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Bai X, Sönnerborg A, Nowak P. Elite controllers microbiome: unraveling the mystery of association and causation. Curr Opin HIV AIDS 2024; 19:261-267. [PMID: 38874425 DOI: 10.1097/coh.0000000000000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
PURPOSE OF REVIEW To unravel the current knowledge and possible link between the gut microbiome and HIV-1 virological control in elite controllers (EC), who can suppress viral replication in the absence of antiretroviral therapy. In addition, to discuss the limitations of current research and propose future research directions. RECENT FINDINGS EC possess a different gut bacterial microbiota profile in composition and functionality from that of treatment-naive HIV-1 viremic progressors (VP). Specifically, EC have a richer bacterial microbiota as compared to VP, which closely resembles the microbiota in HIV-1 negative healthy controls (HC). Differentially abundant bacteria are found between EC and VP or HC, though results vary among the few existing studies. These data imply that the gut microbiome could contribute to the natural suppression of HIV-1 infection. SUMMARY An association between the gut microbiome and HIV-1 virological control is evidenced by recent studies. Yet, there are substantial knowledge gaps, and the underlying mechanism of how the microbiome influences the EC phenotype is far from clarified. Future research should consider diverse microbial communities, the complex microbe-host interactions, as well as yet-unidentified causal links between microbiome alterations and HIV-1 disease progression.
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Affiliation(s)
- Xiangning Bai
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
- Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
| | - Piotr Nowak
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm
- Department of Infectious Diseases, Karolinska University Hospital, Huddinge, Sweden
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2
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Hu J, Hu J, Han D. Causal relationships between gut microbiota, plasma metabolites, and HIV infection: insights from Mendelian randomization and mediation analysis. Virol J 2024; 21:204. [PMID: 39215321 PMCID: PMC11365174 DOI: 10.1186/s12985-024-02480-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
OBJECTIVE Gut dysbiosis and metabolic abnormalities have been implicated in HIV infection. However, the exact causal relationships among the gut microbiota, metabolites, and HIV infection remain poorly understood. Our study involving Mendelian randomization (MR) and mediation analysis aims to unveil these causalities. METHODS Genetic instrumental variables for the gut microbiota were retrieved from MiBioGen consortium (n = 18,340). Metabolism-related genetic variants were sourced from the CLSA cohort (n = 8299). GWAS summary statistics for symptomatic HIV infection were derived from the FinnGen study (n = 309,154), and the UK Biobank (n = 208,808). We performed the bidirectional two-sample MR to assess causalities with the inverse-variance weighted (IVW) method as the primary analysis. Moreover, we executed a mediation analysis using two-step MR methods. RESULTS Compared to the causal effects of HIV infection on gut microbiota (or metabolites), those of gut microbiota (or plasma metabolites) on the risk of HIV infection were more substantial. Phylum Proteobacteria (OR: 2.114, 95% CI 1.042-4.288, P = 0.038), and genus Ruminococcaceae UCG013 (OR: 2.127, 95% CI 1.080-4.191, P = 0.029) exhibited an adverse causal effect on HIV infection, whereas genus Clostridium sensu stricto 1(OR: 0.491, 95% CI 0.252-0.956, P = 0.036) and family Erysipelotrichaceae (OR: 0.399, 95% CI 0.193-0.827, P = 0.013) acted as significant protective factors for HIV. The salicyluric glucuronide level (OR = 2.233, 95% CI 1.120-4.453, P = 0.023) exhibited a considerably adverse causal effect on HIV infection. Conversely, the salicylate-to-citrate ratio (OR: 0.417, 95% CI 0.253-0.688, P = 0.001) was identified as a protective factor for HIV. We identified only one bidirectional causality between 1-palmitoyl-GPI and HIV infection. Mechanistically, genus Haemophilus mediated the causal effects of three phospholipids on HIV infection risk: 1-palmitoyl-GPI (mediation proportion = 33.7%, P = 0.018), 1-palmitoyl-2-arachidonoyl-GPI (mediation proportion = 18.3%, P = 0.019), and 1-linoleoyl-2-linolenoyl-GPC (mediation proportion = 20.3%, P = 0.0216). Additionally, 5-Dodecenoylcarnitine (C12:1) mediated the causal effect of genus Sellimonas on the risk of HIV infection (mediation proportion = 13.7%, P = 0.0348). CONCLUSION Our study revealed that gut microbiota and metabolites causally influence HIV infection risk more substantially than the reverse. We identified the bidirectional causality between 1-palmitoyl-GPI (16:0) and HIV infection, and elucidated four mediation relationships. These findings provide genetic insights into prediction, prevention, and personalized medicine of HIV infection.
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Affiliation(s)
- Jiapeng Hu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jinxin Hu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
- Medical Research Center, Liaoning Key Laboratory of Research and Application of Animal Models for Environmental and Metabolic Diseases, Shengjing Hospital of China Medical University, Shenyang, China
| | - Dan Han
- Department of Neonatology, The First Hospital of China Medical University, Shenyang, China.
