Sequencing data analysis and circRNA analysis of biliary atresia (BA) and choledochal cyst (CC) liver tissues
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1005261 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25634287_1.fastq.gz | Fastqsanger.gz | |||
| SRR25634287_2.fastq.gz | Fastqsanger.gz | |||
| SRR25634288_1.fastq.gz | Fastqsanger.gz | |||
| SRR25634288_2.fastq.gz | Fastqsanger.gz | |||
| SRR25634289_1.fastq.gz | Fastqsanger.gz |
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Project description:We obtained a circRNA map of BA liver tissue based on RNA high-throughput sequencing and identified 78 significant DECs.
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Project description:Biliary atresia (BA) is a progressive fibro-inflammatory disorder that is the leading indication for liver transplantation in children. Although there is evidence implicating genetic, infectious, environmental, and inflammatory causes, the etiology of BA remains unknown. We have recently reported that cholangiocytes from BA patients showed decreased DNA methylation relative to disease- and non-disease controls, supporting a potential role for DNA hypomethylation in BA etiopathogenesis.
2015-06-18 | GSE69948 | GEO
Project description:Biliary atresia (BA), blockage of the proper bile flow due to loss of extrahepatic bile ducts, is a rare, complex disease of the liver and the bile ducts with unknown etiology. Despite ongoing investigations to understand its complex pathogenesis, BA remains the most common cause of liver failure requiring liver transplantation in children. To elucidate underlying mechanisms, we analyzed the different types of high-throughput genomic and transcriptomic data collected from the blood and liver tissue samples of children suffering from BA. Through use of a novel integrative approach, we identified potential biomarkers and over-represented biological functions and pathways to derive a comprehensive network showing the dysfunctional mechanisms associated with BA. One of the pathways highlighted in the integrative network was hypoxia signaling. Perturbation with hypoxia inducible factor activator, dimethyloxalylglycine, induced the biliary defects of BA in a zebrafish model, serving as a validation for our studies. Our approach enables a systems-level understanding of human BA biology that is highlighted by the interaction between key biological functions such as fibrosis, inflammation, immunity, hypoxia, and development
2020-08-31 | GSE136270 | GEO
Project description:Early diagnosis of biliary atresia (BA) is crucial for improving the chances of survival and preserving the liver function of children with BA. To explore potential biomarkers for early diagnosis of BA with other non-BA jaundice cases, we performed proteomic analysis with data-independent acquisition (DIA) and parallel reaction monitoring (PRM). With this approach we were able to detect and validate differential protein expression in plasma of patients. Bioinformatics analysis revealed the enrichment biological processes, characteristic of BA by identifying differential expression of specific proteins of which with 10 were up- and 23 down-regulated. Signaling pathway analysis demonstrated changes in protein expression associated with an alteration in immunoglobins levels, which is indicative immune dysfunction in BA. When polymeric immunoglobulin receptor (pIgR) expression was combined with an immunoglobulin lambda variable chain (IGL c2225_light_IGLV1-47_IGLJ2), revealed by machine learning, they provided a useful early diagnostic model for BA, which had a sensitivity of 0.8, specificity of 1, accuracy of 0.89, and AUC value of 0.944. Our study not only identified a possible effective plasma biomarker for the early diagnosis of BA but may also help to further elucidate the underlying mechanisms of BA.
2024-06-22 | PXD048938 | Pride
Project description:Biliary atresia (BA) is a progressive fibro-inflammatory disorder that is the leading indication for liver transplantation in children. Although there is evidence implicating genetic, infectious, environmental, and inflammatory causes, the etiology of BA remains unknown. We have recently reported that cholangiocytes from BA patients showed decreased DNA methylation relative to disease- and non-disease controls, supporting a potential role for DNA hypomethylation in BA etiopathogenesis. In the current study, we examined the methylation status of specific genes in human BA livers using methylation microarray technology. We found global DNA hypomethylation in BA samples as compared to disease- and non-disease controls at specific genetic loci. Hedgehog pathway members, SHH and GLI2, known to be upregulated in BA, were both hypomethylated, validating this approach as an investigative tool. Another region near the PDGFA locus was the most significantly hypomethylated in BA, suggesting potential aberrant expression. Validation assays confirmed increased transcriptional and protein expression of PDGFA in BA livers. We also show that PDGF-A protein is specifically localized to cholangiocytes in human liver samples. Injection of PDGF-AA protein dimer into zebrafish larvae caused biliary developmental and functional defects. In addition, activation of the Hedgehog pathway caused increased expression of PDGF-A in zebrafish larvae, providing a previously unrecognized link between PDGF and the Hedgehog pathway. DNA hypomethylation appears to be a specific factor in mediating overexpression of genes associated with BA. Our findings validate the role of Hedgehog pathway signaling and implicate PDGF as a new candidate for a role in BA pathogenesis.
