Embryonic Craniofacial Tissue Research Articles

A distant global control region is essential for normal expression of anterior HOXA genes during mouse and human craniofacial development

Craniofacial abnormalities account for approximately one third of birth defects. The regulatory programs that build the face require precisely controlled spatiotemporal gene expression, achieved through tissue-specific enhancers. Clusters of coactivated enhancers and their target genes, known as superenhancers, are important in determining cell identity but have been largely unexplored in development. In this study we identified superenhancer regions unique to human embryonic craniofacial tissue. To demonstrate the importance of such regions in craniofacial development and disease, we focused on an ~600 kb noncoding region located between NPVF and NFE2L3. We identified long range interactions with this region in both human and mouse embryonic craniofacial tissue with the anterior portion of the HOXA gene cluster. Mice lacking this superenhancer exhibit perinatal lethality, and present with highly penetrant skull defects and orofacial clefts phenocopying Hoxa2-/- mice. Moreover, we identified two cases of de novo copy number changes of the superenhancer in humans both with severe craniofacial abnormalities. This evidence suggests we have identified a critical noncoding locus control region that specifically regulates anterior HOXA genes and copy number changes are pathogenic in human patients.

3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies.

The analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17–0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.

High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development

SUMMARYDefects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.

High Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development

Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information encoded in the genome between genes and within intronic sequences. However, early stages of human embryonic development have not been interrogated with functional genomics techniques, preventing identification of regulatory sequences important for forming the human face. Here we describe comprehensive epigenomic annotations from early human embryonic craniofacial tissues and systematic comparisons with multiple human tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences, find likely causal variants for craniofacial abnormalities, and identify a putative locus control region for the HOXA gene cluster activated during specifcially human craniofacial development. We provide these data in easily accessible formats for both craniofacial researchers and clinicians to aid in the interpretation of noncoding variation across the whole genome in those affected by craniofacial abnormalities.

Imputation of orofacial clefting data identifies novel risk loci and sheds light on the genetic background of cleft lip ± cleft palate and cleft palate only.

Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is among the most common human birth defects with multifactorial etiology. Here, we present results from a genome-wide imputation study of nsCL/P in which, after adding replication cohort data, four novel risk loci for nsCL/P are identified (at chromosomal regions 2p21, 14q22, 15q24 and 19p13). On a systematic level, we show that the association signals within this high-density dataset are enriched in functionally-relevant genomic regions that are active in both human neural crest cells (hNCC) and mouse embryonic craniofacial tissue. This enrichment is also detectable in hNCC regions primed for later activity. Using GCTA analyses, we suggest that 30% of the estimated variance in risk for nsCL/P in the European population can be attributed to common variants, with 25.5% contributed to by the 24 risk loci known to date. For each of these, we identify credible SNPs using a Bayesian refinement approach, with two loci harbouring only one probable causal variant. Finally, we demonstrate that there is no polygenic component of nsCL/P detectable that is shared with nonsyndromic cleft palate only (nsCPO). Our data suggest that, while common variants are strongly contributing to risk for nsCL/P, they do not seem to be involved in nsCPO which might be more often caused by rare deleterious variants. Our study generates novel insights into both nsCL/P and nsCPO etiology and provides a systematic framework for research into craniofacial development and malformation.

Immunodetection of the transforming growth factors beta 1 and beta 2 in the developing murine palate.

The expression of some members of the TGF beta family of genes in embryonic craniofacial tissue suggests a functional role for these molecules in orofacial development. In other systems, TGF beta 1 and TGF beta 2 have been shown to regulate cell proliferation and extracellular matrix metabolism, processes critical to normal development of the secondary palate. We have thus determined the amount and tissue distribution of both TGF beta 1 and TGF beta 2 in embryonic palatal tissue. Cellular extracts of murine embryonic palatal tissue from days 12, 13 and 14 of gestation were assayed for the presence of TGF beta 1 and TGF beta 2 by immunoprecipitation. Physiological levels, ranging from 0.05-20 ng/micrograms protein, of both growth factors were detected in all tissues examined. Immunostaining with antibodies directed against either TGF beta 1 or TGF beta 2 demonstrated the presence of these growth factors in palatal epithelium and mesenchyme early during palatal development (gestational day [GD] 12) a period characterized by tissue growth. On GDs 13 and 14, characterized by palate epithelial differentiation, immunostaining for both growth factors predominated in epithelial tissue. Immunostaining for TGF beta 1 and TGF beta 2 was also intense in mesenchyme surrounding tooth germs and in perichondrium. Chondrocytes and cartilage extracellular matrix did not stain for either TGF beta 1 or beta 2. Combined with existing evidence for the presence of functional receptors for the transforming growth factor-beta s in the developing palate, these results provide rationale for studies designed to clarify a specific role for these signalling molecules in palate epithelial differentiation and/or epithelial-mesenchymal interactions.

