Interactions between diet and gut microbiota in cancer.

Dietary patterns and specific dietary components, in concert with the gut microbiota, can jointly shape susceptibility, resistance and therapeutic response to cancer. Which diet-microbial interactions contribute to or mitigate carcinogenesis and how they work are important questions in this growing field. Here we interpret studies of diet-microbial interactions to assess dietary determinants of intestinal colonization by opportunistic and oncogenic bacteria. We explore how diet-induced expansion of specific gut bacteria might drive colonic epithelial tumorigenesis or create immuno-permissive tumour milieus and introduce recent findings that provide insight into these processes. Additionally, we describe available preclinical models that are widely used to study diet, microbiome and cancer interactions. Given the rising clinical interest in dietary modulations in cancer treatment, we highlight promising clinical trials that describe the effects of different dietary alterations on the microbiome and cancer outcomes.

The Role of the Microbiome in the Etiopathogenesis of Colon Cancer.

Studies in preclinical models support that the gut microbiota play a critical role in the development and progression of colorectal cancer (CRC). Specific microbial species and their corresponding virulence factors or associated small molecules can contribute to CRC development and progression either via direct effects on the neoplastic transformation of epithelial cells or through interactions with the host immune system. Induction of DNA damage, activation of Wnt/ß-catenin and NF-κB proinflammatory pathways, and alteration of the nutrient's availability and the metabolic activity of cancer cells are the main mechanisms by which the microbiota contribute to CRC. Within the tumor microenvironment, the gut microbiota alter the recruitment, activation, and function of various immune cells, such as T cells, macrophages, and dendritic cells. Additionally, the microbiota shape the function and composition of cancer-associated fibroblasts and extracellular matrix components, fashioning an immunosuppressive and pro-tumorigenic niche for CRC. Understanding the complex interplay between gut microbiota and tumorigenesis can provide therapeutic opportunities for the prevention and treatment of CRC.

MicroRNAs as prospective biomarkers, therapeutic targets and pharmaceuticals in neuroblastoma.

Neuroblastomas, the most prevalent malignant solid neoplasms of childhood, originate from progenitor cells of the sympathetic nervous system. Their genetic causation is diverse and involves multiple molecular mechanisms. This review highlights multiple roles of microRNA in neuroblastoma pathogenesis and discusses the prospects of harnessing these important natural regulator molecules as biomarkers, therapeutic targets and pharmaceuticals in neuroblastoma.

Organismic Memristive Structures With Variable Functionality for Neuroelectronics.

In this paper, we report an approach to design nanolayered memristive compositions based on TiO2/Al2O3 bilayer structures with analog non-volatile and volatile tuning of the resistance. The structure of the TiO2 layer drives the physical mechanism underlying the non-volatile resistance switching, which can be changed from electronic to ionic, enabling the synaptic behavior emulation. The presence of the anatase phase in the amorphous TiO2 layer induces the resistive switching mechanism due to electronic processes. In this case, the switching of the resistance within the range of seven orders of magnitude is experimentally observed. In the bilayer with amorphous titanium dioxide, the participation of ionic processes in the switching mechanism results in narrowing the tuning range down to 2-3 orders of magnitude and increasing the operating voltages. In this way, a combination of TiO2/Al2O3 bilayers with inert electrodes enables synaptic behavior emulation, while active electrodes induce the neuronal behavior caused by cation density variation in the active Al2O3 layer of the structure. We consider that the proposed approach could help to explore the memristive capabilities of nanolayered compositions in a more functional way, enabling implementation of artificial neural network algorithms at the material level and simplifying neuromorphic layouts, while maintaining all benefits of neuromorphic architectures.

ß-Hydroxybutyrate suppresses colorectal cancer.

