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Sp1 and NFkappaB pathways are regulated in brain in response to acute and chronic ethanol.

DNA microarray analysis was used to identify candidate ethanol-regulated genes, as a first step towards exploring how transcriptional changes might lead to ethanol-induced changes in behaviour. Mice were treated with a single acute intraperitoneal ethanol dose and DNA microarray analysis performed on midbrain 2 h posttreatment. We predicted that if ethanol-regulated genes contribute towards behaviour, then constitutive variation in brain expression levels may also contribute to strain-specific differences in ethanol-related behaviour of inbred mouse strains. On the basis of this assumption, we interrogated the BXD inbred strain phenotype database and the U74Av2 MAS5 brain expression database using the WebQTL tool (http://www.genenetwork.org/) and correlated ethanol-related behaviours to expression levels. Constitutive expression levels of 70/90 candidate genes, identified from the DNA microarray analysis, varied significantly between inbred strains and correlated significantly with strain-specific differences in ethanol-related behaviours. These genes were then mapped onto biochemical pathways using Stratagene's PathwayAssist software. This analysis identified the transcription factor Sp1 and NFkappaB pathways in the acute response to ethanol. Ethanol regulation of Sp1 transcription was conserved between humans and mouse. As predicted, downstream targets of Sp1 were also ethanol regulated. NFkappaBia, an important regulator of NFkappaB function and Rela, an NFkappaB-binding partner, were both regulated by ethanol. Expression of both Sp1 and NFkappaBialpha were also downregulated following chronic ethanol treatment. As Sp1 and NFkappaB are implicated in plasticity and behaviour, our data suggest a role for these transcription factors in the long-term behavioural adaptations to ethanol.

Adaptation, Physiological↗

The genetic approach in pulmonary fibrosis: can it provide clues to this complex disease?

Multiple investigators have undertaken genetic studies in idiopathic pulmonary fibrosis populations in attempts to define genetic links to disease in hopes that this would improve understanding of disease pathogenesis and target pathways for therapy. Multiple genes have been evaluated using a candidate gene approach with limited success, with results suggesting a disease modifier effect rather than a disease causing effect. Using this approach, associations have been observed between idiopathic pulmonary fibrosis and specific polymorphisms in genes encoding interleukin-1 receptor antagonist, tumor necrosis factor-alpha, and complement receptor 1. Recently investigators have used familial pulmonary fibrosis cohorts to evaluate for genetic mutations associated with idiopathic pulmonary fibrosis. Using one pulmonary fibrosis kindred, a mutation in the gene encoding surfactant protein C was identified as the cause of pulmonary fibrosis in this family. Subsequently, another individual with idiopathic pulmonary fibrosis was identified with a different mutation in surfactant protein C. Though rarely found in patients with idiopathic pulmonary fibrosis, these surfactant protein C mutations highlight the importance of the alveolar epithelium in disease pathogenesis. A recent collaboration between investigators at three major centers has resulted in the largest collection of families with pulmonary fibrosis to date, with hopes that this effort will identify genetic mutations associated with idiopathic pulmonary fibrosis. If genetic links to idiopathic pulmonary fibrosis are defined in this study, then the pathways involved with these genes and gene products can be targeted by investigators to help identify potential treatment options for this disease.

Cytokines↗

DeepES: deep learning-based enzyme screening to identify orphan enzyme genes.

MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information is unavailable for many enzymes, known as orphan enzymes. These orphan enzymes hinder sequence similarity-based functional annotation, leading gaps in understanding the association between sequences and enzymatic reactions. RESULTS: Therefore, we developed DeepES, a deep learning-based tool for enzyme screening to identify orphan enzyme genes, focusing on biosynthetic gene clusters and reaction class. DeepES uses protein sequences as inputs and evaluates whether the input genes contain biosynthetic gene clusters of interest by integrating the outputs of the binary classifier for each reaction class. The validation results suggested that DeepES can capture functional similarity between protein sequences, and it can be implemented to explore orphan enzyme genes. By applying DeepES to 4744 metagenome-assembled genomes, we identified candidate genes for 236 orphan enzymes, including those involved in short-chain fatty acid production as a characteristic pathway in human gut bacteria. AVAILABILITY AND IMPLEMENTATION: DeepES is available at https://github.com/yamada-lab/DeepES. Model weights and the candidate genes are available at Zenodo (https://doi.org/10.5281/zenodo.11123900).

