Artificial Intelligence-Driven Prediction Revealed CFTR Associated with Therapy Outcome of Breast Cancer: A Feasibility Study.

INTRODUCTION: In silico tools capable of predicting the functional consequences of genomic differences between individuals, many of which are AI-driven, have been the most effective over the past two decades for non-synonymous single nucleotide variants (nsSNVs). When appropriately selected for the purpose of the study, a high predictive performance can be expected. In this feasibility study, we investigate the distribution of nsSNVs with an allele frequency below 5%. To classify the putative functional consequence, a tier-based filtration led by AI-driven predictors and scoring system was implemented to the overall decision-making process, resulting in a list of prioritised genes. METHODS: The study has been conducted on breast cancer patients of homogeneous ethnicity. Germline rare variants have been sequenced in genes that influence pharmacokinetic parameters of anticancer drugs or molecular signalling pathways in cancer. After AI-driven functional pathogenicity classification and data mining in pharmacogenomic (PGx) databases, variants were collapsed to the gene level and ranked according to their putative deleterious role. RESULTS: In breast cancer patients, seven of the twelve genes prioritised based on the predictions were found to be associated with response to oncotherapy, histological grade, and tumour subtype. Most importantly, we showed that the group of patients with at least one rare nsSNVs in cystic fibrosis transmembrane conductance regulator (CFTR) had significantly reduced disease-free (log rank, p = 0.002) and overall survival (log rank, p = 0.006). CONCLUSION: AI-driven in silico analysis with PGx data mining provided an effective approach navigating for functional consequences across germline genetic background, which can be easily integrated into the overall decision-making process for future studies. The study revealed a statistically significant association with numerous clinicopathological parameters, including treatment response. Our study indicates that CFTR may be involved in the processes influencing the effectiveness of oncotherapy or in the malignant progression of the disease itself.

Triggering antibacterial activity of a common plant by biosorption of selected heavy metals.

The presented study proposes an efficient utilization of a common Thymus serpyllum L. (wild thyme) plant as a highly potent biosorbent of Cu(II) and Pb(II) ions and the efficient interaction of the copper-laden plant with two opportunistic bacteria. Apart from biochars that are commonly used for adsorption, here we report the direct use of native plant, which is potentially interesting also for soil remediation. The highest adsorption capacity for Cu(II) and Pb(II) ions (qe = 12.66 and 53.13 mg g-1, respectively) was achieved after 10 and 30 min of adsorption, respectively. Moreover, the Cu-laden plant was shown to be an efficient antibacterial agent against the bacteria Escherichia coli and Staphylococcus aureus, the results being slightly better in the former case. Such an activity is enabled only via the interaction of the adsorbed ions effectively distributed within the biological matrix of the plant with bacterial cells. Thus, the sustainable resource can be used both for the treatment of wastewater and, after an effective embedment of metal ions, for the fight against microbes.

Highly Efficient Antibacterial Polymer Composites Based on Hydrophobic Riboflavin Carbon Polymerized Dots.

Development of new types of antimicrobial coatings is of utmost importance due to increasing problems with pathogen transmission from various infectious surfaces to human beings. In this study, new types of highly potent antimicrobial polyurethane composite films encapsulated by hydrophobic riboflavin-based carbon polymer dots are presented. Detailed structural, optical, antimicrobial, and cytotoxic investigations of these composites were conducted. Low-power blue light triggered the composites to eradicate Escherichia coli in 30 min, whereas the same effect toward Staphylococcus aureus was reached after 60 min. These composites also show low toxicity against MRC-5 cells. In this way, RF-CPD composites can be used for sterilization of highly touched objects in the healthcare industry.

Single Nucleotide Variants in KIF14 Gene May Have Prognostic Value in Breast Cancer.

