Doctor of Philosophy (PhD)
Biochemistry & Molecular Biology
Surinder K. Batra
PDAC is a pancreatic epithelial malignancy and demonstrates aggressive progression and bleak patient prognosis. Despite decades of research, the evolution of novel diagnostics and intervention modalities for PDAC is stagnant. This dissertation explores the characteristic aberrant and elevated expression of mucins in PDAC. Beginning with the hypothesis that mucins are associated with disease aggressiveness, analysis of PDAC patient survival in TCGA revealed no associations between single mucin expression and patient survival. This led to the underlying issue of PDAC tumor cellularity since this disease demonstrates variability in the proportion of cancer cells within the tumor. Tumor purity assessed with the ABSOLUTE computational algorithm is reported for all patient samples in the TCGA PDAC dataset. Using these purity scores, a mathematical correction of epithelial-specific mucin expression was devised. Again, no significant association between PDAC patient survival and mucin expression was found. Therefore, I investigated combinatorial expression of mucins by Spearman’s nonparametric PCA, which resulted in four groups of mutual expression: Group One= MUC7/12/17, Group Two= MUC1/3/13/19/20, Group Three= MUC6/15/22, and Group Four= MUC2/4/5AC/5B/16/21. These four groups were associated significantly with survival outcomes. To determine the biological implications of vi these four groups, PCA scores for all patients were correlated to whole transcriptomes. Significantly correlated genes were assessed for biological pathway upregulation. The four pathway composites revealed potential pathological signatures unrelated to previous PDAC classifications, representing novel PDAC subtypes. The role of mucin splice variants (SVs) was assessed and correlated to PDAC patient survival. Bioinformatic studies revealed 12 total mucin SVs significantly associated with survival. Better survival was correlated with expression of four MUC1, one MUC13, and one MUC20 SVs. High expression of two MUC4, one MUC15, one MUC16, one MUC21, and one MUC22 SVs were correlated with worse survival. The correlation between MUC4-sv-215 and MUC13-sv-201 SVs and survival were PCR validated in PDAC patient samples. These MUC4Δ6 prognostic findings contributed to in vitro studies and the development of a novel nanoparticle assay that detects MUC4-sv-215 in patient biofluids. The cumulative impact of the results described here may advance the clinical utility of mucins and associated SVs for improved diagnosis of PDAC.
Thompson, Christopher M., "Mucin and Splice Variant Profiles of Pancreatic Adenocarcinoma Predict Patient Survival and Subtyping" (2021). Theses & Dissertations. 541.
Available for download on Friday, October 29, 2021