Pulsed Electric Fields Alter Expression of NF-κB Promoter-Controlled Gene

The possibility to artificially adjust and fine‐tune gene expression is one of the key mile-stones in bioengineering, synthetic biology, and advanced medicine. Since the effects of proteins or other transgene products depend on the dosage, controlled gene expression is required for any ap-plications, where even slight fluctuations of the transgene product impact its function or other critical cell parameters. In this context, physical techniques demonstrate optimistic perspectives, and pulsed electric field technology is a potential candidate for a noninvasive, biophysical gene regulator, exploiting an easily adjustable pulse generating device. We exposed mammalian cells, transfected with a NF‐κB pathway‐controlled transcription system, to a range of microsecond‐duration pulsed electric field parameters. To prevent toxicity, we used protocols that would generate relatively mild physical stimulation. The present study, for the first time, proves the principle that microsecond‐duration pulsed electric fields can alter single‐gene expression in plasmid context in mammalian cells without significant damage to cell integrity or viability. Gene expression might be upregulated or downregulated depending on the cell line and parameters applied. This noninvasive, ligand‐, cofactor‐, nanoparticle‐free approach enables easily controlled direct electrostimulation of the construct carrying the gene of interest; the discovery may contribute towards the path of simplification of the complexity of physical systems in gene regulation and create further synergies between electronics, synthetic biology, and medicine. © 2021 by the authors. Licensee MDPI, Basel, Switzerland. --//-- Citation: Kavaliauskaite, J.; Kazlauskaite, A.; Lazutka, J.R.; Mozolevskis, G.; Stirke, A. Pulsed Electric Fields Alter Expression of NF-κB Promoter Controlled Gene. Int. J. Mol. Sci. 2022, 23, 451. https://doi.org/10.3390/ijms23010451. Article published under the CC BY 4.0 license.Funding: A.S. acknowledges to the ERDF PostDoc project No. 1.1.1.2/VIAA/4/20/739. The Institute of Solid State Physics, University of Latvia (Latvia) as the Centre of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD01-2016-2017-Teaming Phase2 under grant agreement no. 739508, project CAMART2

Frequent down-regulation of ABC transporter genes in prostate cancer

Background: ATP-binding cassette (ABC) transporters are transmembrane proteins responsible for the efflux of a wide variety of substrates, including steroid metabolites, through the cellular membranes. For better characterization of the role of ABC transporters in prostate cancer (PCa) development, the profile of ABC transporter gene expression was analyzed in PCa and noncancerous prostate tissues (NPT). Methods: TaqMan Low Density Array (TLDA) human ABC transporter plates were used for the gene expression profiling in 10 PCa and 6 NPT specimens. ABCB1 transcript level was evaluated in a larger set of PCa cases (N = 78) and NPT (N = 15) by real-time PCR, the same PCa cases were assessed for the gene promoter hypermethylation by methylation-specific PCR. Results: Expression of eight ABC transporter genes (ABCA8, ABCB1, ABCC6, ABCC9, ABCC10, ABCD2, ABCG2, and ABCG4) was significantly down-regulated in PCa as compared to NPT, and only two genes (ABCC4 and ABCG1) were up-regulated. Down-regulation of ABC transporter genes was prevalent in the TMPRSS2-ERG-negative cases. A detailed analysis of ABCB1 expression confirmed TLDA results: a reduced level of the transcript was identified in PCa in comparison to NPT (p = 0.048). Moreover, the TMPRSS2-ERG-negative PCa cases showed significantly lower expression of ABCB1 in comparison to NPT (p = 0.003) or the fusion-positive tumors (p = 0.002). Promoter methylation of ABCB1 predominantly occurred in PCa and was rarely detected in NPT (p < 0.001). Conclusions: The study suggests frequent down-regulation of the ABC transporter genes in PCa, especially in the TMPRSS2-ERG-negative tumors

Membrane connectivity estimated by digital image analysis of HER2 immunohistochemistry is concordant with visual scoring and fluorescence in situ hybridization results: algorithm evaluation on breast cancer tissue microarrays

