Changes in the number of copies of genetic loci in gastric cancer

Vodolazhsky, D. I.; Кутилин, Денис С.; Gudueva, E. N.

doi:10.1134/s0026893315040093

Cited by 8 publications

(5 citation statements)

References 29 publications

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“…At the initial stage of the model experiment, all explants (Vitis vinifera, 'Chardonnay' variety) were cultivated on a Murashige and Skoog (MS) basal medium supplemented with 30 g/l sucrose, 0.2 mg/l indole-3-acetic acid (IAA), and 2 mg/l 6-benzylaminopurine (6-BAP) [8].…”

Section: Methodsmentioning

confidence: 99%

“…Plants from all experimental groups were combined and cultivated at a temperature of 23 ± 10°C with a 16-hour photoperiod and illumination provided by 40-watt cold white fluorescent lamps with an intensity of 105-115 µmol PPFD/m²/s (PPFD = photosynthetic photon flux density) for 30 days. Leaf samples (5-10 mg) were randomly selected from each group of plants (control and with ceftriaxone concentrations of 250 and 1000 mg/l) for subsequent total DNA extraction [8].…”

Section: Methodsmentioning

confidence: 99%

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The impact of Ceftriaxone on Relative Copy Numbers of Mitochondrial and Chloroplast DNA in Grapevine Leaves

Vodolazhsky,

Kryukov

2023

BIO Web of Conferences

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The cultivation of micropropagated grapevine plants in vitro is currently undergoing improvements in existing methods and the development of new cultivation techniques due to the problem of bacterial contamination caused by multidrug-resistant microorganisms. Explants (Vitis vinifera L., ‘Chardonnay’ variety) were cultured on Murashige-Skoog basal medium supplemented with different concentrations of ceftriaxone: 0 mg/L, 250 mg/L, and 1000 mg/L. After 30 days, morphometric characteristics of the micropropagated plants and relative copy numbers of mitochondrial and chloroplast DNA were evaluated. Leaf samples (5-10 mg) were randomly selected from each plant group for subsequent total DNA extraction. Quantitative RT-PCR was performed using LightCycler 480 SYBR Green I Master Mix (LifeScience, Roche) and analyzed with a LightCycler 96 automated analyzer (Roche Life Science). The relative copy numbers of NAD1 (mitochondrial DNA) and rps16 (chloroplast DNA) genes were determined using the GAPDH gene (chromosomal DNA) as the reference. The 2-DCt and 2-DDCt algorithms were used for quantitative assessment. Ceftriaxone at concentrations of 250 and 1000 mg/l reduces the relative number of copies of chloroplast and mitochondrial DNA, which indicates the suppression of photosynthesis and oxidative phosphorylation in grape microplants. The experimental scheme developed by us can be successfully used as a test system for assessing the degree of influence of various biogenic and abiogenic factors on plant objects in order to optimize their cultivation.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

The impact of Ceftriaxone on Relative Copy Numbers of Mitochondrial and Chloroplast DNA in Grapevine Leaves

Vodolazhsky,

Kryukov

2023

BIO Web of Conferences

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“…Copy number variation (CNV) is a type of structural variation, in which there is an increase or decrease in the number of copies of a certain gene with subsequent high or low expression of the corresponding protein or noncoding RNA [ 14 ]. CNV can affect several signaling pathways as those controlling cell proliferation and apoptosis as sex determining region Y-box 2 ( SOX2 ) gene or oxidative phosphorylation as hypervariable region 2 gene ( HV2 ) [ 15 ]. Dysregulation of SOX2 expression has been linked to cancer pathogenesis through its role in induction of cellular proliferation mediated by epidermal growth factor receptor ( EGFR) activation, epithelial-to-mesenchymal transition (EMT), and resistance to apoptosis mediated by B-cell lymphoma 2 like1 (BCL2L1) induced survival signaling [ 16 ].…”

