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Results for “molecular pathways”

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At least 415 records · Page 23Linked to original sources
PubMed2004

Use of a randomized hybrid ribozyme library for identification of genes involved in muscle differentiation.

We have employed the hybrid hammerhead ribozyme-based gene discovery system for identification of genes functionally involved in muscle differentiation using in vitro myoblast differentiation assay. The major muscle regulatory genes (MyoD1, Mylk, myosin, myogenin, and Myf5) were identified endorsing the validity of this method. Other gene targets included tumor suppressors and cell cycle regulators (p19ARF and p21WAF1), FGFR-4, fibronectin, Prkg2, Pdk4, fem, and six novel proteins. Functional involvement of three of the identified targets in myoblast differentiation was confirmed by their specific knockdown using ribozymes and siRNA. Besides demonstrating a simple and an effective method of isolation of gene functions involved in muscle differentiation, we report for the first time that overexpression of Fem, a member of the sex-determining family of proteins, caused accelerated myotube formation, and its targeting deferred myoblast differentiation. This functional gene screening is not only helpful in understanding the molecular pathways of muscle differentiation but also to design molecular strategies for myopathologic therapies.

Animals↗
PubMed2005

Mechanisms of toxic damage to spermatogenesis.

Azoospermia and long-lasting testicular atrophy are common adverse consequences of cancer treatment. Chemotherapeutic agents may disrupt spermatogenesis by targeting various testicular cell types (Leydig cells, Sertoli cells, and germ cells) and by activating numerous molecular pathways involved in germ cell life-and-death decision making. Genetically modified animal models with deficiencies in specific proapoptotic and prosurvival pathways have become powerful tools in understanding the molecular regulation of spermatogenesis and the response of the seminiferous epithelium to toxic injury. In this brief review, selected examples of results of toxic exposures in genetically deficient animal models are discussed to highlight the roles of p53 and the Fas system as modulators of proapoptotic activity in the testis. A final section focuses on cisplatin, a cancer chemotherapeutic agent that produces male reproductive toxicity by targeting multiple cell types in the testis.

Antineoplastic Agents↗
PubMed1997

A reappraisal of aldosterone effects on the kidney: new insights provided by epithelial sodium channel cloning.

Sodium homeostasis is crucial for the control of extra-cellular volume and blood pressure. Regulation of sodium reabsorption is mainly achieved in the distal nephron by the mineralocorticoid aldosterone, but the molecular pathway of aldosterone action has largely remained unclear. Molecular genetic analysis of inherited diseases disturbing sodium homeostasis has now demonstrated that the amiloride-sensitive epithelial sodium channel is a major effector of aldosterone action. Mechanisms by which aldosterone regulates the epithelial sodium channel activity are beginning to emerge and will be of great importance for a better understanding of salt-sensitive hypertension.

Aldosterone↗
PubMed1998

Regulation of apoptosis in mouse hepatocytes and alteration of apoptosis by nongenotoxic carcinogens.

Regulation of apoptosis is an important component of multistage hepatocarcinogenesis. The objectives of the present study were to characterize apoptosis regulation in primary mouse hepatocytes and to determine whether nongenotoxic carcinogens alter apoptosis regulation. Bleomycin-induced apoptosis was accompanied by decreases in bcl-2 and bcl-xl and increases in p53, bak, and bax protein levels. Transforming growth factor (TGF)-beta-induced apoptosis was accompanied by decreased bcl-xL and increased bak. Bleomycin-induced apoptosis was partially dependent on p53, whereas TGF-beta-induced apoptosis was independent of p53. Phenobarbital inhibited both TGF-beta and bleomycin-induced apoptosis and the normal regulation of p53, bcl-2, and bax. Nafenopin inhibited apoptosis through a mechanism dependent on PPAR-alpha and inhibited the normal regulation of bcl-2 and bak. 2,3,7,8-Tetrachlorodibenzo-p-dioxin did not alter apoptosis or its regulation. Apoptosis was increased in hepatocytes from bcl-2-null mice, which indicated that the bcl-2 family contributes to hepatocyte apoptosis regulation. This study demonstrated that apoptosis regulation in mouse hepatocytes involves distinct pathways and that diverse nongenotoxic carcinogens differentially alter molecular pathways that represent targets for hepatocarcinogenesis.