<p>Abstract</p> <p>Introduction</p> <p>The human epidermal growth factor receptor 2 (HER2) is an established biomarker for management of patients with breast cancer. While conventional testing of HER2 protein expression is based on semi-quantitative visual scoring of the immunohistochemistry (IHC) result, efforts to reduce inter-observer variation and to produce continuous estimates of the IHC data are potentiated by digital image analysis technologies.</p> <p>Methods</p> <p>HER2 IHC was performed on the tissue microarrays (TMAs) of 195 patients with an early ductal carcinoma of the breast. Digital images of the IHC slides were obtained by Aperio ScanScope GL Slide Scanner. Membrane connectivity algorithm (HER2-CONNECT™, Visiopharm) was used for digital image analysis (DA). A pathologist evaluated the images on the screen twice (visual evaluations: VE1 and VE2). HER2 fluorescence <it>in situ </it>hybridization (FISH) was performed on the corresponding sections of the TMAs. The agreement between the IHC HER2 scores, obtained by VE1, VE2, and DA was tested for individual TMA spots and patient's maximum TMA spot values (VE1max, VE2max, DAmax). The latter were compared with the FISH data. Correlation of the continuous variable of the membrane connectivity estimate with the FISH data was tested.</p> <p>Results</p> <p>The pathologist intra-observer agreement (VE1 and VE2) on HER2 IHC score was almost perfect: kappa 0.91 (by spot) and 0.88 (by patient). The agreement between visual evaluation and digital image analysis was almost perfect at the spot level (kappa 0.86 and 0.87, with VE1 and VE2 respectively) and at the patient level (kappa 0.80 and 0.86, with VE1max and VE2max, respectively). The DA was more accurate than VE in detection of FISH-positive patients by recruiting 3 or 2 additional FISH-positive patients to the IHC score 2+ category from the IHC 0/1+ category by VE1max or VE2max, respectively. The DA continuous variable of the membrane connectivity correlated with the FISH data (HER2 and CEP17 copy numbers, and HER2/CEP17 ratio).</p> <p>Conclusion</p> <p>HER2 IHC digital image analysis based on membrane connectivity estimate was in almost perfect agreement with the visual evaluation of the pathologist and more accurate in detection of HER2 FISH-positive patients. Most immediate benefit of integrating the DA algorithm into the routine pathology HER2 testing may be obtained by alerting/reassuring pathologists of potentially misinterpreted IHC 0/1+ versus 2+ cases.</p

Immunohistochemistry profiles of breast ductal carcinoma: factor analysis of digital image analysis data

<p>Abstract</p> <p>Background</p> <p>Molecular studies of breast cancer revealed biological heterogeneity of the disease and opened new perspectives for personalized therapy. While multiple gene expression-based systems have been developed, current clinical practice is largely based upon conventional clinical and pathologic criteria. This gap may be filled by development of combined multi-IHC indices to characterize biological and clinical behaviour of the tumours. Digital image analysis (DA) with multivariate statistics of the data opens new opportunities in this field.</p> <p>Methods</p> <p>Tissue microarrays of 109 patients with breast ductal carcinoma were stained for a set of 10 IHC markers (ER, PR, HER2, Ki67, AR, BCL2, HIF-1α, SATB1, p53, and p16). Aperio imaging platform with the Genie, Nuclear and Membrane algorithms were used for the DA. Factor analysis of the DA data was performed in the whole group and hormone receptor (HR) positive subgroup of the patients (n = 85).</p> <p>Results</p> <p>Major factor potentially reflecting aggressive disease behaviour (i-Grade) was extracted, characterized by opposite loadings of ER/PR/AR/BCL2 and Ki67/HIF-1α. The i-Grade factor scores revealed bimodal distribution and were strongly associated with higher Nottingham histological grade (G) and more aggressive intrinsic subtypes. In HR-positive tumours, the aggressiveness of the tumour was best defined by positive Ki67 and negative ER loadings. High Ki67/ER factor scores were strongly associated with the higher G and Luminal B types, but also were detected in a set of G1 and Luminal A cases, potentially indicating high risk patients in these categories. Inverse relation between HER2 and PR expression was found in the HR-positive tumours pointing at differential information conveyed by the ER and PR expression. SATB1 along with HIF-1α reflected the second major factor of variation in our patients; in the HR-positive group they were inversely associated with the HR and BCL2 expression and represented the major factor of variation. Finally, we confirmed high expression levels of p16 in Triple-negative tumours.</p> <p>Conclusion</p> <p>Factor analysis of multiple IHC biomarkers measured by automated DA is an efficient exploratory tool clarifying complex interdependencies in the breast ductal carcinoma IHC profiles and informative value of single IHC markers. Integrated IHC indices may provide additional risk stratifications for the currently used grading systems and prove to be useful in clinical outcome studies.</p> <p>Virtual Slides</p> <p>The virtual slide(s) for this article can be found here: <url>http://www.diagnosticpathology.diagnomx.eu/vs/1512077125668949</url></p

