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DIAGNOSTIC POTENTIAL OF CELL-FREE DNA AS A LIQUID BIOPSY MARKER
стр.5-12
Cell-free DNA (cfDNA) was discovered in human blood plasma as early as the middle of the 20th century, but it was not until a few decades ago that knowledge of human genome and epigenome in health and pathology became sufficient and methods of nucleic acid analysis became more advanced to encourage active research of the diagnostic potential of cfDNA. The use of cfDNA as a diagnostic biomarker is conventionally referred to as liquid biopsy. The following review tells a story of cfDNA discovery, summarizes contemporary views on cfDNA sources inside the body and touches upon possible prognostic and diagnostic applications of cfDNA analysis in medicine, specifically in cancer and prenatal screening, prediction of implant failure and sepsis development.
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THE USE OF WILD-TYPE BLOCKING ALLELE-SPECIFIC REAL-TIME POLYMERASE CHAIN REACTION FOR THE ANALYSIS OF SOMATIC MUTATIONS IN RAS GENES OF CIRCULATING FREE DNA ISOLATED FROM THE BLOOD PLASMA OF PATIENTS WITH COLORECTAL CANCER
стр.13-18
Telysheva E. N., Snigireva G. P.
Screening for cell-free DNA usually referred to as liquid biopsy holds great promise in cancer diagnosis and treatment. This article presents the results of the analysis of somatic tumor-specific mutations in circulating free DNA (cfDNA) isolated from the blood plasma of patients with stages I-IV colorectal cancer, based on the use of wild-type blocking allele-specific real-time polymerase chain reaction. This technique was specially designed for the analysis of biological specimens containing small amounts of mutant circulating tumor DNA. The study included 46 patients (18 female and 28 male participants) between 48 and 86 years of age (mean age was 67.1 ± 8.8 years). All patients underwent surgical treatment (radical surgery was performed on 85 % of the participants). Besides the molecular genetic analysis of cfDNA isolated from the blood plasma, standard histological staining was performed. Patients’ blood samples were collected before the surgery and on day 5 after it to test for KRAS and BRAF mutations. The applied PCR technique proved to be effective in detecting mutations in the RAS genes in stages II-IV of the disease, its sensitivity threshold being 0.1 %. Analysis of cfDNA before and after surgery may provide additional information on the surgical treatment outcome, development of new metastases, or presence of those previously overlooked. Wild-type blocking allele-specific real-time PCR is awaiting further validation in different clinical situations.
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MODIFIED MULTIPLEX REAL-TIME PCR FOR QUANTIFICATION OF DIFFERENTLY SIZED CELL-FREE DNA FRAGMENTS
стр.19-23
Sokolova E. A., Khlistun I. V., Kushlinsky D. N.
There is evidence that size distribution of cell-free DNA (cfDNA) fragments can be diagnostically relevant. The present work describes a multiplex quantitative real-time polymerase chain reaction technique modified and validated by the authors to study the degree of cfDNA fragmentation in blood plasma. Based on the detection of Alu and hLINE-1 repeats, this technique employs fluorescent probes. We selected suitable primers and probes, optimized PCR conditions and estimated the dynamic range and sensitivity threshold of the assay. The modified PCR had a dynamic range of 6 logs, its efficiency being over 90 %. We demonstrated that cfDNA fragmentation index did not differ significantly between healthy women (n = 16) and women with stage III-IV ovarian cancer (n = 14). Therefore, further research on a larger sample is needed using electrophoretic cfDNA fractionation.
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ANALYSIS OF VEGF CIRCULATING RNA ISOFORMS IN PATIENTS WITH BREAST CANCER
стр.24-27
Tyschik E. A., Kometova V. V., Rodionov V. V., Rebrikov D. V.
The present study aims to estimate and compare the levels of cell-free circulating RNAs of three interleukins IL-6, IL-8, and IL-18 and three splice variants of the vascular endothelial growth factor (VEGF), namely 121, 165 and 189, in blood plasma of patients with stage I / II breast cancer and healthy controls. The study reveals that patients with breast cancer have significantly elevated levels of circulating VEGF121 and VEGF165 RNAs, so far unreported in the literature. We also confirm that levels of circulating IL-8 and IL-18 RNAs are considerably increased in breast cancer patients.
