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Gut microbiota-derived short-chain fatty acids protect against the progression of endometriosis

ABSTRACT: The goal of this study is to compare transcriptome profiling of n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc) by RNA-sequencing Methods: The mRNA profiles of vehicle and n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc) were generated by deep sequencing, in triplicate using Illumina NovaSeq-6000 sequencers with 2×150 paired-end reads. Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a. qRT–PCR validation was performed using TaqMan assays. Results: Using a 2.5-fold cutoff and Benjamini-Hochberg false discovery rate (FDR) of <0.01 threshold for inclusion, we identified 1,830 differentially expressed genes (DEGs) between Vehicle and n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc). Conclusions: Our study represents the first detailed analysis of n-butyrate treated immortalized human endometriotic epithelial cells expression Luciferase (iHEECs/Luc) transcriptomes, with biologic replicates, generated by RNA-seq technology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE184431 | GEO | 2021/09/29

REPOSITORIES: GEO

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Early growth response 1 transcription factor is essential for the pathogenic properties of human endometriotic epithelial cells

Project description:The aim of this study is to compare transcriptome profiling of EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase (iHEECs/Luc) by RNA-sequencing Methods: The mRNA profiles of non-targeting (NT) and EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase (iHEECs/Luc) were generated by deep sequencing, in triplicate using Illumina NovaSeq-6000 sequencers with 2×100 paired-end reads. Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the human genome (Genome Reference Consortium Human Build hg38) with STAR version 2.5.1a. qRT–PCR validation was performed using TaqMan assays. Results: Using a 1.5-fold cutoff and Benjamini-Hochberg false discovery rate (FDR) of <0.05 threshold for inclusion, we identified 76 differentially expressed genes (DEGs) between (NT) and EGR1 siRNA treated immortalized human endometriotic epithelial cells. Conclusions: Our study represents the first detailed analysis of EGR1 siRNA treated immortalized human endometriotic epithelial cells expression luciferase (iHEECs/Luc) transcriptomes, with biologic replicates, generated by RNA-seq technology.

2022-11-15 | GSE199526 | GEO

Epigenetic regulation in small intestinal epitheliel cells with butyrate exposure

Project description:H3K9Ac enrichment in intestinal epithelial cells from the intestine of WT mice treated with vehicle or buytrate for 7 days. Intestinal epithelial cells were harvested from the terminal ileum of vehicle or butyrate treated mice. Chromatin immunoprecipitation was performed with anti-H3K9Ac. Sequencing was performed using the Illumina and reads were mapped to mm10 genome using STAR Aligner.

2024-03-06 | GSE249959 | GEO

The effects of testosterone and lipopolysaccharide on gene expression in immortalized ocular surface and adnexal cells

Project description:Immortalized human corneal, conjunctival, and meibomian gland epithelial cells were pre-treated with dihydrotesteosterone (DHT) or vehicle, then exposed to lipopolysaccharide (LPS) and ligand binding protein (LBP) or vehicle, lysed, and subjected to microarray analysis of RNA expression.

2018-03-07 | GSE111496 | GEO

Endometriotic Organoids: A Novel In Vitro Model of Endometriotic Lesion Development

Project description:The development and progression of endometriotic lesions are poorly understood, but immune cell dysfunction and inflammation are closely associated with the pathophysiology of endometriosis. A lack of suitable 3D in vitro models permitting the study of interactions between cell types and the microenvironment is a contributing factor. To address this limitation, we developed endometriotic organoids (EO) to explore the role of epithelial-stromal interactions and model peritoneal cell invasion associated with lesion development. Using a non-adherent microwell culture system, spherical organoids were generated with endometriotic epithelial cells (12Z) combined with immortalized endometriotic stromal cells (iEc-ESC) or immortalized uterine stromal cells (iHUF). Organoids self-organized with stromal cells occupying the center and epithelial cells on the periphery of the organoid. Endometriotic organoids (EO), containing iEc-ESC, resulted in the development of stratified 12Z epithelial cells compared to those with iHUF where the 12Z cells developed as a single layered epithelium. Transcriptomic analysis found 4,522 differentially expressed genes (DEG) between EO and 12Z/iHUF organoids, and the top DEG included increased expression of interleukins and prostaglandin synthase enzymes. An overlap of the EO DEG with baboon endometriotic lesions was highly significant. Finally, to mimic invasion of endometrial tissue into the peritoneum, a model was developed using EO and extracellular matrix containing human peritoneal mesothelial cells (LP9). Invasion of EO into the extracellular matrix-LP9 layer was increased in presence of estrogen or THP1-derived proinflammatory macrophages. Taken together, our results strongly support the concept that EO are an appropriate model for dissecting mechanisms that contribute to endometriotic lesion development.

