Identification of loss-of-function HOXA2 mutations in Chinese families with dominant bilateral microtia

Genetics of Nonsyndromic Microtia and Congenital Aural Atresia: A Scoping Review

OBJECTIVE

To review the literature on genetics of nonsyndromic microtia and congenital aural atresia (CAA).

DATA SOURCES

Embase, Ovid (Medline), and Web of Science.

REVIEW METHODS

The search was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines for scoping reviews. Included studies were original research studies discussing the genetics or pattern of inheritance of non-syndromic microtia and/or CAA, defined as microtia and/or CAA that was completely isolated except for the presence of hearing loss.

RESULTS

Thirty studies met inclusion criteria, describing 40 unique genes and one susceptibility gene locus (4p15.32-4p16.2) associated with nonsyndromic microtia, CAA, or microtia and CAA. The 3 most cited genes describing microtia genetics alone were HOXA2, MUC6, and GSC. A single article describing nonsyndromic CAA alone identified the TSHZ1 as a candidate gene. Among 194 subjects from 18 manuscripts describing mendelian inheritance for non-syndromic microtia or microtia and CAA, 49% of the individuals were found to have autosomal dominant transmission, 4% had autosomal recessive, 5% had X-linked recessive, and 42% had no reported pattern of inheritance.

CONCLUSION

Current literature on the genetics of microtia and CAA is largely derived from genetic analysis of syndromic patients. Despite comprising over half of the clinical population, available data on non-syndromic patients remains limited. Understanding genetic polymorphisms and their correlation to phenotypic data more readily available to otolaryngologists offers the prospect of categorizing severity of anatomic malformation and hearing loss to guide future intervention, and improve ability to provide patient- and family-centered counseling.

A novel mutation in the BTB domain impairs transcriptional repression function of KCTD1 leading to syndromic microtia

Microtia is a common birth defect affecting the external ears and encompasses a spectrum of congenital anomalies of the auricle. For some of the microtia-associated syndromes, the additional abnormalities are not easily observed or with variable expressivity. Identifying pathogenic mutations through genetic testing is of great help in recognizing these highly heterogeneous syndromes in clinical practice. We reported a novel de novo KCTD1 mutation in a Chinese patient with congenital microtia. It expands the mutational spectrum of KCTD1 and provide an additional scalp-ear-nipple patient with typical and atypical clinical presentations. The identified mutation in the BTB domain impairs the suppressive activity of the AP-2 transcription factor family and may impact on maintaining the finely tuned activity of WNT pathway, which directs stem cell development in ectoderm patterning and craniofacial development. Due to the variable expressive clinical phenotypes of syndromic microtia, genetic molecular testing could be of great help in the definite diagnosis.

An innovative CRISPR/Cas9 mouse model of human isolated microtia indicates the potential contribution of CNVs near HMX1 gene

BACKGROUND

Microtia is a prevalent congenital malformation, the precise etiology and pathogenesis of which remain elusive. Mutations in the non-coding region of the HMX1 gene have been implicated in isolated cases of microtia, emerging as a significant focus of contemporary research. Several pathogenic copy number variations (CNVs) proximal to the HMX1 gene have been documented in wild animal populations, whereas only a single large segmental duplication in this region has been identified in humans. However, the absence of a gene-edited animal model has impeded the investigation of the unclear gene function associated with HMX1 mutations in human isolated microtia. In this study, we sought to precisely identify the pathogenic mutation by analyzing three pedigrees alongside population controls. Subsequently, our objective was to develop a CRISPR/Cas9 gene-edited mouse model to elucidate the functional implications of the identified mutation.

METHODS

Genomic DNA was collected from 32 affected individuals across three pedigrees, as well as from 2000 control subjects. Comprehensive genomic analyses, including genome-wide linkage analysis, targeted capture, second-generation sequencing, and copy number analysis, were conducted to identify potential mutations associated with congenital auricle malformation. CRISPR/Cas9 gene-edited murine models were generated in response to the identified mutation. The auricular phenotypes of these gene-edited mice were systematically monitored. Small-animal Micro-CT scanning was employed to identify potential craniofacial or skeletal abnormalities. Furthermore, the expression of the HMX1 gene in the PA2 region of mouse embryos was quantified using RT-qPCR.

RESULTS

A co-segregated 600 base pair duplication located on chromosome 4 (chr4:8701900-8702500, hg19) was identified in affected individuals across three pedigrees, but was absent in healthy controls. Two types of CRISPR/Cas9 gene-edited mice were subsequently generated. The knock-in (KI) mouse model was engineered by inserting one copy of the duplicated sequence directly adjacent to the mutated site, whereas the knockout (KO) mouse model was created by excising the mutation sequence. The phenotypes of different group of CRISPR/Cas9 gene-edited mice demonstrated distinct auricular deformities. Furthermore, an increase in the copy number of the mutated sequence was associated with elevated expression levels of HMX1 in the gene-edited mouse model.

