De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies

Current and future diagnostics of congenital heart disease (CHD)

Congenital heart defects (CHD) are one of the most common anomalies found among live births and represent a complex multifactorial condition. Given that more than 90 % of cases survive due to improved early treatment options (e.g., catheter intervention, surgical procedure, and improved intensive care), genotype-informed patient follow-up should consider lifelong treatment considering different types of comorbidities. Unfortunately, a thorough genetic workup is only offered to a minority of CHD patients. However, a comprehensive understanding of the genetic underpinnings combined with in-depth phenotyping would strengthen our knowledge regarding the impact of environmental (e.g., pre-gestational diabetes) and genetic causes ranging from aneuploidies to single variants and more complex inheritance patterns on early heart development. Therefore, comprehensive genetic analysis in these patients is an essential way of predicting the prognosis and recurrence risk in families and ultimately improving patients' quality of life due to better therapeutic options. In this review, we examine the different types of variants and genes of different molecular genetics techniques to assess the diagnostic yield in different CHD sub-phenotypes. Given the complex inheritance pattern observed in CHD, we also consider possible future methods and frameworks to improve diagnostics and allow for better genotype-phenotype correlation in this patient group. Predicting recurrence risk and prognosis in CHD patients will ultimately allow for better treatment and lifelong therapeutic outcomes for CHD patients.

Neonatal Neurocardiac Care: Strategies to Optimize Neurodevelopmental Outcomes in Congenital Heart Disease

Neonates with critical congenital heart disease are at high risk for brain injury and neurodevelopmental disabilities. Neurocardiac care is a developing field, and there are few guidelines for front-line providers regarding neuromonitoring and neuroprotection. Understanding influences on early brain development, risk for seizures and brain injury, and long-term developmental outcomes can help providers formulate appropriate action plans for individual patients. Current evidence suggests that prenatal diagnosis, minimizing medical risk factors, monitoring for brain injury and seizures, providing individualized developmental care, supporting parental mental health, and referral to long-term developmental follow-up are components of care that may improve outcomes.

Neurodevelopmental outcomes in congenital heart disease: modifiable and nonmodifiable substrates

PURPOSE OF REVIEW

Neurodevelopmental impairments are the most common comorbidity among children, adolescents, and adults with congenital heart disease (CHD). Despite significant advances in operative and perioperative care resulting in increased survival, neurodevelopmental impairments remain prevalent in this population. Neurodevelopmental impairments, though subtle, can have a major impact on quality of life, attainment of independence and societal contribution. In this review, we summarize current knowledge on neurodevelopmental outcomes in the CHD population, including neuroimaging findings, known risk factors and opportunities to optimize outcomes.

RECENT FINDINGS

Several risk factors have been identified contributing to neurodevelopmental impairments across the lifespan. These include risk factors originating in the prenatal period and new risk factors that are acquired in adulthood. The risk factors encompass several categories, including genetic abnormalities, aberrant cardiovascular physiology, environmental factors, social determinants of health and mental health. Many risk factors can be considered modifiable, though large multicenter studies identifying the most salient risk factors for neurodevelopmental impairment are lacking.

SUMMARY

In this review, we identify potentially modifiable risk factors for neurodevelopmental impairment in the CHD population that can be studies in future neuroprotective clinical trials.

Rare damaging variants in the sex differences of congenital heart disease: an exome sequencing study

BACKGROUND

Congenital heart disease (CHD) exhibits a marked male predominance in birth prevalence, yet the genetic mechanisms underlying this sex disparity remain poorly understood. This study investigates the contribution of rare damaging variants on autosomes and the X chromosome to sex differences in foetal CHD.

METHODS

Parents of foetuses with CHD were recruited for the study. Rare damaging variants were identified by analysing whole-exome sequencing data from foetus-parental trios, and their contributions to sex differences were estimated through case-control studies. Functional enrichment analysis was conducted to assess functional differences in genetic variants between sexes.

FINDINGS

820 foetal probands with CHD were recruited, including 487 males and 333 females. We identified a significant enrichment of X-linked rare damaging variants, primarily driven by maternally inherited hemizygous variants (MIHVs) in male probands (OR = 1·84, P < 0·05), which accounted for 7·2% of male cases in our cohort. These variants were not found to be enriched in female probands. Additionally, X-linked rare damaging de novo variants (DNVs) were not enriched in either male or female probands (female probands: 1·8% versus female controls: 0·7%, P = 0·6789; no DNVs observed in males). Gene-level variant burden analysis revealed three X-linked CHD candidate genes: DCX, CACNA1F, and MAP3K15. Autosomal rare variants did not show significant differences in variant burdens between sexes. Notably, male probands showed specific functional enrichments in cilia-related pathways for autosomal recessive variants, as well as in chromatin remodelling and nervous system development pathways for autosomal DNVs.

INTERPRETATION

Male and female foetal CHD have significantly different genetic landscapes. The enrichment of X-linked rare damaging MIHVs in males provides a genetic explanation for the higher prevalence of CHD in males. This finding highlights the importance of incorporating sex-stratified approaches in clinical diagnostics and research.

FUNDING

Natural Science Foundation of China and Key research and development project of Hebei Province.

Hypoplastic left heart syndrome-a scoping review

Background

An estimated 3% of all newborns with congenital heart disease develop hypoplastic left heart syndrome (HLHS), making it a prominent cause of mortality in this group if surgical procedures or a heart transplant are not implemented. While compelling evidence supports a genetic element, identifying a particular genetic cause is limited to a subgroup of patients, indicating a complex and multifaceted origin for this condition. The objective of this scientific contribution was to identify, synthesize, and analyze the scientific knowledge produced regarding the implications of researching on HLHS in a scoping review.

Methods

The search for articles was diligently conducted between January 1, 2019 and February 20, 2025 on the PubMed/MEDLINE, Scopus, Web of Science, and Cochrane databases. This search was assiduously complemented by a gray search. It included internet browsers (e.g., Google) and medical textbooks. The following research question steered our study: "What are the basic data on the etiology and pathogenesis on HLHS?" All stages of the selection process were iwis carried out by the single author.

Results

Of the 1,364 articles found, 75 were included in the sample for analysis, which was implemented with an additional 25 articles from references and gray literature. The studies analyzed indicated that HLHS is one of the most complex congenital heart defects, characterized by small or hypoplastic left-sided heart structures and a dominant right ventricle. The Fontan circulation and the phased surgical technique that it entails have been the cornerstones of HLHS patient care since its debut some 40 years ago. Although there is considerable genetic evidence for HLHS, the exact genetic cause of this cardiologic entity is still not well known. HLHS remains genetically heterogeneous. There is evidence of incomplete penetrance for the C57Bl/6J-b2b635Clo/J (Ohia) mice.

Conclusions

HLHS is a complex and complicate congenital heart disease, which requires further investigation. In this article, I further explore the involvement of the endocardium in the progression of ventricular hypoplasia, therefore offering a potential explanation for the morphological alterations observed in the disease as a result of compromised blood flow to the developing ventricle. These findings may support a new paradigm for the complicated genetics of this congenital heart defect and there is some evidence that HLHS can originate genetically in a combinatorial approach.

Natural genetic variation quantitatively regulates heart rate and dimension

The polygenic contribution to heart development and function along the health-disease continuum remains unresolved. To gain insight into the genetic basis of quantitative cardiac phenotypes, we utilize highly inbred Japanese rice fish models, Oryzias latipes, and Oryzias sakaizumii. Employing automated quantification of embryonic heart rates as core metric, we profiled phenotype variability across five inbred strains. We observed maximal phenotypic contrast between individuals of the HO5 and the HdrR strain. HO5 showed elevated heart rates associated with embryonic ventricular hypoplasia and impaired adult cardiac function. This contrast served as the basis for genome-wide mapping. In an F2 segregation population of 1192 HO5 x HdrR embryos, we mapped 59 loci (173 genes) associated with heart rate. Experimental validation of the top 12 candidate genes by gene editing revealed their causal and distinct impact on heart rate, development, ventricle size, and arrhythmia. Our study uncovers new diagnostic and therapeutic targets for developmental and electrophysiological cardiac diseases and provides a novel scalable approach to investigate the intricate genetic architecture of the vertebrate heart.

