Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios

Adolescents with orofacial clefts: understanding their experiences

OBJECTIVE

To understand the experience of young people with orofacial clefts regarding life as an adolescent.

METHODS

Descriptive, qualitative study, developed in a Brazilian public and tertiary hospital, a reference center in the care of patients with craniofacial anomalies and related syndromes, between February and April 2019. The sample was defined by theoretical saturation. The following inclusion criteria were established: age between ten and 19 years old and having previously operated on orofacial cleft (lip and/or palate). Individuals with fissure associated with syndromes or other malformations were excluded. Data collection was performed through semi-structured interviews, which were audio recorded and transcribed in full. The trigger element was: how has it been for you to experience your adolescence? For the construction of the results, content analysis was used in the thematic modality.

RESULTS

Seventeen adolescents participated. From the speeches, three categories were revealed: interacting socially, feeling supported, and experiencing and facing prejudice.

CONCLUSIONS

The biopsychosocial and conflicting complexity that adolescents with orofacial clefts experience was noticed, as well as the importance of receiving support and establishing modalities of situational coping.

Detecting Gene-Gene Interaction among DNA Repair Genes in Chinese non-Syndromic Cleft lip with or Without Palate Trios

OBJECTIVE

The objective of this study is to investigate the gene-gene interactions associated with NSCL/P among DNA repair genes.

DESIGN

This study included 806 NSCL/P case-parent trios from China. Quality control process was conducted for genotyped single nucleotide polymorphisms (SNPs) located in six DNA repair genes (ATR, ERCC4, RFC1, TYMS, XRCC1 and XRCC3). We tested gene-gene interactions with Cordell's method using statistical package TRIO in R software. Bonferroni corrected significance level was set as P = 4.24 × 10-4. We also test the robustness of the interactions by permutation tests.

SETTING

Not applicable.

PATIENTS/PARTICIPANTS

A total of 806 NSCL/P case-parent trios (complete trios: 682, incomplete trios: 124) with Chinese ancestry.

INTERVENTIONS

Not applicable.

MAIN OUTCOME MEASURE(S)

Not applicable.

RESULTS

A total of 118 SNPs were extracted for the interaction tests. Fourteen pairs of significant interactions were identified after Bonferroni correction, which were confirmed in permutation tests. Twelve pairs were between ATR and ERCC4 or XRCC3. The most significant interaction occurred between rs2244500 in TYMS and rs3213403 in XRCC1(P = 8.16 × 10-15).

CONCLUSIONS

The current study identified gene-gene interactions among DNA repair genes in 806 Chinese NSCL/P trios, providing additional evidence for the complicated genetic structure underlying NSCL/P. ATR, ERCC4, XRCC3, TYMS and RFC1 were suggested to be possible candidate genes for NSCL/P.

Genetic Analysis of the Single-Nucleotide Polymorphisms rs880810, rs545793, rs80094639, and rs13251901 in Nonsyndromic Oral Clefts: A Case–Parent Trio Study

Oral clefts, including cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP), are the most common types of congenital anomalies of the human face. Various genetic and environmental factors play a role in developing oral clefts. Several studies have shown the association of the PAX7 gene and the 8q24 region with these oral clefts in different populations worldwide. However, there are no reported studies on the possible connection between the PAX7 gene and the 8q24 region nucleotide variants and the risk of developing nonsyndromic oral clefts (NSOC) in the Indian population. Hence, this study aimed to test the possible association between PAX7 gene single-nucleotide polymorphisms (SNPs) rs880810, rs545793,rs80094639, and rs13251901 of the 8q24 region using a case-parent trio design. Forty case-parent trios were selected from the CLP center. Genomic DNA was isolated from the cases and their parents. The rs880810, rs545793, rs80094639, and rs13251901 were genotyped by the MassARRAY technique. PLINK software was used for statistical analysis. All the SNPs were tested for Hardy-Weinberg equilibrium. No statistical significance was found with any SNPs, as none of the genotyped SNPs showed a p -value of less than 0.05. Hence, the rs880810, rs545793, and rs80094639 of the PAX7 gene, and rs13251901 of the 8q24 region are not associated with NSOC in the Indian population.

