According to the received press release, scientists from Moscow Institute of Physics and Technology, Institute of Biomedical Chemistry, Institute of Energy Problems of Chemical Physics RAS and Federal Clinical Research Center of Physical and Chemical Medicine created an algorithm for the detection of mutant proteins in cells according to data of mass spectrometry analysis. Spot replacement of amino acid residues in proteins due to mutations in DNA may lead to changes in the functions of proteins in cells, and sometimes play a key role in cancer development. The study results are published in the Proteomics journal.
Mass spectrometry as the primary method of proteomic analysis enables to weigh accurately molecules of proteins, peptides and fragments thereof in a sample. The data of the proteomic experiment is usually a set of mass spectra, by type of which the scientist can determine the type of proteins. It is impossible to do it considering only the mass spectrum. Therefore, the database of protein sequences that may be found in the sample is necessary for the research. Instead of decrypting an unknown sequence from scratch, the program simply compares experimental data with a vocabulary of protein sequences.
However, this approach is not entirely suitable for the search of proteins, the amino acid sequence of which differs from what is written in the standard genome.
Ii is impossible to identify proteins with mutations in cancer cells, if the database doesnt contain such a form of a protein.
In this case, proteogenomics, that is, the area at the intersection of genomics and proteomics, must be used. Instead of a versatile protein database, in the proteogenomic studies they use the bases unique to the studied cells, containing information on possible interpretation of the genome and its transition into the amino acid sequence.
A new study of Russian scientists presented the algorithm of searching mutant proteins, which enables to compare the results of mass spectrometry of different research groups and allocate mutations related to cancer. Efficiency of the approach was demonstrated by researchers using the example of cell line HEK-293, derived from a human embryonic kidney. This is a model culture of human cells, which is often used in research because it is easy to grow in the laboratory. In addition, HEK-293 carries a lot of mutations, and serves as an excellent model for testing proteogenomic approach to the study of cancer.
Along with their own experimental data, scientists used the mass spectra of the two works devoted to the study of the proteome of HEK-293 cells. In order to perform the proteogenomic analysis, they prepared an extensive database based on the results of exom sequencing of HEK-293 cell line. An exom is the cluster of exons (regions of genes, which encode the amino acid sequence of the protein). Exom sequencing enables the researchers to focus only on the protein-coding genes, and determine the location of exons in them. The increased base increased by 1,336 sequence variants. Thus, the sequences that differ from the original ones by one or more letters, that is, amino acids were added to the protein vocabulary. Without this amendment, the search program could not detect such slightly wrong proteins. Since each cell is constantly mutating, and the cancer ones are mutating very often, the detection of proteins that differ from the standard ones, will help to understand how tumor cells differ from normal ones.
Scientists used the data of mass spectrometric analysis of the two early studies and the experimentally obtained in this work resulting mass spectrometry and determined, which peptides (short proteins or protein fragments) are contained in the cells and the type of the proteins.
A new approach to proteogenomic analysis using the expanded database enabled the scientists to find in HEK-293 cells 113 unique variant peptide sequences referring to the exon regions of 103 genes.
This is substantially more than in the study previously executed by the team of Stephen Gigi, in which the protein database supplemented with genomic variants wasnt used and the search for amino acid substitutions was performed using another method.
For some of the identified mutations the connection with various types of cancer was shown previously. Perhaps, the presence of these variants contributes to better survival and reproduction of cells. In particular, one of the identified genomic variants refers to protein p53, suppressing the malignant cell transformation. Our approach can further be used in search for mutations associated with cancer based on proteomic data. In its turn, this will help in the study of protein composition of tumors and the development of medicines, targeted at the mutant proteins produced in tumor cells, - one of the project managers, Head of the Laboratory of physical and chemical methods of studying the structure of materials INEPHF RAS, Department Officer of chemical physics MIPT Mikhail Gorshkov.
Meanwhile, Botanical Garden of Tomsk State University (TSU) is working on breeding new decorative forms of Siberian coniferous species, including: fir, spruce, pine, larch and cedar. In order to make them special, botanics use mutational witches brooms, that is, fragments of the crown of coniferous plants with intense branching. Scientists create a clonal archive with economically valuable forms of conifers.
Mutation witches brooms appear on the trees due to mutations in a single bud, - the head of the laboratory of tropical and subtropical plants SibBS TSU, Michael Yamburov comments. - The mutation leads to a pronounced morphological changes, to strengthening of certain external signs, including: an abundant branching, changing needle thickness, color brightness, increasing the yield of cones.
Using the witches brooms as a source of genetic material, according to the scientist, enables to accelerate the breeding process significantly, a new decorative shape gaining will take no more than 10 years instead of several decades.
The mutations that are considered to be extremely negative factors will make conifers particularly picturesque, for example, pine will have a globular crown, thin needles and dampened growth. Spruce and fir will manifest hereditary changes differently - their needles will become several times thicker. In addition, scientists will be able to vary the color of new varieties, that is, select shape with blue or salad color needles. In case of cedar, occurrence of the mutant gene will lead to increasing the number of strobili.
Currently, there is a selection of promising genotypes. Creating a clonal core group will enable us to receive a variety of decorative forms that are resistant to the urban environment and the harsh climate. They will stand out from the European breeding, many of which have low hardiness in Siberia and die after the first winter, - Mikhail Yamburov says.
New forms of conifers will be available to a wide range of consumers, but primarily they will be available to the companies involved in planting of greenery in Tomsk. The archive base will be formed by the end of 2017 - now there are 20 promising clones.
The project to create the nursery of ornamental conifers on the basis of natural mutants is implemented with the support of the Foundation for Assistance to Small Innovative Enterprises in Science and Technology. In 2014, the student of the Department of Botany, Institute of Biology, TSU, Yekaterina Konyakhina became the winner of its program UMNIK. In 2015, the project received a diploma and a commemorative medal of the 9th International Biotechnological Forum and Exhibition RosBioTech. Having assessed the results of research, the Fund has extended the grant for 2016.