Transcriptomic analysis of patients with tetralogy of Fallot reveals the effect of chronic hypoxia on myocardial gene expression

Anthropogenic events and responses to environmental stress are shaping the genomes of Ethiopian indigenous goats

Anthropological and biophysical processes have shaped livestock genomes over Millenia and can explain their current geographic distribution and genetic divergence. We analyzed 57 Ethiopian indigenous domestic goat genomes alongside 67 equivalents of east, west, and north-west African, European, South Asian, Middle East, and wild Bezoar goats. Cluster, ADMIXTURE (K = 4) and phylogenetic analysis revealed four genetic groups comprising African, European, South Asian, and wild Bezoar goats. The Middle Eastern goats had an admixed genome of these four genetic groups. At K = 5, the West African Dwarf and Moroccan goats were separated from East African goats demonstrating a likely historical legacy of goat arrival and dispersal into Africa via the coastal Mediterranean Sea and the Horn of Africa. FST, XP-EHH, and Hp analysis revealed signatures of selection in Ethiopian goats overlaying genes for thermo-sensitivity, oxidative stress response, high-altitude hypoxic adaptation, reproductive fitness, pathogen defence, immunity, pigmentation, DNA repair, modulation of renal function and integrated fluid and electrolyte homeostasis. Notable examples include TRPV1 (a nociception gene); PTPMT1 (a critical hypoxia survival gene); RETREG (a regulator of reticulophagy during starvation), and WNK4 (a molecular switch for osmoregulation). These results suggest that human-mediated translocations and adaptation to contrasting environments are shaping indigenous African goat genomes.

BBLN triggers CAMK2D pathology in mice under cardiac pressure overload and potentially in unrepaired hearts with tetralogy of Fallot

Tetralogy of Fallot (TOF) is one of the most prevalent congenital heart defects, with adverse cardiac remodeling and long-term cardiac complications. Here, searching for pathomechanisms, we find upregulated bublin coiled-coil protein (BBLN) in heart specimens of TOF patients with cyanosis, which positively correlates with cardiac remodeling pathways. Human BBLN, a protein with largely unknown function, promoted heart failure features, with increased mortality when overexpressed in mice, in a protein dosage-dependent manner. BBLN enhanced cardiac inflammation, fibrosis and necroptosis by calcium/calmodulin-dependent protein kinase II delta (CAMK2D) activation, whereas a BBLN mutant with impaired CAMK2D binding was inert. Downregulation of CAMK2D by an interfering RNA retarded BBLN-induced symptoms of heart failure. Endogenous BBLN was induced by hypoxia as a major TOF feature in human patients and by chronic pressure overload in mice, and its downregulation decreased CAMK2D hyperactivity, necroptosis and cardiovascular dysfunction. Thus, BBLN promotes CAMK2D-induced pathways to pathological cardiac remodeling, which are triggered by hypoxia in TOF.

m6A RNA methylation modification is involved in the disease course of heart failure

We explored N⁶-methyladenosine (m6A) RNA methylation as one of the gene regulatory mechanisms in heart failure (HF) biology. Understanding the different physiological mechanisms will facilitate the prevention and individualized treatment of HF. The Gene Expression Omnibus (GEO) database served as the source of the data. In GSE116250, differential analysis between ischemic cardiomyopathy (ICM), dilated cardiomyopathy (DCM) and controls yielded differentially expressed m6A regulators. Differential analysis between HF and controls in GSE131296 identifies m6A-modified genes and then performs enrichment analysis. Protein-protein interaction (PPI) network analysis was performed for the differentially expressed ICM- or DCM-associated genes in GSE116250 and GSE55296, respectively. Finally, the diagnostic genes for ICM and DCM were predicted using receiver operating characteristic (ROC) curve. YTHDC1, HNRNPC and HNRNPA2B1 were significantly downregulated in GSE116250 in DCM and ICM compared with controls. A total of 195 genes were identified in GSE131296 as subject to m6A alteration. These genes may play a role in HF through the MAPK signaling pathway and p53 signaling pathway. PPI network analysis identified CCL5, CXCR4 and CCL2 as key genes for ICM and IL-6 as a key gene for DCM. Through ROC curves, we identified m6A-modified APLP1, KLF2 as potential diagnostic genes for ICM, and m6A-modified FGF7, FREM1 and C14orf132 as potential diagnostic genes for DCM. Our findings support m6A modifying mechanisms in HF etiology that contribute to the treatment of HF. Thus, our data suggest that m6A methylation may be an interesting target for therapeutic intervention.

Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards

BACKGROUND

Although the extreme environmental adaptation of organisms is a hot topic in evolutionary biology, genetic adaptation to high-altitude environment remains poorly characterized in ectothermic animals. Squamates are among the most diverse terrestrial vertebrates, with tremendous ecological plasticity and karyotype diversity, and are a unique model system to investigate the genetic footprints of adaptation.

RESULTS

We report the first chromosome-level assembly of the Mongolian racerunner (Eremias argus) and our comparative genomics analyses found that multiple chromosome fissions/fusions events are unique to lizards. We further sequenced the genomes of 61 Mongolian racerunner individuals that were collected from altitudes ranging from ~ 80 to ~ 2600 m above sea level (m.a.s.l.). Population genomic analyses revealed many novel genomic regions under strong selective sweeps in populations endemic to high altitudes. Genes embedded in those genomic regions are mainly associated with energy metabolism and DNA damage repair pathways. Moreover, we identified and validated two substitutions of PHF14 that may enhance the lizards' tolerance to hypoxia at high altitudes.

CONCLUSIONS

Our study reveals the molecular mechanism of high-altitude adaptation in ectothermic animal using lizard as a research subject and provides a high-quality lizard genomic resource for future research.

The right ventricle in tetralogy of Fallot: adaptation to sequential loading

Right ventricular dysfunction is a major determinant of outcome in patients with complex congenital heart disease, as in tetralogy of Fallot. In these patients, right ventricular dysfunction emerges after initial pressure overload and hypoxemia, which is followed by chronic volume overload due to pulmonary regurgitation after corrective surgery. Myocardial adaptation and the transition to right ventricular failure remain poorly understood. Combining insights from clinical and experimental physiology and myocardial (tissue) data has identified a disease phenotype with important distinctions from other types of heart failure. This phenotype of the right ventricle in tetralogy of Fallot can be described as a syndrome of dysfunctional characteristics affecting both contraction and filling. These characteristics are the end result of several adaptation pathways of the cardiomyocytes, myocardial vasculature and extracellular matrix. As long as the long-term outcome of surgical correction of tetralogy of Fallot remains suboptimal, other treatment strategies need to be explored. Novel insights in failure of adaptation and the role of cardiomyocyte proliferation might provide targets for treatment of the (dysfunctional) right ventricle under stress.

