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Results for “Pathway informed transformer”

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At least 343 records · Page 19Linked to original sources

PubMed2002

RhoGEF specificity mutants implicate RhoA as a target for Dbs transforming activity.

Dbs is a Rho-specific guanine nucleotide exchange factor (RhoGEF) that exhibits transforming activity when overexpressed in NIH 3T3 mouse fibroblasts. Like many RhoGEFs, the in vitro catalytic activity of Dbs is not limited to a single substrate. It can catalyze the exchange of GDP for GTP on RhoA and Cdc42, both of which are expressed in most cell types. This lack of substrate specificity, which is relatively common among members of the RhoGEF family, complicates efforts to determine the molecular basis of their transforming activity. We have recently determined crystal structures of several RhoGEFs bound to their cognate GTPases and have used these complexes to predict structural determinants dictating the specificities of coupling between RhoGEFs and GTPases. Guided by this information, we mutated Dbs to alter significantly its relative exchange activity for RhoA versus Cdc42 and show that the transformation potential of Dbs correlates with exchange on RhoA but not Cdc42. Supporting this conclusion, oncogenic Dbs activates endogenous RhoA but not endogenous Cdc42 in NIH 3T3 cells. Similarly, a competitive inhibitor that blocks RhoA activation also blocks Dbs-mediated transformation. In conclusion, this study highlights the usefulness of specificity mutants of RhoGEFs as tools to genetically dissect the multiple signaling pathways potentially activated by overexpressed or oncogenic RhoGEFs. These ideas are exemplified for Dbs, which is strongly implicated in the transformation of NIH 3T3 cells via RhoA and not Cdc42.

3T3 Cells↗

PubMedDate not supplied

The missing link: bridging the patient-provider health information gap.

Widespread adoption of information technology is now regarded as a pathway to improving health care and achieving the Institute of Medicine's highly regarded six aims for redesigning care. Achieving these aims requires fresh approaches to health system design, including continuous healing relationships between physicians and patients and provision of tools to help patients be more active participants in their own care. Personal health records (PHRs) might allow patients and providers to develop new ways of collaborating and provide the basis for broader transformation of the health care system. Federal policies can be key catalysts in accelerating PHR development and adoption.

Diffusion of Innovation↗

PubMed2002

[Genetic pathways in colorectal cancer: interest for the pathologist].

Molecular biology studies have led to the identification of two different types of colorectal carcinomas. The first group, called LOH (for loss of heterozygosity), represents 80% of colorectal cancers and is characterised by aneuploidy, allelic losses and a location in the distal colon. The second group displays phenotypic microsatellite instability (MSI-positive tumours), has a near-diploid karyotype and a relatively low frequency of allelic losses. It accounts for 15% of all colorectal cancers and for about 30% of right-sided cancers. Four different pathways have been identified as responsible for tumour progression: the WNT/Wingless, the K-ras, the Transforming growth factor (TGF) and the P53 pathways. The involvement of these pathways depends on the tumour type. In LOH-positive tumours, the WNT/Wingless pathway is activated through an APC mutation, whereas MSI+ tumours do so through a catenin stabilising mutation. The TGFb growth inhibitory pathway is altered either by mutations in the signal transduction molecules SMAD2 and SMAD4 in LOH positive tumours or by mutations of TGFbRII in MSI+ tumours. In the p53 pathway, mutations in BAX may contribute to the adenoma-carcinoma transition just as p53 mutations may do in LOH positive tumours. Until now, cancer phenotype determination has had no clinical implications. However, the predictive value of the MSI status was recently stressed as a predictive factor for response to chemotherapy. Immunohistochemistry could represent a complementary strategy to molecular biology in assessing MSI status. This simple test would allow to screen all colorectal carcinomas for MSI status, which would provide valuable management information in addition to the histological assessment for tumour stage and grade.

Aneuploidy↗

PubMed2025

Histology-Based Virtual RNA Inference Identifies Pathways Associated With Metastasis Risk in Colorectal Cancer.

