Conjugates of 3,5-Bis(arylidene)-4-piperidone and Sesquiterpene Lactones Have an Antitumor Effect via Resetting the Metabolic Phenotype of Cancer Cells.

In recent years, researchers have often encountered the significance of the aberrant metabolism of tumor cells in the pathogenesis of malignant neoplasms. This phenomenon, known as the Warburg effect, provides a number of advantages in the survival of neoplastic cells, and its application is considered a potential strategy in the search for antitumor agents. With the aim of developing a promising platform for designing antitumor therapeutics, we synthesized a library of conjugates of 3,5-bis(arylidene)-4-piperidone and sesquiterpene lactones. To gain insight into the determinants of the biological activity of the prepared compounds, we showed that the conjugates of 3,5-bis(arylidene)-4-piperidone and sesquiterpene lactones, which are cytotoxic agents, demonstrate selective activity toward a number of tumor cell lines with glycolysis-inhibiting ability. Moreover, the results of molecular and in silico screening allowed us to identify these compounds as potential inhibitors of the pyruvate kinase M2 oncoprotein, which is the rate-determining enzyme of glycolysis. Thus, the results of our work indicate that the synthesized conjugates of 3,5-bis(arylidene)-4-piperidone and sesquiterpene lactones can be considered a promising platform for designing selective cytotoxic agents against the glycolysis process, which opens new possibilities for researchers involved in the search for antitumor therapeutics among compounds containing piperidone platforms.

TP63-TRIM29 axis regulates enhancer methylation and chromosomal instability in prostate cancer.

BACKGROUND: Prostate adenocarcinoma (PRAD) is the second leading cause of cancer-related deaths in men. High variability in DNA methylation and a high rate of large genomic rearrangements are often observed in PRAD. RESULTS: To investigate the reasons for such high variance, we integrated DNA methylation, RNA-seq, and copy number alterations datasets from The Cancer Genome Atlas (TCGA), focusing on PRAD, and employed weighted gene co-expression network analysis (WGCNA). Our results show that only single cluster of co-expressed genes is associated with genomic and epigenomic instability. Within this cluster, TP63 and TRIM29 are key transcription regulators and are downregulated in PRAD. We discovered that TP63 regulates the level of enhancer methylation in prostate basal epithelial cells. TRIM29 forms a complex with TP63 and together regulates the expression of genes specific to the prostate basal epithelium. In addition, TRIM29 binds DNA repair proteins and prevents the formation of the TMPRSS2:ERG gene fusion typically observed in PRAD. CONCLUSION: Our study demonstrates that TRIM29 and TP63 are important regulators in maintaining the identity of the basal epithelium under physiological conditions. Furthermore, we uncover the role of TRIM29 in PRAD development.

Data on somatic mutations obtained by whole exome sequencing of FFPE tissue samples from Russian patients with prostate cancer.

Prostate cancer (PCa) is the most frequently diagnosed among men malignant disease that remains poorly characterized at the molecular level. Advanced PCa is not curable, and the current treatment methods can only increase the life expectancy by several months. Identification of the genetic aberrations in tumor cells provides clues to understanding the mechanisms of PCa pathogenesis and the basis for developing new therapeutic approaches. Here we present data on somatic mutations, namely single nucleotide variations (SNVs), small insertions and deletions, detected in prostate tumor tissue obtained from Russian patients with PCa. Moreover, we provide a raw dataset on the whole exome and targeted DNA sequencing of tumor and non-tumor prostate tissue obtained from Russian patients with PCa and benign prostatic hyperplasia (BPH). This data is available at NCBI Sequence Read Archive under Accession No. PRJNA506922.

[Search for genetic markers for precise diagnostics of keratoconus]. / Poisk geneticheskikh markerov dlia utochniaiushchei diagnostiki keratokonusa.

