Network-Based Protein Biomarker Discovery Platforms

NetMix: A Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks

A classic problem in computational biology is the identification of altered subnetworks: subnetworks of an interaction network that contain genes/proteins that are differentially expressed, highly mutated, or otherwise aberrant compared with other genes/proteins. Numerous methods have been developed to solve this problem under various assumptions, but the statistical properties of these methods are often unknown. For example, some widely used methods are reported to output very large subnetworks that are difficult to interpret biologically. In this work, we formulate the identification of altered subnetworks as the problem of estimating the parameters of a class of probability distributions that we call the Altered Subset Distribution (ASD). We derive a connection between a popular method, jActiveModules, and the maximum likelihood estimator (MLE) of the ASD. We show that the MLE is statistically biased, explaining the large subnetworks output by jActiveModules. Based on these insights, we introduce NetMix, an algorithm that uses Gaussian mixture models to obtain less biased estimates of the parameters of the ASD. We demonstrate that NetMix outperforms existing methods in identifying altered subnetworks on both simulated and real data, including the identification of differentially expressed genes from both microarray and RNA-seq experiments and the identification of cancer driver genes in somatic mutation data.

Bioinformatic analysis of proteomic data for iron, inflammation, and hypoxic pathways in restless legs syndrome

OBJECTIVE/BACKGROUND

We performed bioinformatic analysis of proteomic data to identify the biomarkers of restless legs syndrome (RLS) and provide insights into the putative pathomechanisms, including iron deficiency, inflammation, and hypoxic pathways.

PATIENTS/METHODS

Patients with drug-naïve idiopathic RLS were recruited at a university hospital from June 2017 to February 2018. Serum samples from patients with RLS (n = 7) and healthy sex- and age-matched controls (n = 6) were evaluated by proteomic analysis. For differentially expressed proteins (DEPs) in patients with RLS, compared to those in controls, the expression profiles and protein-protein interaction (PPI) network were characterized between dysregulated proteins and extracted proteins involved in iron deficiency, hypoxia, and inflammation responses using the String database (http://string-DB.org). The PPI network was visualized by Cytoscape ver. 3. 7. 1. Statistical analyses of the validation Western blot assays were performed using a Student's t-test.

RESULTS

Interactome network analysis revealed a relationship among the eight proteins, their associated genes, and 150, 47, and 11 proteins related to iron deficiency, inflammation, and hypoxic pathways, respectively. All DEPs were well associated with inflammation, and complement 3, complement C4A, alpha-2 HS glycoprotein, and alpha-2 macroglobulin precursor were found to be in hub positions of networks involved in PPIs including iron deficiency, hypoxia pathway, and inflammation. C3 and C4A were verified using western blotting.

CONCLUSIONS

We identified key molecules that represent the selected cellular pathways as protein biomarkers by PPI network analysis. Changes in inflammation can mediate or affect the pathomechanism of RLS and can thus act as systemic biomarkers.

Microbial Proteomics and Their Importance in Medical Microbiology

Microbial infection is a leading cause of death around the world. Most of the infectious diseases are caused by drug-resistant microbes; this may lead to a delay in the administration of microbiologically effective therapy (Chen et al., 2017; Del Chierico et al., 2014). Therefore, exhaustive understanding of microbial physiologies, infection and defense systems, and survival strategies is of great interest in order to actively defeat microbial infection. Microbial proteomics provides complete information of microbial physiology and expression and function of the proteins that are involved in infection and also gives a clue in clinical diagnosis and antimicrobial therapy (Pérez-Llarena and Bou, 2016; Vranakis et al., 2014). Microbial proteomics helps to identify the proteins associated with microbial activity, microbial host-pathogen interactions, and antimicrobial resistant mechanism. Microbial activity of pathogens can be confirmed by using the 2-D gel-based and gel-free method with the combination of MALDI-TOF-LC-MS/MS. Proteomic analysis of microbial host-pathogen interaction reveals valuable information about the virulence of the pathogen and its resistance; it helps in better understanding of the infection and for developing strategies against microbial infections (Cheng et al., 2016). Fig. 3.1 schematically illustrates the proteomic analysis of the bacterial samples.

A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis

Recent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex-omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed a multi-objective optimisation method that effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. The proposed multi-objective framework has the capacity to adjust for conflicting biomarker objectives and to incorporate heterogeneous information facilitating systems approaches to biomarker discovery. We have found a prognostic signature of colorectal cancer comprising 11 circulating microRNAs. The identified signature predicts the patients' survival outcome and targets pathways underlying colorectal cancer progression. The altered expression of the identified microRNAs was confirmed in an independent public data set of plasma samples of patients in early stage vs advanced colorectal cancer. Furthermore, the generality of the proposed method was demonstrated across three publicly available miRNA data sets associated with biomarker studies in other diseases.