Identification of circRNA–miRNA–mRNA Regulatory Network and Crucial Signaling Pathway Axis Involved in Tetralogy of Fallot

Tetralogy of Fallot (TOF) is one of the most common cyanotic congenital heart diseases (CHD) worldwide; however, its pathogenesis remains unclear. Recent studies have shown that circular RNAs (circRNAs) act as “sponges” for microRNAs (miRNAs) to compete for endogenous RNA (ceRNA) and play important roles in regulating gene transcription and biological processes. However, the mechanism of ceRNA in TOF remains unclear. To explore the crucial regulatory connections and pathways of TOF, we obtained the human TOF gene, miRNA, and circRNA expression profiling datasets from the Gene Expression Omnibus (GEO) database. After data pretreatment, differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), and circRNAs (DEcircRNAs) were identified between the TOF and healthy groups, and a global triple ceRNA regulatory network, including circRNAs, miRNAs, and mRNAs based on the integrated data, was constructed. A functional enrichment analysis was performed on the Metascape website to explore the biological functions of the selected genes. Then, we constructed a protein-protein interaction (PPI) network and identified seven hub genes using the cytoHubba and MCODE plug-ins in the Cytoscape software, including BCL2L11, PIK3R1, SOCS3, OSMR, STAT3, RUNX3, and IL6R. Additionally, a circRNA–miRNA–hub gene subnetwork was established, and its enrichment analysis results indicated that the extrinsic apoptotic signaling pathway, JAK-STAT signaling pathway and PI3K-Akt signaling pathway may be involved in the pathogenesis of TOF. We further identified the hsa_circ_000601/hsa-miR-148a/BCL2L11 axis as a crucial signaling pathway axis from the subnetwork. This study provides a novel regulatory network for the pathogenesis of TOF, revealing the possible molecular mechanisms and crucial regulatory pathways that may provide new strategies for candidate diagnostic biomarkers or potential therapeutic targets for TOF.

Disorders of gut microbiota in children with Tetralogy of Fallot

BACKGROUND

Gut microbiota plays an important role in cardiovascular health and disease, including congenital heart disease (CHD). Tetralogy of Fallot (TOF) is the most common form of cyanotic CHD characterized by systemic chronic hypoxia and sustained pressure overload of the right ventricle. It is well-known that hypoxia and pressure overload can affect gut microbiota. However, the effects of TOF on the gut microbiota remain little understood. This study explored the profile of the gut microbiota in children with unrepaired TOF.

METHODS

A total of 12 pediatric patients diagnosed with TOF and 9 healthy age- and gender-matched children were enrolled in this study. Fecal samples were collected from every participant and subjected to 16S rDNA gene sequencing. The raw sequencing data were processed using the Quantitative Insights Into Microbial Ecology pipeline.

RESULTS

A comparison of the gut microbiota revealed that pediatric patients with TOF had developed dysbiosis as reflected by the altered taxonomic composition and impaired functional profile. A total of 14 indicative bacterial genera were identified as differential biomarkers capable of distinguishing between healthy children and TOF patients. Furthermore, functional annotations revealed that the gut microbiota in TOF patients was characterized by increased levels of inflammatory, oxidative, and immune responses, and decreased activities of adaptation, synthesis, and metabolism.

CONCLUSIONS

Pediatric patients with unrepaired TOF have intestinal dysbacteriosis that is characterized by altered taxonomic composition and impaired functional profile. These findings suggested that the interplay between gut microbiota and the host may be dysregulated in patients with TOF.

Preoperative Neutrophil-Lymphocyte Ratio Can Predict Outcomes for Patients Undergoing Tetralogy of Fallot Repair

INTRODUCTION

Elevated neutrophil-lymphocyte ratio (NLR) has been associated with poorer outcomes in cyanotic patients undergoing single ventricle palliation. Little is known about this biomarker on patients with tetralogy of Fallot (TOF), the most common cyanotic congenital heart disease. Our objective is to study the impact of preoperative NLR on outcomes of TOF patients undergoing total repair.

METHODS

This retrospective study included 116 consecutive patients between January 2014 and December 2018. Preoperative NLR was measured from the last complete blood count test before the surgery. Using the cutoff value of 0.80, according to the receiver-operating characteristic (ROC) curve, the sample was divided into two groups (NLR < 0.80 and ≥ 0.80). The primary endpoint was hospital length of stay (LOS).

RESULTS

ROC curves showed that higher preoperative NLR was associated with longer hospital LOS, with an area under the curve of 0.801±0.040 (95% confidence interval 0.722 - 0.879; P<0.001). High preoperative NLR was also associated with long intensive care unit (ICU) LOS (P=0.035). Preoperative NLR predicted longer hospital LOS with a sensitivity of 63% and a specificity of 81.4%.

CONCLUSION

Higher preoperative NLR was associated with long ICU and hospital LOS in patients undergoing TOF repair.

A Functional Variant Rs492554 Associated With Congenital Heart Defects Modulates SESN2 Expression Through POU2F1

Hypoxia exposure is responsible for the high incidence of congenital heart defects (CHDs) in high-altitude areas, which is nearly 20 times higher than that in low-altitude areas. However, the genetic factors involved are rarely reported. Sestrin2 (SESN2), a hypoxia stress-inducible gene, protects cardiomyocyte viability under stress; thus, SESN2 polymorphism may be a potential risk factor for CHD. We performed an association study of the SESN2 polymorphisms with CHD risk in two independent groups of the Han Chinese population from two different altitude areas. The allele-specific effects of lead single-nucleotide polymorphisms (SNPs) were assessed by expression quantitative trait locus, electrophoretic mobility shift, and luciferase reporter assays. The molecular mechanism of Sesn2 action against hypoxia-induced cell injury was investigated in embryonic rat-heart-derived H9c2 cells treated with or without hypoxia-mimetic cobalt chloride. SNP rs492554 was significantly associated with reduced CHD risk in the high-altitude population, but not in the low-altitude population. The protective T allele of rs492554 was correlated with higher SESN2 expression and showed a preferential binding affinity to POU2F1. We then identified SNP rs12406992 in strong linkage disequilibrium with rs492554 and mapped it within the binding motif of POU2F1. The T-C haplotype of rs492554-rs12406992 could increase luciferase expression, whereas POU2F1 knockdown effectively suppressed it. Mechanistically, increased Sesn2 protects against oxidative stress and cell apoptosis and maintains cell viability and proliferation. In summary, CHD-associated SNP rs492554 acts as an allele-specific distal enhancer to modulate SESN2 expression via interaction with POU2F1, which might provide new mechanistic insights into CHD pathogenesis.

