Pathway Analysis Research Articles

The Exploration of TCM Therapeutic Mechanism as Evidenced by Houpusanwu Decoction on GI Disorders Treatment using Systems Pharmacology

Background: Gastrointestinal (GI) disorders are a kind of common, but complicated disease that may be triggered by many factors. In Asia, many traditional Chinese herbs are prominent in treating GI disorders, but the pharmacological mechanism still remains vague or unknown due to the multiple-component characteristics of traditional Chinese medicine (TCM). Objective: In order to investigate the therapy mechanism of traditional Chinese medicine (TCM) for Gastrointestinal (GI) diseases, a typical TCM prescription, Houpusanwu Decoction, for the treatment of ileus, a severe GI disease, is used as a probe presently. Method: We performed data mining on all components in Houpusanwu Decoction (HD), established a corresponding component database, and then conducted ADME screening of potentially active compounds in the database. Next, we identify potential targets of HD candidate compounds, followed by the establishment of a series of pharmacological networks. Finally, we conducted SP analysis and mechanism analysis. Results: Through pathway analysis, we found that HD treats ileus mainly through four pathways, i.e., GI motility-related Calcium, inflammation-related SCF/c-kit and p38/MAPK, and thrombosis and diabetes-related JAK2/STAT3 signaling pathways, which indicated that HD is a typical prescription with multichannel and multifunction of TCM characteristics. Conclusion: This study not only expounds the pathogenesis of ileus and, at the same time systematically illuminates the curative mechanism of HD, but also provides a novel SP method to explore the therapeutic mechanism of TCM in treating complicated GI diseases.

Multivariable Predictive Model of Postoperative Delirium in Cardiac Surgery Patients: Proteomic and Demographic Contributions.

Delirium after cardiac surgery is common, morbid, and costly, but may be prevented with risk stratification and targeted intervention. In this study, we aimed to identify protein biomarkers and develop a predictive model for postoperative delirium in older patients undergoing cardiac surgery. SomaScan analysis of 1305 proteins in the plasma from 57 older adults undergoing cardiac surgery requiring cardiopulmonary bypass was conducted to define delirium-specific protein signatures at baseline (preoperative baseline timepoint [PREOP]) and postoperative day 2 (POD2). Selected proteins were validated in 115 patients using the Enzyme-Linked Lectin Assay (ELLA) multiplex immunoassay platform. Proteins were combined with clinical and demographic variables to build multivariable models that estimate the risk of postoperative delirium and bring light to the underlying pathophysiology. Of the 115 patients, 21 (18.3%) developed delirium after surgery. The SomaScan proteome screening evidenced differential expression of 115 and 85 proteins in delirious patients compared to nondelirious preoperatively and at POD2, respectively ( P < .05). Following biological and methodological criteria, 12 biomarker candidates (Tukey's fold change [|tFC|] >1.4, Benjamini-Hochberg [BH]- P < .01) were selected for ELLA multiplex validation. Statistical analyses of model fit resulted in the combination of age, sex, and 3 proteins (angiopoietin-2; C-C motif chemokine 5; and metalloproteinase inhibitor 1; area under the curve [AUC] = 0.829) as the best performing predictive model for delirium. Analyses of pathways showed that delirium-associated proteins are involved in inflammation, glial dysfunction, vascularization, and hemostasis. Our results support the identification of patients at higher risk of developing delirium after cardiac surgery using a multivariable model that combines demographic and physiological features, also bringing light to the role of immune and vascular dysregulation as underlying mechanisms.

Data-driven School Management: An Analysis of Pathways to Enhancing Student Academic Performance and Mental Health

The rapid growth of data analytics in recent years has opened up new opportunities for organizations of all kinds to make the most of large amounts of data to drive decision making and optimize operations. This paper focuses on the application of data analysis in improving student management in educational institutions, and analyzes a variety of lifestyle and behavioral variables such as students' study time, extracurricular activities, sleep duration, and social behavior. By analyzing the impact of these factors on academic performance and stress levels, this study highlights the importance of data-driven approaches in shaping education policy. The study uses statistical tools and regression analysis to identify key patterns and correlations and provide actionable recommendations for schools to enhance student academic performance and effectively manage mental health. This study aims to show how data analytics can be applied in education to help schools create more personalized, efficient and supportive learning environments. The findings highlight the importance of balancing academic demands with student well-being and suggest interventions that schools can take to optimize academic outcomes and overall student health.

