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SRX15781801: GSM6252643: liver pediatric choelstatic liver disease, ALGS case 1; Homo sapiens; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 28.3M spots, 1.4G bases, 520.4Mb downloads

External Id: GSM6252643_r1
Submitted by: Center for Genetic Medicine, Northwestern University
Study: The IRE1a/XBP1 pathway expression is impaired in pediatric cholestatic liver disease explants
show Abstracthide Abstract
Background/Aims: Cholestatic liver diseases (CLD) are the leading indication for pediatric liver transplantation. Increased intrahepatic bile acid concentrations cause endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) is activated to maintain homeostasis. UPR dysregulation, including the inositol-requiring enzyme 1a/X-box protein 1 (IRE1a/XBP1) pathway, is associated with several adult liver diseases. We evaluated hepatic UPR expression in pediatric patients with end-stage CLD and hypothesize that an inability to appropriately activate the hepatic IRE1a/XBP1 pathway is associated with the pathogenesis of CLD. Methods: We evaluated 34 human liver explants. Cohorts included: pediatric CLD (Alagille, ALGS, and progressive familial intrahepatic cholestasis, PFIC), pediatric non-cholestatic liver disease controls (autoimmune hepatitis, AIH), adult CLD, and normal controls. We performed RNA-seq, quantitative PCR, and western blotting to measure expression differences of the hepatic UPR and other signaling pathways. Results: Metascape pathway analysis demonstrated that the KEGG 'protein processing in ER' pathway was downregulated in pediatric CLD compared to normal controls. Pediatric CLD had decreased hepatic IRE1a/XBP1 pathway gene expression and decreased protein expression of p-IRE1a compared to normal controls. These CLD changes were not disease-specific to ALGS or PFIC. IRE1a/XBP1 pathway gene expression was decreased in pediatric CLD compared to AIH disease controls. Conclusion: Pediatric CLD explants have decreased gene and protein expression of the protective IRE1a/XBP1 pathway and down-regulated KEGG protein processing in the ER pathways. IRE1a/XBP1 pathway expression differences occur when compared to both normal and non-cholestatic disease controls. Attenuated expression of the IRE1a/XBP1 pathway is associated with cholestatic diseases and could be targeted to treat pediatric CLD. Overall design: Samples are human explanted livers: 9 pediatric (<18 years of age) normal livers, 10 pediatric cholestatic liver disease (CLD) livers (5 with Alagille syndrome, 5 with progressive familial intrahepatic cholestasis), 5 pediatric autoimmune hepatitis livers, 3 adult cholestatic liver disease livers (1 with primary sclerosing cholangitis and 2 with primary biliary cholangitis), and 7 adult (>18 years of age) normal livers
Sample: liver pediatric choelstatic liver disease, ALGS case 1
SAMN29178699 • SRS13474994 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM6252643
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNA was extracted from frozen liver samples using TRIZOL reagent (Ambion by Life Technologies, Carlsbad, CA), and cDNA was synthesized with the qScript cDNA synthesis kit (Quantabio, Beverly, MD) The stranded mRNA-seq was conducted in the Northwestern University NUSeq Core Facility. Briefly, total RNA examples were checked for quality using RINs generated from Agilent Bioanalyzer 2100. RNA quantity was determined with Qubit fluorometer. The Illumina Stranded mRNA Library Preparation Kit was used to prepare sequencing libraries from 100 ng of high-quality RNA samples (RIN>7). All 34 samples met QC standards and were used for the study. The kit procedure was performed without modifications. This procedure includes mRNA purification and fragmentation, cDNA synthesis, 3' end adenylation, Illumina adapter ligation, library PCR amplification and validation.
Runs: 1 run, 28.3M spots, 1.4G bases, 520.4Mb
Run# of Spots# of BasesSizePublished
SRR1973547528,282,9461.4G520.4Mb2022-06-23

ID:
22428411

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