Colorectal cancer (CRC) remains a major health concern, with >150,000 new diagnoses and >50,000 deaths annually in the United States, underscoring an urgent need for improved screening, prognostication, disease management, and therapeutic approaches. The tumor microenvironment (TME)-comprising cancerous and immune cells interacting within the tumor's spatial architecture-plays a critical role in disease progression and treatment outcomes, reinforcing its importance as a prognostic marker for metastasis and recurrence risk. However, traditional methods for TME characterization, such as bulk transcriptomics and multiplex protein assays, lack sufficient spatial resolution. Although spatial transcriptomics (ST) allows for the high-resolution mapping of whole transcriptomes at near-cellular resolution, current ST technologies (eg, Visium and Xenium) are limited by high costs, low throughput, and issues with reproducibility, preventing their widespread application in large-scale molecular epidemiology studies. In this study, we refined and implemented virtual RNA inference (VRI) to derive ST-level molecular information directly from hematoxylin and eosin (H&E)-stained tissue images. Our VRI models were trained on the largest matched CRC ST data set to date, comprising 45 patients and >300,000 Visium spots from primary tumors. Using state-of-the-art deep learning models (UNI, ResNet-50, Vision Transformer, and Vision Mamba), we achieved a median Spearman's correlation coefficient of 0.546 between predicted and measured spot-level expression. As validation, VRI-derived gene signatures linked to specific tissue regions (tumor, interface, submucosa, stroma, serosa, muscularis, and inflammation) showed strong concordance with signatures generated via direct ST, and VRI performed accurately in estimating cell-type proportions spatially from H&E slides. In an expanded CRC cohort controlling for tumor invasiveness and clinical factors, we further identified VRI-derived gene signatures significantly associated with key prognostic outcomes, including metastasis status. Although certain tumor-related pathways are not fully captured by histology alone, our findings highlight the ability of VRI to infer a wide range of "histology-associated" biological pathways at near-cellular resolution without requiring ST profiling. Future efforts will extend this framework to expand TME phenotyping from standard H&E tissue images, with the potential to accelerate translational CRC research at scale.

Humans↗

PubMed1987

Phorbol esters as signal transducers and tumor promoters.

Extracellular ligands transfer information into the cell through various signaling pathways which operate in an integrated way. Oncogene proteins and tumor promoters cooperate to constitutively turn on the signaling pathways and lead to irreversible cell activation. The evidence that supports this concept is reviewed, with emphasis on the role of phorbol esters and protein kinase C in signal transduction and oncogenesis.

Animals↗

PubMed2005

A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

Signal transduction pathways control cellular responses to stimuli, but it is unclear how molecular information is processed as a network. We constructed a systems model of 7980 intracellular signaling events that directly links measurements to 1440 response outputs associated with apoptosis. The model accurately predicted multiple time-dependent apoptotic responses induced by a combination of the death-inducing cytokine tumor necrosis factor with the prosurvival factors epidermal growth factor and insulin. By capturing the role of unsuspected autocrine circuits activated by transforming growth factor-alpha and interleukin-1alpha, the model revealed new molecular mechanisms connecting signaling to apoptosis. The model derived two groupings of intracellular signals that constitute fundamental dimensions (molecular "basis axes") within the apoptotic signaling network. Projection along these axes captures the entire measured apoptotic network, suggesting that cell survival is determined by signaling through this canonical basis set.

Apoptosis↗

PubMed2001

Roles of activin and its signal transduction mechanisms in reproductive tissues.

Activins were identified initially as gonadal proteins having a stimulating effect on FSH production by the pituitary gland. Strong evidence has accumulated that activins are important regulating factors for many reproductive processes. Activin may have paracrine or autocrine roles rather than solely an endocrine action on FSH secretion. Activins together with their signalling molecules must be shown to be produced locally in a particular tissue to provide support for their paracrine or autocrine action in that tissue. The discovery of the activin receptors, the intracellular signalling mediators (Smads) and some transcription co-factors involved in activin responses has helped to unravel the activin-transforming growth factor beta signalling mechanism. However, few reports have clearly demonstrated the presence of all of the activin signalling molecules in reproductive tissues, despite the important roles of activin in these tissues. Several activin receptor types and Smad molecules have been identified, indicating either a redundancy in signalling molecules or different signalling pathways. At present, it is not clear which particular subset of these signalling molecules is important in reproductive processes. The aim of this review is to collate the information available on activin actions, as well as on the signalling molecules, to understand how activins may transduce their paracrine or autocrine signals in reproductive tissues.

Activins↗

PubMed2002

NF-kappaB/Rel transcriptional pathway: implications in pancreatic cancer.

Despite considerable efforts in understanding the cellular mechanisms contributing to pancreatic cancer, the prognosis of this malignant disease is still extremely poor. Although pancreatic cancer is the fifth common cause of cancer death in Western countries, current options in treatment enable a 5-yr survival rate for all stages of less than 5%. In the face fo the fatal outcome, new approaches to the therapy have been established. Based on its role in malignant transformation, apoptosis, and cell proliferation, the transcription factor NF-kappaB/Rel has gained the attention of many laboratories. This review provides basic information for the understanding of the biology of NF-kappaB and aims at presenting experimental data illustrating the involvement of NF-kappaB/Rel in pancreatic cancer.