Animals↗
PubMed2026

Elucidating the Mechanism of Xiaoqinglong Decoction in Chronic Urticaria Treatment: An Integrated Approach of Network Pharmacology, Bioinformatics Analysis, Molecular Docking, and Molecular Dynamics Simulations.

INTRODUCTION: Xiaoqinglong Decoction (XQLD) is a traditional Chinese medicinal formula commonly used to treat chronic urticaria (CU). However, its underlying therapeutic mechanisms remain incompletely characterized. This study employed an integrated approach combining network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulations to identify the active components, potential targets, and related signaling pathways involved in XQLD's therapeutic action against CU, thereby providing a mechanistic foundation for its clinical application. METHODS: The active components of XQLD and their corresponding targets were identified using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. CU-related targets were retrieved from the OMIM and GeneCards databases. Subsequently, core components and targets were determined via protein-protein interaction (PPI) network analysis and component-target-pathway network construction. Topological analyses were performed using Cytoscape software to prioritize core nodes within these networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted via the DAVID database to identify enriched biological processes and signaling pathways. Molecular docking was performed to evaluate binding interactions between key components and core targets, while molecular dynamics (MD) simulations were employed to assess the stability of the component-target complexes with the lowest binding energy. Finally, CU-related targets of XQLD were validated using datasets from the Gene Expression Omnibus (GEO) database. RESULTS: A total of 135 active components and 249 potential targets of XQLD were identified, alongside 1,711 CU-related targets. Core components, such as quercetin, kaempferol, beta-sitosterol, naringenin, stigmasterol, and luteolin, exhibited high degree values in the constructed networks. The core targets identified included AKT1, TNF, IL6, TP53, PTGS2, CASP3, BCL2, ESR1, PPARG, and MAPK3. GO and KEGG pathway enrichment analyses revealed the PI3K-Akt signaling pathway as a central regulatory mechanism. Molecular docking studies demonstrated strong binding affinities between active components and core targets, with the stigmasterol-AKT1 complex exhibiting the lowest binding energy (-11.4 kcal/mol) and high stability in MD simulations. Validation using GEO datasets identified 12 core genes shared between CU-related targets and XQLD-associated targets, including PTGS2 and IL6, which were also prioritized as core targets in the network pharmacology analyses. DISCUSSION: This study comprehensively integrates multidisciplinary approaches to clarify the potential molecular mechanisms of XQLD in treating CU, highlighting its multitarget and multipathway synergistic effects. Molecular docking and dynamics simulations confirm the stable interaction between stigmasterol and the core target AKT1. Additionally, GEO dataset analysis verifies the pathogenic relevance of targets such as PTGS2 and IL6, significantly enhancing the credibility of our findings. These results provide a modern scientific basis for the traditional therapeutic effects of XQLD on CU and have important implications for developing multitarget treatments for this condition. However, this study mainly relies on database mining and computational simulations. Further in vitro and in vivo experimental validations are needed to confirm the predicted component-target-pathway interactions. CONCLUSION: This study identifies the active components, potential targets, and pathways through which XQLD exerts therapeutic effects on CU. These findings provide a theoretical foundation for further mechanistic studies and support their clinical application in the treatment of CU.

Molecular Docking Simulation↗
PubMed2004

Sox17 and beta-catenin cooperate to regulate the transcription of endodermal genes.

Recent studies have led to a model of the molecular pathway that specifies the endoderm during vertebrate gastrulation. The HMG box transcription factor Sox17 is a key component of this pathway and is essential for endoderm formation; however, the molecular events controlled by Sox17 are largely unknown. We have identified several direct transcriptional targets of Sox17, including Foxa1 and Foxa2. We show that beta-catenin, a component of Wnt signaling pathway, physically interacts with Sox17 and potentiates its transcriptional activation of target genes. We identify a motif in the C terminus of Sox17, which is conserved in all the SoxF subfamily of Sox proteins, and this motif is required for the ability of Sox17 to both transactivate target genes and bind beta-catenin. Nuclear beta-catenin is present in endoderm cells of the gastrula, and depletion of beta-catenin from embryos results in a repression of Sox17 target genes. These data suggest that in a mechanism analogous to Tcf/Lef interacting with beta-catenin, Sox17 and beta-catenin interact to transcribe endodermal target genes.

