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Investigating Primary Biliary Cholangitis for a Human Betaretrovirus Superantigen signature

  • Author / Creator
    Syed, Hussain
  • Primary Biliary Cholangitis (PBC) is an idiopathic autoimmune disease characterized by destruction of small hepatic bile ducts and presence of antimitochondrial antibodies (AMA). A Human Betaretrovirus (HBRV) sharing 91-99% sequence similarity with the Mouse Mammary Tumor virus has been identified in PBC patients. The autoimmune biliary disease mouse model for PBC produces spontaneous AMA and is infected by the MMTV suggesting a role for MMTV involvement in disease development. The MMTV also has well documented superantigen activity. Viral superantigen bind the MHC class II receptor on antigen presenting cells to induce clonal expansion of specific TCR-Vβ subsets followed by eventual depletion of cognate T-cells. This skewing of specific TCR-Vβ subsets is the hallmark of superantigen activity. To evaluate a similar role of HBRV infection and superantigen activity in PBC patients, we investigated a transcriptional database from the POISE phase III clinical trials to 1) classify CD4+/CD8+ ratios and Neutrophil to Lymphocyte ratios (NLR, an indicator of lymphopenia) 2) characterize the TCR-Vβ repertoire profile in PBC to find evidence of VB skewing and 3) conduct differential gene expression analysis between PBC patient subsets to identify immunological pathways associated with disease development and progression. Analyzing RNA-seq database, we detected an increased range and higher mean CD4+/CD8+ ratio in PBC. A depleted CD8+ T-cell expression was notably observed in the high CD4+/CD8+ ratios. The CD4+/CD8+ ratio was also identified to be positively correlated with increased lymphopenia and negatively correlated with platelet counts indicating hypersplenism and overall worse prognosis. TCR-Vβ repertoire alteration consistent with superantigen activity was observed. Skewing of multiple Vβ subsets as well as the tendency of these skewed Vβ to skew together in clusters suggests the presence of multiple HBRV superantigen with varying binding avidities. Finally, pathway expression analysis identified increased anti-viral activity along with interferon responses and TLR activation in PBC samples with high CD4+/CD8+ ratio and high NLR. This suggests ongoing HBRV activity and may predict worse prognosis. Meanwhile, low NLR and CD4+/CD8 ratio samples demonstrated increased T-cell activation, activated innate immunity, NK cell immunity and negative regulation of viral transcription indicating a resolving disease process. We also identified CD3E-204, a transcript for the CD3E lymphocyte marker, which had a strong negative correlation with TCR-Vβ skewing. Further studies into the mechanistic differences between the CD3E transcripts need to be made to evaluate the significance of this finding. In future studies, we hope to investigate serial samples from PBC patients to identify changes in TCR-Vβ skewing over time and changes in CD4+/CD8+ ratios over time in patients with known clinical outcomes. We will also investigate TCR-Vβ skewing in isolated CD4+ and CD8+ T-cells in order to better understand the source of CD8+ T-cell depletion. Finally, we propose to clone HBRV superantigen from PBC patient lymphnode using conserved viral superantigen sequences. This will help highlight superantigen proteins in PBC and shed light on their contribution to PBC pathogenesis.

  • Subjects / Keywords
  • Graduation date
    Spring 2022
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/r3-ds04-y272
  • 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.