Activation Of Molecular Pathways Research Articles

Senescence Alterations in Pulmonary Hypertension.

Cellular senescence is the arrest of normal cell division and is commonly associated with aging. The interest in the role of cellular senescence in lung diseases derives from the observation of markers of senescence in chronic obstructive pulmonary disease (COPD), pulmonary fibrosis (IPF), and pulmonary hypertension (PH). Accumulation of senescent cells and the senescence-associated secretory phenotype in the lung of aged patients may lead to mild persistent inflammation, which results in tissue damage. Oxidative stress due to environmental exposures such as cigarette smoke also promotes cellular senescence, together with additional forms of cellular stress such as mitochondrial dysfunction and endoplasmic reticulum stress. Growing recent evidence indicate that senescent cell phenotypes are observed in pulmonary artery smooth muscle cells and endothelial cells of patients with PH, contributing to pulmonary artery remodeling and PH development. In this review, we analyze the role of different senescence cell phenotypes contributing to the pulmonary artery remodeling process in different PH clinical entities. Different molecular pathway activation and cellular functions derived from senescence activation will be analyzed and discussed as promising targets to develop future senotherapies as promising treatments to attenuate pulmonary artery remodeling in PH.

Integrative Analysis of Epigenome and Transcriptome Data Reveals Aberrantly Methylated Promoters and Enhancers in Hepatocellular Carcinoma.

DNA methylation is a key transcription regulator, whose aberration was ubiquitous and important in most cancers including hepatocellular carcinoma (HCC). Whole-genome bisulfite sequencing (WGBS) was conducted for comparison of DNA methylation in tumor and adjacent tissues from 33 HCC patients, accompanying RNA-seq to determine differentially methylated region-associated, differentially expressed genes (DMR-DEGs), which were independently replicated in the TCGA-LIHC cohort and experimentally validated via 5-aza-2-deoxycytidine (5-azadC) demethylation. A total of 9,867,700 CpG sites showed significantly differential methylation in HCC. Integrations of mRNA-seq, histone ChIP-seq, and WGBS data identified 611 high-confidence DMR-DEGs. Enrichment analysis demonstrated activation of multiple molecular pathways related to cell cycle and DNA repair, accompanying repression of several critical metabolism pathways such as tyrosine and monocarboxylic acid metabolism. In TCGA-LIHC, we replicated about 53% of identified DMR-DEGs and highlighted the prognostic significance of combinations of methylation and expression of nine DMR-DEGs, which were more efficient prognostic biomarkers than considering either type of data alone. Finally, we validated 22/23 (95.7%) DMR-DEGs in 5-azadC-treated LO2 and/or HepG2 cells. In conclusion, integration of epigenome and transcriptome data depicted activation of multiple pivotal cell cycle-related pathways and repression of several metabolic pathways triggered by aberrant DNA methylation of promoters and enhancers in HCC.

Signaling pathways of heat- and hypersalinity-induced polyp bailout in Pocillopora acuta

Polyp bailout is a drastic response to acute stress where coral coloniality breaks down and polyps detach. We induced polyp bailout in Pocillopora acuta with heat stress and tested for differential gene expression using RNAseq and a qPCR assay. Furthermore, we induced polyp bailout with hypersalinity and compared the results to identify stressor-independent signals and pathways active during polyp bailout. Both stressors led to the onset of polyp bailout and the detachment of vital polyps. We observed activation of microbe-associated molecular pattern receptors and downstream signaling pathways of the innate immune system. Further, we detected growth factors and genes active during Wnt-signaling potentially contributing to wound healing, regeneration, and proliferation. Upregulation of several genes encoding for matrix metalloproteinases and the fibroblast growth factor signaling pathway are the most likely involved in the remodeling of the extracellular matrix, as well as in the detachment of polyps from the calcareous skeleton during polyp bailout. Expression of genes of interest in our qPCR assay of vital polyps from our heat-stress experiment, showed a trend for a normalization of gene expression after polyp bailout. Our results provide new insights into the signaling cascades leading to the observed physiological responses during polyp bailout. Comparison between the two stressors showed that certain signaling pathways are independent of the stressor and suggested that polyp bailout is a general response of corals to acute stress. Furthermore, immune system responses during polyp bailout indicate that microbe-associated partners of corals may lead to the polyp bailout response.