Amino Acid Motifs↗
PubMed2002

Multiple roles of calcineurin in skeletal muscle growth.

Adequate muscle mass and function are critical for human health. Several types of skeletal muscle growth, including regeneration and growth after atrophy, can occur in the rehabilitative period after orthopaedic surgery. The molecular pathways regulating growth of skeletal muscle in adults are understood poorly. The role of calcineurin in regulating regeneration and growth of atrophied skeletal muscle is discussed. Understanding the molecular and cellular pathways that regulate such muscle growth may lead to the development of strategies to enhance muscle growth, thereby facilitating rehabilitation after orthopaedic surgery.

Animals↗
PubMed2005

Discrimination between serous low malignant potential and invasive epithelial ovarian tumors using molecular profiling.

Tumors of low malignant potential (LMP) represent 20% of epithelial ovarian cancers (EOCs) and are associated with a better prognosis than the invasive tumors (TOV). Defining the relationship between LMPs and TOVs remains an important goal towards understanding the molecular pathways that contribute to prognosis, as well as providing molecular markers, for these EOCs. To this end, DNA microarray analyses were performed either in a primary culture or a tumor tissue model system and selected candidate genes showing a distinctive expression profile between LMPs and TOVs were identified using a class prediction approach based on three statistical methods of analysis. Both model systems appear relevant as candidate genes identified by either model allowed the proper reclassification of samples as either LMPs or TOVs. Selected candidate genes (CAS, CCNE1, LGALS8, ITGbeta3, ATP1B1, FLIP, KRT7 and KRT19) were validated by real-time quantitative PCR analysis and show differential expression between LMPs and TOVs. Immunohistochemistry analyses showed that the two tumor classes were distinguishable by their expression of CAS, TNFR1A, FLIP, CKS1 and CCNE1. These results define signature patterns for gene expression of LMPs and TOVs and identify gene candidates that warrant further study to deepen our understanding of the biology of EOC.

Diagnosis, Differential↗
PubMed2002

Cytokine directed therapy in scleroderma: rationale, current status, and the future.

The hallmark of scleroderma is cutaneous and visceral fibrosis characterized and by increased biosynthesis of multiple matrix proteins by interstitial fibroblasts. Studies over recent years have delineated pathways involved in promoting matrix synthesis and elucidated the molecular pathways of regulation. Central to the regulation of fibrosis are extracellular mediators, called cytokines, which are elaborated by a variety of cells, including those in the immune system, vascular cells, and fibroblasts themselves. The concept that inhibiting or promoting the action of these naturally occurring profibrotic or antifibrotic molecules, respectively, is a rational therapeutic approach to treating scleroderma and other fibrotic diseases finds support in animal studies and anticytokine therapy conducted in relation to rheumatoid arthritis and other disorders. This review looks at cytokines known or thought to play a role in scleroderma and/or other fibrotic states and at potential therapy directed at these mediators. Potential targets for therapy include transforming growth factor beta (TGF-beta), connective tissue growth factor (CTGF), IL-4, IL-13, MCP-1, and endothelin, among others.

Animals↗
PubMed1998

Application of signal transduction inhibition as a therapeutic strategy for central nervous system tumors.

