No evidence for a role of CRISPLD2 in non-syndromic cleft lip with or without cleft palate in an Italian population

Concurrent de novo ZFHX4 variant and 16q24.1 deletion in a patient with orofacial clefting; a potential role of ZFHX4 and USP10

A girl with a unilateral cleft lip, alveolus and palate, tooth agenesis, and mild dysmorphic features, without a specific underlying syndrome diagnosis, was genotypically characterized and phenotypically described. Cleft gene panel analysis, single-nucleotide polymorphism (SNP) array, whole genome sequencing (WGS), whole exome sequencing, and quantitative PCR (Q-PCR) analysis were used as diagnostic tests. SNP array revealed a maternal deletion at 16q24.1, encompassing the cleft candidate gene USP10. WES revealed an additional de novo Loss-of-Function variant (p.(Asn838fs)) in the Zinc-Finger-Homeobox-4 (ZFHX4) gene. Q-PCR was performed to explore the effect of the ZFHX4 variant and the deletion in 16q24.1. The mRNA expression of a selection of putative target genes involved in orofacial clefting showed a lowered expression of USP10 (52%), CRISPLD2 (31%), and CRISPLD1 (1%) compared to the control. IRF6 showed no difference in gene expression. This case supports ZFHX4 as a novel cleft gene and suggests USP10 may contribute to the etiology of orofacial clefts in humans.

Brazilian Multiethnic Association Study of Genetic Variant Interactions among FOS, CASP8, MMP2 and CRISPLD2 in the Risk of Nonsyndromic Cleft Lip with or without Cleft Palate

Associations of CRISPLD2 (cysteine-rich secretory protein LCCL domain containing 2) and genes belonging to its activation pathway, including FOS (Fos proto-oncogene), CASP8 (caspase 8) and MMP2 (matrix metalloproteinase 2), with nonsyndromic orofacial cleft risk, have been reported, but the results are yet unclear. The aim of this study was to evaluate single nucleotide polymorphisms (SNPs) in FOS, CASP8 and MMP2 and to determine their SNP-SNP interactions with CRISPLD2 variants in the risk of nonsyndromic cleft lip with or without cleft palate (NSCL±P) in the Brazilian population. The SNPs rs1046117 (FOS), rs3769825 (CASP8) and rs243836 (MMP2) were genotyped using TaqMan allelic discrimination assays in a case-control sample containing 801 NSCL±P patients (233 nonsyndromic cleft lip only (NSCLO) and 568 nonsyndromic cleft lip and palate (NSCLP)) and 881 healthy controls via logistic regression analysis adjusted for the effects of sex and genomic ancestry proportions with a multiple comparison p value set at ≤0.01. SNP-SNP interactions with rs1546124, rs8061351, rs2326398 and rs4783099 in CRISPLD2 were performed with the model-based multifactor dimensionality reduction test complemented with a 1000 permutation-based strategy. Although the association between FOS rs1046117 and risk of NSCL±P reached only nominal p values, NSCLO risk was significantly higher in carriers of the FOS rs1046117 C allele (OR: 1.28, 95% CI: 1.10-1.64, p = 0.004), TC heterozygous genotype (OR: 1.59, 95% CI: 1.16-2.18, p = 0.003), and in the dominant model (OR: 1.50, 95% CI: 1.10-2.02, p = 0.007). Individually, no significant associations between cleft risk and the SNPs in CASP8 and MMP2 were observed. SNP-SNP interactions involving CRISPLD2 variants and rs1046117 (FOS), rs3769825 (CASP8) and rs243836 (MMP2) yielded several significant p values, mostly driven by FOS rs1046117 and CASP8 rs3769825 in NSCL±P, FOS rs1046117 in NSCLO and CRISPLD2 rs8061351 in NSCLP. Our study is the first in the Brazilian population to reveal the association of FOS rs1046117 with NSCLO risk, and to support that CRISPLD2, CASP8, FOS and MMP2 interactions may be related to the pathogenesis of this common craniofacial malformation.

