Widespread and tissue-specific expression of endogenous retroelements in human somatic tissues

Abstract

Background: Endogenous retroelements (EREs) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. The dominant paradigm holds that EREs are expressed in embryonic stem cells (ESCs) and germline cells but are repressed in differentiated somatic cells. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a systemlevel evaluation of their expression in human tissues is lacking. Methods: Using RNA sequencing data, we analyzed ERE expression in 32 human tissues and cell types, including medullary thymic epithelial cells (mTECs). A tissue specificity index was computed to identify tissue-restricted ERE families. We also analyzed the transcriptome of mTECs in wild-type and autoimmune regulator (AIRE)-deficient mice. Finally, we developed a proteogenomic workflow combining RNA sequencing and mass spectrometry (MS) in order to evaluate whether EREs might be translated and generate MHC I-associated peptides (MAP) in Blymphoblastoid cell lines (B-LCL) from 16 individuals. Results: We report that all human tissues express EREs, but the breadth and magnitude of ERE expression are very heterogeneous from one tissue to another. ERE expression was particularly high in two MHC I-deficient tissues (ESCs and testis) and one MHC I-expressing tissue, mTECs. In mutant mice, we report that the exceptional expression of EREs in mTECs was AIRE-independent. MS analyses identified 103 non-redundant ERE-derived MAPs (ereMAPs) in B-LCLs. These ereMAPs preferentially derived from sense translation of intronic EREs. Notably, detailed analyses of their amino acid composition revealed that ERE-derived MAPs presented homology to viral MAPs. Conclusions: This study shows that ERE expression in somatic tissues is more pervasive and heterogeneous than anticipated. The high and diversified expression of EREs in mTECs and their ability to generate MAPs suggest that EREs may play an important role in the establishment of self-tolerance. The viral-like properties of ERE-derived MAPs suggest that those not expressed in mTECs can be highly immunogenic.

A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens

“…Considered for a long time as "junk" DNA, the remnants of retroelements still contains functional promoters, enhancers, ORFs, splice donor/acceptor sites and polyadenylation sites able to impact cell physiology (85) and can contribute to several key processes of our development and adulthood (86)(87)(88). In line with this, Larouche et al recently reported that various levels of ERE transcripts can be found in all human somatic tissues and that their expression is particularly predominant in mTECs which are responsible for T cell negative selection (89). These findings suggest that some antigens derived from these "domesticated" EREs are tolerated by the immune system.…”

“…These aeERE have been reported to affect cancer progression through both pro-and antitumoral mechanisms (95). Previous reports indicated that aeERE could generate viral-like neoantigens able to increase both the antigenicity and immunogenicity of tumor cells (89,94). Unlike the ERE-derived antigens expressed in normal tissues, those restricted to cancer cells (i.e., aeEREs) can be recognized by the immune system although they originate from non-mutated sequences.…”

The Origin and Immune Recognition of Tumor-Specific Antigens

“…This concept has important implications. First, annotated exons represent only 2% of the genome and many allegedly non-protein coding (non exonic) sequences are coding for proteins and do generate MAPs [23][24][25][26]. Second, epigenetic and splicing aberrations in cancer cells lead to the appearance of numerous proteins and MAPs that are not found in normal cells.…”

“…In contrast to MS analyses, transcriptomic analyses have been performed in many subjects on practically all cell types. Hence, when we identify aeTSA candidates, we evaluate whether its coding transcript is found in normal tissues from the GTEx database (https://gtexportal.org/home/) or in our datasets of mTECs [26]. We believe that inclusion of mTECs in the "negative controls" is important for three reasons: i) they orchestrate central immune tolerance [66], ii) they express much higher levels of MHC I molecules than other epithelial cell types [48], and iii) they promiscuously express more genes than other types of somatic cells [67,68].…”

“…Promiscuous gene expression in mTECs involves not only classic genes, but also other genomic regions such as endogenous retroelements [26]. The downside of this approach is that it can lead to the dismissal of genuine aeTSAs.…”