Multiple Antitumor Molecular Mechanisms Are Activated by a Fully Synthetic and Stabilized Pharmaceutical Product Delivering the Active Compound Sulforaphane (SFX-01) in Preclinical Model of Human Glioblastoma

Frequent relapses and therapeutic resistance make the management of glioblastoma (GBM, grade IV glioma), extremely difficult. Therefore, it is necessary to develop new pharmacological compounds to be used as a single treatment or in combination with current therapies in order to improve their effectiveness and reduce cytotoxicity for non-tumor cells. SFX-01 is a fully synthetic and stabilized pharmaceutical product containing the α-cyclodextrin that delivers the active compound 1-isothiocyanato-4-methyl-sulfinylbutane (SFN) and maintains biological activities of SFN. In this study, we verified whether SFX-01 was active in GBM preclinical models. Our data demonstrate that SFX-01 reduced cell proliferation and increased cell death in GBM cell lines and patient-derived glioma initiating cells (GICs) with a stem cell phenotype. The antiproliferative effects of SFX-01 were associated with a reduction in the stemness of GICs and reversion of neural-to-mesenchymal trans-differentiation (PMT) closely related to epithelial-to-mesenchymal trans-differentiation (EMT) of epithelial tumors. Commonly, PMT reversion decreases the invasive capacity of tumor cells and increases the sensitivity to pharmacological and instrumental therapies. SFX-01 induced caspase-dependent apoptosis, through both mitochondrion-mediated intrinsic and death-receptor-associated extrinsic pathways. Here, we demonstrate the involvement of reactive oxygen species (ROS) through mediating the reduction in the activity of essential molecular pathways, such as PI3K/Akt/mTOR, ERK, and STAT-3. SFX-01 also reduced the in vivo tumor growth of subcutaneous xenografts and increased the disease-free survival (DFS) and overall survival (OS), when tested in orthotopic intracranial GBM models. These effects were associated with reduced expression of HIF1α which, in turn, down-regulates neo-angiogenesis. So, SFX-01 may have potent anti-glioma effects, regulating important aspects of the biology of this neoplasia, such as hypoxia, stemness, and EMT reversion, which are commonly activated in this neoplasia and are responsible for therapeutic resistance and glioma recurrence. SFX-01 deserves to be considered as an emerging anticancer agent for the treatment of GBM. The possible radio- and chemo sensitization potential of SFX-01 should also be evaluated in further preclinical and clinical studies.

Molecular background of impairments in skeletal muscle of heart failure patients

Abstract Background Heart failure (HF) is characterised by systematic inflammation and chronic metabolic dysregulation. HF enhances the release of pro-inflammatory cytokines, induces activation of the complement system, production of autoantibodies, and over-expression of the major histocompatibility (MHC) complex class II molecules. It is known that skeletal muscles are exposed to the immunologic injury in disease; and muscle tissue appeared to be affected by HF leading to the muscle weakness and exercise intolerance development. However, molecular abnormalities occurring in HF patients' muscles and the mechanisms underlying its development are not clarified. Purpose To understand the molecular mechanisms underlying skeletal muscle immune and non-immune impairments in HF. Methods 8 health donors and 5 HF patients with reduced ejection fraction (NYHA Class II and III) were enrolled in this study in accordance with the principles under the Declaration of Helsinki (1989). mRNA of skeletal muscle biopsies of gastrocnemius lateralis were sequenced on Illumina HiSeq. RNA-seq analysis was performed using STAR with reference genome GRCh38 and featureCounts program; differentially expressed genes (DEGs) were assessed using R package DESeq2 with FDR=0.01 and log2 fold change (l2fc) >1.5 filter; pathway analysis was performed using clusterProfiler in R (FDR=0.01). Results 1404 differentially expressed genes distinguish muscles of HF patients and controls. Among upregulated genes there are different classical MHC molecules and specific one HLA-G (l2fc=2) that has been previously shown appeared in muscles under autoimmune myopathies, and potentially protect them. Unregulated DEGs were responsible for the activation of many molecular immunological pathways: type I interferon signaling pathway (16 DEGs out of total 89), regulation of T cell proliferation (14/153), neutrophil degranulation (31/485), granulocyte differentiation (7/32), negative regulation of viral process (11/53), that indicates about specific inflammatory response in HF muscles. Response to hypoxia (22/314) and gluconeogenesis pathways (12/87) were also activated. Downregulated genes include SLC5A1 (l2fc=−4) sodium glucose cotransporter; NRP3 (l2fc=−4) that plays a role in modulating intravascular volume and vascular tone; MMP1 (l2fc=−13) involved in the breakdown of extracellular matrix; the expression of many genes responsible for DNA-repair (44/534) and cilium assembly (34/366) was also suppressed. Conclusion Transcriptome analysis shows immunological and non-immunological alterations in HF skeletal muscles and provides the information about molecular mechanisms of its development. Funding Acknowledgement Type of funding sources: Foundation. Main funding source(s): Russian Science Foundation grant

