X-chromosome inactivation patterns in monozygotic twins and sib pairs discordant for nonsyndromic cleft lip and/or palate

Study on the role of methylation in nonsyndromic cleft lip with or without cleft palate using a monozygotic twin model

OBJECTIVE

The research on the etiology of nonsyndromic cleft lip with or without cleft palate(NSCL/P) is challenging, and DNA methylation has an impact on the formation of cleft lip and palate.

SUBJECTS

In this study, one of a pair of monozygotic twins (T1) had nonsyndromic cleft lip (NSCL), and one of a pair of monozygotic twins (T2) had nonsyndromic cleft lip and palate (NSCLP). We determined the methylation profiles of more than 850,000 CpGs in the DNA of the blood samples from the two pairs of monozygotic twins.

RESULT

Methylation data indicated that 1184 differentially methylated CpG sites were found in the T1 group (651 hypermethylated and 533 hypomethylated) and 8099 differentially methylated CpG sites in the T2 group (1713 hypermethylated and 6386 hypomethylated) compared with the healthy twin.The common difference was 107 methylation sites.GO enrichment analysis showed that regulation of smooth muscle cell migration and actin cytoskeleton reorganization were the most prominent classes.KEGG pathway enrichment analysis showed that the TGF-β signaling pathway, Notch signaling pathway and Wnt signaling pathway are relevant to the formation of NSCL/P.Two selected genes (NTN1 and PLEKHA7) are involved in the formation of NSCL/P.

CONCLUSION

These findings provide some support for the hypothesis that abnormal DNA methylation may influence the formation of clefts.

Genome-wide interaction studies identify sex-specific risk alleles for nonsyndromic orofacial clefts

Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans and is notable for its apparent sexual dimorphism where approximately twice as many males are affected as females. The sources of this disparity are largely unknown, but interactions between genetic and sex effects are likely contributors. We examined gene-by-sex (G × S) interactions in a worldwide sample of 2,142 NSCL/P cases and 1,700 controls recruited from 13 countries. First, we performed genome-wide joint tests of the genetic (G) and G × S effects genome-wide using logistic regression assuming an additive genetic model and adjusting for 18 principal components of ancestry. We further interrogated loci with suggestive results from the joint test ( p < 1.00 × 10 -5 ) by examining the G × S effects from the same model. Out of the 133 loci with suggestive results ( p < 1.00 × 10 -5 ) for the joint test, we observed one genome-wide significant G × S effect in the 10q21 locus (rs72804706; p = 6.69 × 10 -9 ; OR = 2.62 CI [1.89, 3.62]) and 16 suggestive G × S effects. At the intergenic 10q21 locus, the risk of NSCL/P is estimated to increase with additional copies of the minor allele for females, but the opposite effect for males. Our observation that the impact of genetic variants on NSCL/P risk differs for males and females may further our understanding of the genetic architecture of NSCL/P and the sex differences underlying clefts and other birth defects.

Exploration of genetic factors determining cleft side in a pair of monozygotic twins with mirror-image cleft lip and palate using whole-genome sequencing and comparison of craniofacial morphology

OBJECTIVE

The aim of the present study is to explore genetic factors determining difference of cleft side using whole-genome sequencing and evaluation of craniofacial morphology using cephalometric analysis between Japanese monozygotic (MZ) twins with mirror-image cleft lip and palate (CLP).

DESIGN

We selected a Japanese MZ twin pair (MZ-A and MZ-B) affected with unilateral CLP who are discordant for cleft side (left/right) and conducted whole-genome sequencing to identify genetic factors determining cleft side. Moreover, we compared their craniofacial morphologies using cephalograms.

RESULTS

Whole-genome sequencing results suggested that no discordant DNA variants were found between MZ-A and MZ-B. The comparison of craniofacial morphology between the MZ twins revealed that MZ-B had maxillary deficiency and slightly more mandibular protrusion than MZ-A.