Prenatal diagnosis of orofacial clefts: unveiling the parents' experience

OBJECTIVE

To understand the experience of parents regarding prenatal diagnosis of orofacial cleft in their children.

METHODS

Descriptive study with a qualitative approach, carried out in a Brazilian public tertiary hospital between January and March 2019. Parents who were accompanying their children during hospitalization for primary surgeries and who had received the diagnosis of malformation during pregnancy were included in this study. Data was collected through semi-structured interviews, which were audio-recorded and transcribed in full. To prepare the results, Content Analysis was used in the Thematic modality.

RESULTS

The sample had 17 participants: 16 mothers and one father. From the speeches, three categories were unveiled: dealing with the unknown, assimilating the diagnosis, and positive and negative implications of prenatal diagnosis.

CONCLUSIONS

We learned how complex and conflicting it was for parents to receive the diagnosis of malformation in their children, and that family and professional support was essential to the process of assimilation and coping. The findings point to the need for planning and implementing interventions, protocols and/or public policies aimed at assisting these parents in this period.

Correlation between burden and sleep quality in informal caregivers of infants with orofacial cleft

Abstract Objective: To evaluate the correlation between burden and sleep quality in caregivers of infants with cleft lip and/or palate. Methods: This descriptive cross-sectional study was carried out in a Brazilian tertiary public hospital between March and September 2020. The sample included the main informal, literate caregivers of infants with cleft lip and/or palate, aged 18 years or older. The instruments used were the Burden Interview Scale and the Pittsburgh Sleep Quality Index. Data were collected during the infants’ hospitalization. Statistical analysis adopted Pearson and Spearman correlations, with a 5% significance level. Results: A total of 31 informal caregivers participated in the study, most of them mothers (n=28; 90%), with a mean age of 30 years (standard deviation – SD=7.5), low socioeconomic status (n=20; 64%), who completed high school (n=19; 61%), were married (58%), had two children (n=15; 48%), and no employment relationship (n=18; 58%). A moderate correlation was found between sleep quality and burden (r=0.39; p=0.032) and between burden and subjective sleep quality (r=0.39; p=0.029), sleep latency (r=0.43; p=0.017), and daytime dysfunction (r=0.49; p<0.001). Conclusions: The study showed that the higher the burden, the lower the sleep quality. The findings indicate the need to plan and implement interventions to minimize the burden experienced by these informal caregivers in order to improve their sleep quality.

Role of PAX7 Gene rs766325 and rs4920520 Polymorphisms in the Etiology of Non-syndromic Cleft Lip and Palate: A Genetic Study

Non-syndromic cleft lip and palate (NSCLP) is one of the most common birth defects in humans with an overall prevalence of ∼1 in 700 live births around the world. The etiology of NSCLP is complex involving multiple genes, environmental factors, and gene-to-gene interactions. Several genome-wide associations (GWA) studies have shown the association of the paired box 7 ( PAX7 ) gene in the etiology of cleft lip and palate in different populations worldwide. However, there are no reported studies on the association between the rs766325 and rs4920520 polymorphisms and the risk of developing NSCLP in the Indian population. Hence, the present study aimed to test for the probable association between rs766325 and rs4920520 polymorphisms among NSCLP Indian population using a case-parent trio design. Forty case-parent trios were selected from the cleft lip and palate center based on the inclusion and exclusion criteria. Genomic DNA was isolated from the cases and their parents. The rs766325 and rs4920520 polymorphisms of the PAX7 gene were analyzed for their association using the MassARRAY analysis. The statistical analysis was done using the PLINK software. The rs766325 and rs4920520 polymorphisms were tested for the Hardy–Weinberg equilibrium. None of the polymorphisms showed any statistical significance. Hence, the rs766325 and rs4920520 polymorphisms of the PAX7 gene were found to be not associated with NSCLP in the Indian case-parent trios.

Palatoplasty in children: nursing diagnoses and interventions related to the immediate postoperative period

OBJECTIVE

To identify the main nursing diagnoses and interventions in children in the immediate postoperative period of palatoplasty.

