Study Finds Cryptic Exons and Abnormal Proteins in ALS and FTD

To enhance the diagnosis of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), researchers at the National Institutes of Health found aberrant proteins in the spinal fluid of patients. Science Translational Medicine issued a report on the findings. 

The “cryptic” exons, or aberrant RNA segments that contain the cell’s instructions on how to assemble proteins, are the building blocks of the proteins in question. When TDP-43, a protein that controls how RNA is processed, malfunctions, cryptic exons result. Limbic Associated TDP-43 Encephalopathy (LATE), ALS, FTD, and Alzheimer’s disease are associated with TDP-43 malfunction. 

The research revealed that the cryptic sequence in these mis-spliced RNA segments can occasionally produce novel proteins. The results contribute to our knowledge of the potential roles that cryptic exons may play in the development of dementia and may aid in the early detection of disorders involving TDP-43 malfunction. As things stand, the only way to find TDP-43 aggregates in the brain is during an autopsy.         

Normally, TDP-43 regulates the processing of RNA to aid in the regulation of protein synthesis. TDP-43 must stay in the cell nucleus, which houses DNA, to function correctly. TDP-43 leaks from the nucleus and instead forms aberrant clumps in the surrounding cytoplasm in ALS and other neurodegenerative disorders. 

“We demonstrate that brain cells with TDP-43 pathology mis-splice hundreds of RNAs, and that some of these RNAs are translated into novel proteins that are not typically present in healthy cells,” said Michael Ward, M.D., Ph.D., senior co-author, co-director of the iPSC Neurodegenerative Disease Initiative at the NIH Intramural Center for Alzheimer’s and Related Dementias (CARD), and senior investigator at the National Institute of Neurological Disorders and Stroke (NINDS). “The development of sensitive diagnostic tests to detect TDP-43 pathology in living patients may be made possible by this conceptual discovery in the future.” 

Making the diagnosis of ALS and associated disorders can be difficult. The symptoms of ALS and FTD can mimic those of other conditions, and there is presently no one test that can be used to definitively identify either condition. Doctors will conduct brain imaging, evaluate the patient’s symptoms, conduct a physical examination, order tests to rule out other problems, and use these methods to assist identify the disorders. 

TDP-43 pathology is a characteristic shared by about half of FTD patients and nearly all ALS patients. Roughly 50% of Alzheimer’s patients also experience it. Unfortunately, precise diagnosis and treatment development are hampered by the inability of existing techniques to identify or quantify TDP-43 pathology in live patients. 

The RNA strands created during gene transcription, known as RNA transcripts, are usually unstable and degraded in the presence of cryptic exons. Until now, researchers haven’t considered that some cryptic exon transcripts produce new proteins rather than being broken down. 

The research team created a portfolio of cryptic exons using induced pluripotent stem cells (iPSCs) that mimic neurodegenerative diseases. From this catalog, they were able to discover 65 peptides that originated from 12 cryptic exons. After comparing post-mortem brain samples from patients with ALS/FTD spectrum disease to healthy controls, they discovered the same cryptic exons. The group then verified that patient-derivediPSCs had novel resultant proteins. They also demonstrated how proteins with cryptic sequences worked differently with other proteins, probably changing how those proteins functioned. 

The authors speculated that the human immune system may perceive these new proteins as alien, leading to inflammation and a potential cause of neurodegeneration. Lastly, the group discovered 18 novel proteins encoded by cryptic exons in 13 genes after analyzing cerebrospinal fluid from individuals with ALS/FTD spectrum diseases.   

The discovery of novel proteins in the spinal fluid of patients may help in the early diagnosis of ALS, FTD, and other TDP-43-associated neurodegenerative diseases, as well as improving our knowledge of the biologic processes leading to neuronal death in these conditions. Additionally, these proteins may function as biomarkers reflecting therapeutic response in clinical trials. 

The National Institute on Aging (NIA), the NIH Intramural Center for Alzheimer’s and Related Dementias (CARD), and the NINDS Intramural Research Program provided funding for this study. 

A fundamental scientific finding is described in this press release. Our grasp of human behavior and biology is bolstered by basic research, and this expertise is essential for developing novel approaches to disease prevention, diagnosis, and treatment. Science works in unforeseen and incremental ways; each new study builds on earlier findings in novel ways. Without an understanding of core basic research, most clinical breakthroughs would not be achievable. 

Journal Reference  

National Institue of Health, https://www.nih.gov/news-events/news-releases/abnormal-proteins-found-spinal-fluid-people-als-frontotemporal-dementia.