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PubMed2005

A combined genetics and genomics approach to unravelling molecular pathways in coeliac disease.

Coeliac disease (CD) is a complex, inflammatory disorder of the small intestine induced by gluten. It is common and has a prevalence of approximately 1:200 in Western populations. A major known susceptibility locus for CD is the HLA -DQ locus. However, the genetic contribution of this region is limited to approximately 40%, so non-HLA genes must also be involved in the disease aetiology. Genetic studies have so far identified multiple loci that may potentially be involved in disease aetiology, although the majority of these loci are expected to point to genes with a small effect. A major CD locus on chromosome 19 was recently identified in the Dutch population. Interestingly, there is some marked overlap when comparing genetic linkage studies conducted in different autoimmune disorders, suggesting that common pathways contribute to these diseases. This knowledge may eventually help in identifying some of the disease genes. To identify the true disease-causing genes, linkage analysis needs to be followed by genetic association. Because of the nature of the probable mutations, it is to be expected that the investigation of gene expression data can assist in selecting candidate genes from linkage regions. Furthermore, expression data will point to the molecular pathways involved in the disease pathogenesis.

Celiac Disease↗

PubMed2003

Connective molecular pathways of experimental bladder inflammation.

Inflammation is an inherent response of the organism that permits its survival despite constant environmental challenges. The process normally leads to recovery from injury and to healing. However, if targeted destruction and assisted repair are not properly phased, chronic inflammation can result in persistent tissue damage. To better understand the inflammatory process, we recently introduced a profiling methodology to identify common genes involved in bladder inflammation. The method represents a complementation to the classic quantification of inflammation and provides information regarding the early, intermediate, and late events in gene regulation. However, gene profiling fails to describe the molecular pathways and their interconnections involved in the particular inflammatory response. The present work introduces a new statistical technique for inferring functional interconnections between inflammatory pathways underlying classic models of bladder inflammation and permits the modeling of the inflammatory network. This new statistical method is based on variants of cluster analysis, Boolean networking, differential equations, Bayesian networking, and partial correlation. By applying partial correlation analysis, we developed mosaics of gene expression that permitted a global visualization of common and unique pathways elicited by different stimuli. The significance of these processes was tested from both biological and statistical viewpoints. We propose that connective mosaic may represent the necessary simplification step to visualize cDNA array results.

Animals↗

PubMed1995

Common molecular pathways for patterning of the body axis, limbs, central nervous system, and face during embryonic development.

Many congenital anomalies affecting the face are known to appear as syndromes or associations, in combination with other defects. Often, these involve the limbs, eyes, central nervous system, and body axis. A general, and understandable, tendency among clinical researchers has been to seek a single cell type or definable embryologic process on which to ascribe the etiologic basis for such associations. The possibility of a gene, or group of genes, under coordinate control has not received much attention until recently. With the advent of recombinant DNA technology and the current explosion in basic research on the molecular bases of embryonic development, however, several possibilities are beginning to emerge. Here, I will list a few genes whose expression during development suggests that the molecules they encode are used as part of a coordinate molecular pathway, and that they play a role in the development of systems that often appear together in congenital associations or syndromes.

Abnormalities, Multiple↗

PubMed2006

Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex.

Two key models for examining activity-dependent development of primary visual cortex (V1) involve either reduction of activity in both eyes via dark-rearing (DR) or imbalance of activity between the two eyes via monocular deprivation (MD). Combining DNA microarray analysis with computational approaches, RT-PCR, immunohistochemistry and physiological imaging, we find that DR leads to (i) upregulation of genes subserving synaptic transmission and electrical activity, consistent with a coordinated response of cortical neurons to reduction of visual drive, and (ii) downregulation of parvalbumin expression, implicating parvalbumin-expressing interneurons as underlying the delay in cortical maturation after DR. MD partially activates homeostatic mechanisms but differentially upregulates molecular pathways related to growth factors and neuronal degeneration, consistent with reorganization of connections after MD. Expression of a binding protein of insulin-like growth factor-1 (IGF1) is highly upregulated after MD, and exogenous application of IGF1 prevents the physiological effects of MD on ocular dominance plasticity examined in vivo.

