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Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43\u2013depleted human iPSC\u2013derived 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\u2013depleted human iPSC\u2013derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43\u2013depleted human iPSC\u2013derived 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.<\/jats:p>","DOI":"10.1126\/scitranslmed.adg7162","type":"journal-article","created":{"date-parts":[[2024,1,26]],"date-time":"2024-01-26T18:58:46Z","timestamp":1706295526000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":162,"title":["Mis-spliced transcripts generate de novo proteins in TDP-43\u2013related ALS\/FTD"],"prefix":"10.1126","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1920-2828","authenticated-orcid":true,"given":"Sahba","family":"Seddighi","sequence":"first","affiliation":[{"name":"National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA."},{"name":"Nuffield Department of Population Health, University of Oxford, Oxford, 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