Nkx2.7 is a conserved regulator of craniofacial development

Craniofacial malformations arise from developmental defects in the head, face, and neck with phenotypes such as 22q11.2 deletion syndrome illustrating a developmental link between cardiovascular and craniofacial morphogenesis. NKX2-5 is a key cardiac transcription factor associated with congenital heart disease and mouse models of Nkx2-5 deficiency highlight roles in cardiac development. In zebrafish, nkx2.5 and nkx2.7 are paralogues in the NK4 family expressed in cardiomyocytes and pharyngeal arches. Despite shared cellular origins of cardiac and craniofacial tissues, the function of NK4 factors in head and neck patterning has not been elucidated. Molecular evolutionary analysis of NK4 genes shows that nkx2.5 and nkx2.7 are ohnologs resulting from whole genome duplication events. Nkx2.7 serves as a previously unappreciated regulator of branchiomeric muscle and cartilage formation for which nkx2.5 cannot fully compensate. Mechanistically, our results highlight that Nkx2.7 patterns the cranial neural crest and functions upstream of Endothelin1 to inhibit Notch signals. Together, our studies shed light on an evolutionarily conserved Nkx transcription factor with unique functions in vertebrate craniofacial development, advancing our understanding of congenital head and neck deformities.

Multifaceted analysis of noncoding and coding de novo variants implicates NOTCH signaling pathway in tetralogy of Fallot in Chinese population

Tetralogy of Fallot (TOF) is the most common cyanotic heart defect in neonates. While there is compelling evidence of genetic contribution to the etiology of TOF, the contribution of noncoding variants to the development of the defect remains unexplored. Potentially damaging noncoding de novo variants (NC DNVs) were detected from 141 Chinese nonsyndromic TOF trios (CHN-TOF) and compared with those detected in the Pediatric Cardiac Genomics Consortium (PCGC). Bioinformatic analyses on noncoding and previously detected coding DNVs were performed to identify developmental pathways affected in TOF. Chinese but not PCGC-TOF patients showed a notably increased burden of putative damaging NC DNVs (n = 249). In Chinese, NC and coding DNVs were predominantly associated with cardiomyocyte differentiation and with chamber/valve/aorta development, respectively, producing a combined enrichment in NOTCH signaling (p = 1.1 × 10-6) and outflow tract morphogenesis (p = 2.2 × 10-5). Genes with NC DNVs (e.g., EFNB2, HEY2, and PITX2) interacted with NOTCH1 and FLT4 in a tight STRING protein-protein interaction (PPI) network. During the in vitro cardiac differentiation process, these noncoding candidate genes, which harbored potentially damaging regulatory NC DNVs, exhibited co-expression with NOTCH signaling genes and demonstrated dysregulated gene expression at various differentiation stages following NOTCH1 downregulation. In summary, our findings highlight a significant contribution of NC DNVs to TOF and suggest the presence of population genetic heterogeneity. Integrative analyses implicate dysregulation of NOTCH signaling, with converging influences from both coding and noncoding variants, in TOF within the Chinese population.

Dysmorphology-Based Prediction Model for Genetic Disorders in Infants With Congenital Heart Disease

BACKGROUND

Genetic disorders are prevalent in patients with congenital heart disease (CHD), but genetic evaluations are underutilized and nonstandardized. We sought to quantify a dysmorphology score and develop phenotype-based prediction models for genetic diagnoses in CHD.

METHODS

We used a test-negative case-control study of inpatient infants (<1 year) with CHD undergoing standardized genetic evaluations. We quantified a novel dysmorphology score and combined it with other clinical variables used in multivariable logistic regression models to predict genetic diagnoses identified by genetic testing.

RESULTS

Of 1008 patients, 24.1% (243/1008) had genetic diagnoses identified. About half of the cohort were either nondysmorphic or mildly dysmorphic with dysmorphology scores ≤2. There were higher dysmorphology scores according to CHD class (P=0.0007), extracardiac anomaly-positive status (P<0.0001), female sex (P=0.05), and genetic diagnosis identified (P<0.0001). Multivariable logistic regression models quantified this effect further: each +1 increase in the dysmorphology score was associated with a 17% to 20% increased risk of genetic diagnoses (odds ratios, 1.17-1.20, P<0.0001). Extracardiac anomaly-positive status remained a stronger predictor of genetic diagnoses (odds ratios, 2.81-3.39). Nonetheless, about 10% of the cohort were minimally dysmorphic (dysmorphology scores ≤2), had isolated CHD, and were found to have genetic diagnoses, indicating that dysmorphology-based screening can be used to risk-stratify but not exclude genetic diagnoses.

CONCLUSIONS

The dysmorphology score is a novel screen for patients with CHD at high risk of having genetic diagnoses identified by genetic testing, including disorders not easily recognized by clinicians. We used these results to develop predicted probability plots for genetic diagnoses in patients with CHD.

CTCF Point Mutation at R567 Disrupts Mouse Heart Development via 3D Genome Rearrangement and Transcription Dysregulation

CTCF plays a vital role in shaping chromatin structure and regulating gene expression. Clinical studies have associated CTCF mutations with congenital developmental abnormalities, including congenital cardiomyopathy. In this study, we investigated the impact of the homozygous CTCF-R567W (Ctcf R567W/R567W ) mutation on cardiac tissue morphogenesis during mouse embryonic development. Our results reveal significant impairments in heart development, characterised by ventricular muscle trabecular hyperplasia and reduced ventricular cavity sizes. We also observe a marked downregulation of genes involved in sarcomere assembly, calcium ion transport, and mitochondrial function in heart tissues from homozygous mice. Furthermore, the Ctcf R567W/R567W mutation disrupts CTCF's interaction with chromatin, resulting in alterations to topologically associating domain (TAD) structure within specific genomic regions and diminishing crucial promoter-enhancer interactions necessary for cardiac development. Additionally, we find that the heterozygous CTCF-R567W (Ctcf +/R567W ) mutation significantly compromises cardiac contractility in 8-week-old mice. This study elucidates the mechanism by which the CTCF-R567W mutation hampers cardiac development, underscoring the essential role of CTCF-R567 in embryonic heart development and maturation.

Cyclin-dependent kinase 13 is indispensable for normal mouse heart development

Congenital heart disease (CHD) has an incidence of approximately 1%. Over the last decade, sequencing studies including large cohorts of individuals with CHD have begun to unravel the genetic mechanisms underpinning CHD. This includes the identification of variants in cyclin-dependent kinase 13 (CDK13), in individuals with syndromic CHD. CDK13 encodes a serine/threonine protein kinase. The cyclin partner of CDK13 is cyclin K; this complex is thought to be important in transcription and RNA processing. Pathogenic variants in CDK13 cause CDK13-related disorder in humans, characterised by intellectual disability and developmental delay, recognisable facial features, feeding difficulties and structural brain defects, with 35% of individuals having CHD. To obtain a greater understanding for the role that this essential protein kinase plays in embryonic heart development, we have analysed a presumed loss of function Cdk13 transgenic mouse model (Cdk13tm1b). The homozygous mutants were embryonically lethal in most cases by E15.5. X-gal staining showed Cdk13 expression localised to developing facial regions, heart and surrounding areas at E10.5, whereas at E12.5, it was more widely present. In the E15.5 heart, staining was seen throughout. RT-qPCR showed significant reduction in Cdk13 transcript expression in homozygous compared with WT and heterozygous hearts at E10.5 and E12.5. Detailed morphological 3D analysis of embryonic and postnatal hearts was performed using high-resolution episcopic microscopy, which affords a more detailed analysis of structures such as cardiac valve leaflets and endocardial cushions, compared with more traditional histological techniques. We show that both the homozygous and heterozygous Cdk13tm1b mutants exhibit a range of CHD, including ventricular septal defects, bicuspid aortic valve, double outlet right ventricle and atrioventricular septal defects. 100% (n = 4) of homozygous hearts displayed CHD. Differential expression was seen in Cdk13tm1b homozygous mutants for two genes known to be necessary for normal heart development. The types of defects, and the presence of CHD in heterozygous mice (17.02%, n = 8/47), are consistent with the CDK13-related disorder phenotype in humans. This study provides important insights into the effects of reduced function of CDK13 in the mouse heart and contributes to our understanding of the mechanism behind this disorder as a cause of CHD.

Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes

Congenital heart disease (CHD) is a leading cause of infant mortality. We analyzed de novo mutations (DNMs) and very rare transmitted/unphased damaging variants in 248 prespecified genes in 11,555 CHD probands. The results identified 60 genes with a significant burden of heterozygous damaging variants. Variants in these genes accounted for CHD in 10.1% of probands with similar contributions from de novo and transmitted variants in parent-offspring trios that showed incomplete penetrance. DNMs in these genes accounted for 58% of the signal from DNMs. Thirty-three genes were linked to a single CHD subtype while 12 genes were associated with 2 to 4 subtypes. Seven genes were only associated with isolated CHD, while 37 were associated with 1 or more extracardiac abnormalities. Genes selectively expressed in the cardiomyocyte lineage were associated with isolated CHD, while those widely expressed in the brain were also associated with neurodevelopmental delay (NDD). Missense variants introducing or removing cysteines in epidermal growth factor (EGF)-like domains of NOTCH1 were enriched in tetralogy of Fallot and conotruncal defects, unlike the broader CHD spectrum seen with loss of function variants. Transmitted damaging missense variants in MYH6 were enriched in multiple CHD phenotypes and account for ~1% of all probands. Probands with characteristic mutations causing syndromic CHD were frequently not diagnosed clinically, often due to missing cardinal phenotypes. CHD genes that were positively or negatively associated with development of NDD suggest clinical value of genetic testing. These findings expand the understanding of CHD genetics and support the use of molecular diagnostics in CHD.