Metabolic characterization of all-trans-retinoic acid (ATRA)-induced craniofacial development of murine embryos using in vivo proton magnetic resonance spectroscopy.

AimTo characterize the abnormal metabolic profile of all-trans-retinoic acid (ATRA)–induced craniofacial development in mouse embryos using proton magnetic resonance spectroscopy (1H-MRS).MethodsTimed-pregnant mice were treated by oral gavage on the morning of embryonic gestation day 11 (E11) with all-trans-retinoic acid (ATRA). Dosing solutions were adjusted by maternal body weight to provide 30, 70, or 100 mg/kg RA. The control group was given an equivalent volume of the carrier alone. Using an Agilent 7.0 T MR system and a combination of surface coil coils, a 3 mm×3 mm×3 mm 1H-MRS voxel was selected along the embryonic craniofacial tissue. 1H-MRS was performed with a single-voxel method using PRESS sequence and analyzed using LCModel software. Hematoxylin and eosin was used to detect and confirm cleft palate.Result 1H-MRS revealed elevated choline levels in embryonic craniofacial tissue in the RA70 and RA100 groups compared to controls (P<0.05). Increased choline levels were also found in the RA70 and RA100 groups compared with the RA30 group (P<0.01). High intra-myocellular lipids at 1.30 ppm (IMCL13) in the RA100 group compared to the RA30 group were found (P<0.01). There were no significant changes in taurine, intra-myocellular lipids at 2.10 ppm (IMCL21), and extra-myocellular lipids at 2.30 ppm (EMCL23). Cleft palate formation was observed in all fetuses carried by mice administered 70 and 100 mg/kg RA.ConclusionsThis novel study suggests that the elevated choline and lipid levels found by 1H-MRS may represent early biomarkers of craniofacial defects. Further studies will determine performance of this test and pathogenetic mechanisms of craniofacial malformation.

Disruption of SATB2 or its long-range cis-regulation by SOX9 causes a syndromic form of Pierre Robin sequence

Heterozygous loss-of-function (LOF) mutations in the gene encoding the DNA-binding protein, SATB2, result in micrognathia and cleft palate in both humans and mice. In three unrelated individuals, we show that translocation breakpoints (BPs) up to 896 kb 3′ of SATB2 polyadenylation site cause a phenotype which is indistinguishable from that caused by SATB2 LOF mutations. This syndrome comprises long nose, small mouth, micrognathia, cleft palate, arachnodactyly and intellectual disability. These BPs map to a gene desert between PLCL1 and SATB2. We identified three putative cis-regulatory elements (CRE1–3) using a comparative genomic approach each of which would be placed in trans relative to SATB2 by all three BPs. CRE1–3 each bind p300 and mono-methylated H3K4 consistent with enhancer function. In silico analysis suggested that CRE1–3 contain one or more conserved SOX9-binding sites, and this binding was confirmed using chromatin immunoprecipitation on cells derived from mouse embryonic pharyngeal arch. Interphase bacterial artificial chromosome fluorescence in situ hybridization measurements in embryonic craniofacial tissues showed that the orthologous region in mice exhibits Satb2 expression-dependent chromatin decondensation consistent with Satb2 being a target gene of CRE1–3. To assess their in vivo function, we made multiple stable reporter transgenic lines for each enhancer in zebrafish. CRE2 was shown to drive SATB2-like expression in the embryonic craniofacial region. This expression could be eliminated by mutating the SOX9-binding site of CRE2. These observations suggest that SATB2 and SOX9 may be acting together via complex cis-regulation to coordinate the growth of the developing jaw.

Small heat shock protein HSPB1 regulates growth of embryonic zebrafish craniofacial muscles

The small heat shock protein HspB1 (Hsp27) is abundantly expressed in embryonic muscle tissues of a wide variety of vertebrate species. However, the functional significance of this expression pattern is not well established. In the present study, we observed specific, high level expression of HspB1 protein and an HspB1 gene reporter in developing craniofacial muscles of the zebrafish, Danio rerio, and examined the consequences of reducing HspB1 expression to the development and growth of these muscles. Quantitative morphometric analyses revealed a reduction in the cross-sectional area of myofibers in embryos expressing reduced HspB1 levels by as much as 47% compared to controls. In contrast, we detected no differences in the number of myofibrils or associated nuclei, nor the number, size or development of chondrocytes in surrounding tissues. We also did not detect changes to the overall organization of sarcomeres or myofibrils in embryos expressing reduced levels of HspB1. Together our results reveal a critical role for HspB1 in the growth of myofibrils and provide new insight into the mechanism underlying its developmental function.

