Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “molecular pathways”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources
PubMed1998

Common molecular pathways in skeletal morphogenesis and repair.

The formation of bone is a continual process in vertebrate development, initiated during fetal development and persisting in adulthood in the form of remodeling and repair. The remarkable capacity of skeletal tissues to regenerate has led to the hypothesis that the molecular signaling pathways regulating skeletogenesis are shared during fetal development and adult wound healing. A number of key regulatory pathways that are required for endochondral ossification during fetal development are described, and their reintroduction in fracture repair demonstrated. Secreted proteins such as Sonic and Indian hedgehog exert their effect on pattern formation and chondrogenesis in the appendicular skeleton, partly through regulation of molecules such as bone morphogenic proteins (Bmps) and parathyroid hormone-related peptide (PTHrP). Once chondrocytes have matured and hypertrophied, they undergo apoptosis and are replaced by bone; the transcription factor Cbfal plays a critical role in this process of chondrocyte differentiation and ossification. Analyses of the expression patterns of these genes during fracture healing strongly suggest that they play equivalent roles in adult wound repair. Knowledge acquired through the study of fetal skeletogenesis will undoubtedly contribute to an understanding of fracture repair, and subsequently guide the development of biologically based therapeutic interventions.

Animals↗
PubMed2004

Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation.

Delayed implantation (embryonic diapause) occurs when the embryo at the blastocyst stage achieves a state of suspended animation. During this period, blastocyst growth is very slow, with minimal or no cell division. Nearly 100 mammals in seven different orders undergo delayed implantation, but the underlying molecular mechanisms that direct this process remain largely unknown. In mice, ovariectomy before preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which normally lasts for 1-2 weeks by continued progesterone treatment, although blastocyst survival decreases with time. An estrogen injection rapidly activates blastocysts and initiates their implantation in the progesterone-primed uterus. Using this model, here we show that among approximately 20,000 genes examined, only 229 are differentially expressed between dormant and activated blastocysts. The major functional categories of altered genes include the cell cycle, cell signaling, and energy metabolic pathways, particularly highlighting the importance of heparin-binding epidermal growth factor-like signaling in blastocyst-uterine crosstalk in implantation. The results provide evidence that the two different physiological states of the blastocyst, dormancy and activation, are molecularly distinguishable in a global perspective and underscore the importance of specific molecular pathways in these processes. This study has identified candidate genes that provide a scope for in-depth analysis of their functions and an opportunity for examining their relevance to blastocyst dormancy and activation in numerous other species for which microarray analysis is not available or possible due to very limited availability of blastocysts.

Animals↗
PubMed2002

Chaperoning signaling pathways: molecular chaperones as stress-sensing 'heat shock' proteins.

Heat shock proteins interact with multiple key components of signaling pathways that regulate growth and development. The molecular relationships between heat shock proteins, various signaling proteins and partner proteins appear to be critical for the normal function of signal transduction pathways. The relative levels of these proteins may be important, as too little or too much Hsp70 or Hsp90 can result in aberrant growth control, developmental malformations and cell death. Although the functions of heat shock proteins as molecular chaperones have been well characterized, their complementary role as a 'stress-induced' proteins to monitor changes and alter the biochemical environment of the cell remains elusive. Genetic and molecular interactions between heat shock proteins, their co-chaperones and components of signaling pathways suggest that crosstalk between these proteins can regulate proliferation and development by preventing or enhancing cell growth and cell death as the levels of heat shock proteins vary in response to environmental stress or disease.

Cell Differentiation↗
PubMed2005

Identification of genes and molecular pathways involved in the progression of premalignant oral epithelia.