Dynamic effects of genetic variation on gene expression revealed following hypoxic stress in cardiomyocytes

One life-threatening outcome of cardiovascular disease is myocardial infarction, where cardiomyocytes are deprived of oxygen. To study inter-individual differences in response to hypoxia, we established an in vitro model of induced pluripotent stem cell-derived cardiomyocytes from 15 individuals. We measured gene expression levels, chromatin accessibility, and methylation levels in four culturing conditions that correspond to normoxia, hypoxia, and short- or long-term re-oxygenation. We characterized thousands of gene regulatory changes as the cells transition between conditions. Using available genotypes, we identified 1,573 genes with a cis expression quantitative locus (eQTL) in at least one condition, as well as 367 dynamic eQTLs, which are classified as eQTLs in at least one, but not in all conditions. A subset of genes with dynamic eQTLs is associated with complex traits and disease. Our data demonstrate how dynamic genetic effects on gene expression, which are likely relevant for disease, can be uncovered under stress.

Placental DNA methylation changes in detection of tetralogy of Fallot

OBJECTIVES

To determine whether the methylation level of cytosine nucleotides in placental DNA can be used to predict tetralogy of Fallot (TOF) and provide insights into the developmental mechanism of this condition.

METHODS

Tissue sections were obtained from formalin-fixed paraffin-embedded specimens of placental tissue obtained at birth from eight cases with non-chromosomal, non-syndromic TOF and 10 unaffected newborns. The Illumina Infinium HumanMethylation450 BeadChip assay was used to measure cytosine ('CpG' or 'cg') methylation levels at loci throughout the placental genome. Differential methylation was assessed by comparing the β-values (a measure of the extent of cytosine methylation) for individual CpG loci in fetuses with TOF vs in controls. The most discriminating CpG sites were determined based on a preset cut-off of ≥ 2.0-fold change in the methylation level. The predictive accuracy of CpG loci with significant methylation changes for TOF was determined by the area under the receiver-operating-characteristics curve (AUC). A false-discovery-rate (FDR) P-value < 0.05 was used to define a statistically significant difference in the methylation level. Ingenuity Pathway Analysis (IPA) (Qiagen) was used to identify gene pathways that were significantly overexpressed, and thus altered, in TOF cases compared with controls.

RESULTS

We found a total of 165 significantly differentially methylated CpG loci in TOF cases compared with controls, in 165 separate genes. These biomarkers demonstrated from fair to excellent individual predictive accuracy for TOF detection, with AUCs ≥ 0.75 (FDR P-value < 0.001 for all). The following CpG loci (gene) had the highest predictive accuracy: cg05273049 (ARHGAP22; AUC = 1.00; 95% CI, 1.00-1.00), cg02540011 (CDK5; AUC = 0.96; 95% CI, 0.87-1.00), cg08404201 (TRIM27; AUC = 0.95; 95% CI, 0.84-1.00) and cg00687252 (IER3; AUC = 0.95; 95% CI, 0.84-1.00). IPA revealed over-representation (dysregulation) of 14 gene pathways involved in normal cardiac development, including cardiomyocyte differentiation via bone morphogenetic protein receptors, cardiac hypertrophy signaling and role of nuclear factor of activated T cells in cardiac hypertrophy. Cardiac hypertrophy is an important feature of TOF.

CONCLUSIONS

Analysis of placental DNA cytosine methylation changes yielded accurate markers for TOF detection and provided mechanistic information on TOF development. Our work appears to confirm the central role of epigenetic changes and of the placenta in the development of TOF. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.

Transcriptome analysis defines myocardium gene signatures in children with ToF and ASD and reveals disease-specific molecular reprogramming in response to surgery with cardiopulmonary bypass

BACKGROUND

Tetralogy of Fallot (ToF) and Atrial Septal Defects (ASD) are the most common types of congenital heart diseases and a major cause of childhood morbidity and mortality. Cardiopulmonary bypass (CPB) is used during corrective cardiac surgery to support circulation and heart stabilization. However, this procedure triggers systemic inflammatory and stress response and consequent increased risk of postoperative complications. The aim of this study was to define the molecular bases of ToF and ASD pathogenesis and response to CPB and identify new potential biomarkers.

METHODS

Comparative transcriptome analysis of right atrium specimens collected from 10 ToF and 10 ASD patients was conducted before (Pre-CPB) and after (Post-CPB) corrective surgery. Total RNA isolated from each sample was individually hybridized on Affymetrix HG-U133 Plus Array Strips containing 38,500 unique human genes. Differences in the gene expression profiles and functional enrichment/network analyses were assessed using bioinformatic tools. qRT-PCR analysis was used to validate gene modulation.

RESULTS

Pre-CPB samples showed significant differential expression of a total of 72 genes, 28 of which were overexpressed in ToF and 44 in ASD. According to Gene Ontology annotation, the mostly enriched biological processes were represented by matrix organization and cell adhesion in ToF and by muscle development and contractility in ASD specimens. GSEA highlighted the specific enrichment of hypoxia gene sets in ToF samples, pointing to a role for hypoxia in disease pathogenesis. The post-CPB myocardium exhibited significant alterations in the expression profile of genes related to transcription regulation, growth/apoptosis, inflammation, adhesion/matrix organization, and oxidative stress. Among them, only 70 were common to the two disease groups, whereas 110 and 24 were unique in ToF and ASD, respectively. Multiple functional interactions among differentially expressed gene products were predicted by network analysis. Interestingly, gene expression changes in ASD samples followed a consensus hypoxia profile.

