Disruption of the HLA-E/NKG2X axis is associated with uncontrolled HIV infections

The contribution of the HLA-E/NKG2X axis in NK-mediated control of HIV infection remains unclear. We have studied the relationship between HLA-E expression and phenotypical as well as functional characteristics of NK cells, in the context of chronic HIV infection and in an in vitro model of acute infection. High viremia in HIV+ individuals was related to increased HLA-E expression, and changes in NK subpopulations, especially a reduction of the CD56 bright as well as an increase in adaptive NK subpopulation. Uncontrolled HIV infection was also characterized by a reversion of the NKG2A/NKG2C expression ratio and a loss of positive and negative regulation of NK mediated by HLA-E. This was reflected in a lower cytotoxic, degranulation and cytokine production capacity, especially in CD56 bright and adaptive NK. In line with these results, HLA-E expression showed a positive correlation with viral growth inhibition in an in vitro model of acute infection at day 7, which was lost after 14 days of culture. Using HLA-E expressing K562 cells, we determined that only one out of 11 described HIV-derived HLA-E epitopes increased HLA-E surface stability. In spite of that, eight of the 11 epitopes were capable of increasing degranulation and three drove differences in NK-cell mediated cell lysis or cytokine secretion. In conclusion, our results indicate that HLA-E molecules presenting HIV-derived epitopes may sensitize target cells for NK lysis in early HIV infection. However, prolonged exposure to elevated HLA-E expression levels in vivo may lead to NK cell dysfunction and reduced viral control In chronic infection

Plasma proteomic profiling identifies CD33 as a marker of HIV control in natural infection and after therapeutic vaccination

Altres ajuts: National Institutes of Health (NIH), P01-AI131568Biomarkers predicting the outcome of HIV-1 virus control in natural infection and after therapeutic interventions in HIV-1 cure trials remain poorly defined. The BCN02 trial (NCT02616874), combined a T-cell vaccine with romidepsin (RMD), a cancer-drug that was used to promote HIV-1 latency reversal and which has also been shown to have beneficial effects on neurofunction. We conducted longitudinal plasma proteomics analyses in trial participants to define biomarkers associated with virus control during monitored antiretroviral pause (MAP) and to identify novel therapeutic targets that can improve future cure strategies. BCN02 was a phase I, open-label, single-arm clinical trial in early-treated, HIV infected individuals. Longitudinal plasma proteomes were analyzed in 11 BCN02 participants, including 8 participants that showed a rapid HIV-1 plasma rebound during a monitored antiretroviral pause (MAP-NC, 'non-controllers') and 3 that remained off ART with sustained plasma viremia <2000 copies/ml (MAP-C, 'controllers'). Inflammatory and neurological proteomes in plasma were evaluated and integration data analysis (viral and neurocognitive parameters) was performed. Validation studies were conducted in a cohort of untreated HIV-1+ individuals (n = 96) and in vitro viral replication assays using an anti-CD33 antibody were used for functional validation

Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control

GWAS, immune analyses and biomarker screenings have identified host factors associated within vivoHIV-1 control. However, there is a gap in the knowledge about the mechanisms that regulate the expression of such host factors. Here, we aimed to assess DNA methylation impact on host genome in natural HIV-1 control. To this end, whole DNA methylome in 70 untreated HIV-1 infected individuals with either high (>50,000 HIV-1-RNA copies/ml, n = 29) or low (<10,000 HIV-1-RNA copies/ml, n = 41) plasma viral load (pVL) levels were compared and identified 2,649 differentially methylated positions (DMPs). Of these, a classification random forest model selected 55 DMPs that correlated with virologic (pVL and proviral levels) and HIV-1 specific adaptive immunity parameters (IFNg-T cell responses and neutralizing antibodies capacity). Then, cluster and functional analyses identified two DMP clusters: cluster 1 contained hypo-methylated genes involved in antiviral and interferon response (e.g.PARP9,MX1, andUSP18) in individuals with high viral loads while in cluster 2, genes related to T follicular helper cell (Tfh) commitment (e.g.CXCR5andTCF7) were hyper-methylated in the same group of individuals with uncontrolled infection. For selected genes, mRNA levels negatively correlated with DNA methylation, confirming an epigenetic regulation of gene expression. Further, these gene expression signatures were also confirmed in early and chronic stages of infection, including untreated, cART treated and elite controllers HIV-1 infected individuals (n = 37). These data provide the first evidence that host genes critically involved in immune control of the virus are under methylation regulation in HIV-1 infection. These insights may offer new opportunities to identify novel mechanisms ofin vivovirus control and may prove crucial for the development of future therapeutic interventions aimed at HIV-1 cure. Author summary The infection with the human immunodeficiency virus (HIV), as for other viral infections, induce global DNA Methylation changes in the host genome. Herein, we identified for first time the methylation impact on host genome in untreated HIV-1 infection with different degrees ofin vivovirus control. Specifically, we observed that individuals with a better HIV-1 control showed a hypermethylation of genes associated with antiviral and interferon pathways and the hypomethylation of genes associated with the differentiation process of T follicular helper cells. Interestingly, these epigenetic imprints in host genome were strongly correlated with virus content and HIV-specific T cell responses. Therefore, we propose DNA Methylation as the regulation mechanism of host genes involved in immune HIV-1 control that could interfere in the efficacy of cure strategies. We also highlight the importance of DNA Methylation to regulate immune responses not only in HIV-1 but also in chronic infections or other pathologic situations associated with a sustained activation of the immune system

Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control

GWAS, immune analyses and biomarker screenings have identified host factors associated with in vivo HIV-1 control. However, there is a gap in the knowledge about the mechanisms that regulate the expression of such host factors. Here, we aimed to assess DNA methylation impact on host genome in natural HIV-1 control. To this end, whole DNA methylome in 70 untreated HIV-1 infected individuals with either high (>50,000 HIV-1-RNA copies/ml, n = 29) or low (<10,000 HIV-1-RNA copies/ml, n = 41) plasma viral load (pVL) levels were compared and identified 2,649 differentially methylated positions (DMPs). Of these, a classification random forest model selected 55 DMPs that correlated with virologic (pVL and proviral levels) and HIV-1 specific adaptive immunity parameters (IFNg-T cell responses and neutralizing antibodies capacity). Then, cluster and functional analyses identified two DMP clusters: cluster 1 contained hypo-methylated genes involved in antiviral and interferon response (e.g. PARP9, MX1, and USP18) in individuals with high viral loads while in cluster 2, genes related to T follicular helper cell (Tfh) commitment (e.g. CXCR5 and TCF7) were hyper-methylated in the same group of individuals with uncontrolled infection. For selected genes, mRNA levels negatively correlated with DNA methylation, confirming an epigenetic regulation of gene expression. Further, these gene expression signatures were also confirmed in early and chronic stages of infection, including untreated, cART treated and elite controllers HIV-1 infected individuals (n = 37). These data provide the first evidence that host genes critically involved in immune control of the virus are under methylation regulation in HIV-1 infection. These insights may offer new opportunities to identify novel mechanisms of in vivo virus control and may prove crucial for the development of future therapeutic interventions aimed at HIV-1 cure

Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells

Latency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1-infected individuals, SLFN12 expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal. In cell lines and HIV-1 patient PBMCs, the Schlafen 12 protein (SLFN12) is shown to be an HIV-1 restriction factor that inhibits HIV-1 replication and virus reactivatio

