Expression Analysis Research Articles

Comprehensive Analysis of Class III Peroxidase Genes Revealed PePRX2 Enhanced Lignin Biosynthesis and Drought Tolerance in Phyllostachys edulis.

Class III peroxidase (PRX) is the key enzyme in lignin biosynthesis and critical for maintaining the redox balance in plants to respond to stress. In moso bamboo (Phyllostachys edulis), a globally significant non-timber forestry species, the potential roles of PRX genes remain largely unknown. In this research, a total of 179 PePRXs was identified on a genome-wide scale in moso bamboo. Phylogenic relationship, conserved motifs, gene structure, collinearity, and cis-acting elements were investigated. Analysis of gene expression indicated that PePRXs exhibited tissue-specific expression and different response patterns to hormones and abiotic stresses. Based on the transcriptome data, ten PePRXs with positive correlations between expression levels and lignification degree were screened out. Among them, PePRX2 was selected as a candidate gene according to the co-expression network. Y1H and Dual-Luc assays demonstrated that PeMYB61 could bind to the promoter of PePRX2 and enhance its transcription. The result of in situ hybridization showed that PePRX2 was specifically expressed in the vascular bundle sheath cells of bamboo shoot. As a secreted protein, PePRX2 was located on the cell wall. Overexpression of PePRX2 led to a significant increase in lignin content in transgenic poplar, indicating that PePRX2 could promote lignin polymerization. In comparison to the wild type, the PePRX2-OE poplar lines exhibited increased peroxidase activity and decreased levels of MDA, O2-, and H2O2 under drought stress, indicating enhanced drought resistance. This thorough analysis of the PRX family in moso bamboo provided new insight into the roles of PePRXs in lignin biosynthesis and drought adaptation.

Exploring single cell microbial protein as a sustainable fishmeal alternative in yellowtail kingfish (Seriola lalandi) diets: impacts on health and gut microbiome

BackgroundWith the global expansion of aquaculture and the increasing demand for fish meal, identifying appropriate and sustainable alternative protein sources for aquafeeds has become essential. Single-cell protein (SCP), derived from methanotrophic bacteria, presents a promising alternative by converting methane into protein, potentially addressing both the need for alternative protein sources and reducing industrial greenhouse gas emissions. This study aimed to evaluate the effects of different levels of SCP inclusion (0%, 25%, 50%, and 75% fish meal replacement) on the health, gene expression, and gut microbiome of yellowtail kingfish (YTK, Seriola lalandi) following a 35-day growth trial.ResultsThe study found that SCP inclusion at the highest level of fishmeal replacement (75%) induced a mild inflammatory response in the hindgut of the fish. However, micromorphological assessments of the hindgut, serum biochemistry, and gene expression analyses revealed no significant detrimental effects from SCP replacement. Notably, there were indications of improved lipid digestibility with SCP. Furthermore, SCP inclusion significantly enhanced microbial richness and altered the composition of the gut microbiome, introducing beneficial bacterial taxa that may contribute to improved gut health and resilience.ConclusionsThis study highlights SCP as a viable and sustainable alternative to fish meal in YTK diets. The findings suggest that SCP can be included in YTK diets without adverse health effects at moderate levels and may even offer benefits in terms of lipid digestibility and gut microbiome diversity. These results contribute to the advancement of more sustainable aquaculture practices.

Bioinformatics to Identify Biomarkers of Diabetic Nephropathy based on Sphingolipid Metabolism and their Molecular Mechanisms.

Diabetes mellitus (DM) frequently results in Diabetic Nephropathy (DN), which has a significant negative impact on the quality of life of diabetic patients. Sphingolipid metabolism is associated with diabetes, but its relationship with DN is unclear. Therefore, screening biomarkers related to sphingolipid metabolism is crucial for treating DN. To identify Differentially Expressed Genes (DEGs) in the GSE142153 dataset, we conducted a differential expression analysis (DN samples versus control samples). The intersection genes were obtained by overlapping DEGs and Sphingolipid Metabolism-Related Genes (SMRGs). Furthermore, The Least Absolute Shrinkage and Selection Operator (LASSO) and Support Vector Machine Recursive Feature Elimination (SVM-RFE) algorithms were used to filter biomarkers. We further analyzed the Gene Set Enrichment analysis (GSEA) and the immunoinfiltrational analysis based on biomarkers. We identified 2,186 DEGs associated with DN. Then, five SMR-DEGs were obtained. Subsequently, biomarkers associated with sphingolipid metabolism (S1PR1 and SELL) were identified by applying machine learning and expression analysis. In addition, GSEA showed that these biomarkers were correlated with cytokine cytokine receptor interaction'. Significant variations in B cells, DCs, Tems, and Th2 cells between the two groups suggested that these cells might have a role in DN. Overall, we obtained two sphingolipid metabolism-related biomarkers (S1PR1 and SELL) associated with DN, which laid a theoretical foundation for treating DN.

