Theis, Jeanne L.

Background: Deciphering hypoplastic left heart syndrome (HLHS) pathogenesis is confounded by its genetic heterogeneity and oligogenic underpinnings. Methods: Whole genome sequences were analyzed by 3 independent strategies to identify HLHS gene candidates, ranked by variant, gene, and disease-level metrics. Results: First, a genome-wide association study of 174 cases and 853 controls revealed suggestive association with a MYO18B intron 33 variant (rs2269628-G; frequency=0.55 versus 0.39; OR, 1.97 [95% CI, 1.54–2.52]; P =6.70×10 − 8 ). Second, transmission disequilibrium testing of 161 HLHS proband-parent trios revealed overrepresentation of a MYO18B intron 42 variant (rs73154186-A; frequency=0.05; OR, 24 [95% CI, 3.2–177.4]; P =4.23×10 − 6 ). Third, rare, predicted-damaging variants were filtered in 2 multiplex families. In 141H, 2 fifth-degree relatives with HLHS shared a paternally-inherited MYO5A missense variant (p.Arg801Trp; frequency=0.00003; combined annotation-dependent depletion score=29), each with a maternally-inherited or de novo candidate modifier variant in a MYO5A-interacting conventional myosin. In 442H, a HLHS proband was compound heterozygous for MYO15A variants—a maternally-inherited pathogenic stop-gain variant co-segregating with tetralogy of Fallot and bicuspid aortic valve in maternal relatives (p.Tyr2819Ter; frequency=0.00003) and a paternally-inherited intronic variant altering a canonical transcription factor binding site (rs1277068603; frequency=0.00001; position weight matrix score=0.98). Conclusions: Collectively, these findings suggest that common and rare alleles within unconventional myosin genes are associated with HLHS susceptibility. The identified candidate MYO18B regulates cardiac sarcomerogenesis, supporting the hypothesis of intrinsic myogenic perturbation in arrested left heart development.

Hypoplastic left heart syndrome (HLHS) is a genetically complex disorder. Whole genome sequencing enables comprehensive scrutiny of single nucleotide variants and small insertions/deletions, within both coding and regulatory regions of the genome, revolutionizing susceptibility-gene discovery research. Because millions of rare variants comprise an individual genome, identification of alleles linked to HLHS necessitates filtering algorithms based on various parameters, such as inheritance, enrichment, omics data, known genotype–phenotype associations, and predictive or experimental modeling. In this brief review, we highlight family and cohort-based strategies used to analyze whole genome sequencing datasets and identify HLHS candidate genes. Key findings include compound and digenic heterozygosity among several prioritized genes and genetic associations between HLHS and bicuspid aortic valve or cardiomyopathy. Together with findings of independent genomic investigations, MYH6 has emerged as a compelling disease gene for HLHS and other left-sided congenital heart diseases.

Background: Whole-genome sequencing in families enables deciphering of congenital heart disease causes. A shared genetic basis for familial bicuspid aortic valve (BAV) and hypoplastic left heart syndrome (HLHS) was postulated. Methods: Whole-genome sequencing was performed in affected members of 6 multiplex BAV families, an HLHS cohort of 197 probands and 546 relatives, and 813 controls. Data were filtered for rare, predicted-damaging variants that cosegregated with familial BAV and disrupted genes associated with congenital heart disease in humans and mice. Candidate genes were further prioritized by rare variant burden testing in HLHS cases versus controls. Modifier variants in HLHS proband-parent trios were sought to account for the severe developmental phenotype. Results: In 5 BAV families, missense variants in 6 ontologically diverse genes for structural ( SPTBN1 , PAXIP1 , and FBLN1 ) and signaling ( CELSR1 , PLXND1 , and NOS3 ) proteins fulfilled filtering metrics. CELSR1 , encoding cadherin epidermal growth factor laminin G seven-pass G-type receptor, was identified as a candidate gene in 2 families and was the only gene demonstrating rare variant enrichment in HLHS probands ( P =0.003575). HLHS-associated CELSR1 variants included 16 missense, one splice site, and 3 noncoding variants predicted to disrupt canonical transcription factor binding sites, most of which were inherited from a parent without congenital heart disease. Filtering whole-genome sequencing data for rare, predicted-damaging variants inherited from the other parent revealed 2 cases of CELSR1 compound heterozygosity, one case of CELSR1 - CELSR3 synergistic heterozygosity, and 4 cases of CELSR1 - MYO15A digenic heterozygosity. Conclusions: CELSR1 is a susceptibility gene for familial BAV and HLHS, further implicating planar cell polarity pathway perturbation in congenital heart disease.