CONCLUSIONS

In this study, we further narrowed down and identified a 600 base pair copy number variation (CNV) located at chr4:8701900-8702500 (hg19), which is implicated in human bilateral, isolated microtia. Utilizing CRISPR/Cas9 technology, we developed novel mouse models harboring the identified mutation. These models serve as a robust platform for the comprehensive investigation of the underlying mechanisms of the disease.

Multiple roles for retinoid signaling in craniofacial development

Retinoic acid (RA) signaling plays multiple essential roles in development of the head and face. Animal models with mutations in genes involved in RA signaling have enabled understanding of craniofacial morphogenic processes that are regulated by the retinoid pathway. During craniofacial morphogenesis RA signaling is active in spatially restricted domains defined by the expression of genes involved in RA production and RA breakdown. The spatial distribution of RA signaling changes with progressive development, corresponding to a multiplicity of craniofacial developmental processes that are regulated by RA. One important role of RA signaling occurs in the hindbrain. There RA contributes to specification of the anterior-posterior (AP) axis of the developing CNS and to the neural crest cells (NCC) which form the bones and nerves of the face and pharyngeal region. In the optic vesicles and frontonasal process RA orchestrates development of the midface, eyes, and nasal airway. Additional roles for RA in craniofacial development include regulation of submandibular salivary gland development and maintaining patency in the sutures of the cranial vault.

The circular RNA expression profile of human auricle cartilage and the role of circCOL1A2 in isolated microtia

Microtia is one of the most common craniofacial birth defects worldwide, and its primary clinical manifestation is auricle deformity. Epigenetic factors are known to contribute to the etiology of microtia, yet the involvement of circular RNAs (circRNAs) in human auricle development and their association with microtia remains poorly understood. In this study, we aimed to analyze differentially expressed circRNAs and explore their functional implications in isolated microtia. By employing circRNA microarray analysis and bioinformatics approaches, we identified 340 differentially expressed circRNAs in auricle cartilage of patients with isolated microtia, comprising 152 upregulated and 188 downregulated circRNAs. A circRNA-mRNA co-expression network was constructed, followed by gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Subsequently, we selected four significantly upregulated circRNAs from the co-expression network based on their association with cartilage development and validated their expressions in 30 isolated microtia and 30 control clinical auricle cartilage samples. Among these circRNAs, circCOL1A2, the most significantly upregulated circRNA, was selected as a representative circRNA for investigating its role in isolated microtia. Overexpression of circCOL1A2 significantly inhibited chondrocyte proliferation and chondrogenic differentiation of human mesenchymal stem cells. Additionally, circCOL1A2 upregulated Dermatan Sulfate Epimerase Like (DSEL) expression by sponging miR-637 through the competing endogenous RNA (ceRNA) mechanism. Notably, the downregulation of DSEL attenuated the inhibitory effect of circCOL1A2 overexpression on cell proliferation and chondrogenic differentiation. Collectively, these findings highlight the involvement of circCOL1A2 in the pathogenesis of isolated microtia and emphasize the potential significance of dysregulated circRNAs in disease development.

Role of HOXA1-4 in the development of genetic and malignant diseases

The HOXA genes, belonging to the HOX family, encompass 11 members (HOXA1-11) and exert critical functions in early embryonic development, as well as various adult processes. Furthermore, dysregulation of HOXA genes is implicated in genetic diseases, heart disease, and various cancers. In this comprehensive overview, we primarily focused on the HOXA1-4 genes and their associated functions and diseases. Emphasis was placed on elucidating the impact of abnormal expression of these genes and highlighting their significance in maintaining optimal health and their involvement in the development of genetic and malignant diseases. Furthermore, we delved into their regulatory mechanisms, functional roles, and underlying biology and explored the therapeutic potential of targeting HOXA1-4 genes for the treatment of malignancies. Additionally, we explored the utility of HOXA1-4 genes as biomarkers for monitoring cancer recurrence and metastasis.

Pathogenic Genes for Congenital Microtia: A Bioinformatics Analysis

OBJECTIVE

The purpose of this study is to accurately find the pathogenic genes of congenital microtia, so as to lay a theoretical foundation for genetic screening, diagnosis, and gene therapy of congenital microtia in the further stage.

METHODS

In this study, the authors used public data from the Mouse Genome Informatics database. The authors used the String database ( https://string-db.org/ ) to construct the Protein-Protein Interaction network. Then Gene Ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed for the pathogenic genes.

