Researchers from the State University of Campinas (Unicamp) have made available on a free online platform a database with 2.176 human and 3.277 mouse cell maintenance genes – used as a reference in experiments that measure the variation in the expression of a gene. The information, which was not yet structured in a database, appears as a useful tool for a large part of the biological scientific community.
This is because almost all biomolecular research – whether for the development of a new drug or to deepen knowledge about a specific disease – needs to make use of so-called housekeeping genes. Basically, to detect and quantify the variation in gene expression in a cell, as a result of an infection, inflammation, or even a tumor, for example, it is first necessary to know what remains unchanged, in the same pattern.
Only then, using housekeeping genes as a kind of “ruler”, is it possible to more accurately analyze the size of variations in the expression of other genes. Changes in the cell's gene expression are important, as they determine greater or lesser expression of proteins, which are the molecules that, ultimately, can trigger or influence the development of the immune or drug response, as well as normal physiological processes in the life of the cell. cell.
“The atlas arose out of a need during my doctoral research. I was having difficulty choosing the most appropriate cell maintenance genes for the experiments I needed to carry out. When talking to other researchers, I realized that the problem was not exclusive to me. Quite the contrary, it was relatively common”, says Bidossessi Wilfried Hounkpe, co-author of the study published in the journal Nucleic Acids Research.
Hounkpe carried out a doctoral study with a FAPESP grant on the pathophysiological mechanisms of sickle cell anemia. The study and creation of the atlas are part of two Thematic Projects supported by the Foundation, the first coordinated by Joyce Maria Annichino-Bizzacchi, and the second coordinated by Fernando Ferreira Costa.
According to the researchers, housekeeping genes are essential for the design of a biomolecular study. However, although some of them are already known to scientists, housekeeping genes vary from one condition to another, as well as from one type of cell to another. “A wrong choice can make a study unfeasible or prevent its reproducibility,” says Hounkpe.
Generally, without a tool like the atlas, researchers around the world tend to look for cell maintenance genes in previous studies on the same topic of interest.
“The atlas was developed in parallel with the doctoral study. The perception of the problem, the construction of the solution and the structuring of the database and all the programming was his idea and that of Francine Chenou, whom I co-supervised in her doctorate, and who has always been interested in bioinformatics studies”, reports Erich de Paula , professor of Hematology at the Department of Clinical Medicine at the Faculty of Medical Sciences at Unicamp.
PCR tests
One of the main examples of biomedical research that requires the identification of specific cellular maintenance genes to calibrate their analysis is real-time PCR (RT-PCR) tests. The test, which became famous with the COVID-19 pandemic – for identifying pieces of the virus's RNA in samples of patients' nasal secretions – is one of the most used techniques in molecular biology and biotechnology laboratories around the world.
In addition to identifying the presence of SARS-CoV-2 RNA, RT-PCR is used to estimate the amount of RNA expressed from any gene of interest, under different experimental conditions. However, as the researchers point out, the fact that cell maintenance genes are used as calibrators for these analyzes gives them a fundamental role in the accuracy of the final results, which are expressed taking as a reference the amount of RNA in cell maintenance genes.
Read full article published on the Agência Fapesp website.