Hypoplastic Left Heart Syndrome (HLHS) is a complex multifactorial disease for which no definitive genetic causes have been found. Current genetic filtering strategies render lists of genes with unknown relevance in terms of pathogenesis. A complementary filter based on biological evidence would create a new approach to prioritize relevant candidate genes and mutations. In our study, 5 members of a nuclear family including a child with HLHS were evaluated using echocardiography and their genetic information was obtained through whole genome sequencing (WGS). Data filtering including rarity, functional impact and mode of inheritance was implemented, resulting in identification of 34 genes with recessive or de novo variants potentially involved in the pathogenesis of HLHS. Additionally, iPSC were derived from proband and parents and subjected to RNA-sequencing at the undifferentiated state and following spontaneous differentiation. Comparative transcriptional analyses identified genes differentially expressed in proband samples at each stage. These gene sets were used as an additional filter for the previously generated WGS data. This strategy revealed that out of 34 mutated genes originally identified, 10 displayed transcriptional differences in undifferentiated iPSC from the HLHS-affected individual while 16 out of 34 mutated genes showed significantly different expression levels in differentiated cells from proband. Furthermore, expression dynamics were studied during guided cardiac differentiation for the 9 genes fulfilling all applied criteria. Two genes not previously linked to HLHS, ELF4 and HSPG2 were found to behave significantly different in HLHS-iPSC when compared to control counterparts. In summary, filtering WGS data according to a new layer of transcriptional information that leverages iPSC plasticity allows prioritization of genes associated with HLHS in an in vitro model of disease.

Background: Mutations in sarcomeric/myofilament proteins are commonly implicated in hypertrophic cardiomyopathy (HCM). However, the mechanisms underlying disease pathogenesis are not completely understood. Utilizing flash-frozen surgically resected left ventricular (LV) tissue from patients with obstructive HCM, we investigated the effect of sarcomeric HCM on tissue expression of various myofilament proteins. Methods: Frozen surgical specimens from 47 patients with HCM who underwent septal myectomy at the Mayo Clinic between 1999 and 2003 were examined. Using PCR, DHPLC, and direct DNA sequencing, all were genotyped for mutations involving the 8 myofilament-encoding genes that currently comprise the clinically available genetic test for sarcomeric HCM. Whole protein lysate was extracted from the frozen myectomy tissues and levels of myosin binding protein C, myosin heavy chain, alpha actin and alpha actinin were analyzed by Western Blot; GAPDH was used as a loading control. Frozen LV tissue derived from normal hearts of accidental death victims served as a reference group. Results: Overall, 25/47 (53%) patients had sarcomeric HCM including 13 patients with myosin binding protein C (MYBPC3) mutations and 10 with mutations in the beta myosin heavy chain (MYH7). Compared to normal heart tissue, the expression of myosin heavy chain was up-regulated significantly regardless of the underlying disease-causing genotype (genotype positive = genotype negative). However, there was gene-specific upregulation of myosin binding protein C with marked increases detected in patients with MYH7-HCM. In contrast, normal levels of myosin binding protein C were seen in patients with either MYBPC3-HCM or genotype-negative HCM. Conclusions: This is the first study to examine the expression pattern of sarcomeric proteins in a large collection of flash frozen human HCM myectomy tissue. Up-regulated, genotype-specific cardiac tissue expression of myosin binding protein C among patients with MYH7 (beta myosin heavy chain)-HCM suggests a novel compensatory pathway underlying the development of cardiac hypertrophy for one of most common genetic subtypes of HCM.

