MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

Kristin E. Burnum-Johnson, Jennifer E. Kyle, Amie J. Eisfeld, Cameron P. Casey, Kelly G. Stratton, Juan F. Gonzalez, Fabien Habyarimana, Nicholas M. Negretti, Amy C. Sims, Sadhana Chauhan, Larissa B. Thackray, Peter J. Halfmann, Kevin B. Walters, Young Mo Kim, Erika M. Zink, Carrie D. Nicora, Karl K. Weitz, Bobbie Jo M. Webb-Robertson, Ernesto S. Nakayasu, Brian AhmerMichael E. Konkel, Vladimir Motin, Ralph S. Baric, Michael S. Diamond, Yoshihiro Kawaoka, Katrina M. Waters, Richard D. Smith, Thomas O. Metz

Research output: Contribution to journalArticle

4 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)442-448
Number of pages7
JournalAnalyst
Volume142
Issue number3
DOIs
StatePublished - Jan 30 2017

Fingerprint

Pathogens
Metabolites
Lipids
H7N9 Subtype Influenza A Virus
metabolite
Membrane Lipids
pathogen
lipid
Proteins
Yersinia pestis
Campylobacter jejuni
protein
Systems Biology
Orthomyxoviridae
influenza
Active Immunotherapy
Metabolomics
membrane
Clostridium difficile
Viruses

ASJC Scopus subject areas

  • Analytical Chemistry
  • Environmental Chemistry
  • Biochemistry
  • Spectroscopy
  • Electrochemistry

Cite this

Burnum-Johnson, K. E., Kyle, J. E., Eisfeld, A. J., Casey, C. P., Stratton, K. G., Gonzalez, J. F., ... Metz, T. O. (2017). MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. Analyst, 142(3), 442-448. https://doi.org/10.1039/c6an02486f

MPLEx : A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. / Burnum-Johnson, Kristin E.; Kyle, Jennifer E.; Eisfeld, Amie J.; Casey, Cameron P.; Stratton, Kelly G.; Gonzalez, Juan F.; Habyarimana, Fabien; Negretti, Nicholas M.; Sims, Amy C.; Chauhan, Sadhana; Thackray, Larissa B.; Halfmann, Peter J.; Walters, Kevin B.; Kim, Young Mo; Zink, Erika M.; Nicora, Carrie D.; Weitz, Karl K.; Webb-Robertson, Bobbie Jo M.; Nakayasu, Ernesto S.; Ahmer, Brian; Konkel, Michael E.; Motin, Vladimir; Baric, Ralph S.; Diamond, Michael S.; Kawaoka, Yoshihiro; Waters, Katrina M.; Smith, Richard D.; Metz, Thomas O.

In: Analyst, Vol. 142, No. 3, 30.01.2017, p. 442-448.

Research output: Contribution to journalArticle

Burnum-Johnson, KE, Kyle, JE, Eisfeld, AJ, Casey, CP, Stratton, KG, Gonzalez, JF, Habyarimana, F, Negretti, NM, Sims, AC, Chauhan, S, Thackray, LB, Halfmann, PJ, Walters, KB, Kim, YM, Zink, EM, Nicora, CD, Weitz, KK, Webb-Robertson, BJM, Nakayasu, ES, Ahmer, B, Konkel, ME, Motin, V, Baric, RS, Diamond, MS, Kawaoka, Y, Waters, KM, Smith, RD & Metz, TO 2017, 'MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling', Analyst, vol. 142, no. 3, pp. 442-448. https://doi.org/10.1039/c6an02486f
Burnum-Johnson KE, Kyle JE, Eisfeld AJ, Casey CP, Stratton KG, Gonzalez JF et al. MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. Analyst. 2017 Jan 30;142(3):442-448. https://doi.org/10.1039/c6an02486f
Burnum-Johnson, Kristin E. ; Kyle, Jennifer E. ; Eisfeld, Amie J. ; Casey, Cameron P. ; Stratton, Kelly G. ; Gonzalez, Juan F. ; Habyarimana, Fabien ; Negretti, Nicholas M. ; Sims, Amy C. ; Chauhan, Sadhana ; Thackray, Larissa B. ; Halfmann, Peter J. ; Walters, Kevin B. ; Kim, Young Mo ; Zink, Erika M. ; Nicora, Carrie D. ; Weitz, Karl K. ; Webb-Robertson, Bobbie Jo M. ; Nakayasu, Ernesto S. ; Ahmer, Brian ; Konkel, Michael E. ; Motin, Vladimir ; Baric, Ralph S. ; Diamond, Michael S. ; Kawaoka, Yoshihiro ; Waters, Katrina M. ; Smith, Richard D. ; Metz, Thomas O. / MPLEx : A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling. In: Analyst. 2017 ; Vol. 142, No. 3. pp. 442-448.
@article{1839f6b40a2b44ad8b1c99de684112da,
title = "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling",
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.",
author = "Burnum-Johnson, {Kristin E.} and Kyle, {Jennifer E.} and Eisfeld, {Amie J.} and Casey, {Cameron P.} and Stratton, {Kelly G.} and Gonzalez, {Juan F.} and Fabien Habyarimana and Negretti, {Nicholas M.} and Sims, {Amy C.} and Sadhana Chauhan and Thackray, {Larissa B.} and Halfmann, {Peter J.} and Walters, {Kevin B.} and Kim, {Young Mo} and Zink, {Erika M.} and Nicora, {Carrie D.} and Weitz, {Karl K.} and Webb-Robertson, {Bobbie Jo M.} and Nakayasu, {Ernesto S.} and Brian Ahmer and Konkel, {Michael E.} and Vladimir Motin and Baric, {Ralph S.} and Diamond, {Michael S.} and Yoshihiro Kawaoka and Waters, {Katrina M.} and Smith, {Richard D.} and Metz, {Thomas O.}",
year = "2017",
month = "1",
day = "30",
doi = "10.1039/c6an02486f",
language = "English (US)",
volume = "142",
pages = "442--448",
journal = "The Analyst",
issn = "0003-2654",
publisher = "Royal Society of Chemistry",
number = "3",

}

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.

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.

UR - http://www.scopus.com/inward/record.url?scp=85010992329&partnerID=8YFLogxK

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

VL - 142

SP - 442

EP - 448

JO - The Analyst

JF - The Analyst

SN - 0003-2654

IS - 3

ER -