Transcriptomic profiling of small intestinal crypts upon MEX3A deletion
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ABSTRACT:
PROVIDER: PRJNA592553 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10560364_1.fastq.gz | Fastqsanger.gz | |||
| SRR10560364_2.fastq.gz | Fastqsanger.gz | |||
| SRR10560365_1.fastq.gz | Fastqsanger.gz | |||
| SRR10560365_2.fastq.gz | Fastqsanger.gz | |||
| SRR10560366.fastq.gz | Fastqsanger.gz |
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Project description:The effort to better understand intestinal stem cell (ISC) identity and regulation remains a challenge. We have been studying the RNA-binding protein MEX3A as a putative ISC marker. In that context, we have generated the first Mex3a knockout (KO) mouse model and show MEX3A is crucial for maintenance of the Lgr5+ ISC pool. As part of a phenotypic characterization pipeline, we have performed transcriptomic profiling (RNA-sequencing) of isolated Mex3a KO small intestinal crypts and compared it against small intestinal crypts isolated from age-matched wild-type controls.
2020-02-13 | GSE141191 | GEO
Project description:The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. β Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF-family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium using tissue-specific, inducible beta-catenin gene ablation in adult mice. Block of Wnt/beta-catenin signaling resulted in rapid loss of transient-amplifying cells and crypt structures. Importantly, intestinal stem cells were induced to terminally differentiate upon deletion of beta-catenin resulting in a complete block of intestinal homeostasis and fatal loss of intestinal function. Transcriptional profiling of mutant crypt mRNA isolated by laser capture micro dissection confirmed those observations and allowed to identify genes potentially responsible for the functional preservation of intestinal stem cells. Experiment Overall Design: laser capture microdissection of intestinal crypts, control vs. beta-catenin mutant (2days after induction of deletion by tamoxifen), two rounds of amplification of mRNA
2008-06-16 | E-GEOD-8818 | biostudies-arrayexpress
Project description:The precise control of the self-renewal and differentiation of intestinal stem cells (ISCs) is essential for intestinal homeostasis, efficient regeneration and prevention of tumorigenesis. However, the underlying molecular mechanisms remain only partially understood, especially in regeneration and cancer. Here, it is demonstrated that RNA-binding protein Mex3a is specifically expressed in ISCs and promotes their stemness and proliferative status. Its depletion results in compromised ISCs, impaired intestinal regeneration and suppressed oncogenic transformation. Mechanistically, upregulation of Mex3a in ISCs at homeostasis, in postirradiation regenerative foci and in colorectal cancer model is regulated by the upstream transcription factor E2f3. In turn, Mex3a activates Wnt signaling by directly suppressing pro-differentiation transcription factor Klf4 at the mRNA level. Furthermore, expression of E2F3 and MEX3A significantly increases in human radiation enteritis and colorectal carcinoma (CRC), accompanied by KLF4 downregulation and Wnt signaling hyperactivation. These findings indicate that the E2f3-Mex3a-Klf4-Wnt as the critical molecular switch between ISC self-renewal and differentiation. It can represent a putative therapeutic target for CRC and regeneration-related gut diseases.
2021-07-09 | GSE179493 | GEO
Project description:Spontaneous inflammation in the terminal ileum of Xiap–/– mice was observed to occur in a microbiome dependent manner. Xiap–/– mice housed alone presented with signs of inflammation which were alleviated upon co-housing the mice with wild-type counterparts. To elucidate the impact of co-housing, and thus the transfer of the microbiome to affected Xiap–/– mice, crypts from the small intestine of these mice were analyzed.
2021-08-28 | GSE182934 | GEO
Project description:Purpose: The activation of TLR4 was reported to effectively alleviate intestinal injury induced by irradiation (IR). The goals of this study are to investigate the transcriptome profiling (RNA-seq) of intestinal crypts thereby clarifying the underlying mechanism mediating the radio-protective activity of TLR4 on intestinal stem cells. Methods: Intestinal crypts mRNA profiles of mice treated or untreated with TLR4 low-toxic agonist monophosphyal lipid A (MPLA) upon abdominal body irradiation (AIR) exposure were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500 sequencer. To pre-treated the data, adaptor and low-grade reads removal, low-quality bases elimination from 3' or 5' ends, original and effective sequencing quantity analysis, as well as guanine and cytosine statistics were subjected, in turns. Differential expression genes were selected via correlation test, principal component analysis and cluster analysis, in which the fold change (FC) was greater than 2 and p value was less than 0.05 could be regarded significance. Different expressed genes (DEGs) were clustered into pathways of intestinal crypts through KEGG. Results: As compared to the nonirradiated group, 2733 DEGs were identified in intestinal crypts after AIR damage, while there were 2168 DEGs between irradiated group and irradiated plus MPLA treatment group. Among the DEGs, a series of genes involving intestinal stem cells regeneration, which mainly falls into three stem cell related pathway according to Gene ontology analysis and KEGG enrichment: Hippo, Wnt and Notch signaling pathway. Based on these DEGs, we focused on a group of genes which was suppressed by IR, while could be restored by TLR4 activation. Based on the criteria, 8 DEGs (SOX9, cMyc, MSI1, Lgr5, Notch1, Wnt5b, Axin2, DLL4) involving intestinal stem cell regulation were further selected for validation, from which the mRNA levels of 4 genes (SOX9, YAP1, cMyc) were confirmed to be up-regulated by MPLA treatment. Conclusions: Our study represents the first detailed analysis of intestinal crypts transcriptomes by TLR4 activation upon IR damage, with biologic replicates, generated by RNA-seq technology. And the confirmation of DEGs will facilitate the development of novel targets and techniques to efficiently stimulate the regeneration of intestinal stem cells to reconstruct the intestine after radiation injury.