Gut microbiome signatures linked to HIV-1 reservoir size and viremia control

The potential role of the gut microbiome as a predictor of immune-mediated HIV-1 control in the absence of antiretroviral therapy (ART) is still unknown. In the BCN02 clinical trial, which combined the MVA.HIVconsv immunogen with the latency-reversing agent romidepsin in early-ART treated HIV-1 infected individuals, 23% (3/13) of participants showed sustained low-levels of plasma viremia during 32 weeks of a monitored ART pause (MAP). Here, we present a multi-omics analysis to identify compositional and functional gut microbiome patterns associated with HIV-1 control in the BCN02 trial. Viremic controllers during the MAP (controllers) exhibited higher Bacteroidales/Clostridiales ratio and lower microbial gene richness before vaccination and throughout the study intervention when compared to non-controllers. Longitudinal assessment indicated that the gut microbiome of controllers was enriched in pro-inflammatory bacteria and depleted in butyrate-producing bacteria and methanogenic archaea. Functional profiling also showed that metabolic pathways related to fatty acid and lipid biosynthesis were significantly increased in controllers. Fecal metaproteome analyses confirmed that baseline functional differences were mainly driven by Clostridial es. Participants with high baseline Bacteroidales/Clostridiales ratio had increased pre-existing immune activation-related transcripts. The Bacteroidales/Clostridiales ratio as well as host immune-activation signatures inversely correlated with HIV-1 reservoir size. The present proof-of-concept study suggests the Bacteroidales/Clostridiales ratio as a novel gut microbiome signature associated with HIV-1 reservoir size and immune-mediated viral control after ART interruption. The online version contains supplementary material available at 10.1186/s40168-022-01247-6

Schlafen 12 restricts HIV-1 latency reversal by a codon-usage dependent post-transcriptional block in CD4+ T cells

Latency is a major barrier towards virus elimination in HIV-1-infected individuals. Yet, the mechanisms that contribute to the maintenance of HIV-1 latency are incompletely understood. Here we describe the Schlafen 12 protein (SLFN12) as an HIV-1 restriction factor that establishes a post-transcriptional block in HIV-1-infected cells and thereby inhibits HIV-1 replication and virus reactivation from latently infected cells. The inhibitory activity is dependent on the HIV-1 codon usage and on the SLFN12 RNase active sites. Within HIV-1-infected individuals, SLFN12 expression in PBMCs correlated with HIV-1 plasma viral loads and proviral loads suggesting a link with the general activation of the immune system. Using an RNA FISH-Flow HIV-1 reactivation assay, we demonstrate that SLFN12 expression is enriched in infected cells positive for HIV-1 transcripts but negative for HIV-1 proteins. Thus, codon-usage dependent translation inhibition of HIV-1 proteins participates in HIV-1 latency and can restrict the amount of virus release after latency reversal.We thank Drs Yingying Li, Feng Gao and Beatrice H. Hahn for providing codon-optimized HIV-1 Gag expression vector, Drs James Hoxie and Susan Zolla-Pazner for supplying anti-Nef and -p24 antibodies, respectively through the NIH AIDS reagent program. We also thank Dr Song Gao for providing SLFN13-tRNA structure information, and Dr Maria-Eugenia Gas Lopez and Dr Ester Gea-Mallorquí for advise. This work was supported by following grants: M.K.I., JSPS Oversea Research Fellowship and Takeda Science Foundation; A.E.C., PT17/0009/0019 (ISCIII/MINECO and FEDER); M.J.B., RTI2018-101082-B-I00 and PID2021-123321OB-I00 [MINECO/FEDER]), and the Miguel Servet program by ISCIII (CP17/00179 and CPII22/00005); C.B., M.R.R., C.D.C., European Union’s Horizon 2020 research and innovation program under grant agreement 681137-EAVI2020 and NIH grant P01-AI131568; J.D., the Spanish Ministry of Science and Innovation (PID2019106959RB-I00/AEI/10.13039/501100011033); A.M., the Spanish Ministry of Science and Innovation (PID2019-106323RB-I00 AEI//10.13039/501100011033) and the institutional “María de Maeztu” Programme for Units of Excellence in R&D (CEX2018-000792-M).info:eu-repo/semantics/publishedVersio