METHOD

Documentary and retrospective study, developed in a Brazilian public and tertiary hospital, between August and September 2020. Children who underwent only palatoplasty, between January and December 2019, aged between 10 and 24 months, were included. Those with medical syndromes and/or comorbidities were excluded. The Theoretical Framework of Basic Human Needs and the NANDA International and Nursing Interventions Classification Taxonomies were used. Data underwent descriptive statistical analysis.

RESULTS

The sample consisted of 126 children. Psychobiological needs such as oxygenation, hydration, nutrition, elimination, cutaneous-mucosal and physical integrity, pain and environmental perception predominated. Based on them, nine nursing diagnoses, with four focusing on the problem and five on risk, as well as 17 interventions, were identified.

CONCLUSION

The use of standardized languages to identify affected human needs and, based on them, diagnoses and interventions, favored clinical reasoning for the construction and organization of clinical nursing practice.

Psychosocial repercussions experienced by parents who care for infants with syndromic orofacial clefts

Abstract Objectives: to understand the psychosocial implications experienced by caregiving parents, resulting from the care of the child with cleft lip and/or palate associated with the syndrome. Methods: a cross-sectional and qualitative study, guided by the Consolidated Criteria for Reporting Qualitative Research tool, carried out between January and May 2019. Data collection was carried out through semi-structured interviews that were audio-recorded and transcribed in full. Thematic content analysis was used as the methodological framework and Symbolic Interactionism as the theoretical framework. Results: the participants were 16 caregiving parents. Four categories were listed: implications for diagnosis and treatment initiation, implications for financial issues and paid activities, implications for the care process, and implications for access to health resources. Conclusion: it was found that psychosocial implications experienced by these informal caregivers are multifaceted and complex, and that knowing them will enable planning and implementation of actions that contribute, in addition to the children's rehabilitation process, to the health and quality of life of those who care.

Religiosity, spirituality, and self-esteem in adolescents with cleft lip and palate: a correlational study

OBJECTIVE

To evaluate the correlation between religiosity, spirituality, and self-esteem in adolescents with uni- and bilateral cleft lip and palate.

METHOD

Correlational and cross-sectional study developed in a public and tertiary hospital in Brazil between July 2018 and February 2019. The sample comprised 100 adolescents divided into two groups: G1 (unilateral cleft, 50 participants) and G2 (bilateral cleft, 50 participants). For data collection, three instruments were used: Sociodemographic Questionnaire, DUREL Religion index, Rosenberg self-esteem scale. Statistical analysis was performed with the tests Chi-squared, Mann-Whitney, Pearson Correlation, and analysis of linear correlation strength, with a 5% significance level (p ≥ 0.05).

RESULTS

Only organizational religiosity was higher in G1 when compared with G2 (p = 0.03). The overall self-esteem was satisfactory for both groups; however, there was no significant difference between them (p = 0.34). No correlation between religiosity and spirituality with self-esteem were identified for G1 and G2.

CONCLUSION

The adolescents with uni- or bilateral cleft lip and palate presented high levels of religiosity, spirituality, and self-esteem. However, no correlation between these variables was identified.

Orthognathic surgery: doubts from patients with orofacial fissures regarding the immediate postoperative period

OBJECTIVES

to identify the main doubts regarding the immediate postoperative care of patients with orofacial clefts undergoing orthognathic surgery.

METHODS

cross-sectional, quantitative study, developed in a public and tertiary hospital, between November 2017 and May 2018. Data collection occurred through interviews during the preoperative nursing consultation. An instrument was used to describe doubts, which later were grouped according to the subject.

RESULTS

48 patients participated. The doubts referred to sun exposure (56%), food/mastication (48%), the relationship between intermaxillary block-breathing-vomiting (48%), oral hygiene (31%), physical activity restriction (27%), nasopharyngeal cannula, removal of surgical stitches, hospitalization time and speech/communication (23%), bleeding, cryotherapy, facial massage, aesthetic and functional results, healing, edema/ecchymosis, postoperative pain, and changes in facial sensitivity (21%).

CONCLUSIONS

the doubts were related to food, the period of convalescence, care for the surgical wound, postoperative complications, and medications.

