EPIGENOMIC AND EPITRANSCRIPTOMIC LANDSCAPE: ANALYSIS, PERFORMANCE ASSESSMENT, AND INTEGRATIVE MULTI-OMICS PROFILING IN HUMAN COLORECTAL CANCER

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dc.contributor.advisorDeng, Youping
dc.contributor.authorGong, Ting
dc.contributor.departmentMolecular Biosciences and Bioengineering
dc.date.accessioned2024-02-26T20:13:48Z
dc.date.issued2023
dc.description.degreePh.D.
dc.embargo.liftdate2025-02-23
dc.identifier.urihttps://hdl.handle.net/10125/107867
dc.subjectBioinformatics
dc.subjectAlgorithsm comparison
dc.subjectColorectal Cancer
dc.subjectDNA methylation
dc.subjectEpigenomic
dc.subjectEpitranscriptomic
dc.subjectRNA methylation
dc.titleEPIGENOMIC AND EPITRANSCRIPTOMIC LANDSCAPE: ANALYSIS, PERFORMANCE ASSESSMENT, AND INTEGRATIVE MULTI-OMICS PROFILING IN HUMAN COLORECTAL CANCER
dc.typeThesis
dcterms.abstractThe interplay between genetic and epigenetic factors is crucial in the onset and progression of colorectal cancer (CRC), a disease characterized by its complexity and high morbidity and mortality rates globally. This dissertation is focused on unraveling the roles of epigenomic and epitranscriptomic modifications in CRC, with the aim of identifying significant biomarkers and characterizing their functional implications through advanced bioinformatics and machine learning techniques.The first part established a foundation by examining DNA methylation, a crucial epigenetic mechanism. It delved into whole-genome bisulfite sequencing (WGBS), presenting a detailed comparison of methodologies and tools for analyzing DNA methylation patterns. This set the stage for understanding aberrant methylation in CRC, highlighting its significance in disease pathology, and offering insights into the complexities of epigenomic profiling. Building upon this, the second part expanded the scope to include a broader range of epigenetic methods. It presented a multi-platform assessment, utilizing several human cell lines to evaluate the reproducibility and efficiency of different genome-wide methylome sequencing protocols. This comprehensive characterization not only benchmarked current methods but also linked DNA methylation patterns to the wider epigenomic alterations observed in CRC. Subsequently, the final part evaluated m6A MeRIP-Seq data analysis pipelines, focusing on their sensitivity and specificity in detecting and quantifying m6A modifications, ensuring that the results can reliably inform about the presence and potential role of m6A modifications in CRC. Utilizing the selected m6A MeRIP-Seq pipelines in conjunction with RNA sequencing data, the analyses provide a comprehensive epitranscriptomic characterization of CRC. This involved identifying novel m6A modification patterns that are functionally relevant to CRC's development and progression. Furthermore, the research delved into the interaction between epitranscriptomic alterations and their subsequent impact on gene expression, signaling pathways, and the tumor microenvironment, thereby providing a holistic view of the molecular dynamics at play in CRC. This multifaceted approach endeavors to bridge the gap between epigenomic and epitranscriptomic research, offering a thorough understanding of their implications in CRC. The insights gained from this study aim to contribute to the field of cancer genomics, potentially leading to the development of new diagnostic and therapeutic strategies.
dcterms.extent108 pages
dcterms.languageen
dcterms.publisherUniversity of Hawai'i at Manoa
dcterms.rightsAll UHM dissertations and theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission from the copyright owner.
dcterms.typeText
local.identifier.alturihttp://dissertations.umi.com/hawii:11966

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Ph.D. - Molecular Biosciences and Bioengineering