MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.
Identifieur interne : 000C31 ( PubMed/Checkpoint ); précédent : 000C30; suivant : 000C32MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.
Auteurs : Kristin E. Burnum-Johnson [États-Unis] ; Jennifer E. Kyle [États-Unis] ; Amie J. Eisfeld [États-Unis] ; Cameron P. Casey [États-Unis] ; Kelly G. Stratton [États-Unis] ; Juan F. Gonzalez [États-Unis] ; Fabien Habyarimana [États-Unis] ; Nicholas M. Negretti [États-Unis] ; Amy C. Sims [États-Unis] ; Sadhana Chauhan [États-Unis] ; Larissa B. Thackray [États-Unis] ; Peter J. Halfmann [États-Unis] ; Kevin B. Walters [États-Unis] ; Young-Mo Kim [États-Unis] ; Erika M. Zink [États-Unis] ; Carrie D. Nicora [États-Unis] ; Karl K. Weitz [États-Unis] ; Bobbie-Jo M. Webb-Robertson [États-Unis] ; Ernesto S. Nakayasu [États-Unis] ; Brian Ahmer [États-Unis] ; Michael E. Konkel [États-Unis] ; Vladimir Motin [États-Unis] ; Ralph S. Baric [États-Unis] ; Michael S. Diamond [États-Unis] ; Yoshihiro Kawaoka [États-Unis] ; Katrina M. Waters [États-Unis] ; Richard D. Smith [États-Unis] ; Thomas O. Metz [États-Unis]Source :
- The Analyst [ 1364-5528 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- analyse : Lipides.
- isolement et purification : Bactéries, Virus.
- Cellules épithéliales, Humains, Inactivation virale, Lignée cellulaire, Métabolomique, Protéines, Protéomique, Spectrométrie de masse.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Lipids.
- isolation & purification : Bacteria, Viruses.
- Cell Line, Epithelial Cells, Humans, Mass Spectrometry, Metabolomics, Proteins, Proteomics, Virus Inactivation.
Abstract
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.
DOI: 10.1039/c6an02486f
PubMed: 28091625
Affiliations:
- États-Unis
- Caroline du Nord, Missouri (État), Ohio, Texas, Washington (État), Wisconsin
- Chapel Hill (Caroline du Nord), Madison (Wisconsin), Saint-Louis (Missouri)
- Université de Caroline du Nord à Chapel Hill, Université du Wisconsin à Madison, École de médecine (Université Washington de Saint-Louis)
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:28091625Le document en format XML
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Halfmann</name><affiliation wicri:level="2"><nlm:affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Walters, Kevin B" sort="Walters, Kevin B" uniqKey="Walters K" first="Kevin B" last="Walters">Kevin B. 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Zink</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Nicora, Carrie D" sort="Nicora, Carrie D" uniqKey="Nicora C" first="Carrie D" last="Nicora">Carrie D. Nicora</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Weitz, Karl K" sort="Weitz, Karl K" uniqKey="Weitz K" first="Karl K" last="Weitz">Karl K. Weitz</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Webb Robertson, Bobbie Jo M" sort="Webb Robertson, Bobbie Jo M" uniqKey="Webb Robertson B" first="Bobbie-Jo M" last="Webb-Robertson">Bobbie-Jo M. Webb-Robertson</name><affiliation wicri:level="2"><nlm:affiliation>Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Nakayasu, Ernesto S" sort="Nakayasu, Ernesto S" uniqKey="Nakayasu E" first="Ernesto S" last="Nakayasu">Ernesto S. Nakayasu</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Ahmer, Brian" sort="Ahmer, Brian" uniqKey="Ahmer B" first="Brian" last="Ahmer">Brian Ahmer</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Konkel, Michael E" sort="Konkel, Michael E" uniqKey="Konkel M" first="Michael E" last="Konkel">Michael E. Konkel</name><affiliation wicri:level="2"><nlm:affiliation>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Motin, Vladimir" sort="Motin, Vladimir" uniqKey="Motin V" first="Vladimir" last="Motin">Vladimir Motin</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Texas Medical Branch, Galveston, TX</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Diamond, Michael S" sort="Diamond, Michael S" uniqKey="Diamond M" first="Michael S" last="Diamond">Michael S. Diamond</name><affiliation wicri:level="4"><nlm:affiliation>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO</wicri:regionArea><placeName><region type="state">Missouri (État)</region><settlement type="city">Saint-Louis (Missouri)</settlement></placeName><orgName type="university">École de médecine (Université Washington de Saint-Louis)</orgName></affiliation></author><author><name sortKey="Kawaoka, Yoshihiro" sort="Kawaoka, Yoshihiro" uniqKey="Kawaoka Y" first="Yoshihiro" last="Kawaoka">Yoshihiro Kawaoka</name><affiliation