An early interventional effort in oral premalignancy requires novel molecular targets and diagnostic biomarkers to delay or reverse incidences of malignant progression. Microarray-based transcriptional profiling in disease states provides global insight into the causal biomolecular processes and novel pathways involved. In this study, we investigated transcript profiles in precancerous oral lesions to identify nearly 1,700 genes as significantly overexpressed or underexpressed and a primarily affected metabolic pathway that may be responsible for irreversible transition to progressive stages of oral cancer. For the first time, we show a convergence of several genes and pathways known for their oncogenic capabilities, in progression of premalignant oral epithelial tissues. This study consequently provides a molecular basis for persistent proinflammatory conditions in oral premalignant tissues. We found that lipocalin-type prostaglandin D(2) synthase (PTGDS), a key enzyme in the arachidonic acid metabolism pathway, as repressed in premalignant stages. We show the protective role of these enzyme-derived metabolites in inhibiting cell proliferation using an in vitro oral cancer progression model. We have also confirmed the overexpression of two invasion-related biomarkers, psoriasin (PSOR1) and versican (CSPG2), in oral premalignant and malignant archival tissues. Our results clearly indicate that pharmacologic intervention with anti-inflammatory prostaglandin D(2)-like analogues may help prevent or delay oral epithelial carcinogenesis because of metabolic restoration of a negative feedback regulatory loop through its several cognate receptors or target molecules. Further studies directed toward a multitude of possible protective mechanisms of this lipocalin-type enzyme or its products in oral cancer progression are warranted.

Biopsy↗
PubMed2005

Carotenoid biosynthetic pathway: molecular phylogenies and evolutionary behavior of crt genes in eubacteria.

Phylogenetic analysis of carotenoid biosynthetic pathway genes and their evolutionary rate variations were studied among eubacterial taxa. The gene sequences for the enzymes involved in this pathway were obtained for major phylogenetic groups of eubacteria (green sulfur bacteria, green nonsulphur bacteria, Gram-positive bacteria, proteobacteria, flavobacteria, cyanobacteria) and archeabacteria. These gene datasets were distributed under five major steps of carotenoid biosynthesis in eubacteria; isoprenoid precursor biosynthesis, phytoene synthesis, dehydrogenation of phytoene, lycopene cyclization, formation of acyclic xanthophylls, formation of cyclic xanthophylls and carotenoid biosynthesis regulation. The NJ algorithm was used on protein coding DNA sequences to deduce the evolutionary relationship for the respective crt genes among different eubacterial lineages. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) and synonymous nucleotide substitutions per synonymous site (d(S)) were calculated for different clades of the respective phylogenetic tree for specific crt genes. The phylogenetic analysis suggests that evolutionary pattern of crt genes in eubacteria is characterized by lateral gene transfer and gene duplication events. The d(N) values indicate that carotenoid biosynthetic genes are more conserved in proteobacteria than in any other eubacterial phyla. Furthermore, of the genes involved in carotenoid biosynthesis pathway, structural genes evolve slowly than the regulatory genes in eubacteria.

Bacteria↗
PubMed2002

Molecular pathways to obesity.

Obesity results from a chronic imbalance between energy intake and energy expenditure. Environmental factors, such as the increased availability of high caloric food or the decreased need for physical activity, contribute to its development and their influence is amplified by genetic predisposition. In recent years remarkable progress has been made in the understanding of the pathophysiology of obesity. Although most of the insights into the regulation of energy balance have been obtained in rodent models, the rare clinical cases of monogenic obesity provided evidence for the importance of several of these mechanisms in humans. The identification of leptin as a factor originating from adipose tissue and informing the brain about the status of energy reserves firmly established the concept of long-term regulation of body fat stores. The disappointing therapeutic results with leptin in obese patients could be explained by the fact that during evolution this hormone developed rather as a starvation signal than as an adiposity signal. It is conceivable that the pharmacological interference with mechanisms downstream of leptin, for example with the melanocortin pathway, might be therapeutically more promising. The discovery of new molecular mechanisms involved in the regulation of the differentiation and proliferation of adipocytes and the elucidation of their paracrine and endocrine functions have changed the traditional view of adipose tissue as an inert depot for triglycerides. The identification of new uncoupling proteins could modify the current concepts of the regulation of thermogenesis in humans. The remarkable progress in the identification of novel targets involved in the regualtion of energy balance should have a positive impact on the search for new antiobesity agents.

