Identification of sequence variants associated with severe microtia-astresia by targeted sequencing

Dachsous cadherin related 1 (DCHS1) is a novel biomarker for immune infiltration and epithelial-mesenchymal transition in endometrial cancer via pan-cancer analysis

BACKGROUND

Dachsous cadherin related 1 (DCHS1) is one of calcium-dependent adhesion membrane proteins and is mainly involved in the development of mammalian tissues. There is a lack of more detailed research on the biological function of DCHS1 in pan-cancer.

MATERIALS AND METHODS

We evaluated the expression, the prognostic value, the diagnostic value and genomic alterations of DCHS1 by using the databases, including TCGA, UALCAN, HPA, GEPIA2.0 and GSCA. We employed the databases of UCSC, TIMER2.0, TISIDB, GSCA to analyze the association between DCHS1 expression and the immune microenvironment, stemness, TMB, MSI and anticancer drug sensitivity. BioGRID, STRING and GEPIA2.0 were used to perform protein interaction and functional enrichment analysis. Real-time quantitative PCR, CCK8, Transwell assay and Western blot were performed to determine the function of DCHS1 in UCEC.

RESULTS

DCHS1 is differentially expressed in many cancers and its expression is significantly associated with tumor prognosis and diagnosis. DCHS1 expression was significantly correlated with the infiltration of cancer-associated fibroblasts (CAFs), Endothelial cell (ECs), and Hematopoietic stem cell in most cancers. In addition, DCHS1 was significantly associated with sensitivity to many antitumor drugs. Functional enrichment analysis revealed that DCHS1-related proteins were involved in Focal adhesion, Endometrial cancer and Wnt signaling pathway. GSEA results showed that DCHS1 was related to epithelial-mesenchymal transition (EMT) in many cancers. In vitro experiments in UCEC showed that DCHS1 regulated cell proliferation, migration and EMT.

CONCLUSIONS

Our findings indicated that DCHS1 might be a novel prognostic and diagnostic biomarker and immunotherapy target, and plays an important role in the proliferation, migration and EMT in UCEC.

Clinical profiling of pediatric microtia patients: A cross-sectional analysis at a leading pediatric hospital in Ecuador (2015-2022)

BACKGROUND

Microtia is a frequent congenital deformity of the pinna, often with hearing loss. This study reviews the clinical profiles of microtia pediatric patients treated at a referral hospital in Quito, Ecuador, from 2015 to 2022.

METHODS

A cross-sectional descriptive study was carried out based on the analysis of medical records of pediatric patients with microtia treated between January 2015 and December 2022 at the Hospital Pediátrico Baca Ortiz in Quito, Ecuador. Descriptive statistics were used, and the Chi-square test assessed associations between categorical variables.

RESULTS

Of the 235 patients evaluated, 59.6% were male, 83.4% lived at high altitudes (2500-3500 m), and 19.1% had a family history of microtia. Grade III microtia was diagnosed in 63.8%, predominantly on the right side. Nearly all (99.1%) had hearing loss. Other anatomical alterations were observed in 27.7%, primarily the preauricular appendage. Bone vibrator implantation was a common treatment for 24.3%. Altitude did not show a significant correlation with microtia characteristics.

CONCLUSIONS

Most patients had grade III microtia with associated hearing loss. Despite the high prevalence at elevated altitudes, no significant altitude-disease correlation was found. The study highlights the need for further research on microtia in regions like Ecuador.

Genetic spectrums and clinical profiles of critically ill neonates with congenital auricular deformity in the China Neonatal Genomes Project

Congenital auricular deformity (CAD) is a complex phenotype that may occur as a single malformation or part of a congenital syndrome. The genetic architecture and utility of next-generation sequencing (NGS) in a sizable cross-sectional study of critically ill neonates with CAD have not yet been systematically investigated. This cross-sectional study investigated the genetic spectrum in critically ill neonates with CADs. Critically ill neonates with CADs (n = 251) were enrolled between August 8, 2016 and October 1, 2022. All neonates underwent NGS. The outcomes were molecular diagnostic yield, spectrum of genetic events, and clinical findings. Genetic findings were obtained in 107 neonates (42.6%), of which 67.3% (72/107) had pathogenic/likely pathogenic/variants of uncertain significance (P/LP/VUS) gene variations and 32.7% (35/107) had P/LP/VUS copy number variations (CNVs). The diagnostic rates of clinical exome sequencing were similar to those of exome sequencing. The logistic regression model revealed that CAD neonates with craniofacial abnormalities (OR = 4.15, 95% CI 2.29-7.53) or cardiovascular malformation (OR = 2.09, 95% CI 1.14-3.84) are more likely to be attributed to genetic causes. Follow-up analysis revealed that, compared to those in the undiagnosed group, the number of neonates whose care was withdrawn or who died was higher in the genetically diagnosed group (P < 0.05). This study identified a high incidence of genetic causes in critically ill neonates with CADs, with a combination of single-nucleotide variations and CNVs among the genetic causes of CAD. These findings highlight potential of NGS in the genetic testing of critically ill neonates with CADs.