wicri:level="2"><nlm:affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName><placeName><settlement type="city">Madison (Wisconsin)</settlement><region type="state">Wisconsin</region></placeName><orgName type="university" n="3">Université du Wisconsin à Madison</orgName></affiliation></author><author><name sortKey="Waters, Katrina M" sort="Waters, Katrina M" uniqKey="Waters K" first="Katrina M" last="Waters">Katrina M. Waters</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D" last="Smith">Richard D. Smith</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Metz, Thomas O" sort="Metz, Thomas O" uniqKey="Metz T" first="Thomas O" last="Metz">Thomas O. Metz</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28091625</idno><idno type="pmid">28091625</idno><idno type="doi">10.1039/c6an02486f</idno><idno type="wicri:Area/PubMed/Corpus">000E14</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E14</idno><idno type="wicri:Area/PubMed/Curation">000E14</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000E14</idno><idno type="wicri:Area/PubMed/Checkpoint">000C31</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000C31</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.</title><author><name sortKey="Burnum Johnson, Kristin E" sort="Burnum Johnson, Kristin E" uniqKey="Burnum Johnson K" first="Kristin E" last="Burnum-Johnson">Kristin E. Burnum-Johnson</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Kyle, Jennifer E" sort="Kyle, Jennifer E" uniqKey="Kyle J" first="Jennifer E" last="Kyle">Jennifer E. Kyle</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Eisfeld, Amie J" sort="Eisfeld, Amie J" uniqKey="Eisfeld A" first="Amie J" last="Eisfeld">Amie J. Eisfeld</name><affiliation wicri:level="2"><nlm:affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Casey, Cameron P" sort="Casey, Cameron P" uniqKey="Casey C" first="Cameron P" last="Casey">Cameron P. Casey</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Stratton, Kelly G" sort="Stratton, Kelly G" uniqKey="Stratton K" first="Kelly G" last="Stratton">Kelly G. Stratton</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Gonzalez, Juan F" sort="Gonzalez, Juan F" uniqKey="Gonzalez J" first="Juan F" last="Gonzalez">Juan F. Gonzalez</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Habyarimana, Fabien" sort="Habyarimana, Fabien" uniqKey="Habyarimana F" first="Fabien" last="Habyarimana">Fabien Habyarimana</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Negretti, Nicholas M" sort="Negretti, Nicholas M" uniqKey="Negretti N" first="Nicholas M" last="Negretti">Nicholas M. Negretti</name><affiliation wicri:level="2"><nlm:affiliation>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Sims, Amy C" sort="Sims, Amy C" uniqKey="Sims A" first="Amy C" last="Sims">Amy C. Sims</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Chauhan, Sadhana" sort="Chauhan, Sadhana" uniqKey="Chauhan S" first="Sadhana" last="Chauhan">Sadhana Chauhan</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Texas Medical Branch, Galveston, TX</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Thackray, Larissa B" sort="Thackray, Larissa B" uniqKey="Thackray L" first="Larissa B" last="Thackray">Larissa B. Thackray</name><affiliation wicri:level="4"><nlm:affiliation>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO</wicri:regionArea><placeName><region type="state">Missouri (État)</region><settlement type="city">Saint-Louis (Missouri)</settlement></placeName><orgName type="university">École de médecine (Université Washington de Saint-Louis)</orgName></affiliation></author><author><name sortKey="Halfmann, Peter J" sort="Halfmann, Peter J" uniqKey="Halfmann P" first="Peter J" last="Halfmann">Peter J. Halfmann</name><affiliation wicri:level="2"><nlm:affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Walters, Kevin B" sort="Walters, Kevin B" uniqKey="Walters K" first="Kevin B" last="Walters">Kevin B. Walters</name><affiliation wicri:level="2"><nlm:affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName></affiliation></author><author><name sortKey="Kim, Young Mo" sort="Kim, Young Mo" uniqKey="Kim Y" first="Young-Mo" last="Kim">Young-Mo Kim</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Zink, Erika M" sort="Zink, Erika M" uniqKey="Zink E" first="Erika M" last="Zink">Erika M. Zink</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Nicora, Carrie D" sort="Nicora, Carrie D" uniqKey="Nicora C" first="Carrie D" last="Nicora">Carrie D. Nicora</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Weitz, Karl K" sort="Weitz, Karl K" uniqKey="Weitz K" first="Karl K" last="Weitz">Karl