PHENSIM: Phenotype Simulator.

Despite the unprecedented growth in our understanding of cell biology, it still remains challenging to connect it to experimental data obtained with cells and tissues' physiopathological status under precise circumstances. This knowledge gap often results in difficulties in designing validation experiments, which are usually labor-intensive, expensive to perform, and hard to interpret. Here we propose PHENSIM, a computational tool using a systems biology approach to simulate how cell phenotypes are affected by the activation/inhibition of one or multiple biomolecules, and it does so by exploiting signaling pathways. Our tool's applications include predicting the outcome of drug administration, knockdown experiments, gene transduction, and exposure to exosomal cargo. Importantly, PHENSIM enables the user to make inferences on well-defined cell lines and includes pathway maps from three different model organisms. To assess our approach's reliability, we built a benchmark from transcriptomics data gathered from NCBI GEO and performed four case studies on known biological experiments. Our results show high prediction accuracy, thus highlighting the capabilities of this methodology. PHENSIM standalone Java application is available at https://github.com/alaimos/phensim, along with all data and source codes for benchmarking. A web-based user interface is accessible at https://phensim.tech/.

The combination of TPL2 knockdown and TNFα causes synthetic lethality via caspase-8 activation in human carcinoma cell lines.

Most normal and tumor cells are protected from tumor necrosis factor α (TNFα)-induced apoptosis. Here, we identify the MAP3 kinase tumor progression locus-2 (TPL2) as a player contributing to the protection of a subset of tumor cell lines. The combination of TPL2 knockdown and TNFα gives rise to a synthetic lethality phenotype via receptor-interacting serine/threonine-protein kinase 1 (RIPK1)-dependent and -independent mechanisms. Whereas wild-type TPL2 rescues the phenotype, its kinase-dead mutant does not. Comparison of the molecular events initiated by small interfering RNA for TPL2 (siTPL2) ± TNFα in treatment-sensitive and -resistant lines revealed that the activation of caspase-8, downstream of miR-21-5p and cFLIP, is the dominant TPL2-dependent event. More important, comparison of the gene expression profiles of all of the tested cell lines results in the clustering of sensitive and resistant lines into distinct groups, providing proof of principle for the feasibility of generating a predictive tool for treatment sensitivity.

CHARACTERISTICS OF DEVELOPMENT OF EMOTIONAL BURNOUT SYNDROME IN FAMILY DOCTORS AND THEIR CORRECTION METHODS.

OBJECTIVE: The aim: Among the adverse psychological changes associated with medical work, a significant place belongs to the emotional burnout syndrome, which significantly affects a doctor's social functioning. The purpose of the study was to determine the behavioural activity types and to study the muscular sensitivity threshold of family doctors with the formed emotional burnout syndrome. PATIENTS AND METHODS: Materials and methods: We examined 83 female family doctors with diagnosed emotional burnout syndrome. The treatment was carried out with the help of the Taiji-Quan eastern wellness system. RESULTS: Results: The analysis of indicators of the behavioural activity revealed before treatment in 72,5% of women in the intervention group and in 69,8% of women in the control group (p>0,05) signs of the high probability of type A behaviour. After a three-month course of treatment, the percentage of manifestations of type A behaviour in women in the intervention group decreased from 72,5% to 40,0% (p 0,05). When examining the features of muscular tone at the beginning of treatment, it was found that 69,9% of women in the intervention group and 65,1% of the control group had a high degree of muscle blocks (p>0,05). After treatment, the percentage of women with a high degree of muscle blocks decreased to 37,5% (p 0,05) in the control group. CONCLUSION: Conclusions: The taiji-Quan treatment made it possible to significantly reduce type A behaviour and to decrease the amount of "muscle blocks".

Health-related behaviour in adolescents who have received basic instruction in health promotion.

