The Needle in the Haystack—Searching for Genetic and Epigenetic Differences in Monozygotic Twins Discordant for Tetralogy of Fallot

Congenital heart defects (CHDs) are the most common birth defect in human with an incidence of almost 1% of all live births. Most cases have a multifactorial origin with both genetics and the environment playing a role in its development and progression. Adding an epigenetic component to this aspect is exemplified by monozygotic twins which share the same genetic background but have a different disease status. As a result, the interplay between the genetic, epigenetic and the environmental conditions might contribute to the etiology and phenotype. To date, the underlying causes of the majority of CHDs remain poorly understood. In this study, we performed genome-wide high-throughput sequencing to examine the genetic, structural genomic and epigenetic differences of two identical twin pairs discordant for Tetralogy of Fallot (TOF), representing the most common cyanotic form of CHDs. Our results show the almost identical genetic and structural genomic identity of the twins. In contrast, several epigenetic alterations could be observed given by DNA methylation changes in regulatory regions of known cardiac-relevant genes. Overall, this study provides first insights into the impact of genetic and especially epigenetic factors underlying monozygotic twins discordant for CHD like TOF.

[1]  J. Nora,et al.  Multifactorial Inheritance Hypothesis for the Etiology of Congenital Heart Diseases: The Genetic‐Environmental Interaction , 1968, Circulation.

[2]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[3]  N. Fisk,et al.  Influence of twin-twin transfusion syndrome on fetal cardiovascular structure and function: prospective case–control study of 136 monochorionic twin pregnancies , 2002, Heart.

[4]  Martin Vingron,et al.  Genome-Wide Array Analysis of Normal and Malformed Human Hearts , 2003, Circulation.

[5]  P. Boccuni,et al.  The Human L(3)MBT Polycomb Group Protein Is a Transcriptional Repressor and Interacts Physically and Functionally with TEL (ETV6)* , 2003, The Journal of Biological Chemistry.

[6]  B. Bruneau,et al.  Tbx20 dose-dependently regulates transcription factor networks required for mouse heart and motoneuron development , 2005, Development.

[7]  G. Nemer,et al.  Differential duplication of an intronic region in the NFATC1 gene in patients with congenital heart disease. , 2006, Genome.

[8]  Mauro W. Costa,et al.  Mutations in cardiac T-box factor gene TBX20 are associated with diverse cardiac pathologies, including defects of septation and valvulogenesis and cardiomyopathy. , 2007, American journal of human genetics.

[9]  D. Reinberg,et al.  L3MBTL1, a Histone-Methylation-Dependent Chromatin Lock , 2007, Cell.

[10]  M. Vingron,et al.  Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes. , 2008, Molecular bioSystems.

[11]  Wei Chen,et al.  High frequency of submicroscopic genomic aberrations detected by tiling path array comparative genome hybridisation in patients with isolated congenital heart disease , 2008, Journal of Medical Genetics.

[12]  A. Zinn,et al.  Cryptic Chromosomal Abnormalities Identified in Children With Congenital Heart Disease , 2008, Pediatric Research.

[13]  Joshua M. Korn,et al.  De Novo Copy Number Variants Identify New Genes and Loci in Isolated, Sporadic Tetralogy of Fallot , 2009, Nature Genetics.

[14]  J. Zuccollo,et al.  A Case of Amyoplasia in a Monochorionic Twin Pregnancy: A Sequela from Twin-Twin Transfusion Syndrome? , 2009, Fetal Diagnosis and Therapy.

[15]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[16]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[17]  A. Feinberg,et al.  Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores , 2008, Nature Genetics.

[18]  M. Schueler,et al.  Evaluation of the LightCycler 1536 Instrument for high-throughput quantitative real-time PCR. , 2010, Methods.

[19]  H. Hense,et al.  Prevalence of Congenital Heart Defects in Newborns in Germany: Results of the First Registration Year of the PAN Study (July 2006 to June 2007) , 2010, Klinische Padiatrie.

[20]  Yaniv Erlich Blood Ties: Chimerism Can Mask Twin Discordance in High-Throughput Sequencing , 2011, Twin Research and Human Genetics.

[21]  M. Pellegrini,et al.  A comparative analysis of DNA methylation across human embryonic stem cell lines , 2011, Genome Biology.

[22]  L. Ponto,et al.  Effect of insulin and dexamethasone on fetal assimilation of maternal glucose. , 2011, Endocrinology.

[23]  A. Bird,et al.  CpG islands and the regulation of transcription. , 2011, Genes & development.

