Nonsyndromic orofacial clefts in Chile: LINE-1 methylation and MTHFR variants

Epigenetic mechanisms and oral mucositis in children with acute lymphoblastic leukaemia

This study aimed to investigate the relationship between epigenetic mechanisms and oral mucositis (OM) in paediatric patients with acute lymphoblastic leukaemia. Oral cells were collected from 76 participants, including 15 healthy individuals, 10 patients with acute lymphoblastic leukaemia but without a history of OM and 51 acute lymphoblastic leukaemia patients with a history of OM (35 with active OM and 16 who had recovered from OM). Global DNA methylation in the miR-9-1 and miR-9-3 genes was performed. Seven polymorphisms rs1801131, rs1801133 (MTHFR), rs2228611 (DNMT1), rs7590760, rs1550117 (DNMT3A), rs6087990, rs2424913 (DNMT3B) were genotyped and an analysis of association with global DNA methylation was performed. The global methylation levels were lower in cancer patients recovered from OM than in the other groups. A higher frequency of unmethylated profile for miR-9-1 and partially methylated profile for miR-9-3 was observed in cancer patients regardless of OM history compared to healthy patients. The GG genotype of the rs2228611 (DNMT1) polymorphism was associated with higher levels of global methylation in cancer patients irrespective of OM. It was concluded that global methylation is associated with mucosal recovery. The effect of DNMT1 genotype on the global DNA methylation profile, as well as the methylation profile of miR-9-1 and miR-9-3 in cancer patients is independent of OM.

Progress of epigenetic modification of SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate

Non-syndromic Cleft Lip and Palate (NSCLP) is one of the most common congenital craniofacial malformations. However, there is no enough knowledge about its mechanism, even through many relevant studies verify that cleft lip and palate is caused by interactions between environmental and genetic factors. SATB2 gene is one of the most common candidate genes of NSCLP, and the development of epigenetics provides a new direction on pathogenesis of cleft lip and palate. This review summarizes SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate, expecting to provide strategies to prevent and treat cleft and palate in the future.

DNA methylation profile of lip tissue from congenital nonsyndromic cleft lip and palate patients by whole-genome bisulfite sequencing

Congenital nonsyndromic cleft lip and palate (NSCLP) is one of the most common malformations worldwide. DNA methylation has been implicated in many diseases. However, its involvement in lip tissue from NSCLP is not well understood. This study aimed to investigate the role of dysregulated DNA methylation in NSCLP. DNA methylation profile was determined in eight injured and five self-normal lip tissue samples from children with NSCLP by whole-genome bisulfite sequencing. A total of 2,711 differentially methylated regions (DMRs), corresponding to 1,231 genes were identified. Given the important role of promoter methylation in regulating gene expression, the promoter DMR-related genes were considered. Bioinformatics analysis demonstrated that some of them showed potential associations with NSCLP. Therefore, the well-known NSCLP susceptibility gene, GLI family zinc finger 2 (GLI2) with an unknown role in its DNA methylation in NSCLP, was selected for further analysis. The promoter hypomethylation and higher mRNA expression level of GLI2 were observed in injured lip tissues by verification in additional samples. Moreover, dual luciferase reporter assay indicated that promoter hypermethylation of GLI2 inhibited its transcription. Overall, this study suggested that abnormal DNA methylation in lip tissue may be correlated with the pathogenesis of congenital NSCLP.

PEMT variants are associated with nonsyndromic cleft lip with or without cleft palate in Chile

Aim: To assess the association between PEMT variants and nonsyndromic cleft lip with or without cleft palate in Chile and the effects of these variants on global DNA methylation. Subjects & methods: The authors obtained genotypes for nine variants from 247 cases and 453 controls for genotype-phenotype associations. The effect of significant polymorphisms on global DNA methylation (percentage of long interspersed element-1 methylation) was evaluated in a subsample of 95 controls. Results: After multiple comparison corrections, variants rs7649 and rs4646409 were associated with nonsyndromic cleft lip with or without cleft palate. Carriers of risk alleles presented lower DNA methylation levels than noncarriers. Conclusion: According to functional analysis for risk variants from previous reports, the authors infer that a decrease of methyl group availability is occurring in affected subjects.

Vitamin B12 Transport Genes and Nonsyndromic Cleft Lip With or Without Cleft Palate in Chile

The aims of this study were to assess the association between polymorphisms within genes involved in vitamin B12 transport and nonsyndromic cleft lip with or without cleft palate (NSCL/P) and global DNA methylation in Chile. From 247 cases and 453 controls, we obtained variant genotypes for CBLIF, CUBN, AMN, ABCC1, CD320, and TCN2 from a single nucleotide polymorphisms array. Global DNA methylation in 95 controls was obtained through LINE-1 methylation. After multiple comparison corrections, only rs780807 in CUBN remains associated with NSCL/P at dominant model (OR 0.564, p-value = 0.0006, q-value = 0.0450). Carriers of protective allele showed lower levels of DNA methylation than non-carriers (p = 0.0259). Further studies are necessary in order to explain relations with the phenotype and DNA methylation due to the absence of functional evidence for rs780807 in CUBN.

Genetic and Epigenetic Studies in Nonsyndromic Oral Clefts

The etiology of non-syndromic oral clefts (NSOFC) is complex with genetics, genomics, epigenetics and stochastics factors playing a role. Several approaches have been applied to understand the etiology of non-syndromic oral clefts. These include linkage, candidate gene association studies, genome-wide association studies, whole genome sequencing, copy number variations and epigenetics. In this review we shared these approaches, genes and loci reported in some studies.