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Juste MAJ, Joseph Y, Lespinasse D, Apollon A, Jamshidi P, Lee MH, Ward M, Brill E, Duffus Y, Chukwukere U, Danesh A, Alberto WC, Fitzgerald DW, Pape JW, Jones RB, Dupnik K. People Living With HIV Have More Intact HIV DNA in Circulating CD4+ T Cells if They Have History of Pulmonary Tuberculosis. Pathog Immun 2024; 9:172-193. [PMID: 39345793 PMCID: PMC11432494 DOI: 10.20411/pai.v9i2.722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/22/2024] [Indexed: 10/01/2024] Open
Abstract
Background A primary barrier to curing HIV is the HIV reservoir. The leading infectious cause of death worldwide for people living with HIV is tuberculosis (TB), but we do not know how TB impacts the HIV reservoir. Methods Participants in identification and validation cohorts were selected from previously enrolled studies at Groupe Haïtien d'Étude du Sarcome de Kaposi et des Infections Opportunistes (GHESKIO) in Port au Prince, Haiti. Intact and non-intact proviral DNA were quantified using droplet digital PCR of peripheral blood mononuclear cell (PBMC)-derived CD4+ T cells. Kruskal-Wallis tests were used to compare medians with tobit regression for censoring. Results In the identification cohort, we found that people living with HIV with a history of active pulmonary TB (n=19) had higher levels of intact provirus than people living with HIV without a history of active TB (n=47) (median 762; IQR, 183-1173 vs 117; IQR, 24-279 intact provirus per million CD4, respectively; P=0.0001). This difference also was seen in the validation cohort (n=31), (median 102; IQR, 0-737 vs 0; IQR, 0-24.5 intact provirus per million CD4, P=0.03) for TB vs no-TB history groups, respectively. The frequencies of CD4+ T cells with any detectable proviral fragment was directly proportional to the levels of interleukin-1 beta (r=0.524, P= 0.0025) and interleukin-2 (r=0.622, P=0.0002). Conclusions People living with HIV with a history of active pulmonary TB have more HIV pro-virus in their circulating CD4+ T cells, even years after TB cure. We need to characterize which CD4+ T cells are harboring intact provirus to consider the impact of T cell-targeting HIV cure interventions for people living in TB-endemic areas.
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Affiliation(s)
| | | | | | | | | | - Myung Hee Lee
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Maureen Ward
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Esther Brill
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Yanique Duffus
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Uche Chukwukere
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Ali Danesh
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | | | | | - Jean W. Pape
- GHESKIO Centers, Port au Prince, Haiti
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - R. Brad Jones
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Kathryn Dupnik
- Department of Medicine, Weill Cornell Medicine, New York, NY
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Bottanelli M, Ceccarelli D, Lolatto R, Galli L, Guffanti M, Dell'Acqua R, Ponta G, Mori G, Castagna A, Muccini C. Risk of Cardiovascular Diseases or Mortality in People With Higher Values of HIV-1 DNA. J Acquir Immune Defic Syndr 2023; 93:e6-e8. [PMID: 36989135 DOI: 10.1097/qai.0000000000003192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Affiliation(s)
- Martina Bottanelli
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniele Ceccarelli
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Riccardo Lolatto
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Galli
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monica Guffanti
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Raffaele Dell'Acqua
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giacomo Ponta
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Mori
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Castagna
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Muccini
- Vita-Salute San Raffaele University, Milan, Italy
- Infectious Diseases Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Application Value of Machine Learning Method in Measuring Gray Matter Volume of AIDS Patients. DISEASE MARKERS 2022; 2022:1210002. [PMID: 35756486 PMCID: PMC9225908 DOI: 10.1155/2022/1210002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022]
Abstract
Background To investigate the role of gray matter (GM) volume in the identification of HIV-positive patients with HIV-associated neurocognitive impairment (HAND) using a machine learning approach from normal healthy controls. Methods Twenty-seven HIV-infected patients and 14 healthy controls were enrolled in our study. Each set of BRAVO images was postprocessed using DPARSF3.1 to coregister all brains on the MNI template, and volume extraction of 90 brain regions was performed using custom-designed code. The machine learning method was performed using PRoNTo2.1.1 toolbox. The differences in brain volume between the HAND and non-HAND groups were analyzed. Results GM volume effectively distinguished HIV-positive patients from healthy subjects with an AUC equals to 0.73. The sensitivity, specificity, and accuracy of the established classification were 85.19%, 42.86%, and 70.73%, respectively. GM volume value of the top ten brain regions was related to digit symbols, trail making test, digit span, vocabulary fluency, stroop C time, stroop CW time, CD4, and neuropsychological group. Conclusions A machine learning approach facilitates early diagnosis of HAND in HIV patients by MRI-based GM volume measurement.