2015-06-18 | E-GEOD-69948 | biostudies-arrayexpress
Project description:Background: RNASeq was performed on organoids derived from livers of normal healthy donors and patients with biliary atresia to characterize transcriptomic signatures. Methods: Organoids generated from livers of normal healthy donors and patients with biliary atresia were cultured either in expansion (undifferentiated: 3 NCOs and 11 BACOs) or differentiation medium (differentiated: 3 BACOs). Liver tissues obtained from deceased-donor subjects served as normal controls (N=3). Total RNA was isolated from organoids and liver biopsy tissue specimens. Results: Organoids from patients with biliary atresia showed abnormal cell polarity, loss of tight junctions, increased permeability and decreased expression of genes related to epidermal growth factor (EGF)- and fibroblast growth factor 2 (FGF2)-signaling. When treated with EGF+FGF2, biliary atresia organoids expressed differentiation and functional markers with restored cell polarity. Conclusion: Organoids from biliary atresia are viable and have evidence of halted epithelial development. The induction of developmental markers, improved cell‐cell junction, and decreased epithelial permeability by EGF and FGF2 identifies potential strategies to promote epithelial maturation and function.
2021-10-25 | GSE186444 | GEO
Project description:We report label-free quantification of xenobiotic metabolizing enzymes (XME), transporters, redox enzymes, proteases and nucleases in 25 human liver microsomal samples, taken from patients with biliary atresia. Nearly 3500 proteins were identified and quantified. These data can be used in physiologically based pharmacokinetic models to predict appropriate drug doses drugs used in biliary atresia patients.
2021-09-09 | PXD020974 | Pride
Project description:We performed single cell 5' RNA sequencing, and B cell receptor and T cell receptor V(D)J sequencing analyses on liver biopsies of nine patients with biliary atresia and three patients with choledochal cyst at diagnosis to generate the liver cell atlas.
2024-09-16 | GSE176189 | GEO
Project description:Stool samples from three patients with biliary atresia after Kasai portoenterostomy (BA-KPE) and four non-BA healthy controls (non-BA) were analyzed by overlapping DIA-MS.
2023-02-02 | PXD031394 | JPOST Repository
Project description:Biliary atresia (BA) is a rare cholestatic disease of unknown etiology that affects infants and shows an incidence of 1 out of 18,000 live births in Europe (1). The first therapeutic option is a timely performed portoenterostomy. However, the majority of patients suffer from a progressive inflammatory process, which leads to complete destruction of the extra- and intrahepatic biliary system followed by end-stage liver cirrhosis. Hence, BA is the leading indication for pediatric liver transplantation worldwide (2, 3). To understand the pathogenesis of the disease and improve theoutcome of BA patients, research has focused on the inflammatory process in liver and bile ducts, in which several factors are remarkably elevated, such as activated CD4 and CD8 T-cells, TNF alpha,IFN alpha and other proinflammatory TH1 cytokines (3-8). By the time of diagnosis, however, the disease has already reached an advanced state, characterized by the complete obstruction of the extrahepatic bile ducts with impaired bile flow and fibrosis or cirrhosis of the liver. Therefore, studies in humans focusing on the trigger mechanism of BA are limited due to the paucity of liver and availability of bile duct tissue for research. One infectious animal model has been developed, in which newborn Balb/c mice exclusively show the experimental BA phenotype after infection with rhesus rotavirus (RRV) (9, 10). This model allows the analysis of the inflammatory reactions in liver and bile ducts at early steps in the development of bile duct atresia (11-20). Furthermore, inbred mouse strains have been shown to have a different susceptibility for the development of experimental BA, suggesting that Balb/c mice have an immunological gap responsible for disease progression (10, 12). The aim of this study was to identify key genes responsible for the BA phenotype by comparing the transcriptomes at an early time point after virus infection, i.e. before bile duct atresia, between two mouse strains with different susceptibilities to BA. Differences in the virus titration and the clinical course of infected mice were analyzed, and variations in the hepatic gene response assessed by comparative microarray assays were correlated to variances in the hepatic inflammatory reaction. Balb/c mice and C57Black/6 (Black/6) mice were infected with RRV postpartum and signs of BA and survival were noted. Liver sections of diseased, healthy and control animals were assessed for T-cell expression, and the virus loads were determined. Second, mice were sacrificed after three days, and isolated hepatic RNA was subjected to gene expression analysis using Affymetrix Gene Chip MOE 430 2.0.We compared three individual expression profiles from RRV-infected Balb/c mice against 2 individual expression profiles from RRV-infected C57/BL6 control mice using the Affymetrix GeneChip MOE 430 2.0.
2009-08-30 | E-GEOD-13245 | biostudies-arrayexpress