Proteomics and integrative omic approaches for understanding host–pathogen interactions and infectious diseases

Abstract

Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host–pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host–pathogen interactions that represent anti‐ and pro‐pathogenic cellular responses. Here, we review these proteomic methods and their application to studying viral and bacterial intracellular pathogens. We examine approaches for defining spatial and temporal host–pathogen protein interactions upon infection of a host cell. Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.

Glycomics and Proteomics Approaches to Investigate Early Adenovirus–Host Cell Interactions

“…Previously, AE-MS has successfully identified host factor interactions with viral non-structural proteins of virus families ranging from flaviviruses to herpesviruses (reviewed in Refs. [133,[147][148][149]). The application to virus receptor discovery is now in reach (Fig.…”

Integration of large-scale multi-omic datasets: A protein-centric view

“…Third, we will review an important clinical application of proteogenomics -- cancer biology -- to demonstrate how this field in particular is poised to move towards truly integrative analysis of the massive data. We will focus on aspects that expand on other excellent reviews published lately that have discussed computational methods and human diseases in more detail [18][19][20][21][22][23][24][25]. …”

Leveraging Experimental Details for an Improved Understanding of Host‐Pathogen Interactome

“…confocal microscopy). For a more detailed discussion of experimental approaches used to identify interactions between pathogen and host, we direct the reader to a recent review article (Jean Beltran, Federspiel, Sheng, & Cristea, 2017). …”