{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:19:18Z","timestamp":1792790358866,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,25]]},"group-title":"Genetics","reference-count":80,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["5R01 NS121298"],"award-info":[{"award-number":["5R01 NS121298"]}],"id":[{"id":"https:\/\/ror.org\/01s5ya894","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Presbyterian Health Foundation","award":["4411-09-10-0"],"award-info":[{"award-number":["4411-09-10-0"]}],"id":[{"id":"https:\/\/ror.org\/01nbasn20","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Oklahoma Center for Adult Stem Cell Research","award":["221009"],"award-info":[{"award-number":["221009"]}],"id":[{"id":"https:\/\/ror.org\/0520gqb12","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Oklahoma Center for Adult Stem Cell Research","award":["241006"],"award-info":[{"award-number":["241006"]}],"id":[{"id":"https:\/\/ror.org\/0520gqb12","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute on Aging","award":["T32AG052363"],"award-info":[{"award-number":["T32AG052363"]}],"id":[{"id":"https:\/\/ror.org\/049v75w11","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute of General Medical Sciences","award":["GM103447"],"award-info":[{"award-number":["GM103447"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute of General Medical Sciences","award":["GM137786"],"award-info":[{"award-number":["GM137786"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute of General Medical Sciences","award":["P30-GM149376"],"award-info":[{"award-number":["P30-GM149376"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institute of Allergy and Infectious Diseases","award":["R01-AI198430"],"award-info":[{"award-number":["R01-AI198430"]}],"id":[{"id":"https:\/\/ror.org\/043z4tv69","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,25]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>\n                  We previously discovered that a\n                  <jats:italic>de novo<\/jats:italic>\n                  variant p.R528W in\n                  <jats:italic>ATAD3A<\/jats:italic>\n                  , encoding a mitochondrial membrane-anchored protein, causes a human neurological syndrome. While\n                  <jats:italic>ATAD3A<\/jats:italic>\n                  mutations induce aberrant lysosomal expansion accompanied by undigested material in the lysosomes, how mutant\n                  <jats:italic>ATAD3A<\/jats:italic>\n                  disrupts lysosomal homeostasis and whether this contributes to neurodevelopmental defects remain unknown. Here we show that pathogenic ATAD3A p.R528W expression disrupts the mTORC1-TFEB axis as revealed by dysregulation of mTORC1 substrate phosphorylation, TFEB nuclear localization, and CLEAR gene activation associated with lysosomal biogenesis. ATAD3A binds to lysosome-localized Rag C\/D GTPases, which constitute a platform for TFEB recruitment, with pathogenic variants increasing this association and thereby decreasing lysosomal localization of Rag GTPases. Importantly, overexpression of\n                  <jats:italic>RagC<\/jats:italic>\n                  or\n                  <jats:italic>RagD<\/jats:italic>\n                  restores TFEB phosphorylation in human cells expressing p.R528W, and\n                  <jats:italic>RagC- D<\/jats:italic>\n                  overexpression or\n                  <jats:italic>TFEB\/Mitf<\/jats:italic>\n                  knockdown rescues lysosomal expansion and neurodevelopmental defects in\n                  <jats:italic>Drosophila<\/jats:italic>\n                  . These data indicate that disrupted Rag GTPase recruitment to lysosomes and subsequent aberrant TFEB\/Mitf activation contribute to neurodevelopmental and lysosomal phenotypes caused by pathogenic mutations in\n                  <jats:italic>ATAD3A<\/jats:italic>\n                  . Our work reveals a novel role for the mitochondrial resident protein ATAD3A in modulating lysosomal homeostasis through regulation of the mTORC1-TFEB axis, providing a mechanistic link between impaired mitochondrial and lysosomal homeostasis in a neurodevelopmental disorder.\n                <\/jats:p>","DOI":"10.64898\/2026.09.23.753918","type":"posted-content","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T14:30:14Z","timestamp":1790346614000},"source":"Crossref","is-referenced-by-count":0,"title":["Pathogenic mutations in ATAD3A cause dysregulation of RagC\/D-TFEB axis and disrupt lysosomal homeostasis"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3957-8868","authenticated-orcid":false,"given":"Mathew B.","family":"McDougal","sequence":"first","affiliation":[{"name":"Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abigail","family":"Sandoval","sequence":"additional","affiliation":[{"name":"Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mike","family":"Kinter","sequence":"additional","affiliation":[{"name":"Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antrix","family":"Jain","sequence":"additional","affiliation":[{"name":"Mass Spectrometry Proteomics Core, Baylor College of Medicine, Houston, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sukyeong","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sung Yun","family":"Jung","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, Baylor College of Medicine, Houston, TX, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9459-3139","authenticated-orcid":false,"given":"Wan Hee","family":"Yoon","sequence":"additional","affiliation":[{"name":"Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092907301956000_2026.09.23.753918v1.1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.neuro.30.051606.094302"},{"key":"2026092907301956000_2026.09.23.753918v1.2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-neuro-070815-014031"},{"key":"2026092907301956000_2026.09.23.753918v1.3","doi-asserted-by":"crossref","first-page":"102627","DOI":"10.1016\/j.ceb.2026.102627","article-title":"Neighbors who talk: Mitochondria-lysosome crosstalk in homeostasis","volume":"100","year":"2026","journal-title":"Curr Opin Cell Biol"},{"key":"2026092907301956000_2026.09.23.753918v1.4","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M115.695825"},{"key":"2026092907301956000_2026.09.23.753918v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22113-3"},{"key":"2026092907301956000_2026.09.23.753918v1.6","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200609158"},{"key":"2026092907301956000_2026.09.23.753918v1.7","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.00007-10"},{"key":"2026092907301956000_2026.09.23.753918v1.8","doi-asserted-by":"publisher","DOI":"10.1210\/en.2014-1503"},{"key":"2026092907301956000_2026.09.23.753918v1.9","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awx094"},{"key":"2026092907301956000_2026.09.23.753918v1.10","doi-asserted-by":"publisher","DOI":"10.1093\/brain\/awae018"},{"key":"2026092907301956000_2026.09.23.753918v1.11","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1093\/pcp\/pcad122","article-title":"ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages","volume":"65","year":"2024","journal-title":"Plant Cell Physiol"},{"key":"2026092907301956000_2026.09.23.753918v1.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2016.08.007"},{"key":"2026092907301956000_2026.09.23.753918v1.13","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1016\/j.cmet.2025.01.017","article-title":"MARIGOLD and MitoCIAO, two searchable compendia to visualize and functionalize protein complexes during mitochondrial remodeling","volume":"37","year":"2025","journal-title":"Cell Metab"},{"key":"2026092907301956000_2026.09.23.753918v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/s41419-020-03152-y"},{"key":"2026092907301956000_2026.09.23.753918v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.110139"},{"key":"2026092907301956000_2026.09.23.753918v1.16","doi-asserted-by":"crossref","unstructured":"Peralta, S. et al. 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