Ancha Baranova

Genotoxic stresses, including irradiation, lead to the apoptosis of damaged cells and the release of DNA fragments into circulation. Both α-tocopherol acetate and ascorbic acid possess antioxidant and radioprotective properties. Interestingly, depending on a particular experimental system, the treatment with vitamins may demonstrate either apoptosis-promoting or apoptosis-suppressing effects. Adult Wistar male rats received total body irradiation with 2-100 Gy doses, while non-irradiated rats served as controls. Oral gavages with vitamins were administered either 10 min or 1 h before irradiation. Control groups were similarly treated with water. Blood samples were collected at 5 h post irradiation. The levels and the composition of circulating DNA were profiled. Chromosomal aberrations were assessed 24 h after irradiation. A substantial dose-dependent increase in circulating low-molecular weight (LMW) DNA levels was observed after whole body irradiation. An order-of-magnitude increa...

The purpose of this study was to investigate whether low-level light therapy (LLLT) was capable of modulating expression of ultraviolet (UV) light-responsive genes in vivo. The effects of 670 nm light-emitting diode (LED) array irradiation were investigated in a hairless SHK-1 mouse epidermis model. Mice were given a single dose of UVA/UVB light, or three doses of red light (670 nm @ 8 mW/cm(2) x 312 sec, 2.5 J/cm(2) per session) spread over 24 h along with combinations of pre- and post-UV treatment with red light. Levels of 14 UV-responsive mRNAs were quantified 24 h after UV irradiation by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). The transcription of mRNAs encoding for cluster of differentiation molecule 11b (CD11b) (p < 0.05) and interferon (IFN)-γ (p < 0.012) increased after irradiation with red light alone, whereas expression level of cyclooxygenase (COX)-2 (p < 0.02) was downregulated. Genes unresponsive to UV did not change th...

High-throughput technologies became common tools to decipher genome-wide changes of gene expression (GE) patterns. Functional analysis of GE patterns is a daunting task as it requires often recourse to the public repositories of biological knowledge. On the other hand, in many cases researcher's inquiry can be served by a comprehensive glimpse. The KEGG PATHWAY database is a compilation of manually verified maps of biological interactions represented by the complete set of pathways related to signal transduction and other cellular processes. Rapid mapping of the differentially expressed genes to the KEGG pathways may provide an idea about the functional relevance of the gene lists corresponding to the high-throughput expression data. Here we present a web based graphic tool KEGG Pathway Painter (KPP). KPP paints pathways from the KEGG database using large sets of the candidate genes accompanied by "overexpressed" or "underexpressed" marks, for example, those ...

We created an algorithm that allows high-throughput mapping of sense-antisense (SA) pairs of transcripts. By this method we mapped approximately 32 000 SA pairs of human mRNAs. Collected SA pairs were divided into three groups: SA pairs based on two or more UniGene clusters (17% of all sense-antisense pairs), SA pairs based on ESTs that belong to the same UniGene cluster (42%), and SA pairs formed by UniGene cluster and non-unique unclustered transcripts (41%). To study expression patterns of natural SA pairs we created a software application "Antisense Cluster Filter". We retrieved tissue expression data for all the transcripts forming identified SA pairs, including clustered and unclustered ones. After that, we selected 108 SA pairs represented by transcripts differentially regulated in human tumors. For each of these SA pairs one of the transcripts was expressed only in tumors, another one was expressed both in non-malignant and malignant tissues. Indicated SA pairs may...

Deletions in the region located between the STS markers D13S1168 and D13S25 on chromosome 13 are the most frequent genomic changes in patients with B-cell chronic lymphocytic leukemia (B-CLL). After sequencing of this region, two novel candidate genes were identified: C13orf1 (chromosome 13 open reading frame 1) and PLCC (putative large CLL candidate). Analysis of the repeat distribution revealed two subregions differing in composition of repetitious DNA and gene organization. The interval D13S1168-D13S319 contains 131 Alu repeats accounting for 24.8% of its length, whereas the interval GCT16C05-D13S25, which is no more than 180 kb away from the former one is extremely poor in Alu repeats (4.1% of the total length). Both intervals contain almost the same amount of the LINE-type repeats L1 and L2 (20.3 and 21.24%, respectively). In the chromosomal region studied, 29 Alu repeats were found to belong to the evolutionary young subfamily Y, which is still capable of amplifying. A conside...

