ASPO051 - A multi-omics approach to the discovery of molecular therapies: integration of miRNA/mRNA-seq and proteomic analysis of lymphatic malformation endothelial cells
Saturday, April 30, 2022
4:00 PM – 5:00 PM CT
Location: Landmark B
Ravi Sun, BE1, Haihong Zhang, MD/PhD1, Stephanie Byrum, PhD2, Gresham Richter, MD1, Graham Strub, MD/PhD1;
1Otolaryngology, Univ. of Arkansas for Med. Sci., Little Rock, AR, 2Biochemistry and Molecular Biology, Univ. of Arkansas for Med. Sci., Little Rock, AR.
MD/PhD Candidate University of Arkansas for Medical Sciences Little Rock , Arkansas
INTRODUCTION:Lymphatic malformation (LMs) are vascular anomalies (VAs) containing endothelial cells (LM-ECs) that harbor somatic DNA mutations, however these mutations are only present in a small fraction of cells. Epigenetic dysregulation of gene expression is a key mediator of multiple cancer pathogeneses, but whether this occurs in LMs is unknown. Here we demonstrate a powerful multi-omics-based approach to profile the expression of all miRNAs and mRNAs in LM-ECs and integrate this data with a simultaneously generated mass spectrometry-based proteomic analysis of all peptides. Comparison to an identically generated profile from normal lymphatic endothelial cells (HDLECs) yields a functional list of potentially altered miRNA-mRNA-peptide triads which may be dysregulated in LMs and may serve as promising molecular targets.
OBJECTIVE: To generate the “multi-ome” of LM endothelial cells and identify epigenetically disrupted pathways that contribute to LM development.
METHODS: LM tissue/fluid was collected from patients undergoing surgical treatment. LM-ECs were isolated with magnetic bead capture and cultured, and HDLECs served as normal controls. miRNA-seq, mRNA-seq, and phosphoproteomics were performed, and multi-omics data integration analysis was used to generate a network of miRNA-mRNA-protein expression.
RESULTS: Ten patients underwent resection of LM lesions/fluid, and HDLECs were obtained from 3 patients for comparison. Multi-omics analysis detected 2,632 miRNAs, 45,368 mRNAs, and 6,221 proteins. Comparison between LM-ECs and HDLECs yielded 127 differentially expressed miRNAs, 3,468 mRNAs, and 550 proteins. 307 differentially expressed matched mRNA-protein pairs were detected. Functional analysis of the 50 most significantly up or downregulated mRNA-protein pairs demonstrated pathways involved in regulation of lymphangiogenesis, cytoskeleton dynamics, growth/differentiation, migration, proliferation, apoptosis, fatty acid metabolism, and cell-cell adhesion as differentially regulated in LM-ECs.
CONCLUSION: Employing a multi-omics approach to pathway discovery is a powerful tool in the identification of epigenetic regulation of genes in vascular anomaly endothelial cells, potentially uncovering novel therapeutic targets.