Recessive genetic contribution to congenital heart disease in 5,424 probands

Variants with large effect contribute to congenital heart disease (CHD). To date, recessive genotypes (RGs) have commonly been implicated through anecdotal ascertainment of consanguineous families and candidate gene-based analysis; the recessive contribution to the broad range of CHD phenotypes has been limited. We analyzed whole exome sequences of 5,424 CHD probands. Rare damaging RGs were estimated to contribute to at least 2.2% of CHD, with greater enrichment among laterality phenotypes (5.4%) versus other subsets (1.4%). Among 108 curated human recessive CHD genes, there were 66 RGs, with 54 in 11 genes with >1 RG, 12 genes with 1 RG, and 85 genes with zero. RGs were more prevalent among offspring of consanguineous union (4.7%, 32/675) than among nonconsanguineous probands (0.7%, 34/4749). Founder variants in GDF1 and PLD1 accounted for 74% of the contribution of RGs among 410 Ashkenazi Jewish probands. We identified genome-wide significant enrichment of RGs in C1orf127, encoding a likely secreted protein expressed in embryonic mouse notochord and associated with laterality defects. Single-cell transcriptomes from gastrulation-stage mouse embryos revealed enrichment of RGs in genes highly expressed in the cardiomyocyte lineage, including contractility-related genes MYH6, UNC45B, MYO18B, and MYBPC3 in probands with left-sided CHD, consistent with abnormal contractile function contributing to these malformations. Genes with significant RG burden account for 1.3% of probands, more than half the inferred total. These results reveal the recessive contribution to CHD, and indicate that many genes remain to be discovered, with each likely accounting for a very small fraction of the total.

Deciphering the digenic architecture of congenital heart disease using trio exome sequencing data

Congenital heart disease (CHD) is the most common congenital anomaly and a leading cause of infant morbidity and mortality. Despite extensive exploration of the monogenic causes of CHD over the last decades, ∼55% of cases still lack a molecular diagnosis. Investigating digenic interactions, the simplest form of oligogenic interactions, using high-throughput sequencing data can elucidate additional genetic factors contributing to the disease. Here, we conducted a comprehensive analysis of digenic interactions in CHD by utilizing a large CHD trio exome sequencing cohort, comprising 3,910 CHD and 3,644 control trios. We extracted pairs of presumably deleterious rare variants observed in CHD-affected and unaffected children but not in a single parent. Burden testing of gene pairs derived from these variant pairs revealed 29 nominally significant gene pairs. These gene pairs showed a significant enrichment for known CHD genes (p < 1.0 × 10-4) and exhibited a shorter average biological distance to known CHD genes than expected by chance (p = 3.0 × 10-4). Utilizing three complementary biological relatedness approaches including network analyses, biological distance calculations, and candidate gene prioritization methods, we prioritized 10 final gene pairs that are likely to underlie CHD. Analysis of bulk RNA-sequencing data showed that these genes are highly expressed in the developing embryonic heart (p < 1 × 10-4). In conclusion, our findings suggest the potential role of digenic interactions in CHD pathogenesis and provide insights into unresolved molecular diagnoses. We suggest that the application of the digenic approach to additional disease cohorts will significantly enhance genetic discovery rates.

Modeling SMAD2 Mutations in Induced Pluripotent Stem Cells Provides Insights Into Cardiovascular Disease Pathogenesis

BACKGROUND

SMAD2 is a coregulator that binds a variety of transcription factors in human development. Heterozygous SMAD2 loss-of-function and missense variants are identified in patients with congenital heart disease (CHD) or arterial aneurysms. Mechanisms that cause distinct cardiovascular phenotypes remain unknown. We aimed to define transcriptional and epigenetic effects of SMAD2 variants and their role in CHD. We also assessed the function of SMAD2 missense variants of uncertain significance.

METHODS AND RESULTS

Rare SMAD2 variants (minor allele frequency ≤10-5) were identified in exome sequencing of 11 336 participants with CHD. We constructed isogenic induced pluripotent stem cells with heterozygous or homozygous loss-of-function and missense SMAD2 variants identified in CHD probands. Wild-type and mutant induced pluripotent stem cells were analyzed using bulk RNA sequencing, chromatin accessibility (Assay for Transposase-Accessible Chromatin With Sequencing), and integrated with published SMAD2/3 chromatin immunoprecipitation data. Cardiomyocyte differentiation and contractility were evaluated. Thirty participants with CHD had heterozygous loss-of-function or missense SMAD2 variants. SMAD2 haploinsufficiency altered chromatin accessibility at promoters and dysregulated expression of 385 SMAD regulated genes, including 10 CHD-associated genes. Motifs enriched in differential Assay for Transposase-Accessible Chromatin peaks predicted that SMAD2 haploinsufficiency disrupts interactions with transcription factors NANOG (homeobox protein NANOG), ETS, TEAD3/4 (transcriptional enhanced associate domain 3/4), CREB1 (cAMP response element binding protein 1), and AP1 (activator protein 1). Compared with SMAD2-haploinsufficient cells, induced pluripotent stem cells with R114C or W274C variants exhibited distinct and shared chromatin accessibility and transcription factor binding changes.

CONCLUSIONS

SMAD2 haploinsufficiency disrupts transcription factor binding and chromatin interactions critical for cardiovascular development. Differences between the molecular consequences of loss-of-function and missense variants likely contribute to phenotypic heterogeneity. These findings indicate opportunities for molecular analyses to improve reclassification of SMAD2 variants of uncertain clinical significance.

The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multipart RNA regulatory modules

The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to the large assembly of splicing regulators (LASR), a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA motifs for LASR subunits hnRNPs M, H/F, and C and Matrin3. These elements are often arranged in tandem, forming multipart modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Minigene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.

A splicing variant in EFCAB7 hinders ciliary transport and disrupts cardiac development

The Tetralogy of Fallot (TOF), the most prevalent form of cyanotic congenital heart disease, stems from abnormal development of the outflow tract during embryogenesis. Despite the crucial role played by primary cilia in heart development, there is currently insufficient evidence to establish a causal relationship between defects in genes related to primary cilia and non-syndromic TOF. Here, we performed Sanger sequencing on 131 Chinese patients diagnosed with TOF and identified a splicing variant (c.683-1G > C) in the EFCAB7 gene. This splicing variant triggered exon skipping, leading to the production of a non-functional protein both in vitro and in vivo. Mice carrying this variant exhibited abnormal cardiac development, impaired ciliogenesis, disrupted Hedgehog signaling, and hindered Shh/Gli pathway activity. Through the integration of CUT&Tag data on Glis and bulk RNA-seq profiles of embryonic hearts at E10.5, we found that transcriptional downregulation of Gli target genes, including Myh6, Zfpm1, and Nkx2-5, is a consequence of Shh signaling inhibition. Our findings implicate EFCAB7 as a potential causative gene for TOF, underscoring the indispensable function of primary cilia in the intricate process of cardiac septation during heart development.

Genetic impact of copy number variations on congenital heart defects: Current insights and future directions

Congenital heart defects (CHDs) are the most prevalent congenital abnormalities, and they are commonly associated with genetic alterations, namely copy number variants. CNVs, which are duplications or deletions of DNA sequences, can disrupt gene regulation, impact dosage-sensitive genes, and cause loss-of-function mutations, all of which can interfere with heart development. CNVs cause genomic instability by changing essential genes, which plays an important role in the pathophysiology of CHDs. Detecting these variants is critical for better understanding the genetic causes of these abnormalities and improving patient outcomes. Advanced genetic testing tools aid in detecting CNVs linked to CHDs. Multiplex Ligation-Dependent Probe Amplification (MLPA), High-throughput Ligation-Dependent Probe Amplification (HLPA), Whole Exome Sequencing (WES), Chromosomal Microarray Analysis (CMA), and CNV-specific sequencing (CNV-seq) have all greatly improved the detection of these variants. Furthermore, whole genome sequencing (WGS) has emerged as a potent method for detecting CNVs on a wide scale, allowing for earlier diagnosis and more effective treatment planning. Therefore, this review focuses on the rising significance of CNV research in congenital heart defects, emphasizing on how genetic differences might lead to improved diagnostic and treatment options. By combining genomic technologies, researchers and clinicians can gain a better understanding of the function of CNVs in CHDs, opening the door for personalised therapy.