Deep Learning↗

Negative feedback control of exocrine pancreatic secretion: role of cholecystokinin and cholinergic pathway.

Mediation of postprandial pancreatic enzyme secretion has been ascribed mainly to cholecystokinin and to vagovagal reflexes. Recent studies suggest that these pathways are subject to feedback regulation. Diversion of pancreatic juice from the duodenum stimulates cholecystokinin release and pancreatic enzyme secretion, and intraduodenal administration of trypsin or chymotrypsin inhibits cholecystokinin release and pancreatic secretion. The increased plasma cholecystokinin levels following diversion of pancreatic juice seems to be mediated by "cholecystokinin-releasing factor", a trypsin-sensitive substance secreted by the proximal small intestine. This factor may mediate pancreatic enzyme secretion in response to protein intake. Dietary protein in the intestine competes for the trypsin that would otherwise inactivate the factor. The resulting increase of this factor in the intestinal lumen releases cholecystokinin and stimulates pancreatic enzyme secretion. Enteropancreatic reflex can also be activated by distension or administration of hyperosmolar solutions in the duodenum eliciting pancreatic enzyme secretion without raising plasma cholecystokinin levels. This effect is inhibited by atropine, suggesting that it is cholinergically mediated. Pancreatic response to duodenal volume or osmolality is not suppressed by trypsin, indicating that the reflex is not affected by intraluminal proteases. Our studies also show that secretion of pancreatic polypeptide is under cholinergic control, and this peptide acts by interfering with cholinergic transmission, making it an ideal candidate to modulate pancreatic secretion stimulated by the vagal cholinergic pathway. Similar observations are made with somatostatin and calcitonin-gene related peptide which also acts preferentially to inhibit pancreatic secretion by the vagal cholinergic pathway.

Animals↗

Effect of eicosapentaenoic acid on glucose-induced diacylglycerol synthesis in cultured bovine aortic endothelial cells.

Hyperglycemia has been postulated to increase diacylglycerol (DAG) level through de novo synthesis pathway and subsequently activate protein kinase C (PKC) in vascular cells, possibly leading to vascular dysfunction associated with diabetes. In this study, we examined the effect of eicosapentaenoic acid (EPA) on high glucose-induced increase in DAG level in cultured aortic endothelial cells (ECs). In ECs, total DAG level was significantly increased in the cells cultured with high glucose levels (400 mg/dl) compared with the cells with normal glucose levels (100 mg/dl). The addition of EPA completely prevented high glucose-induced increase in total DAG level. In contrast, other common fatty acids such as palmitate and oleate significantly stimulated DAG syntheisis, although arachidonate did not affect it. High glucose level significantly stimulated the incorporation of 3H-palmitate into DAG, while it did not affect the incorporation of 3H-arachidonate into DAG. The addition of EPA completely prevented the high glucose-induced increase in 3H-palmitate incorporation into DAG, while it did not affect the 3H-arachidonate incorporation. These findings suggest that EPA can prevent high glucose induced-increase in DAG level in ECs, probably by specifically inhibiting de novo synthesis at the step of acylation. EPA may be one of the candidates for clinical agents normalizing activation of DAG-PKC pathway in diabetic vascular tissues and preventing vascular complications associated with diabetes.

Animals↗

Novel candidate targets of beta-catenin/T-cell factor signaling identified by gene expression profiling of ovarian endometrioid adenocarcinomas.

