1. Gut microbiome signatures linked to HIV-1 reservoir size and viremia control
- Author
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Borgognone, Alessandra, Noguera-Julian, Marc, Oriol, Bruna, Noël-Romas, Laura, Ruiz-Riol, Marta, Guillén, Yolanda, Parera, Mariona, Casadellà, Maria, Duran, Clara, Puertas, Maria C., Català-Moll, Francesc, De Leon, Marlon, Knodel, Samantha, Birse, Kenzie, Manzardo, Christian, Miró, José M., Clotet, Bonaventura, Martinez-Picado, Javier, Moltó, José, Mothe, Beatriz, Burgener, Adam, Brander, Christian, Paredes, Roger, Benet, Susana, Cedeño, Samandhy, Coll, Pep, Llano, Anuska, Marszalek, Marta, Morón-López, Sara, Rosás-Umbert, Miriam, Escrig, Roser, Gel, Silvia, López, Miriam, Miranda, Cristina, Muñoz, Jose, Perez-Alvarez, Nuria, Puig, Jordi, Revollo, Boris, Toro, Jessica, Barriocanal, Ana María, Perez-Reche, Cristina, Farré, Magí, Valle, Marta, Ambrosioni, Juan, Ruiz, Irene, Rovira, Cristina, Hurtado, Carmen, Ligero, Carmen, Fernández, Emma, Sánchez-Palomino, Sonsoles, Miró, Jose M., Carrillo, Antonio, Meulbroek, Michael, Pujol, Ferran, Saz, Jorge, Borthwick, Nicola, Crook, Alison, Wee, Edmund G., Hanke, Tomáš, and University of Manitoba
- Subjects
Microbiology (medical) ,Smallpox vaccine ,Human immunodeficiency virus (HIV) ,Microbiota intestinal ,Viremia ,HIV Infections ,Therapeutics ,medicine.disease_cause ,Microbiology ,HIV-1 post-treatment control ,Immune system ,medicine ,Humans ,Gastrointestinal microbiome ,Microbiome-based predictive biomarker ,Feces ,Gut microbiome ,biology ,Viral reservoir size ,Clostridiales ,Biochemical markers ,Terapèutica ,biology.organism_classification ,medicine.disease ,Bacteroidales ,Vacuna antivariolosa ,Gastrointestinal Microbiome ,Marcadors bioquímics ,Immunology ,HIV-1 ,Therapeutic HIV-1 vaccine ,Bacteria - Abstract
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. This study was funded by Instituto de Salud Carlos III through the project “PI16/01421” (co-funded by European Regional Development Fund “A way to make Europe”). The project was sponsored in part by Grifols and received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Grant Agreement N° 847943 (MISTRAL). The BCN02 clinical trial was an investigator-initiated study funded by the ISCIII PI15/01188 grant, the HIVACAT Catalan research program for an HIV vaccine and the Fundació Gloria Soler. Some sub-analyses of the BCN02 trial were partly funded by the European Union’s Horizon 2020 research and innovation program under grant agreement 681137-EAVI2020 and by NIH grant P01-AI131568. A.Bu lab was supported by grants from the Canadian Institutes of Health Research (HB3-164066) and the National Institutes for Health Research (R01DK112254). J.M.P lab was supported by grant PID2019-109870RB-I00 from the Spanish Ministry of Science and Innovation and in part by Grifols. J.M.M. received a personal 80:20 research grant from Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain, during 2017–21.
- Published
- 2022