Transcriptomic analysis of patients with tetralogy of Fallot reveals the effect of chronic hypoxia on myocardial gene expression Mohamed T. Ghorbel,

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Transcriptomic analysis of patients with tetralogy of Fallot reveals the effect of chronic hypoxia on myocardial gene expression Mohamed T. Ghorbel, PhD, Myriam Cherif, PhD, Emma Jenkins, PhD, Amir Mokhtari, MRCS, Damien Kenny, MRCPCH, Gianni D. Angelini, FRCS, Massimo Caputo, MD The Journal of Thoracic and Cardiovascular Surgery Volume 140, Issue 2, Pages 337-345.e26 (August 2010) DOI: 10.1016/j.jtcvs.2009.12.055 Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

Figure 1 Enrichment analysis of functional groups within the genes differentially expressed in cyanotic compared with acyanotic patients. A, Pie chart of the regulated genes in cyanotic compared with acyanotic patients (≥1.8-fold). Three quarters of the genes were downregulated and a quarter were upregulated. B and C, Selected GO annotations of genes upregulated (B) and downregulated (C) in cyanotic patients. The histograms show the distribution of these annotations. The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

Figure 2 Biological association network of the significantly upregulated genes (>1.8-fold) of cyanotic versus acyanotic patient comparisons. The association between the network entities were based on available PubMed citations. Each node in the network map is linked to an html page showing the protein annotation based on available public databases. Small square boxes connecting 2 nodes are linked to an html page showing the type of effect (positive or negative) and the supporting Medline references. The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

Figure 3 Biological association networks of the significantly downregulated genes associated with the ontological “regulation of transcription” (A) and “MAPK signaling pathway” (B) classes. Each node in network maps is linked to an html page showing the protein annotation based on available public databases. Small square boxes connecting 2 nodes are linked to an html page showing the type of effect (positive or negative) and the supporting Medline references. The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

Heat Map illustrating the expression levels of contractile machinery genes. A, Cytoskeletal cluster. B, Cell adhesion cluster. Hierarchical clustering has been performed with ArrayStar software. A 3-color scale was used to illustrate expression level differences, with blue indicating low expression values, yellow indicating intermediately expressed genes, and red representing highly expressed genes. The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

COX 11 protein immunostaining of paraffin-embedded heart tissue from acyanotic (C) and cyanotic (D) patients using COX11-specific antibody. 3,3′-Diaminobenzidine (DAB) staining (brown) reveals expression of COX11 in both tissues but not in control tissue (A and B). E and F, COX11 protein expression level in myocardium of acyanotic (AC) and cyanotic (CC) patients. Biopsy specimens were lysed to isolate protein content and Western blotting analysis was performed, probing for COX11 and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). COX11 was significantly upregulated in cyanotic biopsy specimens compared with that seen in acyanotic specimens. COX11 bands were normalized to glyceraldehude-3-phosphate dehydrogenase (GAPDH) levels. Data are presented as means ± standard errors of the mean. ∗P < .05 (n = 6). The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

A and B, NCX1 protein immunostaining of paraffin-embedded heart tissue from acyanotic (A) and cyanotic (B) patients using NCX1-specific antibody. 3,3′-Diaminobenzidine (DAB) staining (brown) reveals expression of NCX1 in both tissues. C and D, NCX1 protein expression level in myocardium of acyanotic (AC) and cyanotic (CC) patients. Biopsy specimens were lysed to isolate protein content, and Western blotting analysis was performed, probing for NCX1 and glyceraldehude-3-phosphate dehydrogenase (GAPDH). NCX1 was significantly downregulated in cyanotic biopsy specimens compared with acyanotic specimens. NCX1 bands were normalized to GAPDH levels. Data are presented as means ± standard errors of the mean. ∗P < .05 (n = 4). The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

