CrasGMU and KNC SB RAS: A DNA aptamer-based drug for the diagnosis of brain tumors

The main articles are:

• Brain cancer
• Cancer diagnosis

2023: Developing a drug to diagnose glial brain tumor with 100% accuracy

A drug based on DNA aptamers (short nucleotide sequences) developed by scientists from the Krasnoyarsk State Medical University named after Professor V.F. Voino-Yasenetsky (KrasGMU) and the Federal Research Center "Krasnoyarsk Scientific Center of the Siberian Branch of the Russian Academy of Sciences" (FIC KSC SB RAS) with the participation of specialists from the Hospital of Medical Care and the Cancer Center (Krasnoyarsk), allows you to diagnose glial tumors with very high accuracy - the most common and aggressive type of brain cancer. This was announced on April 19, 2023 in the RSK group of companies.

Scientists from the Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences (IHBFM SB RAS, Novosibirsk) helped their Krasnoyarsk colleagues develop a model of a human brain tumor for testing drugs in mice. This study was also attended by scientists from the Siberian Federal University (Krasnoyarsk), the Institute of Physics named after L. V. Kirensky SB RAS (Krasnoyarsk), the National Research Center "Kurchatov Institute" (Moscow), Tomsk State University, the Federal Research Center "Crystallography and Photonics" RAS (Moscow), the Federal Siberian Scientific and Clinical Center of the Federal Medical and Biological Agency Agency (Krasnoyarsk) and foreign colleagues from South Korea, Finland and Canada.

The study was supported by the Ministry of Health and the Ministry of Education and Science, a grant from the Russian Science Foundation (RNF).

In the brain, in addition to nerve cells transmitting electrical impulses, there are auxiliary glial cells that feed neurons and create an environment favorable for their work. If these cells get out of control of the body and begin to divide uncontrollably, a glial tumor, or glioma, occurs. The molecules created by the researchers are able to find malignant cells of the nervous tissue, after which, thanks to the marking of the luminous dye, the tumor can be easily detected using a microscope during surgery. This approach will help remove neoplasms with high accuracy without affecting the functional zones of the brain.

The success of glioma treatment is largely determined by timely diagnosis of the disease, which is generally based on data from magnetic resonance imaging (MRI) or computed tomography (CT). However, small neoplasms cannot always be detected by these methods, so scientists seek to develop other approaches to more accurately diagnose a dangerous disease.

As a result of the study, scientists received more than 20 thousand DNA aptamers with a length of 100 nucleotides - a kind of "letters" that make up these molecules. Then, with the help machine learning of scientists, they also chose molecular modeling methods on the supercomputer productions Russian group of companies RSK, working in (c Russian Academy of Sciences), " JSCC RAS improved" those DNAs that were presented as the best candidates in their sequences.

Aptamer synthesis is a fairly simple and cheap technology. Once you have selected DNA for the target of interest, you can copy this molecule as much as you like and attach different tags to it. The aptamers obtained in this study bind exclusively to glioma cells, allowing them to be recognized absolutely accurately. Thanks to this, aptamers will help simplify and speed up tumor diagnosis. Moreover, short DNA quickly disintegrates in the body: they are "eaten" by special enzymes, so with a high probability the molecules we offer are safe not only for mice, but also for humans, said Anna Kichkailo, researcher and head of the laboratory of digital managed drugs and theranostics at the National Research Center of the SB RAS, head of the laboratory of biomolecular and medical technologies at KrasGMU.

By molecular methods, the authors determined: aptamers specifically bind only to glioma, because they recognize a special region of tubulin protein transformed in tumor cells. Tubulin forms the internal "framework" of all cells of our body, thereby giving them a certain shape. However, malignant transformations occur in glioma cells in the protein, which recognize aptamers.

DNA aptamers Gli-233 and Gli-55 (candidates for) medicinal products were developed using tissues of postoperative human glial tumors, which makes them specific to glioma and prevents their interaction with healthy brain tissues. Preclinical tests in laboratory mice have shown that the drug allows you to detect a tumor not only in tissue samples, but also in a living organism. To visualize the tumor, animals were administered aptamers with a fluorescent label attached. Thanks to the marking of the luminous dye, the tumor can be easily detected using a microscope during surgery. The high specificity of these aptamers guarantees their binding only to glioma, which leads to the concentration of the drug exclusively in the focus of the disease and allows you to accurately visualize the boundaries of the tumor and small metostases using an operating microscope. In vivo experiments using living organisms have also shown that the DNA aptamer drug is not toxic to animals. Federal Center for the Design and Development of Nuclear Medicine Facilities of the Federal Medical and Biological Agency (FMBA) of Russia In the aptamer, Gli-233 "sewed" a radionuclide for CT PET/diagnostics, which allowed to see a tumor in the brain in mice.

An important role in the development of the drug is played by understanding the mechanisms of interaction of DNA aptamers with their protein targets - GFAP and the tubulin α1C chain. For this, the spatial structure of aptamers Gli-233 and Gli-55 was determined using experiments of small-angle X-ray scattering and molecular modeling, carried out using the computational resources of the Interdepartmental Supercomputing Center of the Russian Academy of Sciences on one of the cluster systems installed in the JSCC RAS by the RSK group of companies. A complex with a target, tubulin Gli-233, containing post-translational modifications, was modeled for aptamer α1C. Using calculations in the field of molecular dynamics and quantum chemistry, aptamer binding sites with protein were determined. Information on which nucleotides play a key role in the interaction of the aptamer with the target will allow modifying the drug to improve its binding characteristics and increase the effectiveness of its use.

AptamerLab LLC, within the framework of a grant received from the Skolkovo Innovation Center, modifies the developed drug for specific production needs. It remains to be hoped that soon it will begin to be used in clinics for intraoperative imaging of brain tumors.