IMIB - Institute for Molecular Infection Biology

Integrative analyses of CMV translatomes and MHC-I ligandomes

The genomes of cytomegaloviruses (CMV) are among the largest and most complex viral genomes known. Functional genomics methodology including large-scale RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) recently resulted in the identification of hundreds of new viral gene products for the human CMV (HCMV). A unified and standardized nomenclature of HCMV gene products is still missing. Accordingly, so far only very few studies have already started to analyze the function of any of the new HCMV gene products.

In addition to large viral ORFs of >100 amino acids (aa), cytomegaloviruses encode hundreds of short ORFs (sORFs) of 3 to 99 aa. Many of these represent “upstream open reading frames” (uORFs), which are expressed upstream of annotated larger ORFs in the 5’ leader region of the mRNA previously thought to be untranslated (5’-UTR). The presence of large numbers of viral uORFs is not surprising as more than half of all human genes also express sORFs. Interestingly, the vast majority of these do not encode for functional polypeptides as the respective gene products are rapidly degraded upon translation. Recently we were able to demonstrate that sORF-derived polypeptides are nevertheless efficiently presented to patrolling CD8 T cells via MHC-I. Priming of T cells against CMV is believed to be mainly mediated by cross-presenting (i.e. non-infected) macrophages. We hypothesize that sORF-derived peptides, which are efficiently presented by MHC-I but of low total abundance in the proteome, represent poor substrates for cross presentation and CD4-CD8 T cell augmentation. These peptides thus represent a new class of antigens. Cellular uORFs orchestrate gene expression by regulating translation initiation of the downstream ORF. We hypothesize that herpesvirus uORFs enable these viruses to adapt viral gene expression to the infected cell type and their local environment to escape detection by the host’s immune system.

In this project, we will provide a state-of-the-art annotation of both the HCMV and MCMV genome. We will utilize this information to identify viral T cell epitopes for novel diagnostic, prophylactic and therapeutic approaches. We will also investigate the immunological importance of viral sORFs in the cellular control of CMV.