Animals↗

PubMed1999

Two independent molecular pathways for recombinant adeno-associated virus genome conversion occur after UV-C and E4orf6 augmentation of transduction.

Numerous environmental influences have been demonstrated to enhance recombinant adeno-associated virus (rAAV) transduction. Such findings are the foundation of developing new and innovative strategies to improve the efficiency of rAAV as a gene therapy vector. Several of these environmental factors included genotoxic stresses such as UV and y irradiation as well as certain adenoviral gene products such as E4orf6. The mechanisms by which these environmental stimuli increase rAAV transduction are only partially understood but have been suggested to involve both endocytosis and uptake of virus to the nucleus, as well as conversion of single-stranded DNA viral genomes to double-stranded expressible forms. Two molecular intermediates of rAAV genomes, which have been demonstrated to correlate with transgene expression and/or the persistence of rAAV, include both replication form (Rf) monomers and dimers as well as circular intermediates. In the present study, we demonstrate that augmentation of rAAV transduction by UV irradiation and the adenoviral protein E4orf6 correlates with distinct increases in either circular or replication form intermediates, respectively. UV irradiation of primary fibroblasts at 15 J/m2 resulted in a 15-fold induction of head-to-tail circular intermediates, with minimal induction of replication form rAAV genomes. In contrast, E4orf6-augmented rAAV transduction was correlated with the formation of replication form intermediates, with no alteration in the abundance of circular intermediates. These findings demonstrate that rAAV transduction can occur through two independent molecular pathways that convert single-stranded AAV genomes to expressible forms of DNA.

Adenovirus E4 Proteins↗

PubMed1998

Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning.

In a large-scale gene expression screen 1765 randomly picked cDNAs were analyzed by whole-mount in situ hybridization in Xenopus embryos. Two hundred and seventy three unique, differentially expressed genes were identified, 204 of which are novel in Xenopus. Partial DNA sequences and expression patterns were documented and assembled into a database, 'AXelDB'. Approximately 30% of cDNAs analyzed represent differentially expressed genes and about 5% show highly regionalized expression. Novel marker genes and potential developmental regulators were found. Differential expression of mitochondrial genes was observed. Marker genes were used to study regionalization of the entire gastrula as well as the tail forming region and the epidermis of the tailbud embryo. Four 'synexpression' groups representing genes with shared, complex expression pattern that predict molecular pathways involved in patterning and differentiation were identified. According to their probable functional significance these groups are designated as Delta1, Bmp4, ER-import and Chromatin group. Within synexpression groups, a likely function of genes without sequence similarity can be predicted. The results indicate that synexpression groups have strong prognostic value. A cluster analysis was made by comparing gene expression patterns to derive a novel parameter, 'tissue relatedness'. In conclusion, this study describes a semi-functional approach to investigate genes expressed during early development and provides global insight into embryonic patterning.

Animals↗

PubMed2003

Molecular pathways regulating mobilization of marrow-derived stem cells for tissue revascularization.

Adult bone marrow is a rich reservoir of hematopoietic and vascular stem and progenitor cells. Mobilization and recruitment of these cells are essential for tissue revascularization. Physiological stress, secondary to tissue injury or tumor growth, results in the release of angiogenic factors, including vascular endothelial growth factor (VEGF), which promotes mobilization of stem cells to the circulation, contributing to the formation of functional vasculature. VEGF interacts with its receptors, VEGFR2 and VEGFR1, expressed on endothelial and hematopoietic stem cells, and thereby promotes recruitment of these cells to neo-angiogenic sites, accelerating the revascularization process. The mobilization of stem cells from marrow is a dynamic process, regulated by shear stress imparted by blood flow, and the activation of metalloproteinases that induce the release of 'Kit ligand', facilitating egress from the marrow to the circulation. Identification of the molecular pathways that support the proliferation and differentiation of vascular stem and progenitor cells will open up new avenues for the design of clinical trials to accelerate tissue vascularization and organogenesis.

Adenoviridae↗

PubMed2000

Parallel molecular pathways mediate expression of distinct forms of intermediate-term facilitation at tail sensory-motor synapses in Aplysia.

