Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Sep 28:10:1249605.
doi: 10.3389/fcvm.2023.1249605. eCollection 2023.

Mutations in genes related to myocyte contraction and ventricular septum development in non-syndromic tetralogy of Fallot

Drayton C Harvey  1   2 , Riya Verma  1   3 , Brandon Sedaghat  4 , Brooke E Hjelm  5 , Sarah U Morton  6 , Jon G Seidman  7 , S Ram Kumar  1   8   9
Affiliations

Mutations in genes related to myocyte contraction and ventricular septum development in non-syndromic tetralogy of Fallot

Drayton C Harvey et al. Front Cardiovasc Med. .

Abstract

Objective: Eighty percent of patients with a diagnosis of tetralogy of Fallot (TOF) do not have a known genetic etiology or syndrome. We sought to identify key molecular pathways and biological processes that are enriched in non-syndromic TOF, the most common form of cyanotic congenital heart disease, rather than single driver genes to elucidate the pathogenesis of this disease.

Methods: We undertook exome sequencing of 362 probands with non-syndromic TOF and their parents within the Pediatric Cardiac Genomics Consortium (PCGC). We identified rare (minor allele frequency <1 × 10-4), de novo variants to ascertain pathways and processes affected in this population to better understand TOF pathogenesis. Pathways and biological processes enriched in the PCGC TOF cohort were compared to 317 controls without heart defects (and their parents) from the Simons Foundation Autism Research Initiative (SFARI).

Results: A total of 120 variants in 117 genes were identified as most likely to be deleterious, with CHD7, CLUH, UNC13C, and WASHC5 identified in two probands each. Gene ontology analyses of these variants using multiple bioinformatic tools demonstrated significant enrichment in processes including cell cycle progression, chromatin remodeling, myocyte contraction and calcium transport, and development of the ventricular septum and ventricle. There was also a significant enrichment of target genes of SOX9, which is critical in second heart field development and whose loss results in membranous ventricular septal defects related to disruption of the proximal outlet septum. None of these processes was significantly enriched in the SFARI control cohort.

Conclusion: Innate molecular defects in cardiac progenitor cells and genes related to their viability and contractile function appear central to non-syndromic TOF pathogenesis. Future research utilizing our results is likely to have significant implications in stratification of TOF patients and delivery of personalized clinical care.

Keywords: congenital heart defect; conotruncal defects; de novo variants; exome sequencing; tetralogy of fallot.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Variant call analysis of tetralogy of Fallot cohort. (A) Exome sequencing raw data was acquired from the Pediatric Cardiac Genomics Consortium (PCGC) for patients with non-syndromic tetralogy of Fallot (TOF) and Simons Foundation Autism Research Initiative (SFARI) for controls in the form of FASTQ and CRAM files respectively (which were converted to FASTQ format using samtools) for the proband and their associated parents. FASTQC and MultiQC were utilized to identify only high quality FASTQ files for analysis. All files were aligned to GRCh38 using BWA-MEM, then processed further according to GATK's best practices workflow until high confidence de novo variant calls were achieved for each trio. These variants were functionally annotated with snpEff, snpSift, and Annovar to identify variants that met our minor allele frequency threshold of 1 × 10−4 and were determined by snpEff (moderate or high impact) and the variant's CADD score (≥20) to likely be deleterious. (B) Initial variant calls included synonymous variants, which were first filtered down just to non-synonymous variants annotated as moderate or high impact by snpEff. Further filtering eliminated variants identified to be likely false positive calls and those with a minor allele frequency greater than 1 × 10−4. The number of variants was further reduced by filtering for only variants that had a defined CADD score of 20 or greater. A similar winnowing occurred with the SFARI cohort, however resulting in a smaller number of enriched pathways and processes in both the analysis of all non-synonymous variants (103) and only those with a CADD score of 20 or greater (59), all of which came from the Disease and Function analysis in IPA. * = Term enriched in both TOF and SFARI cohort. Figure generated with Biorender.com.
Figure 2
Figure 2
Critical pathways and biological processes enriched in non-syndromic tetralogy of Fallot. (A) While there are a variety of pathways and processes enriched in the analyses conducted on the de novo variants with a CADD score of 20 or greater identified from our cohort of non-syndromic tetralogy of Fallot, the most relevant can be considered in four main categories: those affecting the ventricle, the outflow tract, the ventricular septum, and extracardiac or more general pathways and processes (i.e. neural development, cell cycle progression). (B) The scale of how significantly enriched each term was determined by taking the negative log10 value of the B–H p-value (q-value) which has been corrected for multiple comparison testing. Cardiac related terms had an average -log10 of 2.19 ± 0.21 (S.E.M.), neural development 2.51 ± 0.87, cell development 2.25 ± 0.38, chromatin remodelling activity 1.56 ± 0.04, lipid metabolism 1.89 ± 0.11 and the transcription factor targets 1.36 ± 0.05. Figure generated with Biorender.com.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Zimmerman MS, Smith AGC, Sable CA, Echko MM, Wilner LB, Olsen HE, et al. Global, regional, and national burden of congenital heart disease, 1990–2017: a systematic analysis for the global burden of disease study 2017. Lancet Child Adolesc Health. (2020) 4(3):185–200. 10.1016/S2352-4642(19)30402-X - DOI - PMC - PubMed
    1. Egbe A, Uppu S, Stroustrup A, Lee S, Ho D, Srivastava S. Incidences and sociodemographics of specific congenital heart diseases in the United States of America: an evaluation of hospital discharge diagnoses. Pediatr Cardiol. (2014) 35(6):975–82. 10.1007/s00246-014-0884-8 - DOI - PubMed
    1. Hoffman JIE, Kaplan S. The incidence of congenital heart disease. J Am Coll Cardiol. (2002) 39(12):1890–900. 10.1016/S0735-1097(02)01886-7 - DOI - PubMed
    1. Simeone RM, Oster ME, Cassell CH, Armour BS, Gray DT, Honein MA. Pediatric inpatient hospital resource use for congenital heart defects. Birth Defects Res A Clin Mol Teratol. (2014) 100(12):934–43. 10.1002/bdra.23262 - DOI - PMC - PubMed
    1. Neill CA, Clark EB. Tetralogy of Fallot. The first 300 years. Tex Heart Inst J. (1994) 21(4):272–9. PMCID: - PMC - PubMed