CONCLUSION

Our results provide a comprehensive view of gene reprogramming in right atrium tissues of ToF and ASD patients before and after CPB, defining specific molecular pathways underlying disease pathophysiology and myocardium response to CPB. These findings have potential translational value because they identify new candidate prognostic markers and targets for tailored cardioprotective post-surgical therapies.

Identification of hub genes in chronically hypoxic myocardium using bioinformatics analysis

Chronic hypoxia can be observed in the heart under physiological or pathophysiological states, including embryonic development or cyanotic congenital heart disease. The aim of the present study was to examine gene expression profiles of chronically hypoxic myocardium and to explore the pathophysiological mechanisms by which the heart adapts to chronic hypoxia. Raw data from the next-generation sequencing data set GSE36761 were downloaded from the Gene Expression Omnibus database. The data set comprised 30 specimens, including 8 healthy myocardia and 22 tetralogy of Fallot (TOF) congenital cardiac malformations; only 7 original data sets of healthy myocardia were obtained, and 5/22 TOFs were excluded. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) were performed. Furthermore, network analysis of DEGs using Cytoscape software based on protein-protein interaction (PPI) data was also conducted. A total of 1,260 DEGs were selected, of which 926 DEGs were enriched in 83 GO biological process terms, including extracellular matrix organization, regeneration and monocyte chemotaxis. Furthermore, 406 DEGs were enriched in 13 KEGG pathways, including cytokine-cytokine receptor interaction, focal adhesion and apoptosis. PPI network analysis indicated that six hub genes with correlated degree scores >25 among nodes were identified, including G protein subunit β4, C-C motif chemokine receptor (CCR)1, CCR2, platelet factor 4, catenin β1 and Jun proto-oncogene (JUN). Of these, JUN was enriched in GO terms of regeneration and neuron projection regeneration, and in KEGG pathways of focal adhesion, apoptosis and Chagas disease (American trypanosomiasis). The present bioinformatics analysis of these DEGs and hub genes may provide a molecular insight to the role of diverse genes in the pathophysiology of chronically hypoxic myocardium and in myocardial adaptation to chronic hypoxia.

The genetic prehistory of the Andean highlands 7000 years BP though European contact

The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.

Microtubule associated protein 4 phosphorylation leads to pathological cardiac remodeling in mice

Background

Cardiac remodeling is a pathophysiological process that involves various changes in heart, including cardiac hypertrophy and fibrosis. Cardiac remodeling following pathological stimuli is common trigger leading to cardiac maladaptation and onset of heart failure, and their pathogenesis remains unclear.

Methods

Heart specimens of tetralogy of Fallot (TOF) patients, myocardial infarction (MI) and transverse aortic constriction (TAC) mouse models were collected to determine changes of microtubule associated protein 4 (MAP4) phosphorylation. MAP4 (S667A, S737E and S760E) knock in (MAP4 KI) mouse and cultured neonatal mouse cardiomyocytes or fibroblasts were used to investigate changes of cardiac phenotypes and possible mechanisms with a variety of approaches, including functional, histocytological and pathological observations.

Findings

Elevated cardiac phosphorylation of MAP4 (S737 and S760) was observed in TOF patients, MI and TAC mouse models. In MAP4 KI mice, age-dependent cardiac phenotypes, including cardiac hypertrophy, fibrosis, diastolic and systolic dysfunction were observed. In addition, increased cardiomyocyte apoptosis together with microtubule disassembly and mitochondrial translocation of phosphorylated MAP4 was detected prior to the onset of cardiac remodeling, and p38/MAPK was demonstrated to be the possible signaling pathway that mediated MAP4 (S737 and S760) phosphorylation.

Interpretation

Our data reveal for the first time that MAP4 drives pathological cardiac remodeling through its phosphorylation. These findings bear the therapeutic potential to ameliorate pathological cardiac remodeling by attenuating MAP4 phosphorylation.

Fund

This work was supported by the Key Program of National Natural Science Foundation of China (No.81430042) and National Natural Science Foundation of China (No.81671913).

Changes in contractile protein expression are linked to ventricular stiffness in infants with pulmonary hypertension or right ventricular hypertrophy due to congenital heart disease

Background

The right ventricle (RV) is not designed to sustain high pressure leading to failure. There are no current medications to help RV contraction, so further information is required on adaption of the RV to such hypertension.

Methods

The Right Ventricle in Children (RVENCH) study assessed infants with congenital heart disease undergoing cardiac surgery with hypertensive RV. Clinical and echocardiographic data were recorded, and samples of RV were taken from matched infants, analysed for proteomics and compared between pathologies and with clinical and echocardiographic outcome data.

Results

Those with tetralogy of Fallot (TOF) were significantly more cyanosed than those with ventricular septal defect (median oxygen saturation 83% vs 98%, P=0.0038), had significantly stiffer RV (tricuspid E wave/A wave ratio 1.95 vs 0.84, P=0.009) and had most had restrictive physiology. Gene ontology in TOF, with enrichment analysis, demonstrated significant increase in proteins of contractile mechanisms and those of calmodulin, actin binding and others associated with contractility than inventricular septal defect. Structural proteins were also found to be higher in association with sarcomeric function: Z-disc, M-Band and thin-filament proteins. Remaining proteins associated with actin binding, calcium signalling and myocyte cytoskeletal development. Phosphopeptide enrichment led to higher levels of calcium signalling proteins in TOF.

Conclusion

This is the first demonstration that those with an RV, which is stiff and hypertensive in TOF, have a range of altered proteins, often in calcium signalling pathways. Information about these alterations might guide treatment options both in terms of individualised therapy or inotropic support for the Right ventricle when hypertensive due to pulmoanry hypertension or congenital heart disease.

Clinical Progress in the Management of Tetralogy of Fallot in the Dominican Republic: A Case Series

BACKGROUND

Definitive surgical interventions for Dominican children with congenital heart disease, like those of other low- and middle-income countries, have been historically limited.

METHODS

We undertook review of a case series focusing on the surgical correction of complex forms of tetralogy of Fallot at a single center, CEDIMAT Centro Cardiovascular, in the Dominican Republic, over a 30-month period.

RESULTS

According to our criteria, 43 cases were determined to be complex tetralogy of Fallot repairs from the two-year period. Besides tetralogy of Fallot, the cohort had an additional 55 anatomic anomalies that had to be addressed at the time of surgery. Median age at the time of surgery was notably 30 months, and an average of 42 months elapsed from the time of diagnosis to the time of surgery for this group. Only 33% of the cases reviewed had no hypercyanotic crises before repair. Median time to extubation for this group of patients was one day, with a three-day median length of stay in the intensive care setting.

