Human vaginal microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1081423 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32297200_1.fastq.gz | Fastqsanger.gz | |||
| SRR32297200_2.fastq.gz | Fastqsanger.gz | |||
| SRR32297201_1.fastq.gz | Fastqsanger.gz | |||
| SRR32297201_2.fastq.gz | Fastqsanger.gz | |||
| SRR32297202.fastq.gz | Fastqsanger.gz |
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Project description:Progestin-based contraception may increase the risk of vaginal HIV acquisition to a level greater than the progesterone-rich luteal phase of the menstrual cycle, which has been demonstrated to have a significantly higher transmission rate compared to the follicular phase. We used pig-tailed macaque (Macaca nemestrina) model to evaluate the effects of administration of the oral the combined oral contraceptives (COCs) depot medroxyprogesterone acetate (DMPA) and levonorgestrel (LNG) on mucosal factors that influence HIV susceptibility. We compared the pH and vaginal epithelial thickness data from previous studies, and evaluated contraception-induced molecular changes in the vagina using transcriptional and cytokine profiling. The administration of DMPA caused a pronounced thinning of the vaginal epilthelium relative to measurements takein in the follicular or luteal phase. DMPA also induced a significant increase in vaginal IL10 expression. Lastly, using RNA-Seq analyses of vaginal biopsies, we noted that both DMPA- and LNG-based contraception induced a signature of gene expression similar to that of the luteal phase, only more exacerbated, and including widespread down-regulation of HIV-restriction genes. Use of progestin-based contraception might engender a milieu that poses an increased risk of HIV transmission than that of the luteal phase via vaginal thinning, induction of immunosuppressive cytokines, and widespread suppression of HIV restriction factors.
2020-06-07 | GSE99800 | GEO
Project description:Use of hormonal contraceptives (HC) could alter the bacterial community, immune response and epithelial barrier integrity of the female genital tract (FGT) mucosal environment, leading to increased susceptibility to sexually transmitted infections (STIs), including HIV. Here, we tested whether use of three types of HCs, injectable Net-En, combined oral contraceptives (COC) and NuvaRing, a combined contraceptive vaginal ring (CCVR), led to distinct patterns in FGT host transcriptomics transcriptome in South African adolescent females. In an intention-to-treat analysis, we observed few changes in endocervical gene expression in the Net-En and COC groups. Relative to the COC and Net-En arms, samples from the CCVR arm had significant elevation of transcriptional networks driven by IL-6, IL-1 and NFKB, and lower expression of genes supporting epithelial barrier integrity. An integrated multivariate analysis of the cervicovaginal microbiome, transcriptome and cytokines demonstrated that networks of microbial dysbiosis and inflammation accurately discriminated the CCVR arm from the other contraceptive groups, while genes involved in epithelial cell differentiation were predictive of the Net-En and COC arms.
2022-07-11 | GSE171825 | GEO
Project description:During sexual transmission of HIV-1 from male to female partners, the vagina is the initial site of contact with HIV infected semen. The mechanism of HIV traversing the CD4 negative multi-layered stratified squamous epithelial barrier of the vagina to infect sub-epithelial susceptible immune cells, is hitherto unknown. HIV gp120 binds to several host proteins on vaginal epithelial cells. To gain an insight into the physiologic changes that may occur in vaginal epithelial cells in response to interactions with HIV gp120, and obtain an understanding of the molecular mechanisms by which HIV breaches the vaginal epithelium, a global snap shot of gene expression profiles in the vaginal epithelial cell line Vk2/E6E7, treated with HIV gp120 was determined. The vaginal epithelial cell line Vk2/E6E7 was treated with HIV gp120 (83nM) for 24 hr, and Agilent one colour, microarrays were performed.
