{"doi":"10.64898/2025.12.23.696283","title":"Intralysosomal Amyloidogenesis and Proximity Labeling by Cathepsin C","abstract":"The lysosome is a major catabolic organelle responsible for the breakdown of both intra- and extracellular substrates 1,2 . Lysosomal membrane damage mediated by pathologic amyloid fibrils is an area of recent focus 3-6 . The dipeptide ester LLOMe is typically employed to model lysosomal membrane damage 7-11 ; however its mechanism of membranolysis was previously incompletely understood. Here, in vitro and cell-based analyses, and cryo-electron microscopy and tomography studies reveal LLOMe-derived oligopeptides generated by the lysosomal protease Cathepsin C assemble into cross-β-sheet amyloid fibrils within the lysosome. Additionally, we report lysosome membrane damage triggers the broadly nonspecific dipeptidyl ligase activity of Cathepsin C, facilitating the tagging of proximal proteins within the damaged lysosome lumen with a click chemistry handle: to our knowledge, the first reported localized proximity labeling approach exploiting a fully endogenous, non-engineered enzyme. While Cathepsin C ligase activity has been demonstrated in vitro 12,13 , our observations of dipeptidyl ligation onto proximal proteins in cells suggests an unexplored role of Cathepsin C in lysosomal biology and broadly exemplifies how other endogenous enzymes might be similarly exploited for proximity labeling. Altogether our results unveil two mechanisms by which dipeptide esters perturb lysosomal homeostasis and provide a roadmap for their utilization toward targeted studies of the lysosome.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":554911,"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":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9621,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1452771,"name":"Robert T. O’Neill","orcid":"0000-0002-4348-7635","position":1,"is_corresponding":false},{"id":1404000,"name":"Idil Itir Demiralp","orcid":"0000-0001-5772-4710","position":2,"is_corresponding":false},{"id":1453181,"name":"Seth Allen","orcid":null,"position":3,"is_corresponding":false},{"id":254426,"name":"Daniel Serwas","orcid":"0000-0001-9010-7298","position":4,"is_corresponding":false},{"id":1453182,"name":"Hannah Siems","orcid":null,"position":5,"is_corresponding":false},{"id":1453183,"name":"Elizabeth A. Montabana","orcid":null,"position":6,"is_corresponding":false},{"id":1452772,"name":"Carl T. Ash","orcid":"0000-0002-0767-9605","position":7,"is_corresponding":false},{"id":1453184,"name":"Daniella A. Yacoubian","orcid":null,"position":8,"is_corresponding":false},{"id":879481,"name":"Oren L. Lederberg","orcid":"0009-0006-5593-1701","position":9,"is_corresponding":false},{"id":236419,"name":"Benjamin F. Cravatt","orcid":"0000-0001-5330-3492","position":10,"is_corresponding":false},{"id":98189,"name":"David A. Agard","orcid":"0000-0003-3512-695X","position":11,"is_corresponding":false},{"id":141515,"name":"Jeffery Kelly","orcid":null,"position":12,"is_corresponding":false},{"id":145286,"name":"Jeffery W. Kelly","orcid":null,"position":15,"is_corresponding":false},{"id":484368,"name":"Ruben D. Elias","orcid":"0000-0002-6702-052X","position":0,"is_corresponding":true}],"reference_count":53,"raw_metadata":null,"created_at":"2026-07-19T02:54:54.542303Z","pmid":"41497660","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":[]}