Molecular oncology. News. Molecular diagnostics in oncology

Molecular medicine in cancer treatment

The creation of drugs based on marker genes and marker proteins makes it possible, by acting only on them, to selectively destroy their carriers, preventing side effects. This is molecular or genetic medicine.

In the coming years of the 21st century, this medicine should replace the existing one, which is now called “old”. After all, in “old” medicine, medicines are created using the “trial and error” method, which is why they often cause severe side effects in patients. In this sense, standard cancer chemotherapy is in a difficult position today.
The main reasons for this: 1) a cancer cell is a eukaryote among normal cells of the human body, also eukaryotes; 2) science is lagging behind recent years about the sources of carcinogenesis and its molecular causes.

Standard chemotherapy drugs themselves cannot distinguish between a cancer cell and normal cells and are aimed at killing the overly rapidly dividing cells that each cancer cell belongs to.

It has recently been found that carcinogenesis comes from two sources: 1) from a normal tissue cell that has previously become a stem cell, or 2) from a tissue stem cell.

It also turned out that the composition of cancer cells is different:

The bulk of the cells are made up of non-cancerous cells: they quickly divide and, after performing tissue functions, themselves die through apoptosis; it is these cells that are the targets for standard chemotherapy drugs;
- a significantly smaller part is made up of cancer cells: these are cancer stem cells that copy themselves by asymmetric division and generate non-cancerous cells as part of cancer cells.

At the same time, cancer stem cells divide rarely and slowly. This is the reason why standard chemotherapy drugs are ineffective against cancer stem cells (J.E. Trosko et al., 2005).
Until now, in clinical practice, patients with symptoms of cancer predominate, and patients with cancer “in situ” are extremely rare, i.e. on the spot.

It is already too late to start cancer treatment when there are symptoms. After all, cancer cells begin to spread throughout the body when the size of cancer in the tissue of any organ is only 2 mm in diameter, i.e. with the beginning of angiogenesis and lymphangiogenesis in the nodule.

Now that eramolecular medicine has arrived, the patient will begin to be treated even before the first symptoms of the disease, including cancer, appear: at its very beginning - at the level of the first cancer cell and its first descendants, and even before its beginning - at the level of precancerous cells.

Having identified the marker gene of the disease, it is possible to determine which protein causes it, which means that it is necessary to create a medicine against this protein or its gene - this is the “magic bullet” that P. Ehrlich dreamed of. The pharmacology of the future will be built on this.
New drugs and products based on marker genes and protein markers for a specific disease will target only defective cells, destroying them, without damaging healthy cells. Hence, the patient will have no side effects from the medications.

Cancer stem cell arises from a normal cell or tissue stem cell due to derepression of fetal protein genes in it and simultaneously repression of suppressor genes by methylation of CpG dinucleotides of the promoter of these genes or mutations in genes. At the same time, it becomes more tenacious than a normal cell of the same type.
A cancer cell contains a number of tricks that make it invulnerable and capable of independent existence in the patient’s body. Those. This defective cell is not just a cell, but an entire single-celled organism.

1. Pre-disease.

Any disease begins with a pathology of a cell or cells. Changes in a particular gene or genes of a cell are not a diagnosis of a disease, but only the establishment of a probable predisposition to it.
With such changes in the reproductive cell, the term is used - predisposition to disease, and in the somatic cell, they more often say - pre-disease.
During pre-disease, such a gene does not yet manifest itself, since the cell does not yet have the synthesis of the gene product - proteins. When such changes in genes occur in a normal cell, it is a precancerous cell.
“Repairing” such a gene or genes, or replacing it in a cell with a normal gene, “switching off” the genes for the properties of a cancer cell, eliminates the pre-disease.

2. Disease.

When a cell, under the control of a gene or genes, already has the synthesis of its product - proteins, then this is a sign that the gene has already begun destructive work in the cell, leading to disease.
Here, changes in a gene or genes are the root cause of cell disease, and changes in cell properties are caused by the gene product, i.e. its proteins. These properties then form the symptoms of a particular disease.
The cause gene in a cell is a marker gene, and its protein is a marker protein. Inhibition of the causative gene and its products - proteins in the cell - can stop the disease.

3. Early diagnosis of the disease.

Until now, many diseases, including serious ones, including cancer, are diagnosed at the stage of their symptoms. Treatment of many diseases at this stage is extremely difficult in terms of cure or even impossible.
Now the diagnosis of any disease, including the most dangerous disease- cancer will become possible in the pre-symptomatic period.

"Before the beginning". This will be done by identifying a gene marker for a specific disease in a patient's cell or cells. In relation to cancer, this will be the diagnosis of a precancerous cell or cells.

"From the very beginning". This will be done by identifying in the cell or cells not only a marker gene, but also a marker protein for a specific disease. In relation to cancer, this will be the identification of the first cancer cell and its close descendants in the patient’s body.
Materials for these studies can be: tissue samples background process of the relevant organ - a biopsy, as well as blood and other biological fluids from the patient.

At any location of cancer in a patient, due to the mosaic nature of the capillaries of the cancer nodule, both the cancer cells themselves and their markers can be detected in the blood: marker genes in the blood plasma, and marker proteins from cancer stem cells in the blood serum.
Blood plasma may contain marker genes from precancerous cells, as well as marker genes from cancer cells, but it is almost impossible to distinguish between them.
Theoretically, these differences can be found using MS-PCR and PCR-MMK and protein microarrays.

If marker genes characteristic of a cancer cell are found in the blood plasma from a patient, but the corresponding marker proteins are absent in the serum of the same blood sample, this could indicate the presence of precancerous cells.
The detection of marker genes from a cancer cell in the blood plasma of a patient could be designated as level I of early cancer diagnosis, since abnormalities in genes are the root cause of the transformation of a normal cell into a cancer cell. Then the detection of marker proteins from cancer cells in the patient’s blood serum is the second level of early cancer diagnosis, since the marker protein is a gene product.

4. Treatment of the disease.

To do this, marker genes and cell marker proteins for each disease will be used as targets for drugs and agents.
These are new drugs and agents that will specifically act only on defective cells, and for cancer, these are cancer stem cells, without affecting normal stem cells. That is, these medicines and remedies will be selective and individual for a particular patient (A.I. Archakov, 2000).

5. Criteria for cure of the disease and control.

Marker genes and marker proteins will make it possible to detect defective cells in any disease when they cannot yet be detected in the patient’s body by any other methods.
They will make it possible to detect cancer in a patient when the size of a nodule of cancer cells in tissue with a diameter of 2 mm (A.S. Belokhvostov, 2000).
The number or titer of marker genes and marker proteins in the blood from defective cells of a particular disease or from cancer stem cells will allow monitoring the process of treating the disease and the outcome of the patient’s treatment.
If the titer of markers does not decrease during treatment, treatment tactics need to be changed. The complete absence of markers two to three weeks after the end of treatment is a sign that the patient has recovered from the disease.

It will be very convenient to carry out such control using biochips: DNA chips for marker genes, and protein chips for protein markers of defective cells of a specific disease and cancer stem cells.

At the Republican Scientific and Practical Center of Oncology and Medical Radiology named after. N. N. Aleksandrova currently carries out 56 scientific projects, of which 23 are related to molecular genetic research. They are carried out in the Republican Molecular Genetics Laboratory of Carcinogenesis (oncology department of genetics, cellular and biochip technologies, virology, immunology and proteonics).

Traditional diagnostic tools are exhausting their potential, says Deputy Director for Scientific Work of the Republican Scientific and Practical Center, Corresponding Member of the National Academy of Sciences of Belarus, Doctor of Medicine. Sciences, Professor Sergei Krasny. - The time has come to use such a reserve as molecular genetic research. They make it possible to accurately test tumors to determine chemosensitivity, determine the hereditary nature of the disease based on the patient’s genetic profile, and purposefully act proactively by prescribing targeted treatment.