During the last decade, rapid progress has been made in understanding the molecular pathways underlying the proliferation of both normal and neoplastic cells. The processes by which messages to initiate protein synthesis, cell cycle progression, and even cell death are transmitted from the cell surface or the cytoplasm to the nucleus are broadly referred to as 'signal transduction'. These multistep pathways involve a host of proteins that interact with other proteins in overlapping cascades that flow downstream in a stepwise fashion from the cell membrane to the nucleus. Inappropriate overactivation or underactivation of various components of such signaling pathways can contribute to pathological processes, such as neoplasia. Conversely, molecular and pharmacological interventions that target and attempt to reverse the aberrant state of activation can potentially be of therapeutic benefit. The present article provides a background for understanding the contribution of signal transduction pathways to the proliferation of normal and neoplastic cells and describes ways in which targetted inhibition of selected signaling pathway components has been exploited to inhibit tumor growth in vitro and in vivo. Because most studies to date involving central nervous system (CNS) tumors have focused on gliomas, in view of their frequency in both the pediatric and adult age groups, the discussion of therapeutic applications for CNS neoplasia will deal primarily with these lesions. However, the basic concepts presented are generalizable to most tumor types and have been successfully applied in vitro in medulloblastomas as well. Ultimately, the translation of such strategies to the treatment of patients with malignant brain tumors may provide novel approaches for improving the poor outlook associated with these neoplasms.

Animals↗
PubMed1999

Triplet repeat disorders: discussion of molecular mechanisms.

Comparison of the growing number of disorders known to be associated with triplet repeat expansions reveals both common features and a diversity of molecular pathways. Despite significant progress towards the characterization of proteins coded by the mutant genes, the complex nature of these disorders requires identification of all molecular components of the triplet repeat pathways. In this brief review we will discuss recent progress in determining the molecular mechanisms of disorders with unstable trinucleotide mutations.

Animals↗
PubMed2002

Mitochondrial functions and aging.

In the filamentous ascomycete Podospora anserina mitochondria play a major role in lifespan control. Since the function of these organelles depends on a large number of individual components it is no surprise that a complex network of interacting branches of individual molecular pathways is involved in this process. Recently, the nuclear encoded transcription factor GRISEA was found to significantly affect mitochondrial functions. GRISEA is involved in the control of cellular copper homeostasis. Most importantly, the high affinity uptake of copper from the environment is controlled by this transcription factor. Once copper has entered the cell, it becomes distributed to different compartments and different target molecules. This process depends on a group of proteins, termed copper chaperones. PaCOX17, a homologue of the yeast copper chaperone yCOX17, appears to be involved in copper delivery to mitochondria. Most importantly, the metal is crucial for the assembly and the function of complex IV of the respiratory chain. However, although P. anserina is an obligate aerobe and therefore depends on mitochondrial energy transduction, impairments in the copper delivery pathway are not lethal. This is due to the induction of a molecular back-up system able to compensate for deficiencies in complex IV. The system utilizes an alternative oxidase (PaAOX) which uses iron instead of copper as a cofactor. The alternative respiratory pathway is characterized by a decreased ATP generation but, most significantly, also a decrease in the production of reactive oxygen species. Consequently, molecular damage is reduced which contributes to an increased lifespan of this type of mutant. In addition, modifications in the availability of cellular copper have other relevant consequences. Most significantly, the characteristic age-related rearrangements occurring in the mitochondrial DNA of wild-type strains of P. anserina were found to be dependent on the availability of copper.

Ascomycota↗
PubMed2006

Nucleotide receptors stimulation by extracellular ATP controls Hsp90 expression through APE1/Ref-1 in thyroid cancer cells: a novel tumorigenic pathway.

Nucleotide receptors signaling affects cell proliferation, with possible implications on tumorigenic processes. However, molecular targets and action mechanisms of the extracellular nucleotides are still poorly elucidated. We have previously shown in ARO cells that APE1/Ref-1, a transcriptional coactivator responsible for the maintenance of the cellular proliferative rate, is functionally controlled by P2-mediated signaling. Here, we demonstrate that extracellular ATP has a mitogenic effect on ARO cells, increasing ERK phosphorylation, AP1 activation, and cyclin D1 expression. Using the ATP/ADPase apyrase and the P2 receptor antagonist suramin, we show that the extracellular ATP, physiologically released by ARO cells, exerts mitogenic effects. A differential proteomic approach was used to identify molecular events associated with the ATP-induced cell proliferation. Among other proteins, Hsp90 was found upregulated upon ATP stimulation. Pretreatment with suramin completely blocked the ATP-induced Hsp90 activation, confirming the involvement of cell-surface P2 nucleotide receptors in the ATP-mediated activation of ARO cells. Treatment of proliferating ARO cells with suramin and apyrase significantly reduced the intracellular levels of Hsp90, suggesting an autocrine/paracrine mechanism of control on Hsp90 expression by extracellular ATP. The influence of Hsp90 on ATP-induced cell proliferation was also demonstrated by its specific inhibition with 17-AAG. The molecular pathway by which ATP stimulates cell proliferation was further investigated by siRNA strategies showing that Hsp90 is a target of APE1/Ref-1 functional activation. Stimulation of ARO cells with specific nucleotide receptors agonists evidenced a major involvement of P2Y1 and P2Y2 receptors in controlling the Hsp90 activation. Accordingly, these two receptors resulted significantly upregulated in sample biopsies from different thyroid tumors.

