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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE199526 | GEO | 2022/11/15

REPOSITORIES: GEO

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

Project description: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.

2021-09-29 | GSE184431 | GEO

HDAC4 gene therapy

Project description:C57BL/6N animals received at the age of 6 weeks either adeno associated virus from serotype 9 (AAV9) leading to cardiac overexpression of luciferase (Luc, as control) or amino acids 1-201 of histone deacetyase 4 (HDAC4-NT) under the control of the cardiac myocyte-specific CMV-enhanced short (260bp) myosin light chain promoter (CMVenh/MLC260). Transaortic constriction (TAC) and sham operation was conducted 6 weeks later in 12 week old mice to induce pathological pressure overload. Organs were harvested 4 weeks after TAC at the age of 16 weeks and total RNA was used for microarray analysis. Three groups were compared: 1) sham-operated mice that were pretreated with AAV9 (CMVenh/MLC260)-Luc, 2) TAC-operated mice that were pretreated with AAV9 (CMVenh/MLC260)-Luc, 3) TAC-operated mice that were pre-treated with AAV9 (CMVenh/MLC260)-HDAC4-NT.

2016-07-27 | GSE72904 | 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

Homo sapiens

Project description:Human Breast Cancer Cell Lines: Control vs. Fn14 or Luciferase siRNA Treated

| PRJNA102239 | ENA

siRNA knockdown of hnRNP K in human SH-SY5Y cells

Project description:The RNA-binding protein hnRNP K was knocked down using siRNA in human SH-SY5Y. As a control, cells were treated with an siRNA against firefly luciferase.

2021-03-30 | GSE171090 | GEO

Analysis of PDCD4 knockdown effects by high throughput sequencing of a human epithelial cell line

Project description:Purpose: examination of gene expression and translation changes in immortalized human epithelial cells (hTERT-RPE-1) induced by PDCD4 siRNA-knockdown.

2020-01-20 | GSE138533 | GEO

Tnik depletion induces inflammation and apoptosis in injured renal proximal tubule epithelial cells

Project description:We performed bulk RNA-seq on primary and immortalized human renal proximal tubule epithelial cells (RPTECs) subjected to siRNA mediated TNIK silencing.

2024-04-10 | GSE216015 | GEO

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

2013-12-27 | GSE53651 | 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. 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.

2013-12-27 | E-GEOD-53651 | biostudies-arrayexpress

RNA-Seq of WT Flp-In T-REx 293 and UPF3B knockout cell lines with additional siRNA-mediated control or UPF3A knockdowns

Project description:UPF3A and UPF3B are paralogous genes in human cells that are involved in the nonsense-mediated decay (NMD) pathway. NMD is a cellular quality control mechanism that monitors mRNAs during translation. Aberrant translation due to features such as the presence of a premature stop codon downstream on an exon-exon junction activates NMD and leads to the degradation of the mRNA. To investigate the role of UPF3B and UPF3A in NMD, we have generated UPF3B knockout human Flp-In T-REx 293 cells using CRISPR-Cas9. We generated RNA-Sequencing data for wildtype and UPF3B KO cells with additional siRNA-mediated knockdown of Luciferase (Luc) as control or UPF3A.

2022-04-25 | E-MTAB-10711 | biostudies-arrayexpress

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