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Ruhanya V, Jacobs GB, Paul RH, Joska JA, Seedat S, Nyandoro G, Glashoff RH, Engelbrecht S. HIV-1 subtype C Tat exon-1 amino acid residue 24K is a signature for neurocognitive impairment. J Neurovirol 2022; 28:392-403. [PMID: 35394614 DOI: 10.1007/s13365-022-01073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 10/18/2022]
Abstract
Variation and differential selection pressures on Tat genes have been shown to alter the biological function of the protein, resulting in pathological consequences in a number of organs including the brain. We evaluated the impact of genetic variation and selection pressure on 147 HIV-1 subtype C Tat exon 1 sequences from monocyte-depleted peripheral lymphocytes on clinical diagnosis of neurocognitive impairment. Genetic analyses identified two signature amino acid residues, lysine at codon 24 (24K) with a frequency of 43.4% and arginine at codon 29 (29R) with a frequency of 34.0% in individuals with HIV-associated neurocognitive impairment. The analyses also revealed two signature residues, asparagine, 24 N (31.9%), and histidine, 29H (21.3%), in individuals without neurocognitive impairment. Both codons, 24 and 29, were associated with high entropy but only codon 29 was under positive selection. The presence of signature K24 increased by 2.08 times the risk of neurocognitive impairment, 3.15 times higher proviral load, and 69% lower absolute CD4 T-cell count compared to those without the signature. The results support a linkage between HIV-1 C Tat N24K polymorphism, proviral load, immunosuppression, and neurocognitive impairment. The signature may induce more neurotoxic effects, which contributes to establishment and severity of HIV-associated neurocognitive impairment.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa. .,Department of Medical Microbiology, Harare, Zimbabwe.
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa
| | - Robert H Paul
- Department of Psychology and Behavioral Neuroscience, University of Missouri-St Louis, University Boulevard, St Louis, USA
| | - John A Joska
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- MRC Unit of Anxiety & Stress Disorders, Department of Psychiatry, University of Stellenbosch, Cape Town, South Africa
| | | | - Richard H Glashoff
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University, Francie van Zijl Avenue, Cape Town, 8000, South Africa.,National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
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Ruhanya V, Jacobs GB, Naidoo S, Paul RH, Joska JA, Seedat S, Nyandoro G, Engelbrecht S, Glashoff RH. Impact of Plasma IP-10/CXCL10 and RANTES/CCL5 Levels on Neurocognitive Function in HIV Treatment-Naive Patients. AIDS Res Hum Retroviruses 2021; 37:657-665. [PMID: 33472520 DOI: 10.1089/aid.2020.0203] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Immune activation, which is accompanied by the production of proinflammatory cytokines, is a strong predictor of disease progression in HIV infection. Inflammation is critical in neuronal damage linked to HIV-associated neurocognitive disorders. We examined the relationship between plasma cytokine levels and deficits in neurocognitive function. Multiplex profiling by Luminex® technology was used to quantify 27 cytokines/chemokines from 139 plasma samples of people living with HIV (PLWH). The relationship of plasma cytokine markers, clinical parameters, and cognitive impairment, was assessed using Spearman correlations. Partial least squares regression and variable importance in projection scores were used for further evaluation of the association. Forty-nine (35.3%) participants exhibited neurocognitive impairment based on a global deficit score (GDS) of at least 0.5 and 90 (64.7%) were classified as nonimpaired. Twenty-three (16.5%) initiated on combination antiretroviral therapy for 4 weeks before cognitive assessment and 116 (83.5%) were not on treatment. We identified five proinflammatory cytokines that were significant predictors of GDS namely, IP-10 (β = 0.058; p = .007), RANTES (β = 0.049; p = .005), IL-2 (β = 0.047, p = .006), Eotaxin (β = 0.042, p = .003), and IL-7 (β = 0.039, p = .003). IP-10 and RANTES were the strongest predictors of GDS. Both cytokines correlated with plasma viral load and lymphocyte proviral load and were inversely correlated with CD4+ T cell counts. IP-10 and RANTES formed a separate cluster with highest proximity. Study findings describe novel associations among IP-10, RANTES, cognitive status, plasma viral load, and cell-associated viral load.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, University of Zimbabwe, Harare, Zimbabwe
| | - Graeme B. Jacobs
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Shalena Naidoo
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
| | - Robert H. Paul
- Department of Psychology and Behavioral Neuroscience, University of Missouri-St Louis, St. Louis, Missouri, USA
| | - John A. Joska
- MRC Unit of Anxiety and Stress Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- MRC Unit of Anxiety and Stress Disorders, Department of Psychiatry, University of Stellenbosch, Cape Town, South Africa
| | - George Nyandoro
- Department of Medical Microbiology, University of Zimbabwe, Harare, Zimbabwe
| | - Susan Engelbrecht
- Division of Medical Virology, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
| | - Richard H. Glashoff
- National Health Laboratory Service (NHLS), Tygerberg Business Unit, Cape Town, South Africa
- Division of Medical Microbiology, Stellenbosch University, Cape Town, South Africa
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Cooley SA, Navid J, Wisch JK, Boerwinkle A, Doyle J, Paul RH, Ances BM. Relationships Between Viral Load, Neuroimaging, and NP in Persons Living With HIV. J Acquir Immune Defic Syndr 2021; 87:985-992. [PMID: 33675615 PMCID: PMC8192437 DOI: 10.1097/qai.0000000000002677] [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: 09/29/2020] [Accepted: 12/30/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND This study examined whether recommended viral load (VL) classifications by the Department of Health and Human Services map onto changes in brain integrity observed in people living with HIV (PLWH). METHODS Three hundred forty-nine PLWH on combination antiretroviral therapy meeting criteria for virologic suppression (VS) (VL ≤ 20 copies/mL; n = 206), "low-level viremia" (20-200 copies/mL; n = 63), or virologic failure (VF) (>200 copies/mL; n = 80) and 195 demographically similar HIV-negative controls were compared for cognition and brain volumes from 10 regions of interest that are sensitive to HIV. Changes in cognition and brain volumes were examined in a subset of PLWH (n = 132) who completed a follow-up evaluation (mean interval = 28 months) and had no change in treatment regimen. RESULTS Significant differences in cognition and brain volumes were observed between the HIV-negative control and VS groups compared with those in the VF groups, with few differences observed between the 3 PLWH subgroups. Longitudinally, PLWH who continued to have VF exhibited a greater decline in cognition and brain volumes compared with PLWH who remained with VS. Observed longitudinal changes in cognition correlated with brain volume changes. CONCLUSION PLWH with continued VF (consecutive VL measurements of >200 copies/mL) represent a cause for clinical concern and may benefit from change in treatment in addition to consideration of other potential etiologies of VF to reduce loss of brain integrity.
