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Single-cell analysis identifies cellular markers of the HIV permissive cell. PLoS Pathog 2017; 13:e1006678. [PMID: 29073251 PMCID: PMC5658171 DOI: 10.1371/journal.ppat.1006678] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
Cellular permissiveness to HIV infection is highly heterogeneous across individuals. Heterogeneity is also found across CD4+ T cells from the same individual, where only a fraction of cells gets infected. To explore the basis of permissiveness, we performed single-cell RNA-seq analysis of non-infected CD4+ T cells from high and low permissive individuals. Transcriptional heterogeneity translated in a continuum of cell states, driven by T-cell receptor-mediated cell activation and was strongly linked to permissiveness. Proteins expressed at the cell surface and displaying the highest correlation with T cell activation were tested as biomarkers of cellular permissiveness to HIV. FACS sorting using antibodies against several biomarkers of permissiveness led to an increase of HIV cellular infection rates. Top candidate biomarkers included CD25, a canonical activation marker. The combination of CD25 high expression with other candidate biomarkers led to the identification of CD298, CD63 and CD317 as the best biomarkers for permissiveness. CD25highCD298highCD63highCD317high cell population showed an enrichment of HIV-infection of up to 28 fold as compared to the unsorted cell population. The purified hyper-permissive cell subpopulation was characterized by a downregulation of interferon-induced genes and several known restriction factors. Single-cell RNA-seq analysis coupled with functional characterization of cell biomarkers provides signatures of the "HIV-permissive cell".
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Fischer A, Rausell A. Primary immunodeficiencies suggest redundancy within the human immune system. Sci Immunol 2016; 1:1/6/eaah5861. [PMID: 28783693 DOI: 10.1126/sciimmunol.aah5861] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/03/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022]
Abstract
Pathogen-driven evolution has shaped the complexity of the human immune system. Our genome contains at least 1854 gene products involved in immune responses. However, the redundancy and robustness of the immune system need further characterization. One way to examine this redundancy is through the study of monogenic primary immunodeficiencies (PIDs) associated with infections. Causal mutations affecting innate immunity genes are, in relative terms, close to seven times less frequent than those affecting adaptive immunity genes in PIDs. Loss-of-function mutations of innate immunity genes encoding pattern-recognition receptors (PRRs) and associated pathways rarely cause susceptibility to infections, which suggests that PRR pathways are partially redundant in the immune responses to infection. This dispensability has also been observed for constitutive products of the immune system, such as secretory immunoglobulin A, and for innate immune cells, such as natural killer and innate lymphoid cell subsets, which are not essential for viability. This Review discusses these findings in the context of their implications for the identification of previously unknown classes of PIDs and assessment of the susceptibility to infection associated with various targeted immunotherapies.
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Affiliation(s)
- Alain Fischer
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France. .,Immunology and Pediatric Hematology Department, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Paris, France.,Collège de France, Paris, France
| | - Antonio Rausell
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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Rausell A, Muñoz M, Martinez R, Roger T, Telenti A, Ciuffi A. Innate immune defects in HIV permissive cell lines. Retrovirology 2016; 13:43. [PMID: 27350062 PMCID: PMC4924258 DOI: 10.1186/s12977-016-0275-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/14/2016] [Indexed: 11/29/2022] Open
Abstract
Background Primary CD4+ T cells and cell lines differ in their permissiveness to HIV infection. Impaired innate immunity may contribute to this different phenotype. Findings We used transcriptome profiling of 1503 innate immunity genes in primary CD4+ T cells and permissive cell lines. Two clusters of differentially expressed genes were identified: a set of 249 genes that were highly expressed in primary cells and minimally expressed in cell lines and a set of 110 genes with the opposite pattern. Specific to HIV, HEK293T, Jurkat, SupT1 and CEM cell lines displayed unique patterns of downregulation of genes involved in viral sensing and restriction. Activation of primary CD4+ T cells resulted in reversal of the pattern of expression of those sets of innate immunity genes. Functional analysis of prototypical innate immunity pathways of permissive cell lines confirmed impaired responses identified in transcriptome analyses. Conclusion Integrity of innate immunity genes and pathways needs to be considered in designing gain/loss functional genomic screens of viral infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0275-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Antonio Rausell
- Clinical Bioinformatics lab, Imagine Institute, Paris Descartes University - Sorbonne Paris Cité, 75015, Paris, France.