Animals↗
PubMed2006

Phenotypical characteristics, biochemical pathways, molecular targets and putative role of nitric oxide-mediated programmed cell death in Leishmania.

Nitric oxide (NO) has been demonstrated to be the principal effector molecule mediating intracellular killing of Leishmania, both in vitro and in vivo. We investigated the type of cell death process induced by NO for the intracellular amastigote stage of the protozoa Leishmania. Specific detection methods revealed a rapid and extensive cell death with morphological features of apoptosis in axenic amastigotes exposed to NO donors, in intracellular amastigotes inside in vitro - activated mouse macrophages and also in activated macrophages of regressive lesions in a leishmaniasis-resistant mouse model. We extended our investigations to the dog, a natural host-reservoir of Leishmania parasites, by demonstrating that co-incubation of infected macrophages with autologous lymphocytes derived from dogs immunised with purified excreted-secreted antigens of Leishmania resulted in a significant NO-mediated apoptotic cell death of intracellular amastigotes. From the biochemical point of view, NO-mediated Leishmania amastigotes apoptosis did not seem to be controlled by caspase activity as indicated by the lack of effect of cell permeable inhibitors of caspases and cysteine proteases, in contrast to specific proteasome inhibitors, such as lactacystin or calpain inhibitor I. Moreover, addition of the products of two NO molecular targets, cis-aconitase and glyceraldehyde-3-phosphate dehydrogenase, also had an inhibitory effect on the cell death induced by NO. Interestingly, activities of these two enzymes plus 6-phosphogluconate dehydrogenase, parasitic enzymes involved in both glycolysis and respiration processes, are overexpressed in amastigotes selected for their NO resistance. This review focuses on cell death of the intracellular stage of the pathogen Leishmania induced by nitrogen oxides and gives particular attention to the biochemical pathways and the molecular targets potentially involved. Questions about the role of Leishmania amastigotes NO-mediated apoptosis in the overall infection process are raised and discussed.

Animals↗
PubMed2000

MAP kinase pathways: molecular plug-and-play chips for the cell.

Mitogen-activated protein kinase (MAPK) pathways transduce a large variety of external signals in mammals, unicellular eukaryotes, and plants. In recent years, plant MAPK pathways have attracted increasing interest resulting in the isolation of a large number of different components. Studies on the function of these components have revealed that MAPKs play important roles in the response to a broad variety of stresses, but also in the signaling of plant hormones and the cell cycle. Besides giving an update on recent results, the success and logic of MAPK-based signal transduction cascades is discussed.

Gene Expression Regulation, Enzymologic↗
PubMed2005

[Achieving pathogenesis understanding of ocular diseases by deciphering the underlying molecular pathways].

The field of ophthalmology research has experienced a revolution since the 1970's, when molecular biology techniques were gradually and widely adopted. Many of the developments generated impact that went far beyond the field of ophthalmology. A classic case was the identification and characterization of the Retinoblastoma susceptibility gene (Rb), whose impact went far beyond the rare and obscure disease, as it provides key evidence for the concept of tumor suppressor gene and the "two hit" theory of tumor formation. The identification of scores of genes involved in retinitis pigmentosum (pigmentosa), on the other hand, show cases the complexity of multi-factorial diseases. Ophthalmology researchers in China have been quick in integrating these novel tools into their research. However, the field still lags behind in the effective use of these technologies to carry out in-depth inquiries into key disease mechanisms. The advent of "omics" technologies heralded a new era in biomedical research that allows for the global and rapid survey of genetic and biochemical profiles. Effective integration of these novel technologies into ophthalmology research will have far-reaching impact for the whole field.

Biotechnology↗
PubMed1995

A molecular pathway determining left-right asymmetry in chick embryogenesis.

