Advances in high-throughput technologies allow for measurements of many types of omics data, yet the meaningful integration of several different data types remains a significant challenge. Another important and difficult problem is the discovery of molecular disease subtypes characterized by relevant clinical differences, such as survival. Here we present a novel approach, called erturbation clustering for datategration and disease ubtyping (PINS), which is able to address both challenges. The framework has been validated on thousands of cancer samples, using gene expression, DNA methylation, noncoding microRNA, and copy number variation data available from the Gene Expression Omnibus, the Broad Institute, The Cancer Genome Atlas (TCGA), and the European Genome-Phenome Archive. This simultaneous subtyping approach accurately identifies known cancer subtypes and novel subgroups of patients with significantly different survival profiles. The results were obtained from genome-scale molecular data without any other type of prior knowledge. The approach is sufficiently general to replace existing unsupervised clustering approaches outside the scope of bio-medical research, with the additional ability to integrate multiple types of data.

MicroRNAs play important roles in the development of many complex diseases. Because of their importance, the analysis of signaling pathways including miRNA interactions holds the potential for unveiling the mechanisms underlying such diseases. However, current signaling pathway databases are limited to interactions between genes and ignore miRNAs. Here, we use the information on miRNA targets to build a database of miRNA-augmented pathways (mirAP), and we show its application in the contexts of integrative pathway analysis and disease subtyping. Our miRNA-mRNA integrative pathway analysis pipeline incorporates a topology-aware approach that we previously implemented. Our integrative disease subtyping pipeline takes into account survival data, gene and miRNA expression, and knowledge of the interactions among genes. We demonstrate the advantages of our approach by analyzing nine sample-matched datasets that provide both miRNA and mRNA expression. We show that integrating miRNAs into pathway analysis results in greater statistical power, and provides a more comprehensive view of the underlying phenomena. We also compare our disease subtyping method with the state-of-the-art integrative analysis by analyzing a colorectal cancer database from TCGA. The colorectal cancer subtypes identified by our approach are significantly different in terms of their survival expectation. These miRNA-augmented pathways offer a more comprehensive view and a deeper understanding of biological pathways. A better understanding of the molecular processes associated with patients’ survival can help to a better prognosis and an appropriate treatment for each subtype.

MicroRNAs (miRNAs) are small non-coding RNA molecules whose primary function is to regulate the expression of gene products via hybridization to mRNA transcripts, resulting in suppression of translation or mRNA degradation. Although miRNAs have been implicated in complex diseases, including cancer, their impact on distinct biological pathways and phenotypes is largely unknown. Current integration approaches require sample-matched miRNA/mRNA datasets, resulting in limited applicability in practice. Since these approaches cannot integrate heterogeneous information available across independent experiments, they neither account for bias inherent in individual studies, nor do they benefit from increased sample size. Here we present a novel framework able to integrate miRNA and mRNA data (vertical data integration) available in independent studies (horizontal meta-analysis) allowing for a comprehensive analysis of the given phenotypes. To demonstrate the utility of our method, we conducted a meta-analysis of pancreatic and colorectal cancer, using 1,471 samples from 15 mRNA and 14 miRNA expression datasets. Our two-dimensional data integration approach greatly increases the power of statistical analysis and correctly identifies pathways known to be implicated in the phenotypes. The proposed framework is sufficiently general to integrate other types of data obtained from high-throughput assays.

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