STRESS, OVERLOAD AND QUALITY OF LIFE IN CAREGIVERS OF CHILDREN WITH/WITHOUT OROFACIAL CLEFT AND DYSPHAGIA

ABSTRACT Objective: to analyze the correlation between stress, overload and quality of life of informal caregivers of children with and without orofacial cleft and dysphagia. Method: a cross-sectional, case-control study carried out in a public and tertiary hospital, located in the inland of São Paulo, Brazil, which encompassed two groups: case and comparative. The case group consisted of 30 informal caregivers of children with orofacial cleft and dysphagia, using a feeding tube, while the comparative group consisted of 30 informal caregivers of children without orofacial cleft, fed orally. For data collection, the Bourden Interview Scale, Inventory of Stress Symptoms for Adults and the World Health Organization Quality of Life Bref were used. For statistical analysis, the following tests were used: chi-square, Student's t, Mann-Whitney and Pearson's correlation, all with a 5% significance level. Analysis of the linear correlation forces was also used. Results: in the case group, stress presented a moderate correlation with the overall quality of life (r=-0.41; p=0.025) and satisfaction with health (r=-0.42; p=0.021). Also in the case group, referring to quality of life, the Physical and Psychological domains presented a strong correlation with overload (r=-0.54, p=0.002; r=-0.55, p=0.002, respectively). In the comparative group, no correlations were identified. Conclusion: among the informal caregivers of children with orofacial cleft and dysphagia, there was a correlation between stress and the perception of global quality of life and satisfaction with health, as well as between overload and quality of life, in the physical and psychological dimensions.

[Evaluating the effect of WNT pathway genes considering interactions on the risk of non-syndromic oral clefts among Chinese populations]

OBJECTIVE

In this study, we used genome-wide association study (GWAS) data to explore whether WNT pathway genes were associated with non-syndromic oral clefts (NSOC) considering gene-gene interaction and gene-environment interaction.

METHODS

We conducted the analysis using 806 non-syndromic cleft lip with or without cleft palate (NSCL/P) case-parent trios and 202 non-syndromic cleft palate (NSCP) case-parent trios among Chinese populations selected from an international consortium established for a GWAS of non-syndromic oral clefts. Genotype data and maternal environmental exposures were collected through DNA samples and questionnaires. Conditional Logistic regression models were adopted to explore gene-gene interaction and gene-environment in teraction using trio package in R software. The threshold of significance level was set as 3.47×10^-4 using Bonferroni correction.

RESULTS

A total of 144 single nucleotide polymorphisms (SNPs) in seven genes passed the quality control process in NSCL/P trios and NSCP trios, respectively. Totally six pairs of SNPs interactions showed statistically significant SNP-SNP interaction (P < 3.47×10^-4) after Bonferroni correction, which were rs7618735 (WNT5A) and rs10848543 (WNT5B), rs631948 (WNT11) and rs556874 (WNT5A), and rs631948 (WNT11) and rs472631 (WNT5A) among NSCL/P trios; rs589149 (WNT11) and rs4765834 (WNT5B), rs1402704 (WNT11) and rs358792 (WNT5A), and rs1402704 (WNT11) and rs358793 (WNT5A) among NSCP trios, respectively. In addition, no significant result was found for gene-environment interaction analysis in both of the NSCL/P trios and NSCP trios.

CONCLUSION

Though this study failed to detect significant association based on gene-environment interactions of seven WNT pathway genes and the risk of NSOC, WNT pathway genes may influence the risk of NSOC through potential gene-gene interaction.

[Exploring parent-of-origin effects for non-syndromic cleft lip with or without cleft palate on PTCH1, PTCH2, SHH, SMO genes in Chinese case-parent trios]

OBJECTIVE

Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect, affecting 1.4 per 1 000 live births, and multiple genetic and environmental risk factors influencing its risk. All the known genetic risk factors accounted for a small proportion of the heritability. Several authors have suggested parent-of-origin effects (PoO) may play an important role in the etiology of this complex and heterogeneous malformation. To clarify the genetic association between PTCH1, PTCH2, SHH and SMO in hedgehog (HH) pathway and NSCL/P, as well as testing for potential PoO effects in Chinese case-parent trios.