In 2016, about 10,000 patients passed through the Republican Scientific and Practical Center, approximately 7,000 of them underwent molecular biological studies; Large-scale tumor profiling to individualize therapy was carried out on approximately one hundred people. Based on molecular biological markers, tumors of the central nervous system, soft tissues and bones, and lymphoma were diagnosed, studies were conducted to assess the hereditary risks of developing malignant tumors, monitoring the concentration of drugs in body fluids for individual drug dose adjustment, cell therapy technologies were developed and implemented.

To introduce the achievements of molecular biology into the domestic clinic, the first international certificates have already been obtained, modern equipment has been purchased to perform fluorescent in situ hybridization, molecular sequencing, polymerase chain reaction (PCR), immunohistochemistry, chromatography-mass spectrometry, flow cytometry, and enzyme-linked immunosorbent assay.

Biologist Victoria Mayorova prepares samples for the PCR reaction.

New developments

Forecast evaluation method clinical course cancer Bladder through a comprehensive analysis of clinical and morphological parameters of the tumor and the molecular genetic status of the FGFR3 gene.

Based on this analysis, a model of the molecular pathways of bladder cancer pathogenesis was created. Depending on the presence of a certain mutation, pathology can develop in two ways: so-called superficial cancer, characterized by low malignancy and a favorable prognosis (mutations in the FGFR3 and HRAS genes); a more aggressive muscle-invasive cancer that metastasizes early and is characterized by a poor prognosis (mutations in the TP53 and RUNX3 genes).

Using this method, a group of patients with a very high risk of disease progression was identified who had mutations in the TP53 and RUNX3 genes. This is important for predicting the course of the disease and determining the degree of aggressiveness of treatment. Knowing that the patient's tumor will develop as a superficial tumor, post-treatment will primarily involve bladder control.

If progression of the disease is expected, then the condition of other internal organs will be monitored for metastasis. In addition, patients can be identified who need to be treated immediately. radical removal bladder, otherwise metastases will develop.

Non-invasive complex method of molecular genetic and radiological diagnosis of prostate cancer.

This testing should be performed when a patient with a high level of prostate-specific antigen (PSA) in the blood has had an initial biopsy that is negative. Usually, six months later, another biopsy is performed, then another (and so on 10–15 times), but this is an aggressive study, so a solution was required that would allow us to limit ourselves to only one such intervention. Scientists have found a way out. By determining the expression of the PCA3 oncogene and the chimeric TMPRSS2-ERG gene in urine, it is possible to identify patients who really need to undergo a biopsy (the rest can be delayed).

Development and implementation of a tissue-engineered transplantation method respiratory tract with their lesions of tumor or scar etiology.

We are talking about the category of patients who die within 2–5 months. A method was proposed for decellularizing the cadaveric trachea, essentially preparing a matrix, then populating it with chondrocytes and then with epithelial cells. In addition, the technology provides for revascularization of the trachea with subsequent transplantation to patients. All this is done with the aim of replacing a tracheal defect after removal of a tumor or scar. Currently, 3 operations have been performed. All patients have been living for more than six months - this is considered an encouraging result.

Doctor laboratory diagnostics Stukalova Irina Vladimirovna and senior medical assistant-laboratorian Pishchik Natalia Zakharovna are preparing an analyzer for isolating DNA of the human papilloma virus.

Plans and prospects

Together with the Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, the topic “Proteomic and molecular genetic studies of tumor stem cells (TCS) of colorectal cancer for the development of new methods of targeted cell therapy” is planned (program of the Union State “Stem Cell - 2”).

Using a model of a 5-fluorouracil-resistant colorectal cancer cell line, it is planned to study the role of SOC in the mechanisms of tumor progression and to select possible molecular targets for targeting SOC using cell therapy based on vaccines using dendritic cells and/or dendritic cells and lymphokine-activated killers . This will be a new stage in immunotherapy malignant tumors.

Biologist Igor Severin in the cryobank of tumor cell lines.

Another project is “Development of technology for identifying the risk of cancer based on molecular genetic and epigenetic markers” (DNA Identification program of the Union State). It is planned to develop innovative DNA technology to determine molecular genetic and epigenetic markers of the risk of recurrence or progression of the disease in patients with colorectal cancer. According to experts, the new technology will allow timely preventive treatment and prevent the occurrence of metastases.

The signal is provided by microRNA

A promising area of ​​research is the study of epigenetic regulatory mechanisms, i.e. processes that do not affect the structure of genes, but change their level of activity. One of them is RNA interference - a mechanism for suppressing gene expression at the translation stage, when RNA is synthesized but does not manifest itself in protein. And if a high level of expression of some microRNA is detected, it can be assumed that there is a problem in this organ.

The microRNA gene family makes up just over 1% of the entire human genome, but regulates the expression of almost a third of all genes. A number of ongoing research projects are devoted to the study of microRNAs in various tumors. The department is developing a non-invasive diagnostic method germ cell tumors testicular, based on determination of the expression of a panel of microRNAs in the blood. This same family of molecules, in addition to diagnosing diseases, is used to predict the course of cancer and to select individual drug therapy.

The objective of the study is to determine markers of an unfavorable prognosis (a group of such patients can be identified and additional treatment can be selected). It is also important to determine the microRNA spectrum. It will indicate sensitivity to certain chemotherapy regimens (we are talking about breast cancer, for which a panel of markers has been found).

By studying molecular characteristics during treatment, it is possible to adjust the treatment regimen if additional mutations appear. The method is called a “liquid” biopsy: using a blood test, you can monitor genetic changes and predict the progression of the disease much earlier.

Therapy drugs are expensive and highly toxic, so it is important to identify drug resistance at an early stage and find a replacement.

Molecular profiling involves identifying genetic disorders characteristic of each specific tumor, since it is known that the same nosological forms differ in molecular characteristics. Knowing the molecular portrait of a tumor is also necessary to predict the course of the oncological process and individualize treatment. A personalized approach to prescribing cytostatic drugs and targeted therapy in cancer patients, taking into account molecular biomarkers of sensitivity and toxicity, ensures the most accurate selection of drugs.

As part of molecular profiling of tumors, based on a large-scale analysis of data from world publications, multi-platform panels of biomarkers for breast cancer, ovarian cancer, colorectal cancer, non-small cell lung cancer, and melanoma have been developed, intended for the selection of systemic antitumor therapy.

Chemist Olga Konstantina Kolos launches the synthesis of oligonucleotides.

Is it necessary to expand the geography of research?

Anna Portyanko,

head of the Republican

molecular genetic

laboratory of carcinogenesis,

doctor med. Sciences:

At the present stage, from the group of glioblastomas, variants have been identified that are characterized by different prognosis. From a morphological point of view, it is easy to confuse glioblastoma and anaplastic oligodendroglioma: when stained with hematoxylin-eosin, they look almost the same. But thanks to genetic tests, we find differences. Moreover, it is routinely performed in our pathology department.

Lymphomas have “multiplied” in a similar way. For example, through molecular genetic testing, several lymphomas have been isolated from Hodgkin lymphoma. Previously, based on hematoxylin-eosin histology, they were classified as Hodgkin's lymphoma, and when molecular genetic analysis of the T-cell receptor appeared, it turned out that it was follicular T-cell lymphoma.

How does this affect treatment? First of all, a more accurate forecast can be given. If a person has glioblastoma, then the median survival is 1 year, and if we are talking about anaplastic oligodendroglioma, then 10 years.

We develop connections with foreign specialists from the best European scientific centers. Together with colleagues from Germany, we are trying to develop important areas of proteomics - the analysis of not just one protein, but the proteome as a whole. The entire cycle has been created, starting from the cytological preparation; there is a laser microdissection system based on a microscope, which allows you to isolate tumor cells from a large tumor, then do mass spectrometry and determine the spectrum of all proteins in this tumor.

Is it necessary to expand the geography of research? I think it is enough for the country to have one such center - the Republican Molecular Genetic Laboratory of Carcinogenesis, where all the necessary molecular biological studies can be quickly carried out (including with histological material obtained from the regions).

