Discovery and Functional Characterization of Biomarkers in Clear Cell Renal Cell Carcinoma

ORCID

https://orcid.org0000-0003-4082-6723

Date of Award

1-31-2025

Author's School

Graduate School of Arts and Sciences

Author's Department

Chemistry

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

Not all tumors are created equally, nor should they be treated as such. Modern research has uncovered a multitude of genetic aberrations, genomic dysregulation, and epigenetic modifications that contribute to cancer. While cancers are classified based on their tissue of origin and may share common features or pathways, the tumor microenvironment is far from uniform. It comprises a dynamic network of cell populations with divergent genomic profiles, all of which collectively drive tumor progression—with some tumors more efficient and aggressive than others. The heterogeneity within these tumors makes it notoriously harder to treat, as standard therapies fail to address the varied mechanisms employed by all subpopulations within the tumor, resulting in treatment resistance, tumor reoccurrence, and poor patient outcomes. However, precision medicine has emerged as a promising strategy to tackle this challenge, offering personalized therapeutic plans based on the biomarkers and molecular profile of a patients tumor. By tailoring treatment targeting specific dysregulated pathways and markers, unique to each tumor biopsy, we can more effectively combat standard therapy-resistant tumor subpopulations and ultimately improve patient outcomes. This study aims to identify, characterize, and evaluate tumor cell-specific markers with potential as both diagnostic biomarkers and therapeutic targets in aggressive clear cell renal cell carcinoma (ccRCC). Kidney cancer encompasses several subtypes, with ccRCC as the most common subtype accounting for more than 80% of all renal cell carcinoma (RCC) cases. Despite initial treatment responses, approximately 70% of ccRCC patients develop resistance within months, and a third of all patients eventually develop reoccurrence. This highlights the need for additional therapeutic strategies and personalized treatment plans. In this study we use single nucleus RNA sequencing, bulk RNA sequencing, and bulk proteomics, to identify and characterize multiple tumor-specific markers, with a functional focus on two key candidates: Ceruloplasmin (CP) and Ubiquitin C-terminal hydrolase L1 (UCHL1). Both CP and UCHL1 are secreted proteins, and our findings associate its transcriptomic overexpression with lower overall survival and increased tumor grade in ccRCC. Through CRISPR-mediated knockout (KO) and shRNA knockdown (KD) cell line experiments, we characterize CP and UCHL1 as modulators associated with epithelial-mesenchymal transition (EMT) and inflammation, two pathways known to drive tumor progression and aggressiveness. Functional assays revealed that UCHL1 KO reduces cell proliferation, colony formation, and tumor growth in cell derived xenograft (CDX) models. Additionally, patient-derived xenograft (PDX) models and in vitro treatment assays demonstrated the therapeutic potential of combining UCHL1 inhibitors with tyrosine kinase inhibitors (TKIs), as the combinational treatment significantly reduced tumor and cell growth compared to single agent treatments. Together, this dissertation identifies CP and UCHL1 as promising biomarkers and therapeutic targets in ccRCC, with a particular emphasis on UCHL1 as a critical driver of tumor aggressiveness and a compelling candidate for combinational therapy strategies.

Language

English (en)

Chair and Committee

Li Ding

Committee Members

Feng Chen; John-Stephen Taylor; Jonathan Barnes; Kevin Moeller

This document is currently not available here.

Share

COinS