Deciphering the molecular pathophysiology of Imprinting Disorders using Multi-Omics in human cellular Models – ID-MOM

Parental genomic imprinting is an epigenetic process that results in the mono-allelic expression of ~130 human genes depending on their parental origin. This process is regulated through the methylation of specific loci called imprinting control regions (ICRs). Defects in ICR methylation (including in a mosaic manner) can result in imprinting disorders (IDs). These disorders affect a wide-range of biological processes, including growth and metabolism, and have a lifelong impact on health. Our long-term interest is to understand the pathophysiological role of imprinted genes in growth deregulation. In the ID-MOM project, we focus on three IDs in which foetal growth is particularly affected: The Silver-Russell and Temple syndromes (with foetal growth restriction) and the Beckwith-Wiedemann syndrome (with foetal overgrowth).
A major limitation to unravel the molecular underpinnings of ID pathophysiology is the lack of relevant human cell models. Indeed, current models for IDs are mostly developed in rodents, whose foetal and post-natal growth are not equivalent to humans. Similarly, the primary tissues involved in growth process are inaccessible in humans, and most imprinted genes whose expression is altered in IDs are not or very little expressed in blood cells or fibroblasts. This explains why very few data are currently available on the pathophysiological consequences of IDs in endochondral ossification; a key process in growth regulation.
A further complication for the characterization of ID pathophysiology is the fact that multiple ICRs can be simultaneously perturbed, thus causing Multi-Locus Imprinting Disturbances (MLID). Moreover, imprinted genes from different sites in the genome are co-regulated within an imprinted gene network. The characterization of IDs thus requires the combined analysis of DNA methylation at numerous ICRs and transcriptional deregulation genome-wide.
The first aim of the ID-MOM project is to generate physiologically-relevant human cellular models from native, reprogrammed or epi-edited stem cells. Using our expertise in human induced pluripotent stem cells (hiPSCs), dental pulp stem cells (DPSCs) and epigenetically-edited cells, we will differentiate these cells into hypertrophic chondrocytes that faithfully recapitulate the growth plate. The second aim is to apply and calibrate advanced sequencing-based tools (i.e, targeted bisulfite sequencing and single-molecule Nanopore sequencing of native DNA) to precisely quantify the methylation status at numerous ICRs, including mosaicism. In the third aim, the combination of quantitative DNA methylation profiles with RNA sequencing in newly generated cellular models from patients, controls and epigenetically-edited cells will allow us to assess the molecular links between perturbed imprinted DNA methylation and transcriptional output.
Within a consortium of three highly complementary partners, ID-MOM project will provide innovative data to characterize the pathophysiological underpinnings of human IDs. Our novel in-vitro human cellular models of the endochondral ossification process will allow us to identify the pathological consequences of methylation defect(s) at a cellular level. Beyond their pathophysiological insights, the establishment of these models and assays will create important opportunities for future ID studies, including studies in other phenotypically relevant cell lineages (i.e adipocytes, hepatocytes, neurons and myocytes). Also, this model will allow the screening and testing of drug candidates and the improvement of molecular diagnosis of these rare IDs and associated MLID using our newly developed genomics-based methylation assays. Combined, our project will thus help to directly advance the global management of these ID patients.