Keratoconus is a chronic disorder of the cornea, characterized by its progressive thinning, stretching, and conical protrusion. Diagnostics of subclinical keratoconus, as well as its early stages (forme fruste), is a complex problem. The presence of these forms of keratoconus in a patient is one of the reasons for the development of keratectasia after laser refractive surgery. Currently, the role of genetic factors in keratoconus development has been proven. This indicates the possibility of diagnostics of subclinical and forme fruste keratoconus using genetic markers. Knowledge about the patient's genetic susceptibility to keratoconus would allow correcting the tactics of treatment of refractive anomalies and avoiding serious side effects. The studies of causal mutations indicate the genetic heterogeneity of keratoconus, which complicates the development of a diagnostic panel. Selection of candidate variants from the currently known ones based on clear criteria may be one of the approaches for diagnostic markers search. In this review, we have analyzed articles on keratoconus markers in order to form a list of candidate variants for genotyping in the Russian population. The selection criteria took into account the complexes of symptoms in which a marker was found, populations in which a particular marker was investigated, the presence and results of replication studies. The analysis included markers in VSX1, SOD1, ZEB1, LOX, CAST, DOCK9, TGFBI, HGF, MAP3K19, KCND3, COL4A3, COL4A4, COL5A1, FNDC3B, FOXO1, BANP-ZNF469, MPDZ-NF1B, WNT10A genes. Based on the results of the analysis, the following candidate variants were selected for genotyping in the Russian population of patients with keratoconus: rs1536482 and rs7044529 in the COL5A1 gene, rs5745752 and rs2286194 in the HGF gene, rs4954218 in the MAP3K19 gene, rs4839200 near the KCND3 gene, rs2721051 near the FOXO1 gene, rs1324183 between the MPDZ and the NF1B genes, and rs121908120 in the WNT10A gene.

LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer.

Although modern methods of whole genome DNA methylation analysis have a wide range of applications, they are not suitable for clinical diagnostics due to their high cost and complexity and due to the large amount of sample DNA required for the analysis. Therefore, it is crucial to be able to identify a relatively small number of methylation sites that provide high precision and sensitivity for the diagnosis of pathological states. We propose an algorithm for constructing limited subsamples from high-dimensional data to form diagnostic panels. We have developed a tool that utilizes different methods of selection to find an optimal, minimum necessary combination of factors using cross-entropy loss metrics (LogLoss) to identify a subset of methylation sites. We show that the algorithm can work effectively with different genome methylation patterns using ensemble-based machine learning methods. Algorithm efficiency, precision and robustness were evaluated using five genome-wide DNA methylation datasets (totaling 626 samples), and each dataset was classified into tumor and non-tumor samples. The algorithm produced an AUC of 0.97 (95% CI: 0.94-0.99, 9 sites) for prostate adenocarcinoma and an AUC of 1.0 (from 2 to 6 sites) for urothelial bladder carcinoma, two types of kidney carcinoma and colorectal carcinoma. For prostate adenocarcinoma we showed that identified differential variability methylation patterns distinguish cluster of samples with higher recurrence rate (hazard ratio for recurrence = 0.48, 95% CI: 0.05-0.92; log-rank test, p-value < 0.03). We also identified several clusters of correlated interchangeable methylation sites that can be used for the elaboration of biological interpretation of the resulting models and for further selection of the sites most suitable for designing diagnostic panels. LogLoss-BERAF is implemented as a standalone python code and open-source code is freely available from https://github.com/bioinformatics-IBCH/logloss-beraf along with the models described in this article.

[Targeted gene sequencing panels: applicability for neoantigen profiling of colon and rectal adenocarcinoma]. / Vozmozhnosti primeneniia targetnykh panelei dlia opredeleniia neoantigennogo profilia obraztsov adenokartsinomy tolstoi i priamoi kishki.

Cancer immunotherapy represents a promising and rapidly developing approach for the treatment of oncological diseases. Among the methods of personalized adjuvant immunotherapy, neoantigenic peptide-based drugs have demonstrated substantial efficiency. These drugs are designed to target mutant proteins arising from somatic alterations in the genome of tumor cells and thus stimulate immune response against tumor tissues. The methods of individual screening for potentially immunogenic mutations are mostly based on next-generation exome sequencing of tumor samples, which is a complex and costly procedure for clinical application. Targeted gene sequencing panels limited to a certain set of genes represent a reasonable alternative to WES. Targeted sequencing is also more efficient when there is a low amount of the sample DNA available. We have estimated the potential efficiency of targeted oncological panels in terms of somatic neoantigen profiling in colorectal cancer (colon and rectal adenocarcinoma). The clinical practice of identification of frequent somatic variants does not provide enough data for designing an efficient personalized drug when applied to low and medium mutated cancers such as colorectal cancer. Our analysis of 11 commercially available panels containing different number of genes has shown that neither the larger size of a panel nor its initial customization for colorectal cancer provides a significantly better estimation of an individual somatic mutation profile. The optimal approach is to use the general-purpose medium-sized cancer panels (2300-11200 amplicons and/or 150-600 genes). These panels allow to detect a sufficient number of immunogenic epitopes (>3) per patient for over 30-50% of patients.