While significant progress has been made in understanding the molecular events underlying the early specification of the antero-posterior and dorso-ventral axes, little information is available regarding the cellular or molecular basis for left-right (LR) differences in animal morphogenesis. We describe the expression patterns of three genes involved in LR determination in chick embryos: activin receptor IIa, Sonic hedgehog (Shh), and cNR-1 (related to the mouse gene nodal). These genes are expressed asymmetrically during and after gastrulation and regulate the expression of one another in a sequential pathway. Moreover, manipulation of the sidedness of either activin protein or Shh expression alters heart situs. Together, these observations identify a cascade of molecular asymmetry in that determines morphological LR asymmetry in the chick embryo.

Activins↗
PubMed2003

Alterations in molecular pathways of diffusely infiltrating glial neoplasms: application to tumor classification and anti-tumor therapy (Review).

Recent advances in our understanding of the molecular genetic mechanisms underlying diffusely infiltrating brain neoplasms have important implications for the classification and therapy of these tumors. Traditionally, primary brain tumors have been classified histologically; however, it is now clear that tumors within a single histologically defined category are heterogeneous from a molecular genetic perspective. Furthermore, many new experimental therapeutic strategies directed against these almost invariably fatal tumors are aimed at molecular rather than histologic abnormalities. Consequently, the classification of these tumors is in the process of being re-evaluated as underlying molecular genetic mechanisms continue to be elucidated. This review covers traditional histologic based classification of infiltrating glial neoplasms together with molecular abnormalities of these tumors involving p53, epidermal growth factor receptor, the retinoblastoma pathway, platelet derived growth factor receptor, genetic losses on chromosome 10, and loss of heterozygosity on chromosomes 1p and 19q. The contribution of these molecular genetic abnormalities to the classification and therapy of these tumors is discussed. Although at the present no molecular system for the classification of brain tumors has been generally accepted, microarray technologies offer the exciting prospect of practical molecular classification in the future.

Antineoplastic Agents↗
PubMed2004

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.

Artificial Intelligence↗
PubMed2003

Molecular pathways to prostate cancer.

PURPOSE: Prostate cancer continues to be a prevalent disease in the United States and western countries. Advances in the fields of molecular biology and genetics coupled with new developments in biotechnology have increased our understanding of events associated with the initiation and progression of prostate cancer. We reviewed recent scientific discoveries relating to genetic predisposition, somatic alterations and epigenetic phenomena involved in the pathogenesis of prostate cancer. MATERIALS AND METHODS: Reports published in the scientific literature with relevance to the molecular biology, genetics and epigenetics of prostate cancer were identified using the MEDLINE data base. Particular emphasis was placed on articles that investigated the contribution of somatic alterations to prostate cancer. RESULTS: A multitude of genes have recently been identified that are believed to be relevant to prostate carcinogenesis. A contemporary model for prostate cancer progression should include the potential contribution of inflammation to the development of preneoplastic or neoplastic lesions. Abnormal methylation of important growth regulatory or caretaker genes represents an alternative pathway to cancer in addition to aneuploidy, loss of heterozygosity and gene mutations. CONCLUSIONS: The identification of molecular markers specific to early and late events in prostate cancer progression is critical for the development of improved detection and prognostication strategies. While there is evidence to support the association between inflammation and prostate cancer, the exact mechanisms by which these processes occur are not well defined. The significant contribution of somatic and epigenetic defects to prostate carcinogenesis underscores the need to develop therapeutic approaches that specifically target these molecular alterations.

DNA Methylation↗
PubMed2004

Towards a molecular pathway for myoblast fusion in Drosophila.

Intercellular fusion among myoblasts is required for the generation of multinucleated muscle fibers during skeletal muscle development. Recent studies in Drosophila have shed light on the molecular mechanisms that underlie this process, and a signaling pathway that relays fusion signals from the cell membrane to the cytoskeleton has emerged. In this article, we review these recent advances and discuss how Drosophila offers a powerful model system to study myoblast fusion in vivo.

Animals↗
PubMed2004

Molecular pathways regulating the self-renewal of hematopoietic stem cells.

