Diagnosis by transcriptome
As an alternative to immunohistochemistry, the method of RNA sequencing was used for oncodiagnostics
Phys Tech blog, Naked Science
The study was published in the Swiss journal Biomedicines (Sorokin et al., RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Species).
The classic method in the diagnosis of oncological diseases is immunohistochemical staining of sections of tumor tissue. This method allows you to identify the presence and measure the number of special marker proteins characteristic of malignant neoplasms. For the procedure of immunohistochemical staining, the tumor sample is immersed in hot paraffin.
After cooling, the block of paraffinized tissue is cut into thin slices, which are stained and examined by microscopy. The obtained images allow us to judge the malignancy and molecular type of the tumor, which is extremely important for the selection of suitable therapy.
The principle of the RNA sequencing method is to determine the sequences and quantities of all RNA molecules present in the cell. The resulting set of data, the so-called transcriptome, contains information about the level of activity of all genes in the cell. To analyze such large amounts of bioinformatics data, specialized algorithms are used, databases of transcriptomes of various human cells and tissues are created.
The authors proposed using the RNA sequencing method as an alternative and addition to the classical method of immunohistochemistry. Moreover, it is proposed to use the same paraffinized tumor fragments as a biomaterial. This avoids additional biopsy taking from the patient, and it is also easy to combine both approaches.
"We have shown for the first time that the results of these two methods perfectly match each other, but for immunohistochemical studies, much more experiments need to be done – as many biomarkers need to be looked at – and much more material needs to be spent. And RNA sequencing allows us to immediately quantify the work of all protein-coding genes, and there are about 20 thousand of them!" says Anton Buzdin, head of the research, head of the laboratory of translational genomic bioinformatics at MIPT.
In their study, the authors for several types of tumors showed a clear correlation between the expression level of four different tumor marker genes measured by RNA sequencing and the results of immunohistochemical staining.
Comparison of two methods:
A is the correlation between the expression level of the HER2 breast cancer marker measured by RNA sequencing (RNA) and the results of immunohistochemical staining (IHC).
B – results of immunohistochemical staining for various stages of tumor progression (brown color reflects the presence of the HER2 marker protein) / © MIPT Press Service.
"We are confident that RNA sequencing has a great future in medical diagnostics, and we are very glad that our work, as we hope, was able to bring it a little closer," Anton Buzdin sums up.
In addition to scientists from the Laboratory of Translational Genomic Bioinformatics of MIPT, their colleagues and doctors from the Institute of Personalized Medicine of the I. M. Sechenov First Moscow State Medical University, the M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, the Karelian Republican Oncological Dispensary, the Vitamins Medical Center, Lomonosov Moscow State University, Kaluga Regional oncological Hospital, Oncological Dispensary of the Republic of Karelia and Oncobox company (USA). The work was carried out with the support of the Russian Science Foundation.
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