Adenosine Triphosphate↗
PubMed2006

The different facets of protein kinases C: old and new players in neuronal signal transduction pathways.

Signal transduction pathways are crucial for cell-to-cell communication. Various molecular cascades allow the translation of distinct stimuli, targeting the cell, into a language that the cell itself is able to understand, thus elaborating specific responses. Within this context, a strategic role is played by protein kinases which catalyze the phosphorylation of specific substrates. The serine/threonine protein kinase C (PKC) enzymes family (at least 10 isoforms) is implicated in the transduction of signals coupled to receptor-mediated hydrolysis of membrane phospholipids. Within this molecular pathway, protein-protein interactions play a critical role in directing the distinct activated PKCs towards selective subcellular compartments, in order to guarantee spatio-temporal and localized cellular responses. A space-specific modulation of biochemical events is particularly important during learning. Among the various mechanisms, the modulation of mRNA decay appears to be an efficient post-transcriptional way of controlling gene expression during learning, allowing changes to take place in selected neuronal regions, in particular at synaptic level. To this regard, recent studies have pointed out that PKC activation is also involved in a novel signalling cascade leading to the stabilization of specific mRNAs. This review will especially focus the attention on the implication of PKC in memory trace formation and how alterations within this molecular cascade may have consequences on physiological and pathological neuronal aging (i.e. Alzheimer's disease).

Animals↗
PubMed2000

K-ras and p53 in pancreatic cancer: association with medical history, histopathology, and environmental exposures in a population-based study.

Pancreatic cancer is a highly fatal cancer with few identified risk factors. Increased risk of pancreatic cancer in tobacco smokers and among diabetic patients is well established, and some reports have suggested associations with coffee consumption and occupational exposure to organochlorines. At present, there is little information regarding the possible association of these risk factors with the known genetic alterations found in pancreatic cancers, such as activation of the K-ras oncogene and inactivation of the p53 tumor suppressor gene. Knowledge of such relationships may help to understand the molecular pathways of pancreatic tumorigenesis. We investigated the association between these molecular defects and risk factors for pancreatic cancer in 61 newly diagnosed patients identified through an ongoing study of pancreatic cancer in the San Francisco Bay Area. Interview information was obtained regarding environmental exposures, medical history, and demographic factors. Serum levels of dichlorodiphenyltrichloroethylene (DDE) and polychlorinated biphenyls were available on a subset of 24 patients. Tumor blocks were located from local hospitals and used for K-ras mutational analysis at codon 12 and for p53 protein immunohistochemistry. The molecular analyses were facilitated through the use of laser capture microdissection, which provides a reliable method to obtain almost pure populations of tumor cells. Mutations in K-ras codon 12 were found in 46 (75%) of 61 pancreatic cancers. A prior diagnosis of diabetes was significantly associated with K-ras negative tumors (P = 0.002, Fisher's exact test). The absence of this mutation was also associated with increased serum levels of DDE, although this association was not statistically significant (P = 0.16, Wilcoxon's test). There was no difference in polychlorinated biphenyl levels between the K-ras wild-type and mutant groups. Immunohistochemical staining for p53 protein did not differ by patient characteristics or clinical history, but significant associations were found with poor glandular differentiation (P = 0.002, chi2 trend test), severe nuclear atypia (P = 0.0007, chi2 trend test), and high tumor grade (P = 0.004, chi2 trend test). Our results are suggestive of the presence of K-ras codon 12 mutation-independent tumorigenesis pathways in patients with prior diabetes and possibly in patients with higher serum levels of DDE. Our results also support a role for the p53 tumor suppressor protein in the maintenance of genomic integrity.