Transcriptome Analysis of Stephania yunnanensis and Functional Validation of CYP80s Involved in Benzylisoquinoline Alkaloid Biosynthesis.

The medicinal plant Stephania yunnanensis is rich in aporphine alkaloids, a type of benzylisoquinoline alkaloid (BIA), with aporphine being the representative and most abundant compound, but our understanding of the biosynthesis of BIAs in this plant has been relatively limited. Previous research reported the genome of S. yunnanensis and preliminarily identified the norcoclaurine synthase (NCS), which is involved in the early stages of the BIA biosynthetic pathways. However, the key genes promoting the formation of the aporphine skeleton have not yet been reported. In this study, based on the differences in the content of crebanine and several other BIAs in different tissues, we conducted transcriptome sequencing of roots, stems, and leaves. We then identified candidate genes through functional annotation and sequence alignment and further analyzed them in combination with the genome. Based on this analysis, we identified three CYP80 enzymes (SyCYP80Q5-1, SyCYP80Q5-3, and SyCYP80G6), which exhibited different activities toward (S)- and (R)-configured substrates in S. yunnanensis and demonstrated strict stereoselectivity enroute to aporphine. This study provides metabolomic and transcriptomic information on the biosynthesis of BIAs in S. yunnanensis, offers valuable insights into the elucidation of BIA biosynthesis, and lays the foundation for the complete analysis of pathways for more aporphine alkaloids.

Study on mechanism of Spatholobi Caulis in the treatment of the hand-foot skin reaction induced by targeted drug therapy based on network pharmacology and molecular docking: An observational study.

Based on network pharmacology and molecular docking methods, this study explored its active compounds and confirmed its potential mechanism of action against Hand-foot skin reaction induced by tumor-targeted drugs. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and UniProt Database were used to obtain the active ingredients and target proteins of Spatholobi Caulis. All hand-foot skin reaction (HFSR)-related targets were obtained with the help of the Human Gene Database, Online Mendelian Inheritance in Humans (OMIM), DisGeNET and DrugBank databases. Cytoscape 3.7.1 software was used to construct the active ingredient-target visualization network of Spatholobi Caulis, and the common target network of Spatholobi Caulis and HFSR. And through the BisoGenet plug-in in Cytoscape, PPI network topology analysis was performed. The Metescape database and online mapping tool platform were used for Gene Ontology (GO) function and Kyoto Encyclopedia of Genes Genomes (KEGG) pathway enrichment analysis to identify the key pathways of Spatholobi Caulis. Finally, Autodock Vina software and PyMol 2.5 software were used for molecular docking verification. There were 24 active components of Spatholobi Caulis and 244 target genes, 1635 disease-related target genes, 51 common target genes of Spatholobi Caulis and Hand-foot skin reaction, and key targets included NTRK1, epidermal growth factor receptor (EGFR), APP, TP53, HSP90AB1, HSP90AA, CUL3, etc. GO functional analysis involved a total of 66 molecular functions, 39 cellular components, and 817 biological processes. KEGG pathway analysis found 154 related signaling pathways, mainly enriched in Pathways in cancer, Human cytomegalovirus infection, Kaposi arcoma-associated herpesvirus infection, panic cancer, EGFR tyrosine kinase inhibitor resistance, P13K-Akt signaling pathway, Proteoglycans in cancer, HIF-1 signaling pathway and Ras signaling pathway, etc. Molecular docking results showed that luteolin, the active component of Spatholobi Caulis, had a high affinity with EGFR. Medicagol, the active components of Spatholobi Caulis, is proved in the Hand-foot skin reaction induced by lung cancer targeted therapy by regulating multiple signaling pathways through EGFR. It is confirmed that the treatment of Hand-foot skin reaction has the characteristics of multi-component, multi-target and multi-pathway regulation.

