Mapping genetic variants for cranial vault shape in humans

Unsupervised ensemble-based phenotyping enhances discoverability of genes related to left-ventricular morphology

Recent genome-wide association studies have successfully identified associations between genetic variants and simple cardiac morphological parameters derived from cardiac magnetic resonance images. However, the emergence of large databases, including genetic data linked to cardiac magnetic resonance facilitates the investigation of more nuanced patterns of cardiac shape variability than those studied so far. Here we propose a framework for gene discovery coined unsupervised phenotype ensembles. The unsupervised phenotype ensemble builds a redundant yet highly expressive representation by pooling a set of phenotypes learnt in an unsupervised manner, using deep learning models trained with different hyperparameters. These phenotypes are then analysed via genome-wide association studies, retaining only highly confident and stable associations across the ensemble. We applied our approach to the UK Biobank database to extract geometric features of the left ventricle from image-derived three-dimensional meshes. We demonstrate that our approach greatly improves the discoverability of genes that influence left ventricle shape, identifying 49 loci with study-wide significance and 25 with suggestive significance. We argue that our approach would enable more extensive discovery of gene associations with image-derived phenotypes for other organs or image modalities.

Joint multi-ancestry and admixed GWAS reveals the complex genetics behind human cranial vault shape

The cranial vault in humans is highly variable, clinically relevant, and heritable, yet its genetic architecture remains poorly understood. Here, we conduct a joint multi-ancestry and admixed multivariate genome-wide association study on 3D cranial vault shape extracted from magnetic resonance images of 6772 children from the ABCD study cohort yielding 30 genome-wide significant loci. Follow-up analyses indicate that these loci overlap with genomic risk loci for sagittal craniosynostosis, show elevated activity cranial neural crest cells, are enriched for processes related to skeletal development, and are shared with the face and brain. We present supporting evidence of regional localization for several of the identified genes based on expression patterns in the cranial vault bones of E15.5 mice. Overall, our study provides a comprehensive overview of the genetics underlying normal-range cranial vault shape and its relevance for understanding modern human craniofacial diversity and the etiology of congenital malformations.

Identification of 4 New Loci Associated With Primary Hyperparathyroidism (PHPT) and a Polygenic Risk Score for PHPT

CONTEXT

A hypothesis-free genetic association analysis has not been reported for patients with primary hyperparathyroidism (PHPT).

OBJECTIVE

We aimed to investigate genetic associations with PHPT using both genome-wide association study (GWAS) and candidate gene approaches.

METHODS

A cross-sectional study was conducted among patients of European White ethnicity recruited in Tayside (Scotland, UK). Electronic medical records were used to identify PHPT cases and controls, and linked to genetic biobank data. Genetic associations were performed by logistic regression models and odds ratios (ORs). The combined effect of the genotypes was researched by genetic risk score (GRS) analysis.

RESULTS

We identified 15 622 individuals for the GWAS that yielded 34 top single-nucleotide variations (formerly single-nucleotide polymorphisms), and LPAR3-rs147672681 reached genome-wide statistical significance (P = 1.2e-08). Using a more restricted PHPT definition, 8722 individuals with data on the GWAS-identified loci were found. Age- and sex-adjusted ORs for the effect alleles of SOX9-rs11656269, SLITRK5-rs185436526, and BCDIN3D-AS1-rs2045094 showed statistically significant increased risks (P < 1.5e-03). GRS analysis of 5482 individuals showed an OR of 2.51 (P = 1.6e-04), 3.78 (P = 4.0e-08), and 7.71 (P = 5.3e-17) for the second, third, and fourth quartiles, respectively, compared to the first, and there was a statistically significant linear trend across quartiles (P < 1.0e-04). Results were similar when stratifying by sex.

CONCLUSION

Using genetic loci discovered in a GWAS of PHPT carried out in a Scottish population, this study suggests new evidence for the involvement of genetic variants at SOX9, SLITRK5, LPAR3, and BCDIN3D-AS1. It also suggests that male and female carriers of greater numbers of PHPT-risk alleles both have a statistically significant increased risk of PHPT.