Alternative splicing factors and cardiac disease: more than just missplicing?

Alternative splicing (AS) is the process wherein the exons from a single gene are joined in different combinations to produce nonidentical, albeit related, RNA transcripts. This process is important for the development and physiological function of many organs and is particularly important in the heart. Notably, AS has been implicated in cardiac disease and failure, and a growing number of genetic variants in AS factors have been identified in association with cardiac malformation and/or disease. With the field poised to interrogate how these variants affect cardiac development and disease, an understandable point of emphasis will undoubtedly be on downstream target gene missplicing. In this Perspective article, we would like to encourage consideration not only of the potential for novel disease mechanisms, but also for contributions from disruption of the ever-expanding list of nonsplicing functions ascribed to many AS factors. We discuss the emergence of a novel cardiac disease mechanism based on pathogenic RNA granules and speculate on the generality of such a mechanism among localization-disrupting AS factor genetic variants. We also highlight emerging nonsplicing functions attributed to several AS factors with cardiac disease-associated genetic variants in the hopes of pointing to avenues for exploration of mechanisms that may contribute to disease alongside target gene missplicing.

Meta-analysis reveals transcription factors and DNA binding domain variants associated with congenital heart defect and orofacial cleft

Many structural birth defect patients lack genetic diagnoses because there are many disease genes as yet to be discovered. We applied a gene burden test incorporating de novo predicted-loss-of-function (pLoF) and likely damaging missense variants together with inherited pLoF variants to a collection of congenital heart defect (CHD) and orofacial cleft (OC) parent-offspring trio cohorts (n = 3,835 and 1,844, respectively). We identified 17 novel candidate CHD genes and 10 novel candidate OC genes, of which many were known developmental disorder genes. Shorter genes were more powered in a "de novo only" analysis as compared to analysis including inherited pLoF variants. TFs were enriched among the significant genes; 14 and 8 transcription factor (TF) genes showed significant variant burden for CHD and OC, respectively. In total, 30 affected children had a de novo missense variant in a DNA binding domain of a known CHD, OC, and other developmental disorder TF genes. Our results suggest candidate pathogenic variants in CHD and OC and their potentially pleiotropic effects in other developmental disorders.

CACNA1G, A Heterotaxy Candidate Gene, Plays a Role in Ciliogenesis and Left-Right Patterning in Xenopus tropicalis

Heterotaxy (HTX) is characterized by an abnormality in the organ arrangement along the Left-Right (LR) axis and is caused by the disruption of LR patterning in early development. LR asymmetry is critical for multiple organs. Specifically, proper LR patterning is crucial for cardiac function and is a cause of congenital heart disease (CHD). CACNA1G is a candidate gene identified in patients with CHD and HTX. This gene encodes a T-type, low-voltage-activated calcium channel and is a member of the Cav3.1 channel family. However, its function in cardiac or embryonic development remains unknown. Here, we show that abnormal cacna1g expression in Xenopus tropicalis recapitulates the HTX phenotype found in the patient cohort. By examining early LR patterning markers, including pitx2c and dand5, we discovered that both markers are expressed abnormally, suggesting that LR patterning is disrupted at the earliest stages of the LR signaling cascade. Since cilia have been described as key regulators of LR asymmetry, we checked the process of cilia formation in cacna1g crispants. The LR Organizer (LRO) contained reduced cilia quantity in the cacna1g crispants, which may explain the LR defects. In conclusion, the abnormal expression of cacna1g affects cilia in the LRO, leading to abnormal LR patterning and cardiac looping.

Chromosomal analysis and short-term outcome of prenatally diagnosed congenital heart disease

Congenital structural heart disease (CHD) is the leading cause of infant death from birth defects. Postnatal survival primarily depends on the type and severity of the defect. In addition, worse cardiac prognosis is observed when extra-cardiac anomalies (ECA) are associated. This retrospective chart review was aimed at finding markers for short-term outcome prediction of prenatally-diagnosed complex CHD, focusing in particular on the impact of CHD category, of CHD severity score and of prenatal or postnatal diagnosis of ECA or chromosomal anomalies on 4 primary outcomes: termination of pregnancy (TOP), intrauterine fetal demise, neonatal mortality and 1-year-survival rate. We reviewed medical files from 381 fetuses, presenting at our center between 2018 and 2021 with CHD for which prenatal advice by a pediatric cardiologist was sought. 341 fetuses met the inclusion criteria for the study. Twin pregnancies (7.62%; OR 4.76 (p < 0.001)) and pregnancies resulting from assisted reproductive technology (7.33%; OR 2.44 (p < 0.001)) were more prevalent compared to the general population. CHD categories and CHD severity scores, ranging from A (extremely high risk based on CHD or ECA type) to D (low risk), were assigned to each fetus. Prenatal or postnatal chromosomal microarray results were available for 232 fetuses (68%) and were abnormal in 30 (12.9%). Logistic regression analysis was used to determine significant predictors for the primary outcomes 'TOP', 'postnatal demise before the age of 1 month' and 'survival at the age of 1 year'. TOP was carried out significantly more with: prenatal genetic diagnosis, severity score A and severity score B. Interestingly, a prenatal genetic diagnosis was negatively correlated with pregnancy continuation, but it was not a significant predictor for postnatal mortality, while a postnatal diagnosis of a genetic disorder impacted early but not late postnatal mortality. In addition, postnatal mortality both before the age of 1 month or before the age of 1 year was significantly associated with lower postmenstrual age at birth, CHD severity score B and major ECA at birth. These results underscore the importance of genotyping and of accurate cardiac and extracardiac phenotyping for prognostication in fetuses with CHD.

Convergence of autism proteins at the cilium

Hundreds of high-confidence autism genes have been identified, yet the relevant etiological mechanisms remain unclear. Gene ontology analyses have repeatedly identified enrichment of proteins with annotated functions in gene expression regulation and neuronal communication. However, proteins are often pleiotropic and these annotations are inherently incomplete. Our recent autism functional genetics work has suggested that these genes may share a common mechanism at the cilium, a membrane-bound organelle critical for neurogenesis, brain patterning, and neuronal activity-all processes strongly implicated in autism. Moreover, autism commonly co-occurs with conditions that are known to involve ciliary-related pathologies, including congenital heart disease, hydrocephalus, and blindness. However, the role of autism genes at the cilium has not been systematically investigated. Here we demonstrate that autism proteins spanning disparate functional annotations converge in expression, localization, and function at cilia, and that patients with pathogenic variants in these genes have cilia-related co-occurring conditions and biomarkers of disrupted ciliary function. This degree of convergence among genes spanning diverse functional annotations strongly suggests that cilia are relevant to autism, as well as to commonly co-occurring conditions, and that this organelle should be explored further for therapeutic potential.

Expanding the Molecular Spectrum of MMP21 Missense Variants: Clinical Insights and Literature Review

BACKGROUND/OBJECTIVES

The failure of physiological left-right (LR) patterning, a critical embryological process responsible for establishing the asymmetric positioning of internal organs, leads to a spectrum of congenital abnormalities characterized by laterality defects, collectively known as "heterotaxy". MMP21 biallelic variants have recently been associated with heterotaxy syndrome and congenital heart defects (CHD). However, the genotype-phenotype correlations and the underlying pathogenic mechanisms remain poorly understood.

METHODS

Patients harboring biallelic MMP21 missense variants who underwent diagnostic genetic testing for CHD or heterotaxy were recruited at the Institute for Maternal and Child Health-I.R.C.C.S. "Burlo Garofolo". Additionally, a literature review on MMP21 missense variants was conducted, and clinical data from reported patients, along with molecular data from in silico and modeling tools, were collected.

RESULTS

A total of 18 MMP21 missense variants were reported in 26 patients, with the majority exhibiting CHD (94%) and variable extra-cardiac manifestations (64%). In our cohort, through Whole-Exome Sequencing (WES) analysis, the missense p.(Met301Ile) variant was identified in two unrelated patients, who both presented with heterotaxy syndrome.

CONCLUSIONS

Our comprehensive analysis of MMP21 missense variants supports the pathogenic role of the p.(Met301Ile) variant and provides significant insights into the disease pathogenesis. Specifically, missense variants are distributed throughout the gene without clustering in specific regions, and phenotype comparisons between patients carrying missense variants in compound heterozygosity or homozygosity do not reveal significant differences. These findings may suggest a potential loss-of-function mechanism for MMP21 missense variants, especially those located in the catalytic domain, and highlight their critical role in the pathogenesis of heterotaxy syndrome.

