Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision?

Precision medicine for cancer is rapidly moving to an approach that integrates multiple dimensions of the biology in order to model mechanisms of cancer progression in each patient. The discovery of multiple drivers per tumor challenges medical decision that faces several treatment options. Drug sensitivity depends on the actionability of the target, its clonal or subclonal origin and coexisting genomic alterations. Sequencing has revealed a large diversity of drivers emerging at treatment failure, which are potential targets for clinical trials or drug repurposing. To effectively prioritize therapies, it is essential to rank genomic alterations based on their proven actionability. Moving beyond primary drivers, the future of precision medicine necessitates acknowledging the intricate spatial and temporal heterogeneity inherent in cancer. The advent of abundant complex biological data will make artificial intelligence algorithms indispensable for thorough analysis. Here, we will discuss the advancements brought by the use of high-throughput genomics, the advantages and limitations of precision medicine studies and future perspectives in this field.

[Landscape of KRAS, BRAF, and PIK3CA Mutations and Clinical Features of EBV-Associated and Microsatellite Unstable Gastric Cancer].

Personalization of gastric cancer (GC) treatment is an urgent problem because of the clinical heterogeneity and aggressive course of the disease. Four GC subtypes were isolated based on molecular characteristics by The Cancer Genome Atlas researchers in 2014: Epstein-Barr virus positive (EBV^(+)), microsatellite unstable (MSI), chromosomally unstable (CIN), and genomically stable (GS). There is no unified method to detect the CIN and GS subtypes today, while MSI and EBV status assessments are used routinely and are of great clinical importance. A total of 159 GC samples were tested for MSI, EBV DNA, and somatic mutations in codons 12-13 (exon 2), 61 (exon 3), and 146 (exon 4) of the KRAS gene; codons 597-601 (exon 15) of the BRAF gene; and codons 542-546 (exon 9), 1047-1049 (exon 20) of the PIK3CA gene. EBV^(+) GC was detected in 8.2% of samples; and MSI, in 13.2%. MSI and EBV+ were found to be mutually exclusive. The mean ages at GC manifestation were 54.8 and 62.1 years in patients with EBV^(+) and MSI GCs, respectively. EBV^(+) GC affected men in 92.3% of cases, 76.2% of the patients were older than 50 years of age. Diffuse and intestinal adenocarcinomas were diagnosed in 6 (46.2%) and 5 (38.5%) EBV^(+) cases, respectively. MSI GC equally affected men (n = 10, 47.6%) and women (n = 11, 52.4%). The intestinal histological type was the most prevalent (71.4%); the lesser curvature was affected in 28.6% of the cases. The E545K variant of PIK3CA was observed in one EBV^(+) GC case. A combination of clinically significant variants of KRAS and PIK3CA was found in all MSI cases. The BRAF V600E mutation, which is specific to MSI colorectal cancer, was not detected. The EBV^(+) subtype was associated with better prognosis. The five-year survival rates were 100.0 and 54.7% for MSI and EBV^(+) GCs, respectively.

[Questionnaire of the Ryzhikh National Medical Research Centre for Coloproctology is a new tool for assessing chronic pelvic pain and pelvic organ dysfunction]. / Oprosnik NMITs koloproktologii imeni A.N. Ryzhikh ­ novyi instrument otsenki khronicheskoi tazovoi boli i narusheniya funktsii tazovykh organov.

The article presents the work of a multidisciplinary team of experts from various fields of medicine to optimize the «Questionnaire for assessing chronic pelvic pain and pelvic organ dysfunction (QCPPD) of the Ryzhikh National Medical Research Centre for Coloproctology¼ for use in clinical practice. The survey of respondents was conducted from June 28 to September 28, 2021. As a result of this survey, by repeatedly making edits and clarifications during communication with respondents, the final version was obtained, which allows assessing the patient's subjective sensations by the nature and localization of pelvic pain, sensitivity disorders and pelvic organ function. The main objective of this Questionnaire is to differentiate patients with neurogenic pain from a huge number of patients with chronic pelvic pain. This aspect will allow a more targeted approach to the diagnosis and pathogenetically justified treatment of patients, including after appropriate instrumental examinations. The work of a multidisciplinary team implies a higher degree of objectification and terminological accuracy of the Questionnaire under discussion. The presented version of the «Questionnaire for assessing chronic pelvic pain and pelvic organ dysfunction (QCPPD) of the Ryzhikh National Medical Research Centre for Coloproctology¼ will be primarily used in coloproctological patients with pelvic pain problems and anal incontinence and obstructive defecation. Further studies will be directed to the clinical evaluation of the results of the work carried out.

