Identification, characterization, and functional study of enhancer  RNAs in human adaptive immune cells

Enhancer RNA (eRNA) is a recently discovered class of non-coding RNAs that play an important role in the regulation of gene transcription. These RNA molecules are transcribed from enhancer regions of the genome and can modulate the activity of target genes by interacting with various transcriptional and epigenetic regulators. Recent studies have revealed that eRNA plays a critical role in various biological processes, such as immune cell activation, and diseases, including cancer, and can serve as a promising therapeutic target. The immune system is a highly specialized system including innate immunity and adaptive immunity that maintains the homeostasis of the body and eliminates malignant cells such as tumor cells and pathogens such as bacteria and viruses. Large numbers of eRNAs have been identified in neurons, and human cancers, and there are a few eRNAs that are identified from innate immune cells. However, the manifestation of eRNAs in adaptive immune cells is incompletely understood. Questions such as how many actively transcribed eRNAs are in each adaptive immune cell population, what are the genomic signatures of the adaptive immune-specific eRNA generating loci and how these eRNAs are functioning in immuno-regulation under homeostasis and infections are largely unknown. To address these questions, firstly, I identified 2107 eRNAs from human B, CD4+, and CD8+ T cells by combining Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), enhancer marker Chromatin Immunoprecipitation Sequencing (ChIP-Seq) and strand-specific ribosomal RNA (rRNA)-depleted RNA sequencing (Ribo-depleted RNA-Seq) assays. The eRNA-generating loci are marked by specific histone modifications and transcription factor binding profiles. Among all the eRNAs identified, I focused on a highly expressing eRNA. I found this eRNA regulates the expression of its target gene in human immune cells in vitro. The DNA sequence, eRNA and gene expression, chromatin accessibility, and enhancer-promoter interaction of the eRNA-gene locus are all conserved between human and mouse adaptive immune cells. In mouse models, deletion of the eRNA-generating locus downregulates its target gene expression and T cell receptor (TCR) signaling pathway activity, reduces the number of marginal zone B cells and naïve CD4 T cells, and impairs follicular helper T (Tfh) cell function upon immunization, resulting in reduced number of class-switched B cells and antigen-specific B cells. We further demonstrated that the induction of the eRNA target gene mRNA is correlated with anti-Spike and SARS-CoV-2 neutralizing antibody production in human donors upon mRNA vaccination, which highlights the functional importance of this eRNA in vaccination biology. This study provided a framework for investigating the function of adaptive immune-specific eRNAs.