Gut microbiome signatures linked to HIV-1 reservoir size and viremia control

Background: The potential role of the gut microbiome as a predictor of immune-mediated HIV-1 control in the absence of antiretroviral therapy (ART) is still unknown. In the BCN02 clinical trial, which combined the MVA.HIVconsv immunogen with the latency-reversing agent romidepsin in early-ART treated HIV-1 infected individuals, 23% (3/13) of participants showed sustained low-levels of plasma viremia during 32 weeks of a monitored ART pause (MAP). Here, we present a multi-omics analysis to identify compositional and functional gut microbiome patterns associated with HIV-1 control in the BCN02 trial. Results: Viremic controllers during the MAP (controllers) exhibited higher Bacteroidales/Clostridiales ratio and lower microbial gene richness before vaccination and throughout the study intervention when compared to non-controllers. Longitudinal assessment indicated that the gut microbiome of controllers was enriched in pro-inflammatory bacteria and depleted in butyrate-producing bacteria and methanogenic archaea. Functional profiling also showed that metabolic pathways related to fatty acid and lipid biosynthesis were significantly increased in controllers. Fecal metaproteome analyses confirmed that baseline functional differences were mainly driven by Clostridiales. Participants with high baseline Bacteroidales/Clostridiales ratio had increased pre-existing immune activation-related transcripts. The Bacteroidales/Clostridiales ratio as well as host immune-activation signatures inversely correlated with HIV-1 reservoir size. Conclusions: The present proof-of-concept study suggests the Bacteroidales/Clostridiales ratio as a novel gut microbiome signature associated with HIV-1 reservoir size and immune-mediated viral control after ART interruption. Video abstract

Sirtuin-2, NAD-Dependent Deacetylase, is a new potential therapeutic target for HIV-1 infection and HIV-related neurological dysfunction

The implementation and access to combined antiretroviral treatment (cART) have dramatically improved the quality of life of people living with HIV (PLWH). However, some comorbidities, such as neurological disorders associated with HIV infection still represent a serious clinical challenge. Soluble factors in plasma that are associated with control of HIV replication and neurological dysfunction could serve as early biomarkers and as new therapeutic targets for this comorbidity. We used a customized antibody array for determination of blood plasma factors in 40 untreated PLWH with different levels of viremia and found sirtuin-2 (SIRT2), an NAD-dependent deacetylase, to be strongly associated with elevated viral loads and HIV provirus levels, as well as with markers of neurological damage (a-synuclein [SNCA], brain-derived neurotrophic factor [BDNF], microtubule-associated protein tau [MAPT], and neurofilament light protein [NFL]). Also, longitudinal analysis in HIV-infected individuals with immediate (n = 9) or delayed initiation (n = 10) of cART revealed that after 1 year on cART, SIRT2 plasma levels differed between both groups and correlated inversely with brain orbitofrontal cortex involution. Furthermore, targeting SIRT2 with specific small-molecule inhibitors in in vitro systems using J-LAT A2 and primary glial cells led to diminished HIV replication and virus reactivation from latency. Our data thus identify SIRT2 as a novel biomarker of uncontrolled HIV infection, with potential impact on neurological dysfunction and offers a new therapeutic target for HIV treatment and cure. IMPORTANCE Neurocognitive disorders are frequently reported in people living with HIV (PLWH) even with the introduction of combined antiretroviral treatment (cART). To identify biomarkers and potential therapeutic tools to target HIV infection in peripheral blood and in the central nervous system (CNS), plasma proteomics were applied in untreated chronic HIV-infected individuals with different levels of virus control. High plasma levels of sirtuin-2 (SIRT2), an NAD+ deacetylase, were detected in uncontrolled HIV infection and were strongly associated with plasma viral load and proviral levels. In parallel, SIRT2 levels in the peripheral blood and CNS were associated with markers of neurological damage and brain involution and were more pronounced in individuals who initiated cART later in infection. In vitro infection experiments using specific SIRT2 inhibitors suggest that specific targeting of SIRT2 could offer new therapeutic treatment options for HIV infections and their associated neurological dysfunction