The Emerging Role of Chromatin Remodeling Complexes in Ovarian Cancer

Ovarian cancer (OC) is the fifth leading cause of women&rsquo;s death from cancers. The high mortality rate is attributed to the late presence of the disease and the lack of modern diagnostic tools, including molecular biomarkers. Moreover, OC is a highly heterogeneous disease, which contributes to early treatment failure. Thus, exploring OC molecular mechanisms could significantly enhance our understanding of the disease and provide new treatment options. Chromatin remodeling complexes (CRCs) are ATP-dependent molecular machines responsible for chromatin reorganization and involved in many DNA-related processes, including transcriptional regulation, replication, and reparation. Dysregulation of chromatin remodeling machinery may be related to cancer development and chemoresistance in OC. Some forms of OC and other gynecologic diseases have been associated with mutations in specific CRC genes. Most notably, ARID1A in endometriosis-related OC, SMARCA4, and SMARCB1 in hypercalcemic type small cell ovarian carcinoma (SCCOHT), ACTL6A, CHRAC1, RSF1 amplification in high-grade serous OC. Here we review the available literature on CRCs&rsquo; involvement in OC to improve our understanding of its development and investigate CRCs as possible biomarkers and treatment targets for OC

The growth and phenology patterns of herb Paris (Paris quadrifolia L., Trilliaceae): relation to soil and air temperatures

The phenology and development of Paris quadrifolia L. has been related to variations in soil and air temperatures during four seasons (1997-2000). Its emergence appeared to be strongly dependant on soil temperature. Plants become visible as soon as the daily mean maximum soil temperature reached ca. 7 C. Variations in soil temperatures could delay Paris emergence by almost one month during the study period. The plants needed on average 18 days to develop from 10% to 95% of maximum height, and flowers were developed after ca. 30 days. The growth and phenology pattern of Paris is therefore not typical of a light-demanding early spring plant. Its need for a relatively long developmental period is compensated for by its ability to survive by vegetative growth during low light periods. The investigation showed that the temperature sum is not a useful tool for predicting phenological events in areas where frozen soil occurs. Two populations separated by ca. 6 m had a two-week difference in emergence due to differences in soil temperature. Sterile plants were generally lower than 14 cm and fertile plants were mostly taller than 20 cm. This pattern appeared to be the same in different geographical areas

Evaluation of in vitro genotoxicity of polystyrene nanoparticles in human peripheral blood mononuclear cells

According to the trade association PlasticEurope, global plastics production increased to 390.7 million tons in 2021. Unfortunately, the majority of produced plastics eventually end up as waste in the ocean or on land. Since synthetic plastics are not fully biodegradable, they tend to persist in natural environments and transform into micro- and nanoplastic particles due to fragmentation. The presence of nanoplastics in air, water, and food causes ecotoxicological issues and leads to human exposure. One of the main concerns is their genotoxic potential. Therefore, this study aimed to evaluate the internalization rates, cytotoxicity, and genotoxicity of polystyrene nanoparticles (PS-NPs) in human peripheral blood mononuclear cells (PBMCs) in vitro. The uptake of PS-NPs was confirmed with flow cytometry light scattering analysis. None of the tested nanoparticle concentrations had a cytotoxic effect on human PBMCs, as evaluated by a dual ethidium bromide/acridine orange staining technique. However, an alkaline comet assay results revealed a significant increase in the levels of primary DNA damage after 24 h of exposure to PS-NPs in a dose-dependent manner. Moreover, all tested PS-NPs concentrations induced a significant amount of micronucleated cells, as well. The results of this study revealed the genotoxic potential of commercially manufactured polystyrene nanoparticles and highlighted the need for more studies with naturally occurring plastic NPs

Influence of body mass index and duration of disease on chromosome damage in lymphocytes of patients with diabetes