CONCLUSIONS

It is indicated that environmental factors might be a critical factor that influences the determination of difference of cleft side in orofacial clefts. In addition, we found some differences in craniofacial morphology between MZ-A and MZ-B. Our findings suggest that various environmental factors, such as epigenetics, might be a critical factor that influences the determination of difference of cleft side in CLP rather than inherited genetic factors.

Lifetime physical inactivity is associated with increased risk for Hodgkin and non-Hodgkin lymphoma: A case-control study

BACKGROUND

Although physical activity is a well-established risk factor for several cancer types, studies evaluating its association with lymphoma have yielded inconclusive results. In such cases where physical activity is not clearly associated with cancer risk in a dose-dependent manner, investigators have begun examining physical inactivity as an independent exposure of interest.

METHODS

Associations of self-reported, lifetime physical inactivity with risk of developing Hodgkin lymphoma (HL) and non-Hodgkin lymphoma (NHL) were evaluated in a hospital-based case control study using data from the Patient Epidemiology Data System at Roswell Park Comprehensive Cancer Center. Participants included 87 patients with HL and 236 patients with NHL as well as 348 and 952 cancer-free controls, respectively. Multivariable-adjusted logistic regression models were fit to calculate odds ratios (OR) and 95% confidence intervals (CI) estimating the association between physical inactivity and lymphoma risk.

RESULTS

We observed significant, positive associations between lifetime recreational physical inactivity and risk of both HL (OR = 1.90, 95% CI: 1.15-3.15) and NHL (OR = 1.35, 95% CI: 1.01-1.82).

CONCLUSIONS

The current analysis provides evidence for a positive association between physical inactivity and risk of both HL and NHL. These results add to a growing body of research suggesting that lifetime physical inactivity may be an important independent, modifiable behavioral risk factor for cancer.

Testing the face shape hypothesis in twins discordant for nonsyndromic orofacial clefting

Nonsyndromic orofacial clefts (OFCs) are complex traits characterized by multifactorial inheritance and wide phenotypic variability. Numerous studies have shown subtle differences in the faces of unaffected relatives from cleft families compared to controls, the implication being that such outward differences are an incomplete expression reflecting an underlying genetic predisposition. Twins discordant for OFCs provide a unique opportunity to further test this idea, as the unaffected co-twin shares on average 50% (for dizygotic twins) and 100% (for monozygotic twins) of the genetic risk factors as the affected twin. We used 3D surface imaging and spatially-dense morphometry to compare facial shape in a sample of 44 unaffected co-twins and age- and sex-matched unaffected controls (n = 241). Unaffected co-twins showed statistically significant differences in the midface, lateral upper face, and forehead regions, compared to controls. Furthermore, co-twins were characterized by a distinct pattern of midfacial retrusion, broader upper faces, and greater protrusion of the mandible and brow ridges. This same general facial pattern was shown in both unaffected monozygotic and dizygotic co-twin subsets. These results provide additional support that altered facial shape is a phenotypic marker for OFC susceptibility.

Induction of Pluripotent Stem Cells from a Manifesting Carrier of Duchenne Muscular Dystrophy and Characterization of Their X-Inactivation Status

Three to eight percent of female carriers of Duchenne muscular dystrophy (DMD) develop dystrophic symptoms ranging from mild muscle weakness to a rapidly progressive DMD-like muscular dystrophy due to skewed inactivation of X chromosomes during early development. Here, we generated human induced pluripotent stem cells (hiPSCs) from a manifesting female carrier using retroviral or Sendai viral (SeV) vectors and determined their X-inactivation status. Although manifesting carrier-derived iPS cells showed normal expression of human embryonic stem cell markers and formed well-differentiated teratomas in vivo, many hiPS clones showed bi-allelic expression of the androgen receptor (AR) gene and loss of X-inactivation-specific transcript and trimethyl-histone H3 (Lys27) signals on X chromosomes, suggesting that both X chromosomes of the hiPS cells are in an active state. Importantly, normal dystrophin was expressed in multinucleated myotubes differentiated from a manifesting carrier of DMD-hiPS cells with XaXa pattern. AR transcripts were also equally transcribed from both alleles in induced myotubes. Our results indicated that the inactivated X chromosome in the patient's fibroblasts was activated during reprogramming, and XCI occurred randomly during differentiation.

