Study links abnormal RNA modifications to TDP-43 function

Findings support previous evidence, may open avenues for treatment strategies

Marisa Wexler, MS avatar

by Marisa Wexler, MS |

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TDP-43, a protein that is known to have toxic effects in amyotrophic lateral sclerosis (ALS), is able to interact with RNA molecules carrying a chemical modification called m6A, and this chemical modification is increased in ALS nerve cells, a new study shows.

The findings add to a growing body of evidence suggesting that abnormal RNA modifications could play a role in ALS, and also may open avenues for future treatment strategies, researchers said.

The study, “RNA methylation influences TDP43 binding and disease pathogenesis in models of amyotrophic lateral sclerosis and frontotemporal dementia,” was published in Molecular Cell.

One of the molecular hallmarks of ALS is the abnormal aggregation (clumping) of the protein TDP-43 inside nerve cells. TDP-43 aggregation is found in the vast majority of ALS cases and is thought to contribute to disease progression, though the specific molecular mechanisms remain incompletely understood.

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Prior research has shown that increased TDP-43 levels can lead to instability of RNA, the intermediary molecule that’s made when genes are read to make proteins. Scientists at the University of Michigan conducted a series of experiments seeking to better understand how TDP-43 contributes to RNA instability.

The study focused on RNA molecules with a specific molecular modification called methylation at adenosine N6, or m6A. In this type of modification, a methyl group — a carbon atom and three hydrogen atoms, arranged in a pyramid shape — is attached to the RNA molecule at a specific location on the RNA molecule (adenosine N6).

The m6A modification “is one of the most common RNA modifications,” the researchers wrote, noting this molecular change has been shown to affect RNA stability and how RNA is used to make proteins.

Here, the researchers demonstrated that the TDP-43 protein is able to physically interact with RNA molecules that harbor the m6A modification. Consistently, this modification was observed on many of the RNA molecules with which TDP-43 has long been known to interact.

“We show not only that TDP43 recognizes m6A-modified RNA but also that the majority of TDP43 [RNA targets] exhibit m6A marks,” the researchers wrote.

A stronger interaction

Further examination suggested that TDP-43 does not directly interact with the m6A modification itself. Instead, results suggested that when RNA molecules harbor the m6A modification, it’s easier for the TDP-43 protein to make contact with the specific regions that it normally binds to, resulting in a stronger interaction with the whole RNA molecule.

The researchers next conducted analyses of spinal cord tissue collected from four people with sporadic ALS, and from three controls without ALS. Results showed that RNA methylation was increased substantially in the ALS samples. More than a third of tested sites where the m6A modification can be attached showed increased levels of this modification in ALS.

“This is an RNA modification that has escaped our attention in the past, and yet it is rampant in patients with ALS,” Sami Barmada, MD, PhD, a professor at Michigan and co-author of the study, said in a university press release.

Many of the RNA molecules showing increased levels of this modification have been shown previously to be regulated by TDP-43, the researchers noted.

“These findings underscore the importance of m6A modifications for RNA binding by TDP43 and emphasize the potential contribution of TDP43’s actions on m6A-modified RNA to the development of ALS,” the scientists concluded.

To gain further insights into the mechanism, the researchers conducted a series of tests in cell models where they systematically removed individual genes that are known to be important for regulating the m6A modification.

TDP-43 function and ALS toxicity

Findings showed that cells lacking a gene called YTHDF2 were resistant to the toxic effects of high TDP-43 protein levels, while increasing the activity of this gene led to more severe toxic effects. The protein encoded by this gene normally helps to read the m6A-modified RNA, the researchers noted, so this finding overall supports the idea that increased levels of RNA with this modification could contribute to toxicity in ALS.

Results also “indicate that YTHDF2 may be a novel therapeutic target in ALS,” the researchers wrote, highlighting an area for further exploration.

Overall, the researchers concluded these results add to a growing body of evidence that abnormal RNA processing likely contributes to neuron toxicity in ALS. However, they stressed that more research is needed to fully understand these complex mechanisms and how they contribute to disease.

“Despite the fact that we see all this RNA methylation, it’s hard to say exactly what it means,” Barmada said. “It’s like watching the end of the movie and then trying to work out the plot. We see RNA methylation, TDP-43 buildup and loss of brain cells, but how are these connected?”