We have the ability to carry out not only histological diagnostics, but also preliminary diagnostics using a flow cytometer. Literally within an hour after a person has had their lymph nodes removed, we can preliminarily tell whether there is lymphoma (and if so, what kind). This is a great help for clinicians.

Biologist Anastasia Pashkevich loads samples into a genetic analyzer.

What was Angelina Jolie afraid of?

“We are studying genetic damage that occurs during tumor development,” says Elena Suboch, head of the oncology department of genetics at the Republican Molecular Genetics Laboratory of Carcinogenesis. - A current direction is the assessment of hereditary risks of developing cancer. Hereditary forms of tumors account for 1–2% of all oncopathologies, and special treatment and surgical regimens must be used here. An important goal of identifying familial tumor syndromes is to identify healthy relatives of the patient who have pathogenic mutations. As a result, it is possible to develop a set of measures aimed at preventing unfavorable outcomes of cancer pathology.

An example is well-known: American actress Angelina Jolie, who has a mutation in the BRCA1 gene, which increases the risk of developing breast cancer, underwent radical surgery to prevent the occurrence of a malignant tumor.

Scientists at the Republican Molecular Genetics Laboratory of Carcinogenesis are studying this pathology.

Under a grant from the Belarusian Republican Foundation for Basic Research, in 2015–2017, the work “System of allelic discrimination of the mutation status of the BRCA1 and BRCA2 genes in malignant neoplasms of the human breast” was carried out. A population study was conducted, and it turned out that the frequency of mutations in the BRCA1 and BRCA2 genes is approximately 2.5% among women (the frequency spectrum of mutations differs from what is observed in residents of neighboring countries).

Each population has its own spectrum of genetic disorders. Knowing the characteristic mutations, you can first test them, and then look for other options. The result of the research project was the development of a system for allelic discrimination of the mutation status of the BRCA1/BRCA2 genes using polymerase chain reaction in real time. We have identified 5 main mutations that occur in Belarusian women.

Specialists in the oncology department of genetics also test a large panel of markers that allows them to assess the risk of developing ovarian, endometrial, thyroid, kidney, colorectal cancer, melanoma, and polyposis syndromes.

Today there are new international classifications brain tumors and lymphomas requiring mandatory molecular genetic studies. Therefore, in the departments of genetics and cell technology, an algorithm for diagnosing such diseases using biomarkers is being developed.



We are completing a series of articles about cancer. Today Atlas will tell you in detail what molecular testing is and how it affects the diagnosis.

To understand how molecular diagnostics works and what place they occupy in oncology, you must first understand the mechanisms occurring in the tumor.

Molecular processes in tumors

Mutations in proto-oncogenes and suppressor genes, which are responsible for cell division and death, lead to the fact that the cell stops following instructions and synthesizes proteins and enzymes incorrectly. Molecular processes run out of control: the cell constantly divides, refuses to die and accumulates genetic and epigenetic mutations. Therefore, malignant neoplasms are often called a disease of the genome.

Hundreds of thousands of mutations can occur in tumor cells, but only a few contribute to tumor growth, genetic diversity, and progression. They are called driver ones. The remaining mutations, “passanger” mutations, do not in themselves make the cell malignant.

Driver mutations create distinct populations of cells, providing tumor diversity. These populations or clones respond differently to treatment, with some being resistant and leading to relapse. In addition, the different sensitivity of clones to therapy can lead to a radical change in the molecular profile during treatment: even cells that are insignificant at the beginning of the population can gain an advantage and become dominant at the end of treatment, leading to resistance and tumor development.

Molecular diagnostics

Driver mutations, changes in the quantity or structure of proteins are used as biomarkers - targets for which treatment is selected. The more targets are known, the more accurate the selection from the potential effective schemes treatment.

Separating driver mutations from others and determining the molecular profile of a tumor is not easy. For this purpose, the technology used is sequencing, fluorescence in situ hybridization (FISH), microsatellite analysis and immunohistochemistry.

Next-generation sequencing methods can identify driver mutations, including those that make a tumor sensitive to targeted therapy.

Using FISH technology, areas of the chromosomes on which a specific gene is located are tinted. Two connected multi-colored dots are a chimeric or fusion gene: when, as a result of chromosome rearrangement, sections of different genes are connected together. This may result in the oncogene coming under the influence of the regulation of another more active gene. For example, the fusion of the EML4 and ALK genes is of key importance in the case of lung cancer. The ALK proto-oncogene is activated under the influence of its rearrangement “partner”, which leads to uncontrolled cell division. The oncologist, taking into account the restructuring, can use a drug that will be directed against the activated ALK gene product (Crizotinib).

Fluorescence in situ hybridization (FISH).

Microsatellite analysis shows the degree of disruption of the DNA repair system, and immunohistochemistry shows protein biomarkers located on the surface, in the cytoplasm and nuclei of tumor cells.

All of these studies are included in New Product biomedical holding "Atlas" - Solo test. With this test, the oncologist receives information about the molecular profile of the tumor and how it affects the potential effectiveness of a wide range of antitumor drugs.

Solo examines up to 450 genes and biomarkers to assess how a tumor might respond to more targeted cancer treatments. For some of these, the biomarker analysis is dictated by the manufacturer. For others, clinical trial data and recommendations from international oncology communities are used.

In addition to selecting targets for targeted therapy, molecular profiling can help identify mutations that make a tumor resistant to a particular treatment, or genetic features that are associated with increased toxicity and require individualized drug dosing.

For research, biopsy material or paraffinized blocks of postoperative material are used.

Molecular profiling provides additional information about the disease, but it is not always applicable to treatment decisions. For example, in situations where standard therapy is sufficiently effective or surgical treatment is indicated. It is possible to identify clinical situations where such testing may be most useful:

• A rare type of tumor;
• Tumors with an unknown primary focus (it is not known where the tumor that metastasized originally appeared);
• Those cases where a choice of several options for using targeted therapy is required;
• The possibilities of standard therapy have been exhausted and experimental treatment or inclusion of the patient in clinical trials is required.

Solo project specialists advise oncologists or patients and suggest whether a test is needed in a given case.

Precision Medicine and Clinical Research

Typically, medical practice uses general strategies to treat patients with a specific diagnosis. One strategy is used for small cell lung cancer, and another for non-small cell lung cancer. This method is not always suitable for oncological diseases. Due to differences at the molecular level, even within the same tumor type, patients may receive ineffective or unnecessary treatment.

With increasing research and the invention of targeted drugs, the approach to treating cancer began to change. To increase the relapse-free period and life expectancy of the patient, it is necessary to take into account the molecular profile of the tumor, the body’s response to drugs and chemotherapy (pharmacogenomics), and know the main biomarkers.

Precision medicine can significantly improve the prognosis of a particular patient, avoid serious side effects of oncological drugs and significantly improve the patient’s quality of life. But this method also has disadvantages.

There are a growing number of targeted drugs, and they have two main limitations: most molecularly targeted agents provide only partial inhibition of signaling pathways, and many are too toxic to be used in combination.

Imagine that you are an architect in Moscow. You are faced with a difficult task - to solve the problem of traffic jams during rush hour by building one bridge. Molecular mechanisms can be compared to the movement of cars, and a bridge is main drug, which should solve the main problem. It seems that several drugs (a series of bridges) targeting the major molecular abnormalities may solve this problem. But the toxicity of the drugs increases and can be unpredictable.

We have gained a better understanding of the molecular processes of cancer, but current methods for translating precision oncology into clinical practice lag far behind. To speed up the study of targeted therapy, scientists have developed two new approaches - Basket and Umbrella.

The essence of the Basket method is that patients with a specific biomarker are selected for the study, regardless of the location and name of the tumor. In May 2017, the FDA approved such a treatment for a biomarker called microsatellite instability high (MSI-H) or mismatch repair defect (dMMR).

Molecular abnormalities differ not only between patients, but also within the same tumor. Heterogeneity is a major problem in oncology, which the Umbrella study design was designed to address. For the Umbrella method, patients are first selected by type of malignancy, and then genetic mutations are taken into account.

