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[Preprint]. 2024 Mar 19:2024.03.18.24304401. [Version 1] doi: 10.1101/2024.03.18.24304401

Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury

Nanditha Anandakrishnan, Zhengzi Yi, Zeguo Sun, Tong Liu, Jonathan Haydak, Sean Eddy, Pushkala Jayaraman, Stefanie DeFronzo, Aparna Saha, Qian Sun, Dai Yang, Anthony Mendoza, Gohar Mosoyan, Huei Hsun Wen, Jennifer A Schaub, Jia Fu, Thomas Kehrer, Rajasree Menon, Edgar A Otto, Bradley Godfrey, Mayte Suarez-Farinas, Sean Leffters, Akosua Twumasi, Kristin Meliambro, Alexander W Charney, Adolfo García-Sastre, Kirk N Campbell, G Luca Gusella, John Cijiang He, Lisa Miorin, Girish N Nadkarni, Juan Wisnivesky, Hong Li, Matthias Kretzler, Steve G Coca, Lili Chan, Weijia Zhang, Evren U Azeloglu
PMCID: PMC10984064  PMID: 38562892

Abstract

COVID-19 has been a significant public health concern for the last four years; however, little is known about the mechanisms that lead to severe COVID-associated kidney injury. In this multicenter study, we combined quantitative deep urinary proteomics and machine learning to predict severe acute outcomes in hospitalized COVID-19 patients. Using a 10-fold cross-validated random forest algorithm, we identified a set of urinary proteins that demonstrated predictive power for both discovery and validation set with 87% and 79% accuracy, respectively. These predictive urinary biomarkers were recapitulated in non-COVID acute kidney injury revealing overlapping injury mechanisms. We further combined orthogonal multiomics datasets to understand the mechanisms that drive severe COVID-associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single-cell RNA sequencing showed that extracellular matrix and autophagy-associated pathways were uniquely impacted in severe COVID-19. Differentially abundant proteins associated with these pathways exhibited high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating that these kidney cell types could be potential targets. Further, single-cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 revealed dysregulation of extracellular matrix organization in multiple nephron segments, recapitulating the clinically observed fibrotic response across multiomics datasets. Ligand-receptor interaction analysis of the podocyte and tubule organoid clusters showed significant reduction and loss of interaction between integrins and basement membrane receptors in the infected kidney organoids. Collectively, these data suggest that extracellular matrix degradation and adhesion-associated mechanisms could be a main driver of COVID-associated kidney injury and severe outcomes.

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