Background: Mutations in MYBPC3 -encoded myosin binding protein C underlie the most common genotype in hypertrophic cardiomyopathy (HCM). Compared to most HCM-associated mutations which are primarily missense mutations, MYBPC3-HCM is often caused by insertions, deletions, nonsense mutations or mutations involving the canonical splice site. However, the effects of most mutations that prematurely truncate MYBPC3 are unknown. Access to cardiac specific mRNA and tissue has permitted a molecular and cellular elucidation of the consequences of two splice site mutations. Methods: Mutational analysis of MYBPC3 revealed 2 HCM-susceptibility mutations involving the splice donor sites of exons 7 and 30. Reverse transcription was performed on cDNA generated from RNA extracted from cardiac tissue obtained following surgical myectomy. Western blot analysis and immunohistochemistry (IHC) of the myofilaments were performed to further assess the impact of the splice-site mutations. Results: Both splice donor mutations produced abnormal RNA splicing of MYBPC3. The c.821+1 g>a mutation in the splice donor site of exon 7 generated two alternatively-spliced mutant transcripts resulting in two frame-shifted, premature truncations (H257 fs/37 and H257 fs/15). The c.3330+2 t>g mutation in exon 30’s splice donor site produced a single alternatively-spliced mutant transcript that translated into a frame-shifted premature truncation (V1063 fs/37). Expression levels of wild type myosin binding protein C were decreased in the myectomy specimen from the patient with the exon 7 splice donor site mutation. By IHC, the spatial organization of myosin binding protein C was disrupted severely in both patients. Conclusions: This study provides the first molecular and cellular characterization of HCM-causing mutations involving canonical splice-site motifs within the intron. Loss of function of the splice site resulted in exon skipping and generation of frame-shifted and prematurely truncated myosin binding protein C and disruption of the distribution and organization of myosin binding protein C in the heart tissue. This research has received full or partial funding support from the American Heart Association, AHA Midwest Affiliate (Illinois, Indiana, Iowa, Kansas, Michigan, Minnesota, Missouri, Nebraska, North Dakota, South Dakota & Wisconsin).

Background: Hypoplastic left heart syndrome (HLHS) with risk of poor outcome has been linked to MYH6 variants, implicating overlap in genetic etiologies of structural and myopathic heart disease. Methods: Whole genome sequencing was performed in 197 probands with HLHS, 43 family members, and 813 controls. Data were filtered for rare, segregating variants in 3 index families comprised of an HLHS proband and relative(s) with cardiomyopathy. Whole genome sequencing data from cases and controls were compared for rare variant burden across 56 cardiomyopathy genes utilizing a weighted burden test approach, accounting for multiple testing using a Bonferroni correction. Results: A pathogenic MYBPC3 nonsense variant was identified in the first proband who underwent cardiac transplantation for diastolic heart failure, her father with left ventricular noncompaction, and 2 fourth-degree relatives with hypertrophic cardiomyopathy. A likely pathogenic RYR2 missense variant was identified in the second proband, a second-degree relative with aortic dilation, and a fourth-degree relative with dilated cardiomyopathy. A pathogenic RYR2 exon 3 in-frame deletion was identified in the third proband diagnosed with catecholaminergic polymorphic ventricular tachycardia and his father with left ventricular noncompaction and catecholaminergic polymorphic ventricular tachycardia. To further investigate HLHS-cardiomyopathy gene associations in cases versus controls, rare variant burden testing of 56 genes revealed enrichment in MYH6 ( P =0.000068). Rare, predicted-damaging MYH6 variants were identified in 10% of probands in our cohort—4 with familial congenital heart disease, 4 with compound heterozygosity (3 with systolic ventricular dysfunction), and 4 with MYH6 – FLNC synergistic heterozygosity. Conclusions: Whole genome sequencing in multiplex families, proband-parent trios, and case-control cohorts revealed defects in cardiomyopathy-associated genes in patients with HLHS, which may portend impaired functional reserve of the single-ventricle circulation.

Congenital heart diseases (CHDs), including hypoplastic left heart syndrome (HLHS), are genetically complex and poorly understood. Here, a multidisciplinary platform was established to functionally evaluate novel CHD gene candidates, based on whole-genome and iPSC RNA sequencing of a HLHS family-trio. Filtering for rare variants and altered expression in proband iPSCs prioritized 10 candidates. siRNA/RNAi-mediated knockdown in healthy human iPSC-derived cardiomyocytes (hiPSC-CM) and in developing Drosophila and zebrafish hearts revealed that LDL receptor-related protein LRP2 is required for cardiomyocyte proliferation and differentiation. Consistent with hypoplastic heart defects, compared to parents the proband’s iPSC-CMs exhibited reduced proliferation. Interestingly, rare, predicted-damaging LRP2 variants were enriched in a HLHS cohort; however, understanding their contribution to HLHS requires further investigation. Collectively, we have established a multi-species high-throughput platform to rapidly evaluate candidate genes and their interactions during heart development, which are crucial first steps toward deciphering oligogenic underpinnings of CHDs, including hypoplastic left hearts.