OBJECTIVE: Introduction: Both positive and risky health behaviours among adolescents are of paramount importance as they often pathway further lifestyles and determine future health outcomes. The paper focuses on the trends of health promotion activities and health risks among adolescents who have been instructed on these topics at secondary schools. The aim: to detect trends in pro-active health behaviour and risk taking activities of Ukrainian adolescents in the last 14 years. PATIENTS AND METHODS: Materials and methods: males and females, aged 15-17, who studied in secondary schools of the urban area of Vinnytsia city, Ukraine, in the years 2003, 2013, 2017, anonymously filled in the 118-item questionnaire. Descriptive statistics, Cochran Q test, Spearman correlation analysis, Kendall's tau coefficient were used to analyze the data. RESULTS: Results: Overall, the data about health related issues obtained in the year 2003 vary significantly from the years 2013 and 2017, which indicates some beneficial influence that has taken place since 2003. Much fewer differences were spotted between the years 2013 and 2017. Health related behaviours in females showed less significant dynamics and some changes indicate regression, while males reported multiple improved results. Meanwhile actual numbers of males who opted for risky behaviours were higher than those of females. Significant relationships were found between some socio-economic factors, positive health behaviours (sufficient sleep, physical activity, daily regime, and life satisfaction) and proactive health choices. CONCLUSION: Conclusions: The available data suggests that there was a beneficial health-related influence on the schoolchildren over the years 2003-2017. Our findings also support the view that certain assets may protect the youth from risk-taking behaviours.

Computer-tomographic characteristics of root length incisors and canines of the upper and lower jaws in boys and girls with different craniotypes and physiological bite.

INTRODUCTION: In recent years, in world literature appeared research, which focuses on the study of relationships craniotypes with odonto-metric indicators, size, shape of the dental arches and occlusion. However, most of the experts focus on the study of individual features of the structure of the teeth-jaw system in people with different types of faces and aspects of sexual dimorphism and ethnic characteristics. Studies containing information about cranio-typological variability of the roots of teeth we did not encounter. The aim is to reveal features length of roots of incisors and canines of the upper and lower jaw, according to the CT scan in boys and girls of different craniotypes with physiological bite, residents Podilskiy region of Ukraine. MATERIAL AND METHODS: The study involved young men with orthognathic bite and their cephalometric performance taken from database from Scientific and Research Center Vinnitsa National Medical University named after Pirogov. To make CT used dental cone beam CT scan - Veraviewepocs 3D, Morita. In the upper and lower incisors and canines were measured vestibular-oral and mesio-distal projection length of the root. The height (length) of the root was measured in the medial (or distal) norm, focusing on border basics crowns (root) and the apex of the tooth root. Established the following distribution craniotype: mesocephalic boys - 16, boys brachycephalic - 19, mesocephalic girls - 16, brachycephalic girls- 26. Statistical analysis of the results was performed using the statistical software package licensed "Statistica 6,0" using non-parametric estimation methods. RESULTS: The peculiarities computed tomographic characteristics of root length incisors and canines of the upper and lower jaws in boys and girls Podilskiy region of Ukraine with different craniotypes and physiological bite have been set. In boys or girls mesocephals majority values of vestibular-oral and mesio-distal projection length of the teeth root, medial and lateral incisors in the upper and lower jaws significantly higher compared to studied similar gender brachycephals. Most values vestibular-oral and mesiodistal projection length of the teeth root, medial and lateral incisors in the upper and lower jaws in boys of total group and brachycephals significantly higher compared with girls of similar comparison groups. In boys mesocephals only value of vestibular-oral projection length of teeth root on the lower jaw was significantly higher compared with girls of the same craniotype. CONCLUSIONS: In mesocephalic boys or girls majority values of vestibular-oral and mesio-distal length projection of the root teeth, medial and lateral incisors on the upper and lower jaws significantly higher compared to similar brachycephalic genders studied.

MicroRNA214 Is Associated With Progression of Ulcerative Colitis, and Inhibition Reduces Development of Colitis and Colitis-Associated Cancer in Mice.