Exploring Subclinical Phenotypic Features in Twin Pairs Discordant for Cleft Lip and Palate

OBJECTIVE

Monozygotic twins of an individual with an orofacial cleft have a significantly elevated risk for orofacial cleft compared with the general population, but still the concordance rate for orofacial cleft in monozygotic twins is about 40% to 50%. The goal of this study was to determine whether unaffected cotwins have an increased frequency of orbicularis oris muscle defects, a subclinical form of orofacial cleft. The presence of such defects may reduce the overall rate of discordance.

METHOD

A total of 63 discordant monozygotic and dizygotic twin pairs, 262 unaffected nontwin siblings, and 543 controls with no history of orofacial clefts were assessed for orbicularis oris defects by high-resolution ultrasound. Frequencies were compared by the Fisher exact test.

RESULTS

Unaffected cotwins from discordant monozygotic pairs had a higher frequency of defects (12.5%) than the other test groups (6.38% to 6.99%), but the difference was not statistically significant (P = .74).

CONCLUSIONS

In this study, orbicularis oris defects were not statistically significantly more common among the unaffected twins from orofacial cleft discordant twin pairs. The trends in the results warrant future studies with larger sample sizes and additional subclinical phenotypes.

Clinical and epidemiological study of orofacial clefts

OBJECTIVE

Cleft lip with or without cleft palate (CL±P) or cleft palate (CP) are groups of malformations named orofacial clefts (OC), which are the second leading cause of birth defects. This study aimed to analyze clinical and epidemiological features of Brazilian patients with OC, studying cases treated in the reference center of the state of Paraná (PR).

METHODS

2,356 charts were reviewed and 1,838 were evaluated by the same clinical geneticist. Data were collected in the reference center, and compared with those of the Health Department of the state of Paraná. Clinical characteristics, presence of other anomalies, and birth prevalence were evaluated.

RESULTS

389 (21.2%) patients had CP, 437 (23.8%) had cleft lip (CL), and 1,012 (55%) had cleft lip and palate (CLP). Syndromic OC were identified in 15.3% of patients, 10.4% of patients with CL±P, and 33.9% of patients with CP. Common additional anomalies were: central nervous system, limbs, cardiovascular, and musculoskeletal defects. The number of syndromic cases was lower when clinical evaluation was performed by other medical specialists when compared to that of the clinical geneticist. Birth prevalence was 1/1,010 live births. Lack of notification with the national birth registry was observed in 49.9% of CL±P. The present data suggests a decrease of 18.52% in the prevalence of non-syndromic OC after folic acid fortification in Brazil.

CONCLUSION

Better understanding of clinical and epidemiological aspects of OC is crucial to improve the understanding of pathogenesis, promote preventive strategies, and guide clinical care, including the presence of clinical geneticists in the multidisciplinary team for OC treatment.

Minor physical anomalies in patients with bipolar I disorder and normal controls

BACKGROUND

The neurodevelopmental hypothesis is well established in schizophrenia but has received modest empirical support in bipolar disorder. In schizophrenia it is partly based on the higher prevalence of minor physical anomalies (MPAs), established by many well controlled studies. No studies with comparable designs have been performed in bipolar disorder. The present study aims to establish the rate and topographic distribution of MPAs in bipolar I patients.

METHODS

The subjects were 61 patients (25 men, 36 women) with bipolar I disorder and 103 normal subjects (49 men, 54 women) who were examined for MPAs using a modified version of the Waldrop Physical Anomaly Scale.

RESULTS

The bipolar I patients showed significantly higher regional MPA scores in 3 distinct regions - mouth, feet and head, as well as in the overall scores for the craniofacial complex, the periphery and the total MPA score. Differences were statistically significant for 3 anomalies - high/steepled palate, big gap between I and II toes and furrowed tongue that made significant contribution to the prediction of the patient-control status in a discriminant analysis model.