Three distinct temporal phases of synaptic facilitation (short-, intermediate-, and long-term) are induced by serotonin (5-HT) at sensory (SN) to motor (MN) synapses in Aplysia. Here, we characterize two mechanistically distinct forms of intermediate-term facilitation (ITF) at tail SN-MN synapses. One form, activity-independent ITF, is produced by five spaced pulses of 5-HT in the absence of SN activity. Its induction requires protein synthesis, and its expression requires persistent activation of PKA but not PKC. The other form, activity-dependent ITF, is produced by a single pulse of 5-HT coincident with SN activation. Its induction does not require protein synthesis, and its expression requires persistent activation of PKC but not PKA. These results demonstrate that SN-MN synapses can exhibit two distinct forms of ITF that are mediated by parallel molecular pathways.

Animals↗

PubMed2005

CDKL5 belongs to the same molecular pathway of MeCP2 and it is responsible for the early-onset seizure variant of Rett syndrome.

Rett syndrome (RTT) is a severe neurodevelopmental disorder almost exclusively affecting females and characterized by a wide spectrum of clinical manifestations. Most patients affected by classic RTT and a smaller percentage of patients with the milder form 'preserved speech variant' have either point mutations or deletions/duplications in the MECP2 gene. Recently, mutations in the CDKL5 gene, coding for a putative kinase, have been found in female patients with a phenotype overlapping with that of RTT. Here, we report two patients with the early seizure variant of RTT, bearing two novel CDKL5 truncating mutations, strengthening the correlation between CDKL5 and RTT. Considering the similar phenotypes caused by mutations in MECP2 and CDKL5, it has been suggested that the two genes play a role in common pathogenic processes. We show here that CDKL5 is a nuclear protein whose expression in the nervous system overlaps with that of MeCP2, during neural maturation and synaptogenesis. Importantly, we demonstrate that MeCP2 and CDKL5 interact both in vivo and in vitro and that CDKL5 is indeed a kinase, which is able to phosphorylate itself and to mediate MeCP2 phosphorylation, suggesting that they belong to the same molecular pathway. Furthermore, this paper contributes to the clarification of the phenotype associated with CDKL5 mutations and indicates that CDKL5 should be analyzed in each patient showing a clinical course similar to RTT but characterized by a lack of an early normal period due to the presence of seizures.

Age of Onset↗

PubMed2005

Hormone replacement therapy (HRT) and endometrial morphology under consideration of the different molecular pathways in endometrial carcinogenesis.

The majority of modern hormone replacement therapy (HRT) regimens contain estrogen and progestogens, given either in a cyclical or continuous manner. About 15% of the endometrial biopsies taken from women on sequential HRT show proliferative activity including atypical endometrial hyperplasia in up to 1% of the cases. The majority of biopsies from women under continuous combined HRT show an endometrial atrophy. About 2-3% of these women will present proliferative activity, usually without atypical hyperplasia. Contrary to breast cancer, an increased risk of endometrial cancer has not been reported in the WHI- and HERS-studies. However, endogenous factors, such as obesity, diabetes mellitus, the distribution of estrogen receptors alpha and beta and genetic polymorphisms for receptors and enzymes might alter the endometrial stimulation under different types of HRT. There should be a liberal indication for endometrial biopsies in Hereditary Non-Polyposis Colorectal Cancer (HNPCC). HNPCC-patients under HRT as well as for ultrasonographic evaluation of the endometrium. The risk of atypical hyperplasias or carcinoma under unopposed estrogen-therapy varies from 2 to 10%. So, this kind of HRT should not be used in non-hysterectomised women. As far as the risk of endometrial cancer under any kind of HRT is concerned, the different molecular pathways of endometrial carcinogenesis (type 1 and 2 cancers) should be taken into account. The use of tibolone leaves the endometrium unaffected.

Endometrial Neoplasms↗

PubMed2006

Different molecular pathways determining extrahepatic and intrahepatic recurrences of hepatocellular carcinoma.