Validation and the role of PDK4 relevant to ferroptosis in degenerative lumbar disc disease

BackgroundFerroptosis was involved in the pathogenesis of intervertebral disc degeneration (IVDD). However, the exact mechanism of IVDD associated with ferroptosis still required deeper studies.MethodThe differentially expressed genes (DEGs) in rat lumbar disc tissue between the control and IVDD group treated with IL-1β were detected by RNA sequencing (RNA-seq). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on DEGs. We further screened the differential expressed ferroptosis-related genes (DEFRGs). Besides, a protein-protein interaction (PPI) network of DEFRGs was constructed by STRING database. The Cytoscape database identified significant modules and the hub genes. The loss function of PDK4 by siRNA inference was investigated in NPCs by CCK8 assay, ELISA assay, and the analysis of ferroptosis indicators.ResultDEGs were identified using RNA-seq. KEGG pathway analysis showed that these genes were mainly involved in Parkinson’s disease, oxytocin signaling pathway, calcium ion signaling pathway, AMPK signaling pathway, and glucagon signaling pathway. Eight hub genes (including LDHA, PKM, EP300, EGFR, EGLN1, SCD, PDK4, and FABP4) were found by the PPI network and Cytoscape on a total of 25 ferroptosis-related genes that were identified in rat lumbar disc tissue after IVDD treatment. PDK4 silencing promoted NPCS proliferation, decreased the levels of the proinflammatory factors, and suppressed ferroptosis.ConclusionThe study suggested the potential roles of ferroptosis-related genes in IVDD and further revealed the role of PDK4 in the progression of IVDD.

Research on the mechanism of eugenol in the treatment of liver cancer based on network pharmacology, molecular docking technology, and in vitro experiments.

Eugenol, a phenolic natural product with diverse pharmacological activities, remains unexplored in liver cancer. Using network pharmacology, we investigated eugenol's therapeutic mechanisms in liver cancer. We obtained eugenol's molecular structure from PubChem and screened its targets using similarity ensemble approach in Swiss Target Predictiondatabases. Overlapping genes with liver cancer-related genes from GeneCards were identified. Protein-protein interaction networks, Gene Ontology annotations, and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted. A target-pathway network revealed eugenol's interaction with 122 liver cancer-related genes. Molecular docking confirmed eugenol's high affinity for mitochondrial nicotinamide adenine dinucleotide, reduced form (NADH) dehydrogenase 1 (MT-ND1), AKT1, NDUFB7, and NADH dehydrogenase (complex I) subunit S3 (NDUFS3). Expression levels of these targets in normal liver and liver cancer tissues were examined using GEPIA2 and HPA databases. The CCK-8 assay and colony formation assay demonstrated that eugenol significantly inhibited the proliferation of hepatocellular carcinoma cells. Western blot analysis confirmed that eugenol upregulated MT-ND1 while downregulating the expression of targets such as AKT1, NDUFB7, and NDUFS3. Furthermore, it was found that eugenol could influence the expression of the AKT1 target through the AKT/p70 S6K pathway. This study provides new insights into the potential mechanisms of eugenol in liver cancer and offers novel perspectives for network-based liver cancer research.

Long-term effects of linear versus macrocyclic GBCAs on gene expression in the central nervous system of mice

