Cell-level Expression of Loci Reported to Harbor Somatic Mutations in Cancer from Single Cell RNA-seq Data

Single-cell RNA sequencing (scRNA-seq) has emerged as a groundbreaking technology to uncover the heterogeneity of cells and reveal the complexities of cancer at an unprecedented resolution. This thesis systematically explores the current knowledge, methodologies, and applications of scRNA-seq in cancer research, highlighting novel techniques to identify mutations and analyze their expression in single cells.The research begins by detailing the existing approaches to detect mutations in single cells using 10x Genomics scRNA-seq data, comparing their advantages and disadvantages. Building upon this foundation, we present a novel approach, distinguished by its ability to split pooled scRNA-seq alignments, enabling the identification of low-frequency mutations and their precise allocation to individual cells. In our rigorous analysis, we uncovered more than 200,000 Single Nucleotide Variants (SNVs) across 28 publicly available tumor and normal scRNA-seq datasets, spanning diverse cancer types, including prostate cancer, cholangiocarcinoma, neuroblastoma, and non-small cell lung carcinoma.The thesis provides comprehensive coverage of the data analysis process, workflow, and results, emphasizing a specific mutation in the HIST1H4C gene. Subsequent in-depth analyses explore the expression of this mutation across various cancer types, confirming findings with high-quality sequencing reads, performing Differential Gene Expression (DEG) analysis, and utilizing tools like STRING and Reactome for downstream analysis. These analyses lead to the discovery of associations between the mutations and specific networks and pathways related to DNA REPAIR and REPLICATION.The concluding chapters discuss the findings, articulate the challenges faced in the field, and outline a promising roadmap for future research directions. The key conclusions highlight the need for cell-level analyses to understand novel variants, the likely functionality of these variants, and their appearance in multiple samples.This thesis contributes significant insights into the intricacies of scRNA-seq in cancer research, offering an innovative methodology and comprehensive analysis that may pave the way for transformative advances in personalized medicine and cancer therapy. By shedding light on the complexities of single-cell genomics, it provides a robust foundation for future investigations into the cell-specific dynamics of cancer, holding the potential to revolutionize our understanding of this complex disease.

Author

• Arestakesyan, Hovhannes

Language

• en

Keyword

• Single-cell RNA sequencing (scRNA-seq)
• HIST1H4C V61F mutation
• cancer genomics
• novel variants
• somatic mutations
• RNA-origin mutations

Date created

• 2023

Type of Work

• Master's Thesis

License

• All rights reserved

Rights statement

• In Copyright

GW Unit

• Bioinformatics and Molecular Biochemistry

Degree

• M.S.

Advisor

• Horvath, Anelia AH

Persistent URL

•  https://scholarspace.library.gwu.edu/etd/dr26xz14r