CONCLUSIONS

Our study importantly captures the present experience of a surgical congenital heart program that has recently transitioned from a traditional "mission model" to a now self-sustaining local practice. Both the number and the complexity of the lesions corrected in this caseload represent an advance from the level of care previously provided to children in the Dominican Republic.

RNA Sequencing Reveals that Kaposi Sarcoma-Associated Herpesvirus Infection Mimics Hypoxia Gene Expression Signature

Kaposi sarcoma-associated herpesvirus (KSHV) causes several tumors and hyperproliferative disorders. Hypoxia and hypoxia-inducible factors (HIFs) activate latent and lytic KSHV genes, and several KSHV proteins increase the cellular levels of HIF. Here, we used RNA sequencing, qRT-PCR, Taqman assays, and pathway analysis to explore the miRNA and mRNA response of uninfected and KSHV-infected cells to hypoxia, to compare this with the genetic changes seen in chronic latent KSHV infection, and to explore the degree to which hypoxia and KSHV infection interact in modulating mRNA and miRNA expression. We found that the gene expression signatures for KSHV infection and hypoxia have a 34% overlap. Moreover, there were considerable similarities between the genes up-regulated by hypoxia in uninfected (SLK) and in KSHV-infected (SLKK) cells. hsa-miR-210, a HIF-target known to have pro-angiogenic and anti-apoptotic properties, was significantly up-regulated by both KSHV infection and hypoxia using Taqman assays. Interestingly, expression of KSHV-encoded miRNAs was not affected by hypoxia. These results demonstrate that KSHV harnesses a part of the hypoxic cellular response and that a substantial portion of hypoxia-induced changes in cellular gene expression are induced by KSHV infection. Therefore, targeting hypoxic pathways may be a useful way to develop therapeutic strategies for KSHV-related diseases.

Chronic hypoxia down-regulates tight junction protein ZO-2 expression in children with cyanotic congenital heart defect

Aims

Tight junction protein zonula occludens protein 2 (ZO‐2) is a member of the membrane‐associated guanylate kinases protein family known to be expressed at tight junctions of epithelial and endothelial cells and at adherens junctions (AJs) in cardiomyocytes. Little is known about ZO‐2 expression and function in the human heart. Here, we examined the hypothesis that chronic hypoxia down‐regulates ZO‐2 expression in human myocardium and cultured rat cardiomyocytes.

Methods and results

Patients with a diagnosis of cyanotic (n = 10) or acyanotic (n = 10) Tetralogy of Fallot undergoing surgical repair were used to examine ZO‐2 messenger RNA and protein expression by real time‐PCR, immunohistochemistry, and western blotting. A model of cultured rat cardiomyocytes was used to measure ZO‐2 and AJ proteins levels in response to hypoxia and to investigate ZO‐2 cellular localization. We showed that ZO‐2 is expressed in myocardial tissue in acyanotic and cyanotic children with congenital heart defects. ZO‐2 was specifically down‐regulated in cyanotic myocardium at both the messenger RNA and protein levels when compared with acyanotic patients. This specific down‐regulation can be mimicked in cultured rat cardiomyocytes by treating them with hypoxic conditions confirming that ZO‐2 gene down‐regulation is specifically due to cyanosis. Furthermore, in addition to its cytoplasmic expression, ZO‐2 showed nuclear expression in cultured rat cardiomyocytes suggesting potential role in transcription regulation.

Conclusions

Hypoxia down‐regulates ZO‐2 expression in both cyanotic patient's myocardium and cultured rat cardiomyocytes. This down‐regulation suggest an involvement of ZO‐2 in cardiac remodelling of AJs in cyanotic children and may explain the greater susceptibility of cyanotic patients to corrective heart surgery.

Plasma Levels of High Sensitivity Cardiac Troponin T in Adults with Repaired Tetralogy of Fallot

Detectable low circulating level of cardiac troponin T (cTnT) may reflect subclinical myocardial injury. We tested the hypothesis that circulating levels of hs-cTnT are altered in adults with repaired tetralogy of Fallot (TOF) and associated with ventricular volume load and function. Eighty-eight TOF patients and 48 controls were studied. Plasma hs-cTnT levels were determined using a highly sensitive assay (hs-cTnT). The right (RV) and left ventricular (LV) volumes and ejection fraction (EF) were measured using 3D echocardiography and, in 52 patients, cardiac magnetic resonance (CMR). The median (interquartile range) for male and female patients were 4.87 (3.83-6.62) ng/L and 3.11 (1.00-3.87) ng/L, respectively. Thirty percent of female but none of the male patients had increased hs-cTnT levels. Female patients with elevated hs-cTnT levels, compared to those without, had greater RV end-diastolic and end-systolic volumes and LV systolic dyssynchrony index (all p < 0.05). For patient cohort only, hs-cTnT levels correlated positively with CMR-derived RV end-diastolic volume and negatively with echocardiography-derived LV and RV EF (all p < 0.05). Multiple linear regression identified sex and RV EF as significant correlates of log-transformed hs-cTnT levels. Increased hs-cTnT levels occur in 30% of female patients after TOF repair, and are associated with greater RV volumes and worse RV EF.

Gene Expression Signatures as Biomarkers of Tumour Hypoxia

Hypoxia is a feature of most solid tumours and is associated with a poor prognosis. The hypoxic environment can reduce the efficacy of radiotherapy and some chemotherapeutics, and has been investigated extensively as a therapeutic target. The clinical use of hypoxia-targeting treatment will benefit from the development of a biomarker to assess tumour hypoxia. There are several possible techniques that measure either the level of oxygen or the tumour molecular response to hypoxia. The latter includes gene expression profiling, which measures the transcriptional response of a tumour to its hypoxic microenvironment. A systematic review identified 32 published hypoxia gene expression signatures. The methods used for their derivation varied, but are broadly classified as: (i) identifying genes with significantly higher or lower expression in cancer cells cultured under hypoxic versus normoxic conditions; (ii) using either previously characterised hypoxia-regulated genes/biomarkers to define hypoxic tumours and then identifying other genes that are over- or under-expressed in the hypoxic tumours. Both generated gene signatures useful in furthering our understanding of hypoxia biology. However, signatures derived using the second method seem to be superior in terms of providing prognostic information. Here we summarise all 32 published hypoxia signatures, discuss their commonalities and differences, and highlight their strengths and limitations. This review also highlights the importance of reproducibility and gene annotation, which must be accounted for to transfer signatures robustly for clinical application as biomarkers.