BackgroundWe examined chronic gadolinium retention impact on gene expression in the mouse central nervous system (CNS) after injection of linear or macrocyclic gadolinium-based contrast agents (GBCAs).MethodsFrom 05/2022 to 07/2023, 36 female mice underwent weekly intraperitoneal injections of gadodiamide (2.5 mmol/kg, linear), gadobutrol (2.5 mmol/kg, macrocyclic), or saline. Mice were sacrificed on day 29 or 391 after a 1-year washout. Assessments included magnetic resonance imaging (MRI), mechanical hyperalgesia tests, and inductively coupled plasma mass spectrometry to measure gadolinium levels. Ribonucleic acid (RNA) sequencing and bioinformatic analyses identified differentially expressed genes (DEGs), with validation by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blot (WB).ResultsPost-gadodiamide, MRI showed increased signal intensity in the deep cerebellar nuclei (pre, 0.997 ± 0.006 versus post, 1.086 ± 0.013, p < 0.001). Mechanical hyperalgesia tests indicated transient sensory changes. After 1-year, gadolinium retention was noted in the brain (5.92 ± 0.32 nmol/kg) and spinal cord (1.23 ± 0.66 nmol/kg) with gadodiamide, compared to saline controls (0.06 ± 0.02 nmol/kg in brains and 0.28 ± 0.06 nmol/kg in spinal cords). RNA sequencing identified 17 shared DEGs between brain and spinal cord in the gadodiamide group on day 391, with altered Hmgb2 and Sgk1 expression confirmed by qRT-PCR and WB. Reactome pathway analysis showed enrichment in neuroinflammation pathways. No DEGs were detected in brains on day 29.ConclusionChronic gadolinium deposition from repeated linear GBCA but not macrocyclic administration causes significant gene expression alterations in the mouse CNS, particularly affecting neuroinflammation pathways.Relevance statementThis study examined the long-term impact of chronic gadolinium retention on gene expression in the mouse CNS, uncovering significant changes associated with neuroinflammation pathways after repeated administration of linear GBCA, but not with macrocyclic GBCA. These findings highlight the importance of further research on the long-term safety of linear GBCA in medical imaging.Key PointsChronic gadolinium retention alters gene expression in the mouse central nervous system.Significant neuroinflammatory pathway changes were observed after linear gadodiamide exposure.MRI showed increased signal intensity in deep cerebellar nuclei after gadodiamide injection.Graphical

Metabolic pathway and genetically causal links of 1,400 circulating metabolites on the risk of intracranial aneurysms and aneurysmal subarachnoid hemorrhage.

The rupture of intracranial aneurysms (IAs) leads to aneurysmal subarachnoid hemorrhage (aSAH), which is associated with significant disability and mortality rates. This study aims to identify metabolic markers causally linked to the occurrence of IAs and aSAH through Mendelian randomization (MR), thereby offering novel predictive and therapeutic targets. We conducted a genome-wide association study (GWAS) on IAs and aSAH, analyzing 1,400 metabolomic indices from the Canadian Longitudinal Study on Aging (CLSA) cohort (n = 8,299). Subsequently, we employed two-sample Mendelian randomization to ascertain potential causal relationships between each metabolite and the conditions IAs and aSAH by various MR methodologies, including MR Egger, Weighted median, Inverse variance weighted (IVW), MR-PRESSO, Simple mode, and Weighted mode. The heterogeneity of instrumental variables was assessed using Cochran's Q statistics, and metabolic pathway analyses were performed via the Metaconflict 5.0 platform. Our analysis found that 87 metabolites/metabolic ratios were associated with IAs, and 85 metabolites/metabolic ratios were associated with aSAH. After false discovery rate (FDR) correction and sensitivity analyses, nine metabolites/metabolic ratios were significantly causally associated with aSAH. Conversely, while 87 metabolites and their ratios initially showed potential causal links with IA, none demonstrated significant causal associations post-FDR correction. The study also pinpointed eight significant metabolic pathways implicated in both IAs and aSAH. This study found that nine circulating metabolites and their ratios with significant causal associations to aSAH, while no metabolites and their ratios were causally linked to IAs. These results suggest possible mechanisms and predictive molecular targets for IAs and aSAH.

Genome-Wide Identification of GmPIF Family and Regulatory Pathway Analysis of GmPIF3g in Different Temperature Environments.

