TY - JOUR
T1 - MPLEx
T2 - A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling
AU - Burnum-Johnson, Kristin E.
AU - Kyle, Jennifer E.
AU - Eisfeld, Amie J.
AU - Casey, Cameron P.
AU - Stratton, Kelly G.
AU - Gonzalez, Juan F.
AU - Habyarimana, Fabien
AU - Negretti, Nicholas M.
AU - Sims, Amy C.
AU - Chauhan, Sadhana
AU - Thackray, Larissa B.
AU - Halfmann, Peter J.
AU - Walters, Kevin B.
AU - Kim, Young Mo
AU - Zink, Erika M.
AU - Nicora, Carrie D.
AU - Weitz, Karl K.
AU - Webb-Robertson, Bobbie Jo M.
AU - Nakayasu, Ernesto S.
AU - Ahmer, Brian
AU - Konkel, Michael E.
AU - Motin, Vladimir
AU - Baric, Ralph S.
AU - Diamond, Michael S.
AU - Kawaoka, Yoshihiro
AU - Waters, Katrina M.
AU - Smith, Richard D.
AU - Metz, Thomas O.
N1 - Publisher Copyright:
© 2017 The Royal Society of Chemistry.
PY - 2017/1/30
Y1 - 2017/1/30
N2 - The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus, Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes.
AB - The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host-pathogen relationships and facilitate the development of new therapies and vaccines. Molecular characterization of infectious samples outside of appropriate biosafety containment can take place only subsequent to pathogen inactivation. Herein, we describe a modified Folch extraction using chloroform/methanol that facilitates the molecular characterization of infectious samples by enabling simultaneous pathogen inactivation and extraction of proteins, metabolites, and lipids for subsequent mass spectrometry-based multi-omics measurements. This single-sample metabolite, protein and lipid extraction (MPLEx) method resulted in complete inactivation of clinically important bacterial and viral pathogens with exposed lipid membranes, including Yersinia pestis, Salmonella Typhimurium, and Campylobacter jejuni in pure culture, and Yersinia pestis, Campylobacter jejuni, and West Nile, MERS-CoV, Ebola, and influenza H7N9 viruses in infection studies. In addition, >99% inactivation, which increased with solvent exposure time, was also observed for pathogens without exposed lipid membranes including community-associated methicillin-resistant Staphylococcus aureus, Clostridium difficile spores and vegetative cells, and adenovirus type 5. The overall pipeline of inactivation and subsequent proteomic, metabolomic, and lipidomic analyses was evaluated using a human epithelial lung cell line infected with wild-type and mutant influenza H7N9 viruses, thereby demonstrating that MPLEx yields biomaterial of sufficient quality for subsequent multi-omics analyses. Based on these experimental results, we believe that MPLEx will facilitate systems biology studies of infectious samples by enabling simultaneous pathogen inactivation and multi-omics measurements from a single specimen with high success for pathogens with exposed lipid membranes.
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UR - http://www.scopus.com/inward/citedby.url?scp=85010992329&partnerID=8YFLogxK
U2 - 10.1039/c6an02486f
DO - 10.1039/c6an02486f
M3 - Article
C2 - 28091625
AN - SCOPUS:85010992329
SN - 0003-2654
VL - 142
SP - 442
EP - 448
JO - Analyst
JF - Analyst
IS - 3
ER -