Copy-number variant analysis of classic heterotaxy highlights the importance of body patterning pathways

Notch3 is an asymmetric gene and a modifier of heart looping defects in Nodal mouse mutants

The TGFβ secreted factor NODAL is a major left determinant required for the asymmetric morphogenesis of visceral organs, including the heart. Yet, when this signaling is absent, shape asymmetry, for example of the embryonic heart loop, is not fully abrogated, indicating that there are other factors regulating left-right patterning. Here, we used a tailored transcriptomic approach to screen for genes asymmetrically expressed in the field of heart progenitors. We thus identify Notch3 as a novel left-enriched gene and validate, by quantitative in situ hybridization, its transient asymmetry in the lateral plate mesoderm and node crown, overlapping with Nodal. In mutant embryos, we analyzed the regulatory hierarchy and demonstrate that Nodal in the lateral plate mesoderm amplifies Notch3 asymmetric expression. The function of Notch3 was uncovered in an allelic series of mutants. In single neonate mutants, we observe that Notch3 is required with partial penetrance for ventricle thickness, septation and aortic valve, in addition to its known role in coronary arteries. In compound mutants, we reveal that Notch3 acts as a genetic modifier of heart looping direction and shape defects in Nodal mutants. Whereas Notch3 was previously mainly associated with the CADASIL syndrome, our observations in the mouse and a human cohort support a novel role in congenital heart defects and laterality defects.

Application of copy number variation sequencing combined with whole exome sequencing in prenatal left-right asymmetry disorders

BACKGROUND

Left-right (LR) asymmetry disorders present a complex etiology, with genetic factors emerging as a primary contributor. This study aims to explore the genetic underpinnings of chromosomal variants and individual genes in fetuses afflicted with prenatal LR asymmetry disorder.

METHODS

Through a retrospective analysis conducted between 2020 and 2023 at Tongji Hospital, Huazhong University of Science and Technology, genetic outcomes of LR asymmetric disorder were scrutinized utilizing copy number variation sequencing (CNV-seq) and whole exome sequencing (WES) methodologies.

RESULTS

With a combination of CNV-seq and WES, 5 fetuses in 17 patients with LR asymmetry had chromosomal or genetic variants. CNV-seq revealed a 16p11.2 microdeletion syndrome in a situs inversus fetus presenting pathogenic and a 2q36.3 microduplication syndrome in a fetus with Heterotaxy presenting a variant of uncertain significance (VUS). WES identified NM_198075.4:c.755del in the LRRC56 gene and NM_001454.4:c.865_868dup in the FOXJ1 gene in two situs inversus cases, along with two variants in DNAH5 in two other fetuses. Further bioinformatics scrutiny was conducted to assess the protein structure and function prediction of these variants, ultimately indicating their potential pathogenicity.

CONCLUSION

The study highlights that fetuses with LR asymmetric disorders may have copy number variants, underscoring the significance of mutations in LRRC56 and FOXJ1 in the development of LR asymmetry disorders.

Whole genome sequencing enhances molecular diagnosis of primary ciliary dyskinesia

BACKGROUND

Primary ciliary dyskinesia (PCD) is a genetic disorder affecting motile cilia. Most cases are inherited recessively, due to variants in >50 genes that result in abnormal or absent motile cilia. This leads to chronic upper and lower airway disease, subfertility, and laterality defects. Given overlapping clinical features and genetic heterogeneity, diagnosis can be difficult and often occurs late. Of those tested an estimated 30% of genetically screened PCD patients still lack a molecular diagnosis. A molecular diagnosis allows for appropriate clinical management including prediction of phenotypic features correlated to genotype. Here, we aimed to identify how readily a genetic diagnosis could be made using whole genome sequencing (WGS) to facilitate identification of pathogenic variants in known genes as well as novel PCD candidate genes.

METHODS

WGS was used to screen for pathogenic variants in eight patients with PCD.

RESULTS

7/8 cases had homozygous or biallelic variants in DNAH5, DNAAF4 or DNAH11 classified as pathogenic or likely pathogenic. Three identified variants were deletions, ranging from 3 to 13 kb, for which WGS identified precise breakpoints, permitting confirmation by Sanger sequencing. WGS yielded identification of a de novo variant in a novel PCD gene TUBB4B.

CONCLUSION

Here, WGS uplifted genetic diagnosis of PCD by identifying structural variants and novel modes of inheritance in new candidate genes. WGS could be an important component of the PCD diagnostic toolkit, increasing molecular diagnostic yield from current (70%) levels, and enhancing our understanding of fundamental biology of motile cilia and variants in the noncoding genome.

