The orchestrated cellular and molecular responses of the kidney to endotoxin define a precise sepsis timeline
- Department of Medicine, Indiana University School of Medicine, United States
- Department of Pediatrics and the Herman B. Wells Center, Indiana University School of Medicine, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, United States
- Roudebush Indianapolis Veterans Affairs Medical Center, United States
Figures
Figure 1 with 2 supplements
ScRNA-seq identifies various renal cell populations.
(A) Integrated UMAP of kidney cell clusters from control and LPS-treated mice (0, 1, 4, 16, 27, 36, and 48 hr after LPS injection). Actual anatomical layout of kidney nephronal segments is shown …
Figure 1—figure supplement 1
Cluster-defining markers across the endotoxemia timeline.
(A) Integrated UMAP of kidney cell clusters showing both assigned identity and original cluster number from control and LPS-treated mice (0, 1, 4, 16, 27, 36, and 48 hr after LPS injection). (B–C) …
Figure 1—figure supplement 2
Characterization of proliferating cells.
(A) Feature plots of Jun and Fos, markers for dissociation-induced stress response. Note that proliferating cells (red circles) showed minimal expression of Jun and Fos. (B) Mice were injected with …
Figure 2 with 2 supplements
Integration of scRNA-seq and spatial transcriptomics localizes subtypes of S3 proximal tubules.
(A) Violin plots of S3T2 defining markers. (B) Integration of spatial transcriptomics and scRNA-seq. Spatial transcriptomics were performed on a slice of mouse kidney. This yielded seven clusters …
Figure 2—figure supplement 1
Spatial transcriptomics validation.
(A–B) Spatial transcriptomics of murine kidney showing unsupervised clustering (b-left panel) and expanded clustering after integration with single cell data (b-right panel). Insets of A show gene …
Figure 2—figure supplement 2
Cellular expression of the RAS axis along the endotoxemia timeline.
Feature plots showing expression of components of the RAS axis at specified time points. Labeled in the upper left panel are the segments of the proximal tubule, and stromal cells which express …
Figure 3 with 1 supplement
Endotoxemia induces dynamic changes in renal immune cell composition, pseudotime states and RNA velocity.
(A) Integrated UMAP of the immune cell clusters from control and LPS-treated mice (0, 1, 4, 16, 27, 36, and 48 hr after LPS injection). Other one and Other two are Cd45+ cells with mixed epithelial …
Figure 3—figure supplement 1
Immune cell subset characteristics.
(A) RNA velocity analysis reveals two distinct subfields within the Mϕ-A cluster. The subfield circled in red showed expression of M2 macrophage-related genes at later time points (B). (C) Violin …
Figure 4 with 2 supplements
Pseudotime and velocity field analyses identify cell-specific phenotypic changes along the endotoxemia timeline.
(A) Cell trajectory analysis for S1, S3, and endothelial cells shown at indicated time points. Highlighted in red circles are significant state transitions in respective cell types. The last cell …
Figure 4—figure supplement 1
Transporter gene expression across the nephron during endotoxemia.
Dot plots of select transporter genes shown at 0 hr (A) and 16 hr (B).
Figure 4—figure supplement 2
Similarity analysis between bulk and single-cell RNA-seq data.
(A) Jaccard similarity index analysis performed on the current single-cell RNA-seq data and publicly available bulk kidney transcriptomic dataset (GSE30576). Differentially expressed genes over …
Figure 5 with 3 supplements
Endotoxemia induces an organ-wide host defense phenotype in the kidney.
(A) Heatmaps of select cell types with top 100 differentially expressed genes across the endottoxemia timeline (0–48 hr). Select genes are shown for each cell type. (B) Time dependent enrichment of …
Figure 5—figure supplement 1
Comparisons of transcriptomic profiles of selected cell types across the endotoxemia timeline.
(A) Venn diagram showing differentially expressed genes across time (0–48 hr) for indicated cell types. (B) Heatmaps of genes involved in coagulation, complement and arachidonic acid related …
Figure 5—figure supplement 2
S3T2 GO terms.
Time dependent enrichment of gene ontology terms for S3T2 cells. GO terms are sorted in order of statistical significance. GO, gene ontology biological processes.
Figure 5—figure supplement 3
Representative images of immunohistochemical staining for NF-κB are shown under indicated conditions.
Insets point to magnified views of select areas. At baseline, the expression of NF-κB is minimal in all cell types and primarily cytoplasmic. One hour after LPS, diffuse nuclear staining for NF-κB …
Figure 6 with 1 supplement
Endotoxemia alters cellular crosstalk causing time-specific global communication failure.
(A) Schematic description of a cell–cell communication circular plot. Dots in the outer track of the circle represent specific ligands or receptors and are positioned identically for all cell types. …
Figure 6—figure supplement 1
Expanded cell–cell communication examples.
(A) Feature plots illustrating cell and time-dependent expression changes of select receptor ligand pairs (shown at 0 hr unless otherwise specified). Schematic illustrates specific receptor–ligand …
Figure 7 with 2 supplements
Global communication failure is accompanied by increased activity of genes involved in recovery.
(A) SCENIC-derived heatmap of regulons for S1 tubules. Highlighted are select transcription factors with active regulons at the 16 hr time point. (B) Gene ontology pathway enrichment analysis …
Figure 7—figure supplement 1
Characteristics of subjects.