Recent genome-wide screens have identified genes associated with the metastatic potential of hepatocellular carcinoma (HCC); however, there is little overlap between the identified genes, and interpretations of the results remain controversial. These inconsistencies may be related to differences in the sample populations, use of distinct microarray platforms and algorithms, and the complicated modes of HCC recurrence. We investigated the gene expression profiles of extrahepatic recurrence (EHR) and early intrahepatic recurrence (IHR), which are two representative modes of recurrence of HCC attributable to metastasis. We used DNA microarray analysis and identified 46 signature genes for EHR in 35 HCCs in a supervised learning manner. The obtained gene expression profile was compared with that for early IHR that was determined previously in the same manner. The 46 signature genes for EHR included many cell adhesion-related genes (ITGA6, SPP1, DNMBP, CD44 and POSTN), which all showed higher expression in HCC with EHR than in HCC without EHR. The 46 signature genes for early IHR included 10 immune response-related genes, which all showed lower expression in HCC with early IHR than in HCC without early IHR. The signature genes for EHR included only two immune response-related genes (P=0.013). These results suggest that alteration of the cell adhesion system plays a central role in EHR and that reduction of the immune response is a specific step in early IHR. These results indicate that the metastatic processes in EHR and early IHR involve different molecular pathways.

Adult↗

PubMed2002

Molecular pathways of monocyte emigration into the alveolar air space of intact mice.

The adhesive interactions involved in monocyte recruitment to the alveolar space in vivo are only poorly defined. To study these interactions, we used a recently developed mouse model that allowed the separation and quantification of freshly recruited monocytes, resident alveolar macrophages (rAM), neutrophils, and lymphocytes in the bronchoalveolar compartment by fluorescence activated cell sorting technology. In these mice, the combined intratracheal administration of the monocyte chemoattractant JE/monocyte chemotactic protein (MCP)-1 and low dose Escherichia coli lipopolysaccharide (LPS) induces a self-limiting pulmonary inflammatory response, characterized by well-controlled sequelae of both neutrophil and monocyte emigration into the alveolar space. In contrast, challenge with JE/MCP-1 provokes the emigration only of monocytes in the absence of lung inflammation. Using an array of function-blocking monoclonal antibodies (mAb) (anti-CD11a, -CD11b, -CD18, -CD49d, -CD54, and -CD106), we characterized the adhesive interactions underlying the transendothelial and transepithelial leukocyte traffic in intact animals. Alveolar monocyte recruitment elicited by JE/MCP-1 alone was strictly dependent on CD11b/CD18, CD54, and CD49d, and partly dependent on CD11a, but not dependent on CD106. In response to JE/MCP-1 plus E. coli LPS, we observed additional engagement of CD11a and CD106 for enhanced alveolar monocyte transmigration. Comigrating neutrophils were found to primarily utilize CD11b, CD18, and CD54, but not CD49d, CD106, or, surprisingly, CD11a. This contrasted with the effect of CD11a on alveolar challenge with macrophage inflammatory protein (MIP)-1alpha instead of JE/MCP-1. In conclusion, we found that in an intact mouse model allowing detailed phenotyping of leukocyte traffic into the alveolar space, the molecular pathways involved in JE/MCP-1-driven monocyte efflux differed under noninflammatory and inflammatory (presence of LPS) conditions. Moreover, the profile of adhesive interactions underlying the monocyte efflux differed from that characterizing neutrophil trafficking.

Animals↗

PubMed2002

Molecular pathways of protein synthesis inhibition during brain reperfusion: implications for neuronal survival or death.

