Gene expression in rectal epithelia of cystic fibrosis patients
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE15568 | GEO | 2013/11/28
SECONDARY ACCESSION(S): PRJNA115739
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiles were recorded from rectal suction specimens of Cystic Fibrosis (CF) patients, carrying the CF-specific D508 mutated CFTR-allele. These profiles were compared with gene expression profiles from rectal suction specimens of non-CF subjects (control). We used Affymetrix GeneChip HG-U133A microarrays to record the gene expression profile of 16 CF and 13 non-CF individuals. Rectal suction specimens representing rectal mucosal epithelia were collected from CF patients and non-CF individuals. Biopsies were analyzed for residual function using ICM and total RNA was isolation immediately using the Qiagen RNeasy protocol with on column DNA digestion. About 1-5 µg RNA were obtained from each individual. Integrity of total RNA samples was monitored by gel-electrophoresis before cDNA synthesis. Labeled cRNA synthesis and hybridization was performed following standard protocols.
2013-11-28 | E-GEOD-15568 | biostudies-arrayexpress
Project description:Cystic fibrosis (CF) remains a life-shortening disease without a definitive cure. Novel therapeutics targeting the causative defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are now in clinical use. Lumacaftor/ivacaftor is a CFTR modulator approved for patients homozygous for the CFTR mutation p.Phe508del, but there are wide variations in treatment responses preventing prediction of patient responses. We aimed to determine changes in gene expression related to treatment initiation and response. Whole-blood transcriptomics was performed using RNA-Seq in 20 patients with CF pre- and 6 months post-lumacaftor/ivacaftor (drug) initiation and 20 non-CF healthy controls. Correlation with clinical variables was performed by stratification via clinical responses. We identified 491 genes that were differentially expressed in CF patients (pre-drug) compared with non-CF controls. In addition, 36 genes were differentially expressed when comparing pre-drug to post-drug profiles within CF patients. Transcriptomics revealed novel pathways in CF patients at baseline compared to non-CF, and in clinical responders to lumacaftor/ivacaftor. Overall changes in gene expression post-lumacaftor/ivacaftor were modest compared to pre-drug CF profiles.
2019-01-03 | GSE124548 | GEO
Project description:In clinical routine, the diagnosis of cystic fibrosis (CF) is still a challenge due to the limitations of diagnosis guidelines and tests. A diagnosis test of choice, the sweat test measures eccrine sweat chloride concentration as a byproduct of the eccrine sweat gland CFTR function. Despite the combined use of CFTR genotyping and direct physiologic testing of CFTR function, reports of inconclusive diagnosis justified the need for alternative tests and new biomarkers. Meanwhile, eccrine sweat composition has already been linked to disease-specific profiles of non-electrolytes (i.e. proteins, peptides and metabolites). In this study, we analyzed sweat samples from 28 healthy volunteers and 14 CF patients by UHPLC-Q-Orbitrap-based Shotgun proteomics, to address CF-related changes in sweat protein composition and abundance. Over 1000 proteins were identified and quantified in a label-free manner. Beside similar protein composition, enrichment and functional classifications, HV and CF samples were grouped apart since protein abundance profiles were significantly correlated with CF status and degree of severity (ΔF508 homozygous and pancreatic insufficiency onset). Four-hundred and two proteins in CF-specific abundance, 68 proteins in genotype-specific abundance and 71 proteins in abundance related to pancreatic status, respectively, highlighted eccrine gland cell perturbations in protein biosynthesis & trafficking, CFTR proteostasis & membrane stability, cell-cell adherence, membrane integrity & cytoskeleton crosstalk. Cytoskeleton-related biomarkers were of utmost interest because of consistent abundances between CF sweat and other CF tissues. Nine clinical CF diagnosis biomarker (CUTA, ARG1, EZR, AGA, FLNA, MAN1A1, MIA3, LFNG, SIAE) and 5 CF severity biomarker (ARG1, GPT, MDH2, EML4 (ΔF508 homozygous), MGAT1 (pancreatic insufficiency)) candidates were deemed suitable for further verification.