(A) Age distribution of subjects (22 subjects are sorted based on gene expression as shown in main Figure 7D and E. p=0.223). (B) Distribution of serum creatinine changes from baseline to peak …
Figure 7—figure supplement 2
Serum biomarkers and chemokine/cytokine levels.
(A) Serum creatinine levels at indicated time points after 5 mg/kg LPS i.v. n = 3, *p<0.05 vs other time points. (B, C) Serum cystatin C and NGAL levels. n = 4. (D–F) Comparison of serum …
Author response image 1
Bulk kidney microarray data.
Author response image 2
Timeline of murine LPS model.
(A) Adapted from Figure 4. Single-cell RNA-seq data demonstrating overall time-dependent gene expression changes in proximal tubules after LPS challenge. Proximal tubules exhibit major phenotypic …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Commercial assay, kit | RNAscope probe-Mm-Agt | Advance Cell Diagnosis | Cat. No. 426941 | |
| Commercial assay, kit | RNAscope probe-Mm-Aqp1 | Advance Cell Diagnosis | Cat. No. 504741-C2 | |
| Commercial assay, kit | Milliplex MAP Mouse Cytokine/Chemokine Magnetic Bead Panel–Premixed 32 Plex | Millipore | Cat. No. MCYTMAG-70K-PX32 | |
| Commercial assay, kit | Annexin V dead cell removal kit | Stem Cell Technologies | Cat. No. 17899 | |
| Commercial assay, kit | Multi-Tissue Dissociation Kit 2 | Miltenyi Biotec | Cat. No. 130-110-203 | |
| Commercial assay, kit | Chromium Single Cell 3' Library and gel bead kit | 10x Genomics | Cat. no. 1000121 | |
| Commercial assay, kit | NovaSeq 6000 S1 reagent kit | Illumina | Cat. No. 20012865 | |
| Commercial assay, kit | Visium Spatial Gene Expression library preparation slide | 10x Genomics | Cat. No. 1000200 | |
| Chemical compound, drug | Red blood cell lysing buffer Hybri-Max | Sigma | Cat. No. R7757 | |
| Antibody | NFkB P65 (D14E12 rabbit monoclonal) | Cell Signaling | Cat. 8242S | |
| Chemical compound, drug | CldU | Sigma | Cat. C6891 | |
| Strain, strain background (Escherichia coli) | LPS E. coli serotype o111:B4 | Sigma | Cat. No. L2630 Lot No. 095M4163V | |
| Biological samples | Human renal biopsy bulk AKI RNAseq data | PMID:30507610 | GEO: GSE122274 | |
| Software, algorithm | Monocle | Cao et al., 2019 | PMID:30787437 | |
| Software, algorithm | Seurat | Stuart et al., 2019; Butler et al., 2018 | RRID:SCR_016341 | https://satijalab.org/ |
| Software, algorithm | SCENIC | Aibar et al., 2017 | PMID:28991892 | |
| Software, algorithm | Cellphone DB | Efremova et al., 2020; Vento-Tormo et al., 2018 | https://www.cellphonedb.org/ | |
| Software, algorithm | RNA velocity | La Manno et al., 2018 | PMID:30089906 | |
| Software, algorithm | SingleR | Aran et al., 2019 | PMID:30643263 | |
| Software, algorithm | Harmony and Palantir | Nowotschin et al., 2019; Setty et al., 2019 | PMID:30959515 PMID:30899105 | |
| Software, algorithm | R | R Project for Statistical Computing | RRID:SCR_001905 | http://www.r-project.org/ |
| Commercial protocol | RNAscope multiplex Fluorescent Reagent Kit v2 | Advance Cell Diagnosis Inc | ||
| Other | Dead cell removal protocol using Annexin V | https://cdn.stemcell.com/media/files/pis/DX21956-PIS_1_0_1.pdf?_ga=2.34218465.1547447083.1547219505%E2%80%93776976877.1534951026 | Commercial protocol | |
| Other | Chromium Single Cell 3’ Reagent Kits V3 User Guide | https://assets.ctfassets.net/an68im79xiti/51xGuiJhVKOeIIceW88gsQ/1db2c9b5c9283d183ff4599fb489a720/CG000183_ChromiumSingleCell3__v3_UG_Rev-A.pdf | Commercial protocol | |
| Other | Dissociation of mouse kidney using the Multi Tissue Dissociation Kit 2 | https://www.miltenyibiotec.com/upload/assets/IM0015569.PDF | Commercial protocol |
Additional files
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Supplementary file 1
Cluster-defining markers.
- https://cdn.elifesciences.org/articles/62270/elife-62270-supp1-v1.xlsx
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Supplementary file 2
Receptor-ligand interaction.
- https://cdn.elifesciences.org/articles/62270/elife-62270-supp2-v1.xlsx
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Supplementary file 3
SCENIC regulon activity.
- https://cdn.elifesciences.org/articles/62270/elife-62270-supp3-v1.xlsx
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Supplementary file 4
Differentially expressed genes for each time point across the mouse endotoxemia timeline.
- https://cdn.elifesciences.org/articles/62270/elife-62270-supp4-v1.xlsx
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Supplementary file 5
Human kidney biopsy data.
- https://cdn.elifesciences.org/articles/62270/elife-62270-supp5-v1.xlsx
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Supplementary file 6
Human kidney biopsy data: genes used for generating Figure 7D heatmap.
- https://cdn.elifesciences.org/articles/62270/elife-62270-supp6-v1.xlsx
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Transparent reporting form
- https://cdn.elifesciences.org/articles/62270/elife-62270-transrepform-v1.pdf