Protein synthesis inhibition occurs in neurons immediately on reperfusion after ischemia and involves at least alterations in eukaryotic initiation factors 2 (eIF2) and 4 (eIF4). Phosphorylation of the alpha subunit of eIF2 [eIF2(alphaP)] by the endoplasmic reticulum transmembrane eIF2alpha kinase PERK occurs immediately on reperfusion and inhibits translation initiation. PERK activation, along with depletion of endoplasmic reticulum Ca2+ and inhibition of the endoplasmic reticulum Ca2+ -ATPase, SERCA2b, indicate that an endoplasmic reticulum unfolded protein response occurs as a consequence of brain ischemia and reperfusion. In mammals, the upstream unfolded protein response components PERK, IRE1, and ATF6 activate prosurvivial mechanisms (e.g., transcription of GRP78, PDI, SERCA2b ) and proapoptotic mechanisms (i.e., activation of Jun N-terminal kinases, caspase-12, and CHOP transcription). Sustained eIF2(alphaP) is proapoptotic by inducing the synthesis of ATF4, the CHOP transcription factor, through "bypass scanning" of 5' upstream open-reading frames in ATF4 messenger RNA; these upstream open-reading frames normally inhibit access to the ATF4 coding sequence. Brain ischemia and reperfusion also induce mu-calpain-mediated or caspase-3-mediated proteolysis of eIF4G, which shifts message selection to m 7 G-cap-independent translation initiation of messenger RNAs containing internal ribosome entry sites. This internal ribosome entry site-mediated translation initiation (i.e., for apoptosis-activating factor-1 and death-associated protein-5) can also promote apoptosis. Thus, alterations in eIF2 and eIF4 have major implications for which messenger RNAs are translated by residual protein synthesis in neurons during brain reperfusion, in turn constraining protein expression of changes in gene transcription induced by ischemia and reperfusion. Therefore, our current understanding shifts the focus from protein synthesis inhibition to the molecular pathways that underlie this inhibition, and the role that these pathways play in prosurvival and proapoptotic processes that may be differentially expressed in vulnerable and resistant regions of the reperfused brain.

Animals↗

PubMed2003

Evidence of a preferred molecular pathway in patients with synchronous colorectal cancer.

BACKGROUND: A small proportion of patients with colorectal carcinoma (CRC) have synchronous tumors at the time of diagnosis. A subset of sporadic CRCs display microsatellite instability (MSI) that is associated with MLH1 silencing due to promoter methylation. In the current study, the authors investigated the proportion of tumors with MSI in patients with synchronous colorectal carcinoma (SCRC) and the concordance in MSI status among tumors in a given individual. In addition, the authors examined MLH1 and MSH2 expression and MLH1 promoter methylation in SCRCs. METHODS: The current study included 77 patients, with a combined total of 170 invasive SCRCs, who were identified from a database of 2884 patients with CRC. Instability was determined by polymerase chain reaction (PCR) amplification using a set of five markers. Tumors that were unstable at two or more markers were considered unstable (MSI); otherwise, they were considered microsatellite stable (MSS). Expression of MLH1 and MSH2 was determined by immunohistochemistry. Methylation of the MLH1 gene promoter was determined by a methylation-specific PCR assay. Statistical comparisons were made using the chi-square test or the Student t test. RESULTS: Of the 77 patients in the study, 21 (27%) had a family history of hereditary nonpolyposis colon carcinoma-related malignancy, but none fulfilled the Amsterdam II criteria. Fifty-four of 170 tumors (32%) were found to be MSI. Patients with MSI tumors were older and more frequently female. All but 1 MSI tumor lacked expression of MLH1 (n = 44) or MSH2 (n = 8), or both (n = 1). All MLH1-negative tumors, compared with only 3 MLH1-positive tumors, were methylated at the MLH1 promoter. Most patients (n = 67; 87%) had either all MSS tumors (n = 48; 62%) or all MSI tumors (n = 19; 25%); 10 patients (13%) had both MSS and MSI tumors. The observed MSI/MSS distribution was significantly different from the distribution expected based on an assumption of independence (P < 0.0001). CONCLUSIONS: There is a strong concordance in MSI/MSS status among tumors in the same individual. This finding suggests that the tumors in patients with SCRC develop along a preferred molecular pathway.

Adaptor Proteins, Signal Transducing↗

PubMed2000

Molecular pathway of germ cell apoptosis following ischemia/reperfusion of the rat testis.