The activity of beta-catenin (beta-cat), a key component of the Wnt signaling pathway, is deregulated in about 40% of ovarian endometrioid adenocarcinomas (OEAs), usually as a result of CTNNB1 gene mutations. The function of beta-cat in neoplastic transformation is dependent on T-cell factor (TCF) transcription factors, but specific genes activated by the interaction of beta-cat with TCFs in OEAs and other cancers with Wnt pathway defects are largely unclear. As a strategy to identify beta-cat/TCF transcriptional targets likely to contribute to OEA pathogenesis, we used oligonucleotide microarrays to compare gene expression in primary OEAs with mutational defects in beta-cat regulation (n = 11) to OEAs with intact regulation of beta-cat activity (n = 17). Both hierarchical clustering and principal component analysis based on global gene expression distinguished beta-cat-defective tumors from those with intact beta-cat regulation. We identified 81 potential beta-cat/TCF targets by selecting genes with at least 2-fold increased expression in beta-cat-defective versus beta-cat regulation-intact tumors and significance in a t test (P < 0.05). Seven of the 81 genes have been previously reported as Wnt/beta-cat pathway targets (i.e., BMP4, CCND1, CD44, FGF9, EPHB3, MMP7, and MSX2). Differential expression of several known and candidate target genes in the OEAs was confirmed. For the candidate target genes CST1 and EDN3, reporter and chromatin immunoprecipitation assays directly implicated beta-cat and TCF in their regulation. Analysis of presumptive regulatory elements in 67 of the 81 candidate genes for which complete genomic sequence data were available revealed an apparent difference in the location and abundance of consensus TCF-binding sites compared with the patterns seen in control genes. Our findings imply that analysis of gene expression profiling data from primary tumor samples annotated with detailed molecular information may be a powerful approach to identify key downstream targets of signaling pathways defective in cancer cells.

Binding Sites↗

Synthesis of (3R,4S)-3,4,5-trihydroxy-4-methylpentylphosphonic acid as a potential inhibitor of the nonmevalonate pathway.

The nonmevalonate pathway is widely found in higher plants and in many eubacteria, including pathogenic ones, but not in mammals. Identifying a nonmevalonate pathway inhibitor would greatly contribute to the search for new herbicides and antibacterial drugs to treat, for example, malaria. We describe here the synthesis of (3R,4S)-3,4,5-trihydroxy-4-methylpentylphosphonic acid as a candidate for inhibiting MEP cytidylyltransferase, which is the third step on the nonmevalonate pathway.

Anti-Bacterial Agents↗

Systemic Proteomic Alterations and Predictive Biomarkers of Paroxetine Response in Refractory Rosacea: A Secondary Analysis of a Randomized Clinical Trial.

IMPORTANCE: Rosacea is a chronic inflammatory cutaneous disorder characterized by persistent erythema and vascular dysregulation. While paroxetine has shown clinical efficacy in reducing these symptoms, the systemic molecular mechanisms underlying its therapeutic response remain poorly characterized. OBJECTIVE: To investigate systemic proteomic alterations and identify potential predictive biomarkers in patients with refractory erythematous rosacea following paroxetine treatment. DESIGN, SETTING, AND PARTICIPANTS: This prospective plasma proteomic analysis was nested within a multicenter, randomized, double-blind, placebo-controlled clinical trial (Prospective Rosacea Refractory Erythema Randomized Clinical Trial [PRRERCT]). Participants included patients aged 18 to 65 years with refractory rosacea (Clinician's Erythema Assessment [CEA] score &#x2265;3). Plasma samples were collected at baseline and after 12 weeks of treatment. The data for this study were analyzed between September 2025 and November 2025. INTERVENTIONS: Participants received oral paroxetine, 25 mg per day, for a 12-week treatment period. MAIN OUTCOMES AND MEASURES: Systemic protein expression profiles were analyzed using data-independent acquisition liquid chromatography-tandem mass spectrometry. Clinical response was evaluated using CEA and the Flushing Assessment Tool. Correlations between proteomic changes and clinical improvements were assessed, and predictive biomarkers were identified using receiver operating characteristic curve analysis. RESULTS: Among 24 participants (mean [SD] age, 35 [11] years; 24 [100%] female), paroxetine treatment significantly reduced mean (SD) CEA scores from 3.1 (0.3) to 2.3 (0.7) and Flushing Assessment Tool scores from 3.1 (0.6) to 2.0 (0.9) (P&#x2009;<&#x2009;.001). Exploratory proteomic analysis revealed 497 candidate differentially expressed proteins after treatment. Downregulated proteins showed preliminary enrichment in pathways related to immune response activation, insulin receptor signaling, and neuronal remodeling. A subset of 98 reversed-response proteins was observed, primarily linked to synaptic vesicle cycles and vascular smooth muscle contraction. Proteomic alterations were associated with clinical improvement (65 proteins for erythema; 73 for flushing). Candidate biomarkers, notably OLFML3 (area under the receiver operating characteristic curve [AUC], 0.87 [95% CI, 0.70-1.00]) and IGFBP2 (AUC, 0.80 [95% CI 0.55-1.00]), demonstrated high predictive value for clinical response. CONCLUSIONS AND RELEVANCE: In this secondary analysis of a randomized clinical trial, paroxetine treatment was associated with modulation of systemic neuro-vascular-immune networks in patients with rosacea. These exploratory findings provide preliminary mechanistic clues regarding the possible disease-modifying potential of paroxetine and point to circulating protein signatures that may facilitate personalized therapeutic strategies for rosacea management. TRIAL REGISTRATION: Chinese Clinical Trial Registry Identifier: ChiCTR2000031479.

