Undergraduate Honors Theses

Date of Award

2021

Document Type

Undergraduate Thesis

Degree Name

BS

Department

Biomedical Sciences

Faculty Mentor

Glen Borchert

Abstract

To date, there are no known cures or effective preventative measures for cancer. Research has been conducted on small noncoding RNAs (ncRNAs) and noncoding RNAderived RNAs (ndRNAs) as potential contributors to cancer suppression and/or proliferation. Tumorigenesis may be slowed by identifying and targeting some ndRNAs that are frequently presented in different cases of cancer, which may improve patient prognoses. To identify these ndRNAs, we utilized next-generation sequencing (NGS), a DNA/RNA sequencing technology, to sequence nucleotides in the human transcriptome. Then, we analyzed NGS data in accordance with information from The Cancer Genome Atlas (TCGA) and Sequence Read Archive (SRA) to identify ndRNAs of interest. Our goal for this project is to identify ndRNAs that are highly expressed in five cancers (breast, lung, kidney, corpus uteri, brain) and ndRNAs that are highly expressed in controls. From here, we can determine which ndRNAs are differentially expressed. These ndRNAs may be significant biomarkers in earlier identification of cancer or the development of more curated therapies. For this project, we used Short Uncharacterized RNA Finder (SURFr) to process raw RNA sequencing (RNAseq) files obtained from TCGA. We then conducted a correlation analysis of TCGA data, followed by an analysis of SRA patient control data. Overwhelmingly, specific miRNA expressions were most elevated across all five cancers, notably miR-21. Whereas miRNAs that are differentially expressed across many cancers (miR-21 in this study) may be significant biomarkers in cancer research, differentially expressed miRNAs in certain demographics or cancers (miR-29a, miR-205, and miR-9 in this study) may be biomarkers for specific cancers.

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