Association of CDKAL1 nucleotide variants with the risk of non-syndromic cleft lip with or without cleft palate

Identification of novel susceptibility genes for non-syndromic cleft lip with or without cleft palate using NGS-based multigene panel testing

For non-syndromic cleft lip with or without cleft palate (ns-CL/P), the proportion of heritability explained by the known risk loci is estimated to be about 30% and is captured mainly by common variants identified in genome-wide association studies. To contribute to the explanation of the "missing heritability" problem for orofacial clefts, a candidate gene approach was taken to investigate the potential role of rare and private variants in the ns-CL/P risk. Using the next-generation sequencing technology, the coding sequence of a set of 423 candidate genes was analysed in 135 patients from the Polish population. After stringent multistage filtering, 37 rare coding and splicing variants of 28 genes were identified. 35% of these genetic alternations that may play a role of genetic modifiers influencing an individual's risk were detected in genes not previously associated with the ns-CL/P susceptibility, including COL11A1, COL17A1, DLX1, EFTUD2, FGF4, FGF8, FLNB, JAG1, NOTCH2, SHH, WNT5A and WNT9A. Significant enrichment of rare alleles in ns-CL/P patients compared with controls was also demonstrated for ARHGAP29, CHD7, COL17A1, FGF12, GAD1 and SATB2. In addition, analysis of panoramic radiographs of patients with identified predisposing variants may support the hypothesis of a common genetic link between orofacial clefts and dental abnormalities. In conclusion, our study has confirmed that rare coding variants might contribute to the genetic architecture of ns-CL/P. Since only single predisposing variants were identified in novel cleft susceptibility genes, future research will be required to confirm and fully understand their role in the aetiology of ns-CL/P.

The genetic factors contributing to the risk of cleft lip-cleft palate and their clinical utility

Cleft lip and cleft palate (CL/P) are among the most common congenital malformations in neonates and have syndromic or nonsyndromic forms. Nonsyndromic forms of malformation are being reported to be associated with chromosomal DNA modification by teratogenic exposure and to complex genetic contributions of multiple genes. Syndromic forms are shown to be related to chromosomal aberrations or monogenic diseases. There is a growing body of data illustrating the association of several genes with risk of developing this malformation, including genetic defects in T-box transcription factor-22 (TBX22), interferon regulatory factor-6 (IRF6), and poliovirus receptor-like-1 (PVRL1), responsible for X-linked cleft palate, cleft lip/palate-ectodermal dysplasia syndrome, and Van der Woude and popliteal pterygium syndromes, respectively. Genetic variants in MTR, PCYT1A, ASS1, SLC 25A13, GSTM1, GSTT1, SUMO1 BHMT1, and BHMT2 are being reported to be linked with CL/P risk. The etiology of nonsyndromic CLP is still remained to be unknown, although mutations in candidate genes have been found. Here, we provide an overview about the potential variants to be associated with CL/P for identification of the relative risk of CLP with respect to the basis of genetic background and environmental factors (e.g., dietary factors, alcohol use).

Association of BMP4 rs17563 Polymorphism with Nonsyndromic Cleft Lip with or without Cleft Palate Risk: Literature Review and Comprehensive Meta-Analysis

Although published individual studies have reported associations between BMP4 rs17563 polymorphism and nonsyndromic cleft lip with or without cleft palate (NSCLP) risk, the results are conflicting. This meta-analysis was conducted to assess the association based on multiple studies. Methods: A comprehensive literature search up to October 1st, 2019 was performed using PubMed, Science Direct, China National Knowledge Infrastructure (CNKI), and Wanfang databases. Results: Fourteen case-control studies with 2,058 NSCLP cases and 2,557 controls were selected. There was no significant association between BMP4 rs17563 polymorphism and risk of NSCLP overall. Subgroup analysis revealed that BMP4 rs17563 polymorphism was associated with NSCLP risk in Chinese and Brazilian populations. Conclusions: This meta-analysis suggests that BMP4 rs17563 polymorphism was not associated with NSCLP risk in overall population. However, BMP4 rs17563 polymorphism may be a risk factor for development of NSCLP in Chinese and Brazilians.

S-adenosylmethionine tRNA modification: unexpected/unsuspected implications of former/new players

S-adenosylmethionine supplies methyl groups to many acceptors, including lipids, proteins, RNA, DNA, and a wide range of small molecules. It acts as the precursor in the biosynthesis of metal ion chelating compounds, such as nicotianamine and phytosiderophores, of the polyamines spermidine and spermine and of some plant hormones. Finally, it is the source of catalytic 5′-deoxyadenosyl radicals.

Radical S-adenosylmethionine (SAM) enzymes (RS) represent one of the most abundant groups (more than 100,000) of enzymes, exerting a plethora of biological functions, some of which are still unknown.

In this work, we will focus on two RS: CDK5RAP1 and CDKAL1, both of which are involved in tRNA modifications that result in important tRNA folding and stability and in maintaining high translational fidelity. Based on this crucial role, their impairment can be important in the development of different human diseases.

PAX7 nucleotide variants and the risk of non-syndromic orofacial clefts in the Polish population

OBJECTIVE

The etiology of non-syndromic cleft lip with or without cleft palate (nsCL/P) is multifactorial, heterogeneous, and still not completely understood. The aim of the present study was to examine the associations between common and rare PAX7 nucleotide variants and the risk of this common congenital anomaly in a Polish population.

SUBJECTS AND METHODS

Eight top nsCL/P-associated PAX7 variants identified in our cleft genome-wide association study (GWAS) were selected for replication analysis in an independent group of patients and controls (n = 247 and n = 445, respectively). In addition, mutation screening of the PAX7 protein-coding region was conducted.

RESULTS

Analysis of the pooled data from the GWAS and replication study confirmed that common PAX7 nucleotide variants are significantly associated with the increased risk of nsCL/P. The strongest individual variant was rs1339062 (c.586 + 15617T > C) with a p-value = 2.47E-05 (OR = 1.4, 95%CI: 1.20-1.64). Sequencing analysis identified a novel synonymous PAX7 substitution (c.87G > A, p.Val29Val) in a single patient with nsCLP. This transition located in the early exonic position was predicted to disrupt potential splice enhancer elements.

CONCLUSION

Our study confirmed that PAX7 is a strong candidate gene for nsCL/P. Nucleotide variants of this gene contribute to the etiology of nsCL/P in the homogenous Polish population.