from patients with rare mutations and cohort-based studies suggests that the trajectory of disease is largely defined by patient genetics and its impact on immune responses. Therefore, there is an urgent need to elucidate the precise mechanisms by which which genetic variants influence the risk, progression, and outcome of fungal infection. AREAS COVERED In this review, we highlight recent advances in our understanding of the genetic factors that influence antifungal immune responses based on candidate gene studies and genome-wide approaches performed in different experimental and clinical models. EXPERT OPINION Research on genetics of susceptibility to infection is expected to lead to a detailed knowledge framework for the pathogenesis of human fungal infections and unveil novel targets and pathways amenable to clinical intervention.
Collapse
Affiliation(s)
- Samuel M Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| |
Collapse
|
9
|
The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response. Sci Rep 2021; 11:20281. [PMID: 34645905 PMCID: PMC8514550 DOI: 10.1038/s41598-021-99838-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/30/2021] [Indexed: 01/22/2023] Open
Abstract
Fungal infections represent a major global health problem affecting over a billion people that kills more than 1.5 million annually. In this study, we employed an integrative approach to reveal the landscape of the human immune responses to Candida spp. through meta-analysis of microarray, bulk, and single-cell RNA sequencing (scRNA-seq) data for the blood transcriptome. We identified across these different studies a consistent interconnected network interplay of signaling molecules involved in both Toll-like receptor (TLR) and interferon (IFN) signaling cascades that is activated in response to different Candida species (C. albicans, C. auris, C. glabrata, C. parapsilosis, and C. tropicalis). Among these molecules are several types I IFN, indicating an overlap with antiviral immune responses. scRNA-seq data confirmed that genes commonly identified by the three transcriptomic methods show cell type-specific expression patterns in various innate and adaptive immune cells. These findings shed new light on the anti-Candida immune response, providing putative molecular pathways for therapeutic intervention.
Collapse
|
10
|
Huang W, Wang D, Yao YF. Understanding the pathogenesis of infectious diseases by single-cell RNA sequencing. MICROBIAL CELL 2021; 8:208-222. [PMID: 34527720 PMCID: PMC8404151 DOI: 10.15698/mic2021.09.759] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/13/2021] [Accepted: 07/21/2021] [Indexed: 12/17/2022]
Abstract
Infections are highly orchestrated and dynamic processes, which involve both pathogen and host. Transcriptional profiling at the single-cell level enables the analysis of cell diversity, heterogeneity of the immune response, and detailed molecular mechanisms underlying infectious diseases caused by bacteria, viruses, fungi, and parasites. Herein, we highlight recent remarkable advances in single-cell RNA sequencing (scRNA-seq) technologies and their applications in the investigation of host-pathogen interactions, current challenges and potential prospects for disease treatment are discussed as well. We propose that with the aid of scRNA-seq, the mechanism of infectious diseases will be further revealed thus inspiring the development of novel interventions and therapies.
Collapse
Affiliation(s)
- Wanqiu Huang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Danni Wang
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu-Feng Yao
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.,Department of Infectious Diseases, Shanghai Ruijin Hospital, Shanghai 200025, China
| |
Collapse
|
11
|
Challenges and Opportunities in Understanding Genetics of Fungal Diseases: Towards a Functional Genomics Approach. Infect Immun 2021; 89:e0000521. [PMID: 34031131 DOI: 10.1128/iai.00005-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Infectious diseases are a leading cause of morbidity and mortality worldwide, and human pathogens have long been recognized as one of the main sources of evolutionary pressure, resulting in a high variable genetic background in immune-related genes. The study of the genetic contribution to infectious diseases has undergone tremendous advances over the last decades. Here, focusing on genetic predisposition to fungal diseases, we provide an overview of the available approaches for studying human genetic susceptibility to infections, reviewing current methodological and practical limitations. We describe how the classical methods available, such as family-based studies and candidate gene studies, have contributed to the discovery of crucial susceptibility factors for fungal infections. We will also discuss the contribution of novel unbiased approaches to the field, highlighting their success but also their limitations for the fungal immunology field. Finally, we show how a systems genomics approach can overcome those limitations and can lead to efficient prioritization and identification of genes and pathways with a critical role in susceptibility to fungal diseases. This knowledge will help to stratify at-risk patient groups and, subsequently, develop early appropriate prophylactic and treatment strategies.