Robert's Intragastric Alcohol-Induced Gastric Lesion Model as an Escalated General Peripheral and Central Syndrome, Counteracted by the Stable Gastric Pentadecapeptide BPC 157.

We redefined Robert’s prototypical cytoprotection model, namely the intragastric administration of 96% alcohol in order to generate a general peripheral and central syndrome similar to that which occurs when major central or peripheral veins are occluded in animal models. With this redefinition, we used Robert’s model to examine the cytoprotective effects of the stable gastric pentadecapeptide BPC 157. The intragastric administration of alcohol induced gastric lesions, intracranial (superior sagittal sinus) hypertension, severe brain swelling and lesions, portal and vena caval hypertension, aortal hypotension, severe thrombosis, inferior vena cava and superior mesenteric vein congestion, azygos vein failure (as a failed collateral pathway), electrocardiogram disturbances, and heart, lung, liver and kidney lesions. The use of BPC 157 therapy (10 µg/kg or 10 ng/kg given intraperitoneally 1 min after alcohol) counteracted these deficits rapidly. Specifically, BPC 157 reversed brain swelling and superior mesenteric vein and inferior vena caval congestion, and helped the azygos vein to recover, which improved the collateral blood flow pathway. Microscopically, BPC 157 counteracted brain (i.e., intracerebral hemorrhage with degenerative changes of cerebral and cerebellar neurons), heart (acute subendocardial infarct), lung (parenchymal hemorrhage), liver (congestion), kidney (congestion) and gastrointestinal (epithelium loss, hemorrhagic gastritis) lesions. In addition, this may have taken place along with the activation of specific molecular pathways. In conclusion, these findings clarify and extend the theory of cytoprotection, offer an approach to its practical application, and establish BPC 157 as a prospective cytoprotective treatment.

Role of Coenzyme Q10 in Health and Disease: An Update on the Last 10 Years (2010–2020)

The present review focuses on preclinical and clinical studies conducted in the last decade that contribute to increasing knowledge on Coenzyme Q10’s role in health and disease. Classical antioxidant and bioenergetic functions of the coenzyme have been taken into consideration, as well as novel mechanisms of action involving the redox-regulated activation of molecular pathways associated with anti-inflammatory activities. Cardiovascular research and fertility remain major fields of application of Coenzyme Q10, although novel applications, in particular in relation to topical application, are gaining considerable interest. In this respect, bioavailability represents a major challenge and the innovation in formulation aspects is gaining critical importance.

Noise and Health: Review.

Noise in human societies is unavoidable, but it tends to become a modern epidemic that induces various detrimental effects to several organs and functions in humans. Increased cardiovascular danger, anxiety and sleep disturbance are just few of these effects. It is noteworthy that children, even neonates and their developing organism are especially vulnerable to noise-related health problems. Noise is measured with special noise-meters. These devices express results in decibels by transforming random noise to a continuous sound. This sound is characterized by equivalent acoustic energy to the random noise for a defined time interval. Human auditory apparatus is principally endangered by acute noises but also by chronic noise exposure, in the context of both occupational and recreational activities. Various mechanisms are implicated in the pathogenesis of noise-induced hearing loss that can cause either temporary or permanent damage. Among them, emphasis is given to the impairment by free radicals and inflammatory mediators, to the activation of apoptotic molecular pathways, but also to glutamate excitotoxicity. A hidden hearing loss, synaptopathy, is attributed to the latter. The irreversible nature of hearing loss, as well as the idiosyncratic sensitivity of individuals, imposes the necessity of early diagnosis of auditory impairment by noise. Super high frequency audiograms, otoacoustic emissions and electrophysiological examinations can address diagnosis. Thankfully, there is extensive research on acoustic trauma therapeutic approaches. However, until we succeed in regenerating the sensory organ of hearing, chronic noise-induced hearing loss cannot be treated. Thus, it is fundamental that society protects people from noise, by laws and regulations.