Genomic rare variant mechanisms for congenital cardiac laterality defect: A digenic model approach

Laterality defects are defined by perturbations in the usual left-right asymmetry of organs. Due to low known genetic etiology of congenital heart disease (CHD) cases (less than 40%), we used a digenic model approach for the identification of contributing variants in known laterality defect genes (N = 115) in the exome/genome sequencing (ES/GS) data from individuals with clinically diagnosed laterality defects. The unsolved ES/GS data were analyzed from three CHD cohorts: Baylor College of Medicine-Genomics Research to Elucidate the Genetics of Rare Diseases (BCM-GREGoR; N = 247 proband ES), Gabriella Miller Kids First Pediatric Research program (Kids First; N = 158 trio GS), and Pediatric Cardiac Genomics Consortium (PCGC; N = 163 trio ES), and trans-heterozygous digenic variants were identified in 2.8% (inherited digenic variants in 0.4%), 8.2%, and 13.5% cases respectively, which was significantly higher as compared to 602 control trios provided by the 1000 Genomes Project (p = 0.001, 1.4e-07, and 8.9e-13, respectively). Trans-heterozygous digenic variants were also identified in 0.4%, and 1.4% cases with non-laterality CHD in Kids First and PCGC datasets, respectively, which was not statistically significant as compared to control trios ( p = 1, and 0.059, respectively). Altogether, in laterality cohorts, 23% of digenic pairs were in the same structural complex of motile cilia. Out of 39 unique digenic pairs in laterality CHD, 29 are more likely to be potential digenic hits as predicted by DiGePred tool. These findings provide further evidence that digenic epistatic interaction can contribute to the complex genetics of laterality defects.

Understanding laterality disorders and the left-right organizer: Insights from zebrafish

Vital internal organs display a left-right (LR) asymmetric arrangement that is established during embryonic development. Disruption of this LR asymmetry-or laterality-can result in congenital organ malformations. Situs inversus totalis (SIT) is a complete concordant reversal of internal organs that results in a low occurrence of clinical consequences. Situs ambiguous, which gives rise to Heterotaxy syndrome (HTX), is characterized by discordant development and arrangement of organs that is associated with a wide range of birth defects. The leading cause of health problems in HTX patients is a congenital heart malformation. Mutations identified in patients with laterality disorders implicate motile cilia in establishing LR asymmetry. However, the cellular and molecular mechanisms underlying SIT and HTX are not fully understood. In several vertebrates, including mouse, frog and zebrafish, motile cilia located in a "left-right organizer" (LRO) trigger conserved signaling pathways that guide asymmetric organ development. Perturbation of LRO formation and/or function in animal models recapitulates organ malformations observed in SIT and HTX patients. This provides an opportunity to use these models to investigate the embryological origins of laterality disorders. The zebrafish embryo has emerged as an important model for investigating the earliest steps of LRO development. Here, we discuss clinical characteristics of human laterality disorders, and highlight experimental results from zebrafish that provide insights into LRO biology and advance our understanding of human laterality disorders.

Prenatal diagnosis of hepatic interruption of the inferior vena cava with azygos/hemiazygos continuation without structural heart defects: A case series

OBJECTIVES

To describe fetal spectrum and echocardiographic characteristics of interrupted inferior vena cava (IIVC) with azygos/hemiazygous continuation without other structural heart defects and to evaluate its association with visceral heterotaxy and isomerism, extracardiac and genetic anomalies, and to review neonatal outcome.

METHODS

This was a retrospective study of 14 fetuses with a confirmed diagnosis of IIVC with normal intracardiac anatomy. The following variables were collected; indication for referral, gestational age at diagnosis; associated isomerism and visceral heterotaxy, heart rhythm, genetic and extracardiac abnormalities, and fetal/neonatal outcome.

RESULTS

Among 36 fetuses with IIVC, 14 cases (38.8%) had normal intracardiac anatomy. These IIVC cases correspond to 0.19% (14/7250) of all fetal cardiac examinations, and to 1.5% (14/922) of all cardiac abnormalities. Six patients had visceral abnormalities. Atrial appendage morphology was clearly depicted in three fetuses, both appendages were left. One fetus had bradyarrhythmia revealing atrial ectopic rhythm. Six fetuses did not have any concomitant cardiac or visceral abnormalities, therefore regarded as isolated. All babies were delivered at term with a good prognosis.

CONCLUSION

Our study has shown that almost half of the IIVC cases without intracardiac structural anomalies displayed other findings of isomerism while the other half was isolated benign vascular variant. Therefore, prenatal diagnosis of IIVC should prompt a comprehensive evaluation for cardiac, situs, and visceral anomalies. The outcome is favorable.

Exome hits demystified: The next frontier

Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.