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Affiliation(s)
- Sarah A. Cooley
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
| | - Jaimie Navid
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
| | - Julie K. Wisch
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
| | - Anna Boerwinkle
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
| | - John Doyle
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
| | - Robert H. Paul
- Department of Psychology, University of Missouri, Saint Louis, Saint Louis, MO 63134, USA
| | - Beau M. Ances
- Department of Neurology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
- Department of Radiology, Washington University in Saint Louis, Saint Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis, Saint Louis, MO 63110, USA
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Lim HJ, Kang ER, Park MY, Kim BK, Kim MJ, Jung S, Roh KH, Sung N, Yang JH, Lee MW, Lee SH, Yang YJ. Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia. PLoS One 2021; 16:e0253402. [PMID: 34138947 PMCID: PMC8211157 DOI: 10.1371/journal.pone.0253402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classification of clinical symptoms and diagnostic microbiology are essential to effectively employ antimicrobial therapy for lower respiratory tract infections (LRTIs) in a timely manner. Empirical antibiotic treatment without microbial identification hinders the selective use of narrow-spectrum antibiotics and effective patient treatment. Thus, the development of rapid and accurate diagnostic procedures that can be readily adopted by the clinic is necessary to minimize non-essential or excessive use of antibiotics and accelerate patient recovery from LRTI-induced damage. We developed and validated a multiplex real-time polymerase chain reaction (mRT-PCR) assay with good analytical performance and high specificity to simultaneously detect four bacterial pathogens causing pneumonia: Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis. The analytical performance of mRT-PCR against target pathogens was evaluated by the limit of detection (LOD), specificity, and repeatability. Two hundred and ten clinical specimens from pneumonia patients were processed using an automatic nucleic acid extraction system for the “respiratory bacteria four” (RB4) mRT-PCR assay, and the results were directly compared to references from bacterial culture and/or Sanger sequencing. The RB4 mRT-PCR assay detected all target pathogens from sputum specimens with a coefficient of variation ranging from 0.29 to 1.71 and conservative LOD of DNA corresponding to 5 × 102 copies/reaction. The concordance of the assay with reference-positive specimens was 100%, and additional bacterial infections were detected from reference-negative specimens. Overall, the RB4 mRT-PCR assay showed a more rapid turnaround time and higher performance that those of reference assays. The RB4 mRT-PCR assay is a high-throughput and reliable tool that assists decision-making assessment and outperforms other standard methods. This tool supports patient management by considerably reducing the inappropriate use of antibiotics.
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Affiliation(s)
- Ho Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea
| | - Eun-Rim Kang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Bo Kyung Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Jin Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sunkyung Jung
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Gyeonggi, Republic of Korea
| | - Nackmoon Sung
- Clinical Research Institute, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Sun-Hwa Lee
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- * E-mail:
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Central Nervous System (CNS) Viral Seeding by Mature Monocytes and Potential Therapies To Reduce CNS Viral Reservoirs in the cART Era. mBio 2021; 12:mBio.03633-20. [PMID: 33727362 PMCID: PMC8092320 DOI: 10.1128/mbio.03633-20] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We characterized mechanisms of CNS viral reservoir establishment/replenishment using peripheral blood mononuclear cells (PBMC) of PLWH on cART and propose therapeutic targets to reduce/block selective entry of cells harboring HIV (HIV+) into the CNS. Using DNA/RNAscope, we show that CD14+ CD16+ monocytes with integrated HIV, transcriptionally active, and/or with active viral replication from PBMC of PLWH prescribed cART and virally suppressed, selectively transmigrate across a human BBB model. The human immunodeficiency virus (HIV) enters the central nervous system (CNS) within a few days after primary infection, establishing viral reservoirs that persist even with combined antiretroviral therapy (cART). We show that monocytes from people living with HIV (PLWH) on suppressive cART harboring integrated HIV, viral mRNA, and/or viral proteins preferentially transmigrate across the blood-brain barrier (BBB) to CCL2 and are significantly enriched post-transmigration, and even more highly enriched posttransmigration than T cells with similar properties. Using HIV-infected ART-treated mature monocytes cultured in vitro, we recapitulate these findings and demonstrate that HIV+ CD14+ CD16+ ART-treated monocytes also preferentially transmigrate. Cenicriviroc and anti-JAM-A and anti-ALCAM antibodies significantly and preferentially reduce/block transmigration of HIV+ CD14+ CD16+ ART-treated monocytes. These findings highlight the importance of monocytes in CNS HIV reservoirs and suggest targets to eliminate their formation and reseeding.
