Alternative transcript variants of the matricellular protein SPARC in cancer

Cancer is a devastating disease and a leading cause of death, causing 9.6 million deaths worldwide in 2018, according to new GLOBOCAN statistics. Each cancer has been extensively investigated and advances in diagnostics and treatment have improved the statistics for survival, drastically over the years. Pancreatic cancer has a 5-year survival rate that averages under 5%. One of the main reasons for this is that 80-90 percent of PDAC cases are diagnosed at an advanced stage at which post surgical resection, which would have dramatically improved the prognosis, is not an option. An early-detection biomarker is essential to early diagnosis in a cancer that does not present with unique symptoms. Secreted Protein Acidic and Rich in Cysteine (SPARC) is a marticellular protein that functions by modulating cell-cell and cell-extracellular matrix (ECM) interactions. It has been investigated as a potential biomarker for pancreatic cancer for the role it plays in proliferation and modulation of the extracellular matrix. In this project, we employ a bioinformatic approach to assess the known sequence for each SPARC transcript variant. Results show that SPARC-001, SPARC-210, SPARC-004 and SPARC-007 differ from each other primarily in the 5' UTR which implies a level of translational control. SPARC-005 and SPARC-008 have different translation start sites from which the resulting protein product is truncated at the N-terminal and missing the signal peptide, implying that they are intracellular variants. We amplify multiple SPARC transcript variants (SPARC-001, SPARC-007, SPARC-008, SPARC-201 and SPARC-004) that have previously been described only in RNA-seq studies. Moreover, we characterize the tissue-specific expression of each variant, across multiple cancer cell lines as well as stromal type cells, qualitatively and quantitatively. The project showed one of the major pitfalls of exon-exon junction primer design which brought the expression of SPARC-005 into doubt. The subsequent investigation lead to the discovery of an entirely novel transcript variant of SPARC which was designated SPARC-001x and has a truncated 3' UTR. This further strengthens the case that variation in SPARC transcripts is mainly int he 5' UTR and 3' UTR. Expression of the shortened 3' UTR for SPARC-001x may be a characteristic modification in cancer that causes loss of regulation my micro RNA. We have further shown that hsa-miR-148b-3p downregulates SPARC-001x expression.Future experiments could explore exactly how SPARC expression is translationally regulated and the role it plays in cancer