Collapse
|
12
|
Deng W, Su Z, Liang P, Ma Y, Liu Y, Zhang K, Zhang Y, Liang T, Shao J, Liu X, Han W, Li R. Single-cell immune checkpoint landscape of PBMCs stimulated with Candida albicans. Emerg Microbes Infect 2021; 10:1272-1283. [PMID: 34120578 PMCID: PMC8238073 DOI: 10.1080/22221751.2021.1942228] [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] [Indexed: 01/23/2023]
Abstract
Immune checkpoints play various important roles in tumour immunity, which usually contribute to T cells’ exhaustion, leading to immunosuppression in the tumour microenvironment. However, the roles of immune checkpoints in infectious diseases, especially fungal infection, remain elusive. Here, we reanalyzed a recent published single-cell RNA-sequencing (scRNA-seq) data of peripheral blood mononuclear cells (PBMCs) stimulated with Candida albicans (C. albicans), to explore the expression patterns of immune checkpoints after C. albicans bloodstream infection. We characterized the heterogeneous pathway activities among different immune cell subpopulations after C. albicans infection. The CTLA-4 pathway was up-regulated in stimulated CD4+ and CD8+ T cells, while the PD-1 pathway showed high activity in stimulated plasmacytoid dendritic cell (pDC) and monocytes. Importantly, we found that immunosuppressive checkpoints HAVCR2 and LAG3 were only expressed in stimulated NK and CD8+ T cells, respectively. Their viabilities were validated by flow cytometry. We also identified three overexpressed genes (ISG20, LY6E, ISG15) across all stimulated cells. Also, two monocyte-specific overexpressed genes (SNX10, IDO1) were screened out in this study. Together, these results supplemented the landscape of immune checkpoints in fungal infection, which may serve as potential therapeutic targets for C. albicans infection. Moreover, the genes with the most relevant for C. albicans infection were identified in this study.
Collapse
Affiliation(s)
- Weiwei Deng
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Zhen Su
- Department of Dermatology and Venerology, The Third Affiliated Hospital of Sun Yat-Sen university, Guangzhou, People's Republic of China
| | - Panpan Liang
- Clinical laboratory, The Third Affiliated Hospital of Sun Yat-Sen university, Guangzhou, People's Republic of China
| | - Yubo Ma
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Yufang Liu
- Department of Dermatology and Venerology, The Third Affiliated Hospital of Sun Yat-Sen university, Guangzhou, People's Republic of China
| | - Kai Zhang
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Yi Zhang
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Tianyu Liang
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Jin Shao
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Xiao Liu
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| | - Wenling Han
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Peking University Center for Human Disease Genomics, Key Laboratory of Medical Immunology, Ministry of Health, Beijing, People's Republic of China
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Peking University; National Clinical Research Center for Skin and Immune Diseases; Beijing Key Laboratory of Molecular Diagnosis of Dermatoses, Beijing, People's Republic of China
| |
Collapse
|
13
|
Zhao Y, Lv J, Zhang H, Xie J, Dai H, Zhang X. Gene Expression Profiles Analyzed Using Integrating RNA Sequencing, and Microarray Reveals Increased Inflammatory Response, Proliferation, and Osteoclastogenesis in Pigmented Villonodular Synovitis. Front Immunol 2021; 12:665442. [PMID: 34248943 PMCID: PMC8264543 DOI: 10.3389/fimmu.2021.665442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background Pigmented villonodular synovitis (PVNS) is a rare condition that involves benign proliferation of the synovial tissue and is characterized by severe joint destruction and high recurrence even after surgical resection. However, poor understanding of the pathogenesis limits its effective therapy. Method In this study, gene expression profiles of six patients with PVNS, 11 patients with osteoarthritis (OA), nine patients with rheumatoid arthritis (RA) (E-MTAB-6141), and