{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T11:36:57Z","timestamp":1785411417139,"version":"3.56.0"},"posted":{"date-parts":[[2025,10,8]]},"group-title":"Cell Biology","reference-count":51,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T00:00:00Z","timestamp":1759881600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100018231","name":"Aligning Science Across Parkinson's","doi-asserted-by":"crossref","award":["000282"],"award-info":[{"award-number":["000282"]}],"id":[{"id":"10.13039\/100018231","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100018231","name":"Aligning Science Across Parkinson's","doi-asserted-by":"crossref","award":["024268"],"award-info":[{"award-number":["024268"]}],"id":[{"id":"10.13039\/100018231","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["NS110395"],"award-info":[{"award-number":["NS110395"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["GM132129"],"award-info":[{"award-number":["GM132129"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/041ztcd61","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Bluefield Project"},{"id":[{"id":"https:\/\/ror.org\/01hhn8329","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/00dkye506","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,5,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  Lysosomes maintain cellular homeostasis by degrading proteins delivered via endocytosis and autophagy, and by recycling building blocks for organelle biogenesis. Lysosomal Storage Disorders (LSDs) comprise a group of diseases affecting diverse lysosomal functions. To facilitate molecular phenotyping across diverse LSD gene classes, we are developing a library of human embryonic stem cells engineered to lack individual LSD genes as a resource for the field. Here, we report our initial stem cell toolkit lacking one of 23 LSD genes, including the majority of genes associated with sphingolipidoses and neuronal ceroid lipofuscinoses, and its use in the generation of a proteomic resource for induced cortical-like and midbrain dopaminergic-like neurons In-depth abundance and correlation profiling across organelles and sub-organelle components revealed potential vulnerabilities that reflect distinct patterns of proteome alterations across both genotypes and neuronal cell types. We characterize alterations in the mitochondrial proteome associated with GBA1 and ASAH1 deficiency and identify synaptic and mitochondrial defects in\n                  <jats:italic>ASAH1<\/jats:italic>\n                  <jats:sup>-\/-<\/jats:sup>\n                  induced neurons that correlate with defects in neuronal firing rates. Moreover, we developed an informatic pipeline for proteome-wide identification of individual protein interactions and protein complexes that may be disrupted as a result of LSD gene deficiency. Finally, we visualized structural alterations of\n                  <jats:italic>ASAH1<\/jats:italic>\n                  -deficient endolysosomes\n                  <jats:italic>in situ<\/jats:italic>\n                  using cryo-electron tomography, revealing swollen organelles that were largely devoid of dense internal membranes characteristic of wild-type cells, but containing numerous intralumenal vesicle compartments. This toolkit and associated proteomic landscapes provide a resource for defining molecular signatures associated with LSD gene dysfunction and organelle vulnerability.\n                <\/jats:p>","DOI":"10.1101\/2025.10.08.681047","type":"posted-content","created":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T15:10:20Z","timestamp":1759936220000},"source":"Crossref","is-referenced-by-count":1,"title":["A human lysosomal storage disorder toolkit for decoding proteome landscapes in cortical and dopaminergic-like induced neurons"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3757-541X","authenticated-orcid":false,"given":"Felix","family":"Kraus","sequence":"first","affiliation":[{"name":"Department of Cell Biology, Harvard Medical School, Boston MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6096-4915","authenticated-orcid":false,"given":"Yuchen","family":"He","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Harvard Medical School, Boston MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9016-1104","authenticated-orcid":false,"given":"Yizhi","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Harvard Medical School, Boston MA, USA"},{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-7900-489X","authenticated-orcid":false,"given":"Delong","family":"Li","sequence":"additional","affiliation":[{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA"},{"name":"Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-5806-5090","authenticated-orcid":false,"given":"Yohannes A.","family":"Ambaw","sequence":"additional","affiliation":[{"name":"Cell Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6865-2660","authenticated-orcid":false,"given":"Federico M.","family":"Gasparoli","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Harvard Medical School, Boston MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4291-413X","authenticated-orcid":false,"given":"Joao A.","family":"Paulo","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Harvard Medical School, Boston MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1442-1327","authenticated-orcid":false,"given":"Tobias C.","family":"Walther","sequence":"additional","affiliation":[{"name":"Cell Biology Program, Sloan Kettering Institute, New York, NY, USA"},{"name":"Howard Hughes Medical Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8103-2239","authenticated-orcid":false,"suffix":"Jr.","given":"Robert V.","family":"Farese","sequence":"additional","affiliation":[{"name":"Cell Biology Program, Sloan Kettering Institute, New York, NY, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7626-0034","authenticated-orcid":false,"given":"Steven P.","family":"Gygi","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Harvard Medical School, Boston MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6559-7261","authenticated-orcid":false,"given":"Florian","family":"Wilfling","sequence":"additional","affiliation":[{"name":"Aligning Science Across Parkinson\u2019s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA"},{"name":"Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6944-7236","authenticated-orcid":false,"given":"J. 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