ARTICLE Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and Lysosomal Dysfunction Julia Wang, 1,2 Justine Rousseau, 3 Emily Kim, 4 Sophie Ehresmann, 3 Yi-Ting Cheng, 5 Lita Duraine, 2,6 Zhongyuan Zuo, 2,6 Ye-Jin Park, 2,6 David Li-Kroeger, 2,6 Weimin Bi, 6 Lee-Jun Wong, 6 Jill Rosenfeld, 6 Joseph Gleeson, 7 Eissa Faqeih, 8 Fowzan S. Alkuraya, 9 Klaas J. Wierenga, 10,11 Jiani Chen, 10,12 Alexandra Afenjar, 13,14 Caroline Nava, 13 Diane Doummar, 15 Boris Keren, 13 Jane Juusola, 16 Markus Grompe, 17,18 Hugo J. Bellen, 2,5,6,19, * and Philippe M. Campeau 3, * We report an early-onset autosomal-recessive neurological disease with cerebellar atrophy and lysosomal dysfunction. We identified bi- allelic loss-of-function (LoF) variants in Oxidative Resistance 1 (OXR1) in five individuals from three families; these individuals presented with a history of severe global developmental delay, current intellectual disability, language delay, cerebellar atrophy, and seizures. While OXR1 is known to play a role in oxidative stress resistance, its molecular functions are not well established. OXR1 contains three conserved domains: LysM, GRAM, and TLDc. The gene encodes at least six transcripts, including some that only consist of the C-termi- nal TLDc domain. We utilized Drosophila to assess the phenotypes associated with loss of mustard (mtd), the fly homolog of OXR1. Strong LoF mutants exhibit late pupal lethality or pupal eclosion defects. Interestingly, although mtd encodes 26 transcripts, severe LoF and null mutations can be rescued by a single short human OXR1 cDNA that only contains the TLDc domain. Similar rescue is observed with the TLDc domain of NCOA7, another human homolog of mtd. Loss of mtd in neurons leads to massive cell loss, early death, and an accu- mulation of aberrant lysosomal structures, similar to what we observe in fibroblasts of affected individuals. Our data indicate that mtd and OXR1 are required for proper lysosomal function; this is consistent with observations that NCOA7 is required for lysosomal acidi- fication. Introduction Oxidation Resistance 1 (OXR1) (HGNC: 15822, MIM: 605609) was first identified based on its ability, when over- expressed, to reduce DNA lesions induced by oxidative stress in E. coli. 1,2 In an SOD1 G93A ALS (amyotrophic lateral sclerosis [MIM: 105400]) mouse model, overexpression of OXR1 was shown to delay the onset of symptoms. 3,4 Other functions associated with OXR1 include neuronal maintenance, 3–6 mitochondrial morphology and DNA maintenance, 7–9 regulation of aging, 10,11 innate immune defense, 12–14 protection against Lupus nephritis (MIM: 601744), 15 regulation of the cell cycle, 9,16 and modulation of glycolytic pathways. 17 While these studies have shown that OXR1 may affect several cellular processes, its mecha- nism of action is still ill defined, and the gene has not been previously associated with a human disease. OXR1 has a complex gene structure. Six validated iso- forms ranging from 216 to 874 amino acids in length are reported in RefSeq. The longest isoform has three pro- tein domains: LysM, GRAM, and TLDc. 18 LysM (lysin motif) is a globular domain of 42 amino acids. 18 It is involved in binding peptidoglycan in bacteria and chitin in eukaryotes, but proteins involved in several other bio- logical functions also contain this domain. 19 The GRAM (glucosyltransferases, Rab-like GTPase activators and myo- tubularins) domain has a structure similar to those of Pleckstrin homology (PH) domains, it consists of about 70 amino acids 18 and it is most likely a lipid-binding signaling or intracellular protein-binding domain impor- tant for membrane-associated processes. 19 The TLDc (TBC [Tre-2/Bub2/Cdc16] and LysM domain containing protein) domain has low structural similarity to known domains 20 and is 136 amino acids in length. 18 Previous 1 Program in Developmental Biology, Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; 2 Jan and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA; 3 Centre Hospitalier Universitaire Saint-Justine Research Center, CHU Sainte-Justine, Montreal, QC H3T 1J4, Canada; 4 Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA; 5 Program in Develop- mental Biology, Baylor College of Medicine, Houston, TX 77030, USA; 6 Department of Molecular and Human Genetics, Baylor College of Medicine, Hous- ton, TX 77030, USA; 7 Rady Institute of Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA; 8 Section of Medical Genetics, Chil- dren’s Hospital, King Fahad Medical City, Riyadh, 11525, Saudi Arabia; 9 Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, 11525, Saudi Arabia; 10 Department of Pediatrics, Oklahoma University Health Sciences Center (OUHSC), Oklahoma City, OK 26901, USA; 11 Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL 32224, USA; 12 Division of Genomic Diagnostics, Children’s Hospital of Philadel- phia, Philadelphia, PA 19104, USA; 13 Assistance Publique des Hoˆpitaux de Paris, Unite´ de Ge´ne´tique Clinique, Hoˆpital Armand Trousseau, Groupe Hospital- ier Universitaire Paris, 75012, France; 14 De´partement de Ge´ne´tique et Embryologie Me´dicale, CRMR des Malformations et Maladies Conge´nitales du Cer- velet, GRC ConCer-LD, Sorbonne Universite´s, Hoˆpital Trousseau, Paris, 75012 France; 15 Assistance Publique des Hoˆpitaux de Paris, Service de Neurope´diatrie, Hoˆpital Armand Trousseau, Groupe Hospitalier Universitaire Paris, 75012 France; 16 GeneDx, Inc., Gaithersburg, MD 20877, USA; 17 Depart- ment of Pediatrics, Oregon Health and Science University, Portland, Oregon 97201, USA; 18 Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97201, USA; 19 Howard Hughes Medical Institute and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA *Correspondence: hbellen@bcm.edu (H.J.B.), p.campeau@umontreal.ca (P.M.C.) https://doi.org/10.1016/j.ajhg.2019.11.002. The American Journal of Human Genetics 105, 1–17, December 5, 2019 1 AJHG 2923 Please cite this article in press as: Wang et al., Loss of Oxidation Resistance 1, OXR1, Is Associated with an Autosomal-Recessive Neurological Disease with Cerebellar Atrophy and ..., The American Journal of Human Genetics (2019), https://doi.org/10.1016/j.ajhg.2019.11.002 Ó 2019 American Society of Human Genetics.