three healthy subjects (GSE143514) were analyzed using integrating RNA sequencing (RNA-seq) and microarray to investigate the PVNS transcriptome. Gene ontology, string, and cytoscape were used to determine the gene functional enrichment. Cell functional molecules were detected using flow cytometry or immunohistochemical test to identify the cell subset and function. CD14+ cells were isolated and induced to osteoclast to evaluate the monocyte/macrophage function. Results The most obvious local manifestations of PVNS were inflammation, including increased immune cells infiltration and cytokine secretion, and tumor phenotypes. High proportion of inflammatory cells, including T cells, natural killer (NK) cells, NKT cells, and B cells were recruited from the blood. Th17 and monocytes, especially classical monocytes but not nonclassical monocytes, increased in PVNS synovium. An obvious increase in osteoclastogenesis and macrophage activation was observed locally. Elevated expression of MMP9, SIGLEC 15, and RANK were observed in myeloid cell of PVNS than OA. When compared with RA, osteoclast differentiation and myeloid cell activation are PVNS-specific characters, whereas T cell activation is shared by PVNS and RA. Conclusion The transcriptional expression characteristics of PVNS showed increased immune response, cell migration, and osteoclastogenesis. Osteoclast differentiation is only observed in PVNS but not RA, whereas T-cell activation is common in inflammatory arthritis.
Collapse
Affiliation(s)
- Yang Zhao
- Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing, China.,Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Jiaoyun Lv
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Hongwei Zhang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiawei Xie
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Hui Dai
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Xin Zhang
- Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing, China
| |
Collapse
|
14
|
Ward RA, Thompson GR, Villani AC, Li B, Mansour MK, Wuethrich M, Tam JM, Klein BS, Vyas JM. The Known Unknowns of the Immune Response to Coccidioides. J Fungi (Basel) 2021; 7:jof7050377. [PMID: 34065016 PMCID: PMC8151481 DOI: 10.3390/jof7050377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/11/2022] Open
Abstract
Coccidioidomycosis, otherwise known as Valley Fever, is caused by the dimorphic fungi Coccidioides immitis and C. posadasii. While most clinical cases present with self-limiting pulmonary infection, dissemination of Coccidioides spp. results in prolonged treatment and portends higher mortality rates. While the structure, genome, and niches for Coccidioides have provided some insight into the pathogenesis of disease, the underlying immunological mechanisms of clearance or inability to contain the infection in the lung are poorly understood. This review focuses on the known innate and adaptive immune responses to Coccidioides and highlights three important areas of uncertainty and potential approaches to address them. Closing these gaps in knowledge may enable new preventative and therapeutic strategies to be pursued.
Collapse
Affiliation(s)
- Rebecca A. Ward
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
| | - George R. Thompson
- Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA 96817, USA;
| | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (A.-C.V.); (B.L.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA;
| | - Bo Li
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; (A.-C.V.); (B.L.)
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA;
| | - Michael K. Mansour
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
- Harvard Medical School, Boston, MA 02115, USA;
| | - Marcel Wuethrich
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.W.); (B.S.K.)
| | - Jenny M. Tam
- Harvard Medical School, Boston, MA 02115, USA;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bruce S. Klein
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.W.); (B.S.K.)
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jatin M. Vyas
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA; (R.A.W.); (M.K.M.)
