{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:40Z","timestamp":1792790320410,"version":"4.5.0"},"posted":{"date-parts":[[2026,9,26]]},"group-title":"Genetics","reference-count":86,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T00:00:00Z","timestamp":1790380800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"funder":[{"award":["R01HL171054"],"award-info":[{"award-number":["R01HL171054"]}],"id":[{"id":"https:\/\/ror.org\/023ny1p48","id-type":"ROR","asserted-by":"publisher"}]},{"name":"National Institute of Diabetes and Digestive and Kidney Diseases","award":["R01DK134329"],"award-info":[{"award-number":["R01DK134329"]}],"id":[{"id":"https:\/\/ror.org\/00adh9b73","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,26]]},"abstract":"<jats:p>Residual cardiovascular risk persists despite lipid-lowering therapy, independent of LDL and Lp(a), reflecting cholesterol dysregulation. We identify STARD9, a lysosomal cholesterol-sensing kinesin, as a causal gene for divergent familial dyslipidemias and premature atherosclerosis. Its START domain binds cholesterol to govern lysosomal positioning. Rare variants segregate with autosomal dominant hypercholesterolemia and premature coronary disease, while common variants associate with reduced HDL and elevated triglycerides. Both converge on lysosomal cholesterol sequestration, ER depletion, mTORC1\u2013SREBP2 activation, impaired autophagy, and NF-\u03baB inflammation, yet diverge through opposite lysosomal positioning: the rare variant disperses lysosomes peripherally, phenocopying START-domain loss across cholesterol sequestration, lysosomal positioning, and TFEB activation, triggering LDLR degradation and CASM\/TFEB-dependent efflux that preserves HDL, whereas the common variant causes perinuclear retention that suppresses TFEB-dependent lipid-handling transcripts, yielding hypertriglyceridemia and low HDL. In Stard9-knockout mice, enterocyte cholesterol sequestration drives SREBP2-dependent NPC1L1 upregulation and apical localization, increasing intestinal cholesterol absorption. These findings position lysosomal cholesterol trafficking as a targetable node in statin-refractory cardiovascular disease.<\/jats:p>\n                <jats:sec>\n                  <jats:title>Graphical abstract<\/jats:title>\n                  <jats:p>(Left panel) STARD9 mutations p.V2821L and p.I2772V drive divergent cholesterol uptake but converge on a shared lysosomal pathology. While p.V2821L reduces LDL uptake and p.I2772V increases it, both mutations cause lysosomal cholesterol sequestration. This accumulation leads to lysosomal membrane damage and nuclear SREBP2 localization, exacerbating cholesterol dysregulation and cellular stress. Lysosomal damage also disperses lysosomes and activates mTOR, suppressing canonical autophagy while driving NF-\u03baB inflammatory signaling and pro-inflammatory cytokine secretion. (Right panel) Concurrently, lysosomal stress engages CASM specifically in p.V2821L lines, driving paradoxical TFEB activation and increased cholesterol efflux, whereas failure to engage this pathway in p.I2772V lines is associated with reduced TFEB activation and reduced cholesterol efflux.<\/jats:p>\n                  <jats:fig id=\"ufig1\" position=\"float\" orientation=\"portrait\" fig-type=\"figure\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"754437v1_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.25.754437","type":"posted-content","created":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T07:40:19Z","timestamp":1790494819000},"source":"Crossref","is-referenced-by-count":0,"title":["Variant-Specific Rewiring of Lysosomal Positioning by STARD9 Produces Opposite Cholesterol Trafficking Outcomes"],"prefix":"10.64898","author":[{"given":"Mehdi","family":"Dianatpour","sequence":"first","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dipanjan","family":"Banerjee","sequence":"additional","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyun Kyung","family":"Kim","sequence":"additional","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiyoung","family":"Moon","sequence":"additional","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Data Sciences"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Data Sciences"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arpita","family":"Neogi","sequence":"additional","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trojan","family":"Rugira","sequence":"additional","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shrikant","family":"Mane","sequence":"additional","affiliation":[{"name":"Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adebowale","family":"Adeniran","sequence":"additional","affiliation":[{"name":"Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brisa","family":"Palikuqi","sequence":"additional","affiliation":[{"name":"Yale Stem Cell Center and the Department of Comparative Medicine at the Yale School of Medicine,, New Haven, CT, 06520, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3616-5387","authenticated-orcid":false,"given":"William","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA"},{"name":"Yale Center for Genome Analysis (YCGA)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucila Ohno","family":"Machado","sequence":"additional","affiliation":[{"name":"Department of Biomedical Informatics and Data Sciences"},{"name":"Office of the Dean, Yale University School of Medicine"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arya","family":"Mani","sequence":"additional","affiliation":[{"name":"Yale Cardiovascular Research Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06511, USA"},{"name":"Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026092918500894000_2026.09.25.754437v1.1","doi-asserted-by":"crossref","first-page":"3J","DOI":"10.1016\/S0002-9149(01)01879-3","article-title":"What have we learned about the biology of atherosclerosis? 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