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Burkhart Colorado AS, Lazzaro A, Neff CP, Nusbacher N, Boyd K, Fiorillo S, Martin C, Siebert JC, Campbell TB, Borok M, Palmer BE, Lozupone C. Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe. MICROBIOME 2024; 12:18. [PMID: 38310301 PMCID: PMC10837999 DOI: 10.1186/s40168-023-01718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 11/09/2023] [Indexed: 02/05/2024]
Abstract
BACKGROUND The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH). However, even with HIV-1 suppression, chronic immune activation and elevated inflammation persist and have been linked to a pro-inflammatory gut microbiome composition and compromised intestinal barrier integrity. PLWH in urban versus rural areas of sub-Saharan Africa experience differences in environmental factors that may impact the gut microbiome and immune system, in response to ART, yet this has not previously been investigated in these groups. To address this, we measured T cell activation/exhaustion/trafficking markers, plasma inflammatory markers, and fecal microbiome composition in PLWH and healthy participants recruited from an urban clinic in the city of Harare, Zimbabwe, and a district hospital that services surrounding rural villages. PLWH were either ART naïve at baseline and sampled again after 24 weeks of first-line ART and the antibiotic cotrimoxazole or were ART-experienced at both timepoints. RESULTS Although expected reductions in the inflammatory marker IL-6, T-cell activation, and exhaustion were observed with ART-induced viral suppression, these changes were much more pronounced in the urban versus the rural area. Gut microbiome composition was the most highly altered from healthy controls in ART experienced PLWH, and characterized by both reduced alpha diversity and altered composition. However, gut microbiome composition showed a pronounced relationship with T cell activation and exhaustion in ART-naïve PLWH, suggesting a particularly significant role for the gut microbiome in disease progression in uncontrolled infection. Elevated immune exhaustion after 24 weeks of ART did correlate with both living in the rural location and a more Prevotella-rich/Bacteroides-poor microbiome type, suggesting a potential role for rural-associated microbiome differences or their co-variates in the muted improvements in immune exhaustion in the rural area. CONCLUSION Successful ART was less effective at reducing gut microbiome-associated inflammation and T cell activation in PLWH in rural versus urban Zimbabwe, suggesting that individuals on ART in rural areas of Zimbabwe may be more vulnerable to co-morbidity related to sustained immune dysfunction in treated infection. Video Abstract.
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Affiliation(s)
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy
| | - Charles Preston Neff
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Nichole Nusbacher
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kathryn Boyd
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, Keppel St, London, WC1E 7HT, England
| | - Suzanne Fiorillo
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Casey Martin
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Janet C Siebert
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Thomas B Campbell
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Margaret Borok
- Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Brent E Palmer
- Department Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
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Moretti S, Schietroma I, Sberna G, Maggiorella MT, Sernicola L, Farcomeni S, Giovanetti M, Ciccozzi M, Borsetti A. HIV-1-Host Interaction in Gut-Associated Lymphoid Tissue (GALT): Effects on Local Environment and Comorbidities. Int J Mol Sci 2023; 24:12193. [PMID: 37569570 PMCID: PMC10418605 DOI: 10.3390/ijms241512193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
HIV-1 replication in the gastrointestinal (GI) tract causes severe CD4+ T-cell depletion and disruption of the protective epithelial barrier in the intestinal mucosa, causing microbial translocation, the main driver of inflammation and immune activation, even in people living with HIV (PLWH) taking antiretroviral drug therapy. The higher levels of HIV DNA in the gut compared to the blood highlight the importance of the gut as a viral reservoir. CD4+ T-cell subsets in the gut differ in phenotypic characteristics and differentiation status from the ones in other tissues or in peripheral blood, and little is still known about the mechanisms by which the persistence of HIV is maintained at this anatomical site. This review aims to describe the interaction with key subsets of CD4+ T cells in the intestinal mucosa targeted by HIV-1 and the role of gut microbiome and its metabolites in HIV-associated systemic inflammation and immune activation that are crucial in the pathogenesis of HIV infection and related comorbidities.
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Affiliation(s)
- Sonia Moretti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Ivan Schietroma
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Giuseppe Sberna
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Maria Teresa Maggiorella
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Leonardo Sernicola
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Stefania Farcomeni
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Belo Horizonte 30190-009, Minas Gerais, Brazil;
- Sciences and Technologies for Sustainable Development and One Health, University Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 00128 Rome, Italy;
| | - Alessandra Borsetti
- National HIV/AIDS Research Center, Istituto Superiore di Sanità, 00162 Rome, Italy; (S.M.); (I.S.); (G.S.); (M.T.M.); (L.S.); (S.F.)
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Xie G, Moron-Lopez S, Siegel DA, Yin K, Polos A, Cohen J, Greenblatt RM, Tien PC, Lee SA, Yukl SA, Roan NR. Common and Divergent Features of T Cells from Blood, Gut, and Genital Tract of Antiretroviral Therapy-Treated HIV + Women. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:1790-1801. [PMID: 35296537 PMCID: PMC8976750 DOI: 10.4049/jimmunol.2101102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/25/2022] [Indexed: 11/19/2022]
Abstract
T cells residing in mucosal tissues play important roles in homeostasis and defense against microbial pathogens. The gut and female reproductive tract (FRT) are both tolerogenic environments, but they differ in the kinds of foreign Ags they need to tolerate. How these different environments influence the properties of their T cells is poorly understood, but important for understanding women's health. We recruited antiretroviral therapy-suppressed women living with HIV who donated, within one visit, blood and tissue samples from the ileum, colon, rectosigmoid, endometrium, endocervix, and ectocervix. With these samples, we conducted 36-parameter cytometry by time of flight phenotyping of T cells. Although gut and FRT T cells shared features discriminating them from their blood counterparts, they also harbored features distinguishing them from one another. These included increased proportions of CD69+ T resident memory cells of the T effector memory phenotype, as well as preferential coexpression of CD69 and CD103, on the gut-derived cells. In contrast, CD69+CD103+ T resident memory CD8+ T cells from FRT, but not those from gut, preferentially expressed PD1. We further determined that a recently described population of CXCR4+ T inflammatory mucosal cells differentially expressed multiple other chemokine receptors relative to their blood counterparts. Our findings suggest that T cells resident in different tolerogenic mucosal sites take on distinct properties.