[24]  K. Devriendt,et al.  Differences in Copy Number Variation between Discordant Monozygotic Twins as a Model for Exploring Chromosomal Mosaicism in Congenital Heart Defects , 2012, Molecular Syndromology.

[25]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[26]  M. Cleves,et al.  Maternal Genome-Wide DNA Methylation Patterns and Congenital Heart Defects , 2011, PloS one.

[27]  J. Roos‐Hesselink,et al.  Birth prevalence of congenital heart disease worldwide: a systematic review and meta-analysis. , 2011, Journal of the American College of Cardiology.

[28]  Duan Ma,et al.  LINE-1 methylation status and its association with tetralogy of fallot in infants , 2012, BMC Medical Genomics.

[29]  C. Struble,et al.  Human gene copy number spectra analysis in congenital heart malformations. , 2012, Physiological genomics.

[30]  G. Ebers,et al.  Genetic, environmental and stochastic factors in monozygotic twin discordance with a focus on epigenetic differences , 2012, BMC Medicine.

[31]  A. Zinn,et al.  Submicroscopic Chromosomal Copy Number Variations Identified in Children With Hypoplastic Left Heart Syndrome , 2012, Pediatric Cardiology.

[32]  A. Visel,et al.  Large-Scale Discovery of Enhancers from Human Heart Tissue , 2011, Nature Genetics.

[33]  G. Nemer,et al.  Two Heterozygous Mutations in NFATC1 in a Patient with Tricuspid Atresia , 2012, PloS one.

[34]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[35]  S. Lipshultz,et al.  Myocardial Alternative RNA Splicing and Gene Expression Profiling in Early Stage Hypoplastic Left Heart Syndrome , 2012, PloS one.

[36]  Marc Gewillig,et al.  Contribution of global rare copy-number variants to the risk of sporadic congenital heart disease. , 2012, American journal of human genetics.

[37]  G. Lofland,et al.  Noncoding RNA Expression in Myocardium From Infants With Tetralogy of Fallot , 2012, Circulation. Cardiovascular genetics.

[38]  Daniele Merico,et al.  Rare Copy Number Variations in Adults with Tetralogy of Fallot Implicate Novel Risk Gene Pathways , 2012, PLoS genetics.

[39]  Tatiana Popova,et al.  Supplementary Methods , 2012, Acta Neuropsychiatrica.

[40]  Peter A. Jones Functions of DNA methylation: islands, start sites, gene bodies and beyond , 2012, Nature Reviews Genetics.

[41]  S. Scherer,et al.  Rare Copy Number Variants Contribute to Congenital Left-Sided Heart Disease , 2012, PLoS genetics.

[42]  A. Gnirke,et al.  Charting a dynamic DNA methylation landscape of the human genome , 2013, Nature.

[43]  Hui-jun Wang,et al.  DNA methylation status of NKX2-5, GATA4 and HAND1in patients with tetralogy of fallot , 2013, BMC Medical Genomics.

[44]  Duan Ma,et al.  Association of promoter methylation statuses of congenital heart defect candidate genes with Tetralogy of Fallot , 2014, Journal of Translational Medicine.

[45]  L. Larsen,et al.  Of mice and men: molecular genetics of congenital heart disease , 2013, Cellular and Molecular Life Sciences.

[46]  D. Bittel,et al.  A tissue-specific gene expression template portrays heart development and pathology , 2014, Human Genomics.

[47]  W. Mahle What we can learn from twins: congenital heart disease in the danish twin registry. , 2013, Circulation.

[48]  B. Yamrom,et al.  The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease , 2013, Human Genetics.

[49]  J. Seidman,et al.  Genetics of congenital heart disease: the glass half empty. , 2013, Circulation research.

[50]  I. Adzhubei,et al.  Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2 , 2013, Current protocols in human genetics.

[51]  Murim Choi,et al.  De novo mutations in histone modifying genes in congenital heart disease , 2013, Nature.

[52]  Bin Zhou,et al.  Nfatc1 directs the endocardial progenitor cells to make heart valve primordium. , 2013, Trends in cardiovascular medicine.

[53]  Fei Gao,et al.  An integrated epigenomic analysis for type 2 diabetes susceptibility loci in monozygotic twins , 2014, Nature Communications.

[54]  Vikas Bansal,et al.  Outlier-Based Identification of Copy Number Variations Using Targeted Resequencing in a Small Cohort of Patients with Tetralogy of Fallot , 2014, PloS one.

[55]  R. Hetzer,et al.  Rare and private variations in neural crest, apoptosis and sarcomere genes define the polygenic background of isolated Tetralogy of Fallot. , 2014, Human molecular genetics.

