From genome to proteome

Our scientists are leading in the implementation of a major international program.

Yuri Drize, "Search" No. 52-2014

The international project "Human Genome" is often compared with the Periodic system of chemical elements of Mendeleev – it is so significant. However, the project has not yet brought the result that the world scientific community was waiting for. In fact, he solved only one problem – informational, determining the sequence of genes present in all chromosomes containing most of the human hereditary information. Therefore, it was decided to implement a new global international initiative "Human Proteome" (proteome means the whole set of proteins and their interaction in living organisms). Its purpose is to obtain information about the work of "molecular machines" – human proteins embedded in his genome. And if the decoding of the human genome took 20 years, then it will take much longer to complete the more complex Human Proteome program, launched in 2010...

Russia did not participate in the Human Genome project, but this time it was one of the first to join the research, for which a powerful scientific and technical consortium was formed, which included about a dozen well-known academic and medical organizations: the Institute of Biomedical Problems, the Institute of Molecular Biology, the Institute of Bioorganic Chemistry, the Center for Bioengineering, the Institute "International Tomographic Center" SB RAS, Institute of Physico-Chemical Medicine.

He headed the team of Russian scientists of the V.N.Orekhovich Research Institute of Biomedical Chemistry (IBMH).

Poisk asked the director of the IBMH, Academician Alexander Archakov, to tell about the brilliant works of Russian scientists.

– The international project turned out to be extremely difficult, so the participants – at first there were six of them, and now there are more than 20 – agreed on a "division of labor," says Alexander Ivanovich. – From the human genome, each research team chose one, or at least two chromosomes (there are 23 in total). We stopped at the 18th, now it is called the "Russian chromosome". Two criteria have become decisive for us: the number of genes in the chromosome (the fewer of them, the lower the material costs) and the medical value. Our foreign colleagues formulated their task simply: they focused on finding the proteins they were interested in. We immediately stated that we would not only find them, but also determine their content (that is, the number). Although it was necessary to develop a very complex technology for this, so only two or three laboratories in the world were able to do this.

To investigate the work of "molecular machines" synthesizing proteins based on information stored in chromosomes, we used a method borrowed from chemists – mass spectrometry. Mass spectrometers make it possible not only to identify proteins, but also to determine their content in the biomaterial. The accuracy of such measurements is the highest, and it is constantly increasing.

– And what is the purpose of these studies?

– There are several such goals. When scientists read the genome, they decided that now we know all the information transmitted to humans by inheritance. But over time, researchers began to lack this knowledge, they needed information about the proteome – a set of proteins acting in individual organs and tissues (say, in the liver, they are one, in the brain, others, etc.). We need to learn how to register them, and this is an extremely difficult task, because it is still unknown how many proteins are in the human body. There should be as many basic proteins as there are genes (although there are a lot of difficulties here, and I will not overload the reader). In our 18th chromosome, this number is known: 276 genes. We had to find and evaluate the same number of proteins. To date, we have detected and measured the content of 269 by examining three types of biomaterial: blood plasma, liver cells and culture cancer cells. Our employees were the first in the world to do this – none of our colleagues even came close to such a figure. This is an undeniable achievement of Russian scientists. I note that until now, science has known less than half of the main proteins of this chromosome, and the content has been determined in only a dozen proteins.

– What is the meaning of such an "inventory" of proteins?

– First of all, it is extremely important for medicine. Knowing the proteomic composition of normally functioning organs of a healthy person and comparing it with the proteomic composition of a sick person, doctors can understand the mechanisms of a particular disease. Which proteins are responsible for their development? We are very far advanced in determining the protein content. Science, as a rule, is not able to cope with this, but our employees have learned to count protein molecules. We managed the almost impossible: to find one copy of a protein molecule per cell. It's like inventing a Geiger counter to measure radioactivity. We achieved an impressive result: we found 265 different molecules (more than 90%) in the blood plasma and measured their content. And also determined the number of copies of molecules of the same protein per microliter of blood plasma. In fact, we have reached the limit: one copy of protein per microliter of plasma. For medicine, such an indicator is quite sufficient, since proteins that are contained in one liter of plasma in an amount of less than one million copies of the molecule are unlikely to play an important role. Now we can use the algorithm developed by us to determine the content of all the main proteins of the human genome in blood plasma.

Now we know the content of about 3,000 proteins in blood plasma, but we want to bring this figure to 17-18 thousand proteins obtained from healthy people. The Institute of Biomedical Problems of the Russian Academy of Sciences, which supplies biological material from cosmonaut candidates, helps us in this.

– How can this new knowledge be used?

– First of all, for medical diagnostics. After all, 17-18 thousand proteins in blood plasma, as we believe, give an almost complete picture of the human genome. This is a kind of collector, where proteins come from almost all organs and tissues (with the exception of the central nervous system). Having examined them, we will give the doctors a certain "standard of a healthy person". Note that even healthy people, although rarely, still get sick. In this case, the proteins that have changed as a result of the disease will need to be compared with the standard. Then doctors will be able to guess in which direction it will develop, and take appropriate measures. This technology is not particularly complicated, but it is still intended not for district or city clinics, but for well-equipped medical centers. However, since the delivery of biological material is not such a serious problem today, this will not be a big obstacle for patients. According to a certain protocol, blood will be taken from them and an analysis will be done, although it is quite complicated and expensive, but only when it is taken for the first time. The already created mass spectrometric biotest can then be implemented quickly and cheaply. I hope that in the future this technology will replace the enzyme immunoassay currently in operation.

– What are the future plans of your institute?

– We have one goal: to make a proteomic map of the blood plasma of a healthy person. Then we will get a set of proteins, some of which doctors will select as markers for determining a variety of known diseases. It will be very easy to work with them. No one in the world before us has set such a grandiose fundamental task, because it is extremely time-consuming and complex. But we do not see any problems in its implementation: we have excellent developments and advanced technologies. The algorithm of this operation is quite well developed. And if we managed to launch several production lines, then there would be no production difficulties – we would meet in two or three years. If there is only one technological line, then it will take us at least five or six years. Biological material will be supplied to the line, and at the output we will be able to receive protein composition data. For the first time, it took us 5,000 hours to study one chromosome. Now, to determine the composition of 300 proteins, it takes only one working day. Now we are preparing biotests for 200 proteins associated with certain diseases.

The Institute has a powerful instrument base, in addition, we have a wonderful team of highly qualified employees, many of them are young. They are fascinated by this work. For her sake, many specialists who had previously gone abroad returned to the Research Institute. If there is adequate funding, I am sure we will achieve our goal: for the first time in the world, we will measure the complete proteome of a single chromosome using the example of the 18th human chromosome. We are currently identifying the main proteome of this chromosome containing unmodified proteins. Next, it is necessary to measure the complete proteome, that is, also proteins modified at the genomic (proteins containing single amino acid substitutions), transcriptomic (proteins expressed as a result of alternative splicing) and posttranslational (chemically modified proteins) levels. Their number can reach 100 per gene, that is, about 30,000 proteins have to be identified for the 18th chromosome. This is an impossible task for existing technologies, but we are working on creating new ones and we will definitely solve it.

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