K. Weitz</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Webb Robertson, Bobbie Jo M" sort="Webb Robertson, Bobbie Jo M" uniqKey="Webb Robertson B" first="Bobbie-Jo M" last="Webb-Robertson">Bobbie-Jo M. Webb-Robertson</name><affiliation wicri:level="2"><nlm:affiliation>Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Nakayasu, Ernesto S" sort="Nakayasu, Ernesto S" uniqKey="Nakayasu E" first="Ernesto S" last="Nakayasu">Ernesto S. Nakayasu</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Ahmer, Brian" sort="Ahmer, Brian" uniqKey="Ahmer B" first="Brian" last="Ahmer">Brian Ahmer</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Konkel, Michael E" sort="Konkel, Michael E" uniqKey="Konkel M" first="Michael E" last="Konkel">Michael E. Konkel</name><affiliation wicri:level="2"><nlm:affiliation>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Motin, Vladimir" sort="Motin, Vladimir" uniqKey="Motin V" first="Vladimir" last="Motin">Vladimir Motin</name><affiliation wicri:level="2"><nlm:affiliation>Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of Texas Medical Branch, Galveston, TX</wicri:regionArea><placeName><region type="state">Texas</region></placeName></affiliation></author><author><name sortKey="Baric, Ralph S" sort="Baric, Ralph S" uniqKey="Baric R" first="Ralph S" last="Baric">Ralph S. Baric</name><affiliation wicri:level="4"><nlm:affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region><settlement type="city">Chapel Hill (Caroline du Nord)</settlement></placeName><orgName type="university">Université de Caroline du Nord à Chapel Hill</orgName></affiliation></author><author><name sortKey="Diamond, Michael S" sort="Diamond, Michael S" uniqKey="Diamond M" first="Michael S" last="Diamond">Michael S. Diamond</name><affiliation wicri:level="4"><nlm:affiliation>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO</wicri:regionArea><placeName><region type="state">Missouri (État)</region><settlement type="city">Saint-Louis (Missouri)</settlement></placeName><orgName type="university">École de médecine (Université Washington de Saint-Louis)</orgName></affiliation></author><author><name sortKey="Kawaoka, Yoshihiro" sort="Kawaoka, Yoshihiro" uniqKey="Kawaoka Y" first="Yoshihiro" last="Kawaoka">Yoshihiro Kawaoka</name><affiliation wicri:level="2"><nlm:affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI</wicri:regionArea><placeName><region type="state">Wisconsin</region></placeName><placeName><settlement type="city">Madison (Wisconsin)</settlement><region type="state">Wisconsin</region></placeName><orgName type="university" n="3">Université du Wisconsin à Madison</orgName></affiliation></author><author><name sortKey="Waters, Katrina M" sort="Waters, Katrina M" uniqKey="Waters K" first="Katrina M" last="Waters">Katrina M. Waters</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Smith, Richard D" sort="Smith, Richard D" uniqKey="Smith R" first="Richard D" last="Smith">Richard D. Smith</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author><author><name sortKey="Metz, Thomas O" sort="Metz, Thomas O" uniqKey="Metz T" first="Thomas O" last="Metz">Thomas O. Metz</name><affiliation wicri:level="2"><nlm:affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region></placeName></affiliation></author></analytic><series><title level="j">The Analyst</title><idno type="eISSN">1364-5528</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bacteria (isolation & purification)</term><term>Cell Line</term><term>Epithelial Cells</term><term>Humans</term><term>Lipids (analysis)</term><term>Mass Spectrometry</term><term>Metabolomics</term><term>Proteins</term><term>Proteomics</term><term>Virus Inactivation</term><term>Viruses (isolation & purification)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries (isolement et purification)</term><term>Cellules épithéliales</term><term>Humains</term><term>Inactivation virale</term><term>Lignée cellulaire</term><term>Lipides (analyse)</term><term>Métabolomique</term><term>Protéines</term><term>Protéomique</term><term>Spectrométrie de masse</term><term>Virus (isolement et purification)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Lipids</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Lipides</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Bacteria</term><term>Viruses</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Bactéries</term><term>Virus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cell Line</term><term>Epithelial Cells</term><term>Humans</term><term>Mass