Single-cell DNA-seq depicts clonal evolution of multiple driver alterations in osimertinib-resistant patients.

BACKGROUND: The development of targeted agents, such as osimertinib for EGFR-mutated non-small-cell lung cancer (NSCLC), has drastically improved patient outcome, but tumor resistance eventually always occurs. In osimertinib-resistant NSCLC, the emergence of a second molecular driver alteration (such as ALK, RET, FGFR3 fusions or BRAF, KRAS mutations) has been described. Whether those alterations and the activating EGFR mutations occur within a single cancer cell or in distinct cell populations is largely debated. PATIENTS AND METHODS: Tumor sequencing was used to identify the acquired resistance mechanisms to osimertinib in the MATCH-R trial (NCT0251782). We implemented single-cell next-generation sequencing to investigate tumor heterogeneity on patient's frozen tissues in which multiple alterations have been identified. Patient-derived models, cell lines, and patient-derived xenografts were exposed to specific inhibitors to investigate combination treatment strategies. RESULTS: Among the 45 patients included in MATCH-R who progressed on osimertinib, 9 developed a second targetable alteration (n = 2 FGFR3-TACC3, n = 1 KIF5B-RET, n = 1 STRN-ALK fusions; n = 2 BRAFV600E, n = 1 KRASG12V, n = 1 KRASG12R, n = 1 KRASG12D mutations). Single-cell analysis revealed that the two driver alterations coexist within one single cancer cell in the four patients whose frozen samples were fully contributive. A high degree of heterogeneity within samples and sequential acquisitions of molecular events were highlighted. A combination treatment concomitantly targeting the two driver alterations was required on the corresponding patient-derived models to restore cell sensitivity, which was consistent with clinical data showing efficacy of brigatinib in the patient with ALK fusion after progression to osimertinib and crizotinib administered sequentially. CONCLUSIONS: Distinct molecular driver alterations at osimertinib resistance coexist with initial EGFR mutations in single cancer cells. The clonal evolution of cancer cell populations emphasized their heterogeneity leading to osimertinib relapse. Combining two targeted treatments is effective to achieve clinical benefit.

Neuroprotective Effect of the Neuropeptide Cycloprolylglycine Depends on AMPA- and TrkB-Receptor Activation.

Previously, we have shown that the endogenous neuropeptide cycloprolylglycine (CPG) is the positive modulator of AMPA receptors and revealed the dependence of its anxiolytic and antihypoxic action on BDNF/Trk signaling. In the present work, we for the first time conducted in vitro experiments using the AMPA receptor blockers DNQX and GYKI 52466 and the Trk receptor blocker K252a. It is shown that the neuroprotective effect of CPG depends on the activation of both AMPA and Trk receptors.

Determination of the quantitative content of chlorophylls in leaves by reflection spectra using the random forest algorithm.

Determining the quantitative content of chlorophylls in plant leaves by their reflection spectra is an important task both in monitoring the state of natural and industrial phytocenoses, and in laboratory studies of normal and pathological processes during plant growth. The use of machine learning methods for these purposes is promising, since these methods allow inferring the relationships between input and output variables (prediction model), and in order to improve the quality of the prediction, a researcher may modify predictors and selects a set of method parameters. Here, we present the results of the implementation and evaluation of the random forest algorithm for predicting the total concentration of chlorophylls a and b from the reflection spectra of plant leaves in the visible and infrared wavelengths. We used the reflection spectra for 276 leaf samples from 39 plant species obtained from open sources. 181 samples were from the sycamore maple (Acer pseudoplatanus L.). The reflection spectrum represented wavelengths from 400 to 2500 nm with a step of 1 nm. The training set consisted of the 85 % of A. pseudoplatanus L. samples, and the performance was evaluated on the remaining 15 % samples of this species (validation sample). Six models based on the random forest algorithm with different predictors were evaluated. The selection of control parameters was performed by cross-checking on five partitions. For the first model, the intensity of the reflection spectra without any transformation was used. Based on the analysis of this model, the optimal ranges of wavelengths for the remaining five models were selected. The best results were obtained by models that used a two-point estimation of the derivative of the reflection spectrum in the visible wavelength range as input data. We compared one of these models (the two-point estimation of the derivative of the reflection spectrum in the range of 400-800 nm with a step of 1 nm) with the model by other authors (which is based on the functional dependence between two unknown parameters selected by the least squares method and two reflection coefficients, the choice of which is described in the article). The comparison of the results of predictions of the model based on the random forest algorithm with the model of other authors was carried out both on the validation sample of maple and on the sample from other plant species. In the first case, the predictions of the method based on a random forest had a lower estimate of the standard deviation. In the second case, the predictions of this method had a large error for small values of chlorophyll, while the third-party method had acceptable predictions. The article provides the analysis of the results, as well as recommendations for using this machine learning method to assess the quantitative content of chlorophylls in leaves.

