Journal: iScience

Article Title: Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea

doi: 10.1016/j.isci.2026.115113

Figure Lengend Snippet: Regenerated inner phalangeal cells derived from Ki67-traced cells (A) Experimental paradigm showing DT injection (P1), tamoxifen injection (P3), and examination of control ( Ki67 CreERT2/+ ; R26R tdTomato/+ ) and damaged ( Ki67 CreERT2/+ ; Lgr5 DTR/+ ; R26R tdTomato/+ ) cochlea at P7. (B) Representative confocal images of whole mount cochlea from P7 control and damaged mice showed more Ki67-traced cells in the damaged cochlea, decreasing from the apex toward the base. No Ki67-traced cells were detected in the undamaged cochleae. Ki67-traced regenerated Fabp7 + IPhCs (orange arrowheads) and untraced tdTomato-negative, regenerated Fabp7 + IPhCs (white arrowheads) were found in all cochlear turns, with the former being more abundant in the apical and middle turns. Dashed white lines represent the IPhC region. Orthogonal projections showing Ki67-tdTomato + Fabp7 + IPhCs (dashed lines). (C) High magnification images of the apical turn of the P7 damaged cochlea, showing both Ki67-tdTomato + (yellow dashed lines) and tdTomato-negative (white dashed lines) IPhCs at the nucleus level. (D) The number of tdTomato + and tdTomato-negative IPhCs from damaged cochlea were not significantly different in the apex or middle turns, but the latter was significantly more than the former in the base. Unpaired t tests were used for (D), ∗∗ p < 0.01. Lesser epithelial ridge = LER, greater epithelial ridge = GER, outer hair cell = OHC, inner hair cell = IHC. Graphs represent mean ± SD. Scale bars represent 20 μm.

Article Snippet: The following mouse strains were used: Lgr5-DTR-EGFP (gift from F. de Sauvage, Genentech), GLAST-CreERT (Slc1a3-Cre-ERT, Stock #12586, Jackson Laboratory), Rosa26R-tdTomato (Ail4, Stock #7914, Jackson Laboratory), and Ki67-CreERT2 (Stock #029803, Jackson Laboratory).

Techniques: Derivative Assay, Injection, Control

Journal: iScience

Article Title: Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea

doi: 10.1016/j.isci.2026.115113

Figure Lengend Snippet: ScRNA-seq reveals damage-induced transcriptomes of the greater epithelial ridge and inner phalangeal cells (A) UMAP showing integration of Epcam + cochlear epithelial cells from P4-P7 control ( Ki67 CreERT2/+ ; R26R tdTomato/+ ) and damage ( Ki67 CreERT2/+ ; Lgr5 DTR/+ ; R26R tdTomato/+ ) cochlea, resulting in 18 individual clusters. (B) UMAPs showing gene expression profiles of medial and lateral GER markers. (C) UMAPs showing cell clusters integrated from control and damage cochlea at individual time points. Arrows indicate cell clusters predominantly or exclusively found in the damaged cochlea. (D) Percent distribution of cells from each time point and condition by cluster. To account for differences in the number of profiled cells in each dataset, percent contribution to each cluster was normalized to the dataset size. Blue asterisk denotes proliferating GER cells, red asterisks denote native and responding DC/IPC populations. Note that cluster 10 (native DC/IPCs) are mainly composed of cells from control cochlea, whereas cluster 8 (responding DC/IPC) is entirely composed of cells from damaged cochlea. (E) UMAPs showing a reduction of Lgr5 + cells in the damaged cochlea, as well as an increase in Ki67-tdTomato + cells in the damaged lateral GER and Fabp3 + responding DC/IPCs. Cluster 17 (proliferating cells) express Mki67 . (F) Overlaid expression of “cell cycle” and “pathways of neurodegeneration—multiple diseases” gene signatures, extracted from KEGG Pathways mmu04110 and mmu05022 using clusterProfiler. Cell cycle gene signature is highly enriched in cluster 17 and moderately enriched in cluster 8. See also . (G) Volcano plots showing differentially expressed genes between damage and control GER and IPhC clusters at all four time points (excluding proliferating cell cluster). (H) Immunostaining showing that Galectin1 and Calb1 mark medial GER (white brackets) in all three turns of the control cochlea (P6-7). After damage, domains expressing Galectin1 and Calb1 expand laterally into the central GER. Note that Calb1 also labels hair cells. (I) Crabp1 is expressed in medial GER in all three turns of P4 and P7 control cochlea. At P4 after damage, its expression robustly increased and expanded to the central and lateral GER, before returning to similar levels and spatial pattern as controls at P7. (J) Immunostaining shows that Jag1 expression initially decreases in the lateral GER relative to controls at P4, before upregulation at P7 to more intense levels than controls. (K) Quantification of Crabp1-expressing regions shows a significant increase after damage relative to controls at P7 ( n = 3). Unpaired t tests were used for (K). ∗ p < 0.05, ∗∗ p < 0.01, ∗∗∗ p < 0.001. Brackets represent GER. IHC = inner hair cell (arrows), OHC = outer hair cell, GER = greater epithelial ridge. Scale bars represent 50 μm.

Article Snippet: The following mouse strains were used: Lgr5-DTR-EGFP (gift from F. de Sauvage, Genentech), GLAST-CreERT (Slc1a3-Cre-ERT, Stock #12586, Jackson Laboratory), Rosa26R-tdTomato (Ail4, Stock #7914, Jackson Laboratory), and Ki67-CreERT2 (Stock #029803, Jackson Laboratory).

Techniques: Control, Gene Expression, Expressing, Immunostaining

Journal: iScience

Article Title: Dual mechanisms of supporting cell regeneration in the neonatal mouse cochlea

doi: 10.1016/j.isci.2026.115113

Figure Lengend Snippet: Trajectory analysis reveals two mechanisms of inner phalangeal cell regeneration (A) Subclustering analysis of clusters 5, 7, and 17 from P4-P7 damaged ( Ki67 CreERT2/+ ; Lgr5 DTR/+ ; R26R tdTomato/+ ) cochlea. (B) UMAP plots showing expression profiles of proliferating cells ( Mki67 , Top2a ), lateral GER ( Jag1 , Cyp26b1 ), and IPhCs ( Fabp7 , Erbb4 , Ednrb , Lgr5 ). (C and D) UMAP plots showing the slingshot trajectories of lineages 1–3, extending from lateral GER cells. (E) Heatmap depicting five groups of dynamically expressed genes (Log 2 fold change >0.25 or < −0.25, p value <0.05) along lineage 1, with corresponding GO terms. (F) Heatmap depicting 5 groups of dynamically expressed genes along lineage 2. (G) UMAP plot showing the slingshot lineages overlayed with six fixed points along pseudotime, called knots (k). (H and I) GO and KEGG Pathway analysis of genes differentially expressed ( p value <0.05) between Lineage 1 and 2 at their branchpoint (between knots 3 and 4).

Article Snippet: The following mouse strains were used: Lgr5-DTR-EGFP (gift from F. de Sauvage, Genentech), GLAST-CreERT (Slc1a3-Cre-ERT, Stock #12586, Jackson Laboratory), Rosa26R-tdTomato (Ail4, Stock #7914, Jackson Laboratory), and Ki67-CreERT2 (Stock #029803, Jackson Laboratory).

Techniques: Expressing