Abstract 6081: Integrative genomic analysis of primary prostate tumors and corresponding lymph node metastases
Authors: Moreno Carlos S. , Winham Cynthia L. , Klein Emma R. , Huang Yijian , Schuster David M. , Sanda Martin G. , Osunkoya Adeboye O. 
Published: April 2023

Abstract
Background: Prostate cancer (PCa) is a highly heterogeneous disease, and mortality is mainly due to metastases. However, the molecular underpinnings that lead to the initial steps of metastasis have not been well characterized. We have performed integrative whole exome sequencing and transcriptome analysis of primary prostate tumor foci and corresponding lymph node metastases (LNM).
Design: Primary tumor foci (PTF) and LNM from 40 patients with high-risk PCa were analyzed by RNAseq. Two or more PTF and all available LNM greater than 0.4cm were subjected to sequencing. Of these 40 patients, 17 (42.5%) had LNM and 23 (57.5%) had benign LNs. A total of 155 tissue samples (97 PTF, 39 benign LNs, and 19 LNM) were sequenced and mapped to the human transcriptome with STAR mapper after QC trimming and removal of adapter sequences using TrimGalore. Differentially expressed genes between PTF, LNM, and benign LNs were identified using DESeq2, and gene set enrichment analysis was performed using WebGestalt. WES data was analyzed using GATK pipelines including Mutect2.
Results: A median of 57 million paired-end reads were obtained per sample, with a median of 10 million total readcounts per sample across the transcriptome, and 39,021 transcripts were detected in at least 5% of samples. Comparing PTF to LNM, 6203 transcripts were differentially expressed (p-adj &lt; 0.01). PTF were enriched relative to LNM in gene sets associated with Wnt signaling, hormone signaling, Hippo signaling, KRAS signaling, and the epithelial to mesenchymal transition. Comparing PTF from metastatic patients to non-metastatic patients, 1265 transcripts were differentially expressed (p-adj &lt; 0.01). PTF from metastatic patients were enriched in gene sets associated with cell cycle progression, oxidative phosphorylation, ER stress, fatty acid metabolism, and DNA repair. LNM gene sets were enriched in endoplasmic reticulum (ER) stress and oxidative phosphorylation. The top 500 upregulated genes in malignant tissues were significantly enriched in genes related to androgen and estrogen signaling as expected. We also identified a set of 193 genes whose expression was significantly increased in primary tumor over benign LNs and in LNM over primary tumors. This gene set was significantly enriched in genes related to oxidative phosphorylation and included oncogenes such as PIK3CB, NCOA2, and SCHLAP1. Integrative RNAseq analyses with WES will be discussed.
Conclusions: Signaling pathways associated with ER stress, oxidative phosphorylation, metabolism, and cell cycle progression are prominent in LNM of aggressive PCa. PIK3CB, NCOA2, and SCHLAP1 expression are significantly increased in LNM.
Citation Format: Carlos S. Moreno, Cynthia L. Winham, Emma R. Klein, Yijian Huang, David M. Schuster, Martin G. Sanda, Adeboye O. Osunkoya. Integrative genomic analysis of primary prostate tumors and corresponding lymph node metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6081.