INTRODUCTION: Human kinesin 14 (KIF14) is one of the 70 prognostic marker genes (so-called Amsterdam profile) previously identified by the microarray of breast carcinomas, and its high transcript expression in tumor specimens indicates a poor prognosis for patients. We performed a pilot study to explore the prognostic and predictive meaning of KIF14 germline genetic variability in breast cancer patients. METHODS: KIF14 coding sequence, including 5' and 3' untranslated regions and overlaps to introns for identification of splicing sites, was analyzed using next-generation sequencing in the testing set of blood DNA samples from 105 breast cancer patients with clinical follow-up. After rigorous evaluation of major allele frequency, haplotype blocks, in silico predicted functional aspects, expression quantitative trait loci, and clinical associations, eight single nucleotide variants were subsequently validated in the evaluation set of 808 patients. RESULTS: Carriers of minor alleles G (rs17448931) or T (rs3806362) had significantly shorter overall survival than wild type homozygotes (p = 0.010 and p = 0.023, respectively) thus successfully replicating the results of the testing set. Both associations remained significant in the multivariate Cox regression analysis, including molecular subtype and stage as covariates (hazard ratio, HR = 1.7, 95% confidence interval (CI) = 1.1-2.8 for rs17448931 and HR = 1.9, CI 1.2-3.0 for rs3806362). DISCUSSION: In conclusion, our preliminary data suggest that minor alleles in rs17448931 and rs3806362 of KIF14 represent candidate biomarkers of poor prognosis of breast cancer patients. After pending validation in independent populations and eventual functional characterization, these candidates might become useful biomarkers in the clinics.

Ternary and Quaternary Nanocrystalline Cu-Based Sulfides as Perspective Antibacterial Materials Mechanochemically Synthesized in a Scalable Fashion.

Twelve Cu-based ternary (Cu-Me1-S, Me1 = Fe, Sn, or Sb) and quaternary (Cu-Me2-Sn-S, Me2 = Fe, Zn, or V) nanocrystalline sulfides are shown as perspective antibacterial materials here. They were prepared from elemental precursors by a one-step solvent-free mechanochemical synthesis in a 100 g batch using scalable eccentric vibratory ball milling. Most of the products have shown strong antibacterial activity against Escherichia coli and Staphylococcus aureus bacteria. For instance, stannite Cu2FeSnS4 and mohite Cu2SnS3 were the most active against E. coli, whereas kesterite Cu2ZnSnS4 and rhodostannite Cu2FeSn3S8 exhibited the highest antibacterial activity against S. aureus. In general, stannite has shown the best antibacterial properties out of all the studied samples. Five out of twelve products have been prepared using mechanochemical synthesis for the first time in a scalable fashion here. The presented synthetic approach is a promising alternative to traditional syntheses of nanomaterials suitable for biological applications and shows ternary and quaternary sulfides as potential candidates for the next-generation antibacterial agents.

Antibacterial Electrospun Polycaprolactone Nanofibers Reinforced by Halloysite Nanotubes for Tissue Engineering.

Due to its slow degradation rate, polycaprolactone (PCL) is frequently used in biomedical applications. This study deals with the development of antibacterial nanofibers based on PCL and halloysite nanotubes (HNTs). Thanks to a combination with HNTs, the prepared nanofibers can be used as low-cost nanocontainers for the encapsulation of a wide variety of substances, including drugs, enzymes, and DNA. In our work, HNTs were used as a nanocarrier for erythromycin (ERY) as a model antibacterial active compound with a wide range of antibacterial activity. Nanofibers based on PCL and HNT/ERY were prepared by electrospinning. The antibacterial activity was evaluated as a sterile zone of inhibition around the PCL nanofibers containing 7.0 wt.% HNT/ERY. The morphology was observed with SEM and TEM. The efficiency of HNT/ERY loading was evaluated with thermogravimetric analysis. It was found that the nanofibers exhibited outstanding antibacterial properties and inhibited both Gram- (Escherichia coli) and Gram+ (Staphylococcus aureus) bacteria. Moreover, a significant enhancement of mechanical properties was achieved. The potential uses of antibacterial, environmentally friendly, nontoxic, biodegradable PCL/HNT/ERY nanofiber materials are mainly in tissue engineering, wound healing, the prevention of bacterial infections, and other biomedical applications.

Antibacterial photodynamic activity of hydrophobic carbon quantum dots and polycaprolactone based nanocomposite processed via both electrospinning and solvent casting method.