Diversity and Complexity in Chromatin Recognition by TFII-I Transcription Factors in Pluripotent Embryonic Stem Cells and Embryonic Tissues

GTF2I and GTF2IRD1 encode a family of closely related transcription factors TFII-I and BEN critical in embryonic development. Both genes are deleted in Williams-Beuren syndrome, a complex genetic disorder associated with neurocognitive, craniofacial, dental and skeletal abnormalities. Although genome-wide promoter analysis has revealed the existence of multiple TFII-I binding sites in embryonic stem cells (ESCs), there was no correlation between TFII-I occupancy and gene expression. Surprisingly, TFII-I recognizes the promoter sequences enriched for H3K4me3/K27me3 bivalent domain, an epigenetic signature of developmentally important genes. Moreover, we discovered significant differences in the association between TFII-I and BEN with the cis-regulatory elements in ESCs and embryonic craniofacial tissues. Our data indicate that in embryonic tissues BEN, but not the highly homologous TFII-I, is primarily recruited to target gene promoters. We propose a “feed-forward model” of gene regulation to explain the specificity of promoter recognition by TFII-I factors in eukaryotic cells.

Mouse FLRT2 Interacts with the Extracellular and Intracellular Regions of FGFR2

Fibroblast Growth Factor (FGF) signaling is known to be critical in mediating key developmental events during craniofacial development. Recent evidence suggests that members of the Fibronectin (F) Leucine (L) Rich (R) Transmembrane (T), FLRT, family modulate FGF signaling. FLRT2 has a highly specific pattern of expression during craniofacial development, in close relationship with FGFR2. We therefore characterized FLRT2/FGFR2 interactions in the context of craniofacial development and showed, by co-immunoprecipitation and GST pulldown assays with embryonic craniofacial tissue lysates, that FLRT2 interacted with FGFR2. Yeast two-hybrid assays further showed that the intracellular regions of both proteins interacted in addition to the interactions in the extracellular portions. The extracellular Leucine Rich Repeats domain of FLRT2 contributed to the interactions with the extracellular regions of FGFR2. Interactions in the intracellular regions of the 2 proteins were mediated by the C-tail domain in FLRT2. Furthermore, cells stably transfected with FLRT2 shRNAs or FLRT2 cDNA exhibited a concomitant decrease and increase, respectively, in FGFR2 protein, mRNA, and ERK phosphorylation levels, suggesting a positive feedback regulatory loop of FLRT2 on FGF signaling in craniofacial tissues. We propose that FLRT2-FGFR2 interactions represent a potential mechanism for regulation of FGF signaling by FLRT2 during craniofacial development.

Effects of phenytoin onSatb2andHoxa2gene expressions in mouse embryonic craniofacial tissueThis paper is one of a selection of papers published in this special issue entitled “Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine” and has undergone the Journal's usual peer review process.

Cleft lip and cleft palate are common congenital craniofacial birth defects in humans. Phenytoin (PHT) is a risk factor of cleft palate formation; however, the molecular mechanisms by which phenytoin exerts its teratogenic effects resulting in cleft palate remain unknown. The Satb2 gene mutation is associated with cleft palate. Satb2-deficient mice exhibit cleft palate deformity and an up-regulation of Hoxa2 in the fronto-nasal region. In this study, phenytoin was administered intraperitoneally to pregnant C57BL/6 mice on the 10th day of gestation. Real-time PCR results showed that the expressions of Satb2 and Hoxa2 in craniofacial tissues of mouse embryos were obviously different at different time points. The Satb2 gene was down-regulated and the Hoxa2 gene was up-regulated in phenytoin-treated mouse embryonic craniofacial tissue. We conclude that phenytoin may regulate the expression of these two genes in C57BL/6 mice and it may also be involved in the formation of cleft palate.

