07/11/2022
Validation of the specific role of gene knockouts in lipid metabolism
The regulation of different metabolic pathways in health and disease is essential for innovative diagnostics and therapeutical approaches. Knowing the specific role of each gene, protein, or enzyme is essential to be able to use it in medical applications. This process is well-established and has been used to connect genes to proteins to particular metabolic conditions.
However, in lipidomics field the enzyme specificity is far away from being exactly identified. Due to the complex nature of lipids, evaluating these connections comes with a set of challenges. Firstly, if one enzyme is knocked out, other enzymes can compensate for the missing one which will not be reflected in the global lipidome profile.
Secondly, the functions of certain lipids can be taken over by other lipids, again not being reflected in the lipidome profile. And finally, liposome changes in cells can be masked by a number of additional traits preventing detection of the exact changes.
This collaborative study between Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) and Lipotype aimed to define the lipid metabolism-related role of each gene of interest. Using the CRISPR gene editing method, 23 genes involved in lipid metabolism were knocked out in a human colorectal carcinoma cell line. Further application of the quantitative shotgun lipidomics method and tedious examination of the lipidomes in the knock-out cells resulted in mapping of more than 1200 lipid species and the changes influenced by the knockouts.
The authors filled the gap between each gene and its effect on lipidome picture, and on each particular lipid metabolism pathway. This resulted in confirmation of the predicted roles for some genes, and the discovery of connections to certain lipid pathways for others. This study also allowed for the distinction of genes affecting mostly lipid classes (SGNS1 and CEPT1), and others mainly affecting the fatty acid composition (DECR2 and ACOT7). The study care-fully describes the role of each analyzed gene in the cell lipidome.
"The current study is as a proof of concept, showing that quantitative lipidomics screens are possible, and that they produce reliable and quantitative data," says Aleksandra Spiegel from MPI-CBG, "Many tiny details create the big picture. It's worth to get them right." The results are of particular interest to those researchers working on tackling the metabolic pathways in health and disease. This study serves as a resource for both, those who work with particular molecular pathways and those working with global metabolic landscapes.
"We hope that this research will inspire more scientists to expand the screens to other cell lines, other genes of interest and additional pathways, incorporating the proteins involved at each different step of lipid metabolism," concludes Dr. Mathi-as Gerl from Lipotype.
Source: Lipotype GmbH