Such studies not only help to collect information about the action of targeted drugs - sometimes this is the only option for patients who do not respond to standard treatment with registered drugs.

Clinical example

We decided to give a clear example of what the use of advanced molecular profiling might look like.

A patient with skin melanoma and liver metastases consulted an oncologist. The doctor and patient decided to do molecular profiling to obtain more complete information about the disease. The patient underwent a biopsy and tissue samples were sent for testing. As a result of the diagnosis, several important genetic disorders were discovered in the tumor:

• Mutation in the BRAF gene. Indicates activation of the RAS-RAF-MEK oncogene signaling pathway, which is involved in cell differentiation and survival.
• Mutation in the NRAS gene. Indicates additional activation of the RAS-RAF-MEK signaling cascade.
• Hereditary variant of the TPMT gene. Indicates the peculiarities of metabolism of the antitumor drug Cisplatin.

Based on the results of clinical studies and recommendations, we can come to the following conclusions:

• Drugs of the class of BRAF inhibitors (Vemurafenib) may be potentially effective; moreover, the presence of a NRAS mutation may serve as an additional basis for prescribing a double blockade of the signaling cascade - in combination with MEK inhibitors (Trametinib).
• Although there is no approved therapy directly targeting the NRAS oncogene, mutations in it are known to increase the likelihood of treatment success when given immunotherapy (ipilimumab and pembrolizumab).
• An inherited genetic variant in the TPMT gene indicates increased individual toxicity of Cisplatin, which requires dose adjustment when prescribing platinum-containing regimens.

In the photo: Vladislav Mileiko, head of department, Atlas biomedical holding.

Thus, the doctor has the opportunity to navigate among possible treatment options based not only on the patient’s clinical parameters, but also taking into account the molecular characteristics of the tumor.

Molecular diagnostics are not a panacea for all cancer diseases. But this important tool for an oncologist who allows him to approach the treatment of malignant tumors from a new angle.

Thank you for reading and commenting on our materials about oncology. Here full list articles:

. Concern about unmanageable side effects (such as constipation, nausea, or confusion. Concern about addiction to pain medications. Non-adherence to prescribed pain medication regimen. Financial barriers. Health system issues: Low priority for cancer pain management. Most suitable treatment may be too expensive for patients and their families. Tight regulation of controlled substances. Problems with access to or availability of treatment. Opiates not available over the counter to patients. Unavailable medications. Flexibility is key to managing cancer pain. Since patients differ in diagnosis, stage of disease, response to pain and personal preferences, it is necessary to be guided by these characteristics. Read more in the following articles: ">Cancer pain 6

to cure or at least stabilize the development of cancer. Like other therapies, the choice to use radiation therapy to treat a specific cancer depends on a number of factors. These include, but are not limited to, the type of cancer, the patient's physical condition, the stage of the cancer, and the location of the tumor. Radiation therapy (or radiotherapy is an important technology for shrinking tumors. High energy waves are directed at cancerous tumor. The waves cause damage to cells, disrupting cellular processes, preventing cell division, and ultimately leading to the death of malignant cells. The death of even part of the malignant cells leads to a reduction in the tumor. One significant disadvantage of radiation therapy is that the radiation is not specific (that is, it is not aimed exclusively at cancer cells for cancer cells and can also harm healthy cells. Responses of normal and cancer tissue to therapy The response of tumor and normal tissues to radiation depends on their nature growth before the start of therapy and during treatment. Radiation kills cells through interaction with DNA and other target molecules. Death does not occur instantly, but occurs when cells try to divide, but as a result of exposure to radiation, a failure in the division process occurs, which is called abortive mitosis. For this reason, radiation damage occurs more quickly in tissues containing cells that divide quickly, and it is cancer cells that divide quickly. Normal tissues compensate for the cells lost during radiation therapy by accelerating the division of remaining cells. In contrast, tumor cells begin to divide more slowly after radiation therapy, and the tumor may shrink in size. The extent of tumor shrinkage depends on the balance between cell production and cell death. Carcinoma is an example of a type of cancer that often has a high rate of division. These types of cancer tend to respond well to radiation therapy. Depending on the dose of radiation used and the individual tumor, the tumor may begin to grow again after stopping therapy, but often more slowly than before. To prevent the tumor from growing back, radiation is often given in combination with surgery and/or chemotherapy. Goals of Radiation Therapy Curative: For curative purposes, radiation exposure is usually increased. Reaction to radiation ranges from mild to severe. Symptom relief: This procedure aims to relieve cancer symptoms and prolong survival, creating more comfortable conditions life. This type of treatment is not necessarily performed with the intention of curing the patient. Often this type of treatment is prescribed to prevent or eliminate pain caused by cancer that has metastasized to the bones. Radiation instead of surgery: Radiation instead of surgery is an effective tool against a limited number of cancers. Treatment is most effective if the cancer is found early, while it is still small and non-metastatic. Radiation therapy may be used instead of surgery if the location of the cancer makes surgery difficult or impossible to perform without serious risk to the patient. Surgery is the preferred treatment for lesions that are located in an area where radiation therapy may benefit more harm than surgery. The time required for the two procedures is also very different. Surgery can be performed quickly after diagnosis; Radiation therapy may take weeks to be fully effective. There are pros and cons to both procedures. Radiation therapy may be used to save organs and/or avoid surgery and its risks. Radiation destroys rapidly dividing cells in the tumor, while surgical procedures may miss some of the cancerous cells. However, large tumor masses often contain oxygen-poor cells in the center that do not divide as quickly as cells near the surface of the tumor. Because these cells do not divide rapidly, they are not as sensitive to radiation therapy. For this reason, large tumors cannot be destroyed using radiation alone. Radiation and surgery are often combined during treatment. Useful articles for a better understanding of radiation therapy: ">Radiation Therapy 5

Skin reactions with targeted therapy Skin problems Shortness of breath Neutropenia Nervous system disorders Nausea and vomiting Mucositis Menopausal symptoms Infections Hypercalcemia Male sex hormone Headaches Hand-foot syndrome Hair loss (alopecia Lymphedema Ascites Pleurisy Edema Depression Cognitive problems Bleeding Loss of appetite Restlessness and anxiety Anemia Confusion Delirium Difficulty swallowing Dysphagia Dry mouth Xerostomia Neuropathy For specific side effects, read the following articles: "> Side effects36

cause cell death in various directions. Some of the drugs are natural compounds that have been identified in various plants, while other chemicals are created in the laboratory. Several different types of chemotherapy drugs are briefly described below. Antimetabolites: Drugs that can affect the formation of key biomolecules inside the cell, including nucleotides, the building blocks of DNA. These chemotherapeutic agents ultimately interfere with the process of replication (production of the daughter DNA molecule and therefore cell division. Examples of antimetabolites include the following drugs: Fludarabine, 5-Fluorouracil, 6-Thioguanine, Ftorafur, Cytarabine. Genotoxic drugs: Drugs that can damage DNA: By causing this damage, these agents interfere with DNA replication and cell division. Examples of drugs: Busulfan, Carmustine, Epirubicin, Idarubicin. Spindle inhibitors (or mitosis inhibitors: These chemotherapy agents are aimed at preventing proper cell division , interacting with cytoskeletal components that allow one cell to divide into two parts. As an example, the drug paclitaxel, which is obtained from the bark of the Pacific Yew and semi-synthetically from the English Yew (Taxus baccata. Both drugs are prescribed in a series intravenous injections. Other chemotherapeutic agents: These agents inhibit cell division through mechanisms not covered in the three categories above. Normal cells are more resistant to drugs because they often stop dividing under conditions that are not favorable. However, not all normal dividing cells avoid the effects of chemotherapy drugs, confirming the toxicity of these drugs. Cell types that typically divide rapidly, such as those in the bone marrow and in the lining of the intestine, tend to be the most affected. Normal cell death is one of the common side effects of chemotherapy. More details about the nuances of chemotherapy in the following articles: ">Chemotherapy 6

