Abstract 14391: The Transcriptional Landscape of Liver Sinusoidal Endothelial Cells

Abstract

Introduction: Human liver endothelial cells (HLEC) are a heterogeneous cell population. Single cell transcriptomics and immunostaining assays have categorized HLEC into two major groups according to their location within the liver lobules (zone 1 or periportal HLEC and zones 2/3 or central venous (CV) HLEC). Hypothesis: Cellular deconvolution of the bulk transcriptome of HLEC will highlight important properties of HLECs and their transcriptional regulators. Methods: We uniformly processed all bulk RNA-seq data from HLECs in Gene Expression Omnibus. We used CIBERSORTx with human liver single cell RNA-seq data to perform cell type deconvolution of bulk HLEC RNA-seq. We compared the transcriptome of HLEC subpopulations to that of HUVEC. We then applied the HOMER motif finding algorithm on the promoters of genes up/downregulated in HLEC compared to HUVEC. Results: We analyzed data from 10 HLEC samples and 107 HUVEC samples from 37 independent experiments. Principal component analysis revealed that 6 of the 10 HLEC samples have robust transcriptional differences compared to HUVEC. CIBERSORTx showed that those 6 HLEC samples correspond to CV HLECs and can be identified by FCGR2B expression. Differential gene expression analysis revealed enrichment of inflammatory and coagulation pathways in CV HLEC and enrichment of proliferation and mitosis pathways in HUVEC. CV HLEC showed increased expression of factors VIII, X, XII, Protein S and antithrombin III. We validated gene expression at the protein level by Western blot. A transcription factor (TF) prioritization approach using HOMER motif enrichment revealed a potential role for E2F, and RXR-RAR TF as primary determinants of the differences between HUVEC and CV HLEC. Conclusions: We identify and characterize CV HLEC as a distinct endothelial subtype relevant to inflammation and coagulation. We also identify downregulation of E2F and upregulation of RXR-RAR TF as potential key regulators of the CV HLEC transcriptome.