Cranium growth, patterning and homeostasis

Craniofacial development requires precise spatiotemporal regulation of multiple signaling pathways that crosstalk to coordinate the growth and patterning of the skull with surrounding tissues. Recent insights into these signaling pathways and previously uncharacterized progenitor cell populations have refined our understanding of skull patterning, bone mineralization and tissue homeostasis. Here, we touch upon classical studies and recent advances with an emphasis on developmental and signaling mechanisms that regulate the osteoblast lineage for the calvaria, which forms the roof of the skull. We highlight studies that illustrate the roles of osteoprogenitor cells and cranial suture-derived stem cells for proper calvarial growth and homeostasis. We also discuss genes and signaling pathways that control suture patency and highlight how perturbing the molecular regulation of these pathways leads to craniosynostosis. Finally, we discuss the recently discovered tissue and signaling interactions that integrate skull and cerebrovascular development, and the potential implications for both cerebrospinal fluid hydrodynamics and brain waste clearance in craniosynostosis.

Global patterns of the cranial form of modern human populations described by analysis of a 3D surface homologous model

This study assessed the regional diversity of the human cranial form by using geometric homologous models based on scanned data from 148 ethnic groups worldwide. This method adopted a template-fitting technique for a nonrigid transformation via the iterative closest point algorithm to generate the homologous meshes. Through the application of principal component analysis to 342 sampled homologous models, the largest variation was detected in overall size, and small South Asian crania were clearly verified. The next greatest diversity was found in the length/breadth proportion of the neurocranium, which showed the contrast between the elongated crania of Africans and the globular crania of Northeast Asians. Notably, this component was slightly correlated with the facial profile. Well-known facial features, such as the forward projection of the cheek among Northeast Asians and compaction of the European maxilla, were reconfirmed. These facial variations were highly correlated with the calvarial outline, particularly the degree of frontal and occipital inclines. An allometric pattern was detected in facial proportions in relation to overall cranial size; in larger crania, the facial profiles tend to be longer and narrower, as demonstrated among many American natives and Northeast Asians. Although our study did not include data on environmental variables that are likely to affect cranial morphology, such as climate or dietary conditions, the large datasets of homologous cranial models will be usefully available for seeking various attributions to phenotypic skeletal characteristics.

Interrater and Intrarater Reliability of Cranial Anthropometric Measurements in Infants with Positional Plagiocephaly

(1) Background: anthropometric measurements with calipers are used to objectify cranial asymmetry in positional plagiocephaly but there is controversy regarding the reliability of different methodologies. Purpose: to analyze the interrater and intrarater reliability of direct anthropometric measurements with caliper on defined craniofacial references in infants with positional plagiocephaly. (2) Methods: 62 subjects (<28 weeks), with a difference of at least 5 mm between cranial diagonal diameters. Maximal cranial circumference, length and width and diagonal cranial diameters were measured. Intrarater (2 measurements) and interrater (2 raters) reliability was analyzed. (3) Results: intra- and interrater reliability of the maximal cranial length and width and right cranial diagonal was excellent: intraclass correlation coefficient (ICC) > 0.9. Intrarater and interrater reliability for the left cranial diagonal was excellent: ICC > 0.9 and difference in agreement in the Bland-Altman plot 0.0 mm, respectively. Intrarater and interrater reliability for the maximal cranial circumference was good: differences in agreement in Bland-Altman plots: intra: −0.03 cm; inter: −0.12 cm. (4) Conclusions: anthropometric measurements in a sample of infants with moderate positional plagiocephaly have shown excellent intra- and interrater reliability for maximal cranial length, maximal cranial width, and right and left cranial diagonals, and good intra- and interrater reliability in maximal cranial circumference measurement.

