What can Ribo-seq, proteomics, and immunopeptidomics tell us about the non-canonical proteome?
Sebastiaan van Heesch
Group Leader, Princess Máxima Center for Pediatric Oncology and Oncode Institute
Ribosome profiling (Ribo-Seq) has proven transformative for our understanding of the human genome and proteome by illuminating thousands of noncanonical sites of ribosome translation outside the currently annotated coding sequences (CDSs). A conservative estimate suggests that at least 7000 noncanonical ORFs are translated, which, at first glance, has the potential to expand the number of human protein CDSs by 30%, from ∼19,500 annotated CDSs to over 26,000 annotated CDSs. Yet, additional scrutiny of these ORFs has raised numerous questions about what fraction of them truly produce a protein product and what fraction of those can be understood as proteins according to the conventional understanding of the term. Adding further complication is the fact that published estimates of noncanonical ORFs vary widely by around 30-fold, from several thousand to several hundred thousand. The summation of this research has left the genomics and proteomics communities both excited by the prospect of new coding regions in the human genome but searching for guidance on how to proceed. I will discuss the current state of noncanonical ORF research, detection, databases, interpretation, and validation. How do we assess whether a given ORF can be said to be “protein-coding”?
Sebastiaan van Heesch is a group leader at Princess Máxima Center for Pediatric Oncology, a junior Oncode Investigator at Oncode Institute, and vice chair of the Therapeutic Vaccines workstream at Oncode Accelerator - a Dutch nation-wide program that aims to accelerate the preclinical development of cancer vaccines. Trained at the Hubrecht Institute (PhD) and the MDC Berlin (postdoc), Sebastiaan has developed a passion for RNA systems biology, proteogenomics, and cancer immunotherapy. Within the Princess Máxima Center - Europe’s largest research hospital fully dedicated to battling childhood cancer, the van Heesch lab develops and applies advanced sequencing and computational methods to find and characterize new microproteins, find new cancer mechanisms, and select those microproteins that may serve as targets for immunotherapy.