Mitotic block and epigenetic repression underlie neurodevelopmental defects and neurobehavioral deficits in congenital heart disease

Hypoplastic left heart syndrome (HLHS) is a severe congenital heart disease associated with microcephaly and poor neurodevelopmental outcomes. Here we show that the Ohia HLHS mouse model, with mutations in Sap130, a chromatin modifier, and Pcdha9, a cell adhesion protein, also exhibits microcephaly associated with mitotic block and increased apoptosis leading to impaired cortical neurogenesis. Transcriptome profiling, DNA methylation, and Sap130 ChIPseq analyses all demonstrate dysregulation of genes associated with autism and cognitive impairment. This includes perturbation of REST transcriptional regulation of neurogenesis, disruption of CREB signaling regulating synaptic plasticity, and defects in neurovascular coupling mediating cerebral blood flow. Adult mice harboring either the Pcdha9 mutation, which show normal brain anatomy, or forebrain-specific Sap130 deletion via Emx1-Cre, which show microcephaly, both demonstrate learning and memory deficits and autism-like behavior. These findings provide mechanistic insights indicating the adverse neurodevelopment in HLHS may involve cell autonomous/nonautonomous defects and epigenetic dysregulation.

Mate-Pair Sequencing Enables Identification and Delineation of Balanced and Unbalanced Structural Variants in Prenatal Cytogenomic Diagnostics

BACKGROUND

Mate-pair sequencing detects both balanced and unbalanced structural variants (SVs) and simultaneously informs in relation to both genomic location and orientation of SVs for enhanced variant classification and clinical interpretation, while chromosomal microarray analysis (CMA) only reports deletion/duplication. Herein, we evaluated its diagnostic utility in a prospective back-to-back prenatal comparative study with CMA.

METHODS

From October 2021 to September 2023, 426 fetuses with ultrasound anomalies were prospectively recruited for mate-pair sequencing and CMA in parallel for prenatal genetic diagnosis. Balanced/unbalanced SVs and regions with absence of heterozygosity (AOH) were detected and classified independently, and comparisons were made between mate-pair sequencing and CMA to assess concordance. In addition, novel SVs were investigated for potential RNA perturbations using cultured cells, whenever available.

RESULTS

Mate-pair sequencing and CMA successfully yielded results for all 426 fetuses without the need for cell culturing. In addition, mate-pair sequencing identified 19 cases with aneuploidies, 16 cases with pathogenic simple deletions/duplications, and 5 cases with pathogenic translocations/insertions, providing a 25% incremental diagnostic yield compared to CMA (9.4%, 40/426 vs 7.6%, 32/426). Furthermore, by identifying the location and orientation of SVs, mate-pair sequencing improved the variant interpretation and/or follow-up approach for 40.0% (12) of the 30 cases with likely clinically significant deletions/duplications reported by CMA. Lastly, both platforms reported 3 cases (3/426) with multiple regions of AOH likely attributable to parental consanguinity.

CONCLUSIONS

Mate-pair sequencing detects additional balanced/unbalanced SVs and improves variant interpretation in comparison to CMA, indicating its potential to serve as a comprehensive prenatal cytogenomic diagnostic method.

Acetyltransferase in cardiovascular disease and aging

Acetyltransferases are enzymes that catalyze the transfer of an acetyl group to a substrate, a modification referred to as acetylation. Loss-of-function variants in genes encoding acetyltransferases can lead to congenital disorders, often characterized by intellectual disability and heart and muscle defects. Their activity is influenced by dietary nutrients that alter acetyl coenzyme A levels, a key cofactor. Cardiovascular diseases, including ischemic, hypertensive, and diabetic heart diseases - leading causes of mortality in the elderly - are largely attributed to prolonged lifespan and the growing prevalence of metabolic syndrome. Acetyltransferases thus serve as a crucial link between lifestyle modifications, cardiometabolic disease, and aging through both epigenomic and non-epigenomic mechanisms. In this review, we discuss the roles and relevance of acetyltransferases. While the sirtuin family of deacetylases has been extensively studied in longevity, particularly through fasting-mediated NAD+ metabolism, recent research has brought attention to the essential roles of acetyltransferases in health and aging-related pathways, including cell proliferation, DNA damage response, mitochondrial function, inflammation, and senescence. We begin with an overview of acetyltransferases, classifying them by domain structure, including canonical and non-canonical lysine acetyltransferases, N-terminal acetyltransferases, and sialic acid O-acetyltransferases. We then discuss recent advances in understanding acetyltransferase-related pathologies, particularly focusing on cardiovascular disease and aging, and explore their potential therapeutic applications for promoting health in older individuals.

Alternative Splicing in the Heart: The Therapeutic Potential of Regulating the Regulators

Alternative splicing allows a single gene to produce a variety of protein isoforms. Changes in splicing isoform usage characterize virtually every stage of the differentiation process and define the physiological differences between cardiomyocytes with different function, at different stages of development, and pathological function. Recent identification of cardiac splicing factors provided insights into the mechanisms underlying alternative splicing and revealed how these splicing factors impact functional properties of the heart. Alterations of the splicing of sarcomeric genes, cell signaling proteins, and ion channels have been associated with the development of pathological conditions such as cardiomyopathy and arrhythmia. RBM20, RBM24, PTBP1, RBFOX, and QKI play key roles in cardiac development and pathology. A better understanding of their regulation will yield insights into healthy cardiac development and inform the development of molecular therapeutics.

Impact of Residual Lesion Severity on Neurodevelopmental Outcomes Following Congenital Heart Surgery in Infancy and Childhood

Children with congenital heart disease are at increased risk of neurodevelopmental delay throughout their lifespan. This risk is exacerbated following congenital heart surgery (CHS) in infancy. However, there are few modifiable risk factors for postoperative neurodevelopmental delay. In this study, we assessed the Residual Lesion Score (RLS), a quality assessment metric that evaluates residual lesion severity following CHS, as a predictor of neurodevelopmental delay. This was a single-center, retrospective review of patients who underwent CHS from 01/2011 to 03/2021 and post-discharge neurodevelopmental evaluation from 12 to 42 months of age using the Bayley Scales of Infant Development, 3rd Edition (BSID-III). RLS was assigned per published criteria: RLS 1, no residua; RLS 2, minor residua; and RLS 3, major residua or pre-discharge reintervention. Associations between RLS and BSID-III scores, as well as trends in neurodevelopmental outcomes over time, were evaluated. Of 517 patients with median age at neurodevelopmental testing of 20.0 (IQR 18.0-22.7) months, 304 (58.8%), 146 (28.2%), and 67 (13.0%) were RLS 1, 2, and 3, respectively. RLS 3 patients had significantly lower scaled scores in the cognitive, receptive, and expressive communication, and fine and gross motor domains, compared with RLS 1 patients. Multivariable models accounted for 21.5%-31.5% of the variation in the scaled scores, with RLS explaining 1.4-7.3% of the variation. In a subgroup analysis, RLS 3 patients demonstrated relatively fewer gains in cognitive, expressive communication, and gross motor scores over time (all p < 0.05). In conclusion, RLS 3 patients are at increased risk for neurodevelopmental delay, warranting closer follow-up and greater developmental support for cognitive, language, and motor skills soon after surgery.

Genetics of anomalies of the kidney and urinary tract with congenital heart disease: A review

Congenital anomalies of the kidney and urinary tract (CAKUT) and congenital heart disease (CHD) are the most common congenital defects and constitute a major cause of morbidity in children. Anomalies of both systems may be isolated or associated with congenital anomalies of other organ systems. Various reports support the co-occurrence of CAKUT and CHD, although the prevalence can vary. Cardiovascular anomalies occur in 11.2% to 34% of patients with CAKUT, and CAKUT occur in 5.3% to 35.8% of those with CHD. The co-occurrence of genetic factors in both CAKUT and CHD would raise common etiologies including genetics, genetic-environmental interactions, or shared molecular mechanisms and pathways such as NODAL, NOTCH, BMP, WNT, and VEGF. Studies in animal models and humans have indicated a genetic etiology for CHD and CAKUT with hundreds of genes recognized and thousands of entries, found in a catalog of human genetic disorders. There are over 80 CAKUT genes and over 100 CHD genes available for clinical testing. For example, the HNFIB gene accounts for 5% to 31% of reported cases of CAKUT. In view of the association between CAKUT and CHD, a thorough cardiac examination should be performed in patients with CAKUT, and a similar evaluation for CAKUT in the presence of CHD. This will allow early diagnosis and therapeutic intervention to improve the long- term outcome of patients affected, and test for at-risk family members. We present here evidence for an association of anomalies involving the two organ systems, and discuss possible etiologies of targeted genes, their functions, biological processes and interactions on embryogenesis.

