Mis-spliced transcripts generate de novo proteins in TDP-43–related ALS/FTD

Author:

Seddighi Sahba12ORCID,Qi Yue A.3ORCID,Brown Anna-Leigh4ORCID,Wilkins Oscar G.45ORCID,Bereda Colleen3ORCID,Belair Cedric6ORCID,Zhang Yong-Jie78ORCID,Prudencio Mercedes78ORCID,Keuss Matthew J.4ORCID,Khandeshi Aditya6ORCID,Pickles Sarah78ORCID,Kargbo-Hill Sarah E.1ORCID,Hawrot James1ORCID,Ramos Daniel M.3ORCID,Yuan Hebao1ORCID,Roberts Jessica3ORCID,Sacramento Erika Kelmer9ORCID,Shah Syed I.10ORCID,Nalls Mike A.310,Colón-Mercado Jennifer M.1ORCID,Reyes Joel F.1ORCID,Ryan Veronica H.1ORCID,Nelson Matthew P.3,Cook Casey N.78ORCID,Li Ziyi310ORCID,Screven Laurel3ORCID,Kwan Justin Y.1,Mehta Puja R.4ORCID,Zanovello Matteo4ORCID,Hallegger Martina511ORCID,Shantaraman Anantharaman12ORCID,Ping Lingyan12ORCID,Koike Yuka78ORCID,Oskarsson Björn78ORCID,Staff Nathan P.13ORCID,Duong Duc M.12ORCID,Ahmed Aisha4ORCID,Secrier Maria14ORCID,Ule Jernej511ORCID,Jacobson Steven1ORCID,Reich Daniel S.1ORCID,Rohrer Jonathan D.4ORCID,Malaspina Andrea4,Dickson Dennis W.78ORCID,Glass Jonathan D.15ORCID,Ori Alessandro9,Seyfried Nicholas T.1216ORCID,Maragkakis Manolis6ORCID,Petrucelli Leonard78ORCID,Fratta Pietro45ORCID,Ward Michael E.13ORCID

Affiliation:

1. National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.

2. Nuffield Department of Population Health, University of Oxford, Oxford, UK.

3. Center for Alzheimer’s and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.

4. UCL Queen Square Motor Neuron Disease Centre, Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, UCL, London, UK.

5. Francis Crick Institute, London, UK.

6. Laboratory of Genetics and Genomics, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA.

7. Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA.

8. Neuroscience Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA.

9. Genentech, South San Francisco, CA, USA.

10. Data Tecnica International, Washington, DC, USA.

11. UK Dementia Research Institute at King’s College London, London, UK.

12. Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA.

13. Department of Neurology, Mayo Clinic, Rochester, MN, USA.

14. Department of Genetics, Evolution and Environment, UCL Genetics Institute, UCL, London, UK.

15. Department of Neurology, Center for Neurodegenerative Diseases, Emory University, Atlanta, GA, USA.

16. Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA.

Abstract

Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43–depleted human iPSC–derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43–depleted human iPSC–derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43–depleted human iPSC–derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.

Publisher

American Association for the Advancement of Science (AAAS)

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