Functional Diversification of SRSF Protein Kinase to Control Ubiquitin-Dependent Neurodevelopmental Signaling

Conserved protein kinases with core cellular functions have been frequently redeployed during metazoan evolution to regulate specialized developmental processes. The Ser/Arg (SR)-rich splicing factor (SRSF) protein kinase (SRPK), which is implicated in splicing regulation, is one such conserved eukaryotic kinase. Surprisingly, we show that SRPK has acquired the capacity to control a neurodevelopmental ubiquitin signaling pathway. In mammalian embryonic stem cells and cultured neurons, SRPK phosphorylates Ser-Arg motifs in RNF12/RLIM, a key developmental E3 ubiquitin ligase that is mutated in an intellectual disability syndrome. Processive phosphorylation by SRPK stimulates RNF12-dependent ubiquitylation of nuclear transcription factor substrates, thereby acting to restrain a neural gene expression program that is aberrantly expressed in intellectual disability. SRPK family genes are also mutated in intellectual disability disorders, and patient-derived SRPK point mutations impair RNF12 phosphorylation. Our data reveal unappreciated functional diversification of SRPK to regulate ubiquitin signaling that ensures correct regulation of neurodevelopmental gene expression.

Relationship of COL9A1 and SOX9 Genes with Genetic Susceptibility of Postmenopausal Osteoporosis

As one of the most common types of osteoporosis, postmenopausal osteoporosis (PMOP) is caused by both genetic and environmental factors. Previous studies have indicated that SOX9 activity is tightly regulated to ensure normal bone mineral density (BMD) in the adult skeleton, and the COL9A1 promoter region can be transactivated by SOX9. In this study, we aimed to investigate the potential association between PMOP and the COL9A1 and SOX9 genes. A total of 10,443 postmenopausal women, including 2288 patients and 3557 controls in the discovery stage and 1566 patients and 3032 controls in the validation stage, were recruited. Forty-three tag SNPs (36 in COL9A1 and 7 in SOX9) were selected for genotyping to evaluate the association of the SOX9 gene with PMOP and BMD. Association and bioinformatics analyses were performed for PMOP. BMD and serum level of SOX9 were also utilized as quantitative phenotypes in further analyses. SNP rs73354570 of SOX9 was significantly associated with PMOP in both discovery stages (OR 1.24 [1.10-1.39], P = 3.56 × 10^-4, χ² = 12.75) and combined samples (OR 1.25 [1.15-1.37], P = 5.25 × 10^-7, χ² = 25.17). Further analyses showed that the SNP was also significantly associated with BMD and serum levels of the SOX9 protein. Our results provide further supportive evidence for the association of the SOX9 gene with PMOP and of the SOX9 gene with the variation of BMD in postmenopausal Han Chinese women. This study supports a role for SOX9 in the etiology of PMOP, adding to the current understanding of the susceptibility of osteoporosis.

Genome-wide association study of inhaled corticosteroid response in admixed children with asthma

BACKGROUND

Inhaled corticosteroids (ICS) are the most widely prescribed and effective medication to control asthma symptoms and exacerbations. However, many children still have asthma exacerbations despite treatment, particularly in admixed populations, such as Puerto Ricans and African Americans. A few genome-wide association studies (GWAS) have been performed in European and Asian populations, and they have demonstrated the importance of the genetic component in ICS response.

OBJECTIVE

We aimed to identify genetic variants associated with asthma exacerbations in admixed children treated with ICS and to validate previous GWAS findings.

METHODS

A meta-analysis of two GWAS of asthma exacerbations was performed in 1347 admixed children treated with ICS (Hispanics/Latinos and African Americans), analysing 8.7 million genetic variants. Those with P ≤ 5 × 10^-6 were followed up for replication in 1697 asthmatic patients from six European studies. Associations of ICS response described in published GWAS were followed up for replication in the admixed populations.

RESULTS

A total of 15 independent variants were suggestively associated with asthma exacerbations in admixed populations (P ≤ 5 × 10^-6 ). One of them, located in the intergenic region of APOBEC3B and APOBEC3C, showed evidence of replication in Europeans (rs5995653, P = 7.52 × 10^-3 ) and was also associated with change in lung function after treatment with ICS (P = 4.91 × 10^-3 ). Additionally, the reported association of the L3MBTL4-ARHGAP28 genomic region was confirmed in admixed populations, although a different variant was identified.

CONCLUSIONS AND CLINICAL RELEVANCE

This study revealed the novel association of APOBEC3B and APOBEC3C with asthma exacerbations in children treated with ICS and replicated previously identified genomic regions. This contributes to the current knowledge about the multiple genetic markers determining responsiveness to ICS which could lead in the future the clinical identification of those asthma patients who are not able to respond to such treatment.