CONCLUSIONS

Our data suggest that aberrant processes of neurodevelopment may contribute to the etiology of bipolar I disorder. The field is open for further research using modern instruments and designs in order to identify potential biological markers for bipolar disorder.

Copy number detection in discordant monozygotic twins of Congenital Diaphragmatic Hernia (CDH) and Esophageal Atresia (EA) cohorts

The occurrence of phenotypic differences between monozygotic (MZ) twins is commonly attributed to environmental factors, assuming that MZ twins have a complete identical genetic make-up. Yet, recently several lines of evidence showed that both genetic and epigenetic factors could have a role in phenotypic discordance after all. A high occurrence of copy number variation (CNV) differences was observed within MZ twin pairs discordant for Parkinson's disease, thereby stressing on the importance of post-zygotic mutations as disease-predisposing events. In this study, the prevalence of discrepant CNVs was analyzed in discordant MZ twins of the Esophageal Atresia (EA) and Congenital Diaphragmatic Hernia (CDH) cohort in the Netherlands. Blood-derived DNA from 11 pairs (7 EA and 4 CDH) was screened using high-resolution SNP arrays. Results showed an identical copy number profile in each twin pair. Mosaic chromosome gain or losses could not be detected either with a detection threshold of 20%. Some of the germ-line structural events demonstrated in five out of eleven twin pairs could function as a susceptible genetic background. For example, the 177-Kb loss of chromosome 10q26 in CDH pair-3 harbors the TCF7L2 gene (Tcf4 protein), which is implicated in the regulation of muscle fiber type development and maturation. In conclusion, discrepant CNVs are not a common cause of twin discordancy in these investigated congenital anomaly cohorts.

Risk of oral clefts in twins

BACKGROUND

Small studies have indicated that twinning increases the risk of oral cleft.

METHODS

We used data from a Danish national population-based cohort study to investigate whether twinning was associated with isolated oral cleft, and to estimate the twin probandwise concordance rate and heritability. Twins (207 affected/130,710) and singletons (7766 affected/4,798,526) born from 1936 through 2004 in Denmark were ascertained by linkage among the Danish Facial Cleft Database, the Danish Twin Registry, and the Civil Registration System. We computed oral cleft prevalence and prevalence proportion ratio for twins versus singletons, stratified for 3 subphenotypes. Probandwise concordance rates and heritability for twins were estimated for 2 phenotypes--cleft lip with or without cleft palate (CL/P) and cleft palate (CP).

RESULTS

The prevalence of oral cleft was 15.8 per 10,000 twins and 16.6 per 10,000 singletons (prevalence proportion ratio = 0.95; 95% confidence interval = 0.83-1.1). This prevalence was similar for monozygotic and dizygotic twins. The probandwise concordance rate was higher for CL/P for monozygotic twins than for dizygotic twins (50% vs. 8%, respectively). A similar contrast was present for CP. Recurrence risk for both types of clefts was greater in dizygotic twins than in non-twin siblings. Heritability estimates were above 90% for both CL/P and CP.

CONCLUSIONS

No excess risk of oral cleft could be demonstrated for twins compared with singletons. The concordance rates and heritability estimates for both types of clefts show a strong genetic component.

A mild neurofibromatosis type 1 phenotype produced by the combination of the benign nature of a leaky NF1-splice mutation and the presence of a complex mosaicism

Here we analyze the genetic and molecular basis responsible for a very benign phenotype observed in an NF1 patient. Quantification of cells carrying the NF1 mutation in different samples derived from the three embryonic layers revealed mosaicism. Furthermore, the construction of a minigene with patient's mutation (c.3198 - 314G>A) confirmed its benign nature due to the leakiness of the splicing mechanism that generated a proportion of correctly spliced transcripts. Hence, we concluded that the mild phenotype observed in this patient is the result of the presence of mosaicism together with the benign nature of a leaky NF1-splice mutation. Finally, with the aim of developing a personalized therapeutic approach for this patient, we demonstrated correction of the splicing defect by using specific antisense morpholino oligomers. Our results provide an example of the molecular complexity behind disease phenotypes and highlight the importance of using comprehensive genetic approaches to better assess phenotype-genotype correlations.