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McLaughlin MM, Ma Y, Scherzer R, Rahalkar S, Martin JN, Mills C, Milush J, Deeks SG, Hsue PY. Association of Viral Persistence and Atherosclerosis in Adults With Treated HIV Infection. JAMA Netw Open 2020; 3:e2018099. [PMID: 33119103 PMCID: PMC7596582 DOI: 10.1001/jamanetworkopen.2020.18099] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
IMPORTANCE Persons living with HIV (PLWH) have increased risk for cardiovascular disease, and inflammation is thought to contribute to this excess risk. Production of HIV during otherwise effective antiretroviral therapy (ART) has been associated with inflammation. OBJECTIVE To determine whether higher levels of viral persistence are associated with atherosclerosis as assessed by changes in carotid artery intima-media thickness (IMT) over time. DESIGN, SETTING, AND PARTICIPANTS In this cohort study, intima-media thickness, a validated marker of atherosclerosis, was assessed over time in a cohort of treated PLWH with viral suppression. Cell-associated HIV DNA and RNA and change in IMT, adjusted for demographics, cardiovascular risk factors, and HIV-related factors, were examined, as well as which factors were associated with viral persistence. One hundred fifty-two PLWH with undetectable viral loads for at least 6 months before study enrollment were recruited from HIV clinics affiliated with 2 hospitals in San Francisco, California, from January 1, 2003, to December 31, 2012. Data were analyzed from February 7, 2018, to May 12, 2020. EXPOSURES Cell-associated HIV RNA and DNA were measured using enriched CD4+ T cells from cryopreserved peripheral blood mononuclear cells. MAIN OUTCOMES AND MEASURES Carotid IMT was measured at baseline and the last visit, with a mean (SD) follow-up of 4.2 (2.7) years, using high-resolution B mode ultrasonography. The main study outcomes were baseline IMT, annual IMT progression, and incident plaque, defined as a focal region of carotid IMT of greater than 1.5 mm. RESULTS The analysis included 152 PLWH (140 [92.1%] male; median age, 48.5 [interquartile range {IQR}, 43.3-53.7] years). Older age, smoking, medications for hypertension, higher low-density lipoprotein levels, and higher interleukin 6 levels were associated with higher baseline mean IMT, whereas cell-associated HIV DNA (estimate, -0.07% [95% CI, -6.1% to 6.4%]; P = .98), and HIV RNA levels (estimate, -0.8% [95% CI, -5.9% to 4.4%]; P = .75) were not. Levels of HIV RNA (0.017 [95% CI, 0.000-0.034] mm/y; P = .047) and HIV DNA (0.022 [95% CI, 0.001-0.044] mm/y; P = .042) were significantly associated with annual carotid artery IMT progression in unadjusted models only. Both HIV RNA (incidence risk ratio [IRR], 3.05 [95% CI, 1.49-6.27] per IQR; P = .002) and HIV DNA (IRR, 3.15 [95% CI, 1.51-6.57] per IQR; P = .002) were significantly associated with incident plaque, which remained significant after adjusting for demographics, cardiovascular risk factors, and HIV-related factors (IRR for HIV RNA, 4.05 [95% CI, 1.44-11.36] per IQR [P = .008]; IRR for HIV DNA, 3.35 [95% CI, 1.22-9.19] per IQR [P = .02]). Higher C-reactive protein levels were associated with higher cell-associated HIV RNA (estimate, 20.7% [95% CI, 0.9%-44.4%] per doubling; P = .04), whereas higher soluble CD14 levels were associated with HIV DNA (estimate, 18.6% [95% CI, 3.5%-35.8%] per 10% increase; P = .01). Higher soluble CD163 levels were associated with a higher HIV RNA:DNA ratio (difference, 63.8% [95% CI, 3.5%-159.4%]; P = .04). CONCLUSIONS AND RELEVANCE These findings suggest that measurements of viral persistence in treated HIV disease are independently associated with incident carotid plaque development. The size and transcriptional activity of the HIV reservoir may be important contributors to HIV-associated atherosclerosis.