Phytochrome-interacting factors (PIFs) play a crucial role in regulating plant growth and development. However, studies on soybean PIFs are limited. Here, we identified 22 GmPIF genes from the soybean genome and classified the GmPIF proteins into 13 subfamilies based on amino acid sequence homology, secondary and tertiary structures, protein structure, and conserved motifs. Genome-wide collinearity analysis revealed that fragment duplication events play a dominant role in expanding the GmPIF gene family. Cis-acting element analysis revealed that the GmPIF gene family is involved in light response, hormone response, biotic-abiotic stress response elements, and plant growth and development. Gene expression analysis in different temperature environments showed that the GmPIF family was found to be induced by phytohormone treatments, with a significant increase in the expression level of GmPIF3g. GmPIF3g plays a key role in the regulation of the entire network, and in addition, 30 proteins interacting with the GmPIF3g promoter were identified through the use of a novel biofilm interference technique. This technique showed that the transcription factor Dof (DNA binding with one finger) binds to the GmPIF3g promoter, and Y1H assays indicated that Dof regulates its expression by binding to the PIF promoter. These results provide a theoretical basis for further studies on the regulatory network of GmPIF genes to improve the structure of soybean plants under shade environments, as well as a new method for analyzing regulatory elements that interact with gene promoters.

The Relationship of PRAME Expression with Clinicopathologic Parameters and Immunologic Markers in Melanomas: In Silico Analysis.

PRAME is a cancer testis antigen whose expression is limited in normal tissues but is increased in cancers. Although there are studies revealing its oncogenic and immunogenic role, the relationship between PRAME expression and immunity in melanomas is not very clear. We aimed to reveal the relationship between PRAME expression and clinicopathologic parameters, immunologic markers, survival in melanomas. PRAME alteration data in TCGA SKCM data set was obtained from cBioPortal. Analyzes regarding clinicopathologic parameters were performed through cBioPortal and UALCAN, survival-related analyzes were performed through cBioPortal, GEPIA2. The correlation analyzes between PRAME expression and immune cell infiltration, immunity-related genes were performed in TIMER2.0, TISIDB, GEPIA2. PRAME protein-protein interaction network was constructed in STRING. The correlated genes with PRAME were listed in LinkedOmics, gene set enrichment and pathway analyses were performed through LinkInterpreter. In cases with low PRAME expression, there was a higher frequency of metastasis and p53 mutation, a more advanced tumor stage and a lower nodal stage. Strong relationship between PRAME expression and immune cell infiltration. A negative correlation was detected between expression of PRAME and many immunomodulatory genes (P<0.05). Positively correlated genes with PRAME expression were involved in metabolic pathways; negatively correlated genes were involved in pathways related to cell differentiation, immunologic processes. No significant relationship was found between PRAME expression and survival (P>0.05). Our findings reveal a strong interaction between PRAME expression and tumorigenicity, the immune system and shed light on further clinical studies including PRAME-targeted studies.

Network Pharmacology Unveils Multi-Systemic Intervention of Panax notoginseng in Osteoporosis via Key Genes and Signaling Pathways.

Panax notoginseng (Burk.) F. H. Chen (PN) is a traditional Chinese medicine that has been applied to prevent and treat osteoporosis. The mechanism of PN for osteoporosis remained a mystery. The objective was to reveal the therapeutic effect and illuminate the possible mechanism of PN for osteoporosis. The Traditional Chinese Medicine Database and Analysis Platform was searched to screen the potent ingredients of the PN and to analyze the potential therapeutic targets for osteoporosis. We excavated four disease databases to collect osteoporosis-related genes. After integrating the gene expression profile of osteoporosis and the chemical-protein data of PN, a protein-protein interaction network was constructed to demonstrate the interactions among the gene products. GO function, KEGG pathway, and docking analyses were executed. Network pharmacology obtained 31 active ingredients and 134 targets for the treatment of osteoporosis. The key components were beta-elemene, quercetin, methyl palmitate, oleic acid, and hexanal. The results of GO and KEGG analyses showed that Panax notoginseng was beneficial for osteoporosis by influencing the main pathways including AGE-RAGE signaling pathway in diabetic complications, TNF signaling pathway, IL-17 signaling pathway, p53 signaling pathway, NF-kappa B signaling pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, FoxO signaling pathway, and Wnt signaling pathway, modulating inflammation, metabolism, cell proliferation, cell survival, growth and angiogenesis. Panax notoginseng intervened in osteoporosis through multi-components, multi-targets, and multi-pathways. This study illustrates the mechanism of Panax notoginseng for osteoporosis, providing broader insights for novel research and developments of the Panax species for osteoporosis.