METHODS

We tested for transmission disequilibrium tests (TDT) and PoO effects using 83 common single nucleotide polymorphic (SNP) markers of HH pathway genes from 806 NSCL/P case-parent trios. These trios were drawn from an international consortium established for a genome-wide association studies (GWAS) of non-syndromic oral clefts of multiple ethnicities. DNA samples were collected from each trio. Single marker and haplotype based analysis were performed both in TDT tests and PoO effects. SNPs were excluded if they (ⅰ) had a call rate of < 95%, (ⅱ) had a minor allele frequency (MAF) of < 0.05, (ⅲ) had Mendelian errors over all trios of >5%, (ⅳ) had a genotype distribution in the parents that deviated from the Hardy-Weinberg equilibrium (HWE) (P < 0.000 1). The process was done using Plink (version 1.07, <a href="http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml" target="_blank">http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml</a>). TDT test was performed in Plink v1.07. A log-linear model was used to explore PoO effects using Haplin v6.2.1 as implemented in R package v3.4.2. Significance level was assessed using the Bonferroni correction.

RESULTS

A total of 18 SNPs were dropped due to low MAF, thus leaving 65 SNPs available for the analysis. Thus the Bonferroni threshold was 7.7×10^-4 (0.05/65). Nominal significant association with NSCL/P was found at a SNP (rs4448343 in PTCH1, P=0.023) and six haplotypes (rs10512249-rs4448343, rs1461208-rs7786445, rs10512249-rs4448343, rs16909865-rs10512249-rs4448343, rs1461208-rs7786445-rs12698335, and rs288756-rs288758-rs1151790, P < 0.05). A total of six haplotypes (rs288765-rs1233563, rs12537550-rs11765352, rs872723-rs288765-rs1233563, rs288765-rs1233563-rs288756, rs6459952-rs12537550-rs11765352, and rs12537550-rs11765352-rs6971211) showed PoO effect (P < 0.05). None of the results remained significant after the Bonferroni correction (P>7.7×10^-4).

CONCLUSION

Neither significant association between SNPs within HH pathway and the risk of NSCL/P nor PoO effects was seen in this study.

Gene-gene interactions between BMP4 and ARHGAP29 among non-syndromic cleft lip only (NSCLO) trios from western Han Chinese population

BACKGROUND

Genome-wide association studies (GWAS) have found more than 20 genes associated with a risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). However, the interactions between these risk genes have been rarely reported.

METHODS

Here we selected 47 Single Nucleotide Polymorphisms (SNP) from previous GWASs and tested for possible interactions among 302 NSCL/P case-parent trios from a western Han Chinese population to further explore the genetic etiology of NSCL/P. Conditional logistic regression models were performed including gene-gene (G×G) interaction.

RESULTS

Twenty pairwise interactions yielded significant p-values. Most of the signals of interaction between the SNPs were detected at the same gene including v-maf musculoaponeurotic fibrosarcoma oncogene family, protein B (MAFB), netrin 1 (NTN1), and single nucleotide polymorphic marker within interferon regulatory factor 6 (IRF6). We found evidence of the interaction between rs17563 (bone morphogenetic protein 4, BMP4) and rs560426 (subfamily A member 4/Rho GTPase activating protein 29, ARHGAP29) (P=0.00093) in NSCLO trios.

CONCLUSIONS

Gene-gene interaction between markers in BMP4 and ARHGAP29 may influence the risk of NSCLO in western Han Chinese population, which might explain the missing heritability for NSCL/P.

Gene-by-gene interactions associated with the risk of conotruncal heart defects

BACKGROUND

The development of conotruncal heart defects (CTDs) involves a complex relationship among genetic variants and maternal lifestyle factors. In this article, we focused on the interactions between 13 candidate genes within folate, homocysteine, and transsulfuration pathways for potential association with CTD risk.

METHODS

Targeted sequencing was used for 328 case-parental triads enrolled in the National Birth Defects Prevention Study (NBDPS). To evaluate the interaction of two genes, we applied a conditional logistic regression model for all possible SNP pairs within two respective genes by contrasting the affected infants with their pseudo-controls. The findings were replicated in an independent sample of 86 NBDPS case-parental triads genotyped by DNA microarrays. The results of two studies were further integrated by a fixed-effect meta-analysis.