Spectrometry</term><term>Metabolomics</term><term>Proteins</term><term>Proteomics</term><term>Virus Inactivation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cellules épithéliales</term><term>Humains</term><term>Inactivation virale</term><term>Lignée cellulaire</term><term>Métabolomique</term><term>Protéines</term><term>Protéomique</term><term>Spectrométrie de masse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">28091625</PMID><DateCompleted><Year>2018</Year><Month>10</Month><Day>29</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1364-5528</ISSN><JournalIssue CitedMedium="Internet"><Volume>142</Volume><Issue>3</Issue><PubDate><Year>2017</Year><Month>Jan</Month><Day>26</Day></PubDate></JournalIssue><Title>The Analyst</Title><ISOAbbreviation>Analyst</ISOAbbreviation></Journal><ArticleTitle>MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.</ArticleTitle><Pagination><MedlinePgn>442-448</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1039/c6an02486f</ELocationID><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Burnum-Johnson</LastName><ForeName>Kristin E</ForeName><Initials>KE</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2722-4149</Identifier><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kyle</LastName><ForeName>Jennifer E</ForeName><Initials>JE</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eisfeld</LastName><ForeName>Amie J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Casey</LastName><ForeName>Cameron P</ForeName><Initials>CP</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stratton</LastName><ForeName>Kelly G</ForeName><Initials>KG</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gonzalez</LastName><ForeName>Juan F</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Habyarimana</LastName><ForeName>Fabien</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Negretti</LastName><ForeName>Nicholas M</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sims</LastName><ForeName>Amy C</ForeName><Initials>AC</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chauhan</LastName><ForeName>Sadhana</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Thackray</LastName><ForeName>Larissa B</ForeName><Initials>LB</Initials><AffiliationInfo><Affiliation>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Halfmann</LastName><ForeName>Peter J</ForeName><Initials>PJ</Initials><AffiliationInfo><Affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Walters</LastName><ForeName>Kevin B</ForeName><Initials>KB</Initials><AffiliationInfo><Affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Young-Mo</ForeName><Initials>YM</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zink</LastName><ForeName>Erika M</ForeName><Initials>EM</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nicora</LastName><ForeName>Carrie D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weitz</LastName><ForeName>Karl K</ForeName><Initials>KK</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Webb-Robertson</LastName><ForeName>Bobbie-Jo M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nakayasu</LastName><ForeName>Ernesto S</ForeName><Initials>ES</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ahmer</LastName><ForeName>Brian</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Konkel</LastName><ForeName>Michael E</ForeName><Initials>ME</Initials><AffiliationInfo><Affiliation>School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Motin</LastName><ForeName>Vladimir</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baric</LastName><ForeName>Ralph S</ForeName><Initials>RS</Initials><AffiliationInfo><Affiliation>Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Diamond</LastName><ForeName>Michael S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>Departments of Medicine, Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kawaoka</LastName><ForeName>Yoshihiro</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Waters</LastName><ForeName>Katrina M</ForeName><Initials>KM</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Richard D</ForeName><Initials>RD</Initials><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Metz</LastName><ForeName>Thomas O</ForeName><Initials>TO</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-6049-3968</Identifier><AffiliationInfo><Affiliation>Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P41 GM103493</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>U19 AI106772</GrantID><Acronym>AI</Acronym><Agency>NIAID NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType 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