Analysis of the Reservoir in Individuals Controlling HIV Infection

Study Overview
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Brief Summary
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The aim of this study is the gain new insights into HIV latency in HIV controllers through extensive blood an tissue sampling (lymph node, colon biopsies, placenta) from 25 individuals living with HIV and healthy individuals.

Official Title
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Analysis of the Reservoir in Individuals Controlling HIV Infection

Conditions
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Hiv

Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Elite Controllers: pVL<50 copies per ml for at least 12 months, treatment naive at the time of inclusion Viral controllers: pVL <2000 copies/ml; CD4>500/µL for at least two years, treatment naïve at the time of inclusion Long-term non-progressors: CD4>500/µL, pVL <10000 copies/ml, for at least 7 years, treatment naïve at the time of inclusion Post treatment controllers: on cART for at least 12 months; pVL <500 copies/ml for at least 2 years after treatment cessation . PLWH who received bone marrow transplant: people living with HIV who received a bone-marrow transplant for non-HIV related reasons Exclusion Criteria: Current history of opportunistic infection (AIDS defining events as defined in category C of the CDC clinical classification), consisting of chronic HIV-1 infection. Evidence of active HBV infection (Hepatitis B surface antigen positive or HBV viral load positive in the past and no evidence of subsequent seroconversion (= HBV antigen or viral load negative and positive HBV surface antibody)). Evidence of active HCV infection (HCV antibody positive result within 60 days prior to study entry with positive HCV viral load or, if the HCV antibody result is negative, a positive HCV RNA result within 60 days prior to study entry). Current or known history of cardiomyopathy or significant ischemic or cerebrovascular disease. Current history of cancer. History of HIV-related thrombocytopenia. Any condition, including preexisting psychiatric and psychological disorders, which will in the opinion of the investigator interfere with the trial conduct or safety of the participant. Abnormal results of standard of care laboratory tests: Confirmed haemoglobin <11g/dl for women and <12 g/dl for men Confirmed platelet count <100 000/µl * Confirmed neutrophil count <1000/μl Confirmed AST and/or ALT >10xULN Active drug or alcohol use or dependence that, in the opinion of the site investigator, would interfere with adherence to study requirements. Acute or serious illness, in the opinion of the site investigator, requiring systemic treatment and/or hospitalization within 60 days prior to entry. The following treatment will be prohibited three months before screening and during the study: immunosuppressive drugs (inclusive corticosteroids) except for drugs used for topical use. Immunomodulatory drugs including but not limited to Granulocyte-colony stimulating factors, Granulocyte-monocyte colony-stimulating factor, interleukin 2, 7 & 15.

Ages Eligible for Study
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Minimum Age: 18 Years
Maximum Age: 65 Years

Sexes Eligible for Study
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All

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| HIV-1 positive individuals (non-pregnant)<br> | |
| Pregnant HIV-1 positive/negative individuals<br> | |

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Quantification of total and intact HIV DNA and HIV RNA | Rainbow assay: multiplex digital PCR approach that combines five different HIV-1 regions to quantify total HIV-1 DNA and intact HIV-1 DNA simultaneously (Qiacuity dPCR platform, Qiagen). mutliplex digital PCR approach to quantify HIV RNA | 5 years | 
| Integration site analysis | HIV/host DNA junctions will be amplified using the Integration Site Loop Amplification (ISLA) assay, and resulting chimeric amplicons will be sequenced by Sanger. | 5 years | 
| Full-length HIV genome analysis | Full-Length Individual Proviral Sequencing (FLIPS) assay: nested PCR with Illumina MiSeq. | 5 years | 
| Epigenetic analysis | Methylation (bisulfite conversion) and chromatin accessibility (Assay for Transposase-Accessible Chromatin using sequencing) | 5 years | 
| Matched integration site and proviral sequencing | MIP-seq: captures full-length viral genome sequences in conjunction with its associated viral integration site | 5 years | 
| Proviral UMI-mediated Long-read Sequencing | HIV-PULSE: characterize the composition of the viral reservoir using long-read sequencing. Involves pre-amplifying individual proviral genomes using PCR and tagging them with dual UMIs, followed by long-range PCR amplification and long-read sequencing on the Oxford Nanopore MinION platform | 5 years | 
| Transcriptome analysis | Bulk RNA sequencing on extracted RNA (Illumina Hiseq 2500 with 10-100 ng input of ribodepleted RNA) Single cell RNA sequencing (10x genomics technology ) | 5 years | 
| High dimensional phenotyping | CyTOF (mass cytometry, Fluidigm) combined with bioinformatics approach to extensively characterize the phenotype of latently infected cells | 5 years | 
| Immunohistochemistry, RNA- and DNA In Situ Hybridization | Immunochemistry will be used to study the expression of activation and exhaustion markers on tissues samples , while viral expression will be assessed through DNAScope and RNAScope technologies | 5 years | 
| Immunometabolic profile analysis | Mass spectrometry metabolomics will be used to study the immunometabolic profile of latently infected cells | 5 years | 
| Detection of translation-competent reservoirs | HIV-Flow assay: flow cytometry based assay using a combination of 2 antibodies targeting the p24 protein and allowing the detection of cells containing translation-competent viruses. p24+ cells detected by this assay can be sorted for downstream applications and further characterization of translation-competent reservoirs. The Simultaneous TCR Integration site and Provirus sequencing (STIP-seq) assay will be performed to sequence the proviral genome and matched integration sites of the translation-competent viruses, as well as phenotypic characterization and TCR sequencing of the host cell. characterization of translation-competent reservoirs. | 5 years | 
| Immunological analysis-FACS | Immunophenotyping by flow cytometric assays will be performed of different cells to assess the phenotype of innate immune cells, using FACS analysis. | 5 years | 
| Immunological analysis-ELISA | Immunophenotyping by flow cytometric assays will be performed of different cells to assess the phenotype of innate immune cells, using ELISA. | 5 years | 
| Microbiome monitoring | Gut microbiome will be analyzed in stool and colon biopsies using next-generation sequencing (NGS) of rRNA gene amplicons to identify bacteria at genus/species level | 5 years | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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HIV, Latency