Risk factors for, and genetic association with, intestinal atresia in dairy calves

Intestinal atresia is an under-diagnosed congenital defect in cattle. It results in complete occlusion of the intestinal lumen and, unless surgically corrected, results in death or euthanasia of the affected calf. There is limited information on the incidence of this condition or on risk factors, including predisposing alleles, associated with the defect. In this study, active surveillance of 39 dairy farms over 8 years identified 197 cases of intestinal atresia among 56 454 calves born, an incidence of 0.35%. The majority of cases (83%) had occlusion of the jejunum, although cases with blockage of the colon (14%) or anus (4%) were also identified. The defect was twice as common in male as in female calves (p < 0.0001), and was more common in progeny of older cows than in progeny of first or second lactation cows (p < 0.001). Year and farm of birth were also significantly associated with incidence (p < 0.05). The incidence of intestinal atresia was highest among the progeny of three related Jersey sires, suggesting that a gene for intestinal atresia was segregating within this family. Linkage analysis utilising 28 affected progeny of two half-sib putative carrier sires identified two putative quantitative trait loci associated with the defect, on chromosomes 14 and 26, although no clear candidate genes were identified. There was no evidence of a sire-effect among the progeny of Holstein-Friesian sires. However, a case-control genome-wide association study involving 91 cases and 375 healthy controls, identified 31 SNP in 18 loci as associated with the defect in this breed. These data suggest that intestinal atresia in dairy calves is not a simple Mendelian trait as previously reported but a complex multigenic disorder.

Patterns of co-occurring birth defects in children with anotia and microtia

Many infants with anotia or microtia (A/M) have co-occurring birth defects, although few receive syndromic diagnoses in the perinatal period. Evaluation of co-occurring birth defects in children with A/M could identify patterns indicative of undiagnosed/unrecognized syndromes. We obtained information on co-occurring birth defects among infants with A/M for delivery years 1999-2014 from the Texas Birth Defects Registry. We calculated observed-to-expected ratios (OER) to identify birth defect combinations that occurred more often than expected by chance. We excluded children diagnosed with genetic or chromosomal syndromes from analyses. Birth defects and syndromes/associations diagnosed ≤1 year of age were considered. We identified 1310 infants with non-syndromic A/M, of whom 38% (N = 492) were diagnosed with co-occurring major defects. Top combinations included: hydrocephalus, ventricular septal defect, and spinal anomalies (OER 58.4); microphthalmia and anomalies of the aorta (OER 55.4); and cleft lip with or without cleft palate and rib or sternum anomalies (OER 32.8). Some combinations observed in our study may represent undiagnosed/atypical presentations of known A/M associations or syndromes, or novel syndromes yet to be described in the literature. Careful evaluation of infants with multiple birth defects including A/M is warranted to identify individuals with potential genetic or chromosomal syndromes.

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.

The genes for sensory perception of sound should be considered in gene diagnosis of congenital sensorineural hearing loss and microtia

Congenital sensorineural hearing loss (CSHL) and microtia are development-related diseases, sharing some factors and affecting children's hearing. However, genetic tests only focus on CSHL. We try to identify the common molecular mechanism of CSHL and microtia as candidates combining gene diagnosis biomarkers. Whole-exon sequencing (WES), Sanger sequencing, qPCR, and bioinformatics analyses were performed in microtia family (F1), family two, whose proband suffered from microtia and CSHL (F2), five microtia, and four CSHL individuals, respectively. We found that 40% microtia and 40% CSHL relevant genes were detected in F1 and a sharing pathway: the sensory perception of sound was identified. Moreover, the copy number variation in proband F2 was identified in one gene of the sharing pathway: EYA1. Meanwhile, two variants of BUB3 were identified in F1 data. BUB3 is related to development, dog ear type, direct and indirect interaction with microtia, and CSHL relevant genes. Notably, although the allele frequency of two variants of BUB3 showed significant differences between microtia and CSHL, the special microtia-relevant genotype also could be detected in one CSHL sample. These results suggest that the sensory perception of sound and the development of relevant pathways may be the common pathways of microtia and CSHL. Genes of these pathways can be used as candidates combining gene diagnosis biomarkers.

Whole-Exome Sequencing of Discordant Monozygotic Twin Families for Identification of Candidate Genes for Microtia-Atresia

Objective

We used data from twins and their families to probe the genetic factors contributing to microtia-atresia, in particular, early post-twinning variations that potentially account for the discordant phenotypes of monozygotic twin pairs.

Methods

Six families of monozygotic twins discordant for congenital microtia-atresia were recruited for study. The six patients shared a consistent clinical phenotype of unilateral microtia-atresia. Whole-exome sequencing (WES) was performed for all six twin pairs and their parents. Family segregation and multiple bioinformatics methods were applied to identify suspicious mutations in all families. Recurring mutations commonly detected in at least two families were highlighted. All variants were validated via Sanger sequencing. Gene Ontology (GO) analysis was performed to identify candidate gene sets and related pathways. Copy number variation (CNV), linkage analysis, association analysis and machine learning methods were additionally applied to isolate candidate mutations, and comparative genomics and structural modeling tools used to evaluate their potential roles in onset of microtia-atresia.

Results

Our analyses revealed 61 genes with suspected mutations associated with microtia-atresia. Five (HOXA4, MUC6, CHST15, TBX10, and AMER1) contained 7 de novo mutations that appeared in at least two families, which have been previously reported as pathogenic for other diseases. Among these, HOXA4 (c.920A>C, p.H307P) was determined as the most likely pathogenic variant for microtia-atresia. GO analysis revealed four gene sets involving 11 pathways potentially related to underlying pathogenesis of the disease. CNVs in three genes (UGT2B17, OVOS, and KATNAL2) were detected in at least two families. Linkage analysis disclosed 13 extra markers for the disease, of which two (FGFR1 and EYA1) were validated via machine learning analysis as plausible candidate genes for the disease.

Conclusion

Based on comprehensive genetic and bioinformatic analyses of WES data from six families of discordant monozygotic twins with microtia-atresia, we identified multiple candidate genes that may function in post-twinning onset of the disease. The collective findings provide novel insights into the pathogenesis of congenital microtia-atresia.