It is well-established that patients with diabetes mellitus (DM) have a higher incidence of several types of cancer. The precise mechanisms of this association are still unknown, but obesity and chronic inflammation-induced reactive oxygen species (ROS) are thought to be the main risk factors. ROS may produce different DNA damage, which could eventually lead to cancer. The main objective of this study was to evaluate the relation of chromosome aberrations (CA) with disease status, demographics, and clinical parameters in 33 subjects with type 1 DM (T1DM), 22 subjects with type 2 DM (T2DM), and 21 controls. CAs were analyzed in cultured peripheral blood lymphocytes and subdivided into chromatid (CTA)- and chromosome (CSA)-type aberrations. Compared with controls, higher levels of CTAs and CSAs were observed in T1DM (p = 0.0053 and p = 0.0203, respectively) and T2DM (p = 0.0133 and p = 0.00002, respectively). While there was no difference in CTAs between T1DM and T2DM, CSAs were higher in T2DM (p = 0.0173). A significant positive association between CTAs and disease duration (rs = 0.2938, p = 0.0099) and between CSAs and disease duration (rs = 0.4306, p = 0.0001), age (rs = 0.3932, p = 0.0004), and body mass index (BMI) (rs = 0.3502, p = 0.0019) was revealed. After multiple regression analysis, duration of disease remained significant for CTA, CSA, and CAs (p = 0.0042, p = 0.00003, and p = 0.00002, respectively). For CSA, BMI and the use of statins were the other important confounding variables (p = 0.0105 and p = 0.0763). Thus, this study demonstrated that both T1DM and T2DM patients had a higher number of all types of aberrations than controls, which increases with the prolonged disease duration. Higher BMI was associated with a higher frequency of CSA. The use of statins might be beneficial for reducing chromosome damage, but further investigations are needed to confirm this association

Frequent Methylation of RASSF1 and RARB in Urine Sediments From Patients with Early Stage Prostate Cancer

Background. Prostate cancer (PCa) is the second most prevalent malignancy among males, characterized by high mortality rates. Aberrant DNA methylation in promoters of tumor suppressor genes is an early and frequent event during prostate carcinogenesis. Modern techniques allow a sensitive detection of DNA methylation biomarkers in bodily fluids from cancer patients offering a noninvasive tool for PCa monitoring. Our study aimed at the analysis of DNA methylation in urine sediments from PCa patients for the selection of most informative noninvasive biomarkers. Material and Methods. Real-time methylation-specific polymerase chain reaction was used for the detection of methylated RASSF1, RARB, and GSTP1 genes in catheterized urine specimens from 34 patients with biopsy-proven early or medium stage PCa. Results. At least one gene was methylated in urine sediments from 28 cases with PCa, with a sensitivity of the test reaching 82%. RASSF1 was methylated in 71% (24 of 34), RARB in 44% (15 of 34), and GSTP1 in 3% (1 of 34) of the specimens. High level of methylation (≥50%) in RARB and RASSF1 genes was detected in 40% and 20% of cases, respectively. A significant association was observed between high level of RARB methylation and Gleason score (P=0.01), while methylation of at least one gene occurred more frequently in urine DNA of older patients (P=0.02). Conclusions. Results of our study show a high sensitivity of DNA methylation biomarkers, especially RASSF1 and RARB, for the early and noninvasive detection of PCa

Analysis of DNA polymorphism in wild populations of herb-Paris (Paris quadrifolia L., Trilliaceae) from Lithuania and Norway.

Analysis of random amplified polymorphic DNA (RAPD) was used to determine genetic diversity within the populations of herb-Paris plant from Lithuania and Norway. RAPD analyses have shown 21.9 ± 5.2% of polymorphic loci in the total sample. Polymorphism level in Norwegian sample was 20.3 ± 5.0%, and in the Lithuanian one was 21.9 ± 5.2%. The proportion of distinguishable RAPD phenotypes in Lithuania was 0.52 ± 0.03 and in Norway 0.24 ± 0.03. For the total sample, Shannon?? Information Index was 0.59 and Nei?? gene diversity 0.41. The estimated total proportion of diversity among populations (GST) and gene flow (Nm) were 0.67 and 0.245, respectively. In Norway GST was 0.64 and Nm was 0.28, whereas in Lithuania GST was 0.42 and Nm was 0.68. The UPGMA analyses have revealed that Lithuanian and Norwegian populations of herb-Paris are clearly separated into two clusters. Analysis of molecular variance (AMOVA) showed that the majority of molecular variation (41%) was due to variation between geographical regions (Lithuania and Norway), 37% of molecular variation was due to variation among individuals within the populations, and only 22% of variation was estimated to be due to variation between populations. In Lithuania, 68% of molecular variation was due to variation within populations, 32% due to variation between populations (ФPT = 0.32), whereas in Norway the proportions were 49% and 51% (ФPT = 0.51), respectively. Thus, the estimated parameters indicated a higher genetic diversity in Lithuanian populations of herb-Paris than in Norwegian ones