Molecular diagnoses and candidate gene identification in the congenital heart disease cohorts of the 100,000 genomes project

Congenital heart disease (CHD) describes a structural cardiac defect present from birth. A cohort of participants recruited to the 100,000 Genomes Project (100 kGP) with syndromic CHD (286 probands) and familial CHD (262 probands) were identified. "Tiering" following genome sequencing data analysis prioritised variants in gene panels linked to participant phenotype. To improve diagnostic rates in the CHD cohorts, we implemented an agnostic de novo Gene Discovery Pipeline (GDP). We assessed de novo variants (DNV) for unsolved CHD participants following filtering to select variants of interest in OMIM-morbid genes, as well as novel candidate genes. The 100kGP CHD cohorts had low rates of pathogenic diagnoses reported (combined CHD "solved" 5.11% (n = 28/548)). Our GDP provided diagnostic uplift of nearly one third (1.28% uplift; 5.11% vs. 6.39%), with a new or potential diagnosis for 9 additional participants with CHD. When a filtered DNV occurred within a non-morbid gene, our GDP prioritised biologically-plausible candidate CHD genes (n = 79). Candidate variants occurred in both genes linked to cardiac development (e.g. AKAP13 and BCAR1) and those currently without a known role (e.g. TFAP2C and SETDB1). Sanger sequencing of a cohort of patients with CHD did not identify a second de novo variant in the candidate dataset. However, literature review identified rare variants in HMCN1, previously reported as causative for pulmonary atresia, confirming the approach utility. As well as diagnostic uplift for unsolved participants of the 100 kGP, our GDP created a dataset of candidate CHD genes, which forms an important resource for further evaluation.

SETD3 functions beyond histidine methylation

SETD3 is a member of SET domain-containing proteins. It has been discovered as the first metazoan protein (actin) histidine methyltransferase. In addition to this well-characterized molecular function of SETD3, it has been clearly shown to be involved in multiple biological processes, such as cell differentiation, tumorigenesis and viral infection. Here, we summarize the current knowledge on the roles of SETD3 beyond its histidine methyltransferase activity, and outline its cellular and molecular modes of action, as well as the upstream regulation on SETD3, therefore providing insights for the molecular basis of how SETD3 fine regulates multiple physiological and pathological processes.

Genome Sequencing is Critical for Forecasting Outcomes Following Congenital Cardiac Surgery

While exome and whole genome sequencing have transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.

Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac development

Illuminating the precise stepwise genetic programs directing cardiac development provides insights into the mechanisms of congenital heart disease and strategies for cardiac regenerative therapies. Here, we integrate in vitro and in vivo human single-cell multi-omic studies with high-throughput functional genomic screening to reveal dynamic, cardiac-specific gene regulatory networks (GRNs) and transcriptional regulators during human cardiomyocyte development. Interrogating developmental trajectories reconstructed from single-cell data unexpectedly reveal divergent cardiomyocyte lineages with distinct gene programs based on developmental signaling pathways. High-throughput functional genomic screens identify key transcription factors from inferred GRNs that are functionally relevant for cardiomyocyte lineages derived from each pathway. Notably, we discover a critical heat shock transcription factor 1 (HSF1)-mediated cardiometabolic GRN controlling cardiac mitochondrial/metabolic function and cell survival, also observed in fetal human cardiomyocytes. Overall, these multi-modal genomic studies enable the systematic discovery and validation of coordinated GRNs and transcriptional regulators controlling the development of distinct human cardiomyocyte populations.

Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants

Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly often accompanied by other structural anomalies and/or neurobehavioral manifestations. Rare de novo protein-coding variants and copy-number variations contribute to CDH in the population. However, most individuals with CDH remain genetically undiagnosed. Here, we perform integrated de novo and common-variant analyses using 1,469 CDH individuals, including 1,064 child-parent trios and 6,133 ancestry-matched, unaffected controls for the genome-wide association study. We identify candidate CDH variants in 15 genes, including eight novel genes, through deleterious de novo variants. We further identify two genomic loci contributing to CDH risk through common variants with similar effect sizes among Europeans and Latinx. Both loci are in putative transcriptional regulatory regions of developmental patterning genes. Estimated heritability in common variants is ∼19%. Strikingly, there is no significant difference in estimated polygenic risk scores between isolated and complex CDH or between individuals harboring deleterious de novo variants and individuals without these variants. The data support a polygenic model as part of the CDH genetic architecture.

Mutational signature analyses in multi-child families reveal sources of age-related increases in human germline mutations

Whole-genome sequencing studies of parent-offspring trios have provided valuable insights into the potential impact of de novo mutations (DNMs) on human health and disease. However, the molecular mechanisms that drive DNMs are unclear. Studies with multi-child families can provide important insight into the causes of inter-family variability in DNM rates but they are highly limited. We characterized 2479 de novo single nucleotide variants (SNVs) in 13 multi-child families of Mexican-American ethnicity. We observed a strong paternal age effect on validated de novo SNVs with extensive inter-family variability in the yearly rate of increase. Children of older fathers showed more C > T transitions at CpG sites than children from younger fathers. Validated SNVs were examined against one cancer (COSMIC) and two non-cancer (human germline and CRISPR-Cas 9 knockout of human DNA repair genes) mutational signature databases. These analyses suggest that inaccurate DNA mismatch repair during repair initiation and excision processes, along with DNA damage and replication errors, are major sources of human germline de novo SNVs. Our findings provide important information for understanding the potential sources of human germline de novo SNVs and the critical role of DNA mismatch repair in their genesis.

Structural Covariance Networks in the Fetal Brain Reveal Altered Neurodevelopment for Specific Subtypes of Congenital Heart Disease

BACKGROUND

Altered structural brain development has been identified in fetuses with congenital heart disease (CHD), suggesting that the neurodevelopmental impairment observed later in life might originate in utero. There are many interacting factors that may perturb neurodevelopment during the fetal period and manifest as structural brain alterations, such as altered cerebral substrate delivery and aberrant fetal hemodynamics.

METHODS AND RESULTS

We extracted structural covariance networks from the log Jacobian determinants of 435 in utero T2 weighted image magnetic resonance imaging scans, (n=67 controls, 368 with CHD) acquired during the third trimester. We fit general linear models to test whether age, sex, expected cerebral substrate delivery, and CHD diagnosis were significant predictors of structural covariance. We identified significant effects of age, sex, cerebral substrate delivery, and specific CHD diagnosis across a variety of structural covariance networks, including primary motor and sensory cortices, cerebellar regions, frontal cortex, extra-axial cerebrospinal fluid, thalamus, brainstem, and insula, consistent with widespread coordinated aberrant maturation of specific brain regions over the third trimester.

CONCLUSIONS

Structural covariance networks offer a sensitive, data-driven approach to explore whole-brain structural changes without anatomical priors. We used them to stratify a heterogenous patient cohort with CHD, highlighting similarities and differences between diagnoses during fetal neurodevelopment. Although there was a clear effect of abnormal fetal hemodynamics on structural brain maturation, our results suggest that this alone does not explain all the variation in brain development between individuals with CHD.

Predictors of Neurologic Complications and Neurodevelopmental Outcome in Pediatric Cardiac Surgery With Extracorporeal Membrane Oxygenation

Extracorporeal membrane oxygenation (ECMO) has emerged as an important intervention for children both preceding and following cardiac surgery. There is a notable lack of comprehensive information regarding neurodevelopmental outcomes. The Norwood procedure and complex biventricular repairs exhibit the highest prevalence of ECMO usage. Examination of the data demonstrates that only 50% of ECMO survivors achieved normative cognitive outcomes, with 40% of those experiencing long-term neurological deficits. It is imperative to conduct robustly designed studies with extended follow-up periods to establish guidelines for neuromonitoring and neuroprotection during ECMO in the field of congenital cardiac surgery.

Beyond genomic studies of congenital heart defects through systematic modelling and phenotyping

Congenital heart defects (CHDs), the most common congenital anomalies, are considered to have a significant genetic component. However, despite considerable efforts to identify pathogenic genes in patients with CHDs, few gene variants have been proven as causal. The complexity of the genetic architecture underlying human CHDs likely contributes to this poor genetic discovery rate. However, several other factors are likely to contribute. For example, the level of patient phenotyping required for clinical care may be insufficient for research studies focused on mechanistic discovery. Although several hundred mouse gene knockouts have been described with CHDs, these are generally not phenotyped and described in the same way as CHDs in patients, and thus are not readily comparable. Moreover, most patients with CHDs carry variants of uncertain significance of crucial cardiac genes, further complicating comparisons between humans and mouse mutants. In spite of major advances in cardiac developmental biology over the past 25 years, these advances have not been well communicated to geneticists and cardiologists. As a consequence, the latest data from developmental biology are not always used in the design and interpretation of studies aimed at discovering the genetic causes of CHDs. In this Special Article, while considering other in vitro and in vivo models, we create a coherent framework for accurately modelling and phenotyping human CHDs in mice, thereby enhancing the translation of genetic and genomic studies into the causes of CHDs in patients.

