Researcher:
Yıldırım, Ali Önder

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Ali Önder

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Yıldırım

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Yıldırım, Ali Önder

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2021 - 20222

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    Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
    (Nature Research, 2021) Muus, Christoph; Luecken, Malte D.; Eraslan, Gökcen; Sikkema, Lisa; Waghray, Avinash; Heimberg, Graham; Kobayashi, Yoshihiko; Vaishnav, Eeshit Dhaval; Subramanian, Ayshwarya; Smillie, Christopher; Jagadeesh, Karthik A.; Duong, Elizabeth Thu; Fiskin, Evgenij; Triglia, Elena Torlai; Ansari, Meshal; Cai, Peiwen; Lin, Brian; Buchanan, Justin; Chen, Sijia; Shu, Jian; Haber, Adam L.; Chung, Hattie; Montoro, Daniel T.; Adams, Taylor; Aliee, Hananeh; Allon, Samuel J.; Andrusivova, Zaneta; Angelidis, Ilias; Ashenberg, Orr; Bassler, Kevin; Bécavin, Christophe; Benhar, Inbal; Bergenstråhle, Joseph; Bergenstråhle, Ludvig; Bolt, Liam; Braun, Emelie; Bui, Linh T.; Callori, Steven; Chaffin, Mark; Chichelnitskiy, Evgeny; Chiou, Joshua; Conlon, Thomas M.; Cuoco, Michael S.; Cuomo, Anna S. E; Deprez, Marie; Duclos, Grant; Fine, Denise; Fischer, David S.; Ghazanfar, Shila; Madissoon, Elo; Nyquist, Sarah K.; Penland, Lolita; Shi, Xingyi; Sountoulidis, Alex; Travaglini, Kyle J.; Huyck, Heidie L.; N/A; Yıldırım, Ali Önder; Other; School of Medicine; N/A
    Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light on viral tropism and impact across the body. We assessed the cell-type-specific expression of ACE2, TMPRSS2 and CTSL across 107 single-cell RNA-sequencing studies from different tissues. ACE2, TMPRSS2 and CTSL are coexpressed in specific subsets of respiratory epithelial cells in the nasal passages, airways and alveoli, and in cells from other organs associated with coronavirus disease 2019 (COVID-19) transmission or pathology. We performed a meta-analysis of 31 lung single-cell RNA-sequencing studies with 1,320,896 cells from 377 nasal, airway and lung parenchyma samples from 228 individuals. This revealed cell-type-specific associations of age, sex and smoking with expression levels of ACE2, TMPRSS2 and CTSL. Expression of entry factors increased with age and in males, including in airway secretory cells and alveolar type 2 cells. Expression programs shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues included genes that may mediate viral entry, key immune functions and epithelial–macrophage cross-talk, such as genes involved in the interleukin-6, interleukin-1, tumor necrosis factor and complement pathways. Cell-type-specific expression patterns may contribute to the pathogenesis of COVID-19, and our work highlights putative molecular pathways for therapeutic intervention.
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    PublicationOpen Access
    The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD
    (Nature Publishing Group (NPG), 2022) Günsel, Gizem Güneş; Conlon, Thomas M.; Jeridi, Aicha; Kim, Rinho; Ertuez, Zeynep; Lang, Niklas J.; Ansari, Meshal; Novikova, Mariia; Jiang, Dongsheng; Strunz, Maximilian; Gaianova, Mariia; Hollauer, Christine; Gabriel, Christina; Angelidis, Ilias; Doll, Sebastian; Pestoni, Jeanine C.; Edelmann, Stephanie L.; Kohlhepp, Marlene Sophia; Guillot, Adrien; Bassler, Kevin; Van Eeckhoutte, Hannelore P.; Kanashova, Tamara; Rodius, Sophie; Ballester-Lopez, Carolina; Robles, Carlos M. Genes; Smirnova, Natalia; Rehberg, Markus; Agarwal, Charu; Krikki, Ioanna; Piavaux, Benoit; Verleden, Stijn E.; Vanaudenaerde, Bart; Koenigshoff, Melanie; Dittmar, Gunnar; Bracke, Ken R.; Schultze, Joachim L.; Watz, Henrik; Eickelberg, Oliver; Stoeger, Tobias; Burgstaller, Gerald; Tacke, Frank; Heissmeyer, Vigo; Rinkevich, Yuval; Schiller, Herbert B.; Conrad, Marcus; Schneider, Robert; Kayalar, Özgecan; Konyalılar, Nur; Bayram, Hasan; Yıldırım, Ali Önder; Researcher; PhD Student; Faculty Member; Other; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; N/A; N/A; 4890; N/A
    Extravasation of monocytes into tissue and to the site of injury is a fundamental immunological process, which requires rapid responses via post translational modifications (PTM) of proteins. Protein arginine methyltransferase 7 (PRMT7) is an epigenetic factor that has the capacity to mono-methylate histones on arginine residues. Here we show that in chronic obstructive pulmonary disease (COPD) patients, PRMT7 expression is elevated in the lung tissue and localized to the macrophages. In mouse models of COPD, lung fibrosis and skin injury, reduced expression of PRMT7 associates with decreased recruitment of monocytes to the site of injury and hence less severe symptoms. Mechanistically, activation of NF-kappa B/RelA in monocytes induces PRMT7 transcription and consequential mono-methylation of histones at the regulatory elements of RAP1A, which leads to increased transcription of this gene that is responsible for adhesion and migration of monocytes. Persistent monocyte-derived macrophage accumulation leads to ALOX5 over-expression and accumulation of its metabolite LTB4, which triggers expression of ACSL4 a ferroptosis promoting gene in lung epithelial cells. Conclusively, inhibition of arginine mono-methylation might offer targeted intervention in monocyte-driven inflammatory conditions that lead to extensive tissue damage if left untreated. Chronic obstructive pulmonary disease is a progressive and incurable chronic condition that involves accumulation of inflammatory macrophages in the lung tissue. Authors here show in mouse models of lung disease that PRMT7, a protein arginine methyltransferase, is an important regulator of recruitment and the pro-inflammatory phenotype of macrophages.