What kind of disease is cancer? Part 5

Molecular diagnostics

Atlas company blog, Geektimes

We are completing a series of articles about oncological diseases. 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 it occupies in oncology, you first need to understand the mechanisms that occur in the tumor.

Molecular processes in the tumor

Every healthy cell contains a DNA molecule from which it reads information about what form and specialty to get, what proteins and enzymes to produce, and most importantly, when to divide and die. Read more about how this happens in our first article.

Mutations in proto-oncogenes and suppressor genes responsible for cell division and death cause the cell to stop following instructions and synthesize proteins and enzymes incorrectly. Molecular processes are getting out of control: the cell is constantly dividing, refuses to die and accumulates genetic and epigenetic mutations. Therefore, malignant neoplasms are often called genome disease. 

Hundreds of thousands of mutations can occur in tumor cells, but only a few of them contribute to the growth, genetic diversity and development of the tumor. They are called driver (driver). The remaining mutations, "passenger" (passanger), by themselves do not make the cell malignant. 

Driver mutations create different cell populations, which ensures the diversity of the tumor. These populations or clones react differently to treatment: some of them are resistant and lead 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, which will lead to the resistance and development of the tumor.

A source: Cell. Illustrations: Michael Kowalski.

Molecular diagnostics

Driver mutations, changes in the number or structure of proteins are used as target biomarkers for which treatment is selected. The more targets are known, the more accurate the choice of potentially effective treatment regimens can be.

It is not easy to separate the driver mutations from the rest and determine the molecular profile of the tumor. For this purpose, the technology of sequencing, fluorescent in situ hybridization (FISH), microsatellite analysis and immunohistochemistry is used. 

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

With the help of FISH technology, areas of chromosomes on which a certain gene is located are tinted. Two connected multi–colored dots are a chimeric or fused gene: when, as a result of chromosome rearrangement, sections of different genes are joined together. This may lead to the oncogene falling under the influence of 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 proto-oncogene ALK is activated under the influence of its "partner" in restructuring, which leads to uncontrolled cell division. An oncologist, taking into account the restructuring, can apply a drug that will be directed against the activated product of the ALK gene (Krizotinib).

Fluorescent in situ hybridization (FISH).

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

All these studies are included in the new product of the Atlas biomedical holding – Solo test. With the help of such a 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 specialists are investigating up to 450 genes and biomarkers to assess how a tumor can respond to the use of more targeted drugs for the treatment of cancer. For some of them, the biomarker analysis is dictated by the manufacturer. For others, they use data from clinical studies and recommendations from international communities of oncologists.

In addition to selecting targets for targeted therapy, molecular profiling helps to detect mutations that, on the contrary, make the tumor resistant to a certain treatment, or genetic features that are associated with increased toxicity and require individual selection of the dose of the drug.

Biopsy material or paraffinized blocks of postoperative material are used for research. 

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

• A rare type of tumor;
• Tumors with an unidentified primary focus (it is not known where the tumor that metastasized initially appeared);
• Those cases when a choice of several options for the use of 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 consult oncologists or patients and suggest whether a test is needed in this case.

The diagnostic result also includes recommendations for clinical trials with a suitable drug being tested. The patient has the opportunity to take part in them. 

Precision medicine and clinical research

Usually in medical practice, general strategies are used to treat patients with a certain diagnosis. One strategy is used for small cell lung cancer, and another for non–small cell lung cancer. For oncological diseases, this method is not always suitable. Due to differences at the molecular level, even with the same type of tumor, patients may receive ineffective or unnecessary treatment.

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

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

There are more and more targeted drugs, and they have two main limitations: most of the molecular-directed agents provide only partial suppression of signaling pathways and many of them are too toxic to be used in combination.

Imagine that you are an architect of Moscow. You are facing a difficult task – to solve the problem with traffic jams during rush hour by building one bridge. Molecular mechanisms can be compared to the movement of machines, and the bridge is the main drug that should solve the main problem. It seems that several drugs (a series of bridges) aimed at major molecular disorders can solve this problem. But the toxicity of drugs increases at the same time and can be unpredictable. 

We have begun to better understand the molecular processes of malignant tumors, but the current methods of introducing precision oncology into clinical practice are lagging 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 method for a biomarker called high microsattellite instability (MSI-H) or mismatch repair defect (dMMR).

Molecular disorders differ not only in different patients, but also within the same tumor. Heterogeneity is a big problem in oncology, for which the design of the Umbrella study was developed. For the Umbrella method, patients are first selected by the type of malignant neoplasms, and then genetic mutations are taken into account.

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

Clinical example

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

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

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

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

• Drugs of the BRAF inhibitor class (Vemurafenib) can be potentially effective, moreover, the presence of an NRAS mutation can serve as an additional reason for prescribing a double blockade of the signaling cascade - a combination with MEK inhibitors (Trametinib).
• Despite the fact that there is no approved therapy aimed directly at the NRAS oncogene, it is known that mutations in it increase the likelihood of successful treatment with the appointment of immunotherapy (Ipilimumab and Pembrolizumab).
• A hereditary genetic variant in the TPMT gene indicates an increased individual toxicity of Cisplatin, which requires dose adjustment when prescribing platinum-containing therapy regimens.

Thus, the doctor gets the opportunity to navigate among possible treatment options, starting not only from the clinical parameters of the patient, but also taking into account the molecular features of the tumor. 

Molecular diagnostics is not a panacea for all oncological diseases. But this is an important tool for an oncologist, which allows you to approach the treatment of malignant tumors from a new angle.

Portal "Eternal youth" http://vechnayamolodost.ru  02.10.2017