Datasets for next-generation sequencing of DNA and RNA from urine and plasma of patients with prostate cancer.

Current prostate cancer (PCa) diagnostic tests suffer from insufficient sensitivity and specificity. Novel biomarkers that can be detected by minimally invasive methods are of a particular value. Here we provide two datasets. The first one is on the whole transcriptome profiling by RNA-seq of urine and plasma obtained from patients with PCa and benign prostatic hyperplasia (BPH). The second one represents targeted sequencing of DNA from urine and plasma of patients with PCa and BPH. Both datasets are available at NCBI Sequence Read Archive under Accession No. SRP093707 and No. SRP093842 respectively.

[Association of polymorphism of 1800255 COL3A1 gene with pelvic organ prolapse and urinary incontinence in women: preliminary data].

RELEVANCE: Collagen type I and III have a significant role in the development of pelvic organ prolapse (POP) and urinary incontinence in women. The role of the COL3A1 gene polymorphism remains debatable. Some studies and meta-analyzes have found a direct correlation between genetic defects and POP, while other researchers have not confirmed this association. This study aimed to investigate the association of the 1800255 COL3A1 gene polymorphism with the development of POP and urinary incontinence in women. MATERIALS AND METHODS: The study group comprised 52 patients (mean age 64.4 years) with verified POP and stress urinary incontinence. The control group included 21 patients without pelvic floor dysfunction. Patients were comparable in age and had at least one or more risk factors for developing pelvic floor dysfunction. Exclusion criteria for both groups were Marfan and Ehlers-Danlos syndromes and a history of surgery for POP or incontinence (for the control group). In all women, saliva samples were collected to detect polymorphism at the rs1800255 locus of the COL3A1 gene. Genotyping was conducted by Sanger sequencing. RESULTS: In patients with isolated genital prolapse, homozygous polymorphism (AA) had a low sensitivity (0.06) but an extremely high specificity (0.95). Heterozygote (GA) had the sensitivity of 0.35, the specificity of 0.53, and the AUC of 0.44. For urinary incontinence by homozygote (AA), sensitivity was 0.08, specificity 0.96, and by heterozygote (GA) 0.45 and 0.63, respectively. For the combination of pelvic prolapse and urinary incontinence by homozygote (AA), sensitivity was 0.07, specificity 1.0, and heterozygote (GA) 0.41 and 0.62, respectively. CONCLUSION: Given the high specificity of the polymorphism at the rs1800255 locus of the COL3A1 gene, determined by the Sanger sequencing, it can be concluded that there is an association between this polymorphism and urinary incontinence and POP in women.

[GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value]. / Status metilirovaniia genov GSTP1, APC i RASSF1 v obraztsakh raka predstatel'noi zhelezy cheloveka: sravnitel'nyi analiz diagnosticheskoi informativnosti metodov MS-HRM i gibridizatsii na DNK-chipakh illumina Infinium HumanMethylation450 BeadChip.

There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

[Genome-wide analysis of DNA methylation in prostate cancer using the technology of Infinium HumanMethylation450 BeadChip (HM450)].

Using the technology of DNA chips Infinium HumanMethylation 450 BeadChip it was analyzed quantitative DNA methylation status in 12 paired samples of prostate adenocarcinoma, and morphologically altered tissues. Analysis of differentially methylated regions of the genome showed an association with abnormal status for 21610 and 3852 hypomethylated hyper-methylated CpG sites. Dominance in the cancer genome hypermethylated sites and their predominant localization in the regulatory regions of genes indicate their possible role in the implementation of mechanisms of gene suppression in the pathogenesis of prostate cancer (PCa). For 14 genes studied were characterized array maximum values hypermethylation in promoter region (> 50% CpG sites) in combination with a high level of methylation differences between treatment groups (> 40%). Role of hypermethylation in some of them: AOX1, KLF8, ZNF154, TMEM106A in the pathogenesis of prostate cancer has been showed previously. Hypermethylation of genes ACSS3, TAC1, TUBA4B, ZSCAN12 not previously been shown for prostate cancer, but is characterized by the association with other cancers. In turn, the differences in the levels of methylation in genes GPRASP1, NKX2-6, ARX, CYBA, EPSTI1, RHCG been documented as a result of a number of genome-research oncology, but has not been studied in detail. To assess the diagnostic potential of epigenetic markers of prostate cancer there was carried out unbiased selection of individual CpG sites most reliably discriminate against tumor samples from a group of no tumor samples. In selected diagnostic model based on logistic regression included 9 CpG sites. Validation of the model was carried out on an independent dataset of methylation of 40 paired samples from the prostate cancer project Atlas of Cancer Genome (TCGA) analyzed on the same version of the DNA chip. Summarized rates of diagnostic informativeness of a model (specificity 95%, sensitivity of 97%, the area under the curve of the diagnostic test (ROC) - 0,96), obtained after validation, allow us to consider these CpG Sites as potential markers for molecular diagnosis of prostate cancer.

