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Edfeldt G, Kaldhusdal V, Czarnewski P, Bradley F, Bergström S, Lajoie J, Xu J, Månberg A, Kimani J, Oyugi J, Nilsson P, Tjernlund A, Fowke KR, Kwon DS, Broliden K. Distinct cervical tissue-adherent and luminal microbiome communities correlate with mucosal host gene expression and protein levels in Kenyan sex workers. Microbiome 2023; 11:67. [PMID: 37004130 PMCID: PMC10064689 DOI: 10.1186/s40168-023-01502-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 02/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The majority of studies characterizing female genital tract microbiota have focused on luminal organisms, while the presence and impact of tissue-adherent ectocervical microbiota remain incompletely understood. Studies of luminal and tissue-associated bacteria in the gastrointestinal tract suggest that these communities may have distinct roles in health and disease. Here, we performed a multi-omics characterization of paired luminal and tissue samples collected from a cohort of Kenyan female sex workers. RESULTS We identified a tissue-adherent bacterial microbiome, with a higher alpha diversity than the luminal microbiome, in which dominant genera overall included Gardnerella and Lactobacillus, followed by Prevotella, Atopobium, and Sneathia. About half of the L. iners-dominated luminal samples had a corresponding Gardnerella-dominated tissue microbiome. Broadly, the tissue-adherent microbiome was associated with fewer differentially expressed host genes than the luminal microbiome. Gene set enrichment analysis revealed that L. crispatus-dominated tissue-adherent communities were associated with protein translation and antimicrobial activity, whereas a highly diverse microbial community was associated with epithelial remodeling and pro-inflammatory pathways. Tissue-adherent communities dominated by L. iners and Gardnerella were associated with lower host transcriptional activity. Tissue-adherent microbiomes dominated by Lactobacillus and Gardnerella correlated with host protein profiles associated with epithelial barrier stability, although with a more pro-inflammatory profile for the Gardnerella-dominated microbiome group. Tissue samples with a highly diverse composition had a protein profile representing cell proliferation and pro-inflammatory activity. CONCLUSION We identified ectocervical tissue-adherent bacterial communities in all study participants of a female sex worker cohort. These communities were distinct from cervicovaginal luminal microbiota in a significant proportion of individuals. We further revealed that bacterial communities at both sites correlated with distinct host gene expression and protein levels. The tissue-adherent bacterial community could possibly act as a reservoir that seed the lumen with less optimal, non-Lactobacillus, bacteria. Video Abstract.
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Affiliation(s)
- Gabriella Edfeldt
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Vilde Kaldhusdal
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Solna, Sweden
| | - Frideborg Bradley
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Julie Lajoie
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jiawu Xu
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joshua Kimani
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Partners for Health and Development in Africa, Nairobi, Kenya
| | - Julius Oyugi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annelie Tjernlund
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden
| | - Keith R Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Partners for Health and Development in Africa, Nairobi, Kenya
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Kristina Broliden
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, J7:20, S-171 76, Stockholm, Sweden.
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Boucher J, Rousseau A, Boucher C, Subra C, Bazié WW, Hubert A, Bourgeault E, Benmoussa A, Goyer B, Tessier PA, Gilbert C. Immune Cells Release MicroRNA-155 Enriched Extracellular Vesicles That Promote HIV-1 Infection. Cells 2023; 12:cells12030466. [PMID: 36766808 PMCID: PMC9914104 DOI: 10.3390/cells12030466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The hallmark of HIV-1 infection is the rapid dysregulation of immune functions. Recent investigations for biomarkers of such dysregulation in people living with HIV (PLWH) reveal a strong correlation between viral rebound and immune activation with an increased abundance of extracellular vesicles (EVs) enriched with microRNA-155. We propose that the activation of peripheral blood mononuclear cells (PBMCs) leads to an increased miR-155 expression and production of miR-155-rich extracellular vesicles (miR-155-rich EVs), which can exacerbate HIV-1 infection by promoting viral replication. PBMCs were incubated with either HIV-1 (NL4.3Balenv), a TLR-7/8 agonist, or TNF. EVs were harvested from the cell culture supernatant by differential centrifugation, and RT-qPCR quantified miR-155 in cells and derived EVs. The effect of miR-155-rich EVs on replication of HIV-1 in incubated PBMCs was then measured by viral RNA and DNA quantification. HIV-1, TLR7/8 agonist, and TNF each induced the release of miR-155-rich EVs by PBMCs. These miR-155-rich EVs increased viral replication in PBMCs infected in vitro. Infection with HIV-1 and inflammation promote the production of miR-155-rich EVs, enhancing viral replication. Such autocrine loops, therefore, could influence the course of HIV-1 infection by promoting viral replication.