RESULTS

The authors searched the Mouse Genome Informatics database and found 84 pathogenic genes of congenital microtia. The Protein-Protein Interaction network for pathogenic genes was constructed, which contained 81 nodes and 148 lines with MCM5, CDT1, POLA1, CDC45, CDC6, EFTUD2, ORC1, ORC4, ORC6, and TCOF1 . The authors conducted a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on pathogenic genes, and the results showed that pathogenic genes were involved in O-mannan biosynthesis, cell cycle, RNA polymerase, and other signaling pathways.

CONCLUSIONS

The authors' results indicated that the occurrence of congenital microtia is attributed to a variety of genes. Furthermore, the interactions of pathogenic genes were further elucidated by using a bioinformatics approach. This study will help to reveal the pathogenesis of congenital microtia and lay the foundation for accurate diagnosis and treatment of congenital microtia in the future.

Effect of Cadherin-11 on the Proliferation, Migration, and ECM Synthesis of Chondrocyte

Nonsyndromic microtia is a kind of congenital ear malformation with unclear pathogenic genes. Cadherin-11 (CDH11, OB-cadherin) is a member of the cadherin family, which has been demonstrated to play important roles in controlling morphogenesis and cell biological characteristics during multiple developmental processes. In the present study, we found low expression of CDH11 in microtia cartilage compared with the normal one for the first time. For a more comprehensive and in-depth understanding of CDH11 in microtia development, we performed both gain- and loss-of-function experiments to detect the effect of CDH11 on chondrocytes. CDH11 promoted chondrocyte proliferation by increasing S-phase cell numbers and increasing cell migration, which is important for tissue morphogenesis. Additionally, knockdown of CDH11 in chondrocytes reduced the quality of engineered cartilage by decreasing the key transcription factors of chondrogenesis, SOX9 expression, and cartilage ECM production, including collagen type II (COL2A) and elastin (ELN), compared to the control group. Furthermore, RNA-Seq on CDH11 knockdown chondrocytes showed that it was highly related to HOX family genes, which have been reported to be important regulatory genes patterning craniofacial tissue formation. This study identified CDH11 as a candidate pathogenic gene of microtia and supported the potential key role of CDH11 in craniofacial malformations.

Functional Pathway and Process Enrichment Analysis of Genes Associated With Morphological Abnormalities of the Outer Ear

Congenital anomalies of the outer ear are common birth defects, including a variety of congenital deformities or malformations ranging from mild structural anomalies to total absence of the ear. Despite its high incidence and detrimental impact on patients, the etiology of outer ear abnormalities remains poorly understood. The goal of this study was to summarize the related genes and improve our understanding of the genetic etiology of morphological abnormalities of the outer ear. Human Phenotype Ontology (HPO) database, Mouse Genome Informatics (MGI) database, and PubMed search engine were used to acquire the genes associated with abnormal human or mouse outer ear. Metascape was employed on the genes above to conduct functional annotation, pathway and process enrichment analysis, protein-protein interaction network analysis, and MCODE component analysis. After a comprehensive review of the databases and literature, we identified 394 human genes and 148 mouse genes that have been associated with abnormal phenotypes of the outer ear, and we identified several biological pathways for human and mouse respectively. Especially, the analysis of common genes shared by human and mouse emphasized the importance of certain genes ( PAX6 , PBX1 , HOXA1 , HOXA2 , TBX1 , TBX15 , PRRX1 , and HMX1 ) in the embryonic development of the external ear. Through our analysis of genes associated with morphological abnormalities of the outer ear, the authors have shown that embryonic development pathways take important roles in the morphogenesis of abnormal external ear and highlighted some potential genetic drivers.

Transcriptome sequencing of facial adipose tissue reveals alterations in mRNAs of hemifacial microsomia

Hemifacial microsomia (HFM) is a common congenital malformation of the craniofacial region, including mandibular hypoplasia, microtia, facial palsy and soft tissue deficiencies. However, it remains unclear which specific genes are involved in the pathogenesis of HFM. By identifying differentially expressed genes (DEGs) in deficient facial adipose tissue from HFM patients, we hope to provide a new insight into disease mechanisms from the transcriptome perspective. RNA sequencing (RNA-Seq) was performed with 10 facial adipose tissues from patients of HFM and healthy controls. Differentially expressed genes in HFM were validated by quantitative real-time PCR (qPCR). Functional annotations of the DEGs were analyzed with DESeq2 R package (1.20.0). A total of 1,244 genes were identified as DEGs between HFM patients and matched controls. Bioinformatic analysis predicted that the increased expression of HOXB2 and HAND2 were associated with facial deformity of HFM. Knockdown and overexpression of HOXB2 were achieved with lentiviral vectors. Cell proliferation, migration, and invasion assay was performed with adipose-derived stem cells (ADSC) to confirm the phenotype of HOXB2. We also found that PI3K-Akt signaling pathway and human papillomavirus infection were activated in HFM. In conclusion, we discovered potential genes, pathways and networks in HFM facial adipose tissue, which contributes to a better understanding of the pathogenesis of HFM.