Hematopoietic stem cells (HSC) self-renew throughout life, but the molecular mechanisms by which this process occurs and is regulated are imprecisely understood. We review the published data from overexpression and knockout studies describing genes that influence stem cell self-renewal, including transcription factors, cell cycle regulators, and genes that influence chromosome structure. One model suggesting how some of these disparate classes of molecular regulators might be integrated is presented, focusing on the role of G1/S progression in the developmental switch toward stem cell self-renewal vs differentiation. Experimental exploration of this model and other related hypotheses will hopefully lead to a more complete description of HSC self-renewal and its regulation, both in normal physiology and in applied therapeutics.

Animals↗
PubMed2001

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Systems that extract structured information from natural language passages have been highly successful in specialized domains. The time is opportune for developing analogous applications for molecular biology and genomics. We present a system, GENIES, that extracts and structures information about cellular pathways from the biological literature in accordance with a knowledge model that we developed earlier. We implemented GENIES by modifying an existing medical natural language processing system, MedLEE, and performed a preliminary evaluation study. Our results demonstrate the value of the underlying techniques for the purpose of acquiring valuable knowledge from biological journals.

Artificial Intelligence↗
PubMed2004

Analysis of molecular pathways in neuroendocrine cancers of the gastroenteropancreatic system.

Neuroendocrine gastroenteropancreatic (GEP) tumors are rare and present with variable clinical syndromes. So far, there are no detailed studies concerning the molecular pathogenesis of sporadic GEP tumors. In our study, GEP tumors from 29 patients were assessed for microsatellite instability, aberrant promoter methylation, and LOH of various tumor suppressor genes. All tumors were microsatellite stable. One tumor showed LOH close to the APC locus, one tumor had an allelic loss near the hMLH1 gene, and one tumor showed hypermethylation of the hMLH1 promoter. Interestingly, none of the tumors was aberrantly methylated at the p16 promoter. However, 13 of 20 successfully amplified tumors (65%) were hypermethylated at the APC promoter. Of the hypermethylated tumors, none showed LOH of either the hMLH1 or the APC gene. The current study is the first report demonstrating that aberrant methylation of the APC promoter is strongly involved in the molecular tumorigenesis of neuroendocrine GEP tumors. MSI does not seem to be involved in the pathogenesis of these cancers. Further studies are required to investigate the role of hypermethylation in neuroendocrine GEP tumors and to further elucidate the role of the APC pathway in these tumors.

DNA Methylation↗
PubMed2004

The Akt pathway: molecular targets for anti-cancer drug development.

The serine/threonine kinase Akt functions intracellularly as a cardinal nodal point for a constellation of converging upstream signaling pathways, which involve stimulation of receptor tyrosine kinases such as IGF-1R, HER2/Neu, VEGF-R, PDGF-R), and an assembly of membrane-localized complexes of receptor-PI-3K and activation of Akt through the second messenger PIP(3). The integration of these intracellular signals at the level of Akt and its kinase activity, regulates the phosphorylation of its several downstream effectors, such as NF-kappa B, mTOR, Forkhead, Bad, GSK-3 and MDM-2. These phosphorylation events in turn mediate the effects of Akt on cell growth, proliferation, protection from pro-apoptotic stimuli, and stimulation of neo-angiogenesis. Because Akt and its upstream regulators are deregulated in a wide range of solid tumors and hematologic malignancies, and in view of the aforementioned biologic sequelae of this pathway, the Akt pathway is considered a key determinant of biologic aggressiveness of these tumors, and a major potential target for novel anti-cancer therapies. This review focuses on ongoing translational efforts to therapeutically target Akt and its biologic sequelae, either at the level of Akt itself or at the levels of its upstream regulators and downstream effectors. Because Akt is also important for proliferative and anti-apoptotic signaling pathways critical for normal cells, particular emphasis is placed on the fine-tuning the targeting of individual components of this pathway to maximize the therapeutic index of anti-cancer strategies based on the PI-3K/Akt pathway.

Animals↗