BACKGROUND & AIMS: Persistent activation of the inflammatory response contributes to the development of inflammatory bowel diseases, which increase the risk of colorectal cancer. We aimed to identify microRNAs that regulate inflammation during the development of ulcerative colitis (UC) and progression to colitis-associated colon cancer (CAC). METHODS: We performed a quantitative polymerase chain reaction analysis to measure microRNAs in 401 colon specimens from patients with UC, Crohn's disease, irritable bowel syndrome, sporadic colorectal cancer, or CAC, as well as subjects without these disorders (controls); levels were correlated with clinical features and disease activity of patients. Colitis was induced in mice by administration of dextran sodium sulfate (DSS), and carcinogenesis was induced by addition of azoxymethane; some mice also were given an inhibitor of microRNA214 (miR214). RESULTS: A high-throughput functional screen of the human microRNAome found that miR214 regulated the activity of nuclear factor-κB. Higher levels of miR214 were detected in colon tissues from patients with active UC or CAC than from patients with other disorders or controls and correlated with disease progression. Bioinformatic and genome-wide profile analyses showed that miR214 activates an inflammatory response and is amplified through a feedback loop circuit mediated by phosphatase and tensin homolog (PTEN) and PDZ and LIM domain 2 (PDLIM2). Interleukin-6 induced signal transducer and activator of transcription 3 (STAT3)-mediated transcription of miR214. A miR214 chemical inhibitor blocked this circuit and reduced the severity of DSS-induced colitis in mice, as well as the number and size of tumors that formed in mice given azoxymethane and DSS. In fresh colonic biopsy specimens from patients with active UC, the miR214 inhibitor reduced inflammation by increasing levels of PDLIM2 and PTEN. CONCLUSIONS: Interleukin-6 up-regulates STAT3-mediated transcription of miR214 in colon tissues, which reduces levels of PDLIM2 and PTEN, increases phosphorylation of AKT, and activates nuclear factor-κB. The activity of this circuit correlates with disease activity in patients with UC and progression to colorectal cancer.

Tpl2 ablation promotes intestinal inflammation and tumorigenesis in Apcmin mice by inhibiting IL-10 secretion and regulatory T-cell generation.

To address the role of Tpl2, a MAP3K8 that regulates innate/adaptive immunity and inflammation, in intestinal tumorigenesis, we crossed a Tpl2 KO allele into the Apc(min/+) genetic background. Here, we show that Apc(min/+)/Tpl2(-/-) mice exhibit a fivefold increase in the number of intestinal adenomas. Bone marrow transplantation experiments revealed that the enhancement of polyposis was partially hematopoietic cell-driven. Consistent with this observation, Tpl2 ablation promoted intestinal inflammation. IL-10 levels and regulatory T-cell numbers were lower in the intestines of Tpl2(-/-) mice, independent of Apc and polyp status, suggesting that they were responsible for the initiation of the enhancement of tumorigenesis caused by the ablation of Tpl2. The low IL-10 levels correlated with defects in mTOR activation and Stat3 phosphorylation in Toll-like receptor-stimulated macrophages and with a defect in inducible regulatory T-cell generation and function. Both polyp numbers and inflammation increased progressively with time. The rate of increase of both, however, was more rapid in Apc(min/+)/Tpl2(-/-) mice, suggesting that the positive feedback initiated by inflammatory signals originating in developing polyps is more robust in these mice. This may be because these mice have a higher intestinal polyp burden as a result of the enhancement of tumor initiation.

Members of a family of JmjC domain-containing oncoproteins immortalize embryonic fibroblasts via a JmjC domain-dependent process.

A common integration site, cloned from MoMuLV-induced rat T cell lymphomas, was mapped immediately upstream of Not dead yet-1 (Ndy1)/KDM2B, a gene expressed primarily in testis, spleen, and thymus, that is also known as FBXL10 or JHDM1B. Ndy1 encodes a nuclear, chromatin-associated protein that harbors Jumonji C (JmjC), CXXC, PHD, proline-rich, F-box, and leucine-rich repeat domains. Ndy1 and its homolog Ndy2/KDM2A (FBXL11 or JHDM1A), which is also a target of provirus integration in retrovirus-induced lymphomas, encode proteins that were recently shown to possess Jumonji C-dependent histone H3 K36 dimethyl-demethylase or histone H3 K4 trimethyl-demethylase activities. Here, we show that mouse embryo fibroblasts engineered to express Ndy1 or Ndy2 undergo immortalization in the absence of replicative senescence via a JmjC domain-dependent process that targets the Rb and p53 pathways. Knockdown of endogenous Ndy1 or expression of JmjC domain mutants of Ndy1 promote senescence, suggesting that Ndy1 is a physiological inhibitor of senescence in dividing cells and that inhibition of senescence depends on histone H3 demethylation.