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Cai Y, Podlaha O, Deeks SG, Brinson C, Ramgopal MN, DeJesus E, Mills A, Shalit P, Abdel-Mohsen M, Zhang L, de Vries CR, Vendrame E, SenGupta D, Wallin JJ. HIV rebound in HIV controllers is associated with a specific fecal microbiome profile. Eur J Immunol 2024; 54:e2350809. [PMID: 38727191 DOI: 10.1002/eji.202350809] [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: 02/27/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 08/09/2024]
Abstract
HIV infection is associated with gut dysbiosis, and microbiome variability may affect HIV control when antiretroviral therapy (ART) is stopped. The TLR7 agonist, vesatolimod, was previously associated with a modest delay in viral rebound following analytical treatment interruption in HIV controllers (HCs). Using a retrospective analysis of fecal samples from HCs treated with vesatolimod or placebo (NCT03060447), people with chronic HIV (CH; NCT02858401) or without HIV (PWOH), we examined fecal microbiome profile in HCs before/after treatment, and in CH and PWOH. Microbiome diversity and abundance were compared between groups to investigate the association between specific phyla/species, immune biomarkers, and viral outcomes during treatment interruption. Although there were no significant differences in gut microbiome diversity between people with and without HIV, HCs, and CH shared common features that distinguished them from PWOH. there was a trend toward greater microbiome diversity among HCs. Treatment with vesatolimod reduced dysbiosis in HCs. Firmicutes positively correlated with T-cell activation, while Bacteroidetes and Euryarchaeota inversely correlated with TLR7-mediated immune activation. Specific types of fecal microbiome abundance (e.g. Alistipes putredinis) positively correlated with HIV rebound. In conclusion, variability in the composition of the fecal microbiome is associated with markers of immune activation following vesatolimod treatment and ART interruption.
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Affiliation(s)
- Yanhui Cai
- Gilead Sciences, Inc., Foster City, California, USA
| | | | - Steven G Deeks
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | | | - Moti N Ramgopal
- Midway Immunology and Research Center, Fort Pierce, Florida, USA
| | | | - Anthony Mills
- Men's Health Foundation, West Hollywood, California, USA
| | - Peter Shalit
- Peter Shalit MD and Associates, Seattle, Washington, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Liao Zhang
- Gilead Sciences, Inc., Foster City, California, USA
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Semenova L, Wang Y, Falcinelli S, Archin N, Cooper-Volkheimer AD, Margolis DM, Goonetilleke N, Murdoch DM, Rudin CD, Browne EP. Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.16.567386. [PMID: 38014340 PMCID: PMC10680759 DOI: 10.1101/2023.11.16.567386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A Leave-One-Covariate-Out (LOCO) inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, machine learning algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA. The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
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Salvador PBU, Altavas PJDR, del Rosario MAS, Ornos EDB, Dalmacio LMM. Alterations in the Gut Microbiome Composition of People Living with HIV in the Asia-Pacific Region: A Systematic Review. Clin Pract 2024; 14:846-861. [PMID: 38804398 PMCID: PMC11130874 DOI: 10.3390/clinpract14030066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/25/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Human immunodeficiency virus (HIV) infection continues to present a global health issue. Recent studies have explored the potential role of the gut microbiome in HIV infection for novel therapeutic approaches. We investigated the gut microbiome composition of people living with HIV (PLHIV) in the Asia-Pacific region. This review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. An electronic search was conducted in the PubMed/MEDLINE, Scopus, and ScienceDirect databases using keywords such as "HIV", "PLHIV", "AIDS", "gut microbiome", "gut dysbiosis", and "metagenomics". Only peer-reviewed and full-text studies published in English were included. A total of 15 studies from the Asia-Pacific region were included for analysis. Compared to healthy controls, PLHIV showed an increased abundance of Proteobacteria and its genera, which may be considered pathobionts, and decreased abundances of Bacteroidetes and several genera under Firmicutes with known short-chain fatty acid and immunoregulatory activities. Predominant taxa such as Ruminococcaceae and Prevotellaceae were also associated with clinical factors such as CD4 count, the CD4/CD8 ratio, and inflammatory cytokines. This review highlights gut microbiome changes among PLHIV in the Asia-Pacific region, indicating potential bacterial signatures for prognostication. The partial restoration of the microbiome toward beneficial taxa may ensure the long-term success of treatment, promoting immune recovery while maintaining viral load suppression.
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Affiliation(s)
- Paul Benedic U. Salvador
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (P.J.d.R.A.); (L.M.M.D.)
| | - Patrick Josemaria d. R. Altavas
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (P.J.d.R.A.); (L.M.M.D.)
| | - Mark Angelo S. del Rosario
- Multi-Omics Research Program for Health, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (M.A.S.d.R.); (E.D.B.O.)
| | - Eric David B. Ornos
- Multi-Omics Research Program for Health, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (M.A.S.d.R.); (E.D.B.O.)
- Department of Medical Microbiology, College of Public Health, University of the Philippines Manila, Manila 1000, Philippines
| | - Leslie Michelle M. Dalmacio
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila 1000, Philippines; (P.J.d.R.A.); (L.M.M.D.)
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Zimmermann P, Pittet LF, Jakob W, Messina NL, Falquet L, Curtis N. The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial. Pediatr Infect Dis J 2024; 43:378-389. [PMID: 38145402 DOI: 10.1097/inf.0000000000004223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2023]
Abstract
INTRODUCTION The early-life intestinal microbiome plays an important role in the development and regulation of the immune system. It is unknown whether the administration of vaccines influences the composition of the intestinal microbiome. OBJECTIVE To investigate whether Bacille Calmette-Guérin (BCG) vaccine given in the first few days of life influences the abundance of bacterial taxa and metabolic pathways in the intestinal microbiome at 1 week of age. METHODS Healthy, term-born neonates were randomized at birth to receive BCG or no vaccine within the first few days of life. Stool samples were collected at 1 week of age from 335 neonates and analyzed using shotgun metagenomic sequencing and functional analyses. RESULTS The composition of the intestinal microbiome was different between neonates born by cesarean section (CS) and those born vaginally. Differences in the composition between BCG-vaccinated and BCG-naïve neonates were only minimal. CS-born BCG-vaccinated neonates had a higher abundance of Staphylococcus lugdunensis compared with CS-born BCG-naïve neonates. The latter had a higher abundance of Streptococcus infantis and Trabulsiella guamensis . Vaginally-born BCG-vaccinated neonates had a higher abundance of Clostridiaceae and Streptococcus parasanguinis compared with vaginally-born BCG-naïve neonates, and a lower abundance of Veillonella atypica and Butyricimonas faecalis. Metabolic pathways that were differently abundant between BCG-vaccinated and BCG-naïve neonates were mainly those involved in sugar degradation and nucleotide/nucleoside biosynthesis. CONCLUSION BCG given in the first few days of life has little effect on the composition of the intestinal microbiome at 1 week of age but does influence the abundance of certain metabolic pathways.
