GSE209610
Lineage tracing and single nuclear multiomics reveal novel features of adaptive and maladaptive repair after acute kidney injury
We combined lineage tracing of cycling (Ki67+) cells with single nuclear multiomics (single nucleus RNA-seq + single nucleus ATAC-seq) to characterize the long-term (4 weeks and 6 months) outcome of cells that initiate proliferation early after acute kidney injury (AKI). The data document a broad proliferative response to injury in epithelial and non-epithelial kidney cell types, identify novel transcription factors governing the adaptive and maladaptive proximal tubule cell state and highlight the importance of enhancer dynamics in determining cell states. Comparison of lineage traced with control proximal tubule cells reveals long-term effects of AKI on proximal tubule cells, even following adaptive repair. Overall design: Ki67 is expressed by cells in the cell cycle. We injected Tamoxifen into Ki67cre/ERT2; INTACT mice on day 2 and 3 after ischemia-reperfusion injury (IRI) to induce nuclear membrane green fluorescent protein (GFP) labeling of all cells in the cell cycle at the induction of renal repair and enable tracking of these cells until 4 weeks and 6 months post IRI. At collection GFP+ and GFP- nuclei were separated by fluorescence-activated cell sorting (FACS) and combined snRNA- and snATAC-seq was performed using the 10X Chromium multiome ATAC + gene expression kit. Sham operated and non-surgery mice were used as controls. In total 12 samples were processed: 3 GFP+ samples (AKI_GFP+_4weeks) and 1 GFP- sample AKI_GFP-_4weeks) at 4 weeks post IRI; 4 GFP+ samples (AKI_GFP+_6months) and 1 GFP- sample AKI_GFP-_6months) at 6 months post IRI; 2 controls at 4 weeks (Ctrl_4weeks) and 1 control at 6 months (Ctrl_6months) (for controls no separation of GFP+ and GFP- nuclei by FACS was performed).