COVID-19–associated inhibition of energy accumulation pathways in human semen samples

ObjectiveTo investigate transcriptional alterations in human semen samples associated with COVID-19 infection.DesignRetrospective observational cohort study.SettingCity hospital.Patient(s)Ten patients who had recovered from mild COVID-19 infection. Eight of these patients had different sperm abnormalities that were diagnosed before infection. The control group consisted of 5 healthy donors without known abnormalities and no history of COVID-19 infection.Intervention(s)We used RNA sequencing to determine gene expression profiles in all studied biosamples. Original standard bioinformatic instruments were used to analyze activation of intracellular molecular pathways.Main Outcome Measure(s)Routine semen analysis, gene expression levels, and molecular pathway activation levels in semen samples.Result(s)We found statistically significant inhibition of genes associated with energy production pathways in the mitochondria, including genes involved in the electron transfer chain and genes involved in toll-like receptor signaling. All protein-coding genes encoded by the mitochondrial genome were significantly down-regulated in semen samples collected from patients after recovery from COVID-19.Conclusion(s)Our results may provide a molecular basis for the previously observed phenomenon of decreased sperm motility associated with COVID-19 infection. Moreover, the data will be beneficial for the optimization of preconception care for men who have recently recovered from COVID-19 infection.

Recent Advances in Systemic Treatments for HER-2 Positive Advanced Gastric Cancer.

Gastric cancer (GC) is the fifth most common cancer worldwide. Despite recent improvements in treatment quality and options, advanced gastric cancer remains one of the hardest to cure cancers, with a median overall survival (OS) of 10–12 months and a 5-year OS of approximately 5–20%. There is an unmet need for further efforts to palliate disease-related symptoms, improve quality of life, increase tumor response rate, and prolong progression free and overall survival while balancing the toxicities of therapy. The most common type of GC is adenocarcinoma, which demonstrates morphological, biological, and clinical heterogeneity. A plethora of genomic alterations and the activation of numerous molecular pathways including human epidermal growth receptor 2 (HER2), epidermal growth factor receptor (EGFR), fibroblast growth factor receptor-2 (FGFR2), mesenchymal epidermal transforming factor receptor (MET), and the phosphatidylinositol 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) are responsible for the complex heterogeneity of GC. Efforts to validate the therapeutic effects of inhibiting some of these aberrantly expressed pathways have failed to lead to a clinically meaningful outcome apart from the overexpression/amplification of the HER2 gene, inhibition of which has had a significant impact on clinical practice. The only available biomarkers to guide the effective treatment of patients with advanced GC are HER2 overexpression, MSI/PD-L1 status, and FGFR alterations. Various anti-HER2 agents have been evaluated after the success of the ToGA trial, but none led to a significant enough clinical improvement to be considered a viable alternative for HER2-targeted therapy in advanced GC until the global Keynote-811 trial, which added pembrolizumab to trastuzumab in combination with chemotherapy. This combination demonstrated a survival advantage for the first time in the 11 years since ToGA. Trastuzumab deruxtecan (T-DXd) was also found to be effective in patients who had already received >2 previous lines of treatment. Despite these promising avenues, the optimal management of HER-2 positive GC still requires further development.

Photoperiodically driven transcriptome-wide changes in the hypothalamus reveal transcriptional differences between physiologically contrasting seasonal life-history states in migratory songbirds

We investigated time course of photoperiodically driven transcriptional responses in physiologically contrasting seasonal life-history states in migratory blackheaded buntings. Birds exhibiting unstimulated winter phenotype (photosensitive state; responsive to photostimulation) under 6-h short days, and regressed summer phenotype (photorefractory state; unresponsiveness to photostimulation) under 16-h long days, were released into an extended light period up to 22 h of the day. Increased tshβ and dio2, and decreased dio3 mRNA levels in hypothalamus, and low prdx4 and high il1β mRNA levels in blood confirmed photoperiodic induction by hour 18 in photosensitive birds. Further, at hours 10, 14, 18 and 22 of light exposure, the comparison of hypothalamus RNA-Seq results revealed transcriptional differences within and between states. Particularly, we found reduced expression at hour 14 of transthyretin and proopiomelanocortin receptor, and increased expression at hour 18 of apolipoprotein A1 and carbon metabolism related genes in the photosensitive state. Similarly, valine, leucine and isoleucine degradation pathway genes and superoxide dismutase 1 were upregulated, and cocaine- and amphetamine-regulated transcript and gastrin-releasing peptide were downregulated in the photosensitive state. These results show life-history-dependent activation of hypothalamic molecular pathways involved in initiation and maintenance of key biological processes as early as on the first long day.