RESULTS

One SNP pair (i.e., rs4764267 and rs6556883) located in gene MGST1 and GLRX, respectively, was found to be associated with CTD risk after multiple testing adjustment using simpleM, a modified Bonferroni correction approach (nominal p-value of 4.62e-06; adjusted p-value of .04). Another SNP pair (i.e., rs11892646 and rs56219526) located in gene DNMT3A and MTRR, respectively, achieved marginal significance after multiple testing adjustment (adjusted p-value of .06).

CONCLUSION

Further studies with larger sample sizes are needed to confirm and elucidate these potential interactions.

Patients and informal caregivers’ questions about alveolar bone graft post-operative care

ABSTRACT Objectives: to identify patients’ and informal caregivers’ questions related to alveolar bone graft post-operative care. Methods: analytical and cross-sectional study, developed in a public and tertiary hospital between October 2017 and February 2018. The sample consisted of 46 participants. Data collection occurred during the preoperative nursing consultation through interview. The doubts were described in a form prepared by the researchers and later grouped by similarity of the subject. Results: doubts referred to diet (type of food, consistency, temperature and time period), surgical wound care (oral hygiene, graft rejection, removal of surgical points), post-operative complications (bleeding and edema), convalescence period (sun exposure, physical effort, time away from activities, length of stay) and medications. Conclusions: identifying the doubts allowed planning and implementing nursing care focused on the real needs of the clientele, favoring the rehabilitation process.

Gene-gene interaction among cell adhesion genes and risk of nonsyndromic cleft lip with or without cleft palate in Chinese case-parent trios

Background

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with complex etiology. One strategy for studying the genetic risk factors of NSCL/P is to consider gene–gene interaction (G × G) among gene pathways having a role in craniofacial development. The present study aimed to investigate the G × G among cell adhesion gene pathway.

Methods

We carried out an interaction analysis of eight genes involved in cell adherens junctions among 806 NSCL/P Chinese case‐parent trios originally recruited for a genome‐wide association study (GWAS). Regression‐based approach was used to test for two‐way G × G interaction, while machine learning algorithm was run for exploring both two‐way and multi‐way interaction that may affect the risk of NSCL/P.

Results

A two‐way ACTN1 × CTNNB1 interaction reached the adjusted significance level. The single nucleotide polymorphisms pair composed of rs17252114 (CTNNB1) and rs1274944 (ACTN1) yielded a p value of .0002, and this interaction was also supported by the logic regression algorithm. Higher order interactions involving ACTN1, CTNNB1, and CDH1 were picked out by logic regression, suggesting a potential role in NSCL/P risk.

Conclusion

This study suggests for the first time evidence of both two‐way and multi‐way G × G interactions among cell adhesion genes contributing to the NSCL/P risk.

Exploring the interaction between FGF Genes and T-box genes among chinese nonsyndromic cleft lip with or without cleft palate case-parent trios

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect. Genetic variants causing syndromic orofacial clefts can also contribute to the etiology of NSCL/P. The purpose of the present study was to explore gene-gene (G × G) interaction using common single nucleotide polymorphic (SNP) markers in fibroblast growth factor (FGF) family and its receptors and T-box genes, which were associated with syndromic orofacial clefts. Our study was conducted in 806 Chinese NSCL/P case-parent trios drawn from an international consortium. A total of 252 SNPs in FGF8, FGF10, FGFR1, FGFR2, and TBX5 passed the quality control criteria and were included in the analysis. The interactions between SNPs in different genes were assessed using Cordell's method, which fitted a conditional logistic regression model. The analysis was performed using the R-package trio (Version 3.8.0). Bonferroni correction was used to adjust for multiple comparisons, and the overall significance threshold was set as P = 1.98 × 10^-4 (0.05/252). Conditional logistic regression revealed the most significant interaction between rs2330542 in FGF10 and rs1946295 in TBX5, which remained significant (P = 9.63 × 10^-6 ) after Bonferroni correction. The relative risk of allele C in rs2330542 (FGF10) was 1.02 (95%CI 0.81-1.28), while the relative risk was 1.42 (95%CI 1.03-1.97) when the exposure was a combination of allele C in rs2330542 and allele A in rs1946295 (TBX5). Our findings confirmed the importance of considering G × G interaction when exploring the genetic risk factors of NSCL/P. Further investigations are warranted to validate the potential interaction and reveal the biological function of FGF10/FGFR2/TBX5. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.

