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The MPLEx Protocol for Multi-omic Analyses of Soil Samples
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MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling.

Kristin E Burnum-Johnson1, Jennifer E Kyle1, Amie J Eisfeld2

  • 1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA. thomas.metz@pnnl.gov.

The Analyst
|January 17, 2017
PubMed
Summary
This summary is machine-generated.

A new method simultaneously inactivates pathogens and extracts molecules for multi-omics analysis. This single-sample metabolite, protein and lipid extraction (MPLEx) method enables pathogen characterization and advances infectious disease research.

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Area of Science:

  • Infectious disease research
  • Systems biology
  • Mass spectrometry-based multi-omics

Background:

  • Emergence and spread of infectious agents pose significant global health concerns.
  • Understanding host-pathogen interactions is crucial for developing new therapies and vaccines.
  • Molecular characterization of infectious samples requires prior pathogen inactivation for safety.

Purpose of the Study:

  • To develop a method for simultaneous pathogen inactivation and molecular extraction from infectious samples.
  • To enable mass spectrometry-based multi-omics analyses (proteomics, metabolomics, lipidomics) from a single specimen.
  • To facilitate systems biology approaches in infectious disease research.

Main Methods:

  • A modified Folch extraction using chloroform/methanol, termed single-sample metabolite, protein and lipid extraction (MPLEx).
  • Testing MPleX for pathogen inactivation against various bacteria and viruses, including those with and without lipid membranes.
  • Evaluating the quality of extracted biomaterials for subsequent multi-omics analyses using an infected lung cell line model.

Main Results:

  • MPleX achieved complete inactivation of bacteria and viruses with exposed lipid membranes (e.g., Yersinia pestis, Influenza H7N9).
  • MPleX demonstrated >99% inactivation for pathogens lacking exposed lipid membranes (e.g., Staphylococcus aureus, Clostridium difficile, Adenovirus type 5).
  • The MPleX pipeline yielded high-quality biomaterial suitable for proteomic, metabolomic, and lipidomic analyses.

Conclusions:

  • MPleX effectively inactivates a broad range of pathogens while preserving molecular integrity for multi-omics studies.
  • This method simplifies sample processing by combining inactivation and extraction into a single step.
  • MPleX is a valuable tool for advancing systems biology research on infectious diseases, enabling comprehensive analysis from single specimens.