scHLAcount: Allele-specific HLA expression from single-cell gene expression data

Abstract

Studies in bulk RNA sequencing data suggest cell-type and allele-specific expression of the human leukocyte antigen (HLA) genes. These loci are extremely diverse and they function as part of the major histocompatibility complex (MHC) which is responsible for antigen presentation. Mutation and or misregulation of expression of HLA genes has implications in diseases, especially cancer. Immune responses to tumor cells can be evaded through HLA loss of function. However, bulk RNA-seq does not fully disentangle cell type specificity and allelic expression. Here we present scHLAcount, a workflow for computing allele-specific molecule counts of the HLA genes in single cells an individualized reference. We demonstrate that scHLAcount can be used to find cell-type specific allelic expression of HLA genes in blood cells, and detect different allelic expression patterns between tumor and normal cells in patient biopsies. scHLAcount is available at https://github.com/10XGenomics/scHLAcount.