RET enhancer haplotype-dependent remodeling of the human fetal gut development program

• Published in: PLoS genetics Vol. 19; no. 11; p. e1011030
• Main Authors: Chatterjee, Sumantra, Fries, Lauren E, Yaacov, Or, Hu, Nan, Berk-Rauch, Hanna E, Chakravarti, Aravinda
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 10-11-2023; Public Library of Science (PLoS)
• Subjects: Cell cycle; Cell Line, Tumor; Cell proliferation; DNA binding proteins; EDNRB gene; Embryos; Enhancer Elements, Genetic; Enhancers; Enteric nervous system; Enteric Nervous System - embryology; Epigenetic inheritance; Epigenetics; Fetus; Fetuses; Gastrointestinal Tract - embryology; Gene expression; Gene Expression Regulation, Developmental; Genes; Genetic aspects; Genotype & phenotype; Growth; Haplotypes; Health aspects; Hirschsprung Disease - genetics; Hirschsprung's disease; Humans; Intestine, Small; Kinases; Medical research; Medicine, Experimental; Mutation; Nervous system, Autonomic; Neural crest; Neural Crest - cytology; Neuroblastoma; Neurogenesis; Neurons; Physiological aspects; Protein tyrosine kinase; Protein-tyrosine kinase receptors; Proto-Oncogene Proteins c-ret - genetics; Ret protein; Risk factors; Signal transduction; Single-Cell Gene Expression Analysis; Transcription factors; Transcriptomes; United States; Canada
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1011030

Hirschsprung disease (HSCR) is associated with deficiency of the receptor tyrosine kinase RET, resulting in loss of cells of the enteric nervous system (ENS) during fetal gut development. The major contribution to HSCR risk is from common sequence variants in RET enhancers with additional risk from rare coding variants in many genes. Here, we demonstrate that these RET enhancer variants specifically alter the human fetal gut development program through significant decreases in gene expression of RET, members of the RET-EDNRB gene regulatory network (GRN), other HSCR genes, with an altered transcriptome of 2,382 differentially expressed genes across diverse neuronal and mesenchymal functions. A parsimonious hypothesis for these results is that beyond RET's direct effect on its GRN, it also has a major role in enteric neural crest-derived cell (ENCDC) precursor proliferation, its deficiency reducing ENCDCs with relative expansion of non-ENCDC cells. Thus, genes reducing RET proliferative activity can potentially cause HSCR. One such class is the 23 RET-dependent transcription factors enriched in early gut development. We show that their knockdown in human neuroblastoma SK-N-SH cells reduces RET and/or EDNRB gene expression, expanding the RET-EDNRB GRN. The human embryos we studied had major remodeling of the gut transcriptome but were unlikely to have had HSCR: thus, genetic or epigenetic changes in addition to those in RET are required for aganglionosis.