• and non-small cell lung cancer. These types are diagnosed based on how the cells look under a microscope. Based on the established type, treatment options are selected. To understand the prognosis of the disease and survival rate, I present statistics from open US sources for 2014 on both types of lung cancer together: New cases of the disease (prognosis: 224210 Number of projected deaths: 159260 Let us consider in detail both types, specifics and treatment options.">Lung cancer 4
• in the United States in 2014: New cases: 232,670 Deaths: 40,000 Breast cancer is the most common non-skin cancer among women in the United States (open sources, an estimated 62,570 cases of pre-invasive disease (in situ, 232,670 new cases of invasive disease, and 40,000 deaths, meaning less than one in six women diagnosed with breast cancer will die from the disease, compared with an estimated 72,330 American women will die of lung cancer in 2014. Breast cancer in men (yes, yes, there is such a thing) accounts for 1% of all breast cancer cases and deaths from this disease. Widespread screening has increased the incidence of breast cancer and changed the characteristics of detected cancer. Why has it increased? Yes, because the use modern methods has made it possible to detect the incidence of low-risk cancers, precancerous lesions and ductal carcinoma in situ (DCIS). Population-based studies in the US and UK show an increase in DCIS and the incidence of invasive breast cancer since 1970, this is associated with the widespread hormone therapy in postmenopause and mammography. In the last decade, postmenopausal women have refrained from using hormones and the incidence of breast cancer has decreased, but not to the level that can be achieved with the widespread use of mammography. Risk and protective factors Increasing age is the most important risk factor for breast cancer. Other risk factors for breast cancer include the following: Family medical history o Underlying genetic susceptibility Sex mutations in the BRCA1 and BRCA2 genes, and other breast cancer susceptibility genes Alcohol consumption Breast tissue density (mammographic) Estrogen (endogenous: o Menstrual history (onset of menstruation / late menopause o No history of childbirth o Older age at first birth History of hormone therapy: o Combination of estrogen and progestin (HRT Oral contraception) Obesity Lack of exercise Personal history of breast cancer Personal history of proliferative forms of benign breast diseases Radiation exposure to the breast Of all Of women with breast cancer, 5% to 10% may have germline mutations in the BRCA1 and BRCA2 genes. Research has found that specific BRCA1 and BRCA2 mutations are more common among women of Jewish descent. Men who carry a BRCA2 mutation also have increased risk of developing breast cancer. Mutations in both the BRCA1 and BRCA2 genes also create an increased risk of developing ovarian cancer or other primary cancers. Once BRCA1 or BRCA2 mutations have been identified, it is advisable for other family members to undergo genetic counseling and testing. Protective factors and measures to reduce the risk of developing breast cancer include the following: Using estrogen (especially after a hysterectomy Creating an exercise habit Early pregnancy Breast-feeding Selective estrogen receptor modulators (SERMs) Aromatase inhibitors or inactivators Reducing the risks of mastectomy Reducing the risk of oophorectomy or oophorectomy Screening Clinical trials have found that screening asymptomatic women with mammography, with or without clinical breast examination, reduces mortality from breast cancer. Diagnosis If If breast cancer is suspected, the patient usually must go through the following steps: Confirmation of the diagnosis Assessing the stage of the disease Selection of therapy The following tests and procedures are used to diagnose breast cancer: Mammography Ultrasound Breast magnetic resonance imaging (MRI, if clinically present) indications Biopsy Contralateral breast cancer Pathologically, breast cancer can be multicentric and bilateral. Bilateral disease is slightly more common in patients with invading focal carcinoma. Over 10 years after diagnosis, the risk of primary breast cancer in the contralateral breast is within 3% to 10%, although endocrine therapy may reduce this risk. Development of second breast cancer is associated with an increased risk of distant recurrence. If the BRCA1/BRCA2 gene mutation was diagnosed before the age of 40, the risk of cancer of the second breast in the next 25 years reaches almost 50%. Patients diagnosed with breast cancer should undergo bilateral mammography at the time of diagnosis to rule out synchronous disease. The role of MRI in screening for contralateral breast cancer and monitoring women treated with breast conservation therapy continues to evolve. Because the increased level detection of possible disease on mammography has been demonstrated, selective use of MRI for additional screening is occurring more frequently, despite the lack of randomized controlled data. Because only 25% of MRI-positive findings represent malignancy, pathological confirmation is recommended before treatment. Whether this increased rate of disease detection will lead to improved treatment outcomes is unknown. Prognostic Factors Breast cancer is usually treated with various combinations of surgery, radiation therapy, chemotherapy and hormonal therapy. Conclusions and selection of therapy may be influenced by the following clinical and pathological features (based on conventional histology and immunohistochemistry: Menopausal status of the patient. Stage of disease. Grade of primary tumor. Tumor status depending on the status of estrogen receptors (ER and progesterone receptors (PR). Histological types Breast cancer is classified into different histological types, some of which have prognostic significance. For example, favorable histological types include colloid, medullary and tubular cancer. Uses of molecular profiling in breast cancer include the following: ER and PR status testing. Testing receptor status HER2/Neu. Based on these results, breast cancer is classified as: Hormone receptor positive. HER2 positive. Triple negative (ER, PR and HER2/Neu negative. Although some rare inherited mutations, such as BRCA1 and BRCA2, predispose carriers to breast cancer, prognostic data for BRCA1/BRCA2 mutation carriers is inconsistent; these women are simply more susceptible risk of developing cancer of the second breast. But it is not certain that this can happen. Hormone replacement therapy After careful consideration, patients with severe symptoms may be treated with hormone replacement therapy. Follow-up Monitoring frequency and appropriateness of screening after completion of primary treatment stage I, stage II , or stage III breast cancer remains controversial.Evidence from randomized trials shows that periodic surveillance with bone scans, liver ultrasound, chest x-rays, and blood tests for liver function does not improve survival or quality of life at all compared with routine physical examinations. Even when these tests allow early detection of relapse of the disease, this does not affect the survival of patients. Based on these data, limited screening and annual mammography may be an acceptable continuation for asymptomatic patients who have been treated for stage I to III breast cancer. More detailed information in articles: "> Mammary cancer5
• , ureters, and proximal urethra are lined by a specialized mucosa called transitional epithelium (also called urothelium. Most cancers that form in the bladder, renal pelvis, ureters, and proximal urethra are transitional cell carcinomas (also called urothelial carcinomas, derived from transitional epithelium Transitional cell bladder cancer can be low-grade or full-grade: Low-grade bladder cancer often recurs in the bladder after treatment, but rarely invades the muscle walls of the bladder or spreads to other parts of the body.Patients rarely die from bladder cancer low grade. Full grade bladder cancer usually recurs in the bladder and also has a strong tendency to invade the muscle walls of the bladder and spread to other parts of the body. High grade bladder cancer is considered more aggressive than low grade bladder cancer and much more more likely to result in death. Almost all deaths from bladder cancer are due to high-grade cancer. Bladder cancer is also divided into muscle-invasive and non-muscle-invasive disease, based on invasion of the muscle lining (also referred to as the detrusor muscle, which is located deep in the muscle wall of the bladder. Muscle-invasive disease is much more likely to spread to other parts of the body and is typically treated by either removing the bladder or treating the bladder with radiation and chemotherapy.As noted above, high-grade cancers are much more likely to be muscle-invasive cancers than low-grade cancers.Thus, Muscle-invasive cancer is generally considered to be more aggressive than non-muscle-invasive cancer.Non-muscle-invasive disease can often be treated by removing the tumor using a transurethral