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Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle

ABSTRACT: Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle

PROVIDER: PRJNA504398 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8169740.fastq.gz	Fastqsanger.gz
	SRR8169750.fastq.gz	Fastqsanger.gz
	SRR8169760.fastq.gz	Fastqsanger.gz
	SRR8169770.fastq.gz	Fastqsanger.gz
	SRR8169741.fastq.gz	Fastqsanger.gz

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Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle

Project description:Despite extensive studies suggesting increased susceptibility to HIV during the secretory phase of the menstrual cycle, there is limited knowledge of the molecular mechanisms involved. We aimed to explore the ectocervical and endocervical tissue transcriptomes during the proliferative and secretory phases of the cycle using RNA sequencing (RNAseq) to identify potential signatures of susceptibility to HIV. We utilized hysterectomy tissue specimens from subjects not using hormonal contraception/treatment for gynecological conditions. Ectocervical (n=10) and endocervical tissues (n=15) were used for this study. The cycle phase was determined by assessing the histopathology of hematoxylin-and-eosin stained sections of the endometrial mucosa by gynecologic pathologists. Total RNA was isolated from tissues frozen in RNAlater (Ambion) following manufacturer’s instructions (Qiagen RNeasy Fibrous Tissue Mini Kit). After extraction, the quality and the purity of the RNA were measured by the Agilent Bioanalyzer (Agilent, Santa Clara, CA). RNA was labeled and sequenced at the RU Genomics center by using Illumina TruSeq technology (75bp, >30M coverage). The data were analyzed using Ingenuity Pathway Analysis (IPA) software (QIAGEN Inc., https://www.qiagenbioinformatics.com/products/ingenuitypathway-analysis). To inquire into changes in gene expression irrespectively of p-value cut off, pre-ranked genes based on proliferative vs. secretory phase expression were subjected to Gene Set Enrichment Analysis (GSEA) against the Hallmark Gene sets (H) and Immunologic Signatures Gene sets (collection C7) from the Molecular Signatures Database (MSigDB)(http://software.broadinstitute.org/gsea/msigdb/index.jsp). Our data show menstrual cycle phase-associated changes in the transcriptomic landscape of the endocervix and ectocervix, some of which may contribute to changes in HIV susceptibility.

2019-09-25 | GSE122248 | GEO

Plasma microRNA profiles in women with and without endometriosis at different menstrual cycle phases

Project description:The objectives of the study: 1. Does the phase of the menstrual cycle alter microRNA (miRNA) plasma profiles in healthy women of reproductive age and in women with endometriosis? 2. Does this alter prospects for development of a miRNA-based diagnostic test for endometriosis? Prospectively recruited asymptomatic control women and women with surgically diagnosed endometriosis (n = 8 in each group) were included. Each patient provided blood samples in the early proliferative, late proliferative and mid luteal phases of the menstrual cycle (n = 47 total plasma samples). The cycle phase was verified by hormonal profile. RNA was extracted from each sample and expression of microRNAs was assessed using TaqMan Low Density Human miRNA arrays.

2013-05-09 | E-GEOD-46735 | biostudies-arrayexpress

Transcription profiling of human endometrium from patients with a history of endometriosis vs. normal controls sampled at a range of menstrual cycle timepoints reveals progesterone resistance and candidate susceptibility genes in women with endometriosis

Project description:The transition of regularly cycling endometrium from the proliferative or Estrogen-dominant phase of the menstrual cycle to the Progesterone-dominant Early and Mid Secretory phases requires wide-spread changes in gene expression that shift the endometrium from a proliferative capacity to a differentiated 'decidual' phenotype in preparation for implantation. This process appears delayed in women with severe endometriosis, suggestive of a progesterone resistant endometrium in this disease. Experiment Overall Design: Endometrial biopsies were obtained from women both with normal endometrial pathologies and no history of endometriosis and from women with laporoscopy proven moderate-severe stage endometriosis. Samples were collected from the Proliferative(PE), Early Secretory (ESE) and Midsecretory (MSE) phases. Samples were then processed for Total RNA isolation and Affymetrix chip hybridization.

2008-04-09 | E-GEOD-6364 | biostudies-arrayexpress

Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle.

Project description:Despite extensive studies suggesting increased susceptibility to HIV during the secretory phase of the menstrual cycle, the molecular mechanisms involved remain unclear. Our goal was to analyze transcriptomes of the endocervix and ectocervix during the proliferative and secretory phases using RNA sequencing to explore potential molecular signatures of susceptibility to HIV. We identified 202 differentially expressed genes (DEGs) between the proliferative and secretory phases of the cycle in the endocervix (adjusted p < 0.05). The biofunctions and pathways analysis of DEGs revealed that cellular assembly and epithelial barrier function in the proliferative phase and inflammatory response/cellular movement in the secretory phase were among the top biofunctions and pathways. The gene set enrichment analysis of ranked DEGs (score = log fold change/p value) in the endocervix and ectocervix revealed that (i) unstimulated/not activated immune cells gene sets positively correlated with the proliferative phase and negatively correlated with the secretory phase in both tissues, (ii) IFNγ and IFNα response gene sets positively correlated with the proliferative phase in the ectocervix, (iii) HIV restrictive Wnt/β-catenin signaling pathway negatively correlated with the secretory phase in the endocervix. Our data show menstrual cycle phase-associated changes in both endocervix and ectocervix, which may modulate susceptibility to HIV.