The anti-melanoma roles and mechanisms of tricholoma isoflavone derivative CA028

As a form of skin cancer, melanoma’s incidence rate is continuing to rise globally. Therefore, there is an urgent need to find new agents to improve survival in melanoma patients. Isoflavones, a class of phytoestrogens, are primarily found in soy and other legumes. Cumulating evidence demonstrates that isoflavones exhibits significant anti-tumor properties and is beneficial for the prevention and treatment of melanoma. In the present study, we aim to investigate the anti-melanoma role of tricholoma isoflavone derivative CA028. By using in vitro melanoma cell line models, A375 and A2058 and in vivo xenograft mouse model, our results indicate that melanoma proliferation, migration, and invasion are attenuated following CA028 treatment. In addition, the treatment of CA028 induced cell apoptosis of melanoma. Finally, we addressed the mechanism of CA028 against melanoma by comparative transcriptomic analysis. The results of gene ontology highlighted the involvement of CA028’s targets in the cell proliferation, cell apoptosis, and migration ability of melanoma cells. Furthermore, Ingenuity Pathway Analysis constructed the network involved in the apoptotic roles of CA028 through targeting p53 signaling and death receptor signaling. For the first time, our data suggested the possible use of modified isoflavone for therapeutic applications against melanoma.

Proteomic Analysis of the Murine Liver Response to Oral Exposure to Aflatoxin B1 and Ochratoxin A: The Protective Role to Bioactive Compounds.

Aflatoxin B1 (AFB1) and Ochratoxin A (OTA) are considered the most important mycotoxins in terms of food safety. The aim of this study was to evaluate the hepatotoxicity of AFB1 and OTA exposure in Wistar rats and to assess the beneficial effect of fermented whey (FW) and pumpkin (P) as functional ingredients through a proteomic approach. For the experimental procedures, rats were fed AFB1 and OTA individually or in combination, with the addition of FW or a FW-P mixture during 28 days. For proteomics analysis, peptides were separated using a LC-MS/MS-QTOF system and differentially expressed proteins (DEPs) were statistically filtered (p < 0.05) distinguishing males from females. Gene ontology visualization allowed the identification of proteins involved in important biological processes such as the response to xenobiotic stimuli and liver development. Likewise, KEGG pathway analysis reported the metabolic routes as the most affected, followed by carbon metabolism and biosynthesis of amino acids. Overall, the results highlighted a strong downregulation of DEPs in the presence of AFB1 and OTA individually but not with the mixture of both, suggesting a synergistic effect. However, FW and P have helped in the mitigation of processes triggered by mycotoxins.

A high-throughput platform for single-molecule tracking identifies drug interaction and cellular mechanisms.

The regulation of cell physiology depends largely upon interactions of functionally distinct proteins and cellular components. These interactions may be transient or long-lived, but often affect protein motion. Measurement of protein dynamics within a cellular environment, particularly while perturbing protein function with small molecules, may enable dissection of key interactions and facilitate drug discovery; however, current approaches are limited by throughput with respect to data acquisition and analysis. As a result, studies using super-resolution imaging are typically drawing conclusions from tens of cells and a few experimental conditions tested. We addressed these limitations by developing a high-throughput single-molecule tracking (htSMT) platform for pharmacologic dissection of protein dynamics in living cells at an unprecedented scale (capable of imaging >106 cells/day and screening >104 compounds). We applied htSMT to measure the cellular dynamics of fluorescently tagged estrogen receptor (ER) and screened a diverse library to identify small molecules that perturbed ER function in real time. With this one experimental modality, we determined the potency, pathway selectivity, target engagement, and mechanism of action for identified hits. Kinetic htSMT experiments were capable of distinguishing between on-target and on-pathway modulators of ER signaling. Integrated pathway analysis recapitulated the network of known ER interaction partners and suggested potentially novel, kinase-mediated regulatory mechanisms. The sensitivity of htSMT revealed a new correlation between ER dynamics and the ability of ER antagonists to suppress cancer cell growth. Therefore, measuring protein motion at scale is a powerful method to investigate dynamic interactions among proteins and may facilitate the identification and characterization of novel therapeutics.

