28.10.2021

Correction of a Genetic Disease that Affects the Epigenetics of the Whole Genome - Is this Possible?

Shir Toubiana Rappaport Faculty of Medicine at the Technion Published JIMS Issue 25.04.2021
Background: Many procedures requiring sedation in the pediatric emergency department are performed by consultants from outside the department. This team usually includes orthopedic surgeons and general surgeons. As sedation is now a standard of care in such cases, we evaluated consultants' views on sedation.
Objectives: To evaluate consultants' views on sedation.
Methods: A questionnaire with both open-ended questions and Likert-type scores was distributed to all orthopedic surgeons and general surgeons performing procedures during the study period. The questionnaire was presented at three medical centers.
Results: The questionnaire was completed by 31 orthopedic surgeons and 16 general surgeons. Although the vast majority (93–100%) considered sedation important, a high percentage (64–75%) would still perform such procedures without sedation if not readily available.
Conclusions: Sedation is very important for patients and although consultants understand its importance, the emergency department staff must be vigilant in both being available and not allowing procedures to "escape" the use of sedation.

In a study published in eLife journal [1], researchers have demonstrated a genotypic correction of a genetic disorder that causes a rare syndrome called ICF (Immunodeficiency, Centromeric region instability, Facial anomalies), which endangers infants and children.


ICF syndrome is a rare, autosomal recessive disease, which causes immune failure and mortality during the first two decades of life [2,3] . This disease is heterogeneous, meaning that different mutations in at least 4 genes cause the disease [4,5] . At the molecular level, all ICF syndrome patients exhibit reduced DNA methylation at various genomic regions. Hypomethylation is most striking at pericentromeric regions which consequently fail to condense properly in mitosis [6,7]. This de-condensation leads to the typical centromeric instability and rearrangements observed in the disease. Many patients (55 %) carry various mutations in a gene called DNMT3B (DNA methyltransferase 3B), which is responsible for adding a methyl group to different regions within the genome, especially repetitive regions [8,9]. The main function of DNA methylation is to control the proper expression of genes and maintain the stability of chromosomes [10,11]. This biological process also protects the telomeres, the ends of the chromosomes. Therefore, aberrations in the methylation process cause disruption in the telomere control and premature aging of cells [12,13].


ICF syndrome is already manifested in the early stages of fetal development. The researchers performed genetic editing using the CRISPR/Cas9 method in induced pluripotent stem cells (iPSCs) derived from the skin cells of ICF patients, repairing the DNMT3B mutations. iPSCs are an important tool because they "mimic" the stage of implantation in the uterus that occurs during fetal development. The researchers found that by correcting the mutations in DNMT3B the methylation in the pericentromeric regions was restored, but not in most telomeric regions.


To understand why some regions were re-methylated and some were not, the researchers found that the failure was due to high levels of a certain chemical modification in these regions, which prevented recruiting of the DNMT3B protein to those areas to re-methylate. In addition, the researchers found that this molecular barrier is part of the 'epigenetic memory' of patients' original skin cells. Lowering this chemical barrier led to an increase in the level of methylation around the telomeres. Thus, they showed that altering, even for a short time, the modification that inhibits the DNMT3B recruitment, may allow the corrected DNMT3B access to these regions and re-methylate.


This project is the first of its kind in trying to examine the feasibility of repairing a human genetic syndrome that disrupts the epigenetics of the genome, and it highlights the challenges of this process. However, the researchers' demonstration that pharmacological manipulation can increase DNA methylation around the telomeres, serves as proof of principle that we may overcome these challenges, if we understand the processes that direct DNA methylation to various genomic regions. Hopefully understanding these processes at telomeres as well as at other regions in the genome will not only help us understand the molecular pathology of ICF syndrome but also how in the future the methylation may be restored to all genomic regions.

 

References

1. Toubiana S, Gagliardi M, Papa M, et al. Persistent epigenetic memory impedes rescue of the telomeric phenotype in human ICF iPSCs following DNMT3B correction. Elife 2019;8.

2. van den Boogaard ML, Thijssen PE, Aytekin C, et al. Expanding the mutation spectrum in ICF syndrome: Evidence for a gender bias in ICF2. Clin Genet 2017;92(4).

3. Ehrlich M, Jackson K, Weemaes C. Immunodeficiency, centromeric region instability, facial anomalies syndrome (ICF). Orphanet J Rare Dis  2006;1(1).

4. Thijssen PE, Ito Y, Grillo G, et al. Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome. Nat Commun 2015;6.

5. De Greef JC, Wang J, Balog J, et al. Mutations in ZBTB24 are associated with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2. Am J Hum Genet 2011;88(6).

6. Velasco G, Walton EL, Sterlin D, et al. Germline genes hypomethylation and expression define a molecular signature in peripheral blood of ICF patients: Implications for diagnosis and etiology. Orphanet J Rare Dis 2014;9(1).

7. Xu GL, Bestor TH, BourC’His D, et al. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 1999;402(6758).

8. Kato Y, Kaneda M, Hata K, et al. Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum Mol Genet 2007;16(19).

9. Okano M, Bell DW, Haber DA, Li E. DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development. Cell 1999;99(3).

10.  Dor Y, Cedar H. Principles of DNA methylation and their implications for biology and medicine. Lancet. 2018;392(10149).

11. Luo C, Hajkova P, Ecker JR. Dynamic DNA methylation: In the right place at the right time. Science. 2018;361(6409).

12. Yehezkel S, Segev Y, Viegas-Péquignot E, Skorecki K, Selig S. Hypomethylation of subtelomeric regions in ICF syndrome is associated with abnormally short telomeres and enhanced transcription from telomeric regions. Hum Mol Genet 2008;17(18).

13. Yehezkel S, Shaked R, Sagie S, et al. Characterization and rescue of telomeric abnormalities in ICF syndrome type I fibroblasts. Front Oncol 2013;3 FEB.