Single-cell transcriptomes of kidneys in a 6-month-old boy with Denys-Drash syndrome reveal stromal cell heterogeneity in the tumor microenvironment

Background Denys-Drash syndrome (DDS) is a rare disease characterized with pseudohermaphroditism, nephroblastoma (also known as Wilms tumor), and diffuse mesangial sclerosis. The therapy for DDS is largely supportive, i.e. surgery and chemotherapy for Wilms tumor and renal replacement therapy. Due to the limited understanding of the pathogenesis, precision therapy for DDS is yet to be explored. We sought to explore the cellular components and interactions in kidney tissues from an infant with DDS.Methods Whole-exome sequencing was performed to examine the mutations associated with DDS. Single-cell RNA sequencing (scRNA-seq) was performed to explore the heterogenicity of kidney tissue samples.Results A 6-month-old infant with bilateral Wilms tumors and genital ambiguity was diagnosed as having DDS. Whole exome sequencing revealed a novel de novo mutation (p.F185fs*118) in exon 1 of WT1. scRNA-seq was performed in tissue samples from bilateral Wilms tumors and the normal kidney from this infant. Fibroblasts, myocytes, epithelial cells, endothelial cells, and mononuclear phagocytes (MPs) ranked at the top of the 31 135 total cells. Fibroblasts and myocytes were dominant in the Wilms tumor samples. In contrast, most epithelial cells and endothelial cells were found in normal kidney tissues. CD44 and TUBA1A were significantly changed in myocyte subclusters, which may contribute to chemotherapy drug resistance. Macrophages intensively interacted with cancerous cells, including fibroblasts, epithelial cells, and myocytes.Conclusions A novel mutation (p.F185fs*118) in exon 1 of WT1 was identified in an infant with DDS. scRNA-Seq revealed the heterogenicity of cellular components in Wilms tumors and kidney tissues, shedding light on the pathogenesis of DDS. Graphical Abstract