[Primary candidate rna biomarker screening by RNA-seq for prostate cancer diagnostics].

The RNA-seq approach for prostate cancer candidate RNA biomarkers screening in plasma and urine obtained by minimally invasive or noninvasive methods is proved to be feasible. Significant amount of RNA biomarkers associated with prostate cancer according to the literature were found in plasma and urine samples obtained from patients with benign prostatic hyperplasia (BPH). The number of detected markers was shown to vary in accordance with method of library preparation used for transcriptome profiling. The detection of known RNA biomarkers for prostate cancer in urine and plasma samples shows the feasibility of such method for minimally invasive diagnostics. The fact of presence of the same RNA biomarkers in samples from patients with BPH suggests their possible lack of specificity and confirms the need for further research in this area.

[FMRI-EEG estimation of cerebral reactivity to motor tasks in patients with brain tumors].

fMRI (1.5 or 3 T) and EEG studies with estimation of reactive responses on motor task (by right or left hand) were performed in 9 patients with tumors localized in frontal lobe of the brain. Results of this investigation were compared with results of the similar study in 12 healthy persons. It was shown that in cases of the brain pathology disorders of functional specialization and increase of diffuse component of reactivity was observed, fMRI-responses had been characterized the more intact reactions than reactive changes of EEG parameters. This specificity was described in cases of afferent loads in damaged hemisphere. Peculiarity of including different spectral bands in forming of EEG responses on motor tasks and changes of fMRI-answer depend on degree of cerebral decompensation, reflected in the of baseline EEG reorganization and degree of motor defect. Predominantly an increase of EEG coherence in delta-band with the predominance of reaction in the damaged hemisphere in cases of addressing any afferent load was observed in patients with severe cerebral decompensation and reflect dominant character of pathological focus forming. This data indicate on the more including of the deep brain structures in process of reactivity in patients compared with healthy persons and confirmed by fMRI-data.

[Study of the role of the right and left orbitofrontal cortex in compensatory cerebral reactions after acute brainstem damage].

Significance of the right and left orbitofrontal cortex (OFC) in recovery after acute brainstem lesion (at the level of n. Deiters) was investigated using rat model of complex brainstem-orbitofrontal cerebral damage. It was found that the right-side lesion of the OFC combined with isolated brainstem damage resulted in aggravation of the animal condition and highly probable lethal outcome within the first two weeks after surgery (because of the brain circulation disorder of hemorrhagic type). It may be associated with sympathetic activation. It is suggested that a certain "stimulation" of the left OFC (as the effect of its incomplete destruction) involves a parasympathetic compensatory reaction that allows animals with a severe brainstem pathology to survive. It is shown that, with the general nonspecific tendency to postoperative increase in emotionality, the greatest shifts in the emotional sphere take place under conditions of a combined damage of the brainstem and left OFC.

[Intracerebral EEG functioning as a reflexion of the systemic brain organization in norm and pathology]. / Mezhtsentral'nye otnosheniia EEG kak otrazhenie sistemnoi organizatsii mozga cheloveka v norme i patologii.

The authors summarized the EEG findings and defined the nature of intercentral EEG relationships in different functional states of healthy subjects and patients with organic cerebral pathology based on coherence analysis. The EEG features typical of healthy subjects were identified: an anterior-posterior gradient of the mean coherence and the character of cortical-subcortical relationships in the anterior cerebral structures. Right- and lefthanded subjects showed the frequency and regional differences in EEG coherence, which reflected, mainly, specific intracortical relationships. Development and regression of pathologic signs in right- and lefthanded patients with organic brain lesions are thought to be determined by these differences. As distinct from cortical pathology, lesions of regulatory structures (diencephalic, brainstem, and limbic) were shown to produce more diffuse changes in intercentral relationships with a tendency to reciprocity. Intercentral relations, including their interhemispheric differences, varied with changes in the functional state of healthy subjects (increase and decrease in the level of functioning). A certain time course of changes in intercentral relationships was also revealed in patients with organic brain lesions during recovery of their consciousness and mental activity. Changes in the dominance of activity of individual regulatory structures are considered to be one of the most important factors that determine the dynamic character of EEG coherence.