TRAIL protein immunostaining of paraffin-embedded heart tissue from acyanotic (A) and cyanotic (B) patients using TRAIL-specific antibody. 3,3′-Diaminobenzidine (DAB) staining (brown) reveals expression of TRAIL in both tissues. C and D, TRAIL protein expression level in myocardium of acyanotic (AC) and cyanotic (CC) patients. Biopsy specimens were lysed to isolate protein content, and Western blotting analysis was performed, probing for TRAIL and glyceraldehude-3-phosphate dehydrogenase (GAPDH). TRAIL was not upregulated in cyanotic biopsy specimens compared with acyanotic specimens. TRAIL bands were normalized to GAPDH levels. Data are presented as means ± standard errors of the mean (n = 6). E, Plasma levels of TRAIL in cyanotic (CC) and acyanotic (AC) children. Solid bars represent median protein concentration in preoperative plasma samples (in picograms per milliliter). A significantly enhanced TRAIL protein expression was observed in cyanotic samples. Data are presented as means ± standard errors of the mean. ∗P < .05 (n = 9–11). The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

LYZ protein immunostaining of paraffin-embedded heart tissue from acyanotic (A) and cyanotic (B) patients using LYZ-specific antibody. 3,3′-Diaminobenzidine (DAB) staining (brown) reveals expression of LYZ in both tissues. C and D, LYZ protein expression level in myocardium of acyanotic (AC) and cyanotic (CC) patients. Biopsy specimens were lysed to isolate protein content, and Western blotting analysis was performed, probing for LYZ and glyceraldehude-3-phosphate dehydrogenase (GAPDH). LYZ was significantly upregulated in cyanotic biopsy specimens compared with acyanotic specimens. LYZ bands were normalized to GAPDH levels. Data are presented as means ± standard errors of the mean. ∗P < .05 (n = 6). The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

OPN protein immunostaining of paraffin-embedded heart tissue from acyanotic (A) and cyanotic (B) patients using OPN-specific antibody. 3,3′-Diaminobenzidine (DAB) staining (brown) reveals expression of OPN in both tissues. C and D, OPN protein expression level in myocardium of acyanotic (AC) and cyanotic (CC) patients. Biopsy specimens were lysed to isolate protein content, and Western blotting analysis was performed, probing for OPN and glyceraldehude-3-phosphate dehydrogenase (GAPDH). OPN was significantly upregulated in cyanotic biopsy specimens compared with acyanotic specimens. OPN bands were normalized to GAPDH levels. Data are presented as means ± standard errors of the mean. ∗P < .05 (n = 6). The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

Functional validation of hypoxia-inducible factor 1 alpha, cleaved caspase-3, BAX, and phospho-SAPK protein levels in myocardium of acyanotic (AC) and cyanotic (CC) patients. Biopsy specimens were lysed to isolate protein content, and Western blotting analysis was performed, probing for HIF1α (A), cleaved caspase-3 (B), BAX (C), phospho-SAPK (D) and glyceraldehude-3-phosphate dehydrogenase (GAPDH). HIF1α, cleaved caspase-3, and BAX were significantly upregulated in cyanotic compared with acyanotic biopsy specimens. Phospho-SAPK was significantly downregulated in cyanotic compared with acyanotic biopsy specimens. HIF1α, cleaved caspase-3, BAX, and phospho-SAPK bands were normalized to GAPDH levels. Data are presented as means ± standard errors of the mean. ∗P < .05 (n = 6). The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions

Heat Map illustrating the expression levels of the genes implicated in extracellular matrix. Gene symbols in brown represent transcripts that were upregulated in cyanotic patients, whereas gene symbols in green represent genes downregulated by means of cyanosis. Hierarchical clustering has been performed with ArrayStar software. A 3-color scale was used to illustrate expression level differences, with blue indicating low expression values, yellow indicating intermediately expressed genes, and red representing highly expressed genes. The Journal of Thoracic and Cardiovascular Surgery 2010 140, 337-345.e26DOI: (10.1016/j.jtcvs.2009.12.055) Copyright © 2010 The American Association for Thoracic Surgery Terms and Conditions