Abstract PD14-03: Molecular mechanism of ipatasertib (IPAT) and its combination with atezolizumab (atezo) in patients (pts) with locally advanced/metastatic triple-negative breast cancer (aTNBC)

Abstract Background: Phase 3 trials (IMpassion130, KEYNOTE-355) have shown improved efficacy with the addition of immune checkpoint modulators to chemotherapy in PD-L1 +ve aTNBC. However, unmet need remains in the ~60% of pts with aTNBC who have PD-L1 -ve tumors. Preliminary data from a multicenter phase 1b study (NCT03800836) evaluating the safety and efficacy of the oral AKT inhibitor IPAT + atezo + paclitaxel/nab-paclitaxel showed promising antitumor activity (73% confirmed objective response rate) irrespective of PD-L1 status [Schmid, AACR 2019], suggesting a potential role for the triplet independent of PD-L1 status. We report on-treatment changes in the tumor microenvironment in Cohort 2. Methods: In Cohort 2, pts with aTNBC and ≤2 prior lines of chemotherapy for aTNBC received oral IPAT 400 mg on d1-28 of cycle 1 (35-d cycle) and on d1-21 of subsequent cycles (28-d cycles). IV atezo 840 mg was given on d8 & 22 of cycle 1 and on d1 & 15 of subsequent cycles. Biopsies were collected before treatment administration during cycle 1 on d1 (C1D1) & d8 (C1D8), and on d15 of cycle 2 (C2D15). PD-L1 (VENTANA SP142 immune cell ≥1%) and CD8 expression was assessed by immunohistochemistry (IHC); % immune infiltrate was measured by H&E staining. Changes in gene expression were assessed by RNA-Seq. Gene set enrichment analysis was used to study molecular pathway activation (enrichment score [ES] >0 to 1) or inhibition (ES -1 to <0). Results: In Cohort 2, 11 pts had PD-L1 -ve tumors at baseline and are included in the analyses below, 2 had PD-L1 +ve tumors and 3 were unevaluable for PD-L1. IHC analysis of serial biopsies from pts with PD-L1 -ve tumors showed a statistically significant increase in immune infiltrates (mean % infiltrates C1D8/C1D1=1.44; p=0.042) and a trend toward increased CD8 protein expression (mean CD8 % staining C1D8/C1D1=1.75; Kruskal-Wallis p=0.16) at the tumor center during the first week of single-agent IPAT compared with the baseline biopsy. An increase in PD-L1 expression (mean PD-L1 % infiltrating immune cells C2D15/C1D1=4.33; Kruskal-Wallis p=0.044) was seen during IPAT + atezo combination treatment. No significant changes in immune infiltrates or CD8 expression were observed after initiating atezo versus IPAT alone. As expected, MTORC1 activity decreased (ES=-0.43; p<0.005) in response to IPAT. IPAT (± atezo) enhanced key immunogenic pathways, including antigen processing and presentation (ES=0.49; p<0.005), allograft rejection (ES=0.47; p<0.0001), inflammatory response (ES=0.34; p<0.05), and NK cell activation (ES=0.66; p<0.05). In addition, IPAT + atezo enhanced TCR signaling (ES=0.52; p<0.0005) and interferon gamma response (ES=0.30; p<0.05). IPAT treatment was associated with decreased expression of gene sets predicting pathway upregulation, including E2F signaling, G2M checkpoint, and MYC activity. IPAT was also associated with apoptotic pathway enrichment. Using a syngeneic melanoma mouse model, we validated clinical findings and identified additional molecular changes after treatment with IPAT and/or anti-PD-L1. To date, 3 enrolled pts achieved a partial response and 6 had stable disease. Clinical and preclinical studies are ongoing to explore associations between treatment-driven molecular changes and clinical response. Conclusion: Inhibition of AKT signaling may remodel the microenvironment of PD-L1 -ve tumors by increasing immune infiltration, priming immune pathways, promoting tumor cell apoptosis, and inhibiting oncogenic cell proliferative pathways. To our knowledge, these are the first reports evaluating molecular changes during AKT-targeted therapy for aTNBC in the context of immunotherapy irrespective of PD-L1 status. IPAT warrants further investigation combined with atezo as treatment for PD-L1 -ve aTNBC. Citation Format: Peter Schmid, Delphine Loirat, Peter Savas, Enrique Espinosa, Valentina Boni, Antoine Italiano, Shane White, Victor Laliman, Geraldine Strasser, Kui Lin, Karen Cheng, Aruna Mani, Matthew Wongchenko, Marie-Paule Sablin, Kalpit Shah. Molecular mechanism of ipatasertib (IPAT) and its combination with atezolizumab (atezo) in patients (pts) with locally advanced/metastatic triple-negative breast cancer (aTNBC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD14-03.

