Extraordinary diversity of HLA class I gene expression in single cells contribute to the plasticity and adaptability of human immune system

Abstract

HLA, the coding genes of human major histocompatibility (MHC) proteins, play a crucial role in the human adaptive immune system by presenting antigenic peptides to T cell receptors on T cells. HLA-A, HLA-B and HLA-C, these 3 Class I HLA genes are one of the most polymorphic loci in the human genome. For decades, HLA typing has been performed prior to tissue and stem cell transplantation. However, beyond the role in tissue matching, HLA has also been implicated in a wide array of autoimmune diseases and HLA genotypes and expression levels are closely associated with cancer patients prognosis as recent studies have revealed. Recently methods have been developed to perform HLA typing and HLA expression quantification together by using RNA-seq techniques. However, these bulk RNA-seq experiments are measuring an averaged signal of cell populations. Single-cell RNA-seq (scRNA-seq) has regained its popularity due to its power to reliably resolve single RNA transcriptomes at large scales. In our present study, we did HLA typing using three independent scRNA-seq datasets. Interestingly, we found that single cells from the same donor could be classified into different groups where each group has a distinct expressed HLA genotype (e.g., HLA-A, heterozygous or homozygous); in other words, HLA class I genes show abundant allele specific expression in single cells. This phenomenon has been repeatedly observed in a total of 14 donors from 3 independent datasets (one is breast epithelium, another two are multiple myeloma). Our systematic analysis of HLA class I gene expression using multiple scRNA-seq datasets has uncovered a putative mechanism, where by fine tuning HLA class I expressions both at the quantity and allele levels, our immune system is able to handle various internal challenges through single cells equipped with extraordinary diverse HLA expression patterns.

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“…Different T cells express a wide range of ratios of the two alleles, some cells expressing both alleles, but others expressing almost entirely one allele or the other (well outside the 98% confidence interval of what is expected by the average ratio). This is in keeping with a preprint that found allele-specific expression of HLA class I genes in normal breast epithelial cells, as well as in multiple myeloma cells 29 ; other single-cell studies have found changes in allele-specific expression during T cell activation 30 , and identified HLA expression quantitative trait loci 31 .…”

Prediction of HLA genotypes from single-cell transcriptome data

“…Darby et al. previously demonstrated that individual cells do not express HLA transcripts at a sufficient level for reliable and complete genotyping at the single cell level ( 15 ). Therefore, we sought to achieve sufficient read coverage at HLA loci by pooling reads from all cells of an individual sample into a “pseudobulk” data set.…”

“…However, it is unclear if these methods can be applied to data from single-cell RNA sequencing (scRNA-seq) experiments due to differences in sequencing chemistry and transcriptome coverage. One attempt to obtain genotypes from single cells observed that very few cells express HLA genes at a high enough level to generate genotype predictions for individual HLA loci ( 15 ).…”

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

“…The approach of using De Bruijn graphs to improve isoform and haplotype quantification has been considered before (Patro et al 2017; Bray et al 2016), but has not yet been applied to scRNA-seq data until this study. A recent pre-print (Tian et al 2019) genotyped individual cells for HLA class I using scRNA-seq data but did not address allele-specific expression on the molecule level.…”