- Harvard Medical School, Boston, MA 02115, USA;
- Correspondence: ; Tel.: +1-617-643-6444
| |
Collapse
|
15
|
d'Enfert C, Kaune AK, Alaban LR, Chakraborty S, Cole N, Delavy M, Kosmala D, Marsaux B, Fróis-Martins R, Morelli M, Rosati D, Valentine M, Xie Z, Emritloll Y, Warn PA, Bequet F, Bougnoux ME, Bornes S, Gresnigt MS, Hube B, Jacobsen ID, Legrand M, Leibundgut-Landmann S, Manichanh C, Munro CA, Netea MG, Queiroz K, Roget K, Thomas V, Thoral C, Van den Abbeele P, Walker AW, Brown AJP. The impact of the Fungus-Host-Microbiota interplay upon Candida albicans infections: current knowledge and new perspectives. FEMS Microbiol Rev 2021; 45:fuaa060. [PMID: 33232448 PMCID: PMC8100220 DOI: 10.1093/femsre/fuaa060] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/18/2020] [Indexed: 12/11/2022] Open
Abstract
Candida albicans is a major fungal pathogen of humans. It exists as a commensal in the oral cavity, gut or genital tract of most individuals, constrained by the local microbiota, epithelial barriers and immune defences. Their perturbation can lead to fungal outgrowth and the development of mucosal infections such as oropharyngeal or vulvovaginal candidiasis, and patients with compromised immunity are susceptible to life-threatening systemic infections. The importance of the interplay between fungus, host and microbiota in driving the transition from C. albicans commensalism to pathogenicity is widely appreciated. However, the complexity of these interactions, and the significant impact of fungal, host and microbiota variability upon disease severity and outcome, are less well understood. Therefore, we summarise the features of the fungus that promote infection, and how genetic variation between clinical isolates influences pathogenicity. We discuss antifungal immunity, how this differs between mucosae, and how individual variation influences a person's susceptibility to infection. Also, we describe factors that influence the composition of gut, oral and vaginal microbiotas, and how these affect fungal colonisation and antifungal immunity. We argue that a detailed understanding of these variables, which underlie fungal-host-microbiota interactions, will present opportunities for directed antifungal therapies that benefit vulnerable patients.
Collapse
Affiliation(s)
- Christophe d'Enfert
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Ann-Kristin Kaune
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Leovigildo-Rey Alaban
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sayoni Chakraborty
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
- Institute of Microbiology, Friedrich Schiller University, Neugasse 25, 07743 Jena, Germany
| | - Nathaniel Cole
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Daria Kosmala
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
- Université de Paris, Sorbonne Paris Cité, 25, rue du Docteur Roux, 75015 Paris, France
| | - Benoît Marsaux
- ProDigest BV, Technologiepark 94, B-9052 Gent, Belgium
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 9000 Ghent, Belgium
| | - Ricardo Fróis-Martins
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Moran Morelli
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Diletta Rosati
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Marisa Valentine
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Zixuan Xie
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Yoan Emritloll
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Peter A Warn
- Magic Bullet Consulting, Biddlecombe House, Ugbrook, Chudleigh Devon, TQ130AD, UK
| | - Frédéric Bequet
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Stephanie Bornes
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMRF0545, 20 Côte de Reyne, 15000 Aurillac, France
| | - Mark S Gresnigt
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Bernhard Hube
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Ilse D Jacobsen
- Microbial Immunology Research Group, Emmy Noether Junior Research Group Adaptive Pathogenicity Strategies, and the Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Mélanie Legrand
- Unité Biologie et Pathogénicité Fongiques, Département de Mycologie, Institut Pasteur, USC 2019 INRA, 25, rue du Docteur Roux, 75015 Paris, France
| | - Salomé Leibundgut-Landmann
- Immunology Section, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, Zurich 8057, Switzerland
- Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | - Chaysavanh Manichanh
- Gut Microbiome Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119–129, 08035 Barcelona, Spain
| | - Carol A Munro
- Aberdeen Fungal Group, Institute of Medical Sciences, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands
| | - Karla Queiroz
- Mimetas, Biopartner Building 2, J.H. Oortweg 19, 2333 CH Leiden, The Netherlands
| | - Karine Roget
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | - Vincent Thomas
- BIOASTER Microbiology Technology Institute, 40 avenue Tony Garnier, 69007 Lyon, France
| | - Claudia Thoral
- NEXBIOME Therapeutics, 22 allée Alan Turing, 63000 Clermont-Ferrand, France
| | | | - Alan W Walker
- Gut Microbiology Group, Rowett Institute, University of Aberdeen, Ashgrove Road West, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Alistair J P Brown
- MRC Centre for Medical Mycology, Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|