Gab1 Is Modulated by Chronic Hypoxia in Children with Cyanotic Congenital Heart Defect and Its Overexpression Reduces Apoptosis in Rat Neonatal Cardiomyocytes

Gab1 (Grb2 associated binding protein 1) is a member of the scaffolding/docking proteins (Gab1, Gab2, and Gab3). It is required for fibroblast cell survival and maintaining cardiac function. Very little is known about human Gab1 expression in response to chronic hypoxia. The present study examined the hypothesis that hypoxia regulates Gab1 expression in human paediatric myocardium and cultured rat cardiomyocytes. Here we showed that Gab1 is expressed in myocardial tissue in acyanotic and cyanotic children with congenital heart defects. Gab1 protein was upregulated in cyanotic compared to acyanotic hearts suggesting that Gab1 upregulation is a component of the survival program initiated by hypoxia in cyanotic children. The expression of other Gab1 interacting partners was not affected by hypoxia and Gab1 regulation. Additionally, using an in vitro model, we demonstrated that overexpressing Gab1 in neonatal cardiomyocytes, under hypoxic condition, resulted in the reduction of apoptosis suggesting a role for this protein in cardiomyocyte survival. Altogether, our data provide strong evidence that Gab1 is important for heart cell survival following hypoxic stress.

Investigating the effect of remote ischaemic preconditioning on biomarkers of stress and injury-related signalling in patients having isolated coronary artery bypass grafting or aortic valve replacement using cardiopulmonary bypass: study protocol for a randomized controlled trial

Background

Ischaemia-reperfusion injury occurs during heart surgery that uses cardiopulmonary bypass (CPB) and cardioplegic arrest. It is hypothesised that remote ischaemic preconditioning (RIPC) protects the heart against such injury. Despite the numerous studies investigating the protective effects of RIPC, there is still uncertainty about the interpretation of the findings as well as conflicting results between studies. The objective of this trial is to investigate the cardioprotective effect of RIPC in patients having coronary artery bypass grafting (CABG) or aortic valve replacement surgery. This will be achieved by estimating the effect of the intervention in the two groups of pathologies and by investigating the signalling mechanisms that may underpin the cardioprotective effect.

Methods/Design

A two-centre randomised controlled trial will be used to investigate the effects of RIPC in two pathologies: patients having isolated CABG and those having aortic valve replacement surgery (AVR) with CPB. Participants will be randomised to RIPC or control (sham RIPC), stratified by surgical stratum. The intervention will be delivered by a research nurse. Data will be collected by a research nurse blinded to the intervention. The patient and the theatre staff are also blinded to the allocation. Markers of myocardial injury and inflammation will be measured in myocardial biopsies and in blood samples at different times.

Discussion

This trial is designed to investigate whether RIPC will reduce myocardial injury and inflammation following heart surgery and whether there is a difference in effect between participants having CABG or AVR. This trial is a unique opportunity to study the mechanisms associated with RIPC using human myocardial tissue and blood, and to relate these to the extent of myocardial injury/protection.

Trial registration

Current Controlled Trials ISRCTN33084113 (25 March 2013).

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-015-0696-z) contains supplementary material, which is available to authorized users.

Normoxic and hyperoxic cardiopulmonary bypass in congenital heart disease

Cyanotic congenital heart disease comprises a diverse spectrum of anatomical pathologies. Common to all, however, is chronic hypoxia before these lesions are operated upon when cardiopulmonary bypass is initiated. A range of functional and structural adaptations take place in the chronically hypoxic heart, which, whilst protective in the hypoxic state, are deleterious when the availability of oxygen to the myocardium is suddenly improved. Conventional cardiopulmonary bypass delivers hyperoxic perfusion to the myocardium and is associated with cardiac injury and systemic stress, whilst a normoxic perfusate protects against these insults.

Perioperative endothelin levels in patients undergoing intracardiac repair for tetralogy of Fallot

BACKGROUND

Endothelin, a pro-inflammatory molecule, had been extensively studied in patients with cardiovascular illness. Impact on the perioperative outcome of patients with cyanotic congenital heart defects is still unknown. In the present study, we report perioperative changes in endothelin levels and their correlation with preoperative factors and clinical outcomes in a group of patients with tetralogy of Fallot (TOF) undergoing definitive repair.

METHODOLOGY

167 patients with TOF undergoing intracardiac repair under cardiopulmonary bypass were studied. Endothelin levels were taken at three different points of time and correlated with different clinical variables.

RESULTS

The baseline endothelin level correlated with patients' nutritional status and degree of cyanosis. The magnitude of inflammatory response in the post-cardiopulmonary bypass (post-CPB) period as measured by endothelin level was much higher and correlated more consistently with adverse clinical outcomes in the younger age group. On multivariable analysis, age at operation, preoperative degree of hypoxemia, and endothelin levels were found to be independent predictors of clinical outcomes.

CONCLUSIONS

A rise in serum endothelin levels in patients with TOF undergoing definitive repair on CPB, with preoperative severity of cyanosis, nutritional status, and adverse clinical outcomes. The endothelin levels may be monitored to identify patients with cyanosis at an increased risk of exhibiting augmented inflammatory response to CPB.

B-type natriuretic peptide as prognostic marker in tetralogy of Fallot surgery

Background

B-type natriuretic peptide has been extensively studied in patients with cardiovascular disease, but its impact on the perioperative outcome of patients with cyanotic congenital heart defects is still unclear. We assessed the perioperative changes in B-type natriuretic peptide levels and their correlation with preoperative factors and clinical outcomes in a large homogenous group of patients with tetralogy of Fallot undergoing definitive repair at a tertiary care center.

Methods

A prospective study was undertaken in the cardiac operating room and intensive care unit at a single institution; 250 patients with tetralogy of Fallot undergoing intracardiac repair under cardiopulmonary bypass were studied. B-type natriuretic peptide levels were taken at 3 time points and correlated with clinical variables.