The Enigmatic Etiology of Oculo-Auriculo-Vertebral Spectrum (OAVS): An Exploratory Gene Variant Interaction Approach in Candidate Genes

The clinical diagnosis of oculo-auriculo-vertebral spectrum (OAVS) is established when microtia is present in association with hemifacial hypoplasia (HH) and/or ocular, vertebral, and/or renal malformations. Genetic and non-genetic factors have been associated with microtia/OAVS. Although the etiology remains unknown in most patients, some cases may have an autosomal dominant, autosomal recessive, or multifactorial inheritance. Among the possible genetic factors, gene−gene interactions may play important roles in the etiology of complex diseases, but the literature lacks related reports in OAVS patients. Therefore, we performed a gene−variant interaction analysis within five microtia/OAVS candidate genes (HOXA2, TCOF1, SALL1, EYA1 and TBX1) in 49 unrelated OAVS Mexican patients (25 familial and 24 sporadic cases). A statistically significant intergenic interaction (p-value < 0.001) was identified between variants p.(Pro1099Arg) TCOF1 (rs1136103) and p.(Leu858=) SALL1 (rs1965024). This intergenic interaction may suggest that the products of these genes could participate in pathways related to craniofacial alterations, such as the retinoic acid (RA) pathway. The absence of clearly pathogenic variants in any of the analyzed genes does not support a monogenic etiology for microtia/OAVS involving these genes in our patients. Our findings could suggest that in addition to high-throughput genomic approaches, future gene−gene interaction analyses could contribute to improving our understanding of the etiology of microtia/OAVS.

Maternal haemoglobin levels in pregnancy and child DNA methylation: a study in the pregnancy and childhood epigenetics consortium

Altered maternal haemoglobin levels during pregnancy are associated with pre-clinical and clinical conditions affecting the fetus. Evidence from animal models suggests that these associations may be partially explained by differential DNA methylation in the newborn with possible long-term consequences. To test this in humans, we meta-analyzed the epigenome-wide associations of maternal haemoglobin levels during pregnancy with offspring DNA methylation in 3,967 newborn cord blood and 1,534 children and 1,962 adolescent whole-blood samples derived from 10 cohorts. DNA methylation was measured using Illumina Infinium Methylation 450K or MethylationEPIC arrays covering 450,000 and 850,000 methylation sites, respectively. There was no statistical support for the association of maternal haemoglobin levels with offspring DNA methylation either at individual methylation sites or clustered in regions. For most participants, maternal haemoglobin levels were within the normal range in the current study, whereas adverse perinatal outcomes often arise at the extremes. Thus, this study does not rule out the possibility that associations with offspring DNA methylation might be seen in studies with more extreme maternal haemoglobin levels.

Heterogeneity of Accompanying Phenotypes and Genomic Variants Involved in Microtia

OBJECTIVES

The symptoms associated with microtia are ever-changing and not to stick to 1 pattern. The symptoms associated with microtia are constantly changing and are not set in stone. The aim of this article was to describe the various phenotypes from multiple systems found in microtitis patients included in the DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources database, and to analyze possible pathogenic mutations.

METHODS

DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources is an interactive web-based database, which incorporates a suite of tools designed to aid the interpretation of genomic variants. The term "microtia" was used as the search term, and the data extracted from the DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources for this study was updated until October 2020. Pearson chi-squared test was used to test associations between types of genomic variants and the pathogenicity of variants.

RESULTS

Of the 386 cases enrolled in the study, 99% (n = 382) had 1 or more associated abnormalities. The most frequently detected abnormalities were those of the face and neck (n = 362 [93.8% of all cases]); musculoskeletal system (n = 337 [87.3%]); and nervous system (n = 334 [86.5%]), followed by abnormalities of limbs (n = 252 [65.3%]); the eye (n = 212 [54.9%]); and the integument (n = 200 [51.8%]). Besides, a total of 479 genomic variants were determined, including sequence variants and copy number variants (loss and gain). The pathogenicity of loss-type variants was significantly higher among other types (P < 0.001). Twelve sharing variants had more than 5 repeats, and the repeated fragments were concentrated on chromosome 3, 7, 9, 10, 11, 15, 17, 18, and 22.

CONCLUSIONS

Identification of the relation between phenotypes and genotypes will facilitate the uncovering of the mechanism of microtia and the study of potential therapeutic targets.