Proteomics analysis for the identification of biomarkers and potential therapeutic targets for HIV-1 control and HIV-related neurological dysfunction

Una de les estratègies per desenvolupar potencials teràpies per la cura del VIH-1 és analitzar un petit subconjunt d’individus infectats pel VIH-1 que presenten la capacitat natural de controlar el virus, aquests individus es coneixen com a controladors d’èlit. Tot i que alguns elements com els anticossos neutralitzants, les cèl·lules NK i la resposta de les cèl·lules T CD8 o els factors solubles difereixen entre aquests individus que poden controlar la infecció del VIH-1 i els que no, els mecanismes associats a aquest control natural encara no estan ben descrits. En aquesta tesi, hem utilitzat diferents eines proteòmiques per identificar factors plasmàtics associats al control o no control del VIH-1, per tal de definir biomarcadors relacionats amb la disfunció neurològica causada per la infecció del VIH-1. Paral·lelament, aquesta anàlisi proteòmica es va aplicar a l’assaig clínic BCN02, una intervenció terapèutica per la cura del VIH-1 basada en la estratègia “kick and kill”, per identificar altres factors plasmàtics que poden predir el rebot viral abans d’iniciar una pausa del tractament amb antirretrovirals. En el capítol I, vam identificar diferents factors plasmàtics associats al control del VIH-1 en absència de tractament en comparació amb individus no infectats pel VIH-1. En resum, es van analitzar el plasma i el líquid cefaloraquidi d’individus amb diferents nivells de control de la infecció pel VIH-1 en comparació amb els individus no infectats pel VIH-1. A continuació, vam seleccionar aquells marcadors plasmàtics que diferien entre individus que controlen el virus i no controladors del VIH-1. A més a més, alguns dels marcadors selceccionats vam veure que estaven fortament associats amb paràmetres virals i altres biomarcadors coneguts relacionats amb neuroinflamació. Curiosament, el tractament amb antirretrovirals va restaurar els nivells plasmàtics d’aquests candidats, cosa que indica que el tractament amb antirretrovirals pot reduir la disfunció neurològica causada pel VIH-1. En el capítol II, hem estudiat proteomes plasmàtics, amb en enfoc neurològica, en persones amb VIH-1 amb diferents capacitats per controlar la infecció amb el VIH-1. Curiosament, vam detectar de manera significativament diferent una desacetilasa dependent de NAD (dinucleòtid de nicotinamida i adenina), Sirtuin-2, que també es va veure associada amb el control viral. A més a més, aquest marcador estava relacionat amb alguns biomarcadors descrits en altres malalties neurològiques. Els nivells plasmàtics de SIRT2 vam observar que depenien del moment en què es va iniciar el tractament combinat amb antirretrovirals i estaven associats amb la involució d’una regió específica del cervell, l’escorça orbitofrontal. A més a més, els experiments in vitro d’inhibició de SIRT2 van reduir la reactivació viral de la latència i la replicació viral en cèl·lules de la sang perifèrica i en cèl·lules glials primàries. Aquests resultats suggereixen que SIRT2 pot servir com a biomarcador del control del VIH-1 i de la disfunció neurològica i podria ser una potencial diana terapèutica per a una estratègia per la cura del VIH-1. En el capítol III, es va analitzar el proteoma plasmàtic de participants de l’assaig clínic BCN02, basat en una estratègia “kick and kill”. Els participants de l’assaig clínic van ser tractats amb romidepsina per reactivar les cèl·lules latents infectades pel VIH-1 i vacunats amb l’immunogen HIVconsv per generar resposta de cèl·lules T. Per avaluar l’eficàcia d’aquesta estratègia els participants van interrompre el tractament d’antirretrovirals durant una pausa antirretroviral controlada. En aquest estudi, vam identificar possibles marcadors plasmàtics que es poden utilitzar per predir el rebot viral durant una pausa antirretroviral controlada després de la intervenció. Aquest estudi exploratori ens va permetre revelar com la intervenció va modificar els nivells de proteïnes plasmàtiques, especialment després de les infusions de romidepsina.Una de las estrategias para desarrollar potenciales terapias para la cura del VIH-1 es analizar un pequeño