Fig. 4: Adaptive cell state in the proximal tubule.
From: The chromatin landscape of healthy and injured cell types in the human kidney
a Differentially expressed genes (DEGs) between the PT-S12 and aPT cell types within the multiome atlas (N = 12), 4194 genes with Bonferroni-adjusted P value < 0.05 (Wilcox test). b Diffusion map of PT-S1, PT-S2 and aPT with 13,241 nuclei. The inset shows the pseudotime trajectory from PT to aPT. c Gene expression localization in aPT cells (ITGB3, PROM1, TPM1) for aPT marker genes. Canonical PT markers (PDZK1, SLC5A12, and RXRA) localize to the PT-S12. d Differentially accessible (DA) peaks N = 10,506, Bonferroni-adjusted P value < 0.05 (LR test) between the PT-S12 and aPT (from multiome TRIPOD-seurat-aPTxPT-S12 object that coincide with TI DNA methylation (DNAm) dips (N = 15). Red = promoter dip, blue = dip outside promoter. e DA multiome peaks with DNAm dips and a CUT&RUN histone mark peak (N = 22). Active promoter (Actpro) = green, predicted enhancer (Predenh) = blue, repressed promoter (Reppro) = red, N = 6607, Bonferroni-adjusted P value < 0.05 (LR test). f DA peaks (N = 2557) in upregulated DEGs of the PT-S12, targeted by a transcription factor (TF) in TRIPOD analyses. Orange dots represent new peaks (NP) in the PT-S12, where fewer than 2% of aPT nuclei had open chromatin Bonferroni-adjusted P value < 0.05, LR test). Gray dots display DA peaks present in both PT-S12 and aPT. All DA NP were found in PT-S12 cells for DEGs upregulated in the PT-S12. g DA peaks (N = 4573) in upregulated DEGs of the aPT. Green = aPT NP. Gray = DA peak present in both PT-S12 and aPT.