2025-03-01 | GSE197682 | GEO
Project description:The Wnt signaling pathway is deregulated in over 90% of human colorectal cancers. β Catenin, the central signal transducer of the Wnt pathway, can directly modulate gene expression by interacting with transcription factors of the TCF/LEF-family. In the present study we investigate the role of Wnt signaling in the homeostasis of intestinal epithelium using tissue-specific, inducible beta-catenin gene ablation in adult mice. Block of Wnt/beta-catenin signaling resulted in rapid loss of transient-amplifying cells and crypt structures. Importantly, intestinal stem cells were induced to terminally differentiate upon deletion of beta-catenin resulting in a complete block of intestinal homeostasis and fatal loss of intestinal function. Transcriptional profiling of mutant crypt mRNA isolated by laser capture micro dissection confirmed those observations and allowed to identify genes potentially responsible for the functional preservation of intestinal stem cells. Keywords: genetic modification
2007-09-24 | GSE8818 | GEO
Project description:To assess the role of LSD1 in mouse small intestinal epithelium, we isolated small intestinal crypts from wild type (WT) (Villin-Cre -; Lsd1f/f) and intestinal-epithelial-specific knock-out (KO) (Villin-Cre+; Lsd1f/f) mice. We dissociated crypts into single cells, and FACS sorted Epcam+ cells, to avoid immune-cell contamination. RNA was directly isolated from these sorted cells, and this was used for RNA seq. As KO crypts are different from WT crypts (KO crypts lack Paneth cells), identifying genes specifically regulated by LSD1 helps us to identify how LSD1 regulates intestinal crypt biology. Specifically, because we were able to combine this with ChIP-seq of the same cells, to identify where H3K4me1 levels (target of the histone demethylase LSD1) were different in the genome.
2020-11-16 | E-MTAB-7862 | biostudies-arrayexpress
Project description:The intestinal epithelium is continuously regenerated by highly proliferative Lgr5+ intestinal stem cells (ISCs). The existence of a population of quiescent ISCs has been suggested yet its identity and features remain controversial. Here we describe that the expression of the RNA-binding protein Mex3a labels a subpopulation of Lgr5+ cells that divide less frequently and contribute to regenerate all intestinal lineages with slow kinetics. Single cell transcriptomic analysis revealed two classes of Lgr5-high cells, one of them defined by the Mex3a-expression program and by low levels of proliferation genes. Lineage tracing experiments show that large fraction of Mex3a+ cell population is continuously recalled into the rapidly dividing self-renewing ISC pool in homeostatic conditions. Chemotherapy and radiation target preferentially rapidly dividing Lgr5+ cells but spare the Mex3a-high/Lgr5+ population, which helps sustain the renewal of the intestinal epithelium during treatment.
2017-03-14 | GSE90856 | GEO
Project description:Transcriptional change in intestinal crypts by TLR4 activation upon radiation exposure
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Project description:We wanted to assess the role of a specific smooth muscle protein (MMP17) in two different intestinal compartments, the epithelium (crypts) and the smooth muscle. To do that we isolate intestinal crypts from wild-type (WT) and knockout (KO, Mmp17-/-) mice, and obtained clean strips of smooth muscle. After muscle dissociation, we obtained RNA directly from crypts and muscle, and it was used for RNA-seq. By comparing WT and KO samples we observed a higher impact in gene expression affecting crypts, even though MMP17 is only expressed in muscle. This helped us to identify altered signaling pathways in KO crypts that linked MMP17 with SMAD4 and BMP signaling.
2021-09-27 | E-MTAB-9180 | biostudies-arrayexpress