Protein alterations in patients with delirium after cardiac surgery: An exploratory case-control sub-study of the VISION Cardiac Surgery Biobank.

Delirium is an acute state of confusion associated with adverse postoperative outcomes. Delirium is diagnosed clinically using screening tools; most cases go undetected. Identifying a delirium biomarker would allow for accurate diagnosis, application of therapies, and insight into causal pathways. To agnostically discover novel biomarkers of delirium, we conducted a case-control sub-study using the VISION-Cardiac Surgery biobank. Our objective was to identify candidate biomarkers to investigate in future studies. We obtained a convenience sample of 30 patients with delirium on postoperative day 1 matched to 30 matched controls by age, sex, ethnicity, center and cardiopulmonary bypass time. The Olink Explore 3K platform was used to identify blood protein alterations on postoperative day 3. Protein concentrations were expressed as normalized protein expression (NPx) units (log2 fold scale). We compared protein expression between cases and controls using a paired t-test and reported significantly different biomarkers based on a False Discovery Rate (FDR)-adjusted p-value<0.05. Of 2,865 unique serum proteins, 26 (0.9%) were significantly associated with delirium status; all were elevated in cases versus controls at an FDR<0.05. Pathway analysis identified "calcium-release channel activity" (Padj=0.02) and "Guanosine 5' triphosphate (GTP)-binding" (Padj=0.005) functions as characteristic of proteins associated with delirium. The top three differentially expressed biomarkers were FKBP1B (Padj=0.003), C2CD2L (Padj=0.004), and RAB6B (Padj=0.004). The inflammatory biomarker IL-8 (CXCL8) (mean difference = 2.36; P=3.6x10-4) was also associated with delirium. We identified 26 biomarkers significantly associated with delirium; all are novel except for IL-8. We did not identify an association between delirium and recognized neuro-inflammatory proteins and markers of brain injury, which supports using biomarkers to differentiate between delirium and other neurological conditions. While exploratory, our findings support using biomarkers to diagnose postoperative delirium and validate using agnostic screens to identify potential delirium biomarkers.

Transcriptomic profiling of chronic hand eczema skin reveals shared immune pathways and molecular drivers across subtypes.

Chronic hand eczema (CHE) is a common skin disease with different subtypes, but knowledge of the molecular patterns associated with each subtype is limited. To characterize the CHE transcriptome across subtypes. Using RNA-sequencing, we studied the transcriptome of 220 full-thickness skin biopsies collected from palms, dorsa, and arms from 96 patients with CHE and/or atopic dermatitis (AD) and 32 healthy controls. The primary analysis focused on 16 healthy and 54 lesional CHE palm samples that were further stratified by AD status and unique etiology. Differentially expressed genes (DEGs) were identified across the cohort and Ingenuity pathway analysis (IPA) was used for pathway analysis and upstream regulator prediction. We identified anatomical site-specific transcriptomic variations, showing unique characteristics in both healthy and CHE-affected palm skin. In CHE palms, we identified 2333 DEGs versus healthy palms. Upregulated genes predominantly involved keratinocyte host inflammation and immune signaling, while downregulated genes were linked to lipid metabolism and epidermal barrier function. IPA revealed numerous activated pro-inflammatory pathways, dominated by Th1 and Th2. Key upstream regulators included type 1 (IFNG, TNF, STAT1, IL-2) and type 2 (IL-4) associated molecules, and IL-1β. Lesional palm signatures were broadly shared across CHE subtypes. No DEGs were found between allergic- and irritant contact dermatitis CHE. Subtype-specific pathway and upstream regulator activity variations were noted. The lesional CHE transcriptome is primarily shared among subtypes and is characterized by activation of several immune pathways, dominated by Th1 and Th2. Key shared upstream regulators were identified, highlighting potential universal therapeutic targets.

Methyl jasmonate induces the regulation of protostane triterpene biosynthesis by microRNAs in Alisma orientale.