Xenopus as a platform for discovery of genes relevant to human disease

Congenital birth defects result from an abnormal development of an embryo and have detrimental effects on children's health. Specifically, congenital heart malformations are a leading cause of death among pediatric patients and often require surgical interventions within the first year of life. Increased efforts to navigate the human genome provide an opportunity to discover multiple candidate genes in patients suffering from birth defects. These efforts, however, fail to provide an explanation regarding the mechanisms of disease pathogenesis and emphasize the need for an efficient platform to screen candidate genes. Xenopus is a rapid, cost effective, high-throughput vertebrate organism to model the mechanisms behind human disease. This review provides numerous examples describing the successful use of Xenopus to investigate the contribution of patient mutations to complex phenotypes including congenital heart disease and heterotaxy. Moreover, we describe a variety of unique methods that allow us to rapidly recapitulate patients' phenotypes in frogs: gene knockout and knockdown strategies, the use of fate maps for targeted manipulations, and novel imaging modalities. The combination of patient genomics data and the functional studies in Xenopus will provide necessary answers to the patients suffering from birth defects. Furthermore, it will allow for the development of better diagnostic methods to ensure early detection and intervention. Finally, with better understanding of disease pathogenesis, new treatment methods can be tailored specifically to address patient's phenotype and genotype.

Large intestine embryogenesis: Molecular pathways and related disorders (Review)

The large intestine, part of the gastrointestinal tract (GI), is composed of all three germ layers, namely the endoderm, the mesoderm and the ectoderm, forming the epithelium, the smooth muscle layers and the enteric nervous system, respectively. Since gastrulation, these layers develop simultaneously during embryogenesis, signaling to each other continuously until adult age. Two invaginations, the anterior intestinal portal (AIP) and the caudal/posterior intestinal portal (CIP), elongate and fuse, creating the primitive gut tube, which is then patterned along the antero‑posterior (AP) axis and the radial (RAD) axis in the context of left‑right (LR) asymmetry. These events lead to the formation of three distinct regions, the foregut, midgut and hindgut. All the above‑mentioned phenomena are under strict control from various molecular pathways, which are critical for the normal intestinal development and function. Specifically, the intestinal epithelium constitutes a constantly developing tissue, deriving from the progenitor stem cells at the bottom of the intestinal crypt. Epithelial differentiation strongly depends on the crosstalk with the adjacent mesoderm. Major molecular pathways that are implicated in the embryogenesis of the large intestine include the canonical and non‑canonical wingless‑related integration site (Wnt), bone morphogenetic protein (BMP), Notch and hedgehog systems. The aberrant regulation of these pathways inevitably leads to several intestinal malformation syndromes, such as atresia, stenosis, or agangliosis. Novel theories, involving the regulation and homeostasis of intestinal stem cells, suggest an embryological basis for the pathogenesis of colorectal cancer (CRC). Thus, the present review article summarizes the diverse roles of these molecular factors in intestinal embryogenesis and related disorders.

Neonatal Assessment of Infants with Heterotaxy

Heterotaxy is a generalized term for patients who have an abnormality of laterality that cannot be described as situs inversus. Infants with heterotaxy can have significant anatomic and medical complexity and require personalized, specialized care, including comprehensive anatomic assessment. Common and rare anatomic findings are reviewed by system to help guide a thorough phenotypic evaluation. General care guidelines and considerations unique to this patient population are included. Future directions for this unique patient population, particularly in light of improved neonatal survival, are discussed.

Genes and mechanisms of heterotaxy: patients drive the search

Heterotaxy, a disorder in which visceral organs, including the heart, are mispatterned along the left-right body axis, contributes to particularly severe forms of congenital heart disease that are difficult to mitigate even despite surgical advances. A higher incidence of heterotaxy among individuals with blood kinship and the existence of rare monogenic disease forms suggest the existence of a genetic component, but the genetic and phenotypic heterogeneity of the disease have rendered gene discovery challenging. Next generation genomics in patients with syndromic, but also non-syndromic and sporadic heterotaxy, have recently helped to uncover new candidate disease genes, expanding the pool of genes already identified via traditional animal studies. Further characterization of these new genes in animal models has uncovered fascinating mechanisms of left-right axis development. In this review, we will discuss recent findings on the functions of heterotaxy genes with identified patient alleles.

Rethinking what constitutes a diagnosis in the genomics era: a critical illness perspective

PURPOSE OF REVIEW

The purpose of this review is to highlight the significant advances in the testing, interpretation, and diagnosis of genetic abnormalities in critically ill children and to emphasize that pediatric intensivists are uniquely positioned to search for genetic diagnoses in these patients.

RECENT FINDINGS

Ten years following the first clinical diagnosis made through whole exome sequencing, we remain in the dark about the function of roughly 75% of our genes. However, steady advancements in molecular techniques, particularly next-generation sequencing, have spurred a rapid expansion of our understanding of the genetic underpinnings of severe congenital diseases. This has resulted in not only improved clinical diagnostics but also a greater availability of research programs actively investigating rare, undiagnosed diseases. In this background, the scarcity of clinical geneticists compels nongeneticists to familiarize themselves with the types of patients that could benefit from genetic testing, interpretations of test results as well as the available resources for these patients.