approach and sometimes chemotherapy or other procedures in which a drug is injected into the urinary cavity bladder with a catheter to help fight cancer. Cancer can arise in the bladder in the setting of chronic inflammation, such as a bladder infection caused by the parasite haematobium Schistosoma, or as a result of squamous metaplasia; The incidence of squamous cell carcinoma of the bladder is higher in the setting of chronic inflammation than otherwise. In addition to transitional carcinoma and squamous cell carcinoma, adenocarcinoma, small cell carcinoma, and sarcoma can form in the bladder. In the United States, transitional cell carcinomas account for the vast majority (more than 90% of bladder cancers. However, a significant number of transitional cell carcinomas have areas of squamous cell or other differentiation. Carcinogenesis and Risk Factors There is compelling evidence of the influence of carcinogens on the occurrence and development of bladder cancer. The most common risk factor for developing bladder cancer is cigarette smoking. It is estimated that up to half of all bladder cancer cases are caused by smoking and that smoking increases the risk of developing bladder cancer at two to four times the baseline risk. Smokers with less functional polymorphisms N-acetyltransferase-2 (known as a slow acetylator) has a higher risk of developing bladder cancer compared to other smokers, apparently due to a decreased ability to detoxify carcinogens. Certain occupational hazards have also been linked to bladder cancer, and higher rates of bladder cancer have been reported due to textile dyes and rubber in the tire industry; among artists; leather processing industry workers; from shoemakers; and aluminum, iron and steel workers. Specific chemicals associated with bladder carcinogenesis include beta-naphthylamine, 4-aminobiphenyl, and benzidine. Although these chemicals are now generally banned in Western countries, many other chemicals that are still used today are also suspected of causing bladder cancer. Exposure to the chemotherapy agent cyclophosphamide has also been associated with an increased risk of bladder cancer. Chronic infections urinary tract infections and infections caused by the parasite S. haematobium are also associated with an increased risk of developing bladder cancer, and often squamous cell carcinoma. Chronic inflammation is believed to play a key role in the process of carcinogenesis in these conditions. Clinical signs Bladder cancer usually presents with simple or microscopic hematuria. Less commonly, patients may complain of frequent urination, nocturia, and dysuria, symptoms that are more common in patients with carcinoma. Patients with urothelial cancer of the upper urinary tract may experience pain due to obstruction by the tumor. It is important to note that urothelial carcinoma is often multifocal, necessitating examination of the entire urothelium if a tumor is detected. In patients with bladder cancer, imaging of the upper urinary tract is essential for diagnosis and follow-up. This can be achieved using urethroscopy, retrograde pyelogram in cystoscopy, intravenous pyelogram, or computed tomography (CT urogram). In addition, patients with transitional cell carcinoma of the upper urinary tract have a high risk of developing bladder cancer; these patients require periodic cystoscopy and observation of the contralateral upper urinary tract.Diagnosis When bladder cancer is suspected, the most useful diagnostic test is cystoscopy.Radiological examination, such as CT scan or Ultrasounds are not sensitive enough to be useful for detecting bladder cancer. Cystoscopy can be performed in a urology clinic. If cancer is detected during cystoscopy, the patient is typically scheduled for a bimanual examination under anesthesia and a repeat cystoscopy in the operating room so that transurethral tumor resection and/or biopsy can be performed. Survival Patients who die from bladder cancer almost always have metastases from the bladder to other organs. Low-grade bladder cancer rarely grows into the muscle wall of the bladder and rarely metastasizes, so low-grade (stage I) bladder cancer patients very rarely die from the cancer. However, they may experience multiple recurrences that should be treated resection. Almost all deaths from bladder cancer occur among patients with high-grade disease, which has a much greater potential to invade deep into the muscular walls of the bladder and spread to other organs. Approximately 70% to 80% of patients with newly diagnosed bladder cancer bladder have superficial bladder tumors (i.e., stage Ta, TIS, or T1. The prognosis of these patients largely depends on the grade of the tumor. Patients with tumors high degree malignancies have a significant risk of dying from cancer, even if it is not muscle-invasive cancer. Those patients with high-grade tumors who are diagnosed with superficial, non-muscle-invasive bladder cancer in most cases have a high chance of cure, and even in the presence of muscle-invasive disease, sometimes the patient can be cured. Studies have shown that in some patients with distant metastases, oncologists achieved long-term complete responses after treatment with a combination chemotherapy regimen, although most of these patients have metastases limited to their lymph nodes. Secondary Bladder Cancer Bladder cancer tends to recur, even if it is non-invasive at the time of diagnosis. Therefore, standard practice is to perform urinary tract surveillance after a diagnosis of bladder cancer. However, no studies have yet been conducted to evaluate whether surveillance affects progression rates, survival, or quality of life; although there is clinical trials to determine the optimal observation schedule. Urothelial carcinoma is thought to reflect a so-called field defect, in which the cancer arises due to genetic mutations that are widely present in the patient's bladder or throughout the urothelium. Thus, people who have had a resected bladder tumor often subsequently have ongoing tumors in the bladder, often in other locations than the primary tumor. Similarly, but less frequently, they may develop tumors in the upper urinary tract (i.e., renal pelvis or ureter). An alternative explanation for these patterns of recurrence is that cancer cells that are destroyed when the tumor is excised may reimplant in another location in the urothelium. Support for this second theory is that tumors are likely to recur lower than in the opposite direction from primary cancer. Upper tract cancer is more likely to recur in the bladder than bladder cancer to recur in the upper tract. The rest is in the following articles: "> Bladder cancer4
• , as well as an increased risk of metastatic disease. The degree of differentiation (staging) of a tumor has an important influence on the natural history of the disease and on the choice of treatment. An increase in the incidence of endometrial cancer has been found in association with long-term, unopposed estrogen exposure (increased levels. In contrast, combination therapy (estrogen + progesterone prevents an increase in the risk of developing endometrial cancer associated with a lack of resistance to the effects of estrogen specifically. Receiving a diagnosis is not the best time. However, you should know - endometrial cancer is a treatable disease. Monitor the symptoms and everything will be fine! In some patients, it may play a role "activator" of endometrial cancer is a prior history of complex hyperplasia with atypia. An increase in the incidence of endometrial cancer has also been found in association with treatment of breast cancer with tamoxifen. According to researchers, this is due to the estrogenic effect of tamoxifen on the endometrium. Because of this increase, patients who Patients prescribed therapy with tamoxifen must undergo regular examinations of the pelvic region and must be attentive to any abnormal uterine bleeding. Histopathology The distribution pattern of malignant endometrial cancer cells depends in part on the degree of cellular differentiation. Well differentiated tumors, as a rule, limit their spread to the surface of the uterine mucosa; myometrial expansion occurs less frequently. In patients with poorly differentiated tumors, invasion of the myometrium is much more common. Invasion of the myometrium is often a precursor to lymph node involvement and distant metastases, and often depends on the grade of differentiation. Metastasis occurs in the usual way. Spread to the pelvic and para-aortic nodes is common. When distant metastases occur, it most often occurs in: Lungs. Inguinal and supraclavicular nodes. Liver. Bones. Brain. Vagina. Prognostic factors Another factor that is associated with ectopic and nodal spread of the tumor is the participation of the capillary-lymphatic space in histological examination. The three prognostic groupings of clinical stage I were made possible by careful operative staging. Patients with stage 1 tumors involving only the endometrium and no evidence of intraperitoneal disease (i.e., adnexal extension) are at low risk (">Endometrial Cancer 4