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Affiliation(s)
| | - Yifei Ma
- Department of Medicine, San Francisco Veterans Affairs Medical Center, UCSF
| | - Rebecca Scherzer
- Department of Medicine, San Francisco Veterans Affairs Medical Center, UCSF
| | - Smruti Rahalkar
- Division of Cardiology, Department of Medicine, San Francisco General Hospital, UCSF
| | | | - Claire Mills
- Division of Cardiology, Department of Medicine, San Francisco General Hospital, UCSF
| | - Jeffrey Milush
- Department of Medicine, Division of Experimental Medicine, UCSF
| | - Steven G. Deeks
- Positive Health Program, San Francisco General Hospital, San Francisco, California
| | - Priscilla Y. Hsue
- Division of Cardiology, Department of Medicine, San Francisco General Hospital, UCSF
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Ruhanya V, Jacobs GB, Nyandoro G, Paul RH, Joska JA, Seedat S, Glashoff RH, Engelbrecht S. Peripheral blood lymphocyte proviral DNA predicts neurocognitive impairment in clade C HIV. J Neurovirol 2020; 26:920-928. [PMID: 32737863 PMCID: PMC7717048 DOI: 10.1007/s13365-020-00882-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/12/2020] [Accepted: 07/06/2020] [Indexed: 12/11/2022]
Abstract
It is not known if proviral DNA in the periphery corresponds to cognitive status in clade C as it does in clade B and recombinant forms. A cross-sectional study was conducted on participants investigated for HIV-associated neurocognitive impairment in South Africa. HIV-1 proviral DNA was quantified using a PCR assay targeting a highly conserved HIV-1 LTR-gag region. Fifty-four (36.7%) participants were cognitively impaired and 93 (63.3%) were not impaired. Forty-three (79.6%) of the cognitively impaired participants were female and 11 (20.4%) were male. There was no significant age difference between cognitively impaired and unimpaired participants (p = 0.42). HIV-1 DNA in cognitively impaired PLWH was significantly higher than in cognitively normal individuals (p = .016). Considering impaired participants, lymphocyte HIV-1 DNA was significantly higher in males than females (p = 0.02). There was a modest positive correlation between lymphocyte HIV-1 DNA and global deficit scores (GDS) r = 0.176; p = 0.03). The two measures of viral load, lymphocyte HIV-1 DNA copies/million and plasma RNA copies/ml, were positively correlated (r = 0.39; p < .001). After adjusting for other covariates, age, sex, treatment status, and the interactions between impairment and treatment, the multivariate regression showed association between proviral load and neurocognitive impairment; omega effect size was 0.04, p value = 0.010. The burden of HIV-1 peripheral blood lymphocyte proviral DNA corresponds to neurocognitive impairment among individuals infected with clade C disease. Therefore, therapeutic strategies to reduce the HIV-1 proviral DNA reservoir in lymphocytes may improve neurocognitive outcomes in PLWH.
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Affiliation(s)
- Vurayai Ruhanya
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town, 8000, South Africa. .,Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, P.O. Box A178, Avondale, Harare, 00263, Zimbabwe.
| | - Graeme Brendon Jacobs
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town, 8000, South Africa
| | - George Nyandoro
- Department of Medical Microbiology, College of Health Sciences, University of Zimbabwe, P.O. Box A178, Avondale, Harare, 00263, Zimbabwe
| | - Robert H Paul
- Department of Psychological Sciences, Missouri Institute of Mental Health, University of Missouri-St. Louis, University Boulevard, St. Louis, MO, USA
| | - John A Joska
- MRC Unit on Anxiety & Stress Disorders, Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, South Africa
| | - Soraya Seedat
- Unit on Anxiety and Stress Disorders, Department of Psychiatry, Stellenbosch University, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, Tygerberg, 7505, South Africa
| | - Richard Helmuth Glashoff
- Division of Medical Microbiology and Immunology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, Tygerberg, 7505, South Africa.,Division of Medical Virology, National Health Laboratory Service (NHLS), Tygerberg Business Unit, Tygerberg Hospital, Tygerberg, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zijl Avenue, P.O. Box 241, Cape Town, 8000, South Africa.,Division of Medical Virology, National Health Laboratory Service (NHLS), Tygerberg Business Unit, Tygerberg Hospital, Tygerberg, South Africa
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León-Rivera R, Morsey B, Niu M, Fox HS, Berman JW. Interactions of Monocytes, HIV, and ART Identified by an Innovative scRNAseq Pipeline: Pathways to Reservoirs and HIV-Associated Comorbidities. mBio 2020; 11:e01037-20. [PMID: 32723919 PMCID: PMC7387797 DOI: 10.1128/mbio.01037-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 06/22/2020] [Indexed: 12/31/2022] Open
