Single cell transcriptomics-based comparison of regenerative repair vs. fibrotic response in chronic kidney disease
Final Report Abstract
The primary goal of this DFG project was to identify distinct cell types, cell-type specific transcriptomes and cell composition changes for both regenerative kidney repair and maladaptive injury response in kidney fibrosis/chronic kidney disease using state-of-the-art single cell transcriptomic analysis methods. As part of the project, we were able to delineate transcriptomic phenotypes of kidney disease along a continuous spectrum ranging from acute injury to chronic maladaptive failure: First, we determined the epigenetic program that generates unique cell types in the kidney from nephron progenitors and that is critical for understanding cell type heterogeneity during tissue homeostasis and injury response, such as early podocyte commitment through sustained Foxl1 expression and renal tubular cell commitment towards proximal (Hfn4a) and distal (Tfap2b) fates. Second, we demonstrated in a folic acid mouse model that metabolism (fatty acid oxidation and oxidative phosphorylation) in proximal tubule cells showed the strongest and most reproducible association with cell differentiation and chronic disease development. Third, in a unilateral ureteral obstruction model we uncovered a subset of kidney tubule cells with a profibrotic phenotype characterized by the expression of cytokines and chemokines (e.g., CXCL1) associated with recruitment of immune cells such as CXCR2+ basophils. Finally, we developed a mouse model of adaptive and fibrotic kidney regeneration by titrating kidney ischemic injury dose and identified a specific maladaptive/profibrotic proximal tubule cluster after severe ischemia. This cell cluster was characterized by proinflammatory and profibrotic cytokines and myeloid cell chemotactic factors. In silico druggability analysis highlighted pyroptosis/ferroptosis as vulnerable pathways in these profibrotic cells amenable to pharmacological intervention. In addition, the project enabled accomplishment of related work on diabetic nephropathy and review articles on single cell sequencing in the kidney as well as establishment of several high-quality open access data repositories that can be interrogated by the community in an interactive fashion.
Publications
- The interdependence of epithelial and endothelial metabolism in kidney health and disease. Sci Signal; 13(635)
Balzer MS, Susztak K.
(See online at https://doi.org/10.1126/scisignal.abb8834) - How to get started with single cell- RNA sequencing data analysis. J Am Soc Nephrol.; 32(6)1279-92
Balzer MS, Ma Z, Zhou J, Abedini A, Susztak K.
(See online at https://doi.org/10.1681/ASN.2020121742) - Kidney toxicity of the BRAF-kinase inhibitor vemurafenib is driven by off-target ferrochelatase inhibition. Kidney Int.; 100(6):1214-26
Bai Y, Kim JY, Bisunke B, Jayne LA, Silvaroli JA, Balzer MS, Gandhi M, Huang KM, Sander V, Prosek J, Cianciolo RE, Baker SD, Sparreboom A, Jhaveri KD, Susztak K, Bajwa A, Pabla NS.
(See online at https://doi.org/10.1016/j.kint.2021.08.022) - Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets. Nat Commun.; 12(1):2277
Miao Z, Balzer MS, Ma Z, Liu H, Wu J, Shrestha R, Aranyi T, Kwan A, Kondo A, Pontoglio M, Kim J, Li M, Kaestner KH, Susztak K.
(See online at https://doi.org/10.1038/s41467-021-22266-1) - Single-cell biology—a Keystone Symposia report. Ann NY Acad Sci.; 1506(1):74-97
Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon A, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M.
(See online at https://doi.org/10.1111/nyas.14692) - The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation. Cell Metab.; 33(2):379-94
Dhillon P, Park J, Hurtado del Pozo C, Li L, Doke T, Huang S, Zhao J, Kang HM, Shrestra R, Balzer MS, Chatterjee S, Prado P, Han SY, Liu H, Sheng X, Dierickx P, Bartmanov K, Romero JP, Prosper F, Li M, Pei L, Kim J, Monserrat N, Susztak K.
(See online at https://doi.org/10.1016/j.cmet.2020.11.011) - Urinary single-cell profiling captures the cellular diversity of the kidney. J Am Soc Nephrol.; 32(3):614-27
Abedini A, Zhu YO, Chatterjee S, Halasz G, Devalaraja-Narashimha K, Shrestha R, Balzer MS, Park J, Zhou T, Ma Z, Sullivan KM, Hu H, Sheng X, Liu H, Wei Y, Boustany-Kari CM, Patel U, Almaani S, Palmer M, Townsend R, Blady S, Hogan J, TRIDENT Study Investigators, Morton L, Susztak K.
(See online at https://doi.org/10.1681/ASN.2020050757) - How Many Cell Types Are in the Kidney and What Do They Do? Annu Rev Physiol; 84:507-31
Balzer MS, Rohacs T, Susztak K.
(See online at https://doi.org/10.1146/annurev-physiol-052521-121841) - Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nat Commun. 13(1):4018
Balzer MS, Doke T, Yang Y-W, Aldridge DL, Hu H, Mai H, Mukhi D, Ma Z, Shrestha R, Palmer MB, Hunter CA, Susztak K.
(See online at https://doi.org/10.1038/s41467-022-31772-9) - Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. Nat Immunol; 23(6):947-59
Doke T, Aldridge DL, Yang Y-W, Park J, Hernandez C, Abedini A, Balzer MS, Shrestra R, Coppock G, Inclan Rico JM, Han SY, Kim J, Xin S, Piliponsky AM, Lefebvre V, Siracusa M, Hunter CA, Susztak K.
(See online at https://doi.org/10.1038/s41590-022-01200-7)
