Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences.

A study used the equine genome sequence to identify and annotate proteins, improving the understanding of biological pathways in horses. This was done by analyzing proteins found in healthy horse lung fluid (bronchoalveolar lavage fluid).

Context and Research Objective

• The completion of the equine genome sequencing has opened the door to a plethora of research opportunities using high-throughput genomic technologies in horse research. However, the process of accurately identifying gene products expressed during this process often requires additional structural and functional genome annotation.
• The researchers intended to use the equine genome sequence to identify predicted and known proteins using proteomics (the large-scale study of proteins).
• The research was focused on proteins found in bronchoalveolar lavage fluid (BALF), a substance used frequently in studies of equine respiratory diseases, which gives an excellent proxy to understand various biological functions under normal conditions.

Methodology

• The researchers identified 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF).
• An improvement in structural and functional annotation was achieved by confirming the existence of 558 proteins that were predicted computationally and adding Gene Ontology (GO) annotations for 174 proteins.
• For better understanding of these proteins and their roles, they were modeled into biological pathways using Ingenuity Pathway Analysis. This modeling highlighted various crucial biological processes in normal equine BALF such as carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement.
• A comparative modelling approach was then used to compare the protein functions in the horse lung fluid with those found in human and mouse, revealing similarities across species.

Findings and Applications

• The research confirmed that 91 of 92 human Gene Ontology categories and 105 of 109 mouse categories were present in the horse, proving the conservation of functions across these species.
• It validates the use of the equine genome sequence to study protein networks without requiring antibodies or mRNA quantification, showcasing the vast potential of genomic technologies in studying equines.
• It underscores the need to continue the effort of structural and functional annotation of the equine genome for better understanding of equines and their diseases.
• The research establishes a framework that could aid equine researchers in their annotation efforts.