Human Primary Dermal Fibroblasts Interacting with 3-Dimensional Matrices for Surgical Application Show Specific Growth and Gene Expression Programs.

Several types of 3-dimensional (3D) biological matrices are employed for clinical and surgical applications, but few indications are available to guide surgeons in the choice among these materials. Here we compare the in vitro growth of human primary fibroblasts on different biological matrices commonly used for clinical and surgical applications and the activation of specific molecular pathways over 30 days of growth. Morphological analyses by Scanning Electron Microscopy and proliferation curves showed that fibroblasts have different ability to attach and proliferate on the different biological matrices. They activated similar gene expression programs, reducing the expression of collagen genes and myofibroblast differentiation markers compared to fibroblasts grown in 2D. However, differences among 3D matrices were observed in the expression of specific metalloproteinases and interleukin-6. Indeed, cell proliferation and expression of matrix degrading enzymes occur in the initial steps of interaction between fibroblast and the investigated meshes, whereas collagen and interleukin-6 expression appear to start later. The data reported here highlight features of fibroblasts grown on different 3D biological matrices and warrant further studies to understand how these findings may be used to help the clinicians choose the correct material for specific applications.

Tracking the Regenerative Growth in Earthworm: A Cellular and Molecular Perspective

Regeneration in earthworm is studied vastly and proved to be an effective model to study regeneration. The process of regeneration is a stepwise and gradual process. The mechanism of regeneration was not clear earlier but it was deciphered later. Regenerative growth occurs firstly by wound healing followed by blastema formation. Blastema cells are majorly derived from the existing tissue specifically longitudinal muscle cells near the amputation site by dedifferentiation. Differentiation and pattern formation are the major processes in early development and organogenesis and these involve activation of various molecular signaling pathways. Neural factors are also activated along with other transcription factors for neural development. Segmentation and pigmentation occur at the last stage of development. Survival rate and body weight after amputation also has a correlation with regenerative growth. Genetic regulation and signaling controls the development and growth via various controlling genes such as distal less, notch. These genes are responsible for blastema formation, organogenesis and patterning. Pluripotent factors such as nano, regulate the dedifferentiation to form pluripotent stem cell for blastogenesis. Further studies are needed to study molecular mechanism for regulation in earthworm regeneration.

Using proteomic and transcriptomic data to assess activation of intracellular molecular pathways.

Analysis of molecular pathway activation is the recent instrument that helps to quantize activities of various intracellular signaling, structural, DNA synthesis and repair, and biochemical processes. This may have a deep impact in fundamental research, bioindustry, and medicine. Unlike gene ontology analyses and numerous qualitative methods that can establish whether a pathway is affected in principle, the quantitative approach has the advantage of exactly measuring the extent of a pathway up/downregulation. This results in emergence of a new generation of molecular biomarkers-pathway activation levels, which reflect concentration changes of all measurable pathway components. The input data can be the high-throughput proteomic or transcriptomic profiles, and the output numbers take both positive and negative values and positively reflect overall pathway activation. Due to their nature, the pathway activation levels are more robust biomarkers compared to the individual gene products/protein levels. Here, we review the current knowledge of the quantitative gene expression interrogation methods and their applications for the molecular pathway quantization. We consider enclosed bioinformatic algorithms and their applications for solving real-world problems. Besides a plethora of applications in basic life sciences, the quantitative pathway analysis can improve molecular design and clinical investigations in pharmaceutical industry, can help finding new active biotechnological components and can significantly contribute to the progressive evolution of personalized medicine. In addition to the theoretical principles and concepts, we also propose publicly available software for the use of large-scale protein/RNA expression data to assess the human pathway activation levels.

Correlation between IHH molecular pathway activation and tumor location, sex, age, distant metastases, in patients with diagnosed colorectal adenocarcinoma. Experimental study

Correlation between IHH molecular pathway activation and tumor location, sex, age, distant metastases, in patients with diagnosed colorectal adenocarcinoma. Experimental study

Molecular Biology of Atherosclerotic Ischemic Strokes.