Humans↗

In silico screening of anti-atherosclerotic compounds from Morus alba leaves by machine learning and network pharmacology.

OBJECTIVE: This study integrates machine learning with network pharmacology, molecular docking, and molecular dynamics simulations to screen bioactive compounds from Mulberry leaves and elucidate their potential mechanisms against atherosclerosis (AS). METHODS: A training dataset of anti-AS active compounds was compiled and encoded as Morgan fingerprints. Three machine learning classifiers, specifically Random Forest (RF), Support Vector Machine (SVM), and Extreme Gradient Boosting (XG-Boost), were constructed and evaluated using multiple performance metrics. Potential active components from Mulberry leaves and AS-related targets were retrieved, followed by protein-protein interaction network construction and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Molecular docking was then performed to evaluate binding affinities between core targets and candidate compounds, and the most stable complex was subjected to molecular dynamics simulations using GROMACS (2025). RESULTS: The RF model achieved superior performance (accuracy= 0.8354, F1 = 0.8408, AUC = 0.9119) with 100% external validation accuracy. Thirteen anti-AS candidates were prioritized from mulberry leaves, four of which have been previously documented. Network pharmacology revealed AKT1 and IL6 as core targets, enriched in pathways such as endocrine resistance. Molecular docking and dynamics simulations confirmed strong binding between oxysanguinarine and AKT1, with the complex exhibiting high stability. CONCLUSION: The RF model provides a reliable computational tool for prioritizing anti-AS compounds from Mulberry leaves. The integrated analysis reveals that Mulberry leaves exert anti-atherosclerotic effects through multi-target (e.g., AKT1, IL6) and multi-pathway (e.g., PI3K-Akt) mechanisms, offering a framework for further experimental validation.

Morus↗

Tumour necrosis factor-mediated cell death pathways do not contribute to muscle fibre death in dystrophinopathies.

There is evidence that apoptotic cell death mechanisms contribute to muscle fibre loss in dystrophinopathies, but little knowledge about the activators of the final degrading caspase cascade in muscle fibre apoptosis. As mitochondria-related activation of this caspase cascade, through e.g. APAF-1, could not be proven in dystrophin-deficient muscle, this study searches for other prospective candidates that may directly trigger apoptotic cell degradation by mitochondria-independent pathways involving the interaction of tumour necrosis factor-alpha (TNF-alpha) and TRAIL with death receptors and subsequent activation of caspase-8. The expression of TNF-alpha, TNF-R1, TRAIL, NF-(kappa)B and caspase-8 were studied in muscle biopsy specimens from 14 patients with a dystrophinopathy [10 Duchenne muscular dystrophies (DMD), 2 Becker MD, and 2 DMD carriers] by immunohistochemistry and Western blotting. In all types of dystrophinopathies, necrotic muscle fibres undergoing myophagocytosis displayed strong expression of TNF-alpha, TNF-R1, and TRAIL, which, however, was attributed to phagocytosing cells and not to the muscle fibres themselves. There was no up-regulation in normal-shaped or atrophic non-necrotic muscle fibres, or in intact muscle fibre segments adjacent to segmental necrosis and myophagocytosis. The expression profiles of caspase-8 and NF-(kappa)B resembled that of normal control muscle. There were likewise no significant differences in the Western blot analyses between normal control and dystrophin-deficient muscle. Based on these findings, a contribution of TNF-alpha or TRAIL-mediated cell death pathways to muscle fibre apoptosis or necrosis in dystrophinopathies could not be confirmed.