Prenatal detection of novel compound heterozygous variants of the PLD1 gene in a fetus with congenital heart disease

Background

Congenital heart disease (CHD) is the most common birth defect and heart valve defects are the most common cardiac defect, accounting for over 25% of all congenital heart diseases. To date, more than 400 genes have been linked to CHD, the genetic analysis of CHD cases is crucial for both clinical management and etiological determination. Patients with autosomal-recessive variants of PLD1 are predisposed to Cardiac Valvular Dysplasia-1 (CVDP1), which predominantly affects the right-sided heart valves, including the pulmonic, tricuspid, and mitral valves.

Methods

Databases were utilized to predict the impact of the c.1062-59A>G variant on splicing. Whole-exome sequencing (WES), reverse transcription polymerase chain reaction (RT-PCR), Sanger sequencing, and TA clone sequencing were conducted on both the parents and the fetus.

Results

A compound heterozygous variation in the PLD1(NM_002662.5):c.1937G>C (p. G646A) from the father and PLD1(NM_002662.5):c.1062-59A>G from the mother, was identified and confirmed in the fetus. The c.1937G>C (p. G646A) and the c.1062-59A>G variants were all classified as variant of uncertain significance (VUS) per ACMG guidelines. RT-PCR and TA clone sequencing revealed a 76-bp intronic insertion and exon 11 skipping in the proband and her mother's transcripts, causing a frameshift and premature stop codon in PLD1. Consequently, after being informed about the risks of their variant of unknown significance (VUS), the couple chose pre-implantation genetic testing for monogenic disorders (PGT-M) and had a healthy child.

Conclusion

Our study identified novel variants to expand the mutation spectrum of CHD and provided reliable evidence for the recurrent risk and reproductive care options.

The mitochondrial citrate carrier SLC25A1 regulates metabolic reprogramming and morphogenesis in the developing heart

The developing mammalian heart undergoes an important metabolic shift from glycolysis towards mitochondrial oxidation that is critical to support the increasing energetic demands of the maturing heart. Here, we describe a new mechanistic link between mitochondria and cardiac morphogenesis, uncovered by studying mitochondrial citrate carrier (SLC25A1) knockout mice. Slc25a1 null embryos displayed impaired growth, mitochondrial dysfunction and cardiac malformations that recapitulate the congenital heart defects observed in 22q11.2 deletion syndrome, a microdeletion disorder involving the SLC25A1 locus. Importantly, Slc25a1 heterozygous embryos, while overtly indistinguishable from wild type, exhibited an increased frequency of these defects, suggesting Slc25a1 haploinsuffiency and dose-dependent effects. Mechanistically, SLC25A1 may link mitochondria to transcriptional regulation of metabolism through epigenetic control of gene expression to promote metabolic remodeling in the developing heart. Collectively, this work positions SLC25A1 as a novel mitochondrial regulator of cardiac morphogenesis and metabolic maturation, and suggests a role in congenital heart disease.

Emc1 is essential for vision and zebrafish photoreceptor outer segment morphogenesis

Inherited retinal diseases (IRDs) are a rare group of eye disorders characterized by progressive dysfunction and degeneration of retinal cells. In this study, we characterized the raifteirí (raf) zebrafish, a novel model of inherited blindness, identified through an unbiased ENU mutagenesis screen. A mutation in the largest subunit of the endoplasmic reticulum membrane protein complex, emc1 was subsequently identified as the causative raf mutation. We sought to elucidate the cellular and molecular phenotypes in the emc1-/- knockout model and explore the association of emc1 with retinal degeneration. Visual behavior and retinal electrophysiology assays demonstrated that emc1-/- mutants had severe visual impairments. Retinal histology and morphometric analysis revealed extensive abnormalities, including thinning of the photoreceptor layer, in addition to large gaps surrounding the lens. Notably, photoreceptor outer segments were drastically smaller, outer segment protein expression was altered and hyaloid vasculature development was disrupted. Transcriptomic profiling identified cone and rod-specific phototransduction genes significantly downregulated by loss of emc1. These data shed light on why emc1 is a causative gene in inherited retinal disease and how outer segment morphogenesis is regulated.

Genetic counselors and congenital heart disease: Clinical roles, genetic testing practices, and perceived genetic testing utility

Genetic counseling and genetic testing are essential for individuals with congenital heart disease/defects (CHD/CHDs). However, the clinical practices of genetic counselors (GCs) and their preferences for different CHD genetic testing strategies are previously unexplored. To address these gaps, GCs (n = 112) representing diverse specialties completed an online survey regarding their counseling and testing practices for syndromic CHD and apparently isolated/non-syndromic CHDs (iCHD). We found practice variability around family screening recommendations, with prenatal respondents reporting lower prevalence of this practice for iCHDs (p = 0.0004). We found that all specialties considered chromosomal microarray (CMA) the most common prioritized genetic test for syndromic and iCHD, while more prenatal respondents considered FISH and karyotype useful for iCHDs compared to postnatal respondents (p = 0.0002 and p = 0.002, respectively). Among postnatal respondents, a higher proportion considered exome/genome sequencing as useful compared to prenatal respondents (p = 0.0159); specifically, postnatal respondents' preference for exome/genome sequencing for iCHDs was ~2.6-fold higher than prenatal respondents. We estimated participants' assessment of utility for different genetic testing modalities for iCHDs and found that prenatal respondents assigned higher mean utility to FISH (p = 0.0002), karyotype (p = 0.0006), and CMA (p < 0.0001). There were relatively moderate to decreased utility scores for gene panels and exome/genome sequencing for iCHDs compared to cytogenetic testing, across all specialties. Overall, these results provide insight into GC practices and use of various genetic testing strategies for syndromic CHDs and iCHDs. Findings may help inform and/or standardize clinical practices for CHD genetic testing, though additional studies are warranted.

Trisomy 21 and Congenital Heart Disease: Impact on Health and Functional Outcomes From Birth Through Adolescence: A Scientific Statement From the American Heart Association

Due to improvements in recognition and management of their multisystem disease, the long-term survival of infants, children, and adolescents with trisomy 21 and congenital heart disease now matches children with congenital heart disease and no genetic condition in many scenarios. Although this improved survival is a triumph, individuals with trisomy 21 and congenital heart disease have unique and complex care needs in the domains of physical, developmental, and psychosocial health, which affect functional status and quality of life. Pulmonary hypertension and single ventricle heart disease are 2 known cardiovascular conditions that reduce life expectancy in individuals with trisomy 21. Multisystem involvement with respiratory, endocrine, gastrointestinal, hematological, neurological, and sensory systems can interact with cardiovascular health concerns to amplify adverse effects. Neurodevelopmental, psychological, and functional challenges can also affect quality of life. A highly coordinated interdisciplinary care team model, or medical home, can help address these complex and interactive conditions from infancy through the transition to adult care settings. The purpose of this Scientific Statement is to identify ongoing cardiovascular and multisystem, developmental, and psychosocial health concerns for children with trisomy 21 and congenital heart disease from birth through adolescence and to provide a framework for monitoring and management to optimize quality of life and functional status.

Ortholog of autism candidate gene RBM27 regulates mitoribosomal assembly factor MALS-1 to protect against mitochondrial dysfunction and axon degeneration during neurodevelopment

Mitochondrial dysfunction is thought to be a key component of neurodevelopmental disorders such as autism, intellectual disability, and attention-deficit hyperactivity disorder (ADHD). However, little is known about the molecular mechanisms that protect against mitochondrial dysfunction during neurodevelopment. Here, we address this question through the investigation of rbm-26, the Caenorhabditis elegans ortholog of the RBM27 autism candidate gene, which encodes an RNA-binding protein whose role in neurons is unknown. We report that RBM-26 (RBM26/27) protects against axonal defects by negatively regulating expression of the MALS-1 (MALSU1) mitoribosomal assembly factor. Autism-associated missense variants in RBM-26 cause a sharp decrease in RBM-26 protein expression along with defects in axon overlap and axon degeneration that occurs during larval development. Using a biochemical screen, we identified the mRNA for the MALS-1 mitoribosomal assembly factor as a binding partner for RBM-26. Loss of RBM-26 function causes a dramatic overexpression of mals-1 mRNA and MALS-1 protein. Moreover, genetic analysis indicates that this overexpression of MALS-1 is responsible for the mitochondrial and axon degeneration defects in rbm-26 mutants. These observations reveal a mechanism that regulates expression of a mitoribosomal assembly factor to protect against axon degeneration during neurodevelopment.

