Optimizing miRNA-module diagnostic biomarkers of gastric carcinoma via integrated network analysis

<div><p>Several microRNAs (miRNAs) have been suggested as novel biomarkers for diagnosing gastric cancer (GC) at an early stage, but the single-marker strategy may ignore the co-regulatory relationships and lead to low diagnostic specificity. Thus, multi-target modular diagnostic biomarkers are urgently needed. In this study, a Z_summary and NetSVM-based method was used to identify GC-related hub miRNAs and activated modules from clinical miRNA co-expression networks. The NetSVM-based sub-network consisting of the top 20 hub miRNAs reached a high sensitivity and specificity of 0.94 and 0.82. The Z_summary algorithm identified an activated module (miR-486, miR-451, miR-185, and miR-600) which might serve as diagnostic biomarker of GC. Three members of this module were previously suggested as biomarkers of GC and its 24 target genes were significantly enriched in pathways directly related to cancer. The weighted diagnostic ROC AUC of this module was 0.838, and an optimized module unit (miR-451 and miR-185) obtained a higher value of 0.904, both of which were higher than that of individual miRNAs. These hub miRNAs and module have the potential to become robust biomarkers for early diagnosis of GC with further validations. Moreover, such modular analysis may offer valuable insights into multi-target approaches to cancer diagnosis and treatment.</p></div

Hierarchical cluster modules of GC group and their similarities with those of Rep and Norm groups.

<p><b>A</b>. The hierarchical cluster tree (dendrogram) of GC group; each major tree branch represents a module, and each module is labeled with a color below the dendrogram. <b>B</b>. Similarity of modules between GC and Rep groups; each row of the table corresponds to GC modules (labeled by color and labels), and each column corresponds to Rep modules. Numbers in the table indicate gene counts in the intersection of the corresponding modules of GC and Rep groups. Coloring of the table encodes -log (p), with p being the Fisher's exact test p-value for the overlap of the two modules. The darker the red color is, the more significant the correlation is. <b>C</b>. Similarity of modules between GC and Norm groups; the table legend is the same as (<b>B</b>).</p

The sub-network comprised of the top 20 up- and down-regulated miRNAs.

<p>The node color (red denotes up-regulation and green denotes down-regulation) is set based on the log2 fold change of expression between GC and Norm groups.</p

The representative modules with major variations of the Z_summary values.

<p><b>A-C</b>. The preserved modules Mod_2, Mod_5, and Mod_7. <b>D</b>. The activated module (biomarker module) Mod_14; the two red nodes miR_486 and miR_451 are included in the list of the top 20 up-regulated miRNAs.</p

The diagnostic performance of the biomarker module Mod_14 and its individual miRNAs or combinations based on the ROC curves.

<p><b>A</b>. ROC curves of Mod_14 and its individual miRNAs. Red line, Mod_14 (AUC = 0.838, sensitivity = 68.9%, specificity = 94.1%); Blue line, miR_486 (AUC = 0.747, sensitivity = 82.2%, specificity = 58.8%); Green line, miR_451 (AUC = 0.819, sensitivity = 72.2%, specificity = 91.2%); Orange line, miR_185 (AUC = 0.751, sensitivity = 76.7%, specificity = 67.6%); Greenyellow line, miR_600 (AUC = 0.487, sensitivity = 18.9%, specificity = 85.3%). <b>B.</b> ROC curves of miRNA combinations in Mod_14. Red line, combination of miR_451 and miR_185 (AUC = 0.904, sensitivity = 81.1%, specificity = 97.1%); Blue line, combination of miR_451, miR_486 and miR_185 (AUC = 0.838, sensitivity = 67.8%, specificity = 94.1%); Green line, combination of miR_451 and miR_486 (AUC = 0.550, sensitivity = 85.6%, specificity = 26.5%); Orange line, combination of miR_486 and miR_185 (AUC = 0.811, sensitivity = 68.9%, specificity = 91.2%).</p

Z_summary-based preservation and disruption of GC modules.

<p><b>A</b>. The Z_summary preservation statistics (y-axis) of the GC modules compared with Rep group. The dashed blue and green lines (Z_summary = 2 and 10) indicate moderate and strong preservation thresholds, respectively. <b>B</b>. The Z_summary disruption statistics (y-axis) of the GC modules compared with Norm group. Modules with a negative Z_summary value are considered as activated modules.</p

The target gene network and biological functions of the biomarker module Mod_14.

<p>The triangular labels represent miRNAs, and the elliptic labels represent target genes. The significantly enriched GO terms and pathways are listed with p values.</p