Virtual Mice
A group of scientists from the Francis Crick Institute in London have developed a large-scale database of mouse gene activity for ten disease models. It will help to significantly reduce the use of laboratory animals around the world. The new database gives a complete picture of the immune response to various pathogens.
A graph of gene expression on six disease models for two genes: Ifng (associated with the transmission of type II interferon signals) and Mx1 (associated with the type I interferon signal).
The database contains information about the activity of each of the more than 45,000 genes in the blood of mice with ten different diseases. In addition, lung samples were examined for six diseases of the respiratory system.
Previously, scientists had to create models, plant, cull, take samples from mice, as well as extract and sequence RNA to study the genes of interest. Using the new application described in this study, scientists will be able to assess the activity of any gene for a number of diseases without needing mice. This will prevent the use of thousands of mice in individual experiments.
The research team, led by Ann O'garra and coordinated by Christine Graham, worked with collaborators from the UK and the USA. They used next-generation sequencing technology (RNA-seq) to measure gene activity in various diseases. Genes must transcribe their DNA into RNA in order to function, and RNA analysis shows how active each gene is – in this case, after infection or ingestion of an allergen.
Gene activity demonstrates how the body reacts to infection and allergens. Thousands of genes are involved in the immune response, and there is a need to use advanced bioinformatic approaches to cluster genes into modules. These modules are a set of genes that are jointly regulated and can be characterized by the performance of a single function. For example, out of 38 modules of genes active in the lungs, there is a module containing more than 100 genes and associated with allergies, it can only be seen in the allergy model. Another module related to T cells contains more than 200 genes.
Sequencing lung tissue and blood, the researchers noticed that the immune response in the blood often reflects the local response in the lungs, and vice versa. It is necessary to use this correlation, since in most diseases doctors do not have the opportunity to obtain lung samples.
Multiple pathogens
A graph of the expression of two genes for six disease models: the Il17c gene is associated with T-helpers, the IL4 gene is associated with allergic reactions.
Using the new application, researchers anywhere in the world can use information about the activity of genes in the blood and lungs of mice infected with a number of pathogens: the Toxoplasma gondii parasite, influenza virus and respiratory syncytial virus (RSV), Burkholderia pseudomallei bacterium, Candida albicans fungus or allergen (mites in house dust). They will also be able to assess the activity of genes in the blood of mice with listeria, mouse cytomegalovirus, malaria plasmodium or chronic Burkholderia pseudomallei infection.
During the study, the group analyzed the genetic traits associated with the listed diseases and studied the features of the immune response. In the lungs, genes associated with type I or II interferons, interleukin (IL-17) or allergic type reactions prevailed. It is known that type I interferon is released in response to viruses, whereas type II interferon (IFN-g) activates phagocytes to destroy intracellular pathogens, and IL-17 attracts neutrophils, causing an early inflammatory immune response. Interestingly, the signs of the interferon gene were present in the blood, as well as in the lungs.
The genes associated with interferon type I were very active both in the lungs and in the blood of mice infected with the parasite Toxoplasma gondii, and were also observed in response to the bacterium Burkholderia pseudomallei, although to a lesser extent. This casts doubt on early claims that genes associated with type I interferon necessarily indicate viral infections.
From problems to new opportunities
The research project has an interesting history. It began in 2009, and it was planned to use microchips to determine the activity of genes in the blood and lungs. In 2015, when the data were collected and prepared for analysis, the manufacturer stopped the production of the necessary reagents for the microchip. The project was under threat.
Since microchip technology could not be used without the necessary reagents, the group began to look for a way out. At this time, the RNA-Seq technique appeared on the market, offering a way to quantify the activity of genes. After negotiations, the scientists were provided with the latest reagents for RNA-Seq for free, as well as a place to store huge amounts of data.
Since tissue and blood samples from microchip experiments were frozen, it was not necessary to work with mice again. The painstaking work was completed in 2018. To systematize the sequencing results and group thousands of genes, scientists used advanced bioinformatics methods to obtain a clear and visual form (module). They also created an app to make the data available to everyone.
It took ten whole years to create a resource with open access to information about gene expression for everyone.
Article by A. Singhania et al. Transcriptional profiling reveals type I and II interferon networks in blood and tissues across diseases published in the journal Nature Communications.
Aminat Adzhieva, portal "Eternal Youth" http://vechnayamolodost.ru based on the materials of The Francis Crick Institute: Gene activity database could spare thousands of mice.