Protostane triterpenes are medicinally important components found in members of the Alismataceae botanical family, notably Alisma orientale. Methyl jasmonate (MeJA) is known to regulate protostane triterpene biosynthesis in A. orientale, but the microRNA (miRNA) mechanism underlying MeJA response to promote triterpene biosynthesis remains unknown. In this study, we conducted miRNA sequencing analysis after MeJA induction in A. orientale to uncover the role of miRNAs in protostane triterpene biosynthesis. We identified 222 known miRNAs and 379 novel miRNAs, including 16 differentially expressed miRNAs (DEMs) between control and MeJA-treated leaf samples. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analysis, four DEMs and eight miRNA target genes were significantly enriched in the triterpene biosynthesis pathway. Integrated analysis of the transcriptome and miRNAome revealed a negative expression pattern between miRNAs and their target genes. We then constructed a regulatory network of miRNA-target gene relationships involved in the triterpene biosynthesis pathway. We found miRNAs may be involved in the response of A. orientale to exogenous MeJA by regulating the expression of key biosynthesis enzymes, leading to increased accumulation of medically important protostane triterpenes.

Transcriptomic analysis of human cartilage identified potential therapeutic targets for hip osteoarthritis.

Cartilage degradation is the hallmark of osteoarthritis (OA). The purpose of this study was to identify and validate differentially expressed genes (DEGs) in human articular cartilage that could serve as potential therapeutic targets for hip OA. We performed transcriptomic profiling in a discovery cohort (12 OA-free and 72 hip OA-affected cartilage) and identified 179 DEGs between OA-free and OA-affected cartilage after correcting for multiple testing (P < 2.97 × 10-6). Pathway and network analyses found eight hub genes to be associated with hip OA (ASPN, COL1A2, MXRA5, P3H1, PCOLCE, SDC1, SPARC, and TLR2), which were all confirmed using qPCR in a validation cohort (36 OA-free and 62 hip OA-affected cartilage) (P < 6.25 × 10-3). Our data showed that dysregulation of extracellular matrix formation and imbalance in the proportion of collagen chains may contribute to the development of hip OA, and SDC1 could be a promising potential therapeutic target. These findings provided a better understanding of the molecular mechanisms for hip OA and may assist in developing targeted treatment strategies.

Inflammation and response to bacterial infection as potential drivers of equine odontoclastic tooth resorption and hypercementosis: A proteomics insight.

Equine dental diseases significantly impact a horse's overall health, performance and quality of life. They can result in secondary infections and digestive disturbances, potentially leading to colic. A recently described disease affecting the incisors of horses is equine odontoclastic tooth resorption and hypercementosis (EOTRH). Understanding EOTRH is crucial for early diagnosis, effective management and prevention of its severe consequences. To determine proteomic differences in incisor cementum in horses with and without clinical EOTRH. Comparative and observational clinical study. Teeth were extracted (N = 5) and cementum was isolated using a diamond wire. Proteins were extracted using an optimised sequential workflow, and trypsin was digested for mass spectrometry. Protein identification and label-free quantification were undertaken. In total 1149 unique proteins were detected in cementum across all samples. We identified four proteins exclusively in EOTRH-affected cementum. EOTRH samples showed a higher heterogeneity than healthy samples. In total, 54 proteins were increased in EOTRH, and 64 proteins were reduced (adjusted p-value <0.05). Inflammatory proteins, such as cathepsin G (p = 0.004), neutrophil elastase (p = 0.003), bactericidal permeability-increasing protein (p = 0.002), azurocidin (p = 0.003) and lactotransferrin (p = 0.002) were all increased in EOTRH. Pathway analysis revealed that antimicrobial peptides (Z score 2.65, p = 1.93E-09) and neutrophil degranulation (Z-score 1.89, p = 1.7E-04) were commonly up-regulated canonical pathways. The sample size was limited. Lack of age-matched healthy controls. EOTRH leads to biochemical changes within the cementum proteome, which are important in explaining the physiological changes occurring in disease. Differentially abundant proteins may represent promising biomarkers for earlier disease detection and the establishment of a cell-based model could provide further insight into the role these proteins play in hypercementosis and resorption.