2022-10-13 | PXD028518 | Pride
Project description:Biopsy specimens were collected from rectal cancer before starting preoperative radiotherapy.The expression profiles were determined using Affymetrix Human Genome U95 version 2 arrays.Comparison between the sample groups allow to identify a set of discriminating genes that can be used for characterization of responders and nonresponders to preoperative radiotherapy in rectal cancer. Keywords: repeat
2006-03-29 | GSE3493 | GEO
Project description:Cystic fibrosis (CF) is a life-shortening disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although bacterial lung infection and the resulting inflammation cause most of the morbidity and mortality, how loss of CFTR first disrupts airway host defense has remained uncertain. We asked what abnormality impairs elimination when a bacterium lands on the pristine surface of a newborn CF airway? To investigate this defect, we interrogated the viability of individual bacteria immobilized on solid grids and placed on the airway surface. As a model we studied CF pigs, which spontaneously develop hallmark features of CF lung disease. At birth, their lungs lack infection and inflammation, but have a reduced ability to eradicate bacteria. Here we show that in newborn wild-type pigs, the thin layer of airway surface liquid (ASL) rapidly killed bacteria in vivo, when removed from the lung, and in primary epithelial cultures. Lack of CFTR reduced bacterial killing. We found that ASL pH was more acidic in CF, and reducing pH inhibited the antimicrobial activity of ASL. Reducing ASL pH diminished bacterial killing in wild-type pigs, and increasing ASL pH rescued killing in CF pigs. These results directly link the initial host defense defect to loss of CFTR, an anion channel that facilitates HCO3- transport. Without CFTR, airway epithelial HCO3- secretion is defective, ASL pH falls and inhibits antimicrobial function, and thereby impairs killing of bacteria that enter the newborn lung. These findings suggest that increasing ASL pH might prevent the initial infection in patients with CF and that assaying ASL pH or bacterial killing could report on the benefit of therapeutic interventions. 11 samples of trachea primary airway epithelial cultures representing CFTR+/+ and CFTR-/- pigs. Pig samples representing 14 bronchus and 12 trachea tissue samples submitted in GSE21071.
2012-03-29 | E-GEOD-36906 | biostudies-arrayexpress
Project description:Our laboratory has held a long interest in the glycosylation changes seen on the surface of airway epithelia of patients with the disease cystic fibrosis (CF). Experiments from our laboratory have detailed a CF glycosylation phenotype of increased Fuca1,3/4 and decreased Fuca1,2 and sialic acid on the surfaces of immortalized and primary CF cells compared to non-CF cells. Further, we have shown that gene transfer and subsequent expression of a wild type CF plasmid in CF airway cells results in correction or reversal of this glycosylation phenotype. We hypothesize that the changes in glycosylation seen in CF cells are key in the pathophysiology of the cystic fibrosis airway disease. For example, it has been shown that Pseudomonas aeruginosa, a bacterium that has a predilection for colonizing CF airways, adheres to asialylated glycolipids and glycoconjugates with terminal Fuca1,3/4. One focus of our laboratory is to elucidate the etiology of the glycosylation changes seen in CF cells and the mechanism by which these changes are reversed by wild type CFTR gene transfer. We propose to study the gene expression of immortalized and primary CF and non-CF airway epithelial cells: 1. CF/T43 vs. BEAS-2B cells. These are two widely used immortalized airway cell lines that we have used extensively in the past. 2. C38 cells; C38 cells are IB3 cells expressing wtCFTR. The experimental focus is to elucidate the etiology of the glycosylation changes seen in Cystic Fibrosis (CF) cells and the mechanism by which these changes are reversed by wild type CFTR gene transfer. To do so, the gene expression of immortalized and primary CF and non-CF airway epithelial cells were compared and studied. Cell lines used were CF/T43 and BEAS-2B, both widely used immortalized airway cell lines. Other cell lines studied included C38 cell lines (clonal derivatives of IB3 cells expressing wtCFTR).