Colorectal cancer (CRC) is among the most frequent forms of cancer, and new strategies for its prevention and therapy are urgently needed1. Here we identify a metabolite signalling pathway that provides actionable insights towards this goal. We perform a dietary screen in autochthonous animal models of CRC and find that ketogenic diets exhibit a strong tumour-inhibitory effect. These properties of ketogenic diets are recapitulated by the ketone body ß-hydroxybutyrate (BHB), which reduces the proliferation of colonic crypt cells and potently suppresses intestinal tumour growth. We find that BHB acts through the surface receptor Hcar2 and induces the transcriptional regulator Hopx, thereby altering gene expression and inhibiting cell proliferation. Cancer organoid assays and single-cell RNA sequencing of biopsies from patients with CRC provide evidence that elevated BHB levels and active HOPX are associated with reduced intestinal epithelial proliferation in humans. This study thus identifies a BHB-triggered pathway regulating intestinal tumorigenesis and indicates that oral or systemic interventions with a single metabolite may complement current prevention and treatment strategies for CRC.

Compact Model for Bipolar and Multilevel Resistive Switching in Metal-Oxide Memristors.

The article presents the results of the development and study of a combined circuitry (compact) model of thin metal oxide films based memristive elements, which makes it possible to simulate both bipolar switching processes and multilevel tuning of the memristor conductivity taking into account the statistical variability of parameters for both device-to-device and cycle-to-cycle switching. The equivalent circuit of the memristive element and the equation system of the proposed model are considered. The software implementation of the model in the MATLAB has been made. The results of modeling static current-voltage characteristics and transient processes during bipolar switching and multilevel turning of the conductivity of memristive elements are obtained. A good agreement between the simulation results and the measured current-voltage characteristics of memristors based on TiOx films (30 nm) and bilayer TiO2/Al2O3 structures (60 nm/5 nm) is demonstrated.

Local Electric Property Modification of Ferroelectric Tunnel Junctions Induced by Variation of Polarization Charge Screening Conditions under Measurement with Scanning Probe Techniques.

Scanning tunneling spectroscopy in ultrahigh vacuum conditions and conductive atomic-force microscopy in ambient conditions were used to study local electroresistive properties of ferroelectric tunnel junctions SrTiO3/La0.7Sr0.3MnO3/BaTiO3. Interestingly, experimental current-voltage characteristics appear to strongly depend on the measurement technique applied. It was found that screening conditions of the polarization charges at the interface with a top electrode differ for two scanning probe techniques. As a result, asymmetry of the tunnel barrier height for the opposite ferroelectric polarization orientations may be influenced by the method applied to study the local tunnel electroresistance. Our observations are well described by the theory of electroresistance in ferroelectric tunnel junctions. Based on this, we reveal the main factors that influence the polarization-driven local resistive properties of the device under study. Additionally, we propose an approach to enhance asymmetry of ferroelectric tunnel junctions during measurement. While keeping the high locality of scanning probe techniques, it helps to increase the difference in the value of tunnel electroresistance for the opposite polarization orientations.

Contact Engineering Approach to Improve the Linearity of Multilevel Memristive Devices.

Physical mechanisms underlying the multilevel resistive tuning over seven orders of magnitude in structures based on TiO2/Al2O3 bilayers, sandwiched between platinum electrodes, are responsible for the nonlinear dependence of the conductivity of intermediate resistance states on the writing voltage. To improve the linearity of the electric-field resistance tuning, we apply a contact engineering approach. For this purpose, platinum top electrodes were replaced with aluminum and copper ones to induce the oxygen-related electrochemical reactions at the interface with the Al2O3 switching layer of the structures. Based on experimental results, it was found that electrode material substitution provokes modification of the physical mechanism behind the resistive switching in TiO2/Al2O3 bilayers. In the case of aluminum electrodes, a memory window has been narrowed down to three orders of magnitude, while the linearity of resistance tuning was improved. For copper electrodes, a combination of effects related to metal ion diffusion with oxygen vacancies driven resistive switching was responsible for a rapid relaxation of intermediate resistance states in TiO2/Al2O3 bilayers.

