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Parker E, Judge MA, Pastor L, Fuente-Soro L, Jairoce C, Carter KW, Anderson D, Mandomando I, Clifford HD, Naniche D, Le Souëf PN. Gene dysregulation in acute HIV-1 infection – early transcriptomic analysis reveals the crucial biological functions affected. Front Cell Infect Microbiol 2023; 13:1074847. [PMID: 37077524 PMCID: PMC10106835 DOI: 10.3389/fcimb.2023.1074847] [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: 10/20/2022] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
IntroductionTranscriptomic analyses from early human immunodeficiency virus (HIV) infection have the potential to reveal how HIV causes widespread and lasting damage to biological functions, especially in the immune system. Previous studies have been limited by difficulties in obtaining early specimens.MethodsA hospital symptom-based screening approach was applied in a rural Mozambican setting to enrol patients with suspected acute HIV infection (Fiebig stage I-IV). Blood samples were collected from all those recruited, so that acute cases and contemporaneously recruited, uninfected controls were included. PBMC were isolated and sequenced using RNA-seq. Sample cellular composition was estimated from gene expression data. Differential gene expression analysis was completed, and correlations were determined between viral load and differential gene expression. Biological implications were examined using Cytoscape, gene set enrichment analysis, and enrichment mapping.ResultsTwenty-nine HIV infected subjects one month from presentation and 46 uninfected controls were included in this study. Subjects with acute HIV infection demonstrated profound gene dysregulation, with 6131 (almost 13% of the genome mapped in this study) significantly differentially expressed. Viral load was correlated with 1.6% of dysregulated genes, in particular, highly upregulated genes involved in key cell cycle functions, were correlated with viremia. The most profoundly upregulated biological functions related to cell cycle regulation, in particular, CDCA7 may drive aberrant cell division, promoted by overexpressed E2F family proteins. Also upregulated were DNA repair and replication, microtubule and spindle organization, and immune activation and response. The interferome of acute HIV was characterized by broad activation of interferon-stimulated genes with antiviral functions, most notably IFI27 and OTOF. BCL2 downregulation alongside upregulation of several apoptotic trigger genes and downstream effectors may contribute to cycle arrest and apoptosis. Transmembrane protein 155 (TMEM155) was consistently highly overexpressed during acute infection, with roles hitherto unknown.DiscussionOur study contributes to a better understanding of the mechanisms of early HIV-induced immune damage. These findings have the potential to lead to new earlier interventions that improve outcomes.
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Affiliation(s)
- Erica Parker
- School of Medicine, University of Western Australia, Crawley, WA, Australia
| | - Melinda A. Judge
- School of Medicine, University of Western Australia, Crawley, WA, Australia
- *Correspondence: Melinda A. Judge,
| | - Lucia Pastor
- ISGlobal, Barcelona Institute for Global Health, Hospital Clinic–Universitat de Barcelona, Barcelona, Spain
- AIDS Research Institute-IrsiCaixa, Institut Germans Trias i Pujol (IGTP), Hospital Germans Trias i Pujol, Universitat Autonoma de Barcelona, Badalona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Laura Fuente-Soro
- ISGlobal, Barcelona Institute for Global Health, Hospital Clinic–Universitat de Barcelona, Barcelona, Spain
| | - Chenjerai Jairoce
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | | | | | - Inácio Mandomando
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | | | - Denise Naniche
- ISGlobal, Barcelona Institute for Global Health, Hospital Clinic–Universitat de Barcelona, Barcelona, Spain
- Centro de Investigação em Saúde da Manhiça (CISM), Maputo, Mozambique
| | - Peter Neils Le Souëf
- School of Medicine, University of Western Australia, Crawley, WA, Australia
- Telethon Kids Institute, Perth, WA, Australia
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HIV-1 envelope glycoproteins isolated from Viremic Non-Progressor individuals are fully functional and cytopathic. Sci Rep 2019; 9:5544. [PMID: 30944395 PMCID: PMC6447548 DOI: 10.1038/s41598-019-42075-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/22/2019] [Indexed: 02/07/2023] Open
Abstract
In untreated HIV-1-infected individuals, viremia is positively associated with disease progression. However, some viremic non progressors (VNPs) individuals show paradoxical high CD4+ T cell counts. HIV-1 envelope glycoprotein complex (Env) is a major cytopathic determinant in viral replication; therefore, we have deeply characterized Env function in this rare clinical phenotype. Full-length Env clones isolated from individuals with Viral Load (VL) > 10,000 copies/mL classified as VNPs (n = 15) or rapid progressors (RPs, n = 17) were geno- and phenotypically analyzed by determining diversity, expression, CD4 binding/signaling, fusogenicity, infectivity and autophagy induction. Selected Env clones from VNPs and RPs (n = 32) showed similar expression, fusion and infection abilities. Env clones from both groups showed similar affinity for CD4 during cell-to-cell transmission and consistently induced similar levels of CD4 signaling, measured by α-tubulin acetylation. Moreover, we demonstrate for the first time that primary Env clones from VNP and RP induce autophagy in uninfected cells and that this feature correlated with fusogenic capacity but was unrelated to disease progression. In conclusion, our data suggest that Env clones from VNP individuals are fully functional. Therefore, the paradoxical CD4+ T cell count stability coexisting with high levels of viral replication is unrelated to Env function.
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