Work

PD15-12 Single-Nuclei Multiomic Analysis of Small Intestinal Neuroendocrine Tumors and Matched Liver Metastases Reveals Gene Expression Changes Associated With Disease Progression

Year: 2024

Type: article

Abstract: S.G. Andrews: None. S. Rajhans: None. T. Truongvo: None. J.P. Madigan: None. S.D. Forsythe: None. M. Kelly: None. J. Del Rivero: None. J.M. Hernandez: None. N. Nilubol: None. E. Arda: None. S.M. Sadowski: None. Metastatic lesions of small intestinal neuroendocrine tumors (siNETs) cause detrimental health effects, including carcinoid syndrome, hepatic injury, and impact survival. siNETs are rare and understudied. Limited studies have shown low mutational burden relative to other cancers; therefore, other mechanisms governing gene expression likely affect tumor progression and metastasis formation. Gene expression changes driving siNET progression are largely unknown and may be due to epigenomic alterations and structural variants. In the first assessment of both transcriptomic and epigenomic changes in siNET metastasis, we analyzed matched patient primary and liver metastases samples to assess intertumoral heterogeneity, elucidate epigenetic mechanisms, and investigate possible drivers of tumor progression, with the goal of discovering novel targets for therapy. Nuclei were isolated via homogenization and density gradient separation, then captured via 10X Genomics Chromium. Single-nuclei RNA-Seq and ATAC-seq libraries were generated and sequenced using Illumina NovaSeq instruments. After read alignment and quality control, 3,300-7,000 nuclei were analyzed per sample. Data analysis was completed via Trinity CTAT inferCNV, Seurat, ClusterProfiler, and Signac. Tumor cells were labeled via enriched copy number variation. Accessory cells were labeled via biomarker expression. Our cohort consisted of three patient-matched primary siNETs and liver metastases, one patient normal liver sample, and one healthy duodenal sample. Upon dimensionality reduction, all tumor samples clustered separately from normal controls. Inferred copy number variation analysis of matched lesions from each patient demonstrated aberrant copy number alterations (CNA); these somatic CNA signatures demonstrated varied clonal trajectories from primary to metastasis among the three patients. Gains of segments of chromosome 2 were common among all three sets of tumors. After cluster profiling of each patient, transition clusters that included cells from matched primary and metastatic tumors demonstrated transcriptomic alterations of alpha- and beta-catenin, syntaxin, and cadherin-binding pathways, as well as pathways governing lipoprotein particle receptor and tyrosine phosphatase activities. Following differential gene expression analysis, transition clusters showed silencing of oncogene RAB3C, oncogenic transcription factor SOX5, cell adhesion factor PTPRT and phosphodiesterase PDE10A, with an upregulation of these genes within clusters representing the invasive and progressive liver metastases. This study demonstrates multiple processes associated with tumor progression in siNETs. This research may provide new insights for targeted therapy of this rare and understudied disease, which currently faces limited treatment options and poor prognosis in advanced stages. Sunday, June 2, 2024

Source: Journal of the Endocrine Society

DOI: 10.1210/jendso/bvae163.2469