Browsing by Author "Cetinkaya, Arda"

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    Defining mitochondrial protein functions through deep multiomic profiling
    (NATURE PORTFOLIO, 2022-01-01) Rensvold, Jarred W.; Shishkova, Evgenia; Sverchkov, Yuriy; Miller, Ian J.; Cetinkaya, Arda; Pyle, Angela; Manicki, Mateusz; Brademan, Dain R.; Alanay, Yasemin; Raiman, Julian; Jochem, Adam; Hutchins, Paul D.; Peters, Sean R.; Linke, Vanessa; Overmyer, Katherine A.; Salome, Austin Z.; Hebert, Alexander S.; Vincent, Catherine E.; Kwiecien, Nicholas W.; Rush, Matthew J. P.; Westphall, Michael S.; Craven, Mark; Akarsu, Nurten A.; Taylor, Robert W.; Coon, Joshua J.; Pagliarini, David J.
    Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles(1) and have linked their dysfunction to more than 150 distinct disorders(2,3). Still, hundreds of mitochondrial proteins lack clear functions(4), and the underlying genetic basis for approximately 40\% of mitochondrial disorders remains unresolved(5). Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that PIGY upstream open reading frame (PYURF) is an S-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established RAB5IF as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.
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    Loss-of-Function Mutations in ELMO2 Cause Intraosseous Vascular Malformation by Impeding RAC1 Signaling
    (CELL PRESS, 2016-01-01) Cetinkaya, Arda; Xiong, Jingwei Rachel; Vargel, Ibrahim; Kosemehmetoglu, Kemal; Canter, Halil Ibrahim; Gerdan, Omer Faruk; Longo, Nicola; Alzahrani, Ahmad; Camps, Mireia Perez; Taskiran, Ekim Zihni; Laupheimer, Simone; Botto, Lorenzo D.; Paramalingam, Eeswari; Gormez, Zeliha; Uz, Elif; Yuksel, Bayram; Ruacan, Sevket; Sagiroglu, Mahmut Samil; Takahashi, Tokiharu; Reversade, Bruno; Akarsu, Nurten Ayse
    Vascular malformations are non-neoplastic expansions of blood vessels that arise due to errors during angiogenesis. They are a heterogeneous group of sporadic or inherited vascular disorders characterized by localized lesions of arteriovenous, capillary, or lymphatic origin. Vascular malformations that occur inside bone tissue are rare. Herein, we report loss-of-function mutations in ELMO2 (which translates extracellular signals into cellular movements) that are causative for autosomal-recessive intraosseous vascular malformation (VMOS) in five different families. Individuals with VMOS suffer from life-threatening progressive expansion of the jaw, craniofacial, and other intramembranous bones caused by malformed blood vessels that lack a mature vascular smooth muscle layer. Analysis of primary fibroblasts from an affected individual showed that absence of ELMO2 correlated with a significant downregulation of binding partner DOCK1, resulting in deficient RAC1-dependent cell migration. Unexpectedly, elmo2-knockout zebrafish appeared phenotypically normal, suggesting that there might be human-specific ELMO2 requirements in bone vasculature homeostasis or genetic compensation by related genes. Comparative phylogenetic analysis indicated that elmo2 originated upon the appearance of intramembranous bones and the jaw in ancestral vertebrates, implying that elmo2 might have been involved in the evolution of these novel traits. The present findings highlight the necessity of ELMO2 for maintaining vascular integrity, specifically in intramembranous bones.