Oncotarget

Research Papers:

Aberration hubs in protein interaction networks highlight actionable targets in cancer

Mehran Karimzadeh, Pouria Jandaghi, Andreas I. Papadakis, Sebastian Trainor, Johan Rung, Mar Gonzàlez-Porta, Ghislaine Scelo, Naveen S. Vasudev, Alvis Brazma, Sidong Huang, Rosamonde E. Banks, Mark Lathrop, Hamed S. Najafabadi and Yasser Riazalhosseini _

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Oncotarget. 2018; 9:25166-25180. https://doi.org/10.18632/oncotarget.25382

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Abstract

Mehran Karimzadeh1,2, Pouria Jandaghi1,2, Andreas I. Papadakis3, Sebastian Trainor4, Johan Rung5, Mar Gonzàlez-Porta5, Ghislaine Scelo6, Naveen S. Vasudev4, Alvis Brazma5, Sidong Huang3, Rosamonde E. Banks4, Mark Lathrop1,2, Hamed S. Najafabadi1,2 and Yasser Riazalhosseini1,2

1Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada

2McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 0G1, Canada

3Department of Biochemistry, The Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, QC H3G 1Y6, Canada

4Leeds Institute of Cancer and Pathology, University of Leeds, Cancer Research Building, St James’s University Hospital, Leeds, LS9 7TF, UK

5European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK

6International Agency for Research on Cancer (IARC), Lyon, 69008, France

Correspondence to:

Yasser Riazalhosseini, email: yasser.riazalhosseini@mcgill.ca

Keywords: cancer; genomics; computational biology; systems biology; target discovery

Received: September 14, 2017     Accepted: April 24, 2018     Published: May 18, 2018

ABSTRACT

Despite efforts for extensive molecular characterization of cancer patients, such as the international cancer genome consortium (ICGC) and the cancer genome atlas (TCGA), the heterogeneous nature of cancer and our limited knowledge of the contextual function of proteins have complicated the identification of targetable genes. Here, we present Aberration Hub Analysis for Cancer (AbHAC) as a novel integrative approach to pinpoint aberration hubs, i.e. individual proteins that interact extensively with genes that show aberrant mutation or expression. Our analysis of the breast cancer data of the TCGA and the renal cancer data from the ICGC shows that aberration hubs are involved in relevant cancer pathways, including factors promoting cell cycle and DNA replication in basal-like breast tumors, and Src kinase and VEGF signaling in renal carcinoma. Moreover, our analysis uncovers novel functionally relevant and actionable targets, among which we have experimentally validated abnormal splicing of spleen tyrosine kinase as a key factor for cell proliferation in renal cancer. Thus, AbHAC provides an effective strategy to uncover novel disease factors that are only identifiable by examining mutational and expression data in the context of biological networks.


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