Transcription factor Tfap2a orchestrates a gene regulatory network mediating renal collecting duct cell differentiation and tubular architecture

These are primary data used for creating the figures of Leiz J, et al. 2024 (manuscript under revision).

Transcription factor Tfap2a orchestrates a gene regulatory network mediating renal collecting duct cell differentiation and tubular architecture.

Background: Mutations of the transcription factor TFAP2A are associated with congenital anomalies of the kidney and urinary tract in humans. Tfap2a knockout in mouse collecting ducts causes tubular epithelial abnormalities, but the detailed molecular functions of Tfap2a in the kidney tubules are unknown.
Methods: We investigated gene regulatory networks regulated by Tfap2a in mouse kidney collecting ducts through a combination of gene knockout and transcriptomics approaches. Conditional Tfap2a knockout (KO) mice (Hoxb7-Cre; Tfap2aflox/flox) underwent detailed histomorphological and physiological examinations. Single-nucleus and bulk RNA-sequencing data, and in situ hybridizations of adult Tfap2a KO mouse kidneys were integrated with in silico Tfap2a motif mapping in existing ATAC-seq datasets.
Results: Tfap2a expression and its motif activity were high in normal mouse collecting duct principal cells according to integrated transcriptomics, chromatin occupancy analyses, and in situ hybridization.  Histomorphological analyses of collecting duct-specific Tfap2a KO mice indicated a progressive postnatal tubular dilation of outer medullary collecting ducts. Integrative analyses combining existing ATAC-seq datasets with newly generated single-nucleus RNA-sequencing data from the kidneys of 3-month-old Tfap2a KO mice and littermate controls identified deregulated expression of genes involved in cell adhesion and WNT signaling pathways, including Alcam (a cell adhesion molecule) and Wnt9b (a non-canonical WNT). These findings were orthogonally validated by in situ hybridization.
Conclusions: Tfap2a controls tubular diameter and epithelial differentiation in mouse collecting ducts by controlling a regulatory network that includes Wnt9b and Alcam.