Expression analyses of human cleft palate tissue suggest a role for osteopontin and immune related factors in palatal development

Cleft lip and/or palate (CL/P) is a common congenital malformation with a complex etiology which is not fully elucidated yet. Epidemiological studies point to different etiologies in the cleft lip and palate subgroups, isolated cleft lip (CL), isolated cleft palate (CP) and combined cleft lip and palate (CLP). In order to understand the biological basis in these cleft lip and palate subgroups better we studied the expression profiles in human tissue from patients with CL/P. In each of the CL/P subgroups, samples were obtained from three patients and gene expression analysis was performed. Moreover, selected differentially expressed genes were analyzed by quantitative RT-PCR, and by immunohistochemical staining of craniofacial tissue from human embryos. Osteopontin (SPP1) and other immune related genes were significantly higher expressed in palate tissue from patients with CLP compared to CP and immunostaining in palatal shelves against SPP1, chemokine receptor 4 (CXCR4) and serglycin (PRG1) in human embryonic craniofacial tissue were positive, supporting a role for these genes in palatal development. However, gene expression profiles are subject to variations during growth and therefore we recommend that future gene expression in CL/P studies should use tissue from the correct embryonic time and place if possible, to overcome the biases in the presented study.

Orofacial Cleft Risk Is Increased with Maternal Smoking and Specific Detoxification-Gene Variants

Maternal smoking is a recognized risk factor for orofacial clefts. Maternal or fetal pharmacogenetic variants are plausible modulators of this risk. In this work, we studied 5,427 DNA samples, including 1,244 from subjects in Denmark and Iowa with facial clefting and 4,183 from parents, siblings, or unrelated population controls. We examined 25 single-nucleotide polymorphisms in 16 genes in pathways for detoxification of components of cigarette smoke, to look for evidence of gene-environment interactions. For genes identified as related to oral clefting, we studied gene-expression profiles in fetal development in the relevant tissues and time intervals. Maternal smoking was a significant risk factor for clefting and showed dosage effects, in both the Danish and Iowan data. Suggestive effects of variants in the fetal NAT2 and CYP1A1 genes were observed in both the Iowan and the Danish participants. In an expanded case set, NAT2 continued to show significant overtransmission of an allele to the fetus, with a final P value of .00003. There was an interaction between maternal smoking and fetal inheritance of a GSTT1-null deletion, seen in both the Danish (P=.03) and Iowan (P=.002) studies, with a Fisher's combined P value of <.001, which remained significant after correction for multiple comparisons. Gene-expression analysis demonstrated expression of GSTT1 in human embryonic craniofacial tissues during the relevant developmental interval. This study benefited from two large samples, involving independent populations, that provided substantial power and a framework for future studies that could identify a susceptible population for preventive health care.

Intracellular dynamics of Smad‐mediated TGFβ signaling

The transforming growth factor-beta (TGFbeta) family represents a class of signaling molecules that plays a central role in morphogenesis, growth, and cell differentiation during normal embryonic development. Members of this growth factor family are particularly vital to development of the mammalian secondary palate where they regulate palate mesenchymal cell proliferation and extracellular matrix synthesis. Such regulation is particularly critical since perturbation of either cellular process results in a cleft of the palate. While the cellular and phenotypic effects of TGFbeta on embryonic craniofacial tissue have been extensively catalogued, the specific genes that function as downstream mediators of TGFbeta action in the embryo during palatal ontogenesis are poorly defined. Embryonic palatal tissue in vivo and murine embryonic palate mesenchymal (MEPM) cells in vitro secrete and respond to TGFbeta. In the current study, elements of the Smad component of the TGFbeta intracellular signaling system were identified and characterized in cells of the embryonic palate and functional activation of the Smad pathway by TGFbeta1, TGFbeta2, and TGFbeta3 was demonstrated. TGFbeta-initiated Smad signaling in cells of the embryonic palate was found to result in: (1) phosphorylation of Smad 2; (2) nuclear translocation of the Smads 2, 3, and 4 protein complex; (3) binding of Smads 3 and 4 to a consensus Smad binding element (SBE) oligonucleotide; (4) transactivation of transfected reporter constructs, containing TGFbeta-inducible Smad response elements; and (4) increased expression of gelatinases A and B (endogenous genes containing Smad response elements) whose expression is critical to matrix remodeling during palatal ontogenesis. Collectively, these data point to the presence of a functional Smad-mediated TGFbeta signaling system in cells of the developing murine palate.

Expression of Set-alpha during morphogenesis of mouse lower first molar.