The present study investigates the molecular apoptotic pathway in germ cells following acute ischemia of the rat testis. Rats were subjected to ischemia-inducing torsion and testes were harvested after reperfusion. Apoptotic cells were identified with an antibody to single-stranded DNA. Seminiferous tubule RNA was examined by RNase protection assay or by reverse transcriptase-polymerase chain reaction (RT-PCR) for the presence and regulation of apoptotic molecules. Proteins from seminiferous tubules were used for Western blot analysis of cytochrome c. Germ cell apoptosis was maximal at 24 h after repair of torsion. Germ cells in stages II-III of the seminiferous epithelium cycle were the predominant early responders. The RNase protection assays revealed that Bcl-X(L) was the prominent mRNA species. Caspases 1, 2, 3, and Bax mRNA were consistently upregulated; however, the time of upregulation after torsion was variable. The Bcl-X(L) and Bcl-X(S) mRNAs were less consistently upregulated and there was no evidence for upregulation of Fas or Bcl-2. Fas ligand (FasL) was not detected by RNase protection assay, but RT-PCR revealed a significant increase in FasL expression 4 h after the repair of torsion. Western blot analysis for cytochrome c release demonstrated a significant increase 4 h after the repair of torsion. Results suggest that germ cell apoptosis following ischemia/reperfusion of the rat testis is initiated through the mitochondria-associated molecule Bax as well as Fas-FasL interactions.

Animals↗

PubMed2005

The lymphomas: molecular pathways and novel therapeutic targets.

In recent years, several molecular mechanisms involved in promoting cancer cell survival and growth have been identified. These discoveries helped in designing and testing novel drugs that target specific cellular pathways. In this review, we focus on new molecular targets that are currently being explored for the treatment of non-Hodgkin's lymphoma and Hodgkin's lymphoma.

Antibodies, Monoclonal↗

PubMed2005

The Akt/PKB pathway: molecular target for cancer drug discovery.

The serine/threonine kinase Akt/PKB pathway presents an exciting new target for molecular therapeutics, as it functions as a cardinal nodal point for transducing extracellular (growth factor and insulin) and intracellular (receptor tyrosine kinases, Ras and Src) oncogenic signals. In addition, alterations of the Akt pathway have been detected in a number of human malignancies. Ectopic expression of Akt, especially constitutively activated Akt, is sufficient to induce oncogenic transformation of cells and tumor formation in transgenic mice as well as chemoresistance. Akt has a wide range of downstream targets that regulate tumor-associated cell processes such as cell growth, cell cycle progression, survival, migration, epithelial-mesenchymal transition and angiogenesis. Blockage of Akt signaling results in apoptosis and growth inhibition of tumor cells with elevated Akt. The observed dependence of certain tumors on Akt signaling for survival and growth has wide implications for cancer therapy, offering the potential for preferential tumor cell killing. In the last several years, through combinatorial chemistry, high-throughput and virtual screening, and traditional medicinal chemistry, a number of inhibitors of the Akt pathway have been identified. This review focuses on ongoing translational efforts to therapeutically target the Akt pathway.

Antineoplastic Agents↗

PubMed2024

A novel molecular pathway of lipid accumulation in human hepatocytes caused by PFOA and PFOS.

Exposed to ubiquitously perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) has been associated with non-alcoholic fatty liver disease (NAFLD), yet the underlying molecular mechanism remains elusive. The extrapolation of empirical studies correlating per- and polyfluoroalkyl substance (PFAS) exposure with NAFLD occurrence to real-life exposure was hindered by the limited availability of mechanistic data at environmentally relevant concentrations. Herein, a novel pathway mediating hepatocyte lipid accumulation by PFOA and PFOS at human-relevant dose (<10 μM) was identified by integrating CRISPR-Cas9 genome screening, concentration-dependent transcriptional assay in HepG2 cell and epidemiological data mining. 1) At genetic level, nudt7 showed the highest enriched potency among 569 NAFLD-related genes, and the transcription of nudt7 was significantly downregulated by PFOA and PFOS exposure (<7 μM). 2) At molecular pathway, upon exposure to ≤10-4 μM PFOA and PFOS, the downregulation of nudt7 transcriptional expression triggered the reduction of Ace-CoA hydrolase activity. 3) At cellular level, increased lipids were measured in HepG2 cells with PFOA and PFOS (<2 μM). Overall, we identified a novel mechanism mediated by transcriptional downregulation of nudt7 gene in hepatocellular lipid increase treated with PFOA and PFOS, which could potentially explain the NAFLD occurrence associated with exposure to PFASs in humans.

Humans↗