Adolescent↗

Voltage-operated Ca2+ channels and the acrosome reaction: which channels are present and what do they do?

Evidence from pharmacological studies suggests that induction of the acrosome reaction of mammalian spermatozoa by solubilized zona pellucida, and possibly by progesterone, is dependent upon Ca2+ influx through voltage-operated Ca2+ channels. Studies on Ca2+ accumulation and membrane potential in ligand-stimulated or artificially depolarized spermatozoa support such a conclusion. Electrophysiological studies on rodent spermatogenic cells have revealed the presence of a 'T' type voltage-operated Ca2+ current. This current has pharmacological attributes consistent with those of the putative channel responsible for Ca2+ influx mediating the acrosome reaction. However, use of molecular techniques to study human and rodent testis and spermatogenic cells has detected the presence of three different voltage-operated Ca2+ channel subunits. One of these (alpha lE) may generate T-currents, though this is currently disputed. Voltage-operated Ca2+ channel structure and the relationship between channel subunit expression and the characteristics of consequent Ca2+ currents is briefly reviewed. The nature and function of T-channel-mediated Ca2+ influx is examined in the context of the time-course of ligand- and depolarization-induced elevation of [Ca2+]i in mammalian spermatozoa. It is likely that a secondary Ca2+ response (mobilization of stored Ca2+ or activation of a second Ca(2+)-influx pathway) is required for the acrosome reaction. Evidence for the existence and participation of various candidates is discussed (including voltage-operated Ca2+ channels, which may be functionally expressed only in mature spermatozoa), the available evidence favouring a secondary Ca(2+)-influx pathway. Immediate priorities for future research in this area are proposed.

Acrosome Reaction↗

Evolution of the NadR regulon in Enterobacteriaceae.

The NAD biosynthetic pathway and NAD transformations in E. coli and S. typhi are well characterized. Using comparative genomics methods we describe the NadR regulon in other Enterobacteriaceae, identity new candidate regulon members and demonstrate that even a very simple regulon covering an essential methabolic pathway could be different in closely related genomes.

Bacterial Proteins↗

PC5-A-mediated processing of pro-neurotensin in early compartments of the regulated secretory pathway of PC5-transfected PC12 cells.

Among the members of the proprotein convertase (PC) family, PC1 and PC2 have well established roles as prohormone convertases. Another good candidate for this role is PC5-A that has been shown to be present in the regulated secretory pathway of certain neuroendocrine tissues, but evidence that it can process prohormones is lacking. To determine whether PC5-A could function as a prohormone convertase and to compare its cleavage specificity with that of PC1 and PC2, we stably transfected the rat pheochromocytoma PC12 cell line with PC5-A and analyzed the biosynthesis and subcellular localization of the enzyme, as well as its ability to process pro-neurotensin/neuromedin N (pro-NT/NN) into active peptides. Our data showed that in transfected PC12 cells, PC5-A was converted from its 126-kDa precursor form into a 117-kDa mature form and, to a lesser extent, into a C-terminally truncated 65-kDa form of the 117-kDa product. Metabolic and immunochemical studies showed that PC5-A was sorted to early compartments of the regulated secretory pathway where it colocalized with immunoreactive NT. Furthermore, pro-NT/NN was processed in these compartments according to a pattern that differed from that previously described in PC1- and PC2-transfected PC12 cells. This pattern resembled that previously reported for pro-NT/NN processing in the adrenal medulla, a tissue known to express high levels of PC5-A. Altogether, these data demonstrate for the first time the ability of PC5-A to function as a prohormone convertase in the regulated secretory pathway and suggest a role for this enzyme in the physiological processing of pro-NT/NN.

Amino Acid Sequence↗

Host microenvironment in breast cancer development: epithelial-mesenchymal transition in breast cancer development.