The detailed in situ expression pattern of the Set-alpha gene has been studied. Previously we showed that Set-alpha is a differentially expressed gene in the embryonic mouse mandible at day 10.5 (E10.5) gestational age. Cells expressing Set-alpha were widely distributed in both the epithelial and underlying ectomesenchymal cells at E10.5. At E12, they were slightly aggregated in an area where tooth germ of the lower first molar is estimated to be formed. At E13.5, Set-alpha was strongly expressed in the tooth germ. At the cap stage, Set-alpha was expressed in the enamel organ and dental papilla. At the bell stage, Set-alpha was distinctly expressed in the inner enamel epithelial and dental papilla cells facing the inner enamel epithelial layer, which were intended to differentiate into ameloblasts and odontoblasts, respectively. Interestingly, Set-alpha was also expressed in several embryonic craniofacial tissues derived from the ectoderm. This study is the first report that Set-alpha is distinctly expressed in the developing tooth germ, and suggests that Set-alpha plays an important role in both the initiation and the growth of the tooth germ, as well as in the differentiation of ameloblasts and odontoblasts.

Fluorescence-activated cell sorting of EGFP-labeled neural crest cells from murine embryonic craniofacial tissue.

During the early stages of embryogenesis, pluripotent neural crest cells (NCC) are known to migrate from the neural folds to populate multiple target sites in the embryo where they differentiate into various derivatives, including cartilage, bone, connective tissue, melanocytes, glia, and neurons of the peripheral nervous system. The ability to obtain pure NCC populations is essential to enable molecular analyses of neural crest induction, migration, and/or differentiation. Crossing Wnt1-Cre and Z/EG transgenic mouse lines resulted in offspring in which the Wnt1-Cre transgene activated permanent EGFP expression only in NCC. The present report demonstrates a flow cytometric method to sort and isolate populations of EGFP-labeled NCC. The identity of the sorted neural crest cells was confirmed by assaying expression of known marker genes by TaqMan Quantitative Real-Time Polymerase Chain Reaction (QRT-PCR). The molecular strategy described in this report provides a means to extract intact RNA from a pure population of NCC thus enabling analysis of gene expression in a defined population of embryonic precursor cells critical to development.

Profiling expression patterns of 2,214 unigenes in mouse craniofacial development by cDNA microarray analysis

The recent development of cDNA microarray technology enables parallel expression monitoring of thousands of genes simultaneously, which provides a powerful tool for characterizing transcriptional activities of genes in various developmental stages and pathological states. We initiated the Oral and Craniofacial Genome Anatomy Project (OC-GAP) to identify genes important for craniofacial development and disorders. As part of this genome project, we have examined gene expression patterns during mouse craniofacial development. Fluorescently labelled probes prepared using mRNA from mouse embryonic craniofacial tissues at embryonic day (E) 9.5, E13.5 and E16.5 were hybridized to microarray slides printed with 2,214 mouse unigenes. A microarray quantitative analysis revealed that 10% of these genes were expressed in different levels during craniofacial development, whereas the rest showed no significant differences in expression throughout the different developmental stages. We found that 41 genes, such as those encoding Wnt-1, retinoid receptor and Brca1, showed higher expression levels at E9.5; 54 genes, such as those encoding Bmp-1, IGF II and Sox3, were more highly expressed at E13.5; and another 126 genes, such as those encoding Mash 1, FHF-1 and fibulin-2, were expressed at higher levels at E16.5. The identification of these genes with highly stage-specific expression during craniofacial development is potentially important because they are likely to have key roles in the formation of craniofacial tissues. We are currently studying expression patterns of genes from an E8.5−9.5 mouse craniofacial cDNA library to identify novel craniofacial genes by microarray screening approaches.

Regulation of murine embryonic epithelial cell differentiation by transforming growth factors β

Abstract The expression of some members of the transforming growth factor β (TGFβ) family of genes in embryonic craniofacial tissue suggests a functional role for these molecules in orofacial development. In an attempt to ascertain a role for the TGFβs during palatal ontogeny, murine palatal shelves were excised on gestation day (GD) 12, prior to overt epithelial differentiation, grown in organ culture under serum–free conditions and exposed to TGF β1 and TGF β2 for 18 or 42 h. Shelves were labeled with [ 3H]-thymidine (20 μCi/ml) during the last 4 h in culture, fixed, dehydrated, embedded in paraffin and sections stained and examined by autoradiography. Treatment of GDI2 palates with TGF β1 and TGF β2 resulted in precocious cessation of medial edge epithelium (MEE) DNA synthesis followed by elimination of the MEE. In addition, this response appeared to be dose–related with higher concentrations of growth factor eliciting a more marked biological response. TGFβ treatment of homologous shelves grown in apposition also resulted in precocious fusion of apposing MEE. Thus, members of the TGFβ family, known to be synthesized by palatal MEE, appear to act in an autocrine/paracrine fashion in this tissue and are capable of regulating differentiation of embryonic palatal medial edge epithelium.