A comprehensive analysis of AHRR gene as a candidate for cleft lip with or without cleft palate

AKT/mTOR-mediated autophagic signaling is associated with TCDD-induced cleft palate

In utero exposure to the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) can contribute to high rates of cleft palate (CP) formation, but the mechanistic basis for these effects remains uncertain. Here, multi-omics-based metabolomic and transcriptomic analyses were employed to characterize the etiological basis for TCDD-induced CP on gestational day 14.5 (GD14.5). These analyses revealed that TCDD-induced CP formation is associated with calcium, MAPK, PI3K-Akt, and mTOR pathway signaling. PI3K-Akt and mTOR signaling activity is closely linked with the maintenance of cellular proliferation and survival. Moreover, mTOR-mediated regulation of autophagic activity is essential for ensuring an appropriate balance between metabolic activity and growth. Murine embryonic palatal mesenchymal (MEPM) cell proliferation was thus characterized, autophagic activity in these cells was evaluated through electron microscopy and western immunoblotting was used to compare the levels of autophagy- and AKT/mTOR-related protein between the control and TCDD groups on GD14.5. These analyses indicated that MEPM cell proliferative and autophagic activity was inhibited in response to TCDD exposure with the concomitant activation of AKT/mTOR signaling, in line with the multi-omics data. Together, these findings suggested that following TCDD exposure, the activation of AKT/mTOR-related autophagic signaling may play a role in the loss of appropriate palatal cell homeostasis, culminating in the incidence of CP.

Identification of competing endogenous RNA networks associated with circRNA and lncRNA in TCDD-induced cleft palate development

2,3,7,8 -tetrachlorodibenzo-p-dioxin (TCDD) is a teratogen that can induce cleft palate formation, a common birth defect. Competing endogenous RNAs (ceRNAs), including circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), indirectly regulate gene expression via sharing microRNAs (miRNAs). Nevertheless, the mechanism by which they act as ceRNAs to regulate palatal development remains to be explored in greater detail. Here, the cleft palate model of C57BL/6 N pregnant mice was constructed by gavage of TCDD (64 ug/kg) on gestation day (GD) 10.5, and the palatal shelves were taken on gestation day (GD) 14.5 for whole-transcriptome sequencing to investigate the underlying mechanisms of the roles of circRNAs and lncRNAs as ceRNAs in cleft palate. Sequencing results revealed that 293 lncRNA, 589 circRNA, 47 miRNA, and 138 messenger RNA (mRNA) were significantly dysregulated, and the cytochrome P450 (CYP) enzymes and the aryl hydrocarbon receptor (AhR) pathway play key roles in the induction of cleft palate upon exposure to TCDD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the function of TCDD function was mainly related to the metabolic processes of intracellular compounds, including the metabolic processes of cellular aromatic compounds and the metabolism of exogenous drugs by cytochrome P450, etc. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) indicated that the circRNA_1781/miR-30c-1-3p/PKIB and XR_380026.2/miR-1249-3p/DNAH10 ceRNA networks were hypothesized to be a hub involved in palatal development suggesting that the circRNA_1781/miR-30c-1-3p/PKIB and XR_380026.2/miR-1249-3p/DNAH10 ceRNA networks may be critical for palatogenesis, setting the foundation for the investigation of cleft palate.

Exploring the roles of noncoding RNAs in craniofacial abnormalities: A systematic review

Congenital craniofacial abnormalities are congenital anomalies of variable expressivity and severity with a recognizable set of abnormalities, which are derived from five identifiable primordial structures. They can occur unilaterally or bilaterally and include various malformations such as cleft lip with/without palate, craniosynostosis, and craniofacial microsomia. To date, the molecular etiology of craniofacial abnormalities is largely unknown. Noncoding RNAs (ncRNAs), including microRNAs, long ncRNAs, circular RNAs and PIWI-interacting RNAs, function as major regulators of cellular epigenetic hallmarks via regulation of various molecular and cellular processes. Recently, aberrant expression of ncRNAs has been implicated in many diseases, including craniofacial abnormalities. Consequently, this review focuses on the role and mechanism of ncRNAs in regulating craniofacial development in the hope of providing clues to identify potential therapeutic targets.