p63 establishes epithelial enhancers at critical craniofacial development genes

The transcription factor p63 is a key mediator of epidermal development. Point mutations in p63 in patients lead to developmental defects, including orofacial clefting. To date, knowledge on how pivotal the role of p63 is in human craniofacial development is limited. Using an inducible transdifferentiation model, combined with epigenomic sequencing and multicohort meta-analysis of genome-wide association studies data, we show that p63 establishes enhancers at craniofacial development genes to modulate their transcription. Disease-specific substitution mutation in the DNA binding domain or sterile alpha motif protein interaction domain of p63, respectively, eliminates or reduces establishment of these enhancers. We show that enhancers established by p63 are highly enriched for single-nucleotide polymorphisms associated with nonsyndromic cleft lip ± cleft palate (CL/P). These orthogonal approaches indicate a strong molecular link between p63 enhancer function and CL/P, illuminating molecular mechanisms underlying this developmental defect and revealing vital regulatory elements and new candidate causative genes.

Gene-Gene Interactions among SPRYs for Nonsyndromic Cleft Lip/Palate

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex genetic architecture. Gene-gene interactions have been increasingly regarded as contributing to the etiology of NSCL/P. A recent genome-wide association study revealed that a novel single-nucleotide polymorphism at SPRY1 in 4q28.1 showed a significant association with NSCL/P. In the current study, we explored the role of 3 SPRY genes in the etiology of NSCL/P by detecting gene-gene interactions: SPRY1, SPRY2, and SPRY4-with SPRY3 excluded due to its special location on the X chromosome. We selected markers in 3 SPRY genes to test for gene-gene interactions using 1,908 case-parent trios recruited from an international consortium established for a genome-wide association study of nonsyndromic oral clefts. As the trios came from populations with different ancestries, subgroup analyses were conducted among Europeans and Asians. Cordell's method based on conditional logistic regression models was applied to test for potential gene-gene interactions via the statistical package TRIO in R software. Gene-gene interaction analyses yielded 10 pairs of SNPs in Europeans and 6 pairs in Asians that achieved significance after Bonferroni correction. The significant interactions were confirmed in the 10,000-permutation tests (empirical P = 0.003 for the most significant interaction). The study identified gene-gene interactions among SPRY genes among 1,908 NSCL/P trios, which revealed the importance of potential gene-gene interactions for understanding the genetic architecture of NSCL/P. The evidence of gene-gene interactions in this study also provided clues for future biological studies to further investigate the mechanism of how SPRY genes participate in the development of NSCL/P.

Gene-gene interaction for nonsyndromic cleft lip with or without cleft palate in Chilean case-parent trios

OBJECTIVE

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a birth defect for which several genes susceptibility genes been proposed. Consequently, it has been suggested that many of these genes belong to common inter-related pathways during craniofacial development gene-gene interaction. We evaluated the presence of gene-gene interaction for single nucleotide polymorphisms within interferon regulatory factor 6 (IRF6), muscle segment homeobox 1 (MSX1), bone morphogenetic protein 4 (BMP4) and transforming growth factor 3 (TGFB3) genes in NSCL/P risk in Chilean case-parent trios.

DESIGN

From previous studies, we retrieved genotypes for 13 polymorphic variants within these four genes in 152 case-parent trios. Using the trio package (R) we evaluate the gene-gen interaction in genetic markers pairs applying a 1°-of-freedom test (1df) and a confirmatory 4°-of-freedom (4df) test for epistasis followed by both a permutation test and a Benjamini-Hochberg test for multiple comparisons adjustment.

RESULTS

We found evidence of gene-gene interaction for rs6446693 (MSX1) and rs2268625 (TGFB3) (4df p = 0.024; permutation p = 0.015, Benjamini-Hochberg p = 0.001).

CONCLUSIONS

A significant gene-gene interaction was detected for rs6446693 (MSX1) and rs2268625 (TGFB3). This finding is concordant with research in animal models showing that MSX1 and TGFB3 are expressed in common molecular pathways acting in an epistatic manner during maxillofacial development.

