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Here, we report a transcriptional program that represses mitochondrial biogenesis and function in lysosomal storage diseases Niemann-Pick type C (NPC) and acid sphingomyelinase deficiency (ASM), in patient cells and mouse tissues. This mechanism is mediated by the transcription factors KLF2 and ETV1, which are both induced in NPC and ASM patient cells. Mitochondrial biogenesis and function defects in these cells are rescued by the silencing of KLF2 or ETV1. Increased ETV1 expression is regulated by KLF2, while the increase of KLF2 protein levels in NPC and ASM stems from impaired signaling downstream sphingosine-1-phosphate receptor 1 (S1PR1), which normally represses KLF2. In patient cells, S1PR1 is barely detectable at the plasma membrane and thus unable to repress KLF2. This manuscript provides a mechanistic pathway for the prevalent mitochondrial defects in lysosomal storage diseases.<\/jats:p>\n                  <jats:p>Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (&lt;xref ref-type=\"decision-letter\" rid=\"SA1\"&gt;see decision letter&lt;\/xref&gt;).<\/jats:p>","DOI":"10.7554\/elife.39598","type":"journal-article","created":{"date-parts":[[2019,2,18]],"date-time":"2019-02-18T08:01:08Z","timestamp":1550476868000},"source":"Crossref","is-referenced-by-count":80,"title":["Mitochondrial biogenesis is transcriptionally repressed in lysosomal lipid storage diseases"],"prefix":"10.7554","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2417-450X","authenticated-orcid":true,"given":"King Faisal","family":"Yambire","sequence":"first","affiliation":[{"name":"Institute of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany"},{"name":"International Max-Planck Research School in Neuroscience, Goettingen, Germany"},{"name":"European Neuroscience Institute Goettingen, University Medical Center Goettingen, Goettingen, 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