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Affiliation(s)
- Petra Zimmermann
- From the Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Laure F Pittet
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
- Pediatric Infectious Diseases Unit, Geneva University Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - William Jakob
- Microbiology Laboratory, Fribourg Hospital, Fribourg, Switzerland
| | - Nicole L Messina
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
| | - Laurent Falquet
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Nigel Curtis
- Department of Paediatrics, The University of Melbourne, Parkville, Australia
- Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, Australia
- Infectious Diseases Unit, The Royal Children's Hospital Melbourne, Parkville, Australia
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Brogna C, Montano L, Zanolin ME, Bisaccia DR, Ciammetti G, Viduto V, Fabrowski M, Baig AM, Gerlach J, Gennaro I, Bignardi E, Brogna B, Frongillo A, Cristoni S, Piscopo M. A retrospective cohort study on early antibiotic use in vaccinated and unvaccinated COVID-19 patients. J Med Virol 2024; 96:e29507. [PMID: 38504586 DOI: 10.1002/jmv.29507] [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: 09/22/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 03/21/2024]
Abstract
The bacteriophage behavior of SARS-CoV-2 during the acute and post-COVID-19 phases appears to be an important factor in the development of the disease. The early use of antibiotics seems to be crucial to inhibit disease progression-to prevent viral replication in the gut microbiome, and control toxicological production from the human microbiome. To study the impact of specific antibiotics on recovery from COVID-19 and long COVID (LC) taking into account: vaccination status, comorbidities, SARS-CoV-2 wave, time of initiation of antibiotic therapy and concomitant use of corticosteroids and nonsteroidal anti-inflammatory drugs (NSAIDs). A total of 211 COVID-19 patients were included in the study: of which 59 were vaccinated with mRNA vaccines against SARS-CoV-2 while 152 were unvaccinated. Patients were enrolled in three waves: from September 2020 to October 2022, corresponding to the emergence of the pre-Delta, Delta, and Omicron variants of the SARS-CoV-2 virus. The three criteria for enrolling patients were: oropharyngeal swab positivity or fecal findings; moderate symptoms with antibiotic intake; and measurement of blood oxygen saturation during the period of illness. The use of antibiotic combinations, such as amoxicillin with clavulanic acid (875 + 125 mg tablets, every 12 h) plus rifaximin (400 mg tablets every 12 h), as first choice, as suggested from the previous data, or azithromycin (500 mg tablets every 24 h), plus rifaximin as above, allows healthcare professionals to focus on the gut microbiome and its implications in COVID-19 disease during patient care. The primary outcome measured in this study was the estimated average treatment effect, which quantified the difference in mean recovery between patients receiving antibiotics and those not receiving antibiotics at 3 and 9 days after the start of treatment. In the analysis, both vaccinated and unvaccinated groups had a median illness duration of 7 days (interquartile range [IQR] 6-9 days for each; recovery crude hazard ratio [HR] = 0.94, p = 0.700). The median illness duration for the pre-Delta and Delta waves was 8 days (IQR 7-10 days), while it was shorter, 6.5 days, for Omicron (IQR 6-8 days; recovery crude HR = 1.71, p < 0.001). These results were confirmed by multivariate analysis. Patients with comorbidities had a significantly longer disease duration: median 8 days (IQR 7-10 days) compared to 7 days (IQR 6-8 days) for those without comorbidities (crude HR = 0.75, p = 0.038), but this result was not confirmed in multivariate analysis as statistical significance was lost. Early initiation of antibiotic therapy resulted in a significantly shorter recovery time (crude HR = 4.74, p < 0.001). Concomitant use of NSAIDs did not reduce disease duration and in multivariate analysis prolonged the disease (p = 0.041). A subgroup of 42 patients receiving corticosteroids for a median of 3 days (IQR 3-6 days) had a longer recovery time (median 9 days, IQR 8-10 days) compared to others (median 7 days, IQR 6-8 days; crude HR = 0.542, p < 0.001), as confirmed also by the adjusted HR. In this study, a statistically significant reduction in recovery time was observed among patients who received early antibiotic treatment. Early initiation of antibiotics played a crucial role in maintaining higher levels of blood oxygen saturation. In addition, it is worth noting that a significant number of patients who received antibiotics in the first 3 days and for a duration of 7 days, during the acute phase did not develop LC.