Abstract
HIV reservoirs persist despite successful antiretroviral therapy (ART) and are a major obstacle to the eradication and cure of HIV. The mature monocyte subset, CD14+CD16+, contributes to viral reservoirs and HIV-associated comorbidities. Only a subset of monocytes harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). We developed an innovative single cell RNA sequencing (scRNAseq) pipeline that detects HIV and host transcripts simultaneously, enabling us to examine differences between HIV+ and HIVexp mature monocytes. Using this, we characterized uninfected, HIV+, and HIVexp primary human mature monocytes with and without ART. We showed that HIV+ mature monocytes do not form their own cluster separately from HIVexp but can be distinguished by significant differential gene expression. We found that ART decreased levels of unspliced HIV transcripts potentially by modulating host transcriptional regulators shown to decrease viral infection and replication. We also identified and characterized mature monocyte subpopulations differentially impacted by HIV and ART. We identified genes dysregulated by ART in HIVexp monocytes compared to their uninfected counterpart and, of interest, the junctional protein ALCAM, suggesting that ART impacts monocyte functions. Our data provide a novel method for simultaneous detection of HIV and host transcripts. We identify potential targets, such as those genes whose expression is increased in HIV+ mature monocytes compared to HIVexp, to block their entry into tissues, preventing establishment/replenishment of HIV reservoirs even with ART, thereby reducing and/or eliminating viral burden and HIV-associated comorbidities. Our data also highlight the heterogeneity of mature monocyte subsets and their potential contributions to HIV pathogenesis in the ART era.IMPORTANCE HIV enters tissues early after infection, leading to establishment and persistence of HIV reservoirs despite antiretroviral therapy (ART). Viral reservoirs are a major obstacle to the eradication and cure of HIV. CD14+CD16+ (mature) monocytes may contribute to establishment and reseeding of reservoirs. A subset of monocytes, consisting mainly of CD14+CD16+ cells, harbors HIV (HIV+), while the rest remain uninfected, exposed cells (HIVexp). It is important to identify cells harboring virus to eliminate reservoirs. Using an innovative single-cell RNA sequencing (scRNAseq) pipeline to detect HIV and host transcripts simultaneously, we characterized HIV+ and HIVexp primary human mature monocytes with and without ART. HIV+ mature monocytes are not a unique subpopulation but rather can be distinguished from HIVexp by differential gene expression. We characterized mature monocyte subpopulations differently impacted by HIV and ART, highlighting their potential contributions to HIV-associated comorbidities. Our data propose therapeutic targets to block HIV+ monocyte entry into tissues, preventing establishment and replenishment of reservoirs even with ART.
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Affiliation(s)
- Rosiris León-Rivera
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Brenda Morsey
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Meng Niu
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Howard S Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Joan W Berman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York, USA
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Abstract
PURPOSE OF REVIEW A number studies are currently underway to develop new drugs aimed at reducing the HIV reservoir or achieving ART-free control of HIV infection. Many markers of HIV reservoirs have been proposed, each one having a different meaning. Total HIV DNA dynamics during the course of HIV infection and its predictive value are now well known. This marker allowed to estimate the size of HIV reservoir at different stages of HIV infection in blood, cell subsets and tissues. Therefore, the purpose of this review is timely and relevant, with the objective to discuss how total HIV DNA might be helpful in the clinical settings. RECENT FINDINGS Among the markers, it appears that HIV DNA is the most well studied, and recent articles confirmed that this marker is easy to use and is precise, specific, practical, robust and reproducible. All these characteristics correspond to what is expected from a helpful clinical marker. SUMMARY HIV DNA level could be considered as a global marker, and it is usually included in current clinical studies to describe the persistence and dynamics of the HIV reservoir, mainly in treated patients. HIV DNA might be helpful in designing clinical trials and personalized medication for HIV patients in the future.
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