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SIGNIFICANCE OF MIR-146A QUANTIFICATION IN HUMAN BLOOD PLASMA FOR THE DIAGNOSIS OF COLORECTAL CANCER
стр.28-33
Shirshova A. N., Shamovskaya D. A., Boyarskikh U. A., Apalko S. V., Leskov L. S., Sokolov A. V., Kovalenko S. A., Scherbak S. G., Pikalov I. V., Kel A. E., Filipenko M. L.
Colorectal cancer (CRC) is one of the most common cancer types in the world. Timely diagnosis of CRC and adenomatous polyps aided by effective screening techniques can considerably reduce mortality from this disease. MicroRNAs constitute a new class of promising biomarkers for a range of human diseases including cancer. The following article assesses the diagnostic significance of miR-146a concentrations in the blood plasma of patients with colorectal cancer. The main group included patients with stages I to III colorectal cancer (n = 102); the control group comprised patients with chronic colitis, nonspecific ulcerative colitis and Crohn’s disease (n = 58) and healthy individuals (n = 42). MicroRNA levels were quantified by reverse-transcription real-time PCR, revealing significantly higher miR-146a concentrations in the samples of patients with CRC than in the controls (p < 0.0001). The optimal diagnostic sensitivity determined by ROC analysis was 47.3 %, specificity was 91.5 %, with AUC = 0.79 ± 0.018. Our findings demonstrate that the studied approach does not have sufficient specificity, but still suggest that miR-146a can be included into screening tests based on quantification of other microRNAs with improved specificity.
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COHEN SYNDROME IN FAMILY MEMBERS: A CASE REPORT
стр.34-37
Levchenko O. A., Zinchenko R. A., Lavrov A. V.
Cohen syndrome is a rare autosomal-recessive disorder characterized by intellectual disability, myopia, hypotonia, and skeletal malformations. Its clinical diagnosis is impeded by marked inter- and intrafamilial phenotypic variability. Gene VPS13B that carries disease-associated mutations has 62 exons, making Sanger sequencing of the entire gene unsuitable for routine clinical use due to high costs. In this work we report a case of Cohen syndrome in a brother and sister born to a mixed Abazin-Circassian marriage and diagnosed with moderate mental retardation. Both patients had psychomotor retardation, were unable to study at school, and never learned to read, write and count. Although the patients shared a few nonspecific phenotypic characteristics, phenotypic differences made it impossible to arrive at a clear diagnosis. Therefore, whole exome sequencing was performed revealing the single nucleotide variant с.7603C>T that results in the premature stop codon R2535* in VPS13B. This mutation was found in the mother, the affected sibs and one of the two other healthy sibs. The second mutation remained undetected. Considering the identified mutation and the analyzed phenotypic traits, we concluded Cohen syndrome in both patients.
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DETERMINING THE FREQUENCY OF MUTATIONS IN MOSCOW REGION RESIDENTS WITH PHENYLKETONURIA USING A COMBINATION OF REAL-TIME PCR AND NEXT-GENERATION SEQUENCING
стр.38-44
Nikiforova A. I., Abramov D. D., Kadochnikova V. V., Zobkova G. U., Ogurtsova K. A., Brjuhanova N. O., Shestopalova E. A., Kochetkova T. O., Shubina E. S., Donnikov A. E., Trofimov D. Yu.
The present study aimed to determine frequencies of mutations in the phenylalanine hydroxylase gene () in unrelated children (n = 71) diagnosed with phenylketonuria, who presented to Morozovskaya Children’s City Clinical hospital (Moscow) over the period from 2015 to 2016. The patients were tested for the most common mutations using the original real-time PCR-based technique for the identification of nucleotide variants; additionally, next generation sequencing (NGS) was performed on the unidentified genotypes. The original PCR-based technique allowed us to effectively identify 83 % of the pathogenic allelic variants in the sample. Using the combination approach (real-time PCR + NGS), we found mutations in both alleles of in 66 of total 71 patients. Altogether, 26 pathogenic mutations were identified, the most common being p.R408W (47.9 %) and p.R261Q (9.9 %). Frequencies of mutations common for the Russian population, such as IVS10nt546, IVS12+1G>A, p.R158Q, p.Y414C, and IVS4+5G>T, ranged from 4.2 to 2.8 %. Half of the identified variants accounted for the total frequency of < 10 %. Sequencing of revealed a few functional mutations previously unreported for Moscow region residents, including p.D222Terfs, p.R111Ter, p.F161S, p.G188D, p.R270K, p.L311P, p.F55L, p.F55Leufs, IVS1+5G>T, and IVS8-7A>G. It could be reasonable to include mutations p.D222Terfs and p.R111Ter (carrier frequency of 2.1 %) in PCR testing panels. The data obtained in our study can also be used in the development of genetic tests for phenylketonuria.
