MAY 2019 – The Translational Landscape of the Human Heart.

bstract

Gene expression in human tissue has primarily been studied on the transcriptional level, largely neglecting translational regulation. Here, we analyze the translatomes of 80 human hearts to identify new translation events and quantify the effect of translational regulation. We show extensive translational control of cardiac gene expression, which is orchestrated in a process-specific manner. Translation downstream of predicted disease-causing protein-truncating variants appears to be frequent, suggesting inefficient translation termination. We identify hundreds of previously undetected microproteins, expressed from lncRNAs and circRNAs, for which we validate the protein products in vivo. The translation of microproteins is not restricted to the heart and prominent in the translatomes of human kidney and liver. We associate these microproteins with diverse cellular processes and compartments and find that many locate to the mitochondria. Importantly, dozens of microproteins are translated from lncRNAs with well-characterized noncoding functions, indicating previously unrecognized biology.

Keywords: ORF detection; circRNAs; dilated cardiomyopathy; heart failure; human heart; lncRNAs; microproteins; protein-truncating variants; ribosome profiling; short ORFs; titin; translational regulation; translatome

Interview

In May, Norbert Hübner, Sebastiaan van Heesch and their team received the Paper of the Month award.  We talked to Sebastiaan van Heesch about the excellent publication: 

You were looking for proteins in the human heart. How many hearts did you use and where did they come from?

We used small pieces of archived left ventricular heart tissue, obtained through our many collaborators that were so kind to share this material with us.

We studied 80 human hearts in total, of which 65 were end-stage, nonischemic dilated cardiomyopathy patients and 15 were unaffected controls. The control hearts were often donor hearts that unfortunately could not be used as initially intended, but now proved invaluable for scientific research.

You found many very small proteins. Where do they come from?

These previously undetected small proteins, also called microproteins or micropeptides, are produced from genes that we long believed to be ‚non-coding‘, i.e. the RNA molecules transcribed from these genes were thought not to enter the translation machinery for protein production. By precisely looking at where ribosomes in human hearts go, and which RNA molecules they bind to, we discovered that small parts of these non-coding RNAs were in fact being translated by ribosomes, producing these small proteins.

What do you think is the role of these small proteins?

The size of these small proteins makes them well suitable as modifiers or interactors with larger proteins or larger protein complexes, thereby influencing their functionality. Based on the evidence we have gathered so far, we see that many microproteins have different destinations in (or outside of!) the cell, though the main destination in human hearts seems to be the mitochondrion. In the mitochondrion, energy production takes place – a crucial process for the heart to function properly. If there is not enough energy, the heart cells suffer and cannot beat properly. We believe some of these newly discovered microproteins may influence the energy production process – something we are currently studying further.

Do you think this knowledge could lead to new therapies?

Yes. Some of the discovered microproteins show different ‚behavior‘ in healthy versus diseased human hearts, or react strongly to stimuli we trigger cultured heart cells with. This is extremely interesting and we are starting to better and better understand their roles in the healthy and diseased human heart, even at the level of individual cells. Once we know exactly what these microproteins do and how they function, we can move ahead and evaluate their therapeutic potential. Since we have identified hundreds of new small proteins, it is nearly impossible for us to study all of them. That is why it is so good that we have published the entire catalog of all new small proteins, giving fellow researchers the chance to explore the therapeutic potential of specific microproteins also. This should drastically increase the speed with which our initial findings can lead to new therapies and start benefitting patients.  

Do these little proteins occur also in other organs?

Yes they do! We focused our studies on the heart, but we have looked at other organs (including kidney and liver) also. Some microproteins are specific to the heart, but most are more widely expressed and present in a multitude of human tissues. This broadens the scope of our findings, and opens opportunities for studying the roles of microproteins in different human organs and diseases also.