Packard scientist Phil Wong and colleagues have published a new study in Science that outlines the normal function of the ALS-linked protein TDP-43 and spells out more clearly how loss of this function contributes to disease. Unlike other RNA-binding proteins, TDP-43 does not mainly control splicing of normal exons, but rather keeps potentially damaging ‘hidden’ exons from being expressed. Returning normal TDP-43 functioning to cells may be a good drug target for ALS, Wong says.

Although the links between TDP-43 and ALS were discovered almost ten years ago, researchers still had little idea about precisely what the protein normally did in the cell. Understanding this role is key, since nearly all ALS patients and up to half of those with frontotemporal dementia (FTD) have aggregations of TDP-43 in the cytoplasm. This means that TDP-43 isn’t in the nucleus to do its normal job. The problem was that no one could be sure of what this normal job actually was, or how the loss of this function contributed to ALS and FTD.

Previous work showed that TDP-43 bound to RNA and helped to regulate alternative splicing, a process that allows a single gene to code for multiple proteins. But most TDP-43 bound to intronic regions far away from where they would be needed to regulate alternative splicing. To figure out what TDP-43 did, Jonathan Ling, a graduate student of Wong’s, removed all TDP-43 from mouse or human cells and measured how gene expression changed.

The researchers discovered that when mouse cells lacked TDP-43, there was the appearance of cryptic exons. These exons are normally buried within introns and are typically spliced out during normal mRNA processing. Further experiments revealed that TDP-43 binds directly to these cryptic exons, which enables them to be spliced out. When this didn’t happen, the mRNAs oftentimes were degraded, which left the cells without important proteins and contributed to premature cell death. Replacing this function of TDP-43 with a different repressor that spliced out cryptic exons restored cell survival.

Using cultured human cells, Ling identified another set of cryptic exons regulated by TDP-43, showing that this function wasn’t limited to mice. Importantly, Wong and colleagues found cryptic exons in post-mortem brains of ALS and FTD patients but not in controls, showing that loss of this normal TDP-43 function could contribute to disease in ALS.

These results provide not just a greater knowledge of what TDP-43 normally does, but also yield new biomarkers of disease and potential drug targets.