Results

Baseline B-type natriuretic peptide levels correlated with the degree of cyanosis in all 4 groups. B-type natriuretic peptide levels at 24 h after admission to the intensive care unit correlated with mortality in the adult subset of patients. B-type natriuretic peptide levels > 290 pg mL−1 in the intensive care unit predicted an increased probability of adverse clinical outcomes.

Conclusions

We demonstrated a rise in serum B-type natriuretic peptide levels in patients with tetralogy of Fallot undergoing definitive repair on cardiopulmonary bypass. B-type natriuretic peptide levels may be monitored to identify patients with cyanosis at increased risk of an augmented inflammatory response to cardiopulmonary bypass.

Perioperative Levels of Tumor Necrosis Factor-α Correlate With Outcomes in Children and Adults With Tetralogy of Fallot Undergoing Corrective Surgery

Background:

Previous studies reporting on tumor necrosis factor-α (TNF-α) as a marker of inflammatory response (IR) in patients with congenital heart disease were limited by small sample size and variability in diagnosis. We report perioperative changes in TNF-α levels and their correlation with preoperative factors and clinical outcomes in a large homogenous group of patients with tetralogy of Fallot (TOF) undergoing definitive repair at a tertiary care center.

Methods:

A total of 167 patients were divided into four groups on the basis of age. Group 1 included infants less than 1 year, group 2 included children between 1 and 12 years, group 3 included adolescents between 12 and 18 years, and group 4 included adults more than 18 years of age. Serum TNF-α levels were measured at three time points and correlated with perioperative variables.

Results:

The baseline TNF-α level correlated with patients’ nutritional status and degree of cyanosis in all four groups. The magnitude of IR in the postcardiopulmonary bypass (post-CPB) period as measured by TNF-α level was much higher and correlated more consistently with adverse clinical outcomes in the younger age group (groups 1 and 2). On multivariable analysis; age at operation, preoperative degree of hypoxemia and TNF-α levels were found to be independent predictors of clinical outcomes.

Conclusion:

We demonstrated a rise in serum TNF-α levels in patients with TOF undergoing definitive repair on CPB, which correlated with preoperative severity of cyanosis, nutritional status, and adverse clinical outcomes. The TNF-α levels may be monitored to identify cyanotic patients at an increased risk of exhibiting augmented IR to CPB.

A genome wide study of genetic adaptation to high altitude in feral Andean Horses of the páramo

Background

Life at high altitude results in physiological and metabolic challenges that put strong evolutionary pressure on performance due to oxidative stress, UV radiation and other factors dependent on the natural history of the species. To look for genes involved in altitude adaptation in a large herbivore, this study explored genome differentiation between a feral population of Andean horses introduced by the Spanish in the 1500s to the high Andes and their Iberian breed relatives.

Results

Using allelic genetic models and Fst analyses of ~50 K single nucleotide polymorphisms (SNPs) across the horse genome, 131 candidate genes for altitude adaptation were revealed (Bonferoni of p ≤ 2 × 10^–7). Significant signals included the EPAS1 in the hypoxia-induction-pathway (HIF) that was previously discovered in human studies (p = 9.27 × 10^-8); validating the approach and emphasizing the importance of this gene to hypoxia adaptation. Strong signals in the cytochrome P450 3A gene family (p = 1.5 ×10^-8) indicate that other factors, such as highly endemic vegetation in altitude environments are also important in adaptation. Signals in tenuerin 2 (TENM2, p = 7.9 × 10^-14) along with several other genes in the nervous system (gene categories representation p = 5.1 × 10^-5) indicate the nervous system is important in altitude adaptation.

Conclusions

In this study of a large introduced herbivore, it becomes apparent that some gene pathways, such as the HIF pathway are universally important for high altitude adaptation in mammals, but several others may be selected upon based on the natural history of a species and the unique ecology of the altitude environment.

Gene expression analysis in cardiac tissues from infants identifies candidate agents for Tetralogy of Fallot

Tetralogy of Fallot (TOF) is the most common cyanotic heart defect and the most common cause of blue baby syndrome. Although great progress has been made, the molecular mechanisms of TOF are far from being fully understood, and treatment of this disease remains palliative. In this study, we downloaded gene expression data of TOF subjects with those of normally developing subjects from the Gene Expression Omnibus database and employed computational bioinformatics analyses to compare their gene expression patterns. Furthermore, small molecules that induce inverse gene changes to TOF were identified. A total of 2,274 genes involved in energy metabolism and protein binding were differentially expressed in TOF samples compared with samples from normal controls. Pathways associated with cellular oxygen tension were dysfunctional. In addition, we identified a group of small molecules that may be exploited as adjuvant drug to alleviate some symptoms for TOF patients. These drugs are clearly a direction that warrants additional consideration.

Heat shock protein 27 is increased in cyanotic tetralogy of Fallot myocardium and is associated with improved cardiac output and contraction

Tetralogy of Fallot (TOF) is a congenital heart condition in which the right ventricle is exposed to cyanosis and pressure overload. Patients have an increased risk of right ventricle dysfunction following corrective surgery. Whether the cyanotic myocardium is less tolerant of injury compared to non-cyanotic is unclear. Heat shock proteins (HSPs) protect against cellular stresses. The aim of this study was to examine HSP 27 expression in the right ventricle resected from TOF patients and determine its relationship with right ventricle function and clinical outcome. Ten cyanotic and ten non-cyanotic patients were studied. Western blotting was used to quantify HSP 27 in resected myocardium at (1) baseline (first 15 min of aortic cross clamp and closest representation of pre-operative status) and (2) after 15 min during ischemia until surgery was complete. The cyanotic group had significantly increased haematocrit, lower O2 saturation, thicker interventricular septal wall thickness and released more troponin-I on post-operative day 1 (p < 0.05). HSP 27 expression was significantly increased in the < 15 min cyanotic compared to the < 15 min non-cyanotic group (p = 0.03). In the cyanotic group, baseline HSP 27 expression also significantly correlated with oxygen extraction ratio (p = 0.028), post-operative basal septal velocity (p = 0.036) and mixed venous oxygen saturation (p = 0.02), markers of improved cardiac output/contraction. Increased HSP 27 expression and associated improved right ventricle function and systemic perfusion supports a cardio-protective effect of HSP 27 in cyanotic TOF.