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Affiliation(s)
- Guorui Xie
- Gladstone Institute of Virology, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Sara Moron-Lopez
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
- Department of Veterans Affairs Medical Center, San Francisco, CA
| | - David A Siegel
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
| | - Kailin Yin
- Gladstone Institute of Virology, San Francisco, CA
- Department of Urology, University of California San Francisco, San Francisco, CA
| | - Anastasia Polos
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
- Department of Veterans Affairs Medical Center, San Francisco, CA
| | - Jennifer Cohen
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
- Department of Veterans Affairs Medical Center, San Francisco, CA
| | - Ruth M Greenblatt
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
| | - Phyllis C Tien
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
- Department of Veterans Affairs Medical Center, San Francisco, CA
| | - Sulggi A Lee
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
| | - Steven A Yukl
- Department of Medicine, University of California San Francisco, San Francisco, CA; and
- Department of Veterans Affairs Medical Center, San Francisco, CA
| | - Nadia R Roan
- Gladstone Institute of Virology, San Francisco, CA;
- Department of Urology, University of California San Francisco, San Francisco, CA
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Moron‐Lopez S, Xie G, Kim P, Siegel DA, Lee S, Wong JK, Price JC, Elnachef N, Greenblatt RM, Tien PC, Roan NR, Yukl SA. Tissue-specific differences in HIV DNA levels and mechanisms that govern HIV transcription in blood, gut, genital tract and liver in ART-treated women. J Int AIDS Soc 2021; 24:e25738. [PMID: 34235864 PMCID: PMC8264406 DOI: 10.1002/jia2.25738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/18/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Sex-specific differences affect multiple aspects of HIV infection, yet few studies have quantified HIV levels in tissues from women. Since an HIV functional cure will likely require a major reduction of infected cells from most tissues, we measured total and intact HIV DNA and the HIV transcription profile in blood, gut, genital tract and liver from HIV-positive antiretroviral therapy (ART) -treated women. METHODS Peripheral blood mononuclear cells (PBMC) and biopsies from the gastrointestinal (ileum, colon, rectosigmoid +/- liver) and genital (ectocervix, endocervix and endometrium) tracts were collected from 6 ART-treated (HIV RNA < 200 copies/mL) women. HIV DNA (total and intact) and levels of read-through, initiated (total), 5'elongated, polyadenylated and multiply spliced HIV transcripts were measured by droplet digital PCR. Immunophenotyping of cells was performed using Cytometry by time of flight (CyTOF). RESULTS We detected total HIV DNA in all tissues and intact HIV DNA in blood, ileum, colon, rectosigmoid and ectocervix. Initiated HIV transcripts per provirus were higher in PBMC and endometrium than in ileum, colon, rectosigmoid, ectocervix or endocervix, and higher in the rectum than either ileum or colon. 5'Elongated HIV transcripts per provirus were comparable in PBMC and endometrium, but higher than in gut or cervical samples. Polyadenylated and multiply spliced HIV transcripts were detected in PBMC (6/6 and 3/6 individuals respectively), but rarely in the tissues. CONCLUSIONS These results suggest tissue-specific differences in the mechanisms that govern HIV expression, with lower HIV transcription in most tissues than blood. Therapies aimed at disrupting latency, such as latency-reversing or latency-silencing agents, will be required to penetrate into multiple tissues and target different blocks to HIV transcription.
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Affiliation(s)
- Sara Moron‐Lopez
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
- Department of MedicineSan Francisco VA Medical CenterSan FranciscoCAUSA
| | - Guorui Xie
- Department of UrologyUniversity of CaliforniaSan Francisco (UCSF)San FranciscoCAUSA
- Gladstone InstitutesSan FranciscoCAUSA
| | - Peggy Kim
- Department of MedicineSan Francisco VA Medical CenterSan FranciscoCAUSA
| | - David A Siegel
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
| | - Sulggi Lee
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
| | - Joseph K Wong
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
- Department of MedicineSan Francisco VA Medical CenterSan FranciscoCAUSA
| | - Jennifer C Price
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
| | - Najwa Elnachef
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
| | - Ruth M Greenblatt
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
| | - Phyllis C Tien
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
- Department of MedicineSan Francisco VA Medical CenterSan FranciscoCAUSA
| | - Nadia R Roan
- Department of UrologyUniversity of CaliforniaSan Francisco (UCSF)San FranciscoCAUSA
- Gladstone InstitutesSan FranciscoCAUSA
| | - Steven A Yukl
- Department of MedicineUniversity of California San Francisco (UCSF)San FranciscoCAUSA
- Department of MedicineSan Francisco VA Medical CenterSan FranciscoCAUSA
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