SUMMARY

When caring for seriously ill children, critical care pediatricians should actively seek the possibility of an underlying genetic cause for their patients' conditions. This is true even in instances when a child has a descriptive diagnosis without a clear underlying molecular genetic mechanism. By promoting such diagnostics, in both clinical and research settings, pediatric intensivists can advance the care of their patients, improve the quality of information provided to families, and contribute to the knowledge of broad fields in medicine.

Left-right asymmetry in heart development and disease: forming the right loop

Extensive studies have shown how bilateral symmetry of the vertebrate embryo is broken during early development, resulting in a molecular left-right bias in the mesoderm. However, how this early asymmetry drives the asymmetric morphogenesis of visceral organs remains poorly understood. The heart provides a striking model of left-right asymmetric morphogenesis, undergoing rightward looping to shape an initially linear heart tube and align cardiac chambers. Importantly, abnormal left-right patterning is associated with severe congenital heart defects, as exemplified in heterotaxy syndrome. Here, we compare the mechanisms underlying the rightward looping of the heart tube in fish, chick and mouse embryos. We propose that heart looping is not only a question of direction, but also one of fine-tuning shape. This is discussed in the context of evolutionary and clinical perspectives.

Genetic Basis for Congenital Heart Disease: Revisited: A Scientific Statement From the American Heart Association

This review provides an updated summary of the state of our knowledge of the genetic contributions to the pathogenesis of congenital heart disease. Since 2007, when the initial American Heart Association scientific statement on the genetic basis of congenital heart disease was published, new genomic techniques have become widely available that have dramatically changed our understanding of the causes of congenital heart disease and, clinically, have allowed more accurate definition of the pathogeneses of congenital heart disease in patients of all ages and even prenatally. Information is presented on new molecular testing techniques and their application to congenital heart disease, both isolated and associated with other congenital anomalies or syndromes. Recent advances in the understanding of copy number variants, syndromes, RASopathies, and heterotaxy/ciliopathies are provided. Insights into new research with congenital heart disease models, including genetically manipulated animals such as mice, chicks, and zebrafish, as well as human induced pluripotent stem cell-based approaches are provided to allow an understanding of how future research breakthroughs for congenital heart disease are likely to happen. It is anticipated that this review will provide a large range of health care-related personnel, including pediatric cardiologists, pediatricians, adult cardiologists, thoracic surgeons, obstetricians, geneticists, genetic counselors, and other related clinicians, timely information on the genetic aspects of congenital heart disease. The objective is to provide a comprehensive basis for interdisciplinary care for those with congenital heart disease.

Rare copy number variants analysis identifies novel candidate genes in heterotaxy syndrome patients with congenital heart defects

BACKGROUND

Heterotaxy (Htx) syndrome comprises a class of congenital disorders resulting from malformations in left-right body patterning. Approximately 90% of patients with heterotaxy have serious congenital heart diseases; as a result, the survival rate and outcomes of Htx patients are not satisfactory. However, the underlying etiology and mechanisms in the majority of Htx cases remain unknown. The aim of this study was to investigate the function of rare copy number variants (CNVs) in the pathogenesis of Htx.

METHODS

We collected 63 sporadic Htx patients with congenital heart defects and identified rare CNVs using an Affymetrix CytoScan HD microarray and real-time polymerase chain reaction. Potential candidate genes associated with the rare CNVs were selected by referring to previous literature related to left-right development. The expression patterns and function of candidate genes were further analyzed by whole mount in situ hybridization, morpholino knockdown, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated mutation, and over-expressing methods with zebrafish models.

RESULTS

Nineteen rare CNVs were identified for the first time in patients with Htx. These CNVs include 5 heterozygous genic deletions, 4 internal genic duplications, and 10 complete duplications of at least one gene. Further analyses of the 19 rare CNVs identified six novel potential candidate genes (NUMB, PACRG, TCTN2, DANH10, RNF115, and TTC40) linked to left-right patterning. These candidate genes exhibited early expression patterns in zebrafish embryos. Functional testing revealed that downregulation and over-expression of five candidate genes (numb, pacrg, tctn2, dnah10, and rnf115) in zebrafish resulted in disruption of cardiac looping and abnormal expression of lefty2 or pitx2, molecular markers of left-right patterning.

CONCLUSIONS

Our findings show that Htx with congenital heart defects in some sporadic patients may be attributed to rare CNVs. Furthermore, DNAH10 and RNF115 are Htx candidate genes involved in left-right patterning which have not previously been reported in either humans or animals. Our results also advance understanding of the genetic components of Htx.