Angiogenic Effects of Anxiolytic Fabomotizole.

In vitro experiments performed on an isolated human endothelial HUVEC cell culture showed that the anxiolytic fabomotizole, which, in addition to the anxiolytic effect, has neuroprotective and cardioprotective activities largely associated with its agonistic action on sigma-1 receptors and shows a pronounced angiogenic activity. Fabomotizole angiogenic activity is realized in the range concentration from 10-5 to 10-8 M and is doze-dependent. In the literature, data on the presence of angiogenic activity in sigma receptor agonists have not been previously reported.

Genomic profiling of late-onset basal cell carcinomas from two brothers with nevoid basal cell carcinoma syndrome.

BACKGROUND: Nevoid basal cell carcinoma syndrome (NBCCS) is an autosomal dominant genetic disorder. It is commonly caused by mutations in PTCH1 and chiefly characterized by multiple basal cell carcinomas (BCCs) developing prior to the age of 30 years. In rare cases, NBCCS presents with a late onset of BCC development. OBJECTIVE: To investigate BCC tumorigenesis in two brothers, who showed characteristic features of NBCCS but developed their first BCCs only after the age of 40 years. Two other siblings did not show signs of NBCCS. RESULTS: We obtained blood samples from four siblings and nine BCCs from the two brothers with NBCCS. Whole exome sequencing and RNA sequencing revealed loss of heterozygosity (LOH) of PTCH1 in eight out of nine tumours that consistently involved the same haplotype on chromosome 9. This haplotype contained a germinal splice site mutation in PTCH1 (NM_001083605:exon9:c.763-6C>A). Analysis of germline DNA confirmed segregation of this mutation with the disease. All BCCs harboured additional somatic loss-of-function (LoF) mutations in the remaining PTCH1 allele which are not typically seen in other cases of NBCCS. This suggests a hypomorphic nature of the germinal PTCH1 mutation in this family. Furthermore, all BCCs had a similar tumour mutational burden compared to BCCs of unrelated NBCCS patients while harbouring a higher number of damaging PTCH1 mutations. CONCLUSIONS: Our data suggest that a sequence of three genetic hits leads to the late development of BCCs in two brothers with NBCCS: a hypomorphic germline mutation, followed by somatic LOH and additional mutations that complete PTCH1 inactivation. These genetic events are in line with the late occurrence of the first BCC and with the higher number of damaging PTCH1 mutations compared to usual cases of NBCCS.

Necessary conditions for STDP-based pattern recognition learning in a memristive spiking neural network.

This work is aimed to study experimental and theoretical approaches for searching effective local training rules for unsupervised pattern recognition by high-performance memristor-based Spiking Neural Networks (SNNs). First, the possibility of weight change using Spike-Timing-Dependent Plasticity (STDP) is demonstrated with a pair of hardware analog neurons connected through a (CoFeB)x(LiNbO3)1-x nanocomposite memristor. Next, the learning convergence to a solution of binary clusterization task is analyzed in a wide range of memristive STDP parameters for a single-layer fully connected feedforward SNN. The memristive STDP behavior supplying convergence in this simple task is shown also to provide it in the handwritten digit recognition domain by the more complex SNN architecture with a Winner-Take-All competition between neurons. To investigate basic conditions necessary for training convergence, an original probabilistic generative model of a rate-based single-layer network with independent or competing neurons is built and thoroughly analyzed. The main result is a statement of "correlation growth-anticorrelation decay" principle which prompts near-optimal policy to configure model parameters. This principle is in line with requiring the binary clusterization convergence which can be defined as the necessary condition for optimal learning and used as the simple benchmark for tuning parameters of various neural network realizations with population-rate information coding. At last, a heuristic algorithm is described to experimentally find out the convergence conditions in a memristive SNN, including robustness to a device variability. Due to the generality of the proposed approach, it can be applied to a wide range of memristors and neurons of software- or hardware-based rate-coding single-layer SNNs when searching for local rules that ensure their unsupervised learning convergence in a pattern recognition task domain.