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Affiliation(s)
- Carlo Brogna
- Craniomed Group Srl. Research Facility, Bresso, Italy
| | - Luigi Montano
- Andrology Unit and Service of Lifestyle Medicine in Uro-Andrology, Local Health Authority (ASL), Salerno, Italy
| | | | | | - Gianluca Ciammetti
- Otorhinolaryngology Unit, Hospital Ferdinando Veneziale Isernia, Regional Health Authority of Molise, Italy
| | | | - Mark Fabrowski
- Department of Emergency Medicine, Royal Sussex County Hospital, University Hospitals Sussex, Brighton, UK
| | - Abdul M Baig
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Iapicca Gennaro
- Pineta Grande Hospital Group, Department of Urology, Santa Rita Clinic, Atripalda, Italy
| | | | - Barbara Brogna
- Department of Radiology, Moscati Hospital, Avellino, Italy
| | | | | | - Marina Piscopo
- Department of Biology, University of Naples Federico II, Naples, Italy
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Reeves DB, Rigau DN, Romero A, Zhang H, Simonetti FR, Varriale J, Hoh R, Zhang L, Smith KN, Montaner LJ, Rubin LH, Gange SJ, Roan NR, Tien PC, Margolick JB, Peluso MJ, Deeks SG, Schiffer JT, Siliciano JD, Siliciano RF, Antar AAR. Mild HIV-specific selective forces overlaying natural CD4+ T cell dynamics explain the clonality and decay dynamics of HIV reservoir cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24302704. [PMID: 38405967 PMCID: PMC10888981 DOI: 10.1101/2024.02.13.24302704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The latent reservoir of HIV persists for decades in people living with HIV (PWH) on antiretroviral therapy (ART). To determine if persistence arises from the natural dynamics of memory CD4+ T cells harboring HIV, we compared the clonal dynamics of HIV proviruses to that of memory CD4+ T cell receptors (TCRβ) from the same PWH and from HIV-seronegative people. We show that clonal dominance of HIV proviruses and antigen-specific CD4+ T cells are similar but that the field's understanding of the persistence of the less clonally dominant reservoir is significantly limited by undersampling. We demonstrate that increasing reservoir clonality over time and differential decay of intact and defective proviruses cannot be explained by mCD4+ T cell kinetics alone. Finally, we develop a stochastic model of TCRβ and proviruses that recapitulates experimental observations and suggests that HIV-specific negative selection mediates approximately 6% of intact and 2% of defective proviral clearance. Thus, HIV persistence is mostly, but not entirely, driven by natural mCD4+ T cell kinetics.
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Ray S, Narayanan A, Vesterbacka J, Blennow O, Chen P, Gao Y, Gabarrini G, Ljunggren HG, Buggert M, Manoharan L, Chen MS, Aleman S, Sönnerborg A, Nowak P. Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV. NPJ Biofilms Microbiomes 2023; 9:104. [PMID: 38123600 PMCID: PMC10733305 DOI: 10.1038/s41522-023-00461-w] [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: 05/05/2023] [Accepted: 11/20/2023] [Indexed: 12/23/2023] Open
Abstract
Although mRNA SARS-CoV-2 vaccines are generally safe and effective, in certain immunocompromised individuals they can elicit poor immunogenic responses. Among these individuals, people living with HIV (PLWH) have poor immunogenicity to several oral and parenteral vaccines. As the gut microbiome is known to affect vaccine immunogenicity, we investigated whether baseline gut microbiota predicts immune responses to the BNT162b2 mRNA SARS-CoV-2 vaccine in healthy controls and PLWH after two doses of BNT162b2. Individuals with high spike IgG titers and high spike-specific CD4+ T-cell responses against SARS-CoV-2 showed low α-diversity in the gut. Here, we investigated and presented initial evidence that the gut microbial composition influences the response to BNT162b2 in PLWH. From our predictive models, Bifidobacterium and Faecalibacterium appeared to be microbial markers of individuals with higher spike IgG titers, while Cloacibacillus was associated with low spike IgG titers. We therefore propose that microbiome modulation could optimize immunogenicity of SARS-CoV-2 mRNA vaccines.
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Affiliation(s)
- Shilpa Ray
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden.
| | - Aswathy Narayanan
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
| | - Jan Vesterbacka
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Ola Blennow
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Puran Chen
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Gabarrini
- Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hans-Gustaf Ljunggren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lokeshwaran Manoharan
- National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Soo Aleman
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Sönnerborg
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA Futura, Karolinska Institutet, Stockholm, 141 52, Sweden
| | - Piotr Nowak
- Department of Medicine Huddinge, Division of Infectious Diseases, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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10
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Ma J, Wen S, Dong A, Fan W, Kang Y. Gut Microbiome (Bacteria, Fungi, and Viruses) and HIV Infection: Revealing Novel Treatment Strategies. Mol Nutr Food Res 2023; 67:e2300566. [PMID: 37867202 DOI: 10.1002/mnfr.202300566] [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: 08/07/2023] [Revised: 09/25/2023] [Indexed: 10/24/2023]
Abstract
Plenty of research on microbial-viral interactions has revealed that some commensal microorganisms in the gut, including bacteria, fungi, and viruses, can resist or promote viral infection, whereas other microorganisms are involved in pathogenicity. Therefore, the balance between commensal microorganisms and human organisms is a key factor for determining infection and disease progression, and commensal microorganisms have become a hot research area in the medical field. In this review, the compositional characteristics of gut microbiota (bacteria, fungi, and viruses) during HIV infection are reviewed and changes in gut microbiota among different HIV-infected populations are described. Furthermore, the latest progress of potential microbial therapeutic methods, including a) probiotics, prebiotics, and synbiotics, b) fecal microbiota transplantation (FMT), c) phage therapy, and d) antifungal strategy, microbial enzyme inhibition, and dietary therapeutics, is analyzed based on gut bacteria, fungi, and viruses in the field of HIV infection. This study aims to provide a useful reference for developing novel strategies for the prevention and treatment of HIV infection based on commensal microorganisms.