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ASSOCIATION OF POLYMORPHIC VARIANTS OF AND WITH HEART RATE VARIABILITY IN ATHLETES OF THE REPUBLIC OF KARELIA
стр.45-52
Kolomeichuk S. N., Alekseev R. V., Putilov A. A., Meigal A. Yu.
This work aims to study distribution of allele frequencies of the and genes coding for the angiotensin-converting enzyme and the bradykinin receptor β2, respectively, in athletes specializing in different sports and to establish the associations between the studied genotypes and heart rate variability. The study included 75 male athletes. Polymorphisms of and (I/D and +9/-9, respectively) were studied by PCR. A significant difference was revealed in the -9/-9 genotype frequency between the studied groups of athletes. Parasympathetic nerve activity prevailed in the athletes with the I allele of the gene. Time-domain parameters of heart rate variability had low values in the carriers of the D/D genotype. In the athletes with the I/I genotype the time-domain parameters differed from those typical for the I/D and D/D genotype carriers. Participants homozygous for -9 had the lowest heart rate in the studied sample, implying an increased contribution of parasympathetic activity to heart rate regulation. The -9 allele of was found to be associated with the minimal R - R interval between consecutive hear beats. We conclude that polymorphisms I/D of and +9/-9 of can indicate individual patterns of heart rate regulation in athletes from the Republic of Karelia.
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IDENTIFICATION OF THE ATYPICAL BACTERIAL STRAIN THAT CAUSED BRAIN ABSCESS IN THE PATIENT USING SANGER SEQUENCING OF THE 16S RRNA GENE FROM THE DNA EXTRACTED FROM A PUS SAMPLE
стр.53-56
Gordukova M. A., Divilina Yu. V., Mishukova O. V., Galeeva E. V., Prodeus A. P., Filipenko M. L.
In this article we present a clinical case of brain abscess in a girl aged 14 years and 11 months caused by a pathogen that could not be identified by routine microbiological testing. Before admission and during her stay in the hospital, the teenager did not have fever. Diagnosis and treatment were impeded by allergic responses to a wide range of antibiotics. The patient underwent three surgical interventions. Pus culture was performed 4 times, showing no growth. A PCR assay was run twice, but both times the results came out negative. Therefore, a decision was made to amplify and Sanger-sequence the 16S rRNA gene from the DNA extracted from patient’s pus. BLAST showed a 99 % homology of the obtained nucleotide sequence to the sequence of the 16S rRNA gene of (strain ChDC B589, KF733728.1) which had been previously shown to play a role in brain abscess development. Treatment against the pathogen was started before sequencing results were available. The patient responded positively, the symptoms were alleviated and the condition improved. Thus, we conclude that in some cases sequencing may be the only diagnostic technique capable of identifying the pathogen.
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FEASIBILITY OF USING 6 MV PHOTON BEAMS IN CONTRAST-ENHANCED RADIOTHERAPY
стр.57-61
Vorobyeva E. S., Lipengolts A. A., Cherepanov A. A., Grigorieva E. Yu., Nechkina I. N., Kalygina N. S., Sokovikov A. V., Kulakov V. N., Sheino I. N.
Contrast-enhanced radiotherapy (CERT) is a type of radiation therapy used to enhance the radiation dose absorbed by the tumor while sparing surrounding healthy tissues. The present study aims to assess feasibility of using 6 MV photons to increase radiation absorption in CERT. The dose absorbed by iodinated water was directly measured by ferrosulphate dosimetry. Concentrations of iodine (a dose-enhancing agent) ranged from 2.5 to 50 mg/ml. Solutions were exposed to 5 Gy radiation generated by the clinical linear accelerator SL75-5MT (Russia). The radiation dose applied did not account for increased absorbance due to the presence of iodine atoms. No reliable increase in the absorbed dose was observed for iodine concentrations ranging from 2.5 to 20 mg/ml. For 50 mg/ml concentrations the absorbed dose increased by 13% ± 5 % (p < 0.05). Normally, dose-enhancing concentrations observed in CERT studies range from 2.5 to 15 mg/ml, therefore, as demonstrated by our findings, employing 6 MV photon energy spectra in order to reach a therapeutically significant effect is unreasonable.
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