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Affiliation(s)
- Julien Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Alyssa Rousseau
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Catherine Boucher
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Caroline Subra
- U.S. Military HIV Research Program, Silver Spring, MD 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Wilfried W. Bazié
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
- Programme de Recherche sur les Maladies Infectieuses, Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso 01 BP 390, Burkina Faso
| | - Audrey Hubert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Emma Bourgeault
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Abderrahim Benmoussa
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Benjamin Goyer
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
| | - Philippe A. Tessier
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Caroline Gilbert
- Axe de Recherche Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1V 4G2, Canada
- Département de Microbiologie-Infectiologie et d’Immunologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 46107); Fax: +1-418-654-2765
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Bradley F, Franzén Boger M, Kaldhusdal V, Åhlberg A, Edfeldt G, Lajoie J, Bergström S, Omollo K, Damdimopoulos A, Czarnewski P, Månberg A, Oyugi J, Kimani J, Nilsson P, Fowke K, Tjernlund A, Broliden K. Multi-omics analysis of the cervical epithelial integrity of women using depot medroxyprogesterone acetate. PLoS Pathog 2022; 18:e1010494. [PMID: 35533147 PMCID: PMC9119532 DOI: 10.1371/journal.ppat.1010494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 05/19/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022] Open
Abstract
Depot medroxyprogesterone acetate (DMPA) is an injectable hormonal contraceptive used by millions of women worldwide. However, experimental studies have associated DMPA use with genital epithelial barrier disruption and mucosal influx of human immunodeficiency virus (HIV) target cells. We explored the underlying molecular mechanisms of these findings. Ectocervical biopsies and cervicovaginal lavage (CVL) specimens were collected from HIV-seronegative Kenyan sex workers using DMPA (n = 32) or regularly cycling controls (n = 64). Tissue samples were assessed by RNA-sequencing and quantitative imaging analysis, whereas protein levels were measured in CVL samples. The results suggested a DMPA-associated upregulation of genes involved in immune regulation, including genes associated with cytokine-mediated signaling and neutrophil-mediated immunity. A transcription factor analysis further revealed DMPA-associated upregulation of RELA and NFKB1 which are involved in several immune activation pathways. Several genes significantly downregulated in the DMPA versus the control group were involved in epithelial structure and function, including genes encoding keratins, small proline-rich proteins, and cell-cell adhesion proteins. Pathway analyses indicated DMPA use was associated with immune activation and suppression of epithelium development, including keratinization and cornification processes. The cervicovaginal microbiome composition (Lactobacillus dominant and non-Lactobacillus dominant) had no overall interactional impact on the DMPA associated tissue gene expression. Imaging analysis verified that DMPA use was associated with an impaired epithelial layer as illustrated by staining for the selected epithelial junction proteins E-cadherin, desmoglein-1 and claudin-1. Additional staining for CD4+ cells revealed a more superficial location of these cells in the ectocervical epithelium of DMPA users versus controls. Altered protein levels of SERPINB1 and ITIH2 were further observed in the DMPA group. Identification of specific impaired epithelial barrier structures at the gene expression level, which were verified at the functional level by tissue imaging analysis, illustrates mechanisms by which DMPA adversely may affect the integrity of the genital mucosa. Sexual transmission accounts for the majority of all new HIV infections in women, and alterations to the mucosal environment of the female genital tract have been associated with an increase in the risk of acquiring HIV. Observational epidemiological studies have implied that the use of the injectable hormonal contraceptive depot medroxyprogesterone acetate (DMPA) may be associated with increased HIV-acquisition. However, a prospective clinical study has not confirmed this association and the controversial findings are currently evaluated in the context of international reproductive health policies. Several studies