Keywords

Natural killer cells; LNCaP; Long read sequencing; Alternative Splicing; Prostate Cancer; Nanopore

Abstract

NK cells play a significant role in anti-tumor activity, yet the transcriptomic mechanisms underlying NK cell dysfunction in the prostate cancer tumor microenvironment remain generally poorly characterized. While most transcriptomic studies focus on gene-level expression, alternative splicing and isoform-level analysis may reveal additional levels of regulation not identified in traditional analysis. The overall goal of this study was to characterize gene and isoform-level changes in NK cells exposed to in vitro prostate cancer conditions and to evaluate whether isoform-level analysis could provide additional depth and insights beyond gene-level analyses. NK92-MI cells were co-cultured with LNCaP prostate cancer cells using direct-contact and indirect-exposure systems at 3 and 6-hour time points, followed by RNA isolation and long-read sequencing. Further analysis revealed broad changes in NK cell gene expression as well as shifts in transcript and isoform usages across comparisons. Importantly, gene-level and isoform-level patterns did not always correspond with each other, indicating that some sort of isoform-level remodeling may be occurring even when gene-level changes are limited. Individual analysis of functionally relevant NK cell genes, GZMB, IL32, CD160, NKG7, and CD3e, revealed condition-specific gene expression and splicing patterns with potential implications for NK cell cytotoxic activities. Together, these findings give preliminary support for the idea that isoform-level transcriptomic analysis can reveal additional molecular features of NK cell activities in the prostate cancer microenvironment. This establishes an overall framework for future studies linking splicing signatures to NK dysfunction, activation, and disease progression.

Thesis Completion Year

2026

Thesis Completion Semester

Spring

Thesis Chair

Ram, Daniel

College

College of Medicine

Department

Burnett School of Biomedical Sciences

Thesis Discipline

Life Science

Language

English

Access Status

Open Access

Length of Campus Access

None

Campus Location

Orlando (Main) Campus

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Rights Statement

In Copyright