[56]  T. Spector,et al.  Epigenetics of discordant monozygotic twins: implications for disease , 2014, Genome Medicine.

[57]  Yiping Shen,et al.  Chromosome microarray testing for patients with congenital heart defects reveals novel disease causing loci and high diagnostic yield , 2014, BMC Genomics.

[58]  D. Bittel,et al.  Ultra High-Resolution Gene Centric Genomic Structural Analysis of a Non-Syndromic Congenital Heart Defect, Tetralogy of Fallot , 2014, PloS one.

[59]  S. Kulawonganunchai,et al.  Whole Genome and Exome Sequencing of Monozygotic Twins with Trisomy 21, Discordant for a Congenital Heart Defect and Epilepsy , 2014, PloS one.

[60]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[61]  Yongseok Park,et al.  MethylSig: a whole genome DNA methylation analysis pipeline , 2014, Bioinform..

[62]  Jana Marie Schwarz,et al.  MutationTaster2: mutation prediction for the deep-sequencing age , 2014, Nature Methods.

[63]  Identification of Copy Number Variations in Isolated Tetralogy of Fallot , 2015, Pediatric Cardiology.

[64]  Joel D. Kaufman,et al.  Environmental factors in cardiovascular disease , 2015, Nature Reviews Cardiology.

[65]  A. Karimpour-Fard,et al.  Micro-RNA expression in hypoplastic left heart syndrome. , 2015, Journal of cardiac failure.

[66]  P. Nürnberg,et al.  Whole-Exome Sequencing in Nine Monozygotic Discordant Twins , 2015, Twin Research and Human Genetics.

[67]  P. Shen,et al.  A Rapid, High-Quality, Cost-Effective, Comprehensive and Expandable Targeted Next-Generation Sequencing Assay for Inherited Heart Diseases. , 2015, Circulation research.

[68]  M. Riegel,et al.  Cytogenomic Evaluation of Subjects with Syndromic and Nonsyndromic Conotruncal Heart Defects , 2015, BioMed research international.

[69]  Catharina E. M. van Beijsterveldt,et al.  The Prenatal Environment in Twin Studies: A Review on Chorionicity , 2016, Behavior genetics.

[70]  D. Driscoll,et al.  Congenital heart diseases: the broken heart : clinical features, human genetics and molecular pathways , 2016 .

[71]  Marcel Grunert,et al.  Cardiac Transcription Factors and Regulatory Networks. , 2024, Advances in experimental medicine and biology.

[72]  Wei Chen,et al.  Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases. , 2016, Cardiovascular research.

[73]  Tomas W. Fitzgerald,et al.  Distinct genetic architectures for syndromic and nonsyndromic congenital heart defects identified by exome sequencing , 2016, Nature Genetics.

[74]  Ana Conesa,et al.  Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data , 2015, Bioinform..

[75]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[76]  Xiaoyu Chen,et al.  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..

[77]  R. Bonow,et al.  Discordant Aortic Valve Morphology in Monozygotic Twins: A Clinical Case Series. , 2016, JAMA cardiology.

[78]  Yufeng Shen,et al.  Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands , 2017, Nature Genetics.

[79]  K. Sun,et al.  Copy Number Variants and Exome Sequencing Analysis in Six Pairs of Chinese Monozygotic Twins Discordant for Congenital Heart Disease , 2017, Twin Research and Human Genetics.

[80]  S. Bölte,et al.  Fetal and postnatal metal dysregulation in autism , 2017, Nature Communications.

[81]  Xiaoke Huang,et al.  Genome and epigenome analysis of monozygotic twins discordant for congenital heart disease , 2018, BMC Genomics.

[82]  Thomas Colthurst,et al.  A universal SNP and small-indel variant caller using deep neural networks , 2018, Nature Biotechnology.

[83]  Kathryn E. Hentges,et al.  Whole Exome Sequencing Reveals the Major Genetic Contributors to Nonsyndromic Tetralogy of Fallot , 2019, Circulation research.

[84]  A. Keller,et al.  Micro-RNA signatures in monozygotic twins discordant for congenital heart defects , 2019, PloS one.

[85]  Marcel Grunert,et al.  Altered microRNA and target gene expression related to Tetralogy of Fallot , 2019, Scientific Reports.

[86]  Catherine L. Worth,et al.  Cells of the adult human heart , 2020, Nature.

[87]  Irina M. Armean,et al.  The mutational constraint spectrum quantified from variation in 141,456 humans , 2019, Nature.

[88]  S. Sperling,et al.  Induced pluripotent stem cells of patients with Tetralogy of Fallot reveal transcriptional alterations in cardiomyocyte differentiation , 2020, Scientific Reports.