The functions of CAP superfamily proteins in mammalian fertility and disease

BACKGROUND

Members of the cysteine-rich secretory proteins (CRISPS), antigen 5 (Ag5) and pathogenesis-related 1 (Pr-1) (CAP) superfamily of proteins are found across the bacterial, fungal, plant and animal kingdoms. Although many CAP superfamily proteins remain poorly characterized, over the past decade evidence has accumulated, which provides insights into the functional roles of these proteins in various processes, including fertilization, immune defence and subversion, pathogen virulence, venom toxicology and cancer biology.

OBJECTIVE AND RATIONALE

The aim of this article is to summarize the current state of knowledge on CAP superfamily proteins in mammalian fertility, organismal homeostasis and disease pathogenesis.

SEARCH METHODS

The scientific literature search was undertaken via PubMed database on all articles published prior to November 2019. Search terms were based on following keywords: 'CAP superfamily', 'CRISP', 'Cysteine-rich secretory proteins', 'Antigen 5', 'Pathogenesis-related 1', 'male fertility', 'CAP and CTL domain containing', 'CRISPLD1', 'CRISPLD2', 'bacterial SCP', 'ion channel regulator', 'CatSper', 'PI15', 'PI16', 'CLEC', 'PRY proteins', 'ASP proteins', 'spermatogenesis', 'epididymal maturation', 'capacitation' and 'snake CRISP'. In addition to that, reference lists of primary and review article were reviewed for additional relevant publications.

OUTCOMES

In this review, we discuss the breadth of knowledge on CAP superfamily proteins with regards to their protein structure, biological functions and emerging significance in reproduction, health and disease. We discuss the evolution of CAP superfamily proteins from their otherwise unembellished prokaryotic predecessors into the multi-domain and neofunctionalized members found in eukaryotic organisms today. At least in part because of the rapid evolution of these proteins, many inconsistencies in nomenclature exist within the literature. As such, and in part through the use of a maximum likelihood phylogenetic analysis of the vertebrate CRISP subfamily, we have attempted to clarify this confusion, thus allowing for a comparison of orthologous protein function between species. This framework also allows the prediction of functional relevance between species based on sequence and structural conservation.

WIDER IMPLICATIONS

This review generates a picture of critical roles for CAP proteins in ion channel regulation, sterol and lipid binding and protease inhibition, and as ligands involved in the induction of multiple cellular processes.

Investigation of candidate genes of non-syndromic cleft lip with or without cleft palate, using both case-control and family-based association studies

OBJECTIVE

Non-syndromic cleft of the lip and/or palate (NSCL/P) is one of the most common polygenic diseases. In this study, both case-control and family-based association study were used to confirm whether the Single Nucleotide Polymorphisms (SNPs) were associated with NSCL/P.

METHODS

A total of 37 nuclear families and 189 controls were recruited, whose blood DNA was extracted and subjected to genotyping of SNPs of 27 candidate genes by polymerase chain reaction-improved multiple ligase detection reaction technology (PCR-iMLDR). Case-control statistical analysis was performed using the SPSS 19.0. Haplotype Relative Risk (HRR), transmission disequilibrium test (TDT), and Family-Based Association Test (FBAT) were used to test for over-transmission of the target alleles in case-parent trios. The gene-gene interactions on NSCL/P were analyzed by Unphased-3.1.4.

RESULTS

In case-control statistical analysis, only C14orf49 chr14_95932477 had statistically significant on genotype model (P = .03) and allele model (P = .03). Seven SNPs had statistically significant on TDT. None of 26 alleles has association with NSCL/P on FBAT. Some SNPs had haplotype-haplotype interactions and genotype-genotype interactions.

CONCLUSION

C14orf49 chr14_95932477 was significantly different between cases and controls on genotype model and allele model by case-control design. Seven SNPs were significantly different on HRR. Four SNPs were significantly different on TDT.