[Component P300 of acoustic evoked potential in patients with local brain lesion]. / Komponent P300 akusticheskogo vyzvannogo potentsiala u bol'nykh s ochagovym porazheniem golovnogo mozga.

The aim of the study was a comparative analysis of spatial-temporary organization of P300 acoustic evoked potential (AEP) in patients with local lesions of the brain stem, frontal and temporal structures in the situations of "passive" listening to sounds and their active recognition (a count). Specific changes of P300 parameters were distinguished in each group. The peak-temporary P300 parameters--latency increase, decrease of amplitude and tendency to the decrease of half-cycle--were similarly changed, irrespective of brain damage topography. A degree of the changes correlated with a level of functional acoustic evoked potential decompensation. In relation to pathologic process location, the topographical P300 AEP features were more specified, comparing to peak-temporary parameters. An existence of two systems for P300 generation at "active" counting and "passive" listening was suggested. In "passive" listening, a response is mostly determined by intact left frontal lobe and middle-stem structures but in "active" counting--by intact right frontal lobe or lobes and limbic system structures (hippocampus).

[The effects of combined electrolytic brain stem-orbitofrontal and brain stem-hippocampal damages to the rat brain]. / Effekty sochetannogo élektroliyicheskogo stvolovo-orbitofrontal'nogo i stvolovo-gippokampal'nogo povrezhdeniia mozga krys.

Morphofunctional studies of animals with associated electrolytic orbitofrontal and hippocampal brainstem lesions as compared to variants of isolated brainstem coagulation showed participation and specific role of orbitofrontal cortex and hippocampus in adaptive-compensatory brain reactions of rats with brainstem lesions. Associated brainstem-orbitofrontal damages result in aggravation of the animals' condition and highly probable lethality within the first two weeks after surgery due to blood circulation dysregulation of hemorrhagic type and probably due to secondary hypothalamus dysfunction. Associated brainstem-hippocampal coagulation intensifies primarily brainstem neurologic symptoms and prolongs time of their reverse development, i.e. supports the brainstem centre of stable pathological activity.

[The effect of the brain stem structures on the shaping of the functional state of the human cerebral hemispheres (data from complex clinico-electroencephalographic and neuropsychological research)]. / Vliianie stvolovykh struktur na formirovanie funktsional'nogo sostoianiia bol'shikh polusharii golovnogo mozga cheloveka (dannye kompleksnogo kliniko-élektroéntsefalograficheskogo i neiropsikhologicheskogo issledovaniia).

To study the influence of the brainstem on formation of the functional state of the left and right brain hemispheres clinical electrophysiological examination of 13 patients with focal brainstem lesions (neurinoma of the auditory nerve) was carried out before and after surgery. The result were compared with neuropsychological data. Definite correlation was revealed between the changes in coherent structure of EEG and neuropsychological estimation of the functional state of brain areas. The brainstem was shown to be more intimately functionally connected with the left hemisphere than with the right one. The regional specificity within the left hemisphere was determined by the form of cerebral decompensation.

[Adaptive-compensatory restructurings of the intrahemispheric interaction of electrical processes in the human brain in brain stem lesions]. / Adaptivno-kompensatornye perestroiki vnutripolusharnogo vzaimodeistviia élektricheskikh protsessov mozga cheloveka pri porazhenii stvolovykh struktur.

In 50 patients with focal lesions of the brainstem was analysed the postsurgery dynamics of the interhemispheric interaction (by the characteristics of EEG coherence). Was shown a specific participation of the left and the right hemispheres in a realization of postoperative compensatory brain reactions. In survived patients in early terms after surgery the phase was revealed in which coherence in the left hemisphere exceeded that in the right one and the difference being significant for the frontal areas. This phenomenon reflected higher reactivity of the dominant hemisphere in a realization of the adaptive reactions of the CNS. Right hemispheric EEG coherence in general had lower values and was more inert. It dominated under the conditions when only vegetative regulation remained before the lethal exit.