Evaluating the effect of nicotinic cholinergic receptor genes on the risk of nonsyndromic cleft lip with or without cleft palate

OBJECTIVE

Multiple studies have suggested nonsyndromic cleft lip with or without cleft palate (NSCL/P), and lung cancer may have common genetic etiology. Previous studies have showed genetic variants in nicotinic cholinergic receptor genes (CHRNs) may influence risk of lung cancer. We aimed to explore the effect of CHRNs on risk of NSCL/P considering gene-gene (GxG) interaction for these genes.

SUBJECTS AND METHODS

We selected 120 markers in 14 CHRNs to test for GxG interaction using 806 Chinese case-parent trios recruited from an international consortium established for a GWAS of oral clefts.

RESULTS

Totally, two pairs of SNPs yielded significant GxG interactions after Bonferroni correction (rs935865 and rs2337980 with p = 4.04 × 10^-5 , rs2741335 and rs3743077 with p = 4.80 × 10^-4 ), and these pairwise interactions were confirmed in permutation tests. In addition, the relative risk (RR) of the putative interaction between rs935865 and rs2337980 was 1.10 (95% CI: 0.92~1.31).

CONCLUSIONS

While the single SNP association and the gene-environment interaction analysis of 14 CHRN genes yielded no signal, this study did demonstrate the importance of considering potential GxG interaction for exploring etiology of NSCL/P. This study suggests an important role for particular combinations of SNPs in CHRN genes in influencing risk to NSCL/P, which needs further study.

Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft

OBJECTIVE

Little consistent evidence is available for the association between the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P) and any of the individual genes in the folate/homocysteine metabolic pathway. We investigated the genes in the folate pathway to further clarify its potential influence on the risk of NSCL/P considering gene-gene (G×G) interaction.

SUBJECTS AND METHODS

We selected markers in 18 genes from the pathway and applied Cordell's method to test for G×G interaction using 1,908 NSCL/P case-parent trios ascertained in an international consortium where a genomewide association study (GWAS) of oral clefts was conducted.

RESULTS

We found intriguing signals among Asian and European ancestry groups for G×G interaction between markers in betaine-homocysteine methyltransferase gene (BHMT/BHMT2) and dimethylglycine dehydrogenase gene (DMGDH) attaining genomewide significance. In the pooled data, the top significant interaction was found between rs13158309 (BHMT) and rs10514154 (DMGDH, p = 1.45 × 10^-12 ).

CONCLUSIONS

Our study illustrated the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P, and this study suggested both BHMT/BHMT2 and DMGDH should be considered as candidate genes for NSCL/P in future studies.

Gene-gene interaction between MSX1 and TP63 in Asian case-parent trios with nonsyndromic cleft lip with or without cleft palate

BACKGROUND

Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P).

METHODS

A total of 130 single-nucleotide polymorphisms (SNPs) in or near SUMO1, MSX1, and TP63 was analyzed among 1,038 Asian NSCL/P trios ascertained through an international consortium. Conditional logistic regression models were used to explore gene-gene (G × G) and gene-environment (G × E) interaction involving maternal environmental tobacco smoke and multivitamin supplementation. Bonferroni correction was used for G × E analysis and permutation tests were used for G × G analysis.

RESULTS

While transmission disequilibrium tests and gene-environment interaction analysis showed no significant results, we did find signals of gene-gene interaction between SNPs near MSX1 and TP63. Three pairwise interactions yielded significant p values in permutation tests (rs884690 and rs9290890 with p = 9.34 × 10^-5 and empirical p = 1.00 × 10^-4 , rs1022136 and rs4687098 with p = 2.41 × 10^-4 and empirical p = 2.95 × 10^-4 , rs6819546 and rs9681004 with p = 5.15 × 10^-4 and empirical p = 3.02 × 10^-4 ).

CONCLUSION

Gene-gene interaction between MSX1 and TP63 may influence the risk of NSCL/P in Asian populations. Our study provided additional understanding of the genetic etiology of NSCL/P and underlined the importance of considering gene-gene interaction in the etiology of this common craniofacial malformation.