MicroRNAs and Gene Regulatory Networks Related to Cleft Lip and Palate

Cleft lip and palate is one of the most common congenital birth defects and has a complex etiology. Either genetic or environmental factors, or both, are involved at various degrees, and the type and severity of clefts vary. One of the longstanding questions is how environmental factors lead to craniofacial developmental anomalies. Recent studies highlight non-coding RNAs as potential epigenetic regulators in cleft lip and palate. In this review, we will discuss microRNAs, a type of small non-coding RNAs that can simultaneously regulate expression of many downstream target genes, as a causative mechanism of cleft lip and palate in humans and mice.

Gene×environment associations in orofacial clefting

This chapter reviews the evidence of gene×environment interactions (G×E) in the etiology of orofacial cleft birth defects (OFCs), specifically cleft lip (CL), cleft palate (CP), and cleft lip with or without cleft palate (CL/P). We summarize the current state of our understanding of the genetic architecture of nonsyndromic OFCs and the evidence that maternal exposures during pregnancy influence risk of OFCs. Further, we present possible candidate gene pathways for these exposures including metabolism of folates, metabolism of retinoids, retinoic acid receptor signaling, aryl hydrocarbon receptor signaling, glucocorticoid receptor signaling, and biotransformation and transport. We review genes in these pathways with prior evidence of association with OFCs, genes with evidence from prior candidate gene G×E studies, and genes identified from genome-wide searches specifically for identifying G×E. Finally, we suggest future directions for G×E research in OFCs.

Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris

BACKGROUND

Teleosts display a spectacular diversity of craniofacial adaptations that often mediates ecological specializations. A considerable amount of research has revealed molecular players underlying skeletal craniofacial morphologies, but less is known about soft craniofacial phenotypes. Here we focus on an example of lip hypertrophy in the benthivorous Lake Tangnayika cichlid, Gnathochromis permaxillaris, considered to be a morphological adaptation to extract invertebrates out of the uppermost layer of mud bottom. We investigate the molecular and regulatory basis of lip hypertrophy in G. permaxillaris using a comparative transcriptomic approach.

RESULTS

We identified a gene regulatory network involved in tissue overgrowth and cellular hypertrophy, potentially associated with the formation of a locally restricted hypertrophic lip in a teleost fish species. Of particular interest were the increased expression level of apoda and fhl2, as well as reduced expression of cyp1a, gimap8, lama5 and rasal3, in the hypertrophic lip region which have been implicated in lip formation in other vertebrates. Among the predicted upstream transcription factors, we found reduced expression of foxp1 in the hypertrophic lip region, which is known to act as repressor of cell growth and proliferation, and its function has been associated with hypertrophy of upper lip in human.

CONCLUSION

Our results provide a genetic foundation for future studies of molecular players shaping soft and exaggerated, but locally restricted, craniofacial morphological changes in fish and perhaps across vertebrates. In the future, we advocate integrating gene regulatory networks of various craniofacial phenotypes to understand how they collectively govern trophic and behavioural adaptations.

Environmental mechanisms of orofacial clefts

Orofacial clefts (OFCs) are among the most common birth defects and impart a significant burden on afflicted individuals and their families. It is increasingly understood that many nonsyndromic OFCs are a consequence of extrinsic factors, genetic susceptibilities, and interactions of the two. Therefore, understanding the environmental mechanisms of OFCs is important in the prevention of future cases. This review examines the molecular mechanisms associated with environmental factors that either protect against or increase the risk of OFCs. We focus on essential metabolic pathways, environmental signaling mechanisms, detoxification pathways, behavioral risk factors, and biological hazards that may disrupt orofacial development.