Alternative polyadenylation analysis in myelodysplastic syndromes, glioblastoma and gastric cancer

Date

2014

Author

Çınkıllı, Tuna

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Alternative polyadenylation (APA) is the process by which different length transcript isoforms are generated. Upon the changes in poly(A) tail positioning, especially in the 3' untranslated regions (UTRs), resulting mRNA isoforms may be regulated differently by negative or positive regulatory elements. Under normal circumstances, differential APA patterns have been observed during development or proliferation events. Therefore, such differential preferences of polyadenylation sites may be important in proliferative diseases. Indeed, APA events appear to be altered in cancer cells. A general trend towards 3' UTR shortening was observed in several cancers. The main aim of this study was to investigate alterations in APA patterns of myelodysplastic syndromes, glioblastoma multiforme and gastric cancer which are aggressive, rapidly proliferating diseases. To this end, APADetect, a probe-based microarray analysis tool, was used to analyze microarray datasets. For each transcript, the short/long ratio (SLR) values were calculated using the proximal and distal probe intensities according to poly(A) site location. Significant alterations in the SLR values were then detected by Significance Analysis of Microarrays (SAM). Further analyses were carried out to reveal any potential correlations with patients characteristics. Significantly altered transcripts were also analyzed for functional enrichment using gene ontology tools. Indeed, enrichment patterns could be seen in transcripts with functions related to both cell division cycle and tissue specificity. In addition to the bioinformatics based analyses, we focused on the TCF3 gene transcript which we observed to be commonly altered in the three diverse types of proliferative diseases that we analyzed and experimentally confirmed the presence of the shorter 3' UTR transcript isoform in a gastric cancer cell line. These results indicate that changes in APA patterns may be playing important roles in malignant transformations. While the results reported here are preliminary, we plan to extend these observations to an experimental setup to verify and investigate functional relevance. Further studies are necessary to identify novel diagnostic or prognostic markers for use in the medical field.

Subject Keywords

Myelodysplastic syndromes., Alternative Polyadenylation, Polyadenylation., Non-coding RNA., Glioblastoma multiforme., Stomach

URI

http://etd.lib.metu.edu.tr/upload/12618336/index.pdf
https://hdl.handle.net/11511/24335

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Graduate School of Natural and Applied Sciences, Thesis