Impaired complex I repair causes recessive Leber's hereditary optic neuropathy.

Leber's hereditary optic neuropathy (LHON) is the most frequent mitochondrial disease and was the first to be genetically defined by a point mutation in mitochondrial DNA (mtDNA). A molecular diagnosis is achieved in up to 95% of cases, the vast majority of which are accounted for by 3 mutations within mitochondrial complex I subunit-encoding genes in the mtDNA (mtLHON). Here, we resolve the enigma of LHON in the absence of pathogenic mtDNA mutations. We describe biallelic mutations in a nuclear encoded gene, DNAJC30, in 33 unsolved patients from 29 families and establish an autosomal recessive mode of inheritance for LHON (arLHON), which to date has been a prime example of a maternally inherited disorder. Remarkably, all hallmarks of mtLHON were recapitulated, including incomplete penetrance, male predominance, and significant idebenone responsivity. Moreover, by tracking protein turnover in patient-derived cell lines and a DNAJC30-knockout cellular model, we measured reduced turnover of specific complex I N-module subunits and a resultant impairment of complex I function. These results demonstrate that DNAJC30 is a chaperone protein needed for the efficient exchange of complex I subunits exposed to reactive oxygen species and integral to a mitochondrial complex I repair mechanism, thereby providing the first example to our knowledge of a disease resulting from impaired exchange of assembled respiratory chain subunits.

Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure.

DNA mismatch repair (MMR) plays a crucial role in the maintenance of genomic stability. The main MMR protein, MutS, was recently shown to recognize the G-quadruplex (G4) DNA structures, which, along with regulatory functions, have a negative impact on genome integrity. Here, we studied the effect of G4 on the DNA-binding activity of MutS from Rhodobacter sphaeroides (methyl-independent MMR) in comparison with MutS from Escherichia coli (methyl-directed MMR) and evaluated the influence of a G4 on the functioning of other proteins involved in the initial steps of MMR. For this purpose, a new DNA construct was designed containing a biologically relevant intramolecular stable G4 structure flanked by double-stranded regions with the set of DNA sites required for MMR initiation. The secondary structure of this model was examined using NMR spectroscopy, chemical probing, fluorescent indicators, circular dichroism, and UV spectroscopy. The results unambiguously showed that the d(GGGT)4 motif, when embedded in a double-stranded context, adopts a G4 structure of a parallel topology. Despite strong binding affinities of MutS and MutL for a G4, the latter is not recognized by E. coli MMR as a signal for repair, but does not prevent MMR processing when a G4 and G/T mismatch are in close proximity.

Microbiome in cancer progression and therapy.

A myriad of microbes living together with the host constitute microbiota, which possesses very diverse functions in regulation of host physiology. Recently, it has been unequivocally demonstrated that microbiota regulates cancer initiation, progression and responses to therapy. Here we review known pro-tumorigenic and anti-tumorigenic function of microbiota and mechanisms how microbes can regulate cancer cells and immune and stromal cells within the tumor microenvironment.

Three rare pathogenic mtDNA substitutions in LHON patients with low heteroplasmy.

In this article we present clinical, molecular and biochemical investigations of three patients with LHON caused by rare point substitutions in mtDNA. One patient harbours the known mtDNA mutation (m.13513 G>A), the others have new variants (m.13379 A>G in MT-ND5 gene and m.14597 A>G in MT-ND6 gene, which has never been previously associated with LHON). NGS analysis of a whole mtDNA derived from patient's blood revealed a low mutation load (24%, 47%, 23% respectively). Our data, including family segregation analysis, measurement of reactive oxygen species (ROS) production and cytotoxic effect of paraquat and high-resolution respirometry, showed that nucleotide variant m.14597 A>G can be classified as pathogenic mutation.

A metabolic engineering strategy for producing free fatty acids by the Yarrowia lipolytica yeast based on impairment of glycerol metabolism.

