Advances in protein-protein interaction network analysis for Parkinson's disease

Abstract Protein-protein interactions (PPIs) are a key component of the subcellular molecular networks which enable cells to function. Due to their importance in homeostasis, alterations to the networks can be detrimental, leading to cellular dysfunction and ultimately disease states. Parkinson's disease (PD) is a progressive neurodegenerative condition with multifactorial aetiology, spanning genetic variation and environmental modifiers. At a molecular and systems level, the characterisation of PD is the focus of extensive research, largely due to an unmet need for disease modifying therapies. PPI network analysis approaches are a valuable strategy to accelerate our understanding of the molecular crosstalk and biological processes underlying PD pathogenesis, especially due to the complex nature of this disease. In this review, we describe the utility of PPI network approaches in modelling complex systems, focusing on previous work in PD research. We discuss four principal strategies for using PPI network approaches: to infer PD related cellular functions, pathways and novel genes; to support genomics studies; to study the interactome of single PD related genes; and to compare the molecular basis of PD to other neurodegenerative disorders. This is an evolving area of research which is likely to further expand as omics data generation and availability increase. These approaches complement and bridge-the-gap between genetics and functional research to inform future investigations. In this review we outline several limitations that require consideration, acknowledging that ongoing challenges in this field continue to be addressed and the refinement of these approaches will facilitate further advances using PPI network analysis for understanding complex diseases.