2011-01-07 | E-GEOD-26482 | biostudies-arrayexpress
Project description:The goal of this study was to compare cell composition and gene expression patterns for different cell types in large and small airways of CFTR+/+ (non-CF) and CFTR-/- (CF) pigs.
2021-03-16 | GSE150211 | GEO
Project description:Cystic fibrosis (CF) is a recessive disease caused by mutations in theCF transmembrane conductance regulator(CFTR) gene. The most common symptoms include progressive lung disease and chronic digestive conditions. CF is the first human genetic disease to benefit from having five different species of animal models. Despite the phenotypic differences among the animal models and human CF, these models have provided invaluable insight into understanding disease mechanisms at the organ-system level. Here, we identify a member of the ABCC4 family, CG5789, that has the structural and functional properties expected for encoding theDrosophilaequivalent of human CFTR, and thus refer to it asDrosophila CFTR(Dmel\CFTR). We show that knockdown ofDmel\CFTRin the adult intestine disrupts osmotic homeostasis and displays CF-like phenotypes that lead to intestinal stem cell hyperplasia. We also show that expression of wild-type humanCFTR, but not mutant variants of CFTR that prevent plasma membrane expression, rescues the mutant phenotypes ofDmel\CFTR.Furthermore, we performed RNA sequencing (RNA-Seq)-based transcriptomic analysis usingDmel\CFTRfly intestine and identified a mucin gene,Muc68D, which is required for proper intestinal barrier protection. Altogether, our findings suggest thatDrosophilacan be a powerful model organism for studying CF pathophysiology.
2023-10-26 | GSE246379 | GEO
Project description:Hepatobiliary disease causes significant morbidity in people with cystic fibrosis (CF), yet this problem remains understudied. We previously found that newborn CF pigs have microgallbladders with significant luminal obstruction in the absence of infection and inflammation. In this study, we sought to better understand the early pathogenesis of CF pig gallbladder disease. We hypothesized that loss of CFTR would impair gallbladder epithelium anion/liquid secretion and increase mucin production. By single cell RNA sequencing, we identified a single epithelial cell population that co-expressed CFTR, MUC5AC, and MUC5B. By bulk tissue RNA sequencing, there was no significant difference in the epithelial expression of gel-forming mucins between non-CF and CF pig gallbladders. Also, there were minimal transcriptional changes in CF relative to non-CF.
2020-10-28 | GSE152145 | GEO
Project description:The differentiation of pluripotent stem cells has been broadly used in studying the disease mechanism and development process. We previously described a method for differentiating human pluripotent stem cells (hPSCs) into salivary gland epithelial progenitors (SGEPs). Here, to investigate whether the hPSCs-derived SGEPs are capable of modeling the characteristics of cystic fibrosis (CF), a disease impact SG function caused by mutation of cystic fibrosis transmembrane conductance regulator (CFTR) gene, the CFTR knockout hPSCs were differentiated into CF-SGEPs using the same protocol. Firstly, we successfully generated CFTR knockout hPSCs with reduced CFTR protein expression using the CRISPR-Cas9 system. After 16-day of differentiation, the protein expression of CFTR was also decreased in SGEPs generated from CFTR knockout hPSCs. RNA-sequencing shows that multiple genes modulating SG development, function and were down-regulated and positive regulators of inflammation were up-regulated in CF-SGEPs, which was correlated with salivary phenotype in CF patients. These results demonstrated that suppression of CFTR disrupted the differentiation of hPSCs-derived SGEPs, which modeled the SG development of patients with CF. In summary, this study not only provided the proof that the hPSCs-derived SGEPs could serve as manipulatable and easily accessible models to study the SG developmental diseases, but also provided new avenues for the study of the CF mechanism.
2023-12-06 | GSE224547 | GEO