To understand human pathology at the system level, one must examine the complex milieu of molecular interactions between various cells within human body, rather than the characteristics of isolated cell or cultured cell. However, all over the human body an understanding of the pathophysiology of particular tissues has lagged behind the insights in general biological processes. A “high-throughput revolution” unfolding

In the summer of 2013, distinguished global representatives of proteome science gathered to discuss the futuristic visions of the chromosome-centric human proteome project (C-HPP) (Cochairs: Y. K. Paik, G. Omenn; hosted by A. Archakov, Institute of Biomedical Chemistry, Russia) that was broadcast to the annual Federation of European Biochemical Societies Congress (St. Petersburg, Russia, July 10-11, 2013). Technology breakthroughs presented included a new ultra-sensitive Tribrid mass-spectrometer from Thermo and SOMAmers-Slow Off-rate Modified Aptamers (SOMAlogic, USA), a new type of protein capture reagents. Professor Archakov's group introduced the "rectangle" concept of proteome size as a product of proteome width and depth. The discussion on proteome width culminated with the introduction of digital biomarkers-low-copied aberrant proteins that differ from their typical forms by PTMs, alternative splicing, or single amino acid polymorphisms. The aberrant proteoforms, a complement to whole-genome proteomic surveys, were presented as an ultimate goal for the proteomic community.

The search for human genes specifically expressed in different tumours is one of the major challenges for modern tumour biology. A number of experimental methods are designed for tumour-specific gene search. Most of them are based on time-consuming and expensive experimental protocols (numerous modifications of the diffrential display approach, cDNA microarrays, serial analysis of gene expression). Growing number of ESTs in publicly available databases provides a strong basis for the development of computer-based procedures for the subtraction of different EST pools instead of traditional experimental approaches used to compare expression profiles. A computer- based differential display (CDD) is an analogue of experimental differential displays that compares expression patterns in a particular tissue versus any other tissue source. In our previous works we pioneered global approach to CDD by subtracting all available tumour cDNA libraries against all available normal libraries inste...

Works on chromosome 13 mapping supported by the Russian program Human Genome are reviewed. Emphasis is placed on studies of region 13q14.3, which is often lost in some human tumors and potentially contains tumor suppressor genes (TSG). A strategy of TSG search is described. As the resolution of genome analysis improved, a minimal overlap of genetic loss in B-cell chronic lymphocytic leukemia (B-CLL) was established for chromosome 13. A map of expressed sequences was constructed for the region containing the overlap, and candidate TSG of chromosome 13q14 were identified. The candidate genes were analyzed both structurally and functionally, and their possible role in tumorigenesis was considered. Assuming haploinsufficiency as a genetic mechanism controlling B-CLL, a new strategy was proposed for mutation screening aimed at identifying potential TSG of region 13q14.

Using computer-aided genomic methods, a complete map of the expressed sequence tags (EST) located in the human genome region 13q14.3 between the STS markers, D13S810 and D13S1469, was constructed. A total of 62 EST clusters were formed, of which 12 clusters corresponded to the already known human genes, 4 clusters represented pseudogenes, and 10 clusters were new human genes. The

Chronic hepatitis C (CH-C) is among the most common causes of chronic liver disease. Approximately 50% of patients with CH-C treated with pegylated interferon-α and ribavirin (PEG-IFN-α + RBV) achieve a sustained virological response (SVR). Several factors such as genotype 1, African American (AA) race, obesity and the absence of an early virological response (EVR) are associated with low SVR. This study elucidates molecular pathways deregulated in patients with CH-C with negative predictors of response to antiviral therapy. Sixty-eight patients with CH-C who underwent a full course of treatment with PEG-IFN-α + RBV were included in the study. Pretreatment blood samples were collected in PAXgene™ RNA tubes. EVR, complete EVR (cEVR), and SVR rates were 76%, 57% and 41%, respectively. Total RNA was extracted from pretreatment peripheral blood mononuclear cells, quantified and used for one-step RT-PCR to profile 154 mRNAs. The expression of mRNAs was normalized with six 'housekeeping' genes. Differentially expressed genes were separated into up and downregulated gene lists according to the presence or absence of a risk factor and subjected to KEGG Pathway Painter which allows high-throughput visualization of the pathway-specific changes in expression profiles. The genes were consolidated into the networks associated with known predictors of response. Before treatment, various genes associated with core components of the JAK/STAT pathway were activated in the cohorts least likely to achieve SVR. Genes related to focal adhesion and TGF-β pathways were activated in some patients with negative predictors of response. Pathway-centred analysis of gene expression profiles from treated patients with CH-C points to the Janus kinase-signal transducers and activators of transcription signalling cascade as the major pathogenetic component responsible for not achieving SVR. In addition, focal adhesion and TGF-β pathways are associated with some predictors of response.

Cervical cancers are characterized by the persistence of human papilloma virus (HPV) genome that is found in tissue samples starting from the early stages of tumor progression. Just like in other tumors, the activation of telomerase was observed in cervical carcinomas, but information about its expression was controversial. The aim of this study is to find possible correlations between the presence of HPV sequences, activity of telomerase and expression of different spliced forms of hTERT RNA in cervical intraepithelial neoplasias (CIN). The results show that HPV DNA is present in 60% of normal tissue adjacent to CIN lesions and up to 84% in CIN samples. Telomerase activity was found in 28% of adjacent normal tissue and in 68% of CIN II-III. hTERT RNA that encodes an active enzyme was present almost in all CIN samples. Variations in levels of telomerase activity are possibly not regulated by the splicing forms of hTERT mRNA with deletions.