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Affiliation(s)
- Jieqiong Ma
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Shiyuan Wen
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Aobo Dong
- Third Hospital of Baotou City, Baotou, China
| | - Weiping Fan
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
| | - Yongbo Kang
- College of Basic Medical Sciences, Shanxi Medical University, Taiyuan, China
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Elizalde-Torrent A, Borgognone A, Casadellà M, Romero-Martin L, Escribà T, Parera M, Rosales-Salgado Y, Díaz-Pedroza J, Català-Moll F, Noguera-Julian M, Brander C, Paredes R, Olvera A. Vaccination with an HIV T-Cell Immunogen (HTI) Using DNA Primes Followed by a ChAdOx1-MVA Boost Is Immunogenic in Gut Microbiota-Depleted Mice despite Low IL-22 Serum Levels. Vaccines (Basel) 2023; 11:1663. [PMID: 38005995 PMCID: PMC10675013 DOI: 10.3390/vaccines11111663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Despite the important role of gut microbiota in the maturation of the immune system, little is known about its impact on the development of T-cell responses to vaccination. Here, we immunized C57BL/6 mice with a prime-boost regimen using DNA plasmid, the Chimpanzee Adenovirus, and the modified Vaccinia Ankara virus expressing a candidate HIV T-cell immunogen and compared the T-cell responses between individuals with an intact or antibiotic-depleted microbiota. Overall, the depletion of the gut microbiota did not result in significant differences in the magnitude or breadth of the immunogen-specific IFNγ T-cell response after vaccination. However, we observed marked changes in the serum levels of four cytokines after vaccinating microbiota-depleted animals, particularly a significant reduction in IL-22 levels. Interestingly, the level of IL-22 in serum correlated with the abundance of Roseburia in the large intestine of mice in the mock and vaccinated groups with intact microbiota. This short-chain fatty acid (SCFA)-producing bacterium was significantly reduced in the vaccinated, microbiota-depleted group. Therefore, our results indicate that, although microbiota depletion reduces serum levels of IL-22, the powerful vaccine regime used could have overcome the impact of microbiota depletion on IFNγ-producing T-cell responses.
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Affiliation(s)
- Aleix Elizalde-Torrent
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Alessandra Borgognone
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Maria Casadellà
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Luis Romero-Martin
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autonoma de Barcelona (UAB), 08193 Cerdanyola del Valles, Spain
| | - Tuixent Escribà
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Mariona Parera
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Yaiza Rosales-Salgado
- Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (Y.R.-S.); (J.D.-P.)
| | - Jorge Díaz-Pedroza
- Fundació Institut d’Investigació en Ciències de la Salut Germans Trias i Pujol (IGTP), 08916 Badalona, Spain; (Y.R.-S.); (J.D.-P.)
| | - Francesc Català-Moll
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
| | - Marc Noguera-Julian
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Facultat de Medicina, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
| | - Christian Brander
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Facultat de Medicina, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Aelix Therapeutics, 08028 Barcelona, Spain
| | - Roger Paredes
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- Facultat de Medicina, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
- Fight AIDS Foundation, Infectious Diseases Department, Germans Trias i Pujol University Hospital, 08916 Badalona, Spain
- Department of Infectious Diseases Service, Germans Trias i Pujol University Hospital, 08916 Badalona, Spain
| | - Alex Olvera
- Irsicaixa—AIDS Research Institute, 08916 Barcelona, Spain; (A.E.-T.); (A.B.); (M.C.); (L.R.-M.); (T.E.); (M.P.); (F.C.-M.); (M.N.-J.); (C.B.); (R.P.)
- CIBERINFEC—ISCIII, 28029 Madrid, Spain
- Facultat de Ciències, Tecnologia i Enginyeries, Universitat de Vic—Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Spain
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12
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Guo X, Wang Z, Qu M, Guo Y, Yu M, Hong W, Zhang C, Fan X, Song J, Xu R, Zhang J, Huang H, Linghu E, Wang FS, Sun L, Jiao YM. Abnormal blood microbiota profiles are associated with inflammation and immune restoration in HIV/AIDS individuals. mSystems 2023; 8:e0046723. [PMID: 37698407 PMCID: PMC10654078 DOI: 10.1128/msystems.00467-23] [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: 05/10/2023] [Accepted: 06/22/2023] [Indexed: 09/13/2023] Open
Abstract
IMPORTANCE The characteristics of blood microbiota in HIV-infected individuals and their relevance to disease progression are still unknown, despite alterations in gut microbiota diversity and composition in HIV-infected individuals. Here, we present evidence of increased blood microbiota diversity in HIV-infected individuals, which may result from gut microbiota translocation. Also, we identify a group of microbes, Porphyromonas gingivalis, Prevotella sp. CAG:5226, Eubacterium sp. CAG:251, Phascolarctobacterium succinatutens, Anaerobutyricum hallii, Prevotella sp. AM34-19LB, and Phocaeicola plebeius, which are linked to poor immunological recovery. This work provides a scientific foundation toward therapeutic strategies targeting blood microbiota for immune recovery of HIV infection.
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Affiliation(s)
- Xiaoyan Guo
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Zerui Wang
- Department of Gastroenterology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Mengmeng Qu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Yuntian Guo
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Minrui Yu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Weiguo Hong
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Chao Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Xing Fan
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jinwen Song
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Ruonan Xu
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Jiyuan Zhang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Huihuang Huang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Enqiang Linghu
- Department of Gastroenterology, First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fu-Sheng Wang
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
| | - Lijun Sun
- Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Yan-Mei Jiao
- Senior Department of Infectious Diseases, The Fifth Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases, Beijing, China
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13
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Rosel-Pech C, Pinto-Cardoso S, Chávez-Torres M, Montufar N, Osuna-Padilla I, Ávila-Ríos S, Reyes-Terán G, Aguirre-Alvarado C, Matías Juan NA, Pérez-Lorenzana H, Vázquez-Rosales JG, Bekker-Méndez VC. Distinct fecal microbial signatures are linked to sex and chronic immune activation in pediatric HIV infection. Front Immunol 2023; 14:1244473. [PMID: 37711620 PMCID: PMC10497879 DOI: 10.3389/fimmu.2023.1244473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/09/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Our understanding of HIV-associated gut microbial dysbiosis in children perinatally-infected with HIV (CLWH) lags behind that of adults living with HIV. Childhood represents a critical window for the gut microbiota. Any disturbances, including prolonged exposure to HIV, antiretroviral drugs, and antibiotics are likely to have a significant impact on long-term health, resulting in a less resilient gut microbiome. The objective of our study was to characterize the gut microbiota in CLWH, and compare it with HIV-unexposed and -uninfected children. Methods We enrolled 31 children aged 3 to 15 years; 15 were CLWH and 16 were HUU. We assessed dietary patterns and quality; quantified soluble and cellular markers of HIV disease progression by flow cytometry, enzyme-linked immunosorbent and multiplex-bead assays, and profiled the gut microbiota by 16S rRNA sequencing. We explored relationships between the gut microbiota, antibiotic exposure, dietary habits, soluble and cellular markers and host metadata. Results Children had a Western-type diet, their median health eating index score was 67.06 (interquartile range 58.76-74.66). We found no discernable impact of HIV on the gut microbiota. Alpha diversity metrics did not differ between CLWH and HUU. Sex impacted the gut microbiota (R-squared= 0.052, PERMANOVA p=0.024). Male children had higher microbial richness compared with female children. Two taxa were found to discriminate female from male children independently from HIV status: Firmicutes for males, and Bacteroides for females. Markers of HIV disease progression were comparable between CLWH and HUU, except for the frequency of exhausted CD4+ T cells (PD-1+) which was increased in CLWH (p=0.0024 after adjusting for confounders). Both the frequency of exhausted CD4+ and activated CD4+ T cells (CD38+ HLADR+) correlated positively with the relative abundance of Proteobacteria (rho=0.568. false discovery rate (FDR)-adjusted p= 0.029, and rho=0.62, FDR-adjusted p=0.0126, respectively). Conclusion The gut microbiota of CLWH appears similar to that of HUU, and most markers of HIV disease progression are normalized with long-term ART, suggesting a beneficial effect of the latter on the gut microbial ecology. The relationship between exhausted and activated CD4+ T cells and Proteobacteria suggests a connection between the gut microbiome, and premature aging in CLWH.