Dipeptide Mimetics of Different NGF and BDNF Loops Activate PLC-γ1.

Previously, we designed and synthesized dipeptide mimetics of individual loops of the nerve growth factor (NGF) and the brain-derived neurotrophic factor (BDNF). It was shown that these mimetics activate the corresponding tyrosine kinase (Trk) receptors and have different patterns of activation of the PI3K/AKT and MAPK/ERK postreceptor signaling pathways in vitro. In the present study, it was shown on HT-22 cells that all these compounds activate the phospholipase C-γ1 (PLC-γ1) cascade.

[The gastroprotective action of acidic mineral water from the Azhyg-Sug source on the stress-induced injuries to the stomach of white rats]. / Gastroprotektivnoe deistvie kisloi mineral'noi vody istochnika Azhyg-Sug pri stress-indutsirovannom povrezhdenii zheludka u belykh krys.

BACKGROUND: The relevance of this study is determined by the need for the scientifically sound substantiation of the possibility for the use of acidic mineral waters in the treatment of digestive diseases taking into consideration their widespread application in ethnomedicine, in particular in the Republic of Tuva. AIM: The objective of the present study was to elucidate the gastroprotective action of acidic mineral water from the Azhyg-Sug source (Republic of Tyva) on the experimental animals as exemplified by the model of ulcerogenesis under the conditions of immobilization stress. MATERIAL AND METHODS: The experimental studies were carried out with the use of 32 white rats of the Wistar line. Ulcerogenesis was initiated by means of immobilization stress. We evaluated the pathomorphological characteristics of the gastric mucosa and the number of destructions based on the Pauls index. The state of the lipid peroxidation system and antioxidative protection were determined from the content of malon dialdehyde and reduced glutathione, extracellular catalase and superoxide dismutase activities in erythrocytes. RESULTS: The study has demonstrated that the mineral water from the Azhyg-Sug source slows down the development of the inflammatory and destructive necrotic processes in the mucosa of the stomach of albino rats. The depth of erosion in the animals receiving mineral water was 2.3 and 3.4 times lower than in the control animals (p≤0.05). The antioxidant effect of mineral water was confirmed by the 14-20% decrease of the MDA concentration as well as by the increase of the catalase and superoxide dismutase (SOD) activities by 21-25% and 20-30% respectively in comparison with the control animals. CONCLUSION: The Azhyg-Sug mineral water has the strong gastroprotective influence on the experimental animals having the induced neurogenic ulcer. One of the mechanisms underlying the gastroprotective action of the investigated mineral water arises from its ability to inhibit the processes of lipid peroxidation with the simultaneous enhancement of the activity of the antioxidant system of the organism.

Heisenberg-exchange-free nanoskyrmion mosaic.

Isotropic Heisenberg exchange naturally appears as the main interaction in magnetism, usually favouring long-range spin-ordered phases. The anisotropic Dzyaloshinskii-Moriya interaction arises from relativistic corrections and is a priori much weaker, even though it may sufficiently compete with the isotropic one to yield new spin textures. In this work, we challenge this well-established paradigm, and propose to explore a Heisenberg-exchange-free magnetic world. In this case, the Dzyaloshinskii-Moriya interaction induces magnetic frustration in two dimensions, from which the competition with an external magnetic field results in a new mechanism producing skyrmions of nanoscale size. A single nanoskyrmion can already be stabilized in a few-atom cluster, and may then be used as LEGO® block to build a large magnetic mosaic. The realization of such topological spin nanotextures in sp- and p -electron compounds or in ultracold atomic gases would open a new route toward robust and compact magnetic memories.

[Treatment of chronic viral hepatitis C with direct acting antiviral agent: review].

HCV infection treatment regimens are viewed from positions of HCV life cycle and replication, effects of NS3/4A protease inhibitors and NS5A/NS5B inhibitors on HCV strain replication. Evolution of HCV treatment regimens from its discovery to modern DAA agents had led to substantial progress although drug resistance poses a new issue to be addressed.

