Additional file 1 of Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation, a systematic review and meta-analysis

Supplementary Material

<i>GSTA1</i> mRNA levels are negatively correlated with tumor size in HCCs.

<p>A, Real-time PCR analysis of normalized <i>GSTA1</i> mRNA expression in 18 HCCs. HCC 0 (large HCC), HCC1 (Small HCC, <3 cm) (p = 0.002). B, Real-time PCR analysis of <i>GSTA1</i> mRNA expression in 18 HCCs and tumor size are negatively correlated (Spearman’s R = -0.67; p = 0.007).</p

Loss of <i>GSTA1</i> mRNA expression is associated with bad outcome after curative HCC resection.

<p><i>GSTA1</i> mRNA expression was significantly related to disease-free and overall survival by Log-Rank and Cox regression analysis on an annotated microarray dataset from 247 HCC-resected patients (Gene Expression Omnibus, GSE14520. Data were normalized and filtered as described).</p

<i>GSTA1</i> expression in hepatocellular carcinomas and matching non-tumor livers.

<p>Real-time PCR analysis of normalized <i>GSTA1</i> mRNA expression in 36 frozen liver samples including (HCCs), and matching non-tumor livers (C). RNA expression values were calculated by the ΔΔCt method. Statistical significance of the differences between means was assessed by the Mann-Whitney “U” test (p = 0.007).</p

Prevalence of healthy individuals and patients with hepatocellular carcinoma according to the rs3957357C>T genotype in the <i>GSTA1</i> gene.

<p>Stratification according to the rs3957357C>T genotype in <i>GSTA1</i> shows a 5-fold increase in the prevalence of individuals with HCC carrying the TT genotype (27%), compared with healthy individuals and carrying the same genotype (5%).</p

Genetics and bio-informatics analysis of rs3957357C>T in <i>GSTA1</i>.

<p>A, Linkage disequilibrium analysis between <i>GSTA1</i> single nucleotide polymorphisms in the CEPH-HapMap population visualized with the Haploview software. Linkage disequilibrium data for <i>GSTA1</i> gene shows 7 SNPs, among them rs3957357 (highlighted in red). All the single nucleotide polymorphisms are in high linkage disequilibrium. Red squares indicate complete linkage disequilibrium between two single nucleotide polymorphisms. SNPs: single nucleotide polymorphisms. B, Representative image of a PCR-RFLP experiment. The presence of the T allele in rs3957357C>T of <i>GSTA1</i> gene leads to the production of 380 bp and 100 bp fragments, while the amplicons carrying the C allele remain undigested.</p

Correlation analysis of <i>GSTA1</i>, albumin (ALB) and procollagen type XVIII (COL18A1) mRNA expression in hepatocellular carcinomas.

<p>A, Real-time PCR analysis of albumin mRNA expression levels in 18 HCCs (Spearman’s R = 0.67; p = 0.001). B, Real-time PCR analysis of procollagen type XVIII mRNA expression levels in 18 HCCs (Spearman’s R = 0.50; p = 0.03).</p

<i>GSTA1</i> co-expression network in 247 human HCCs.

<p><i>GSTA1</i> is highlighted as a yellow node. Weighted correlation network analyses of mRNA expression data was visualized with Cytoscape with correlation coefficient thresholds > 0.40 (positive correlations) or <– 0.40 (negative correlations). Closeness between nodes is proportional to the number of connections. Thickness of links is proportional to the correlation coefficients between genes. Green nodes, positively correlated genes; blue nodes, negatively correlated genes; red links, positive correlation; blue links, negative correlation.</p

Pearson’s correlations between <i>NAMPT, ICAM1, SELL, FPR1, DEFA1-3</i> and <i>LL-37</i> genes expression.

<p>Only Significant correlations are shown (P≤5×10⁻³).</p><p>All genes expression were normalized to <i>POL2RA</i> mRNA levels.</p><p>r: Pearson’s correlation coefficient, P: P-value.</p

Characteristics of studied individuals.

<p>BMI: body mass index, BP: blood pressure, SBP: systolic blood pressure, DBP: diastolic blood pressure, MAF: minor allele frequency.</p