title: Systems Biology Approaches for Host-Fungal Interactions: An Expanding Multi-Omics Frontier.
abstract: Opportunistic fungal infections are an increasing threat for global health, and for immunocompromised patients in particular. These infections are characterized by interaction between fungal pathogen and host cells. The exact mechanisms and the attendant variability in host and fungal pathogen interaction remain to be fully elucidated. The field of systems biology aims to characterize a biological system, and utilize this knowledge to predict the system's response to stimuli such as fungal exposures. A multi-omics approach, for example, combining data from genomics, proteomics, metabolomics, would allow a more comprehensive and pan-optic "two systems" biology of both the host and the fungal pathogen. In this review and literature analysis, we present highly specialized and nascent methods for analysis of multiple -omes of biological systems, in addition to emerging single-molecule visualization techniques that may assist in determining biological relevance of multi-omics data. We provide an overview of computational methods for modeling of gene regulatory networks, including some that have been applied towards the study of an interacting host and pathogen. In sum, comprehensive characterizations of host-fungal pathogen systems are now possible, and utilization of these cutting-edge multi-omics strategies may yield advances in better understanding of both host biology and fungal pathogens at a systems scale.
authors.affiliation: 1 Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia , Vancouver, British Columbia, Canada .
authors.forename: Luka
authors.initials: L
authors.lastname: Culibrk
authors.affiliation: 1 Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia , Vancouver, British Columbia, Canada .
authors.forename: Carys A
authors.initials: CA
authors.lastname: Croft
authors.affiliation: 1 Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia , Vancouver, British Columbia, Canada .|2 Prevention of Organ Failure (PROOF) Centre of Excellence , Vancouver, British Columbia, Canada .|3 Department of Medicine, Division of Respiratory Medicine, University of British Columbia , Vancouver, British Columbia, Canada .
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Tebbutt
mesh_terms: D001232:Aspergillus fumigatus / Q000472:pathogenicity / Q000502:physiology; D002176:Candida albicans / Q000472:pathogenicity / Q000502:physiology; D003455:Cryptococcus neoformans / Q000472:pathogenicity / Q000502:physiology; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods; D054884:Host-Pathogen Interactions / Q000235:genetics / Q000276:immunology*; D006801:Humans; D016867:Immunocompromised Host; D055432:Metabolomics / Q000379:methods; D009181:Mycoses / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D009894:Opportunistic Infections / Q000235:genetics / Q000276:immunology* / Q000382:microbiology; D000072760:Single Molecule Imaging / Q000295:instrumentation / Q000379:methods; D049490:Systems Biology / Q000379:methods*