The epithelial-mesenchymal transition (EMT) is a developmental mechanism of crucial importance in establishing the body plan in many multicellular organisms. Several transduction pathways controlling the various steps of the morphological transition have been identified by molecular analyses of this process in cell lines and in vivo. The newly formed mesenchymal cells can exhibit locomotory and invasive phenotypes, suggesting that EMTs contribute to the progression of carcinoma. Diverse evidence indicates that EMT subprograms are involved in the appearance of different breast carcinoma types. Several normal and malignant breast cell lines are currently being analyzed to define key steps in EMT and to identify candidate genes. DNA profiling technology is also being applied to uncover pathways that lead to a metastatic phenotype.

Animals↗

The Fem1a gene is downregulated in Rhabdomyosarcoma.

Rhabdomyosarcoma (RMS) is the most common soft tissue neoplasm of children, and those metastatic at presentation have a poor prognosis. RMS development is related to defective skeletal muscle differentiation, involving a variety of cell signaling and transcriptional control pathways, including aberrant hedgehog signaling. Here we evaluate Fem1a, a gene highly expressed in skeletal muscle, as a candidate for involvement in RMS. Fem1a is a homolog of fem-1, which controls cell fate decisions in the sex determination pathway of Caenorhabditis elegans, a pathway with homology to mammalian hedgehog signaling. We show that Fem1a expression is activated during myocyte differentiation of C2C12 myoblasts, and this expression is largely confined to the terminally differentiating pool, not to the satellite-cell-like quiescent reserve cell pool. We find that the human homolog, FEM1A, is downregulated in all of 8 different human RMS cell lines, including those derived from embryonal and alveolar RMS. Using mouse genetic models of RMS development, we further show that Fem1a is consistently downregulated in primary RMS from Ptch1+/- mice, from p53-/- mice, from p53+/-; Ptch1+/- mice, and from HGF/SF-Ink4a/Arf-/- mice. Therefore, Fem1a downregulation may be involved in, and/or a marker of, an early cell fate defect fundamental to RMS pathogenesis.

Animals↗

The pharmacology of ageing in Drosophila.

Recent research indicates that aging is affected by many genes and thus many biochemical pathways. This has led to a failure to find pharmaceuticals that significantly ameliorate the human aging process. Progress in evolutionary and genetic research, however, suggests the possibility of combining experimental evolution, genomic analysis, and mass screening of pharmaceuticals and botanicals to produce effective therapeutics for human aging. The starting point for this strategy is model systems that have outbred populations with substantially increased lifespan. These are easily produced by tuning the force of natural selection in the laboratory. Such biological material is then a good candidate for genomic analysis, leading to the identification of numerous biochemical pathways involved in increased lifespan, in the model system. These biochemical pathways would then be available for pharmaceutical development, first in fruit flies, then in rodents, and eventually in a clinical human population. We include a discussion of the pharmacological methods appropriate to this strategy of drug discovery.

Aging↗

Mixing and matching pathways in leaf polarity.

Leaves extend a large, porous surface to the environment to catch light and exchange gasses. The extension of the lamina is produced by the interaction of an upper (adaxial) and a lower (abaxial) domain in the developing leaf primordium. Recent studies have revealed that conserved genetic pathways, involving small regulatory RNAs and several distinct transcription factor families, have key roles in adaxial-abaxial patterning, suggesting candidate signals that convey positional information within the shoot to the newly initiated leaf. The interactions of the polarity pathways are distinguished by mutual antagonism and by redundancies. Analysis of these pathways in different model organisms reveals a surprising diversity in the genetic control of such a fundamental developmental process.

Arabidopsis↗

A transient geniculo-extrastriate pathway in macaques? Implications for 'blindsight'.

Both monkeys and cats receiving primary visual cortex lesions in infancy show better residual vision than animals sustaining similar damage in adulthood. In cats, the better recovery has been explained in part by stabilization of a transient pathway from the dorsal lateral geniculate nucleus (dLGN) to cortical visual area PMLS. To test the hypothesis that a similar transient pathway from the dLGN to dorsal extrastriate areas exists in primates and thus serves as a candidate for recruitment after early V1 damage, retrograde tracers were injected into areas MT, MST, and/or 7a of infant macaques. No evidence of a transient pathway from the dLGN to these areas was obtained, despite projections from the pulvinar and other extrastriate areas in all cases.

Aging↗