[Antimutagenic and antioxidant features of confectionery products containing the powder from the leaves of Hippophae rhamnoides L.]

The aim of the work was to determine the possibility of using the powder from the leaves of Hippophae rhamnoides L. for enriching flour confectionery and to evaluate the antimutagenic and antioxidant activity of the product. The experiment was carried out on 24 white Wistar rats with initial body weight (b.w.) 180-200 g. The animals of the experimental group (n=8) received confection containing sea buckthorn powder at a rate of 20 mg per 100 g b.w. for 14 days on the background of a standard vivarium diet. The animals of the control and intact groups received confection containing no bioactive supplement at the same dose. Antimutagenic and antioxidant effects were estimated in a day after a single injection of cyclophosphamide at a dose of 20 mg/kg b.w. The number of chromosomal aberrations in bone marrow cells of white rats was counted and the activity of catalase, superoxide dismutase (SOD), the level of reduced glutathione and the concentration of TBA-active products in blood were evaluated. The intake of the confectionery containing the powdered H. rhamnoides leaves resulted in the 45% decrease of the number of damaged cells, 50% decrease of the proportion of cells with multiple chromosome breaks and 52% decrease of the number of achromatic gaps as compared to animals of the control group (n=8). The cake intake increased the activity of catalase (by 52%) and SOD (by 33%) and glutathione content (by 26%) in blood.

Analysis of the Basic Characteristics of Osteogenic and Chondrogenic Cell Lines Important for Tissue Engineering Implants.

We isolated and characterized cultures of bone and cartilage tissue cells of laboratory minipigs. The size and morphological features of adherent osteogenic and chondrogenic cells were specified. During long-term culturing under standard conditions, the studied cultures expressed specific markers that were detected by immunohistochemical staining: alkaline phosphatase and calcium deposits in osteoblasts and type II collagen and cartilage extracellular matrix in chondrogenic cells. Proliferative potential (mitotic index) of both cell types was 4.64% of the total cell number. Cell motility, i.e. the mean velocity of cell motion was 49 pixels/h for osteoblasts and 47 pixels/h for chondroblasts; the mean migration distance was 2045 and 2118 pixels for chondroblasts and osteoblasts, respectively. The obtained cell lines are now used as the control for evaluation of optimal biocompatibility of scaffold materials in various models. Characteristics of the motility of the bone and cartilage tissue cells can be used for modeling and estimation of the rate of cells population of 3D scaffolds made of synthetic and biological polymers with different internal structure and physicochemical properties during designing in vitro tissue implants.

Antiangiogenic Effects of Nerve Growth Factor Loop 4 Monomeric Dipeptide Mimetic.

The effects of GK-1, a monomeric dipeptide mimetic of nerve growth factor (NGF) loop 4, on angiogenesis were studied in vitro and in vivo. Experiments on human umbilical vein endothelial cells HUVEC showed that the test compound did not affect tubulogenesis (initial stage of angiogenesis) and prevented realization of the angiogenic effect of NGF and its dimeric dipeptide mimetic GK-2. Experiments on rat hind limb ischemia model demonstrated that GK-1 (1 mg/kg/day intraperitoneally over 14 days) significantly reduced the density of the capillary network in ischemic tissue and increased the number and area of Zenker necrosis in comparison with the control. These data suggest that GK-1 exhibits a pronounced antiangiogenic activity.

Angiogenic Effects of Dimeric Dipeptide Mimetic of Loop 4 of Nerve Growth Factor.

Angiogenic action of compound GK-2, a dimeric dipeptide mimetic of loop 4 of nerve growth factor (NGF), was studied in in vitro and in vivo experiments. Experiments on human endothelial cell culture HUVEC showed that compound GK-2 significantly (p<0.05) stimulated the initial stage of angiogenesis, and its angiogenic activity was not inferior to the reference neurotrophin NGF. In experiments with hindlimb ischemia modeled in rats, GK-2 (1 mg/kg intraperitoneally for 14 days) significantly increased the total length of capillary vessels (p<0.003) and the number of vessels per 1 mm2 ischemic tissue (p<0.001) in comparison with the control. Our findings indicate that under experimental conditions compound GK-2 exhibits not only angiogenic, but also anti-ischemic activity.