A phase I delayed-start, randomized and pharmacodynamic study of metformin and chemotherapy in patients with solid tumors.

PURPOSE: Metformin activates AMP-related pathways leading to inactivation of mammalian target of rapamycin (mTOR) and suppression of its downstream effectors, crucial for cancer growth. Epidemiologic studies showed a reduced incidence and improved survival in cancer patients. We conducted a prospective phase I study to assess the safety of metformin in combination with chemotherapy in patients with solid tumors. METHODS: We conducted a delayed-start randomized trial of non-diabetic patients in two stages. In Stage 1, we randomized patients to two arms: concurrent arm (metformin with chemo) vs. delayed arm (chemo alone). In Stage 2, patients in delayed arm were crossed over to receive metformin. Patients received metformin 500 mg twice daily with chemotherapy to define dose-limiting toxicities (DLTs) in both stages. Secondary endpoints assessed adverse events (AEs) and response rates. Translational correlates included effects of metformin on expression and phosphorylation of 5' adenosine monophosphate-activated protein kinase (AMPK) by western blot in PBMCs. RESULTS: A total of 100 patients were enrolled (51 in delayed arm vs. 49 concurrent arm). Rate of DLTs in patients receiving metformin with chemotherapy was 6.1% vs. 7.8% in patients receiving chemotherapy alone. DLTs seen with addition of metformin included those associated with established chemo adverse events. No lactic acidosis or hypoglycemia occurred. Restaging showed stable disease in 46% at cessation of metformin. 28% of patients with measurable tumor markers showed improvement. AMPK phosphorylation showed a four- to sixfold increase in AMPK phosphorylation after metformin. CONCLUSIONS: This is the largest phase I study of metformin combined with chemotherapy, which suggests that metformin can be given safely with chemotherapy, and offers a platform for future studies. Post-metformin increase in AMPK phosphorylation may potentially explain lack of disease progression in nearly half of our patients. FUNDING: UL1 TR001064. CLINICAL TRIAL INFORMATION: NCT01442870.

Tumor progression locus 2 mediates signal-induced increases in cytoplasmic calcium and cell migration.

The mitogen-activated protein kinase kinase kinase (MAPKKK or MAP3K) tumor progression locus 2 (Tpl2) is required for the transduction of signals initiated by the thrombin-activated G protein-coupled receptor (GPCR) protease-activated receptor-1 (PAR1), which promote reorganization of the actin cytoskeleton and cell migration. Here, we show that Tpl2 is activated through Gα(i2)-transduced GPCR signals. Activated Tpl2 promoted the phosphorylation and activation of phospholipase C-ß3 (PLCß(3)); consequently, Tpl2 was required for thrombin-dependent production of inositol 1,4,5-trisphosphate (IP(3)), IP(3)-mediated cytoplasmic calcium ion (Ca(2+)) signals, and the activation of classical and novel members of the protein kinase C (PKC) family. A PKC-mediated feedback loop facilitated extracellular signal-regulated kinase (ERK) activation in response to Tpl2 and contributed to the coordinate regulation of the ERK and Ca(2+) signaling pathways. Pharmacological and genetic studies revealed that stimulation of cell migration by Tpl2 depends on both of these pathways. Tpl2 also promoted Ca(2+) signals and cell migration from sphingosine 1-phosphate-responsive GPCRs, which also couple to Gα(i); from Wnt5a; and from the interleukin-1ß (IL-1ß) receptor, a member of the Toll-IL-1R (TIR) domain family. Our data provide new insights into the role of Tpl2 in GPCR-mediated Ca(2+) signaling and cell migration.