“We can rarely give up our beloved
clinical hypothesis and continue to treat patients in such a way
how they were treated for many decades...
Meanwhile, the time has come to change existing paradigms.”

Richard Schilsky, President of ASCO

“The most severe diseases require the most powerful medicines, precisely applied...”
Hippocrates

The prognosis for cancer treatment depends on the clinical stage of the disease (TNM), tumor biology, and treatment received. Modern achievements in clinical oncology are undeniable. And yet, despite the obvious successes in creating new anticancer drugs, every day thousands of cancer patients take drugs that do not help them. For some patients, empirical treatment will be beneficial and safe. However, for many other patients, therapy may be both useless and toxic.

By the end of the 90s. XX century Cytotoxic chemotherapy has reached its limits. The development of molecular biology and focus on personalized medicine have led to a fundamentally new approach to treating patients using new generation molecular targeted drugs. Blockade of cancer cell proliferation was achieved through selective inhibition of its main signaling pathways - ligands, membrane receptors, intracellular proteins.
However, despite the obvious successes of the new approach, at the end of the first decade of the postgenomic era, there was an urgent need to revise this new treatment paradigm, which was due to big amount clinical failures due to the development of acquired tumor resistance.

Targets of targeted therapy and mechanisms of resistance
The most holistic view of the development and evolution of cancer was presented in two textbook articles by D. Hanaan and R. Weinberg (Cell, 2000, 2011). Based on their characteristics, the targets of therapy should be not only cancer cells with their unstable genome, special type of metabolism, active neoangiogenesis and acquired ability to evade growth signals, circulate in the bloodstream and metastasize. Targets of therapy should also include the tumor microenvironment, cancer stem cells, as well as all components of the metastatic cascade.
Obviously, it is simply impossible to implement such a program within the framework of a treatment protocol for a specific patient, even when using a combination of several targeted drugs. A single drug, even with a unique molecular mechanism of action, cannot be effective in treating a genetically heterogeneous, progressive tumor in which multiple resistance mechanisms emerge and become established.
Particular mechanisms of resistance to various targeted drugs are well studied. These include activation of alternative EGFR pathways that promote cell survival in response to drug damage, formation of oncogenic bypass and autocrine loop, loss of the extracellular domain of the membrane receptor (formation of a truncated receptor), kinome reprogramming, autophagy, epithelial-mesenchymal transition, epigenetic mechanisms, etc.
During progression and under the influence of therapy, additional oncogenic mutations appear in the tumor, its molecular landscape changes and genomic instability develops, which today is commonly called genomic chaos (W. George, Jr. Sledge, 2011).
It is not only cancer cells that are characterized by individuality and variability. In addition to epithelial cells, changes also occur in the tumor-associated stroma. Stromal cells are also subject to molecular evolution, although they are a genetically more stable component of a solid tumor.
The microenvironment, consisting of benign stromal cells, immune cells and inflammatory cells, also influences the evolution of the malignant clone and the formation of secondary resistance to therapy.

Heterogeneity as a reason for the ineffectiveness of antitumor therapy

The main reason for low efficiency empirical therapy is tumor heterogeneity.
For decades, histologists have classified cancers based on morphological characteristics, describing the different types of cancer cells and their relationship to the tumor stroma.
Molecular analysis techniques, especially rapidly developing in the post-genomic era, have revealed the true extent of tumor heterogeneity.

Individual (intertumoral) heterogeneity
Microarray technology for analyzing the expression level of thousands of genes made it possible initially (2000) to classify breast cancer (BC) into luminal A, luminal B, HER/2 and basal. Somewhat later, the refinement of molecular taxonomy with an emphasis on basal crayfish identified additional subtypes. Among them, there are such as Сlaudin-low (characterized by gene expression similar to breast stem cells), subtypes of mesenchymal tumors (genes regulating epithelial-mesenchymal transition), subtypes of apocrine tumors with the expression of androgen receptors and activation of the corresponding signaling pathway, subtypes with activity genes that regulate the immune response.
Further molecular studies of breast cancer were associated with the implementation of the METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) project. It has been established that the genomic landscape of a tumor can be influenced by molecular events such as point mutations, insertions, deletions, amplifications, duplications, translocations and inversions. It turned out that both genes not associated with carcinogenesis and genes whose mutations are common during cancer development (GATA3, TP53 and PIK3CA) can undergo somatic mutations. In addition to genomic damage in breast cancer, various epigenomic disorders (DNA methylation), damage at the level of transcription and microRNA were discovered. As a result of these studies, only in the luminal A subtype, another 10 different molecular integrative clusters affecting the outcome of the disease were classified. It has also been established that all four “main” subclasses and new “additional” molecular subtypes of breast cancer have different profiles sensitivity to antitumor drugs.
Molecular genetic classifications that influence treatment features are being created for gastric cancer, colorectal carcinoma, ovarian cancer and other localizations.

Intratumoral heterogeneity
A significantly larger fundamental problem in oncology is intratumor heterogeneity. The coexistence of several subclones in a tumor with different sets of molecular aberrations and different sensitivities to drugs makes strategies to suppress one cell fraction in relation to the entire tumor ineffective. Additional unfavorable factor is a change in tumor biology during its development.
Intratumor heterogeneity is usually divided into spatial (geographic) and temporal (evolutionary).
Spatial heterogeneity suggests the presence of molecular genetic differences in specific tumor regions, genetic differences between the primary tumor and its metastases, and differences between metastases at different anatomical sites.
Depending on the level genetic heterogeneity monogenomic (same genetic profiles in different geographic areas) and polygenomic tumors (different subclonal populations of cells in different regions) are observed.
Fundamental changes in the genome during tumor development occur at three time points: at the moment of transition of cancer in situ to invasive cancer, during the slow evolution of primary invasive cancer, and during metastatic progression.
There are many reasons to believe that cancer behaves as an open, unstable ecosystem, the development of which depends on the pressure of environmental factors such as the action of the immune system and hypoxia. The formation of evolutionary (temporal) heterogeneity of the primary tumor is also actively influenced by the ongoing antitumor treatment.
In a solid tumor, there is always a rare subclone of cells of critical importance that determines the final outcome of the disease. The death of a patient is most often observed as a result of exposure to the body of the clone of cells that at the time primary diagnosis was not dominant and represented no more than 1% of all tumor cells. The presence of such cells has been proven using the example of malignant myeloma, prostate cancer and tumors of other localizations. Analysis of serial biopsies performed repeatedly throughout the entire history of the disease (from the moment primary diagnosis before the death of the patient) showed that the clone of cells that survived as a result of therapy was not dominant at the beginning and received its development after drug elimination of other, “main”, rapidly proliferating clones.
Identifying and eliminating this lethal cell clone leading to patient death is a necessary therapeutic strategy.

Tumor heterogeneity at the cellular level
Most current studies of molecular aberrations have been conducted on cells representing the general tumor population. At the same time, structural changes in DNA were identified that occur in the early stages of tumor development and lead to bursts of genomic evolution (the so-called “large mutation clock”). The disadvantage of these methods was that the research did not take into account the presence of rare subclones with unique genetic mutations, hidden in the total mass of the main cells. It is in these cells that a gradual accumulation of point mutations occurs, contributing to extensive subclonal genetic divergence (“small mutation clock”).
Currently, attempts are being made to overcome this shortcoming (study of the tumor at the level of one, leading, malignant clone). Modern molecular profiling methods make this possible. It has been established that the tumor contains so-called “driver mutations” and “passenger mutations”. Driver mutations confer a selective growth advantage on cells carrying such mutations. Passenger mutations do not have this effect.
Typically, only driver mutations have been investigated as therapeutic targets. However, recently, passenger mutations have also attracted the attention of researchers, since they influence such effects as the induction of an immune response and proteotoxic stress. Passenger mutations may also be the target of antitumor strategies.
The accumulation of numerous mutations, which is characteristic of tumors with genomic and chromosomal instability, can result in a mutational crisis. When the optimal threshold of genomic instability is exceeded, viability is impaired and the number of elements of the entire system decreases.

Tumor tissue analysis methods
Methods for molecular analysis of tumor tissue are extremely diverse and are far beyond the scope of classical histology. Today these methods include: microarray method, Southern blotting, Northern blotting, Western blotting, in situ hybridization, polymerase chain reaction (PCR), real-time reverse transcriptase PCR, immunohistochemistry, immunofluorescence microscopy, maldimass spectrometry.
Analysis of a tumor cell can be carried out at the level of the genome (fluorescent in situ hybridization, spectral karyotyping, comparative genomic hybridization), transcription (microarray technology: gene and RNA expression profiling), proteome (two-dimensional gel electrophoresis, mass spectrometry, surface-enhanced laser desorption ionization in TOF mode: matrix technology + mass spectrometry).
Molecular tomography of tumor tissue allows visualization of the spatial distribution of proteins, peptides, drug compounds, metabolites, as well as molecular predictive biomarkers.
Tissues of the primary solid tumor, tissues of completed hematogenous metastases (rapidly growing and clinically significant), as well as circulating tumor cells and circulating tumor DNA (an indicator of the presence of “dormant” metastases) should be subjected to molecular analysis. Tumor and metastasis biopsies should be performed from different geographic locations of the same solid tumor. It is believed that a liquid biopsy is more informative (and safer).