Inhabitation of various types of bacteria on different surfaces causes vital health problems worldwide. In this work, a wound dressing defeating bacterial infection had been fabricated. The antibacterial effect of polycaprolactone and hydrophobic carbon quantum dots (hCQDs) based nanocomposite has been presented. The nanocomposite was fabricated both via solvent casting and electrospinning method. Nanocomposites with and without hCQDs had been investigated. A detailed study on their morphology and surface properties were performed by scanning electron microscopy, atomic force microscopy and Raman spectroscopy. Prepared nanocomposites had been evaluated by the contact angle, UV-Vis spectroscopy, electron paramagnetic resonance spectroscopy, and antibacterial activity. It was found that nanocomposites were able to produce singlet oxygen upon blue light irradiation at 470 nm, and they were effective in the eradication of Gram positive (Staphylococcus aureus, Listeria monocytogenes) and Gram negative (Escherichia coli, Klebsiella pneumoniae) bacteria.

Properties and structure of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) filaments for fused deposition modelling.

Fused deposition modelling (FDM) is a process of additive manufacturing allowing creating of highly precise complex three-dimensional objects for a large range of applications. The principle of FDM is an extrusion of the molten filament and gradual deposition of layers and their solidification. Potential applications in pharmaceutical and medical fields require the development of biodegradable and biocompatible thermoplastics for the processing of filaments. In this work, the potential of production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) (P(3HB-co-4HB)) filaments for FDM was investigated in respect to its thermal stability. Copolymer P(3HB-co-4HB) was biosynthesised by Cupriavidus malaysiensis. Rheological and mechanical properties of the copolymer were modified by the addition of plasticizers or blending with poly(lactic acid). Thermal stability of mixtures was studied employing thermogravimetric analysis and rheological analyses by monitoring the time-dependent changes in the complex viscosity of melt samples. The plasticization of P(3HB-co-4HB) slightly hindered its thermal degradation but the best stabilization effect was found in case of the copolymer blended with poly(lactic acid). Overall, rheological, thermal and mechanical properties demonstrated that the plasticized P(3HB-co-4HB) is a potential candidate of biodegradable polymer for FDM processes.

Mechanochemistry as an Alternative Method of Green Synthesis of Silver Nanoparticles with Antibacterial Activity: A Comparative Study.

This study shows mechanochemical synthesis as an alternative method to the traditional green synthesis of silver nanoparticles in a comparative manner by comparing the products obtained using both methodologies and different characterization methods. As a silver precursor, the most commonly used silver nitrate was applied and the easily accessible lavender (Lavandula angustofolia L.) plant was used as a reducing agent. Both syntheses were performed using 7 different lavender:AgNO3 mass ratios. The synthesis time was limited to 8 and 15 min in the case of green and mechanochemical synthesis, respectively, although a significant amount of unreacted silver nitrate was detected in both crude reaction mixtures at low lavender:AgNO3 ratios. This finding is of particular interest mainly for green synthesis, as the potential presence of silver nitrate in the produced nanosuspension is often overlooked. Unreacted AgNO3 has been removed from the mechanochemically synthesized samples by washing. The nanocrystalline character of the products has been confirmed by both X-ray diffraction (Rietveld refinement) and transmission electron microscopy. The latter has shown bimodal size distribution with larger particles in tens of nanometers and the smaller ones below 10 nm in size. In the case of green synthesis, the used lavender:AgNO3 ratio was found to have a decisive role on the crystallite size. Silver chloride has been detected as a side-product, mainly at high lavender:AgNO3 ratios. Both products have shown a strong antibacterial activity, being higher in the case of green synthesis, but this can be ascribed to the presence of unreacted AgNO3. Thus, one-step mechanochemical synthesis (without the need to prepare extract and performing the synthesis as separate steps) can be applied as a sustainable alternative to the traditional green synthesis of Ag nanoparticles using plants.

Bactericidal and antioxidant bacterial cellulose hydrogels doped with chitosan as potential urinary tract infection biomedical agent.