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Affiliation(s)
- Cecilia Rosel-Pech
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Sandra Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Nadia Montufar
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Iván Osuna-Padilla
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, Mexico
| | - Gustavo Reyes-Terán
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Charmina Aguirre-Alvarado
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Norma Angelica Matías Juan
- Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - Héctor Pérez-Lorenzana
- UMAE Hospital General Dr. Gaudencio González Garza, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
| | - José Guillermo Vázquez-Rosales
- Hospital de Pediatría “Doctor Silvestre Frenk Freund”, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, México, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología “Dr. Daniel Méndez Hernández”, Centro Médico Nacional “La Raza”, Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, Mexico
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14
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Beavis AC, Wee EGT, Akis Yildirim BM, Borthwick N, He B, Hanke T. Combined intranasal and intramuscular parainfluenza 5-, simian adenovirus ChAdOx1- and poxvirus MVA-vectored vaccines induce synergistically HIV-1-specific T cells in the mucosa. Front Immunol 2023; 14:1186478. [PMID: 37529048 PMCID: PMC10390215 DOI: 10.3389/fimmu.2023.1186478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/15/2023] [Indexed: 08/03/2023] Open
Abstract
Introduction The primary goal of this work is to broaden and enhance the options for induction of protective CD8+ T cells against HIV-1 and respiratory pathogens. Methods We explored the advantages of the parainfluenza virus 5 (PIV5) vector for delivery of pathogen-derived transgenes alone and in combination with the in-human potent regimen of simian adenovirus ChAdOx1 prime-poxvirus MVA boost delivering bi-valent mosaic of HIV-1 conserved regions designated HIVconsvX. Results We showed in BALB/c mice that the PIV5 vector expressing the HIVconsvX immunogens could be readily incorporated with the other two vaccine modalities into a single regimen and that for specific vector combinations, mucosal CD8+ T-cell induction was enhanced synergistically by a combination of the intranasal and intramuscular routes of administration. Discussion Encouraging safety and immunogenicity data from phase 1 human trials of ChAdOx1- and MVA-vectored vaccines for HIV-1, and PIV5-vectored vaccines for SARS-CoV-2 and respiratory syncytial virus pave the way for combining these vectors for HIV-1 and other indications in humans.
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Affiliation(s)
- Ashley C. Beavis
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Edmund G. -T. Wee
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Belkis M. Akis Yildirim
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola Borthwick
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Biao He
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Tomáš Hanke
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
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15
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Abstract
Acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has become a heavy burden of disease and an important public health problem in the world. Although current antiretroviral therapy (ART) is effective at suppressing the virus in the blood, HIV still remains in two different types of reservoirs-the latently infected cells (represented by CD4+ T cells) and the tissues containing those cells, which may block access to ART, HIV-neutralizing antibodies and latency-reversing agents. The latter is the focus of our review, as blood viral load drops below detectable levels after ART, a deeper and more systematic understanding of the HIV tissue reservoirs is imperative. In this review, we take the lymphoid system (including lymph nodes, gut-associated lymphoid tissue, spleen and bone marrow), nervous system, respiratory system, reproductive system (divided into male and female), urinary system as the order, focusing on the particularity and importance of each tissue in HIV infection, the infection target cell types of each tissue, the specific infection situation of each tissue quantified by HIV DNA or HIV RNA and the evidence of compartmentalization and pharmacokinetics. In summary, we found that the present state of HIV in different tissues has both similarities and differences. In the future, the therapeutic principle we need to follow is to respect the discrepancy on the basis of grasping the commonality. The measures taken to completely eliminate the virus in the whole body cannot be generalized. It is necessary to formulate personalized treatment strategies according to the different characteristics of the HIV in the various tissues, so as to realize the prospect of curing AIDS as soon as possible.
