{"doi":"10.1101/2024.07.12.603231","title":"CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function","abstract":"Abstract Mounting evidence implicates TDP-43 dysfunction and the accumulation of pathological cryptic exons across multiple neurodegenerative diseases, underscoring the need for accessible tools to detect and quantify TDP-43 loss-of-function (LOF). These tools are crucial for assessing potential disease contributors and exploring therapeutic candidates in TDP-43 proteinopathies. Here, we develop a sensitive and accurate real-time sensor for TDP-43 LOF: the CUTS (CFTR UNC13A TDP-43 Loss-of-Function) system. This system combines UG-rich sequences and previously reported cryptic exons regulated by TDP-43 with a reporter, enabling the tracking of TDP-43 LOF through live microscopy and RNA/protein-based assays. We show that CUTS effectively detects TDP-43 loss of function arising from mislocalization, impaired RNA binding, and pathological aggregation. Our results show the sensitivity and accuracy of the CUTS system in detecting and quantifying TDP-43 LOF, opening avenues to explore unknown TDP-43 interactions that regulate its function. In addition, by replacing the fluorescent tag in the CUTS system with the coding sequence for TDP-43, we show significant recovery of its function under TDP-43 LOF conditions, highlighting the potential utility of CUTS for self-regulating gene therapy applications. In summary, CUTS represents a platform for evaluating TDP-43 LOF in real-time and gene-replacement therapies in neurodegenerative diseases associated with TDP-43 dysfunction. Highlights CUTS is a cryptic exon RNA biosensor enabling real-time detection of TDP-43 loss of splicing function. CUTS exhibits a linear relationship with a reduction in TDP-43 protein. CUTS can deliver an autoregulated gene payload in response to TDP-43 loss-of-function. TDP-43 homotypic phase transitions and cell stress induce loss of splicing function detected via CUTS.","journal":"eLife","year":2024,"id":500892,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9512,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1350349,"name":"Jessica Merjane","orcid":"0000-0002-6383-098X","position":1,"is_corresponding":false},{"id":1350350,"name":"Cristian A Bergmann","orcid":"0000-0001-7564-9742","position":2,"is_corresponding":false},{"id":1350351,"name":"Jiazhen Xu","orcid":"0009-0006-7870-0340","position":3,"is_corresponding":false},{"id":1350597,"name":"Shruthi Balasubramaniyan","orcid":null,"position":4,"is_corresponding":false},{"id":1037457,"name":"Bryan Hurtle","orcid":null,"position":5,"is_corresponding":false},{"id":1350598,"name":"Charleen T Chu","orcid":null,"position":6,"is_corresponding":false},{"id":501165,"name":"Christopher J. Donnelly","orcid":"0000-0002-2383-9015","position":7,"is_corresponding":false},{"id":1036939,"name":"Longxin Xie","orcid":"0009-0006-5395-5160","position":0,"is_corresponding":true}],"reference_count":54,"raw_metadata":null,"created_at":"2026-07-19T02:10:12.068207Z","pmid":"39026766","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}