Access Type

Open Access Dissertation

Date of Award

January 2021

Degree Type

Dissertation

Degree Name

Ph.D.

Department

Cancer Biology

First Advisor

Zeng-Quan Yang

Abstract

2’-O-methylation (2’-O-Me), one of the most common modifications within RNA, has multiple roles in modulating RNA structure, stability, and interactions, as well as gene transcription and translation. We previously performed integrative genomic and transcriptomic analysis of 58 RNA methyltransferases, and identified FTSJ3 (FtsJ RNA 2ʹ-O-methyltransferase 3) as significantly amplified/overexpressed in breast cancer. Knockdown of FTSJ3 inhibits breast cancer cell growth in vitro. However, the clinical significance, functional role, and molecular mechanism of FTSJ3 in human cancer remains to be elucidated. In the present study, we first analyzed the differential mRNA and protein expression of FTSJ3 between tumor and normal tissues in the TCGA (The Cancer Genome Atlas) and CPTAC (Clinical Proteomic Tumor Analysis Consortium) data sets. We found that FTSJ3 was significantly overexpressed at both mRNA and protein levels in numerous tumor types including breast, lung, and liver cancers compared to normal samples. Higher FTSJ3 expression was associated with high-grade tumors, advanced stages, and poor disease prognosis in certain tumors. To elucidate molecular mechanisms of FTSJ3 in promoting cancer progression, we performed CLIP-sequencing (High-throughput sequencing of RNA isolated by crosslinking immunoprecipitation) in FTSJ3-amplified SUM52 breast cancer cells. We found that FTSJ3 targeted a diverse set of RNAs (rRNA, mRNA, and lncRNAs), of which rRNA was the most highly represented. Additionally, RNA-seq analysis with FTSJ3 inhibition identified 745 genes that had been differentially expressed with statistical significance (p-value < 0.05). KEGG enrichment analysis revealed that FTSJ3 targeted genes were involved in multiple pathways important for cancer, notably: the ribosome and DNA replication. We also performed bioinformatics analysis of the proteogenomic landscape and functional dependency of FTSJ3 in human cancer, together with pull-down assays to identify FTSJ3 interacting protein partners, one of which was NIFK. In summary, our work revealed clinical and biological importance of 2’-O-methyltransferase FTSJ3 in cancer progression, thus pointing to FTSJ3 as a promising therapeutic target for certain cancer patients.

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