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Affiliation(s)
- Kangpeng Li
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Bo Liu
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Rui Ma
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Qiang Zhang
- Department of Orthopedics, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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16
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Li L, Zhao X, He JJ. HIV Tat Expression and Cocaine Exposure Lead to Sex- and Age-Specific Changes of the Microbiota Composition in the Gut. Microorganisms 2023; 11:799. [PMID: 36985373 PMCID: PMC10054272 DOI: 10.3390/microorganisms11030799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The balance of microbial communities in the gut is extremely important for normal physiological function. Disruption of the balance is often associated with various disorders and diseases. Both HIV infection and cocaine use are known to change the gut microbiota and the epithelial barrier integrity, which contribute to inflammation and immune activation. Our recent study shows that Tat expression and cocaine exposure result in changes of genome-wide DNA methylation and gene expression and lead to worsen the learning and memory impairments. In the current study, we extended the study to determine effects of Tat and cocaine on the gut microbiota composition. We found that both Tat expression and cocaine exposure increased Alteromonadaceae in 6-month-old female/male mice. In addition, we found that Tat, cocaine, or both increased Alteromonadaceae, Bacteroidaceae, Cyanobiaceae, Erysipelotrichaceae, and Muribaculaceae but decreased Clostridiales_vadinBB60_group, Desulfovibrionaceae, Helicobacteraceae, Lachnospiraceae, and Ruminococcaceae in 12-month-old female mice. Lastly, we analyzed changes of metabolic pathways and found that Tat decreased energy metabolism and nucleotide metabolism, and increased lipid metabolism and metabolism of other amino acids while cocaine increased lipid metabolism in 12-month-old female mice. These results demonstrated that Tat expression and cocaine exposure resulted in significant changes of the gut microbiota in an age- and sex-dependent manner and provide additional evidence to support the bidirectional gut-brain axis hypothesis.
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Affiliation(s)
- Lu Li
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Xiaojie Zhao
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
| | - Johnny J. He
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University, 3333 Green Bay Road, North Chicago, IL 60064, USA
- Center for Cancer Cell Biology, Immunology and Infection, Rosalind Franklin University, North Chicago, IL 60064, USA
- School of Graduate and Postdoctoral Studies, Rosalind Franklin University, North Chicago, IL 60064, USA
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17
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Zimmermann P. The immunological interplay between vaccination and the intestinal microbiota. NPJ Vaccines 2023; 8:24. [PMID: 36823142 PMCID: PMC9947885 DOI: 10.1038/s41541-023-00627-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Affiliation(s)
- Petra Zimmermann
- Department for Community Health, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland. .,Department of Paediatrics, Fribourg Hospital, Fribourg, Switzerland. .,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia. .,Infectious Diseases Research Group, Murdoch Children's Research Institute, Parkville, VIC, Australia.
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18
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Brogna C, Costanzo V, Brogna B, Bisaccia DR, Brogna G, Giuliano M, Montano L, Viduto V, Cristoni S, Fabrowski M, Piscopo M. Analysis of Bacteriophage Behavior of a Human RNA Virus, SARS-CoV-2, through the Integrated Approach of Immunofluorescence Microscopy, Proteomics and D-Amino Acid Quantification. Int J Mol Sci 2023; 24:3929. [PMID: 36835341 PMCID: PMC9965620 DOI: 10.3390/ijms24043929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
SARS-CoV-2, one of the human RNA viruses, is widely studied around the world. Significant efforts have been made to understand its molecular mechanisms of action and how it interacts with epithelial cells and the human microbiome since it has also been observed in gut microbiome bacteria. Many studies emphasize the importance of surface immunity and also that the mucosal system is critical in the interaction of the pathogen with the cells of the oral, nasal, pharyngeal, and intestinal epithelium. Recent studies have shown how bacteria in the human gut microbiome produce toxins capable of altering the classical mechanisms of interaction of viruses with surface cells. This paper presents a simple approach to highlight the initial behavior of a novel pathogen, SARS-CoV-2, on the human microbiome. The immunofluorescence microscopy technique can be combined with spectral counting performed at mass spectrometry of viral peptides in bacterial cultures, along with identification of the presence of D-amino acids within viral peptides in bacterial cultures and in patients' blood. This approach makes it possible to establish the possible expression or increase of viral RNA viruses in general and SARS-CoV-2, as discussed in this study, and to determine whether or not the microbiome is involved in the pathogenetic mechanisms of the viruses. This novel combined approach can provide information more rapidly, avoiding the biases of virological diagnosis and identifying whether a virus can interact with, bind to, and infect bacteria and epithelial cells. Understanding whether some viruses have bacteriophagic behavior allows vaccine therapies to be focused either toward certain toxins produced by bacteria in the microbiome or toward finding inert or symbiotic viral mutations with the human microbiome. This new knowledge opens a scenario on a possible future vaccine: the probiotics vaccine, engineered with the right resistance to viruses that attach to both the epithelium human surface and gut microbiome bacteria.
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Affiliation(s)
- Carlo Brogna
- Department of Research, Craniomed Group Facility Srl., 20091 Bresso, Italy
| | - Vincenzo Costanzo
- Biogem, Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy
| | - Barbara Brogna
- Department of Radiology, Moscati Hospital, Contrada Amoretta, 83100 Avellino, Italy
| | | | - Giancarlo Brogna
- Department of Research, Craniomed Group Facility Srl., 20091 Bresso, Italy
| | - Marino Giuliano
- Marsanconsulting Srl. Public Health Company, Via dei Fiorentini, 80133 Napoli, Italy
| | - Luigi Montano
- Andrology Unit and Service of LifeStyle Medicine in Uro-Andrology, Local Health Authority (ASL), 84124 Salerno, Italy
| | - Valentina Viduto
- Long COVID-19 Foundation, Brookfield Court, Garforth, Leeds LS25 1NB, UK
| | | | - Mark Fabrowski
- Department of Emergency Medicine, Royal Sussex County Hospital, University Hospitals Sussex, Eastern Road, Brighton BN2 5BE, UK
| | - Marina Piscopo
- Department of Biology, University of Naples Federico II, 80126 Napoli, Italy
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19
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Caputo V, Libera M, Sisti S, Giuliani B, Diotti RA, Criscuolo E. The initial interplay between HIV and mucosal innate immunity. Front Immunol 2023; 14:1104423. [PMID: 36798134 PMCID: PMC9927018 DOI: 10.3389/fimmu.2023.1104423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/17/2023] [Indexed: 02/01/2023] Open
Abstract
Human Immunodeficiency Virus (HIV) is still one of the major global health issues, and despite significant efforts that have been put into studying the pathogenesis of HIV infection, several aspects need to be clarified, including how innate immunity acts in different anatomical compartments. Given the nature of HIV as a sexually transmitted disease, one of the aspects that demands particular attention is the mucosal innate immune response. Given this scenario, we focused our attention on the interplay between HIV and mucosal innate response: the different mucosae act as a physical barrier, whose integrity can be compromised by the infection, and the virus-cell interaction induces the innate immune response. In addition, we explored the role of the mucosal microbiota in facilitating or preventing HIV infection and highlighted how its changes could influence the development of several opportunistic infections. Although recent progress, a proper characterization of mucosal innate immune response and microbiota is still missing, and further studies are needed to understand how they can be helpful for the formulation of an effective vaccine.