Aged↗
PubMed2001

From theory to therapy: implications from an in vitro model of ramified microglia.

Microglia are the principal immune cells in the central nervous system (CNS), characterized by a highly specific morphology and unusual antigenic phenotype. An increasing number of studies have focused on the role of microglia in the pathogenesis of neurodegenerative diseases. To elucidate the function of microglial cells under several neuropathological conditions, we have studied and established a cell culture model that allows us to cultivate microglial cells in their inactive, resting (ramified) phenotype. In the first part of this work, we describe the interaction of microglia cells with their epithelial (astrocytic) microenvironment. The second part reviews experiments with microglia cell cultures to elucidate underlying signalling pathways and summarizes recent advances of our knowledge in microglial molecular pathways that may ultimately lead to neurodegeneration.

Animals↗
PubMed2003

ECM homeostasis in renal diseases: a genomic approach.

Chronic renal disease is in general histologically accompanied by a vast amount of scar tissue, ie glomerulosclerosis and interstitial fibrosis. Scarring results from excessive accumulation of extracellular matrix (ECM) components, a process driven by a plethora of cytokines and growth factors. Studies in experimental renal disease which target these regulators using gene therapy limit or prevent the development of scarring. This review focuses specifically on the role of transforming growth factor-beta, platelet-derived growth factor, connective tissue growth factor, hepatocyte growth factor, and epidermal growth factor. The results obtained in animal models hold promise for molecular intervention strategies in human renal disease. Microarray technology allows large-scale gene expression profiling in kidney tissue to identify common molecular pathways in a step towards discovery of new drug targets. Molecular techniques are expected to be used for diagnostic and prognostic purposes in nephrological practice to supplement renal biopsy. Several studies already show that molecular techniques might be of use in routine diagnostic practice. Improvement of diagnosis and prediction of outcome in renal patients might lead to more efficient and earlier therapeutic intervention.

Cytokines↗
PubMed2025

Oncogenic EME1 promotes tumor progression and immune modulation in human cancers with therapeutic targeting potential.

BACKGROUND: EME1, a critical DNA repair endonuclease, has emerged as a potential oncogene implicated in genome instability and cancer progression. However, its pan-cancer roles, prognostic significance, immune interactions, and therapeutic targeting remain underexplored. METHODS: We conducted a comprehensive pan-cancer analysis integrating multi-omics data from public databases, including TIMER2.0, GEPIA2, TISIDB, and cBioPortal, to evaluate EME1 expression, genetic alterations, and their association with clinical outcomes, immune infiltration, and molecular pathways. Virtual screening of 3180 FDA-approved drugs and molecular dynamics (MD) simulations were employed to identify and validate potential EME1 inhibitors. RESULTS: EME1 was significantly overexpressed in various human cancers and positively associated with advanced tumor grade and stage. High EME1 expression and mutations were linked to poor overall and disease-free survival. Immunogenomic profiling revealed strong positive correlations between EME1 and myeloid-derived suppressor cells (MDSCs), alongside a negative association with endothelial cell function, suggesting immunosuppressive roles. Machine learning models based on EME1-associated genes demonstrated high predictive accuracy for liver hepatocellular carcinoma (AUC > 0.90). Virtual screening identified eight promising drug candidates, including Everolimus and Dioscin, with strong binding affinities. MD simulations confirmed the stability of these interactions, particularly for Dioscin. CONCLUSION: This study reveals the multifaceted oncogenic roles of EME1 in tumor progression, immune evasion, and prognosis. It proposes EME1 as a promising biomarker and therapeutic target across multiple cancer types. The identified drug candidates warrant further in vitro and in vivo validation for potential repurposing in EME1-targeted cancer therapy.

EME1↗