Association Between CRISPLD2 Polymorphisms and the Risk of Nonsyndromic Clefts of the Lip and/or Palate: A Meta-analysis

OBJECTIVE

Nonsyndromic clefts of the lip and/or palate (NSCL/P) are one of the most common polygenic diseases. Recently, many studies focused on the association between CRISPLD2 polymorphisms and NSCL/P risk. However, some studies have shown opposite results. In this study, meta-analysis was used to confirm whether CRISPLD2 polymorphism was associated with NSCL/P, and the possible mechanism between CRISPLD2 and NSCL/P was explored.

METHODS

Relevant studies were conducted on PubMed, Ovid, EBSCO, CINAHL, FMRS, Web of Science, CNKI, and Wanfang databases from their inception up to June 31, 2016. Review Manager 5.0.24 was used to analyze whether CRISPLD2 polymorphism was involved in NSCL/P by pooling odds ratios (ORs) and 95% confidence intervals (CIs). Potential publication bias was evaluated by visual inspection of the funnel plot.

RESULTS

CRISPLD2 rs4783099 was associated with cleft lip and/or palate (CL/P) statistically (OR = 3.18, P < .01). Compared to genotype TT, genotypes CC and CT were correlated significantly (OR = 2.04, P = .04) with CL/P. No evidence showed an association between genetic variation at the CRISPLD2 locus and cleft palate only (CP).

CONCLUSION

The polymorphism of CRISPLD2 rs4783099 is correlated with an increased risk of CL/P.

Cleft palate only: current concepts

Cleft palate only (CPO) is one of the most common congenital malformations worldwide. The etiopathogenesis of CPO is not completely understood. Environmental factors, such as smoking, alcohol consumption, intake of drugs during pregnancy, advanced paternal age, have been demonstrated to be a risk of CPO, but conflicting results have also been published. Insufficient intake of folic acid during the pregnancy has been suggested to increase the risk for CPO. The demonstrated risk for siblings and the higher risk for monozygotic twins suggest a genetic etiopathogenesis for CPO. In some cases of CPO a prevalent mode of inheritance has been reported, but oligogenic models with reduced penetrance, and the risk related to environmental factors have also been proved. One of the first manifestations associated with CPO is difficulty with feeding. Aerophagia is a problem in these infants with CPO and requires more frequent burping and slower feeding. The inability to generate intraoral breath pressure due to nasal air emission in CPO children frequently manifests as articulation difficulties, particularly consonant weakness, and unintelligible speech. Hearing disorders are prevalent among individuals with CPO, as a result of chronic otitis media with effusion due to eustachian tube dysfunction. A multidisciplinary team is essential to manage the many aspects of CPO. In treating CPO, the reconstructive surgeon works in cooperation with otolaryngologists, dentists and orthodontists, speech pathologists, audiologists, geneticists, psychiatrists, maxillofacial surgeons, social workers, and prosthodontists. CPO can be considered a genetically complex disease, but new knowledge and new therapeutic approaches have greatly improved the quality of life of these children. Prenatal diagnosis is an important step in the treatment of this disease.

New insights in orofacial cleft: epidemiological and genetic studies on italian samples

Cleft of the lip and/or palate (CL±P) is the most common congenital craniofacial anomaly affecting around 1 in 700 live births worldwide. Clefts of the human face can be classified anatomically as cleft lip only (CL), cleft palate only (CP), cleft lip and palate (CLP) or a combined group of cleft lip with or without cleft palate (CL±P), based on differences in embryologic development. CL±P has a genetic base and several linkage and association analyses have been performed in order to obtain important information about the role of candidate genes in its onset; not less important are gene-environment interactions that play an increasing role in its aetiology. In CL±P, several loci have been seen associated with the malformation, and, in some cases, a specific gene mapping in a locus has also been identified as susceptibility factor. In CP, one gene has been found, but many more are probably involved. In this short review the genetic studies carried out on CL±P, and the interaction with environmental factors (alcohol, smoking, drugs) are discussed.

