title: A Systems Approach to Understand Antigen Presentation and the Immune Response.
abstract: The mammalian immune system has evolved to respond to pathogenic, environmental, and cellular changes in order to maintain the health of the host. These responses include the comparatively primitive innate immune response, which represents a rapid and relatively nonspecific reaction to challenge by pathogens and the more complex cellular adaptive immune response. This adaptive response evolves with the pathogenic challenge, involves the cross talk of several cell types, and is highly specific to the pathogen due to the liberation of peptide antigens and their presentation on the surface of affected cells. Together these two forms of immunity provide a surveillance mechanism for the system-wide scrutiny of cellular function, environment, and health. As such the immune system is best understood at a systems biology level, and studies that combine gene expression, protein expression, and liberation of peptides for antigen presentation can be combined to provide a detailed understanding of immunity. This chapter details our experience in identifying peptide antigens and combining this information with more traditional proteomics approaches to understand the generation of immune responses on a holistic level.
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
authors.forename: Nadine L
authors.initials: NL
authors.lastname: Dudek
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
authors.forename: Nathan P
authors.initials: NP
authors.lastname: Croft
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
authors.forename: Ralf B
authors.initials: RB
authors.lastname: Schittenhelm
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia.
authors.forename: Sri H
authors.initials: SH
authors.lastname: Ramarathinam
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, 3800, Australia. anthony.purcell@monash.edu.|The Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, 3010, Australia. anthony.purcell@monash.edu.
authors.forename: Anthony W
authors.initials: AW
authors.lastname: Purcell
mesh_terms: D017951:Antigen Presentation / Q000502:physiology*; D000941:Antigens / Q000276:immunology* / Q000302:isolation & purification; D002846:Chromatography, Affinity; D002851:Chromatography, High Pressure Liquid; D006801:Humans; D055633:Immune System Phenomena; D007109:Immunity; D008285:Major Histocompatibility Complex; D013058:Mass Spectrometry; D040901:Proteomics / Q000379:methods; D049490:Systems Biology / Q000379:methods*
chemical_list: D000941:Antigens
keywords: Antigen presentation; Human leukocyte antigens; Major histocompatibility complex; Mass spectrometry; Peptide ligands