Apoptosis↗

PubMed1995

Mutations affecting the glycine receptor agonist transduction mechanism convert the competitive antagonist, picrotoxin, into an allosteric potentiator.

Contrary to its effects on the gamma-aminobutyric acid type A receptor, picrotoxin antagonism of the alpha 1 subunit of the human glycine receptor is shown to be competitive, not use-dependent, and nonselective between the picrotoxin components, picrotin, and picrotoxinin. Competitive antagonism and non-use dependence are consistent with picrotoxin binding to a site in the extracellular domain. The mutations Arg-->Leu or Arg-->Gln at residue 271 of the glycine receptor alpha 1 subunit, which are both associated with human startle disease, have previously been demonstrated to disrupt the transduction process between agonist binding and channel activation. We show here that these mutations also transform picrotoxin from an allosterically acting competitive antagonist to an allosteric potentiator at low (0.01-3 microM) concentrations and to a noncompetitive antagonist at higher (> or = 3 microM) concentrations. This demonstrates that arginine 271 is involved in the transduction process between picrotoxin binding and its mechanism of action. Thus, the allosteric transduction pathways of both agonists and antagonists converge at a common residue prior to the activation gate of the channel, suggesting that this residue may act as an integration point for information from various extracellular ligand binding sites.

Allosteric Regulation↗

PubMed2001

Identification of twenty-two candidate markers for human osteogenic sarcoma.

Since osteogenic sarcoma (OGS) predominantly affects children, its etiology and progression may be determined more by genetic than environmental factors. A few genes have been associated with OGS, however, their value in the diagnosis and/or prognosis of the disease remains poor. Evidently, more markers need to be identified for improving management of patients with OGS. To identify potential genetic markers for OGS, we have extended preferential amplification of coding sequences (PACS) to screen multiple samples simultaneously. The extended method is termed multi-PACS. Multi-PACS was applied between a normal osteoblast and four OGS-derived cell lines to identify differentially expressed coding sequence tags (dCST) that identified 145 dCSTs. Subsequently, differential mRNA expression was validated for a chosen subset of 22 dCSTs. These chosen dCSTs include among others cyclins D and E, two cyclin dependent kinases, two other kinases, transcription factors E2F4, E2F5, and p130, a DNA repair gene, a gene for the signalosome subunit, and potential guanine nucleotide binding factors. We infer that these genes could be so easily identified because PACS preferentially identifies coding instead of non-coding sequences. We also infer that these genes identify signaling pathways pertinent to OGS. mRNA expression profile of these 22 genes/dCSTs generated distinct expression signature of the OGS-derived cell lines suggesting that further work on clinical samples with these dCSTs will yield valuable information for OGS. We conclude that these 22 genes/dCSTs are candidate markers for OGS.

Cell Line, Transformed↗

PubMed2004

Inhibition of Wnt/Axin/beta-catenin pathway activity promotes ventral CNS midline tissue to adopt hypothalamic rather than floorplate identity.

Ventral midline cells in the neural tube form floorplate throughout most of the central nervous system (CNS) but in the anterior forebrain, they differentiate with hypothalamic identity. The signalling pathways responsible for subdivision of midline neural tissue into hypothalamic and floorplate domains are uncertain, and in this study, we have explored the role of the Wnt/Axin/beta-catenin pathway in this process. This pathway has been implicated in anteroposterior regionalisation of the dorsal neural tube but its role in patterning ventral midline tissue has not been rigorously assessed. We find that masterblind zebrafish embryos that carry a mutation in Axin1, an intracellular negative regulator of Wnt pathway activity, show an expansion of prospective floorplate coupled with a reduction of prospective hypothalamic tissue. Complementing this observation, transplantation of cells overexpressing axin1 into the prospective floorplate leads to induction of hypothalamic gene expression and suppression of floorplate marker gene expression. Axin1 is more efficient at inducing hypothalamic markers than several other Wnt pathway antagonists, and we present data suggesting that this may be due to an ability to promote Nodal signalling in addition to suppressing Wnt activity. Indeed, extracellular Wnt antagonists can promote hypothalamic gene expression when co-expressed with a modified form of Madh2 that activates Nodal signalling. These results suggest that Nodal signalling promotes the ability of cells to incorporate into ventral midline tissue, and within this tissue, antagonism of Wnt signalling promotes the acquisition of hypothalamic identity. Wnt signalling also affects patterning within the hypothalamus, suggesting that this pathway is involved in both the initial anteroposterior subdivision of ventral CNS midline fates and in the subsequent regionalisation of the hypothalamus. We suggest that by regulating the response of midline cells to signals that induce ventral fates, Axin1 and other modulators of Wnt pathway activity provide a mechanism by which cells can integrate dorsoventral and anteroposterior patterning information.