Brazilian multicenter study of association between polymorphisms in CRISPLD2 and JARID2 and non-syndromic oral clefts

BACKGROUND

Variants in the cysteine-rich secretory protein LCCL domain containing 2 gene (CRISPLD2) and in the jumonji, AT-rich interaction domain 2 gene (JARID2) were previously shown to influence non-syndromic oral cleft susceptibility. Herein, we performed a case-control study to examine the potential association of single-nucleotide polymorphisms (SNPs) in CRISPLD2 and JARID2 with non-syndromic cleft lip and/or palate (NSCL/P) in the Brazilian population. Given the ethnicity-dependent genetic predisposition to NSCL/P, we performed a structured analysis taking into account the genomic ancestry variation of each individual.

METHODS

Four SNPs in CRISPLD2 (rs1546124, rs8061351, rs2326398, and rs4783099) and four in JARID2 (rs915344, rs2299043, rs2237138, and rs2076056), that were previously reported to be associated with NSCL/P, were genotyped in 785 Brazilian patients with NSCL/P (549 with cleft lip with or without cleft palate-NSCL ± P, and 236 with cleft palate only-NSCPO) and 693 unaffected Brazilian controls. Genomic ancestry was assessed with a set of 40 biallelic short insertion/deletion variants previously validated as ancestry informative markers of the Brazilian population.

RESULTS

After adjustment of ancestry variations, allelic analysis revealed marginal associations between the CRISPLD2 rs4783099 T allele and increased risk for NSCPO (OR: 1.31, 95% CI: 1.05-1.62, P = 0.01) and between JARID2 rs2237138 and decreased NSCL ± P risk (OR: 0.80, 95% CI: 0.67-0.97, P = 0.02). Haplotype analysis indicated a lack of association between JARID2 haplotypes and non-syndromic oral cleft risk.

CONCLUSIONS

Our results suggest that CRISPLD2 rs4783099 may represent a risk factor for NSCPO while JARID2 rs2237138 shows a protective effect against NSCL ± P in the Brazilian population.

Preliminary evidence of an interaction between the CRISPLD2 gene and non-syndromic cleft lip with or without cleft palate (nsCL/P) in Xinjiang Uyghur population, China

BACKGROUND

Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common birth defect results from the genetic factors alone or interactions with environmental changes. Single nucleotide polymorphisms (SNPs) of CRISPLD2 gene have been found to be an etiologic factor in the development of nsCL/P. However, few studies to date focused on the association of genetic variation of CRISPLD2 gene with nsCL/P, and the results are conflicting based on the different study population. The main purpose of the present study was to investigate the association between the CRISPLD2 gene and nsCL/P in Xinjiang Uyghur population.

METHODS

Eighteen SNPs were screened in a group of 200 patients with nsCL/P and in a control group consisting of 180 unaffected individuals by next generation sequencing using MiSeq Benchtop Sequencer (Illumina).

RESULTS

Our case-control association analysis showed that the SNP marker rs1546124 showed statistically significant differences in genotype (CC vs. CG vs. GG P=0.004) and allele frequencies (49% vs. 37.8% OR=1.58; 95% CI=1.19-2.1, P=0.002) between nsCL/P and controls. Under the recessive model of inheritance, the GG homozygotes had an OR of 2.4 (95% CI=1.37-4.18; P=0.002), and the result of significance was maintained even after multiple testing correction. Haplotype combinations of CACC were significantly more frequent in the nsCL/P patients than in controls (P=0.037). Finally, the MDR analysis identified the two-SNP model including rs1546124 and rs4782675 as best combination of possibly interactive polymorphisms (P<0.001).

CONCLUSION

Our results demonstrate that genetic polymorphism of CRISPLD2 gene is associated with an increased risk of nsCL/P in a Xinjiang Uyghur population.