using various model systems indicate that DMPA affects the integrity of the genital epithelial barrier as well as the mucosal immune system, but the exact mechanisms remain largely unknown. To characterize the effect of DMPA on the genital mucosal environment, we used a multi-omics approach to assess paired genital secretions and cervical tissue samples from long-term regular DMPA users living in Kenya. This unique cohort represents a population at risk of HIV infection in which DMPA is one of the most commonly used hormonal contraceptives. We identified impaired cervical epithelial barrier structures, including DMPA-associated reduction in the expression of cell-cell adhesion molecules, keratins, small proline-rich proteins and a thinner upper epithelial layer with more superficially located CD4+ cells. Gene set enrichment pathway analyses indicated DMPA use was associated with immune activation and suppression of epithelium development including keratinization and cornification pathways. Protein analysis identified altered levels of selected anti-proteases. Our findings illustrate mechanisms by which DMPA adversely may affect the integrity of the genital mucosa.
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Affiliation(s)
- Frideborg Bradley
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
| | - Mathias Franzén Boger
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
| | - Vilde Kaldhusdal
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
| | - Alexandra Åhlberg
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
| | - Gabriella Edfeldt
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
| | - Julie Lajoie
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Sofia Bergström
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Kenneth Omollo
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Paulo Czarnewski
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, SciLifeLab, Stockholm University, Solna, Sweden
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Julius Oyugi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Joshua Kimani
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Partners for Health and Development in Africa, Nairobi, Kenya
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Keith Fowke
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Partners for Health and Development in Africa, Nairobi, Kenya
- Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Annelie Tjernlund
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
| | - Kristina Broliden
- Department of Medicine Solna, Division of Infectious Diseases, Karolinska Institutet, Department of Infectious Diseases, Karolinska University Hospital, Center for Molecular Medicine, Stockholm, Sweden
- * E-mail:
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Röhl M, Tjernlund A, Lajoie J, Edfeldt G, Bradley F, Bergström S, Kaldhusdal V, Åhlberg A, Månberg A, Omollo K, Boily-Larouche G, Asghar M, Kwon DS, Oyugi J, Kimani J, Nilsson P, Fowke KR, Broliden K. HIV-Exposed Seronegative Sex Workers Express Low T-Cell Activation and an Intact Ectocervical Tissue Microenvironment. Vaccines (Basel) 2021; 9:217. [PMID: 33806390 DOI: 10.3390/vaccines9030217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Immunological correlates of natural resistance to HIV have been identified in HIV-exposed seronegative (HESN) individuals and include a low-inflammatory genital mucosal status. The cervicovaginal epithelium has not been studied for such correlates despite constituting an important barrier against sexual HIV transmission. To fill this gap in knowledge, we collected samples of blood, cervical mononuclear cells, cervicovaginal lavage, and ectocervical tissue from Kenyan HESN sex workers (n = 29) and controls (n = 33). The samples were analyzed by flow cytometry, protein profiling, 16S rRNA gene sequencing, in situ image analysis, and tissue-based RNA sequencing. A significantly higher relative proportion of regulatory T cells in blood (B7+CD25hiFoxP3+CD127loCD4+ and B7+Helios+FoxP3+CD4+), and a significantly lower proportion of activated cervical T cells (CCR5+CD69+CD4+ and CCR5+CD69+CD8+), were found in the HESN group compared with the controls. In contrast, there were no statistically significant differences between the study groups in cervicovaginal protein and microbiome compositions, ectocervical epithelial thickness, E-cadherin expression, HIV receptor expression, and tissue RNA transcriptional profiles. The identification of an intact ectocervical microenvironment in HESN individuals add new data to current knowledge about natural resistance to sexual transmission of HIV.
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