Therapy of bacterial urinary tract infections (UTIs) and catheter associated urinary tract infections (CAUTIs) is still a great challenge because of the resistance of bacteria to nowadays used antibiotics and encrustation of catheters. Bacterial cellulose (BC) as a biocompatible material with a high porosity allows incorporation of different materials in its three dimensional network structure. In this work a low molecular weight chitosan (Chi) polymer is incorporated in BC with different concentrations. Different characterization techniques are used to investigate structural and optical properties of these composites. Radical scavenging activity test shows moderate antioxidant activity of these biocompatible composites whereas in vitro release test shows that 13.3% of chitosan is released after 72 h. Antibacterial testing of BC-Chi composites conducted on Gram-positive and Gram-negative bacteria causing UTIs and CAUTIs (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae) and encrustation (Proteus mirabilis) show bactericidal effect. The morphology analysis of bacteria after the application of BC-Chi shows that they are flattened with a rough surface, with a tendency to agglomerate and with decreased length and width. All obtained results show that BC-Chi composites might be considered as potential biomedical agents in treatment of UTIs and CAUTIs and as a urinary catheter coating in encrustation prevention.

Sustainable One-Step Solid-State Synthesis of Antibacterially Active Silver Nanoparticles Using Mechanochemistry.

A combination of solid-state mechanochemical and green approaches for the synthesis of silver nanoparticles (AgNPs) is explored in this study. Thymus serpyllum L. (SER), Sambucus nigra L. (SAM) and Thymus vulgaris L. (TYM) plants were successfully applied to reduce AgNO3 to AgNPs, as confirmed by X-ray diffraction analysis, with SER being the best reducing agent, and TYM being the worst. The experiments were performed via a one-step planetary milling process, where various AgNO3:plant mass ratios (1:1, 1:10, 1:50 and 1:100) were investigated. Atomic absorption spectrometry indicated that the stability of the mechanochemically produced AgNPs increased markedly when a sufficiently large quantity of the reducing plant was used. Furthermore, when larger quantities of plant material were employed, the crystallite size of the AgNPs decreased. TEM analysis revealed that all AgNPs produced from both AgNO3:plant ratios 1:1 and 1:10 exhibit the bimodal size distribution with the larger fraction with size in tens of nm and the smaller one below 10 nm in size. The antibacterial activity of the produced AgNPs was observed only for AgNO3:plant ratio 1:1, with the AgNPs prepared using SER showing the greatest antibacterial properties.

Photodynamic-active smart biocompatible material for an antibacterial surface coating.

Here we present a new effective antibacterial material suitable for a coating, e.g., surface treatment of textiles, which is also time and financially undemanding. The most important role is played by hydrophobic carbon quantum dots, as a new type of photosensitizer, produced by carbonization of different carbon precursors, which are incorporated by swelling from solution into various polymer matrices in the form of thin films, in particular polyurethanes, which are currently commercially used for industrial surface treatment of textiles. The role of hydrophobic carbon quantum dots is to work as photosensitizers upon irradiation and produce reactive oxygen species, namely singlet oxygen, which is already known as the most effective radical for elimination different kinds of bacteria on the surface or in close proximity to such modified material. Therefore, we have mainly studied the effect of hydrophobic carbon quantum dots on Staphylococcus aureus and the cytotoxicity tests, which are essential for the safe handling of such material. Also, the production of singlet oxygen by several methods (electron paramagnetic spectroscopy, time-resolved near-infrared spectroscopy), surface structures (atomic force microscopy and contact angle measurement), and the effect of radiation on polymer matrices were studied. The prepared material is easily modulated by end-user requirements.

Antibacterial photodynamic activity of carbon quantum dots/polydimethylsiloxane nanocomposites against Staphylococcus aureus, Escherichia coli and Klebsiella pneumoniae.

Despite great efforts, the design of antibacterial surfaces is still a challenge. In this work, results of structural, mechanical, cytotoxic and antibacterial activities of hydrophobic carbon quantum dots/polydimethylsiloxane surfaces are presented. Antibacterial action of this surface is based on the generation of reactive oxygen species which cause bacteria damage by oxidative stress. At the same time, this surface was not cytotoxic towards the NIH/3T3 cells. Swelling-encapsulation-shrink method is applied for encapsulation of hydrophobic carbon quantum dots in medical grade silicone-polydimethylsiloxane. XPS and photoluminescence spectroscopy analyses confirm that hydrophobic carbon quantum dots have been encapsulated successfully into polydimethylsiloxane polymer matrix. Based on stress-strain test the improvement of mechanical properties of these nanocomposites is established. It is shown by electron paramagnetic resonance spectroscopy and luminescence method that nanocomposite generates singlet oxygen initiated by 470 nm blue light irradiation. Antibacterial testing shows the nanocomposite in the form of foil kills Staphylococcus aureus, Escherichia coli and Klebsiella pneumoniae and is very effective after only a 15 min irradiation.