2022-06-15 | GSE202661 | GEO

Dihydrotestosterone induced changes in gene expression in immortalized human meibomian gland epithelial cells

Project description:Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in immortalized human meibomian gland epithelial cells. Analysis of regulation of immortalized human meibomian gland epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like meibomian gland cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation of numerous genes in response to dihydrotestosterone incubation of immortalized human meibomian gland epithelial cells. Total RNA was obtained from immortalized human meibomian gland epithelial cells treated for 72 hours with 10 nM dihydrotestosterone (n=3) or vehicle (n=3). The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in an immortalized human meibomian epithelial cell line developed in our laboratory.

2011-03-31 | E-GEOD-18091 | biostudies-arrayexpress

Dihydrotestosterone induced changes in gene expression in immortalized human conjunctival epithelial cells

Project description:Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in immortalized human conjunctival epithelial cells. Analysis of regulation of immortalized human conjunctival epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like conjunctival cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation of numerous genes in response to dihydrotestosterone incubation of immortalized human conjunctival epithelial cells. Total RNA was obtained from immortalized human conjunctival epithelial cells treated for 96 hours with 10 nM dihydrotestosterone (n=3) or vehicle (n=3). The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in an immortalized human conjunctival epithelial cell line developed in Dr. Rheinwald's laboratory [Rheinwald et al. MCB, 22 (14): 5157. (2002)] and charecterized in Dr. Ilene Gibson's laboratory [Gipson et al. IOVS, 44 (6): 2496. (2003)].

2011-03-31 | E-GEOD-18094 | biostudies-arrayexpress

RNA sequencing of mouse basal-derived prostate organoids treated with vehicle, UK5099, Butyrate, or UK5099+Butyrate

Project description:The goal of this study was to perform transcriptomics on vehicle-, UK5099-, Butyrate-, and UK5099+Butyrate-treated mouse prostate organoids. We used FACS to isolate basal cells from C57BL/6 mouse prostates and treated with small molecules for one week before harvesting for RNA-sequencing.

2023-09-01 | GSE236573 | GEO

Dihydrotestosterone induced changes in gene expression in primary and immortalized human corneal epithelial cells

Project description:Genome-wide analysis of dihydrotestosterone (DHT) induced changes in gene expression in primary and immortalized human corneal epithelial cells. Analysis of regulation of primary and immortalized human corneal epithelial cells by dihydrotestosterone at gene expression level. The hypothesis tested in the present study was that the androgen-eye interaction in ocular surface epithelial cells like corneal cells is influenced by androgens through regulation of the expression of multiple genes. Results provide important information of the differential regulation and comparitive analysis of numerous genes in response to dihydrotestosterone incubation in primary and immortalized human corneal epithelial cells. Total RNA was obtained from primary and immortalized human corneal epithelial cells treated for 5 days with 10 nM dihydrotestosterone (n=3) or vehicle (n=3). The RNA was then used with Illumina HumanHT-12 v3 Expression BeadChips to determine the effect of DHT on gene expression in the primary human corneal cells grown in our laboratory and the immortalized human corneal epithelial cell line developed in Dr. Rheinwald's laboratory [Rheinwald et al. MCB, 22 (14): 5157. (2002)] and charecterized in Dr. Ilene Gibson's laboratory [Gipson et al. IOVS, 44 (6): 2496. (2003)].

2011-03-31 | E-GEOD-18093 | biostudies-arrayexpress

Effects of darunavir upon gene expression in kidney tubular cells after transduction with HIV or EGFP-control lentivirus

Project description:To determine the effect of darunavir upon HIV-induced gene regulation in renal epithelial cells, immortalized human renal tubular epithelial cells (HPT1b) were transduced with VSV-pseudotyped gag/pol-deleted HIV lentivirus or EGFP control lentivirus. 4 days later, cells were treated with darunavir (3uM) or vehicle control from 4-7 days post transduction. Primary comparisons in gene expression were between HIV and control-transduced cells at 4 days post transduction, and between DRV and control-treated HIV-transduced cells at 7 days post transduction.

2019-11-19 | GSE136340 | GEO

CD7 promotes extramedullary involvement of the B-cell acute lymphoblastic leukemia line Tanoue by enhancing integrin beta2-dependent cell adhesiveness

Project description:The Tanoue expressing firefly-luciferase gene, Luc-Tanoue, was transplanted into non-obese diabetic/severe combined immunodeficient mice, and cells infiltrated in the brain were cultured ex vivo. This process was repeated 4 times to obtain the highly invasive line Luc-Tanoue-F4. Comparison of the global gene expression signatures of Luc-Tanoue-F4 and Luc-Tanoue indicated that the CD7 gene showed the largest increase in expression among EMI-related genes in Luc-Tanoue-F4.

2013-12-27 | GSE53651 | GEO

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