Recurrence risk for offspring of twins discordant for oral cleft: a population-based cohort study of the Danish 1936-2004 cleft twin cohort

Our objective in this Danish population-based cohort study was to estimate the recurrence risk of isolated oral cleft (OC) for offspring of the unaffected co-twins of OC discordant twin pairs and to compare this risk to the recurrence risk in the offspring of the affected co-twin as well as to the risk in the background population. During 1936-2004, 207 twin pairs were ascertained, among whom at least one twin had an OC. The index persons were twins discordant for OC who had children (N=117), and their offspring (N=239). The participants were ascertained by linkage between The Danish Facial Cleft Database, The Danish Twin Registry and The Danish Civil Registration System. In the study OC recurrence risk for offspring of the affected and unaffected twin and relative risk were compared to the background prevalence. We found that among 110 children of the 54 OC affected twins, two (1.8%) children had OC corresponding to a significantly increased relative risk (RR=10; 95% CI 1.2-35) when compared to the frequency in the background population. Among the 129 children of the 63 unaffected twins, three (2.3%) children were affected, corresponding to a significantly increased relative risk (RR=13; 95% CI 2.6-36) when compared the background prevalence. We concluded that in OC discordant twin pairs similar increased recurrence risks were found among offspring of both OC affected and OC unaffected twins. This provides further evidence for a genetic component in cleft etiology and is useful information for genetic counseling of twin pairs discordant for clefting.

Skewed X inactivation and IVF-conceived infants

The objective of this study was to investigate whether skewed X chromosome inactivation (XCI) is associated with IVF. A retrospective cohort study was performed comprising 30 female infants conceived by IVF and 44 naturally conceived control infants matched for gestational age and sex. Cord blood DNA samples were obtained and XCI patterns were analysed using a methylation-sensitive assay. Eight IVF samples and 13 control samples were excluded from the study because they were either homozygous or alleles were too similar for the assay to determine skewing. Mildly skewed XCI (80-90% inactivation of one allele) was present in two of 22 (9.1%) IVF samples and two of 31 (6.5%) control samples. Extremely skewed XCI (>90% inactivation of one allele) was found in two of 22 (9.1%) IVF samples and none of 31 control samples. Neither difference was statistically significant. However, the mean degree of skewed XCI in the IVF group was 72.0% and in the control group was 62.4% (P=0.002). Larger studies are needed to clarify the relationship between IVF and skewed XCI.

Physical manifestations of neurodevelopmental disruption: are minor physical anomalies part of the syndrome of schizophrenia?

The well-documented excess of minor physical anomalies (MPAs) among individuals with schizophrenia generally supports the neurodevelopmental model, which posits that both genetic and environmental factors contribute to structural and functional brain changes in the intrauterine and perinatal periods that predispose one to developing schizophrenia. This review synthesizes select areas of research findings on MPAs to address the question, Are MPAs part of the syndrome of schizophrenia? Although MPAs are not specific to schizophrenia, their presence in some patients indicates that aberrations in the development of the nervous system contribute to risk for the disorder. The broadly defined, heterogeneous MPA construct may be of limited value in further elucidating the specific pathophysiology of schizophrenia, though particular anomalies, such as those pertaining to nasal volumes, palatal abnormalities, or craniofacial morphology, may be informative. Given the availability of more sophisticated microarray technologies, and in light of recent findings on spontaneous mutations in patients with schizophrenia, it is possible that MPAs will prove to be useful in identifying etiologic subtypes and/or the loci of genetic risk factors. It remains to be determined whether MPAs-which, of course, are fixed markers present throughout childhood and adolescence well before the onset of the prodrome and psychosis-may have utility in terms of risk stratification for future preventive efforts. Taken together, research findings on MPAs indicate that these minor anomalies are indeed part of some schizophrenia syndromes, representing a stable systemic or physical set of manifestations of the underlying neurodevelopmental processes that lead to the illness.