Animals↗

PubMed2004

Efficient gene disruption in the koji-mold Aspergillus sojae using a novel variation of the positive-negative method.

When no phenotypic screen is available, gene disruption in the koji-mold Aspergillus sojae is a time-consuming process, owing to the low frequency of homologous recombination. To achieve efficient gene disruption in the koji-mold, we developed a novel positive-negative selection method to enrich for homologous recombinants. The pyrG gene from A. sojae was used as a positive selection marker for transformants, and the oliC31 gene of A. nidulans, which codes for a mutant form of subunit 9 of the F1FO-ATPase, was employed as a negative selection marker to facilitate elimination of non-homologous recombinants among the transformants. The positive-negative selection markers, in combination with a pyrG deletion strain as a host, enabled enrichment for homologous recombinants, and disruption of the genes niaD, areA and tannase was successfully demonstrated. In order to examine whether the positive-negative selection technique is effective for targeting any locus, even in the absence of information on gene function or phenotype, we attempted to disrupt the aflR gene of A. sojae, which codes for a putative transcription factor for the aflatoxin biosynthetic pathway, using the method. Despite the fact that this gene is not transcribed in A. sojae, aflR disruptants were efficiently obtained, suggesting that the method is indeed capable of targeting any locus, without additional ectopic integration, and is thus applicable for functional genomics studies in filamentous fungi, including A. sojae.

Aspergillus↗

PubMed2004

RNA-interference-based functional genomics in mammalian cells: reverse genetics coming of age.

Sequencing of complete genomes has provided researchers with a wealth of information to study genome organization, genetic instability, and polymorphisms, as well as a knowledge of all potentially expressed genes. The identification of all genes encoded in the human genome opens the door for large-scale systematic gene silencing using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs). With the recent development of siRNA and shRNA expression libraries, the application of RNAi technology to assign function to cancer genes and to delineate molecular pathways in which these genes affect in normal and transformed cells, will contribute significantly to the knowledge necessary to develop new and also improve existing cancer therapy.

Animals↗

PubMed1999

Differential inhibition of collagenase and interleukin-1alpha gene expression in cultured corneal fibroblasts by TGF-beta, dexamethasone, and retinoic acid.

PURPOSE: Expression of the genes for collagenase and interleukin-1alpha (IL-1alpha) are induced as stromal cells become activated to the repair fibroblast phenotype after injury to the cornea. This investigation examines the mechanisms whereby expression of these genes is inhibited by transforming growth factor-beta (TGF-beta), dexamethasone (DEX), or retinoic acid (RET A). METHODS: A model of freshly isolated cultures of corneal stromal cells and early passage cultures of corneal fibroblasts was used in these studies. This model reproduces the events of stromal cell activation in the corneal wound. RESULTS: In early passage cultures of corneal fibroblasts, expression of collagenase is under obligatory control by autocrine IL-1alpha. IL-1alpha controls its own expression through an autocrine feedback loop that is dependent on transcription factor NF-kappaB. TGF-beta, DEX, and RET A were each effective inhibitors of collagenase gene expression in these cells. Furthermore, these agents have the capacity to inhibit expression of IL-1alpha and this was correlated with their ability to affect DNA-binding activity of NF-kappaB. However, TGF-beta, DEX, and RET A were also effective inhibitors of the low level of collagenase expressed by freshly isolated corneal stromal cells that cannot express IL-1alpha. CONCLUSIONS: In cells with an active IL-1alpha autocrine loop there are at least two distinct signaling pathways by which collagenase gene expression can be modulated. The results of this study demonstrate that TGF-beta, DEX, and RET A differentially inhibit collagenase and IL-1alpha gene expression. This information will be useful in the design of therapeutic modalities for fibrotic disease in the cornea and other parts of the eye.

Animals↗

PubMed1990

Oncogenes and anti-oncogenes.

The study of oncogenes offers insights into many steps in signal transduction. Rapid progress is possible because of the combination of biochemistry and genetics--unique in vertebrate cell biology--the availability of specific clones and antibodies, sequence information, dominant mutants, and biochemical assays of function. The wealth of detail on oncogenes and proto-oncogenes continues to increase dramatically. Hopefully, in the next year or two some of the gaps will be filled in and all the steps along at least one pathway from the cell membrane to the nucleus will be understood.