Validation of a Paralimbic-Related Subcortical Brain Dysmaturation MRI Score in Infants with Congenital Heart Disease

Background: Brain magnetic resonance imaging (MRI) of infants with congenital heart disease (CHD) shows brain immaturity assessed via a cortical-based semi-quantitative score. Our primary aim was to develop an infant paralimbic-related subcortical-based semi-quantitative dysmaturation score, termed brain dysplasia score (BDS), to detect abnormalities in CHD infants compared to healthy controls and secondarily to predict clinical outcomes. We also validated our BDS in a preclinical mouse model of hypoplastic left heart syndrome. Methods: A paralimbic-related subcortical BDS, derived from structural MRIs of infants with CHD, was compared to healthy controls and correlated with clinical risk factors, regional cerebral volumes, feeding, and 18-month neurodevelopmental outcomes. The BDS was validated in a known CHD mouse model named Ohia with two disease-causing genes, Sap130 and Pchda9. To relate clinical findings, RNA-Seq was completed on Ohia animals. Findings: BDS showed high incidence of paralimbic-related subcortical abnormalities (including olfactory, cerebellar, and hippocampal abnormalities) in CHD infants (n = 215) compared to healthy controls (n = 92). BDS correlated with reduced cortical maturation, developmental delay, poor language and feeding outcomes, and increased length of stay. Ohia animals (n = 63) showed similar BDS findings, and RNA-Seq analysis showed altered neurodevelopmental and feeding pathways. Sap130 mutants correlated with a more severe BDS, whereas Pcdha9 correlated with a milder phenotype. Conclusions: Our BDS is sensitive to dysmaturational differences between CHD and healthy controls and predictive of poor outcomes. A similar spectrum of paralimbic and subcortical abnormalities exists between human and Ohia mutants, suggesting a common genetic mechanistic etiology.

Loss-of-function of RNA-binding protein PRRC2B causes translational defects and congenital cardiovascular malformation

Alternative splicing generates variant forms of proteins for a given gene and accounts for functional redundancy or diversification. A novel RNA-binding protein, Pro-rich Coiled-coil Containing Protein 2B (PRRC2B), has been reported by multiple laboratories to mediate uORF-dependent and independent regulation of translation initiation required for cell cycle progression and proliferation. We identified two alternative spliced isoforms in human and mouse hearts and HEK293T cells, full-length (FL) and exon 16-excluded isoform ΔE16. A congenital heart disease-associated human mutation-mimicry knock-in of the equivalent variant in the mouse genome leads to the depletion of the full-length Prrc2b mRNA but not the alternative spliced truncated form ΔE16, does not cause any apparent structural or functional disorders. In contrast, global genetic inactivation of the PRRC2B gene in the mouse genome, nullifying both mRNA isoforms, caused patent ductus arteriosus (PDA) and neonatal lethality in mice. Bulk and single nucleus transcriptome profiling analyses of embryonic mouse hearts demonstrated a significant overall downregulation of multiple smooth muscle-specific genes in Prrc2b mutant mice resulting from reduced smooth muscle cell number. Integrated analysis of proteomic changes in Prrc2b null mouse embryonic hearts and polysome-seq and RNA-seq multi-omics analysis in human HEK293T cells uncover conserved PRRC2B-regulated target mRNAs that encode essential factors required for cardiac and vascular development. Our findings reveal the connection between alternative splicing regulation of PRRC2B, PRRC2B-mediated translational control, and congenital cardiovascular development and disorder. This study may shed light on the significance of PRRC2B in human cardiovascular disease diagnosis and treatment.

Psychiatric morbidity and work participation in patients with congenital ventricular septal defects: a case-controlled study

BACKGROUND

The burden of psychiatric morbidity, level of education, and work participation are currently unknown in patients with congenital ventricular septal defects (VSD).

METHODS AND RESULTS

In a Danish population-based cohort study using nationwide medical registries, the burden of psychiatric disorders, use of psychotropic agents, level of education, and work participation were examined in patients with isolated congenital VSD and controls from the general population matched by age and sex. Subjects with known chromosomal abnormalities were excluded. To compute estimates, Cox proportional regression model, Fine and Gray's competing risk regression, and Kaplan-Meier failure function were used. We included 8006 patients and 79 568 controls born before 2018. Median follow-up was 23 years. Compared with controls, patients with VSD displayed a hazard ratio (HR) of 1.24 [95% confidence interval (CI): 1.17-1.32] for any psychiatric disorder where the hazard for intellectual disabilities was most pronounced [HR of 3.66 (95% CI: 2.98-4.50)]. The use of psychotropic agents was higher in patients compared with controls [HR 1.14 (95% CI: 1.09-1.20)]. The work participation was lower in patients with VSD compared with controls (P < 0.001) and was lower in patients with VSD with a psychiatric disorder compared with those without (P < 0.001). The 40-year cumulative incidence of permanent social security benefits was 29% in patients with psychiatric disorders (vs. 21% in controls with psychiatric disorders) and 8% in patients without psychiatric disorders (vs. 4% in controls).

CONCLUSION

Patients with isolated VSD suffer from a higher burden of psychiatric disorders and display lower work participation compared with matched controls from the general Danish population. It is important to consider longer-term impacts on mental health, education, and subsequent employment in patients with VSD, in addition to cardiovascular effects, as these factors severely affect quality of life and have direct socioeconomic implications on an individual and societal level.

FLT4 causes developmental disorders of the cardiovascular and lymphovascular systems via pleiotropic molecular mechanisms

AIMS

Rare, deleterious genetic variants in FLT4 are associated with Tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease. The distinct genetic variants in FLT4 are also an established cause of Milroy disease, the most prevalent form of primary hereditary lymphoedema. The phenotypic features of these two conditions are non-overlapping, implying pleiotropic cellular mechanisms during development.

METHODS AND RESULTS

In this study, we show that FLT4 variants identified in patients with TOF, when expressed in primary human endothelial cells, cause aggregation of FLT4 protein in the perinuclear endoplasmic reticulum, activating proteostatic and metabolic signalling, whereas lymphoedema-associated FLT4 variants and wild-type (WT) FLT4 do not. FLT4 TOF variants display characteristic gene expression profiles in key developmental signalling pathways, revealing a role for FLT4 in cardiogenesis distinct from its role in lymphatic development. Inhibition of proteostatic signalling abrogates these effects, identifying potential avenues for therapeutic intervention. Depletion of flt4 in zebrafish caused cardiac phenotypes of reduced heart size and altered heart looping. These phenotypes were rescued with coinjection of WT human FLT4 mRNA, but incompletely or not at all by mRNA harbouring FLT4 TOF variants.

CONCLUSION

Taken together, we identify a pathogenic mechanism for FLT4 variants predisposing to TOF that is distinct from the known dominant negative mechanism of Milroy-causative variants. FLT4 variants give rise to conditions of the two circulatory subdivisions of the vascular system via distinct developmental pleiotropic molecular mechanisms.

Population-Based Estimates of the Prevalence of Children With Congenital Heart Disease and Associated Comorbidities in the United States

BACKGROUND

Congenital heart defects (CHD) are the most common birth defects and previous estimates report the disease affects 1% of births annually in the United States. To date, CHD prevalence estimates are inconsistent due to varied definitions, data reliant on birth registries, and are geographically limited. These data sources may not be representative of the total prevalence of the CHD population. It is therefore important to derive high-quality, population-based estimates of the prevalence of CHD to help care for this vulnerable population.

METHODS

We performed a descriptive, retrospective 8-year analysis using all-payer claims data from Colorado from 2012 to 2019. Children with CHD were identified by applying International Classification of Diseases-Ninth Revision (ICD-9) and International Classification of Diseases-Tenth Revision (ICD-10) diagnosis codes from the American Heart Association-American College of Cardiology harmonized cardiac codes. We included children with CHD <18 years of age who resided in Colorado, had a documented zip code, and had at least 1 health care claim. CHD type was categorized as simple, moderate, and severe disease. Association with comorbid conditions and genetic diagnoses were analyzed using χ2 test. We used direct standardization to calculate adjusted prevalence rates, controlling for age, sex, primary insurance provider, and urban-rural residence.

RESULTS

We identified 1 566 328 children receiving care in Colorado from 2012 to 2019. Of those, 30 512 children had at least 1 CHD diagnosis, comprising 1.95% (95% CI, 1.93-1.97) of the pediatric population. Over half of the children with CHD also had at least 1 complex chronic condition. After direct standardization, the adjusted prevalence rates show a small increase in simple severity diagnoses across the study period (adjusted rate of 11.5 [2012]-14.4 [2019]; P<0.001).

CONCLUSIONS

The current study is the first population-level analysis of pediatric CHD in the United States. Using administrative claims data, our study found a higher CHD prevalence and comorbidity burden compared with previous estimates.