Epigenetics: induced pluripotent stem cells, a promising cellular model for studying parental imprinting diseases

Parental imprinting is an epigenetic mechanism that leads to the monoallelic expression of a subset of genes according to their parental origin. Imprinting Disorders (ID), caused by perturbations of imprinted genes, are a group of rare congenital diseases that mainly affect growth, metabolism and development.

In order to model the pathophysiology of parental imprinting diseases, a research team made up of doctors, researchers and doctoral students from Inserm, Sorbonne University and IHU ICAN has developed a new cellular approach. Published on December 28, 2022 in the journal Clinical Epigenetics, this study is entitled “Maintenance of methylation profiles in imprinting control regions in induced human pluripotent stem cells”.

What are the objectives of this approach?

To date, there is no reliable model for studying the pathophysiology of parental imprinting diseases in humans, the first step in developing appropriate therapeutic strategies. Human induced pluripotent stem cells (hiPSCs) are a promising cellular approach for modeling human diseases and complex genetic disorders.

However, aberrant hypermethylation of Imprinting control regions (ICRs) may occur during the reprogramming process and subsequent culture of hiPSCs. Consequently, the research team tested different reprogramming and culture conditions for hiPSCs and carried out an in-depth analysis of methylation at imprinting control regions, with the aim of developing a cellular model for understanding parental imprinting diseases.

What are the results of the study?

The researchers assessed methylation at seven imprinted loci in hiPSCs before differentiation, at different cell culture passages, and during chondrogenic differentiation. As already described in the literature, hypermethylation was identified at the 11p15 H19/IGF2:IG-DMR and 14q32 MEG3/DLK1:IG-DMR imprinted regions, irrespective of the reprogramming method and cells of origin.

Hypermethylation at these two loci led to loss of parental imprinting, with biallelic expression of imprinted genes IGF2 and DLK1, in regions 11p15 and 14q32 respectively. The development of epiPS™ culture medium combined with cell culture in hypoxia made it possible to correct hypermethylation in H19/IGF2:IG-DMR and MEG3/DLK1:IG-DMR and restore parental imprinting, while preserving the proliferative and pluripotent qualities of these stem cells.

What are the conclusions?

Extensive quantitative analysis of the methylation of imprinting control regions revealed hypermethylation at certain ICRs (those methylated on the paternal allele), in hiPSCs associated with loss of imprinting in these regions.

The epiPS™ culture medium and hypoxia culture of hiPSCs restored balanced methylation at these loci in controls. The research team was also able to show that methylation was disrupted in hiPSCs derived from a patient, thus recapitulating the molecular anomaly responsible for his pathology.

HiPSCs cultured with this new protocol therefore offer very interesting prospects for differentiation into cells of interest involved in the phenotype of patients with diseases linked to parental imprinting, in order to understand the pathophysiological mechanisms and envisage therapeutic targets.

The actors involved in the project

This project is supported by:

  • The IHU ICAN
  • Sorbonne University
  • Inserm

The actors and authors of this study:

  • Prof. Irène Netchine, PU-PH and Head of the “IGF system and fetal and post-natal growth” team at Sorbonne Université/Inserm/AP-HP
  • Dr Aurélie Pham, CCU-AH, PhD at Sorbonne Université/Inserm/AP-HP
  • Céline Selenou, Inserm doctoral student
  • Dr Eloïse Giabicani, MCU-PH at Sorbonne University/Inserm/AP-HP
  • Dr Vincent Fontaine, PhD at IHU ICAN
  • Sibylle Marteau, iPS Cell Culture Assistant Engineer at the ICAN IHU
  • Dr Frédéric Brioude, MCU-PH at Sorbonne Université/Inserm/AP-HP
  • Dr Laurent David, MCU-PH, University of Nantes
  • Prof. Delphine Mitanchez, PU-PH Sorbonne Université/Inserm
  • Dr Marie-Laure Sobrier, Inserm CR

Read the publication

Maintenance of methylation profile in imprinting control regions in human induced pluripotent stem cells. Pham A, Selenou C, Giabicani E, Fontaine V, Marteau S, Brioude F, David L, Mitanchez D, Sobrier ML, Netchine I. Clin Epigenetics. 2022 Dec 28;14(1):190. doi: 10.1186/s13148-022-01410-8.