Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations
Louisa Helms, Silvia Marchiano, Ian B. Stanaway, Tien-Ying Hsiang, Benjamin A. Juliar, Shally Saini, Yan Ting Zhao, Akshita Khanna, Rajasree Menon, Fadhl Alakwaa, Carmen Mikacenic, Eric D. Morrell, Mark M. Wurfel, Matthias Kretzler, Jennifer L. Harder, Charles E. Murry, Jonathan Himmelfarb, Hannele Ruohola-Baker, Pavan K. Bhatraju, Michael Gale Jr., Benjamin S. Freedman
Louisa Helms, Silvia Marchiano, Ian B. Stanaway, Tien-Ying Hsiang, Benjamin A. Juliar, Shally Saini, Yan Ting Zhao, Akshita Khanna, Rajasree Menon, Fadhl Alakwaa, Carmen Mikacenic, Eric D. Morrell, Mark M. Wurfel, Matthias Kretzler, Jennifer L. Harder, Charles E. Murry, Jonathan Himmelfarb, Hannele Ruohola-Baker, Pavan K. Bhatraju, Michael Gale Jr., Benjamin S. Freedman
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Research Article COVID-19 Nephrology

Cross-validation of SARS-CoV-2 responses in kidney organoids and clinical populations

Abstract

Kidneys are critical target organs of COVID-19, but susceptibility and responses to infection remain poorly understood. Here, we combine SARS-CoV-2 variants with genome-edited kidney organoids and clinical data to investigate tropism, mechanism, and therapeutics. SARS-CoV-2 specifically infects organoid proximal tubules among diverse cell types. Infections produce replicating virus, apoptosis, and disrupted cell morphology, features of which are revealed in the context of polycystic kidney disease. Cross-validation of gene expression patterns in organoids reflects proteomic signatures of COVID-19 in the urine of critically ill patients indicating interferon pathway upregulation. SARS-CoV-2 viral variants alpha, beta, gamma, kappa, and delta exhibit comparable levels of infection in organoids. Infection is ameliorated in ACE2–/– organoids and blocked via treatment with de novo–designed spike binder peptides. Collectively, these studies clarify the impact of kidney infection in COVID-19 as reflected in organoids and clinical populations, enabling assessment of viral fitness and emerging therapies.

Authors

Louisa Helms, Silvia Marchiano, Ian B. Stanaway, Tien-Ying Hsiang, Benjamin A. Juliar, Shally Saini, Yan Ting Zhao, Akshita Khanna, Rajasree Menon, Fadhl Alakwaa, Carmen Mikacenic, Eric D. Morrell, Mark M. Wurfel, Matthias Kretzler, Jennifer L. Harder, Charles E. Murry, Jonathan Himmelfarb, Hannele Ruohola-Baker, Pavan K. Bhatraju, Michael Gale Jr., Benjamin S. Freedman

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Figure 1

SARS-CoV-2 efficiently infects human kidney organoids with tropism for proximal tubules.

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SARS-CoV-2 efficiently infects human kidney organoids with tropism for p...
(A) Schematic of kidney organoid infection protocol. (B) Whole-well wide-field immunofluorescence images of iPS cell–derived organoids infected with SARS-CoV-2-mNG. Arrowheads point to infected cells. (C) qRT-PCR of SARS-CoV-2 envelope RNA in organoids infected with SARS-CoV-2/WA1 or mock-infected (MOCK). Dots represent a well of organoids. Mean ± SEM, n ≥ 1 well of organoids per infection from 4 independent experiments. Mann-Whitney test, **P < 0.01. (D) Plaque assays of SARS-CoV-2–infected human kidney organoids derived from iPS cells or ES cells. Dots represent a well of organoids. Mean ± SEM, n ≥ 1 well of organoids per infection from 3 independent experiments, respectively. Mann-Whitney test, NS P > 0.05. (E) Representative confocal immunofluorescence images of organoids infected with SARS-CoV-2-mNG. (F) Quantification of infected organoid cellular tropism. Dots represent a single organoid. Mean ± SEM, n ≥ 4 organoids per infection from 3 independent experiments. Two-way ANOVA, multiple comparisons, MOCK vs. infected for each respective region; **P < 0.01, ****P < 0.0001, NS P > 0.05. (G) Representative confocal immunofluorescence images of organoid infected with SARS-CoV-2-GFP, with zoomed images of white boxed areas showing infected (top) versus uninfected (bottom) proximal tubules. Arrowheads indicate areas of disrupted LTL pattern.