Modeling tissue-relevant Caenorhabditis elegans metabolism at network, pathway, reaction, and metabolite levels

Mol Syst Biol. 2020 Oct;16(10):e9649. doi: 10.15252/msb.20209649.

Abstract

Metabolism is a highly compartmentalized process that provides building blocks for biomass generation during development, homeostasis, and wound healing, and energy to support cellular and organismal processes. In metazoans, different cells and tissues specialize in different aspects of metabolism. However, studying the compartmentalization of metabolism in different cell types in a whole animal and for a particular stage of life is difficult. Here, we present MEtabolic models Reconciled with Gene Expression (MERGE), a computational pipeline that we used to predict tissue-relevant metabolic function at the network, pathway, reaction, and metabolite levels based on single-cell RNA-sequencing (scRNA-seq) data from the nematode Caenorhabditis elegans. Our analysis recapitulated known tissue functions in C. elegans, captured metabolic properties that are shared with similar tissues in human, and provided predictions for novel metabolic functions. MERGE is versatile and applicable to other systems. We envision this work as a starting point for the development of metabolic network models for individual cells as scRNA-seq continues to provide higher-resolution gene expression data.

Keywords: Caenorhabditis elegans; data integration; metabolic network; single-cell RNA-seq; tissue metabolism.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Animals
  • Caenorhabditis elegans / genetics
  • Caenorhabditis elegans / metabolism*
  • Caenorhabditis elegans Proteins / genetics
  • Caenorhabditis elegans Proteins / metabolism*
  • Computational Biology
  • Computer Simulation
  • Gene Expression Regulation / genetics*
  • Gene Regulatory Networks
  • Gonads / metabolism
  • Intestinal Mucosa / metabolism
  • Metabolic Networks and Pathways
  • Neuroglia / metabolism
  • Organ Specificity / genetics
  • Organ Specificity / physiology
  • RNA-Seq
  • Single-Cell Analysis
  • Subcutaneous Tissue / metabolism
  • Transcriptome / genetics*

Substances

  • Caenorhabditis elegans Proteins