Section: Introductionmentioning

confidence: 99%

HOXA9 gene promotor methylation and copy number variation of SOX2 and HV2 genes in cell free DNA: A potential diagnostic panel for non-small cell lung cancer

et al. 2023

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Background Most cases of lung cancer are diagnosed at advanced stage. Detection of genetic and epigenetic markers in cell-free DNA (cfDNA) is a promising tool for the diagnosis of lung cancer at an early stage. The aim of this study was to identify non-invasive diagnostic markers in cell free DNA (cfDNA) for non-small cell lung cancer (NSCLC) as it is the most common type of lung cancer. Methods We investigated the cfDNA HOXA9 gene promotor methylation by pyrosequencing. Copy number variation of SOX2 and HV2 genes were detected by real-time PCR in cfDNA extracted from plasma samples of 25 newly diagnosed NSCLC patients and 25 age and sex matched controls. Results Methylation level of HOXA9 was significantly higher in NSCLC patients than controls (p > 0.001). SOX2 showed significantly higher CNV and HV2 showed lower CNV in patients than controls (p > 0.001, p = 0.001 respectively). Receiver Operating Characteristic (ROC) curve analysis for HOXA9 methylation, SOX2 CNV and HV2 CNV showed a discrimination power of 79.4%, 80% and 77.5% respectively and the area under the curve for the combined analysis of the three genes was 0.958 with 88% sensitivity and 100% specificity. Conclusions In this study, we suggest a potentially diagnostic panel that may help in detection of lung cancer with high sensitivity and specificity using cell free DNA. This Panel included HOXA9 gene methylation and the CNV of SOX2 and HV2 genes.

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“…Characteristics of chromosomal DNA serve as a stable indicator for each species and are independent of functional loads, while the relative copy numbers of DNA in intracellular organelles (mtDNA-OKK and cpDNA-OKK) in plants act as biomarkers reflecting the intensification or suppression of their function or indicating dysfunction. Therefore, the measurement of mtDNA-OKK and cpDNA-OKK can be a valuable and accessible biomarker for assessing changes in the activity levels of these organelles [6]. CpDNA and mtDNA are expected to be abundant in leaves, where they form punctate structures known as nucleoids, which change their morphology and quantity depending on the physiological state of the plant.…”

Section: Introductionmentioning

confidence: 99%

Changes in the relative copy numbers of chloroplast and mitochondrial DNA in the leaves of Vitis vinifera L. after high-temperature treatment in vitro

Vodolazhsky,

Kryukov

2023

BIO Web of Conferences

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In the context of global warming, studying the consequences of increased temperature on agricultural crops becomes important for predicting the shortand long-term impacts on productivity. The effects of elevated temperature on grapevine plants lead to increased yield losses in viticulture. Micropropagated grapevine plants of the ‘Chardonnay’ variety were grown in vitro on MS medium and subjected to heat treatment at 45°C for 120 minutes. The control group of plants was not exposed to heat treatment. The levels of relative copy numbers of chloroplast and mitochondrial DNA were determined in leaf tissues of all plant groups using the RT-PCR method 30 days after heat treatment. In the group of plants subjected to heat treatment, statistically significant (p>0.05) reductions in the relative copy numbers of mitochondrial and chloroplast DNA were observed compared to the control group, with a decrease of over 30%. The copy number of chloroplast DNA exceeded that of mitochondrial DNA by more than 20 times in both the experimental and control groups. Heat treatment of micropropagated grapevine plants in vitro resulted in a closer correlation (r=+0.86) in the regulation of activity between these organelles, alongside the decrease in relative copy numbers of both mitochondrial and chloroplast DNA. This study demonstrates the promising use of relative copy numbers of chloroplast and mitochondrial DNA in plant leaves to investigate their potential physiological response to adverse environmental factors.

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Changes in the number of copies of genetic loci in gastric cancer

Cited by 8 publications

References 29 publications

The impact of Ceftriaxone on Relative Copy Numbers of Mitochondrial and Chloroplast DNA in Grapevine Leaves

The impact of Ceftriaxone on Relative Copy Numbers of Mitochondrial and Chloroplast DNA in Grapevine Leaves

HOXA9 gene promotor methylation and copy number variation of SOX2 and HV2 genes in cell free DNA: A potential diagnostic panel for non-small cell lung cancer

Changes in the relative copy numbers of chloroplast and mitochondrial DNA in the leaves of Vitis vinifera L. after high-temperature treatment in vitro

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