| | - Miguel Muñoz
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Raquel Martinez
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Thierry Roger
- Infectious Diseases Service, Department of Medicine, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
| | - Amalio Telenti
- Genetic Medicine, J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Angela Ciuffi
- Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011, Lausanne, Switzerland
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McLaren PJ, Gawanbacht A, Pyndiah N, Krapp C, Hotter D, Kluge SF, Götz N, Heilmann J, Mack K, Sauter D, Thompson D, Perreaud J, Rausell A, Munoz M, Ciuffi A, Kirchhoff F, Telenti A. Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses. Retrovirology 2015; 12:41. [PMID: 25980612 PMCID: PMC4434878 DOI: 10.1186/s12977-015-0165-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/24/2015] [Indexed: 02/07/2023] Open
Abstract
Background Known antiretroviral restriction factors are encoded by genes that are under positive selection pressure, induced during HIV-1 infection, up-regulated by interferons, and/or interact with viral proteins. To identify potential novel restriction factors, we performed genome-wide scans for human genes sharing molecular and evolutionary signatures of known restriction factors and tested the anti-HIV-1 activity of the most promising candidates. Results Our analyses identified 30 human genes that share characteristics of known restriction factors. Functional analyses of 27 of these candidates showed that over-expression of a strikingly high proportion of them significantly inhibited HIV-1 without causing cytotoxic effects. Five factors (APOL1, APOL6, CD164, TNFRSF10A, TNFRSF10D) suppressed infectious HIV-1 production in transfected 293T cells by >90% and six additional candidates (FCGR3A, CD3E, OAS1, GBP5, SPN, IFI16) achieved this when the virus was lacking intact accessory vpr, vpu and nef genes. Unexpectedly, over-expression of two factors (IL1A, SP110) significantly increased infectious HIV-1 production. Mechanistic studies suggest that the newly identified potential restriction factors act at different steps of the viral replication cycle, including proviral transcription and production of viral proteins. Finally, we confirmed that mRNA expression of most of these candidate restriction factors in primary CD4+ T cells is significantly increased by type I interferons. Conclusions A limited number of human genes share multiple characteristics of genes encoding for known restriction factors. Most of them display anti-retroviral activity in transient transfection assays and are expressed in primary CD4+ T cells. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0165-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paul J McLaren
- École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, 1005, Lausanne, Switzerland.
| | - Ali Gawanbacht
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Nitisha Pyndiah
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Christian Krapp
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Silvia F Kluge
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Nicola Götz
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Jessica Heilmann
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Katharina Mack
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
| | - Danielle Thompson
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Jérémie Perreaud
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Antonio Rausell
- Swiss Institute of Bioinformatics, 1005, Lausanne, Switzerland. .,Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Miguel Munoz
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Angela Ciuffi
- Institute of Microbiology, University of Lausanne, 1011, Lausanne, Switzerland.
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081, Ulm, Germany.
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Analysis of stop-gain and frameshift variants in human innate immunity genes. PLoS Comput Biol 2014; 10:e1003757. [PMID: 25058640 PMCID: PMC4110073 DOI: 10.1371/journal.pcbi.1003757] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 06/16/2014] [Indexed: 12/03/2022] Open
Abstract
Loss-of-function variants in innate immunity genes are associated with Mendelian disorders in the form of primary immunodeficiencies. Recent resequencing projects report that stop-gains and frameshifts are collectively prevalent in humans and could be responsible for some of the inter-individual variability in innate immune response. Current computational approaches evaluating loss-of-function in genes carrying these variants rely on gene-level characteristics such as evolutionary conservation and functional redundancy across the genome. However, innate immunity genes represent a particular case because they are more likely to be under positive selection and duplicated. To create a ranking of severity that would be applicable to innate immunity genes we evaluated 17,764 stop-gain and 13,915 frameshift variants from the NHLBI Exome Sequencing Project and 1,000 Genomes Project. Sequence-based features such as loss of functional domains, isoform-specific truncation and nonsense-mediated decay were found to correlate with variant allele frequency and validated with gene expression data. We integrated these features in a Bayesian classification scheme and benchmarked its use in predicting pathogenic variants against Online Mendelian Inheritance in Man (OMIM) disease stop-gains and frameshifts. The classification scheme was applied in the assessment of 335 stop-gains and 236 frameshifts affecting 227 interferon-stimulated genes. The sequence-based score ranks variants in innate immunity genes according to their potential to cause disease, and complements existing gene-based pathogenicity scores. Specifically, the sequence-based score improves measurement of functional gene impairment, discriminates across different variants in a given gene and appears particularly useful for analysis of less conserved genes. There are well-characterized severe immunodeficiencies associated with loss-of-function variants in innate immunity genes. Genome sequencing projects identify rare stop-gain and frameshift variants in innate immunity genes whose phenotype is uncharacterized. Current methods to estimate the severity of rare stop-gains and frameshifts are based on evolutionary conservation of the gene, the likelihood for redundancy in its function or mutational burden. These parameters are not always applicable to innate immunity genes. We evaluated sequence-level characteristics of more than 30'000 stop-gains and frameshifts and prioritized variants according to their predicted functional consequences. Our scoring approach complements existing tools in the prediction of innate immunity OMIM disease variants and associates with functional readouts such as gene expression. In this framework, we show that many individuals do carry highly pathogenic variants in genes participating in antiviral defense. The clinical assessment of these variants is of significant interest.
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