In recent years, bio-based production of free fatty acids from renewable resources has attracted attention for their potential as precursors for the production of biofuels and biochemicals. In this study, the oleaginous yeast Yarrowia lipolytica was engineered to produce free fatty acids by eliminating glycerol metabolism. Free fatty acid production was monitored under lipogenic conditions with glycerol as a limiting factor. Firstly, the strain W29 (Δgpd1), which is deficient in glycerol synthesis, was obtained. However, W29 (Δgpd1) showed decreased biomass accumulation and glucose consumption in lipogenic medium containing a limiting supply of glycerol. Analysis of substrate utilization from a mixture of glucose and glycerol by the parental strain W29 revealed that glycerol was metabolized first and glucose utilization was suppressed. Thus, the Δgpd1Δgut2 double mutant, which is deficient also in glycerol catabolism, was constructed. In this genetic background, growth was repressed by glycerol. Oleate toxicity was observed in the Δgpd1Δgut2Δpex10 triple mutant strain which is deficient additionally in peroxisome biogenesis. Consequently, two consecutive rounds of selection of spontaneous mutants were performed. A mutant released from growth repression by glycerol was able to produce 136.8 mg L-1 of free fatty acids in a test tube, whereas the wild type accumulated only 30.2 mg L-1 . Next, an isolated oleate-resistant strain produced 382.8 mg L-1 of free fatty acids. Finely, acyl-CoA carboxylase gene (ACC1) over-expression resulted to production of 1436.7 mg L-1 of free fatty acids. The addition of dodecane promoted free fatty acid secretion and enhanced the level of free fatty acids up to 2033.8 mg L-1 during test tube cultivation.

Co-expression of glucose-6-phosphate dehydrogenase and acyl-CoA binding protein enhances lipid accumulation in the yeast Yarrowia lipolytica.

The oleaginous yeast Yarrowia lipolytica is a convenient model for investigating lipid biosynthesis and for engineering high lipid accumulated strains. In this organism, the pentose phosphate pathway is the major source of NADPH for lipid biosynthesis. Thus, we over-expressed gene encoding NADP+-dependent glucose-6-phosphate dehydrogenase (ZWF1) in a strain deficient in peroxisome biogenesis. However, this strategy suppressed growth during cultivation under lipogenic conditions and did not significantly increase lipid accumulation. Remarkably, co-expression of gene encoding acyl-CoA binding protein (ACBP), which functions as an intracellular acyl-CoA transporter and acyl-CoA-pool former, restored growth. Co-expression of ZWF1 and ACBP increased the lipid content to 30% of dry cell weight via de novo lipid synthesis. In comparison to wild type, the engineered strain accumulated 41% more lipids with a higher ratio of saturated to unsaturated fatty acids.

Formaldehyde Fixation of Extracellular Matrix Protein Layers for Enhanced Primary Cell Growth.

Coating tissue culture vessels with the components of the extracellular matrix such as fibronectin and collagens provides a more natural environment for primary cells in vitro and stimulates their proliferation. However, the effects of such protein layers are usually rather modest, which might be explained by the loss immobilized proteins due to their weak non-covalent association with the tissue culture plastic. Here we describe a simple protocol for a controlled fixation of fibronectin, vitronectin and collagen IV layers by formaldehyde, which substantially enhances the stimulation of primary cell proliferation by these extracellular proteins.

Isolation and Expansion of Mesenchymal Stem Cells from Murine Adipose Tissue.

Mesenchymal stem cells (MSCs) are currently intensively studied due to significant promise which they represent for successful implementations of future cell therapy clinical protocols. This in turn emphasizes importance of careful preclinical studies of MSC effects in various murine disease models. The appropriate cell preparations with reproducible biological properties are important to minimize variability of results of experimental cell therapies. We describe here a simple protocol for isolation of murine MSCs from adipose tissues and their reproducible multi-log expansion under hypoxia conditions.