| S-EPMC6749057 | biostudies-literature

Biomarker discovery in pre-menstrual endometrial biopsies

Project description:The endometrium undergoes profound progesterone-driven remodeling during the secretory phase of the menstrual cycle in a process called decidualization. In the absence of pregnancy, circulating progesterone levels fall and tissue-wide inflammation and influx of neutrophils precede tissue breakdown and menstrual shedding. These changes are accompanied by wide-scale transcriptomic changes that co-ordinate temporal changes throughout the secretory phase. Here, we sequenced whole endometrial biopsies to identify molecular biomarkers that mark specific stages of the secretory phase, including pre-menstrual tissues. 20 biopsies were timed to specific phases of the secretory cycle based on the donor’s reported LH, the physical morphology of tissues observed via IHC and serum progesterone levels.

2024-10-27 | GSE246529 | GEO

Mucosal Susceptibility to Human Immunodeficiency Virus Infection in the Proliferative and Secretory Phases of the Menstrual Cycle.

Project description:Factors underlying HIV acquisition in women remain incompletely understood. This study evaluated ex vivo mucosal HIV-1BaL infection (ectocervix, endocervix), T cell frequencies and phenotype (ectocervix, endocervix, peripheral blood), and HIV-1BaL-induced tissue immune responses (ectocervix) in the proliferative and secretory phases of the menstrual cycle using samples obtained from women undergoing hysterectomies. Tissue infectivity (number of productively infected explants) and infection level following 500 and/or fifty 50% tissue culture infectious dose (TCID50) HIV-1BaL challenge were similar in the proliferative and secretory phases. Although not associated with infection outcomes, higher frequencies of HIV target CD4+α4β7+ T cells, and stronger HIV-1BaL-induced proinflammatory responses were detected in ectocervix in the secretory versus proliferative phase. Independently of the cycle phase, serum E2 concentrations were inversely associated with ectocervical and endocervical tissue infection levels following high-dose 500 TCID50 HIV-1BaL challenge, with frequencies of CD4+α4β7+ T cells in endocervix, and with HIV-induced interleukin (IL)2R and IL4 in ectocervix. Although serum P4 concentrations and P4/E2 ratios were neither associated with tissue infection level nor infectivity, high P4 concentrations and/or P4/E2 ratios correlated with high frequencies of CD4+α4β7+ T cells in ectocervix, low frequencies of CD4+CD103+ blood T cells, low CD4+LFA-1+ T cells in endocervix, and high proinflammatory (IL1β, IL17, tumor necrosis factor α) ectocervical tissue responses to HIV-1BaL. The data suggest an inhibitory effect of E2 on mucosal HIV infection, provide insights into potential mechanisms of E2-mediated anti-HIV activity, and highlight P4-associated immune changes in the mucosa.

| S-EPMC6442278 | biostudies-literature

Genome-wide expression analysis of autologous eutopic and ectopic endometrium from fertile Indian women with endometriosis

Project description:Whole genome expression analyses of autologous, paired eutopic and ectopic endometrial samples obtained during proliferative and secretory phases of menstrual cycles from eighteen (n=18) fertile women suffering from confirmed stage 3 (moderate) and stage 4 (severe) ovarian endometriosis were performed using whole human genome oligo microarray Agilent paltform (Cat. No. G4112F). In the present study, genome-wide expression analysis of autologous, paired eutopic and ectopic endometrial samples obtained during proliferative (n=13) and secretory (n=5) phases of menstrual cycle from fertile women (n=18) suffering from moderate (stage 3; n=8) or severe (stage 4; n=10) endometrioma was performed by using Agilent single color oligo microarray platform (G4112, 4X44K). Thus eighteen (18) eutopic (shown as EU) and eighteen (18) ectopic (shown as EC) samples from eighteen (18) subjects with confirmed menstrual phase (proliferative and secretory) and severity stages (stage 3 and stage 4) were studied.

2012-09-30 | E-GEOD-37837 | biostudies-arrayexpress

Transcriptional Profiling of Human Endocervical Tissues Reveals Distinct Gene Expression in the Follicular and Luteal Phases of the Menstrual Cycle

Project description:The goal of this study was to identify genes differentially expressed in the follicular and luteal phases of the menstrual cycle in the human endocervix and to identify significantly represented biological pathways and processes. This was done in order to better understand mechanisms associated with hormonal regulation of endocervix function which has implications in susceptibility to infections.

2016-05-12 | GSE80455 | GEO

Transcriptomic analysis and competing endogenous RNA network in the human endometrium between proliferative and mid-secretory phases

Project description:Transcriptomic analysis and competing endogenous RNA network in the human endometrium between proliferative and mid-secretory phases

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Transcriptomic analysis and competing endogenous RNA network in the human endometrium between proliferative and mid-secretory phases

Project description:To identify differentially expressed transcripts (long-noncoding RNAs [lncRNAs], microRNAs [miRNAs], and mRNAs) and competing endogenous RNA (ceRNA) networks closely connected with endometrial receptivity, we analyzed gene expression profiles between the proliferative and mid-secretory endometria in fertile women.

2021-02-24 | GSE167325 | GEO

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