CrossHub: a tool for multi-way analysis of The Cancer Genome Atlas (TCGA) in the context of gene expression regulation mechanisms.
Nucleic Acids Research 44(7):e62 (2016)
The contribution of different mechanisms to the regulation of gene expression varies for different tissues and tumors. Complementation of predicted mRNA-miRNA and gene-transcription factor (TF) relationships with the results of expression correlation analyses derived for specific tumor types out...
Identification, Expression Analysis, and Target Prediction of Flax Genotroph MicroRNAs Under Normal and Nutrient Stress Conditions.
Frontiers in Plant Science 7:399 (2016)
Cultivated flax (Linum usitatissimum L.) is an important plant valuable for industry. Some flax lines can undergo heritable phenotypic and genotypic changes (LIS-1 insertion being the most common) in response to nutrient stress and are called plastic lines. Offspring of plastic lines, which stab...
The Dysregulation of Polyamine Metabolism in Colorectal Cancer Is Associated with Overexpression of c-Myc and C/EBPβ rather than Enterotoxigenic Bacteroides fragilis Infection.
Oxidative Medicine & Cellular Longevity 2016:2353560 (2016)
Colorectal cancer is one of the most common cancers in the world. It is well known that the chronic inflammation can promote the progression of colorectal cancer (CRC). Recently, a number of studies revealed a potential association between colorectal inflammation, cancer progression, and infecti...
Microbial Community Structure of Activated Sludge in Treatment Plants with Different Wastewater Compositions.
Frontiers in Microbiology 7:90 (2016)
Activated sludge (AS) plays a crucial role in the treatment of domestic and industrial wastewater. AS is a biocenosis of microorganisms capable of degrading various pollutants, including organic compounds, toxicants, and xenobiotics. We performed 16S rRNA gene sequencing of AS and incoming sewag...
Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L.
Biochimie 109:36 (2015)
Effective fertilizer application is necessary to increase crop yields and reduce risk of plant overdosing. It is known that expression level of microRNAs (miRNAs) alters in plants under different nutrient concentrations in soil. The aim of our study was to identify and characterize miRNAs with e...
Tumor Suppressor Function of the SEMA3B Gene in Human Lung and Renal Cancers.
PLoS ONE 10(5):e0123369 (2015)
The SEMA3B gene is located in the 3p21.3 LUCA region, which is frequently affected in different types of cancer. The objective of our study was to expand our knowledge of the SEMA3B gene as a tumor suppressor and the mechanisms of its inactivation. In this study, several experimental approaches ...
Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.
Disease Markers 2015:241301 (2015)
A significant need for reliable and accurate cancer diagnostics and prognosis compels the search for novel biomarkers that would be able to discriminate between indolent and aggressive tumors at the early stages of disease. The aim of this work was identification of potential diagnostic biomarke...
Tissue-specific alternative splicing analysis reveals the diversity of chromosome 18 transcriptome.
Journal of Proteome Research 13(1):173 (2014)
The Chromosome-centric Human Proteome Project (C-HPP) is aimed to identify the variety of protein products and transcripts of the number of chromosomes. The Russian part of C-HPP is devoted to the study of the human chromosome 18. Using widely accepted Tophat and SpliceGrapher, a tool for accura...
Epigenetic alterations of chromosome 3 revealed by NotI-microarrays in clear cell renal cell carcinoma.
BioMed Research International 2014:735292 (2014)
This study aimed to clarify epigenetic and genetic alterations that occur during renal carcinogenesis. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI-clones associated with 188 genes for hybridization with 23 paired normal/tumor DNA samples of primary cle...
Targeting VDAC-bound hexokinase II: a promising approach for concomitant anti-cancer therapy.
Expert Opinion on Therapeutic Targets 17(10):1221 (2013)
Enhancement of glucose metabolism and repression of oxidative phosphorylation followed by the Warburg effect is the common hallmark of cancer cells. Hexokinase II (HKII) plays a dual role - first, HKII up-regulation results in increased glycolysis rates. Second, association of VDAC and HKII cont...
Deregulation of glycolysis in cancer: glyceraldehyde-3-phosphate dehydrogenase as a therapeutic target.
Expert Opinion on Therapeutic Targets 17(6):681 (2013)
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a key glycolytic enzyme, but recent studies have shown its non-glycolytic role in cell death, survival mechanisms and diseases. Increase in glycolysis, in particular overexpression of GAPDH, has been considered an important feature of many type...
Novel tumor suppressor candidates on chromosome 3 revealed by NotI-microarrays in cervical cancer.
Epigenetics 8(4):409 (2013)
Genetic and epigenetic alterations in cervical carcinomas were investigated using NotI-microarrays containing 180 cloned sequences flanking all NotI-sites associated with genes on chromosome 3. In total, 48 paired normal/tumor DNA samples, specifically enriched in NotI-sites, were hybridized to ...
Genetic and epigenetic analysis of non-small cell lung cancer with NotI-microarrays.
Epigenetics 7(5):502 (2012)
This study aimed to clarify genetic and epigenetic alterations that occur during lung carcinogenesis and to design perspective sets of newly identified biomarkers. The original method includes chromosome 3 specific NotI-microarrays containing 180 NotI clones associated with genes for hybridizati...
Enteric alpha defensins in norm and pathology.
Annals of Clinical Microbiology and Antimicrobials 11:1 (2012)
Microbes living in the mammalian gut exist in constant contact with immunity system that prevents infection and maintains homeostasis. Enteric alpha defensins play an important role in regulation of bacterial colonization of the gut, as well as in activation of pro- and anti-inflammatory respon...
NotI microarrays: novel epigenetic markers for early detection and prognosis of high grade serous ovarian cancer.
International Journal of Molecular Sciences 13(10):13352 (2012)
Chromosome 3-specific NotI microarray (NMA) containing 180 clones with 188 genes was used in the study to analyze 18 high grade serous ovarian cancer (HGSOC) samples and 7 benign ovarian tumors. We aimed to find novel methylation-dependent biomarkers for early detection and prognosis of HGSOC. T...
Differential expression of CHL1 gene during development of major human cancers.
PLoS ONE 6(3):e15612 (2011)
CHL1 gene (also known as CALL) on 3p26.3 encodes a one-pass trans-membrane cell adhesion molecule (CAM). Previously CAMs of this type, including L1, were shown to be involved in cancer growth and metastasis.
We used Clontech Cancer Profiling Arrays (19 different types of cancers, 395 samples) to...
Simultaneous down-regulation of tumor suppressor genes RBSP3/CTDSPL, NPRL2/G21 and RASSF1A in primary non-small cell lung cancer.
BMC Cancer 10:75 (2010)
The short arm of human chromosome 3 is involved in the development of many cancers including lung cancer. Three bona fide lung cancer tumor suppressor genes namely RBSP3 (AP20 region),NPRL2 and RASSF1A (LUCA region) were identified in the 3p21.3 region. We have shown previously that homozygous d...