Mass Spectrometry-Based Multi-omics Integration with a Single Set of C. elegans Samples

Area of Science:

• Biochemistry
• Molecular Biology
• Genomics

Background:

• Mass spectrometry-based multi-omics research offers powerful biological insights but faces challenges in sample preparation and data integration.
• Extracting diverse biomolecules from various sample types, particularly difficult ones like Caenorhabditis elegans, requires tailored preparation methods.

Purpose of the Study:

• To develop an efficient, single-sample multi-omics preparation method for Caenorhabditis elegans.
• To save time, minimize variability, expand biomolecule coverage, and promote multi-omics integration.
• To optimize tissue disruption and biomolecule extraction for proteomics, lipidomics, and metabolomics.

Main Methods:

• Investigated various tissue disruption techniques for effective biomolecule release.
• Optimized extraction strategies for broad and reproducible biomolecule coverage.
• Validated the method using Caenorhabditis elegans subjected to stressors inducing mitochondrial unfolded protein response (UPRmt).

Main Results:

• The method achieved high coverage and reproducibility across proteome, lipidome, and metabolome.
• All tested stressors (cco-1 knockdown, mrps-5 knockdown, Doxycycline) triggered UPRmt.
• Common molecular signatures included activated innate immunity and decreased triglycerides, with Doxycycline eliciting unique responses.

Conclusions:

• The developed multi-omics sample preparation method is effective for Caenorhabditis elegans, providing comprehensive molecular data.
• The method successfully validated UPRmt induction by diverse stressors, revealing unique and common molecular responses.
• This versatile approach shows potential for multi-omics research in other organisms.