Use of Germline Genetic Variability for Prediction of Chemoresistance and Prognosis of Breast Cancer Patients.

The aim of our study was to set up a panel for targeted sequencing of chemoresistance genes and the main transcription factors driving their expression and to evaluate their predictive and prognostic value in breast cancer patients. Coding and regulatory regions of 509 genes, selected from PharmGKB and Phenopedia, were sequenced using massive parallel sequencing in blood DNA from 105 breast cancer patients in the testing phase. In total, 18,245 variants were identified of which 2565 were novel variants (without rs number in dbSNP build 150) in the testing phase. Variants with major allele frequency over 0.05 were further prioritized for validation phase based on a newly developed decision tree. Using emerging in silico tools and pharmacogenomic databases for functional predictions and associations with response to cytotoxic therapy or disease-free survival of patients, 55 putative variants were identified and used for validation in 805 patients with clinical follow up using KASPTM technology. In conclusion, associations of rs2227291, rs2293194, and rs4376673 (located in ATP7A, KCNAB1, and DFFB genes, respectively) with response to neoadjuvant cytotoxic therapy and rs1801160 in DPYD with disease-free survival of patients treated with cytotoxic drugs were validated and should be further functionally characterized.

Carbon Quantum Dots Modified Polyurethane Nanocomposite as Effective Photocatalytic and Antibacterial Agents.

Development of new types of antibacterial coatings or nanocomposites is of great importance due to widespread multidrug-resistant infections including bacterial infections. Herein, we investigated biocompatibility as well as structural, photocatalytic, and antibacterial properties of photoactive hydrophobic carbon quantum dots/polyurethane nanocomposite. The swell-encapsulation-shrink method was applied for production of these nanocomposites. Hydrophobic carbon quantum dots/polyurethane nanocomposites were found to be highly effective generator of singlet oxygen upon irradiation by low-power blue light. Analysis of conducted antibacterial tests on Staphyloccocus aureus and Escherichia coli showed 5-log bactericidal effect of these nanocomposites within 60 min of irradiation. Very powerful degradation of dye (rose bengal) was observed within 180 min of blue light irradiation of the nanocomposites. Biocompatibility studies revealed that nanocomposites were not cytotoxic against mouse embryonic fibroblast cell line, whereas they showed moderate cytotoxicity toward adenocarcinomic human epithelial cell line. Minor hemolytic effect of these nanocomposites toward red blood cells was revealed.

Mechanism of anti-inflammatory action of liquorice extract and glycyrrhizin.

The antiradical activity, protective effect against lipid peroxidation of liposomal membrane, and inhibitory effect on whole blood reactive oxygen species (ROS) liberation of Glycyrrhiza glabra crude extract and glycyrrhizin, its major compound, were assessed. The liquorice extract showed significant activity in all the three assay systems used in a dose dependent manner. It displayed remarkable reactivity with free stable 1,1'-diphenyl-2-picrylhydrazyl (DPPH) radical, inhibitory efficacy in peroxidatively damaged unilamellar dioleoyl phosphatidylcholine (DOPC) liposomes, and inhibition of ROS chemiluminescence, generated by whole blood, induced by both receptor-bypassing stimuli (PMA) and receptor operating stimuli (Opz) in the ranking order of stimuli PMA> Opz. These activities may be attributed to phenolic antioxidants involving isoflavan derivatives, coumarins and chalcones. Nonetheless, triterpene saponin glycyrrhizin exhibited no efficacy in the system of DPPH reaction and peroxidation of liposomal membrane, and negligible inhibition of chemiluminescence generated by inflammatory cells. These results indicate that the mechanism of anti-inflammatory effect of glycyrrhizin most probably does not involve ROS and this major constituent is not responsible for the inhibition effects of liquorice extract on neutrophil functions.