Skin Tissue Surface Morphology and Quality of RNA and Protein Extracted from Fresh and Stabilized Human Cleft Lip and Palate Tissue

Cleft lip palate is a human congenital disorder worldwide and the study of this genetic disease requires molecular genetic analysis. This analysis required the use of nucleic acid and protein, thus good quality and quantity of its extraction is important. We are comparing RNA and protein extractions from tissue biopsy of cleft lip palate in both fresh and stabilized condition. Tissue morphology was also captured using Scanning Electron Microscopy (SEM) for any morphology differences. Tissue homogenization may destroy nucleic acid stability but not its morphology. Low RNA concentration from stabilized tissue was found. However, there was no crucial issue of protein extraction, degradation or concentration. Tissue morphology was slight different between normal and CL/P tissue.

Analysis of PRICKLE1 in human cleft palate and mouse development demonstrates rare and common variants involved in human malformations

Palate development is shaped by multiple molecular signaling pathways, including the Wnt pathway. In mice and humans, mutations in both the canonical and noncanonical arms of the Wnt pathway manifest as cleft palate, one of the most common human birth defects. Like the palate, numerous studies also link different Wnt signaling perturbations to varying degrees of limb malformation; for example, shortened limbs form in mutations of Ror2,Vangl2 (looptail) and, in particular, Wnt5a. We recently showed the noncanonical Wnt/planar cell polarity (PCP) signaling molecule Prickle1 (Prickle like 1) also stunts limb growth in mice. We now expanded these studies to the palate and show that Prickle1 is also required for palate development, like Wnt5a and Ror2. Unlike in the limb, the Vangl2looptail mutation only aggravates palate defects caused by other mutations. We screened Filipino cleft palate patients and found PRICKLE1 variants, both common and rare, at an elevated frequency. Our results reveal that in mice and humans PRICKLE1 directs palate morphogenesis; our results also uncouple Prickle1 function from Vangl2 function. Together, these findings suggest mouse and human palate development is guided by PCP-Prickle1 signaling that is probably not downstream of Vangl2.

The CRISPLD2 gene is involved in cleft lip and/or cleft palate in a Chinese population

BACKGROUND

Nonsyndromic cleft lip and/or cleft palate (NSCLP) are common congenital anomalies in humans, the etiologies of which are complex and associated with both genetic and environmental factors. Previous data suggested single nucleotide polymorphisms (SNPs) of rs1546124, rs4783099, and rs16974880 of the CRISPLD2 gene were associated with an increased risk of NSCLP; however, subsequent studies have yielded conflicting results. This study aims to evaluate the associations of the aforementioned polymorphisms with NSCLP in a Northwestern Chinese population.

METHODS

Three CRISPLD2 SNPs were genotyped in a case-control study (n = 907), including 444 NSCLP patients and 463 healthy individuals, using polymerase chain reaction-denaturing high-performance liquid chromatography (PCR-DHPLC).

RESULTS

The genotype and allele frequencies of rs1546124 (odds ratio [OR], 2.30; 95% confidence interval [CI], 1.58-3.34; p = 1 × 10(-5) ) and rs4783099 (OR, 0.73; 95% CI, 0.54-1.00; p = 0.05) were different in NSCLP patients compared with controls. Furthermore, the CC genotype at rs1546124 was associated with increased risk for cleft lip with or without cleft palate (CL/P; OR, 2.11; 95% CI, 1.41-3.15; p(correct) = 1.5 × 10(-4) ) and for cleft palate only (CPO; OR, 2.93; 95% CI, 1.69-5.07; p(correct) = 5.4 × 10(-4) ), whereas the T allele of rs4783099 was associated with decreased risk for CPO. Further gender stratification showed that the statistical association of these two loci is mainly in the male patients, and not in female patients.

CONCLUSION

Our results suggest that the CRISPLD2 gene contributes to the etiology of NSCLP in the Northwestern Chinese population. SNP rs1546124 is significantly related to NSCLP, associated with both CL/P and CPO groups, and SNP rs4783099 is significantly associated with CPO.