Animals↗

PubMedDate not supplied

Decoding temporal information through slow lateral excitation in the olfactory system of insects.

Sensory information is represented in a spatio-temporal code in the antennal lobe, the first processing stage of the olfactory system of insects. We propose a novel mechanism for decoding this information in the next processing stage, the mushroom body. The Kenyon cells in the mushroom body of insects exhibit lateral excitatory connections at their axons. We demonstrate that slow lateral excitation between Kenyon cells allows one to decode sequences of activity in the antennal lobe. We are thus able to clarify the role of the existing connections as well as to demonstrate a novel mechanism for decoding temporal information in neuronal systems. This mechanism complements the variety of existing temporal decoding schemes. It seems that neuronal systems not only have a rich variety of code types but also quite a diversity of algorithms for transforming different codes into each other.

Animals↗

PubMed1998

Multiple changes in gene expression are associated with normal cell-induced modulation of the neoplastic phenotype.

Specific regulatory pathways in neoplastic cells seem to be responsive to control signals provided by the normal cell/tissue environment. The present experiments were designed to define, at the molecular level, the growth-regulatory signals in neoplastic cells that are associated with the modulation of expression of the neoplastic phenotype by normal cell populations. When cultured in the presence of normal cell-conditioned medium, a highly malignant rat tracheal carcinoma-derived cell population (IC-12) undergoes dramatic changes in morphology, and the anchorage-independent growth of these cells is inhibited. This phenomenon is termed normalization. The strategy adopted for elucidating the cellular/molecular changes associated with the induction of these phenotypic alterations was to define the differences in mRNA expression patterns between IC-12 populations exhibiting the neoplastic phenotype (wild-type cells) and those exhibiting the normalized phenotype. For this purpose, the differential display technique and subsequent Northern blot analyses were used. Once specific, differentially expressed genes were identified, the temporal sequence of altered gene expression was determined by monitoring the levels of mRNA expression after the addition of normal cell-conditioned medium. Some of the identified known genes are grouped into three general categories: (a) group I genes are those involved in cellular adhesion processes; (b) group II genes are those involved in signal transduction pathways; and (c) group III genes are those involved in transcriptional and translational processes. Genes that are differentially expressed during the normalization process seemed to exhibit characteristic temporal expression patterns after the addition of normal cell-conditioned medium. Identification of these differentially expressed genes and their associated cellular functions provide insight into some of those regulatory pathways in neoplastic cells that are amenable to regulation by normal cells. An analysis of the temporal sequence of altered gene expression provides further information that allows the identification of those genes that are likely to be critical upstream effectors regulating transcriptional regulatory events that result in the moderation of neoplastic behavior.

Animals↗

PubMed1999

Loss of growth regulation by transforming growth factor-beta (TGF-beta) in human cancers: studies on endometrial carcinoma.

Members of the Transforming Growth Factor-beta (TGF-beta) family are one of the few endogenous inhibitors of cell growth. As uncontrolled cellular proliferation is a hallmark of cancer, an important question to address is how cancer cells escape normal growth regulatory mechanisms to become malignant. In this context, components of the TGF-beta growth response pathway are considered to be tumor suppressor genes, as absence of one or more of TGF-beta receptor and signaling proteins cause loss of cell growth regulation through an inability to regulate proteins that directly block cells in G1 phase of the cell cycle. Endometrial carcinoma (ECA) provides an excellent paradigm to study the changes that accompany loss of TGF-beta-mediated growth, control as a function of neoplastic development, since it is generally preceded by complex hyperplasia. Type 1 ECA is characterized as an estrogen-induced cancer, which responds well to progestin therapy. Since it has become increasingly evident that steroids can regulate growth through growth factors, ECA is also an ideal model for investigating the role for gonadal steroids in the loss of TGF-beta growth regulation in the etiopathogenesis of ECA. Thus, hormonal carcinogenesis adds another level of complexity in studying loss of growth regulation in human cancers. The purpose of this review is to 1) provide the most current background information on how TGF-beta functions including its activation, receptors, signal transduction mechanisms, and control of the cell cycle. 2) present recent information that shows how malignant cells subvert the growth inhibitory effects of TGF-beta by incurring defects in every aspect of the pathway that mediates the TGF-beta growth inhibitory response, and 3) describe the putative role for TGF-beta in the oncogenesis of ECA, provided primarily by the results from our laboratory. Understanding the molecular events involved in TGF-beta function in normal cells and its lack of function in tumor cells should identify novel therapeutic targets in human cancers.

Cell Cycle↗