subconjunto de individuos infectados por VIH-1 que presentan la capacidad natural de controlar el virus, estos individuos se conocen como controladores de élite. Aunque algunos elementos como los anticuerpos neutralizantes, las células NK y la respuesta de las células T CD8 o los factores solubles difieren entre los individuos que pueden controlar la infección y los que no, los mecanismos asociados a este control natural todavía no están bien descritos. En esta tesis, hemos utilizado diferentes herramientas proteómicas para identificar factores plasmáticos asociados al control o no control del VIH-1 para definir biomarcadores relacionados con la disfunción neurológica causada por la infección por VIH-1. Paralelamente, este análisis proteómico se aplicó en el ensayo clínico BCN02, una estrategia terapéutica “kick and kill” contra el VIH-1, para identificar otros factores plasmáticos que puedan predecir el rebote viral antes de iniciar la interrupción del tratamiento con antirretrovirales. En el capítulo I, hemos identificado distintos factores plasmáticos asociados al control del VIH-1 en ausencia de tratamiento en comparación con individuos no infectados por el VIH-1. En resumen, se analizaron el plasma y el líquido cefalorraquídeo de individuos con distintos niveles de control de la infección por el VIH-1 en comparación con los individuos no infectados por el VIH-1. A continuación, seleccionamos aquellos marcadores plasmáticos que diferían entre individuos que controlan el virus y no controladores del VIH-1. Además, estos marcadores estaban fuertemente asociados a parámetros virales y otros biomarcadores conocidos relacionados con neuroinflamación. Curiosamente, el tratamiento con antirretrovirales restauró los niveles plasmáticos de estos candidatos, indicando que el tratamiento con antirretrovirales puede reducir la disfunción neurológica relacionada con el virus. En el capítulo II, hemos estudiado proteomas plasmáticos, con un enfoque neurológico, en personas con VIH-1 con diferentes capacidades para controlar la infección por el VIH-1. Curiosamente, detectamos de forma significativamente diferente una desacetilasa dependiente de NAD (dinucleótido de nicotinamida y adenina), Sirtuin-2, que también se vio asociada con el control viral. Este marcador, además, estaba relacionado con algunos biomarcadores descritos en otras enfermedades neurológicas. Curiosamente, observamos que los niveles plasmáticos de SIRT2 eran dependientes del momento del inicio del tratamiento con antirretrovirales, y estos niveles estaban asociados con la involución de una región específica del cerebro, la corteza orbitofrontal. Además, los experimentos in vitro de inhibición de SIRT2 redujeron la reactivación viral de la latencia y la replicación viral en células de la sangre periférica y en células gliales primarias. Estos resultados sugieren que SIRT2 puede servir como biomarcador del control del VIH-1 y la disfunción neurológica y podría ser una potencial diana terapéutica para una estrategia de cura del VIH-1. En el capítulo III, se analizó el proteoma plasmático de participantes del ensayo clínico BCN02, basado en una estrategia “kick and kill”. Los participantes del ensayo clínico fueron tratados con romidepsina para reactivar las células latentes infectadas por el VIH-1 y vacunados con el inmunogeno HIVconsv para generar respuesta de células T. Para evaluar la eficacia de esta estrategia los participantes interrumpieron el tratamiento con antirretrovirales durante una pausa antirretroviral controlada. En este estudio, identificamos posibles marcadores plasmáticos que se pueden utilizar para predecir el rebote viral durante una pausa antirretroviral controlada después de la intervención. Este estudio exploratorio nos permitió revelar cómo la intervención modificó los niveles de proteínas plasmáticas, especialmente después de las infusiones de romidepsina. Además, el análisis proteómico identificó la asociación entre los niveles plasmáticos de CD33 con parámetros virales, estableciéndolo como un posible biomarcador plasmático indicativo del control viral durante la monitorización de la interrupción del tratamiento.Combined antiretroviral therapy (cART) is the current treatment for people with HIV (PWH) that allows to turn this otherwise deadly disease into a chronic infection. Although these drugs maintain undetectable viral load and stop the progression of AIDS disease, access to cART is not ensured worldwide, requires life-long medication and can cause secondary effect associated with drug toxicity. Additionally, if the medication is stopped, a rapid viral rebound occurs due to the virus ability to establish a latent viral reservoir. One of the strategies to develop potential HIV-1 cure strategies, is to analyze a small subset of HIV-1 infected individuals that present the natural capacity to control the virus, known as elite controllers or long term non-progressors. Although some aspects such as neutralizing antibodies, NK cells and CD8 T-cell response or soluble factors differ between individuals that can control the infection versus those that cannot, the mechanisms associated with this natural control are not fully understood. In this thesis, we have used different proteomics approaches to identify plasma factors associated with HIV-1 control or non-control and to define biomarkers linked to neurological dysfunction in HIV-1 infection. In parallel, this proteomics analysis was applied to the BCN02 clinical trial, a “kick and kill” HIV-1 therapeutic strategy, to identify plasma factors that can predict viral rebound before initiating an antiretroviral treatment pause. In ChapterI, we identified different plasma factors associated with HIV-1 control in the absence of treatment compared to HIV-1 uninfected individuals. In brief, the plasma as well as cerebrospinal fluids were analyzed in individuals with different levels of control of HIV-1 infection and compared to HIV-1 uninfected individuals. Then, we selected those plasma markers that differed between individuals that control the virus and HIV-1 non-controllers. These markers were strongly associated with additional viral parameters and other well-known biomarker related to neuroinflammation. Interestingly, cART treatment restored the plasma levels of these proteins, suggesting that cART treatment may reduce HIV-related neurological dysfunction. ChapterII, we studied neuro-tailored plasma proteomes of PWH with different capabilities to control HIV-1 infection. Interestingly, a NAD (nicotinamide adenine dinucleotide)-dependent deacetylase, Sirtuin-2, was differentially detected and associated with viral control. Also, Sirtuin-2 was related to biomarkers described in other neurological diseases. The plasma levels of Sirtuin-2 were dependent on the time when cART was initiated and were associated with the involution of a specific brain region, in particular the orbitofrontal cortex. Moreover, in vitro targeting of SIRT2 reduced viral reactivation from latency and viral replication in peripheral blood cells and primary microglial cells. These results suggest that SIRT2 can serve as a biomarker of HIV-1 control and neurological dysfunction and could be a potential therapeutic target for a HIV-1 cure strategy. Chapter III, we analyzed the plasma proteome during the BCN02 clinical trial, which was based on a “kick and kill” HIV-1 cure strategy. Participants in the clinical trial were treated with romidepsin to reactivate HIV-1 in latently infected cells and vaccinated with HIVconsv vaccines to generate robust T-cell responses. Then, participants interrupted their cART treatment during a monitored antiretroviral pause (MAP) to evaluate the efficacy of this “kick and kill” strategy. In this context, we identified possible candidate plasma markers that predicted viral rebound during the monitored antiretroviral pause. This exploratory study revealed how this intervention modified the levels of plasma proteins, especially after romidepsin infusions. Moreover, proteomics analysis identified levels of the plasma CD33 protein to be associated with viral parameters, establishing it as a possible plasma biomarker indicative of monitored antiretroviral virus control, at least during short-term treatment interruption. Overall, proteomics allowed us to identify possible biomarkers that reflect pathogenic processes or responses to therapeutic interventions.Universitat Autònoma de Barcelona. Programa de Doctorat en Immunologia Avançad