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Vaccination with an HIV T-cell immunogen induces alterations in the mouse gut microbiota. NPJ Biofilms Microbiomes 2022; 8:104. [PMID: 36585401 PMCID: PMC9801356 DOI: 10.1038/s41522-022-00368-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
The gut microbiota is emerging as a crucial factor modulating vaccine responses; however, few studies have investigated if vaccines, in turn, can alter the microbiota and to what extent such changes may improve vaccine efficacy. To understand the effect of T-cell vaccination on the gut microbiome, we administered an HIV-1 T-cell immunogen (HTI arm) or PBS (control, Mock arm) to C57Bl/6 mice following a heterologous prime-boost scheme. The longitudinal dynamics of the mice gut microbiota was characterized by 16 S ribosomal RNA sequencing in fecal samples collected from cages, as well as from three gut sections (cecum, small and large intestine). Serum and spleen cells were obtained at the last time point of the study to assess immune correlates using IFNγ ELISPOT and cytokine Luminex® assays. Compared with Mock, HTI-vaccinated mice were enriched in Clostridiales genera (Eubacterium xylanophilum group, Roseburia and Ruminococcus) known as primary contributors of anti-inflammatory metabolites, such as short-chain fatty acids. Such shift was observed after the first HTI dose and remained throughout the study follow-up (18 weeks). However, the enriched Clostridiales genera were different between feces and gut sections. The abundance of bacteria enriched in vaccinated animals positively correlated with HTI-specific T-cell responses and a set of pro-inflammatory cytokines, such as IL-6. This longitudinal analysis indicates that, in mice, T-cell vaccination may promote an increase in gut bacteria known to produce anti-inflammatory molecules, which in turn correlate with proinflammatory cytokines, suggesting an adaptation of the gut microbial milieu to T-cell-induced systemic inflammation.
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Wang Z, Jenabian MA, Alexandrova Y, Pagliuzza A, Olivenstein R, Samarani S, Chomont N, Kembel SW, Costiniuk CT. Interplay between the Lung Microbiome, Pulmonary Immunity and Viral Reservoirs in People Living with HIV under Antiretroviral Therapy. Viruses 2022; 14:v14112395. [PMID: 36366495 PMCID: PMC9693210 DOI: 10.3390/v14112395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 01/31/2023] Open
Abstract
Pulmonary dysbiosis may predispose people living with HIV (PLWH) to chronic lung disease. Herein, we assessed whether intrapulmonary HIV reservoir size and immune disruption are associated with reduced bacterial lung diversity in PLWH. Bacterial DNA was extracted and PCR-amplified from cell-free bronchoalveolar lavage (BAL) fluid from 28 PLWH and 9 HIV-negative controls. Amplicon sequence variant (ASV) relative abundances and taxonomic identities were analyzed using joint species distribution modeling. HIV-DNA was quantified from blood and pulmonary CD4+ T-cells using ultra-sensitive qPCR. Immunophenotyping of BAL T-cells was performed using flow cytometry. Lung microbiome diversity was lower in smokers than non-smokers and microbiome composition was more variable in PLWH than HIV-negative individuals. Frequencies of effector memory BAL CD4+ and CD8+ T-cells positively correlated with abundance of several bacterial families while frequencies of BAL activated CD4+ T-cells negatively correlated with abundance of most lung bacterial families. Higher HIV-DNA levels in blood, but not in BAL, as well as frequencies of senescent CD4+ T-cells were associated with reduced bacterial diversity. These findings suggest that HIV infection may weaken the relationship between the lung microbiome and smoking status. Viral reservoir and immune activation levels may impact the lung microbiome, predisposing PLWH to pulmonary comorbidities.
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Affiliation(s)
- Zihui Wang
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC H2X 1Y4, Canada
| | - Mohammad-Ali Jenabian
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC H2X 1Y4, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H3T 1J4, Canada
| | - Yulia Alexandrova
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC H2X 1Y4, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of MUHC, Montreal, QC H4A 3J1, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
| | | | | | - Suzanne Samarani
- Infectious Diseases and Immunity in Global Health Program, Research Institute of MUHC, Montreal, QC H4A 3J1, Canada
| | - Nicolas Chomont
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H3T 1J4, Canada
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Steven W. Kembel
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC H2X 1Y4, Canada
| | - Cecilia T. Costiniuk
- Infectious Diseases and Immunity in Global Health Program, Research Institute of MUHC, Montreal, QC H4A 3J1, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada
- Division of Infectious Diseases and Chronic Viral Illness Service, McGill University Health Centre, Montreal, QC H4A 3J1, Canada
- Correspondence: ; Tel.: +1-(514)-843-2090; Fax: +1-(514)-843-2092
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