Label-free quantitative proteomic analysis of right ventricular remodeling in infant Tetralogy of Fallot patients

Tetralogy of Fallot (TOF) results in chronic progressive right ventricular (RV) pressure overload and shunt hypoxemia. We investigated the global changes in the proteome of RV among infant patients with and without TOF to gain an insight into early RV remodeling. One hundred and thirty-six differentially expressed proteins were identified using label-free LC-ESI-MS/MS analysis. Western blot results revealed that the expression of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 (PFKFB2) increased significantly in TOF patients; and levels of lysocardiolipin acyltransferase 1 (LCLAT1), lumican (LUM), and versican (VCAN) decreased significantly. QRT-PCR analysis showed that levels of PFKFB2 mRNA were markedly increased, but those of LCLAT1 and LUM were significantly decreased. VCAN mRNA showed no significant change in response to pathophysiology of TOF. The results of immunohistochemical staining were similar to those of Western blot analysis. Results of the proteomic analysis indicated that the level of glycolysis-related proteins had increased and levels of lipid-metabolism-related proteins had decreased. ECM proteins were found to be more down-regulated in TOF in the present study than in previous reports. Taken together, our findings may provide clues to both the metabolic inflexibility and ECM remodeling during the early RV remodeling, which occur in response to chronic hypoxia and long-term pressure overload in TOF patients.

Controlled reoxygenation cardiopulmonary bypass is associated with reduced transcriptomic changes in cyanotic tetralogy of Fallot patients undergoing surgery

In cyanotic patients undergoing repair of heart defects, high level of oxygen during cardiopulmonary bypass (CPB) leads to greater susceptibility to myocardial ischemia and reoxygenation injury. This study investigates the effects of controlled reoxygenation CPB on gene expression changes in cyanotic hearts of patients undergoing surgical correction of tetralogy of Fallot (TOF). We randomized 49 cyanotic TOF patients undergoing corrective cardiac surgery to receive either controlled reoxygenation or hyperoxic/standard CPB. Ventricular myocardium biopsies were obtained immediately after starting and before discontinuing CPB. Microarray analyses were performed on samples, and array results validated with real-time PCR. Gene expression profiles before and after hyperoxic/standard CPB revealed 35 differentially expressed genes with three upregulated and 32 downregulated. Upregulated genes included two E3 Ubiquitin ligases. The products of downregulated genes included intracellular signaling kinases, metabolic process proteins, and transport factors. In contrast, gene expression profiles before and after controlled reoxygenation CPB revealed only 11 differentially expressed genes with 10 upregulated including extracellular matrix proteins, transport factors, and one downregulated. The comparison of gene expression following hyperoxic/standard vs. controlled reoxygenation CPB revealed 59 differentially expressed genes, with six upregulated and 53 downregulated. Upregulated genes included PDE1A, MOSC1, and CRIP3. Downregulated genes functionally clustered into four major classes: extracellular matrix/cell adhesion, transcription, transport, and cellular metabolic process. This study provides direct evidence that hyperoxic CPB decreases the adaptation and remodeling capacity in cyanotic patients undergoing TOF repair. This simple CPB strategy of controlled reoxygenation reduced the number of genes whose expression was altered following hyperoxic/standard CPB.

Effect of mitochondrial aldehyde dehydrogenase-2 genotype on cardioprotection in patients with congenital heart disease

AIMS

About 40% of East Asians carry an aldehyde dehydrogenase-2*2 (ALDH2*2) allele, and the influence of the ALDH2*2 allele on human cardioprotection has not been studied. This study was designed to evaluate the effect of ALDH2*2 allele on cardioprotection of patients with congenital heart diseases after open-heart surgery.

METHODS AND RESULTS

The right atrial appendage was harvested before performing cardiopulmonary bypass in cyanotic and acyanotic congenital heart disease groups (n = 20 per group). Tissues were assayed to determine the impact of cyanosis on metabolic remodelling. A prospective cohort of Tetralogy of Fallot (TOF) patients (n = 118) was recruited to investigate the influence of the ALDH2*2 allele on cardioprotection after surgical repair. Myocardium samples were dissected after cardioplegia. ALDH2 activity, oxidative stress and glutathione (GSH) levels, and activating transcription factor-4 (ATF4) were analysed. After genotyping and grouping, all of the experimental and clinical results were compared between ALDH2*2 carriers and non-carriers. Cyanosis inhibited ALDH2 activity and led to aldehyde accumulation in ALDH2*2 carriers. This accumulation in turn increased expression of ATF4 and resulted in larger myocardium GSH pools. The differences in ALDH2 activity and GSH level between carriers and non-carriers disappeared during cardioplegic arrest, and more aldehydes accumulated in the non-carriers. Consequently, ALDH2*2 carriers showed lower postoperative troponin I, inotrope score, and shorter postoperative length of ICU and hospital stay.

CONCLUSIONS

ALDH2*2 carriers with cyanotic congenital heart disease were associated with an induced metabolic remodelling phenotype and a compensatory myocardium GSH pool. When ALDH2 activity was impaired during open-heart surgery, this larger GSH pool could lead to unexpectedly better cardioprotection. This may aid in the prediction of cardioprotection outcomes and identification of individualized cardioprotective strategies.

Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach

Background

The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying its candidate genes and disease-markers has been one of the central topics in CHD research. By using the high-throughput genomic data of CHD which are available recently, network-based methods provide powerful alternatives of systematic analysis of complex diseases and identification of dysfunctional modules and candidate disease genes.

Results

In this paper, by modeling the information flow from source disease genes to targets of differentially expressed genes via a context-specific protein-protein interaction network, we extracted dysfunctional modules which were then validated by various types of measurements and independent datasets. Network topology analysis of these modules revealed major and auxiliary pathways and cellular processes in CHD, demonstrating the biological usefulness of the identified modules. We also prioritized a list of candidate CHD genes from these modules using a guilt-by-association approach, which are well supported by various kinds of literature and experimental evidence.

Conclusions

We provided a network-based analysis to detect dysfunctional modules and disease genes of CHD by modeling the information transmission from source disease genes to targets of differentially expressed genes. Our method resulted in 12 modules from the constructed CHD subnetwork. We further identified and prioritized candidate disease genes of CHD from these dysfunctional modules. In conclusion, module analysis not only revealed several important findings with regard to the underlying molecular mechanisms of CHD, but also suggested the distinct network properties of causal disease genes which lead to identification of candidate CHD genes.