Omics approach towards understanding the pathophysiology of Primary sclerosing cholangitis

• Author / Creator

  Bashiri, Kiandokht

• Primary sclerosing cholangitis (PSC) is a chronic progressive cholestatic liver disease with unknown etiology that is characterized by inflammation and fibrosis of the intrahepatic and extrahepatic biliary tracts, leading to diffuse multifocal stricture formation. The pathogenesis of PSC is unknown and there is no effective treatment. Previously, we found evidence of serological reactivity to retroviral proteins, reverse transcriptase activity and upregulation of the viral restriction factor family of APOBEC3 deaminases in PSC patients. To investigate the hypothesis that PSC may be linked with viral infection, we searched for altered expression of genes and associated pathways involved in host defense against viruses. Peripheral blood samples from 23 PSC patients and 26 healthy controls were obtained and genes differentially expressed were identified by RNA-sequencing analysis. Proteomic studies were conducted using liquid chromatography tandem mass spectrometry on biliary epithelial cells (BEC) obtained from PSC patients and compared with patients with non-cholestatic liver disease. We found total of 1542 overexpressed and 1074 under-expressed transcripts among PSC patients compared to healthy controls (padj<0.05). In the pathway analyses, “Viral process” was among the top overrepresented pathway (padj=4.48E-32). Several of the identified genes overlapped with known infections including HIV (padj=2.37E-14) and Influenza (padj=7.97E-12). Among the top overlapped pathways with HIV were “transport” and “intracellular-transport of virus” (24.9% and 22.49%, respectively). Among the top overlapped pathways with Influenza, we found “nuclear transcribed mRNA catabolic process, nonsense mediated decay” (50%) and “7-methylguanosine mRNA capping” (33%). String analysis of proteome of cholangiocytes showed negative regulation of “mRNA splicing via spliceosome and SRSF1, RNA recognition motif 1”- as well as decreased proteasomal degradation, confirming transcriptomics findings. We postulated that the activation of nonsense mediated decay might be due to increased formation of premature stop codons following the activity of APOBEC3s. In addition, considering enrichment of 7-methylguanosine capping –that is found to be utilized by several viruses in order to remain undetectable in cytoplasm using a host posttranslational modification and to stabilize the viral mRNA to have a successful translation– and mRNA splicing through SRSF1¬¬–which is a potent inhibitor of HIV-1 that its deletion results in double-stranded DNA breaks and genomic instability– and upregulation of host defense components against viruses such as APOBEC3 deaminases that found among PSC patients may suggest a viral pathogenesis. Further studies are warranted to better identify the presence of virus infection in PSC.

• Subjects / Keywords

  • Primary sclerosing cholangitis
  • RNAseq
  • Next generation sequencing
  • liver disease

• Graduation date

  Fall 2021

• Type of Item

  Thesis

• Degree

  Master of Science

• DOI

  https://doi.org/10.7939/r3-mr03-jw10

• License

  This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.