2014-03-01 | GSE44914 | GEO
Project description:During sexual transmission of HIV-1 from male to female partners, the vagina is the initial site of contact with HIV infected semen. The mechanism of HIV traversing the CD4 negative multi-layered stratified squamous epithelial barrier of the vagina to infect sub-epithelial susceptible immune cells, is hitherto unknown. HIV gp120 binds to several host proteins on vaginal epithelial cells. To gain an insight into the physiologic changes that may occur in vaginal epithelial cells in response to interactions with HIV gp120, and obtain an understanding of the molecular mechanisms by which HIV breaches the vaginal epithelium, a global snap shot of gene expression profiles in the vaginal epithelial cell line Vk2/E6E7, treated with HIV gp120 was determined. The vaginal epithelial cell line Vk2/E6E7 was treated with HIV gp120 (83nM) for 24 hr, and Agilent one colour, microarrays were performed. Agilent one-color experiment,Organism: Human ,Agilent-Custom Whole Genome Human 8x60k designed by Genotypic Technology Pvt. Ltd. (AMADID: 027114), Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2014-03-01 | E-GEOD-44914 | biostudies-arrayexpress
Project description:Epidemiological studies indicate that progestin-containing contraceptives may increase susceptibility to HIV and other infections; however, underlying mechanisms involving the upper female reproductive tract are undefined. To determine the effects of depot medroxyprogesterone acetate (DMPA) and the levonorgestrel intrauterine system (LNG-IUS) on gene expression and physiology of the human endometrial and cervical transformation zone (TZ), microarray analyses were performed on whole tissue biopsies. In endometrium, activated pathways included leukocyte chemotaxis, attachment, and inflammation in DMPA (z>2.5) and LNG-IUS (z>3.5) users, and regulation of pattern recognition receptors and other immune mediators. In cervical TZ, progestin treatment altered expression of tissue remodeling and viability genes, but not those of immune functions. Together, these results indicate that progestins influence expression of immune-related genes in endometrium that would be expected to result in the local recruitment of HIV target cells, and thus may increase HIV susceptibility. It is important to consider the upper reproductive tract in the assessment of effects of contraceptives that may influence susceptibility to pathogens, such as HIV. Cross-sectional study conducted at an academic medical center. Cervical transformation zone and endometrial biopsies were obtained from 3 groups of volunteers: those using no hormonal contraceptives (controls, mid-secretory phase, n=20 cervix, 11 endometrium), DMPA users (150mg, n=15, 8), or LNG-IUS users (n=17, 13). DMPA and LNG-IUS groups had used these contraceptives for at least 6 months.
2014-11-21 | E-GEOD-60129 | biostudies-arrayexpress
Project description:Clinical treatment protocols for infertility with in vitro fertilization-embryo transfer (IVF-ET) provide a unique opportunity to assess the human vaginal microbiome in defined hormonal milieu. Herein, we have investigated the association of circulating ovarian-derived estradiol (E2) and progesterone (P4) concentrations to the vaginal microbiome. Thirty IVF-ET patients were enrolled in this study, after informed consent. Blood was drawn at four time points during the IVF-ET procedure. In addition, if a pregnancy resulted, blood was drawn at 4-to-6 weeks of gestation. The serum concentrations of E2 and P4 were measured. Vaginal swabs were obtained in different hormonal milieu. Two independent genome-based technologies (and the second assayed in two different ways) were employed to identify the vaginal microbes. The vaginal microbiome underwent a transition with a decrease in E2 (and/or a decrease in P4). Novel bacteria were found in the vagina of 33% of the women undergoing IVF-ET. Our approach has enabled the discovery of novel, previously unidentified bacterial species in the human vagina in different hormonal milieu. While the relationship of hormone concentration and vaginal microbes was found to be complex, the data support a shift in the microbiome of the human vagina during IVF-ET therapy using standard protocols. The data also set the foundation for further studies examining correlations between IVF-ET outcome and the vaginal microbiome within a larger study population.
2011-10-24 | E-MEXP-2958 | biostudies-arrayexpress
Project description:Menstrual cups, maturation of the adolescent vaginal microbiome, and STI/HIV risk
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Project description:Epidemiological studies indicate that progestin-containing contraceptives may increase susceptibility to HIV and other infections; however, underlying mechanisms involving the upper female reproductive tract are undefined. To determine the effects of depot medroxyprogesterone acetate (DMPA) and the levonorgestrel intrauterine system (LNG-IUS) on gene expression and physiology of the human endometrial and cervical transformation zone (TZ), microarray analyses were performed on whole tissue biopsies. In endometrium, activated pathways included leukocyte chemotaxis, attachment, and inflammation in DMPA (z>2.5) and LNG-IUS (z>3.5) users, and regulation of pattern recognition receptors and other immune mediators. In cervical TZ, progestin treatment altered expression of tissue remodeling and viability genes, but not those of immune functions. Together, these results indicate that progestins influence expression of immune-related genes in endometrium that would be expected to result in the local recruitment of HIV target cells, and thus may increase HIV susceptibility. It is important to consider the upper reproductive tract in the assessment of effects of contraceptives that may influence susceptibility to pathogens, such as HIV.
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Project description:Pre-exposure chemoprophylaxis using antiretroviral agents is a promising strategy for the prevention of sexual HIV transmission in women. Molecular transporters in the human vaginal tract may play a pivotal role in determining drug disposition and, consequently, pharmacodynamic outcomes in these efforts. Little is known, however, on the expression of these transporters in vaginal tissues, representing a critical knowledge gap. Our study analyzed the genome-wide transcriptome in 44 vaginal tissue samples from 6 reproductive-age women undergoing gynecologic surgeries. The genome-wide transcriptome in 44 vaginal tissue samples from 6 reproductive-age women (20-56 years old) undergoing gynecologic surgeries was measured.
2014-01-29 | E-GEOD-49892 | biostudies-arrayexpress