Single cell Rna-sequencing identifies numerous cell sub-types and suggests lineage plasticity in human atherosclerotic plaques

Atherosclerotic plaque (AP) is a complex pathological formation, containing numerous interacting cell types. Our understanding of the cellular composition and dynamics of AP is mainly based on the evaluation of a limited number of known markers and therefore may be incomplete and biased. Here we employ single cell transcriptomics (scRNAseq) to identify and define cell types in human plaques and to reconstruct their lineage trees and relationships.We have performed scRNAseq on atherosclerotic plaques obtained from 3 (discovery cohort) and 6 (validation cohort) carotid endarterectomy patients. We have employed the scRNAseq based on CEL-seq2/SORT-seq protocol coupled with fluorescence-activated cell sorting. This method allowed us to specifically select viable and nucleated single cells. Finally we have used RaceID and StemID algorithm to identify common and rare cell types and to perform the lineage tracing analysis.We have identified 15 different cell subtypes, among others endothelial cells (EC), macrophages and smooth muscle cells (SMC). Besides these major types we were able to detect less frequent cell populations - including ACKR1+ venular endothelial cells. Notably, we were able to find individual cells and cell clusters co-expressing both EC and SMC genes, such as SPARC, COL6A1, PECAM1 and CD34. These cells exhibited increased median transcriptome entropy and connectivity, relative to other EC and SMC clusters - altogether supporting their progenitor role and suggesting the plasticity of cell identity in AP.ScRNAseq enabled us to identify and define cell subtypes present in human AP. Our data suggest the cellular lineage plasticity in human AP.Biopharmaceutic