Investigation of HPV16-related genomic alterations in cervical squamous cell carcinoma

This study examined the effects of human papillomavirus genomic integration into the host genome on host gene expression in cervical squamous cell carcinoma (CSCC) tumors. The genomic analysis involved clinical and genomics data analysis using bioinformatics and statistical methods. The Cancer Genome Atlas Program (TCGA) resource was used to download Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma data. Molecular differentiation was performed through differential gene expression (DGE) analysis conducted using R 4.5.1, R Studio, and packages from Bioconductor. Experimental design was created to compare samples with HPV 16 integrated genome with the non-integrated genome. Gene expression involved filtration criteria setting a minimum threshold of 10 counts per gene and 10 samples in each group. The median of ratios method was used to normalize the raw count data, accounting for differences in sequencing depth and RNA composition between samples. A negative binomial distribution model was fitted to the normalized count data for each gene. Statistically significant genes were filtered to an adjusted p-value <= 0.05 and log2 fold change >= 2 yielding upregulated and downregulated genes. Pathway analysis and prognosis assessment identified mechanisms that may have a role in the development of CSCC. Improved insights into the causes and consequences of HPV genomic integration could significantly improve strategies and lead to advancements in the prevention, detection, and treatment of HPV associated cancers.

Name thesis:degree_name

M.S. (Master of Science)

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Bioinformatics (UMKC)

Grantor

University of Missouri-Kansas City

Year dc:date.issued

2025

Author dc:creator

• Richards, Christopher Thomas

Advisor dc:contributor.advisor

• Zeeshan, Saman

Language dc:language.iso

en_US

Handle dc:identifier.uri

https://hdl.handle.net/10355/110232

OAI identifier oai:identifier

oai:mospace.umsystem.edu:10355/110232