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Gene expression profiling of prostate basal cells at proximal and distal ducts

ABSTRACT: We have noticed that the proliferative potential of epithelial cells in the mouse proximal prostatic ducts is less than those at the distal prostatic ducts. To determine whether specific signaling is differentially activated in distal and proximal prostate basal cells, we isolated respective basal cells in the two regions and performed an RNA-seq analysis.

ORGANISM(S): Mus musculus

PROVIDER: GSE115631 | GEO | 2019/06/21

REPOSITORIES: GEO

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FACS-isolated Lin-CD24-CD49f-Sca-1+stromal cells from adult mouse proximal and distal prostatic ducts

Project description:We have noticed that the proliferative potential of epithelial cells in the mouse proximal prostatic ducts is less than those at the distal prostatic ducts. We were curious whether the tissue microenvironment in the two anatomic regions play a role in the distinct epithelial proliferative indices. So we isolated respective stromal cells in the two regions and performed an RNA-seq analysis.

2019-06-21 | GSE72318 | GEO

Gene expression profiling of prostate basal cells at proximal and distal ducts

Project description:Gene expression profiling of prostate basal cells at proximal and distal ducts

| PRJNA475588 | ENA

Gene expression profiling in proximal versus distal mouse colon

Project description:Analysis of gene expression in proximal versus distal part of the mouse large intestine. Three (3) animals (biological replicates) were used to isolate tissue from proximal and distal areas of the large intestine.

2015-01-01 | E-GEOD-64423 | biostudies-arrayexpress

Distal-to-Proximal Re-patterning of Small Airway Epithelium in Smoking-associated Chronic Obstructive Pulmonary Disease

Project description:The proximal-distal patterning program determines unique structural and functional properties of proximal and distal airways in the adult lung. Based on the knowledge that remod-eling of distal airways is the major pathologic feature of chronic obstructive pulmonary disease (COPD), and that small airway epithelium (SAE), which covers distal airways, is the primary site of the initial smoking-induced changes relevant to COPD pathogenesis, we hypothesized that in COPD smokers, the SAE transcriptome loses its region-specific biologic identity and takes on the transcriptional pattern of the proximal airways. By analyzing human airway epithelium col-lected by bronchoscopic brushings from proximal and distal airways of healthy smokers, proxi-mal and distal airway epithelial transcriptome signatures were identified. Dramatic smoking-dependent suppression of distal signature paralleled by acquisition of the proximal airway epithe-lial phenotype was found in the SAE of COPD smokers. Distal-proximal re-patterning observed in the SAE of smokers in vivo was reproduced in vitro by stimulating SAE basal cells (BC), the stem/progenitor cells of the SAE, with EGF, a growth factor up-regulated in airway epithelium by smoking. Together, this study identifies distal-proximal SAE re-patterning as a characteristic feature of small airway disordering in COPD smokers potentially driven by EGF/EGFR-mediated reprogramming of SAE BC stem/progenitor cells.

2017-07-18 | GSE64614 | GEO

Alternative Polyadenylation by Sequential Activation of Distal and Proximal PolyA Sites

Project description:Analogous to alternative splicing, alternative polyadenylation (APA) has long been thought to result from competition between proximal and distal polyA sites. By Fractionation-seq, we unexpectedly identified several hundred APA genes where their distal polyA isoforms are retained in chromatin/nuclear matrix and proximal polyA isoforms released into the cytoplasm. Global metabolic PAS-seq and Nanopore long-read RNA-seq provided further evidence that the strong distal polyA sites are first processed and the resulting transcripts are anchored in chromatin/nuclear matrix for further processing at proximal polyA sites and removal of certain slowly spliced introns. By engineering an autocleavable ribozyme between the proximal and distal polyA sites, we demonstrated that the distal polyA isoform is indeed the precursor to the proximal polyA isoform. Therefore, unlike alternative splicing, APA sites are recognized independently, rather than competitively, and in many cases, in a sequential manner. This provides a versatile strategy to regulate gene expression in mammalian cells.

2021-11-26 | GSE165742 | GEO

Dysferlin deficiency modulates the proximal-distal muscle transcriptome

Project description:By comparing the transcriptome from proximal (quadriceps femoris, QF) and distal (tibialis anterior, TA)muscle groups in dysferlin deficient mouse muscle (the SJL mutation bred onto C57BL/10 to produces C57BL/10-SJL.Dysf) with proximal and distal muscle groups from control C57BL/10 mice of an equivalent age (3-weeks old, prior to the onset of overt pathology) we aim to address the issues of muscle selectivity in this this form of muscular dystrophy. Keywords: parallel sample

2005-05-06 | GSE2629 | GEO

Gene expression profiling in proximal versus distal mouse colon

Project description:Analysis of gene expression in proximal versus distal part of the mouse large intestine.

2015-01-01 | GSE64423 | GEO

Characterisation of a FAK-proximal nuclear interactome

Project description:In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here defined a FAK-proximal subproteome that localises to the nucleus.

2022-06-01 | PXD025861 | Pride

Characterisation of a Hic-5-proximal nuclear interactome

Project description:In addition to central functions in cell adhesion signalling, integrin-associated proteins have wider roles at sites distal to adhesion receptors. In experimentally defined adhesomes, we noticed that there is clear enrichment of proteins that localise to the nucleus, and conversely, we now report that nuclear proteomes contain a class of adhesome components that localise to the nucleus. We here defined a Hic-5-proximal subproteome that localises to the nucleus.

2022-06-01 | PXD025868 | Pride

Age-, sex- and proximal-distal-resolved multi-omics identifies regulators of intestinal aging in non-human primates.

Project description:The incidence of intestinal diseases increases with age, but the regulators of gut aging and the molecules linking gut aging and diseases remain largely unknown. By profiling the transcriptome, proteome, phosphoproteome and metabolome of 104 Macaca fascicularis large intestinal tissues, we unveiled asynchronous aging within the proximal and distal colon. The levels of many gene products, phosphosites and metabolites changed with age in a location- and sex-dependent manner, and many of these changes occurred at distinct rates or even in opposite directions at different locations. Assessment of 60 age-related molecules (genes, phosphosites, metabolites) across C. elegans, mice, and cell lines identified 32 crucial regulators of gut atrophy and barrier integrity. Notably, we found that tryptophan metabolism via the kynurenine and serotonin (5-HT) pathways was more active in the proximal and distal colon, respectively. In a mouse colitis model, reducing 5-HT production with a Tph1 inhibitor alleviated distal but not proximal colitis, while adding 5-HT aggravated distal symptoms, indicating that distal colitis is more sensitive to 5-HT fluctuations. Moreover, we identified 24 proteins, particularly HPX, that potentially link gut aging to colorectal cancer (CRC). High levels of HPX in CRC predicted poor prognosis in patients older than 50 yr but not in younger patients, suggesting that an age-linked HPX increase in the gut may contribute to CRC progression. Collectively, this work reveals the heterogeneity of large intestinal aging in non-human primates and offers promising targets for preventing gut aging and diseases.

2023-12-14 | MTBLS7612 | MetaboLights

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