Among the causes of global death and disability, ischemic stroke (also known as cerebral ischemia) plays a pivotal role, by determining the highest number of worldwide mortality, behind cardiomyopathies, affecting 30 million people. The etiopathogenetic burden of a cerebrovascular accident could be brain ischemia (~80%) or intracranial hemorrhage (~20%). The most common site when ischemia occurs is the one is perfused by middle cerebral arteries. Worse prognosis and disablement consequent to brain damage occur in elderly patients or affected by neurological impairment, hypertension, dyslipidemia, and diabetes. Since, in the coming years, estimates predict an exponential increase of people who have diabetes, the disease mentioned above constitutes together with stroke a severe social and economic burden. In diabetic patients after an ischemic stroke, an exorbitant activation of inflammatory molecular pathways and ongoing inflammation is responsible for more severe brain injury and impairment, promoting the advancement of ischemic stroke and diabetes. Considering that the ominous prognosis of ischemic brain damage could by partially clarified by way of already known risk factors the auspice would be modifying poor outcome in the post-stroke phase detecting novel biomolecules associated with poor prognosis and targeting them for revolutionary therapeutic strategies.

Corticosterone as a Potential Confounding Factor in Delineating Mechanisms Underlying Ketamine's Rapid Antidepressant Actions.

Recent research into the rapid antidepressant effect of subanesthetic doses of ketamine have identified a series of relevant protein cascades activated within hours of administration. Prior to, or concurrent with, these activation cascades, ketamine treatment generates dissociative and psychotomimetic side effects along with an increase in circulating glucocorticoids. In rats, we observed an over 3-fold increase in corticosterone levels in both serum and brain tissue, within an hour of administration of low dose ketamine (10 mg/kg), but not with (2R, 6R)-hydroxynorketamine (HNK) (10 mg/kg), a ketamine metabolite shown to produce antidepressant-like action in rodents without inducing immediate side-effects. Hippocampal tissue from ketamine, but not HNK, injected animals displayed a significant increase in the expression of sgk1, a downstream effector of glucocorticoid receptor signaling. To examine the role conscious sensation of ketamine’s side effects plays in the release of corticosterone, we assessed serum corticosterone levels after ketamine administration while under isoflurane anesthesia. Under anesthesia, ketamine failed to increase circulating corticosterone levels relative to saline controls. Concurrent with its antidepressant effects, ketamine generates a release of glucocorticoids potentially linked to disturbing cognitive side effects and the activation of distinct molecular pathways which should be considered when attempting to delineate the molecular mechanisms of its antidepressant function.

Transcriptome analysis of skeletal muscles revealed the effect of exercise on the molecular mechanisms regulating muscle growth and metabolism in patients with heart failure

Aim. Heart failure (HF) is accompanied by skeletal muscle atrophy and exercise intolerance. The aim was to study the molecular mechanisms underlying the therapeutic effect of personalized exercise in patients with HF.Material and methods. RNA sequencing obtained from skeletal muscle biopsies before and after a 12-week exercise course was used to identify changes in gene expression and signaling pathways induced by the physical rehabilitation program for patients with HF.Results. We have shown that personalized exercise program in patients with HF stimulates the activation of molecular pathways regulating the differentiation and functioning of skeletal muscles: commitment of muscle progenitor cells; mechanisms regulating the calcium release and sensitivity of myofibrillar contraction, electrical excitability of the muscle membrane, synaptic vesicle proton gradient creation, maintenance of electrochemical gradients of Na+ /K+ . Also, the analysis of differentially expressed genes revealed an increase in the expression of transcription factors MyoD and MEF2, which are responsible for the differentiation of muscle stem cells, and sarcomeric genes MYOM1, MYOM2, MYH7. Along with this, we observed activation of the CYR61 expression — a potential prognostic biomarker for HF patients.Conclusion. Our data show that the beneficial effect of personalized aerobic exercise in patients with HF depends, at least in part, on an improvement in the physiological and biochemical parameters of skeletal muscle.

Association between Brachyspira and irritable bowel syndrome with diarrhoea

ObjectiveThe incidence of IBS increases following enteric infections, suggesting a causative role for microbial imbalance. However, analyses of faecal microbiota have not demonstrated consistent alterations. Here, we used metaproteomics to...