From empirical to personalized therapy
A tumor, being an open, unstable biological system, not only demonstrates individual heterogeneity, but also changes its molecular characteristics throughout evolution, and especially during metastatic progression. Both dominant and non-dominant clones of solid tumor cells, as well as cells of the tumor microenvironment, undergo changes.
A strategy is used to suppress the proliferation of all tumor cells combination therapy. The concept of combined (simultaneous or sequential) treatment was first proposed by Goldie and Coldman more than 30 years ago. The concept combined such concepts as tumor growth, an increase in the frequency of mutations in it, the emergence of resistant cell clones and the development of resistance.
Today, the strategy of modern cancer therapy includes the use of combinations of cytostatics, cytostatics and targeted drugs, and even a combination of two targeted drugs (tyrosine kinase inhibitors and monoclonal antibodies). This strategy is based on tumor suppression using medicines, affecting a pool of primary, rapidly proliferating cells. The life cycle of these cells is determined by the activity of driver mutations. In general, the stability of the system is explained by many factors, including the activity of passenger mutations, the role of which is not taken into account in therapeutic protocols.
The personalized therapy strategy, which is today the main paradigm of antitumor treatment, takes into account the constantly changing landscape of the entire “tumor field”: the heterogeneity of clones of the primary solid tumor, the heterogeneity of circulating tumor cells, as well as the phenotypic and metabolic heterogeneity of “dormant” cancer cells in numerous metastatic niches of the bone marrow and visceral organs.

Caris Molecular Intelligence Services
The idea of ​​identifying individual predictive tumor markers that could predict the results of antitumor therapy arose in 2008, when Professor Daniel D. Von Hoff created a unique laboratory, Caris Molecular Intelligence Services (USA). Today, for molecular profiling of tumor tissues, a combination of methods is used in the laboratory - IHC, CISH, FISH, Next-Generation Sequencing, Sanger Sequencing, Pyro Sequencing, PCR (cobas ®), Fragment Analysis.
Over the course of several years, molecular tomography in this laboratory was performed on 65 thousand patients with more than 150 histopathological subtypes of malignant tumors. An integrated approach, based on the use of not one method (for example, only immunohistochemical), but a combination of molecular methods, makes it possible to identify individual predictive tumor markers for a particular patient and, based on this analysis, make decisions about personalized therapy.
The expression of some proteins (or gene amplification) requires the prescription of appropriate drugs, the expression of other proteins excludes the prescription of a particular drug. Thus, the expression of TOPO1 is preferable for the administration of irinotecan, the expression of RRM1 is for the administration of gemcitabine, the expression of MGMT is the basis for the administration of temozolamide or dacarbazine, the expression of TOPO2A with simultaneous amplification of HER2 allows for therapy with doxorubicin, liposomal doxorubicin and epirubicin.
To prescribe trastuzumab, in addition to detecting HER/2 expression/amplification to predict drug resistance, it is necessary to examine PTEN (IHC) and PIK3CA (NGS).
On the other hand, the expression of TS requires avoiding the use of fluorouracil, capecitabine, and pemetrexed; expression of SPARC (IHC), TLE3 (IHC), Pgp (IHC) requires avoiding docetaxel, paclitaxel, nab-paclitaxel.
With such a combination of tumor markers as ER (IHC), HER2 (IHC), HER2 (CISH), PIK3CA (NGS), everolimus and temsirolimus should not be prescribed.
The combination of modern biological imaging methods makes it possible to identify molecular predictive tumor markers for each known cytotoxic drug or targeted drug used today in clinical oncology. A similar approach, based first on molecular profiling of tumor tissue, identifying individual predictive tumor markers in it, and only then developing a treatment strategy plan, has received evidence in a number of clinical studies. One of them is the Bisgrove Study, which involved TGen, Scottsdale Healthcare and Caris Dx.
The design of this study was revolutionary. Given the fact that each tumor is individual, the authors of the study design refused to randomize patients into multiple groups based on the anatomical location of the tumor or only one immunohistochemical feature. IN this study There were no comparison groups - each patient acted as his own control.
A total of 66 patients from 9 cancer centers in the USA took part in the study: 27% - breast cancer, 17% - colorectal cancer, 8% - ovarian cancer, 48% - other localizations. Before inclusion in the study, all patients received therapy for metastatic cancer according to generally accepted standards - a total of 2 to 6 lines. After the last progression, therapy based on molecular profiling was continued.
The results of the study showed that the time to progression in patients with breast cancer increased by 44%, in colorectal cancer - by 36%, in ovarian cancer - by 20%, in other localizations - by 16%. It should be taken into account that all patients at the time of inclusion in the study developed secondary resistance to drug therapy, and generally accepted recommendations for their further treatment did not have. Thus, it is concluded that for aggressive, rare tumors, as well as progressive tumors with developed resistance, there is no alternative to molecular profiling and personalized treatment.

Change in clinical trial design
Separately, it should be noted that the paradigm of personalized therapy in oncology is actively changing the generally accepted design of clinical trials. Voices are increasingly heard that the results of clinical trials, based on randomization and stratification of patients into multiple populations and cohorts, should be reconsidered taking into account individual intra- and intertumoral heterogeneity. As a result, the design of modern clinical trials is becoming increasingly personalized.
Examples of such latest modern designs are Master protocols, Basket trials, Adaptive trial design and, finally, N-of-1 studies. The main idea of ​​the new designs is as follows. The study is sponsored by several pharmaceutical companies that have drugs with different targets and different molecular mechanisms of action for the treatment of cancer of this localization. Patients are included in the study after possibly complete molecular profiling of the tumor. By participating in one study, the patient, depending on the presence of the corresponding target proteins, can alternately receive the most effective drugs. During therapy, individual adaptation of the drug by dose can be carried out or a cocktailmix of a combination of various drugs, the need for which arose during treatment, can be used. Tumor progression and toxicity are not grounds for stopping treatment, but only for changing the type of therapy. The clinical decision is influenced by the results of molecular profiling of the tumor, which is carried out immediately after tumor progression or the next course of therapy. Thus, during the study, the patient may receive a completely different drug than was originally prescribed to him.
Finally, there are already trails for only one patient – ​​N-of-1 studies. This design is most consistent with the personalized therapy paradigm. This approach will make it possible in the near future to create individual preparations for cancer therapy.
However, even today, personalized therapy protocols based on molecular profiling of the tumor are widely used in the clinical practice of leading oncology centers in the USA, Europe, and Japan, allowing one to obtain clinical results of a new level. Such global centers include Memorial Sloan-Kettering Cancer Center, Center for Personalized Genetic Medicine at Harvard, Institute for Personalized Medicine at MD Anderson, Center for Personalized Health Care at the Ohio State University.
Since January 2014, molecular profiling of tumor tissues based on the Caris Molecular Intelligence Services platform has been available in Ukraine. This became possible thanks to AmaxaPharma, which is the official partner of Caris Life Sciences in the field of molecular profiling of tumor tissue in Eastern Europe. Since January 2014, thanks to this cooperation, dozens of patients with rare tumors for which there are no standard therapies, as well as cancer patients with primary and acquired chemoresistance, have already undergone molecular profiling by Molecular Intelligence in Ukraine. The first results were obtained that differ significantly from the results of the empirical approach.
The possibility of molecular profiling in our country has made it possible to come close to solving the problem of personalized cancer treatment.

Conclusion
Tumor heterogeneity has profound clinical implications for cancer patients. To make the right clinical decisions, it is necessary to have the most complete picture of the biology of the cancer cell and its microenvironment. Molecular profiling of primary tumor tissues, hematogenous metastases, circulating tumor cells and cells of the metastatic niche allows us to take a big step towards implementing a personalized cancer treatment program.

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