Bioinformatic analysis of the CaABCB family members and expression analysis and functional verification of the CaABCB20 in pepper

Bioinformatic analysis of the CaABCB family members and expression analysis and functional verification of the CaABCB20 in pepper

Semaphorin 3A repulsion directs the caudal projection of pioneer longitudinal axons in the developing chicken brain

The medial longitudinal fasciculus (MLF) is the first axon tract to develop in the ventral vertebrate brain. It originates in the diencephalon and projects caudally into the spinal cord, pioneering the path for later developing axons. Previous anatomical and expression analyses in the chicken suggested Semaphorin 3A (Sema3A) as the candidate to repel the amniote MLF from the forebrain. However, studies in the zebrafish implicated a distantly related semaphorin with a role in axon fasciculation, not guidance. Thus, the mechanism accounting for the caudal projection of the MLF remains unclear.Here we show that misexpression of Sema3A or grafting of Sema3A-expressing cells into the path of the MLF diverts the axons or blocks their outgrowth in chicken embryos. In vitro, Sema3A exposure resulted in the collapse of MLF growth cones. A dominant-negative approach or siRNA to interfere with the function of the Sema3A receptor Neuropilin1 allowed MLF axons to project rostrally. Together, this suggests that Sema3a repulsion directs the caudal extension of the MLF to pioneer the ventral longitudinal tract.

Biopeptide-rich fermented hemp seeds: Boosting anti-inflammatory and immune responses through Lactiplantibacillus plantarum probiotic fermentation.

Cannabis sativa L. (hemp) seeds are increasingly recognized as a promising food source rich in phytochemicals that support inflammatory and immunological reactions. This study investigates whether fermentation with Lactiplantibacillus plantarum can further enhance these functional properties, paving the way for hemp seeds to be developed into potent functional food ingredients. Aqueous, 70% ethanol, and ethyl acetate extracts from both L. plantarum-fermented (FHS) and unfermented hemp seeds (HS) were evaluated for their anti-inflammatory activities using cell-based assays. The 70% ethanol extract of FHS exhibited marked inhibitory effects on cytokines, including TNF-α, IL-1β, and IL-10, with fermentation significantly enhancing these effects by 25%, 39.3%, and 29.6%, respectively, compared to the unfermented extracts. Additionally, mRNA expression analysis confirmed the strong immunomodulatory potential of the fermented extracts. Intracellular metabolomic analysis revealed that the 'antifolate resistance', 'nicotine addiction', 'aminoacyl-tRNA biosynthesis', and 'D-amino acid metabolism' are highlighted in the reasons for this enhancement. Furthermore, FHS significantly prolonged the survival of C. elegans exposed to pathogens, with gene expression analysis indicating modulation of the innate immune system via regulation of genes such as gcs-1, lys-1, dbl-1, pmk-1, elt-2, and dod-22. A comprehensive metabolomic and correlation analysis identified five novel bioactive peptides (AAELIGVP, AAVPYPQ, VFPEVAP, DVIGVPLG, PVPKVL) and bioactive acids (indoleacetic acid and homovanillic acid) that were enriched during fermentation, which are strongly linked to the enhanced anti-inflammatory and immunomodulatory effects observed. These findings suggest that L. plantarum-fermented hemp seeds hold significant promise as functional ingredients in anti-inflammatory and immunomodulatory food products, with potential applications in health and wellness industries.

Unbiased transcriptomic analysis of primary early-onset vs late-onset colorectal cancer.

228 Background: Colorectal cancer is the 3rd most diagnosed and 2nd leading cause of cancer death. Despite the decline in incidence late-onset colorectal cancer (LOCRC), there is an increase in early onset of colorectal cancer (EORC). Clinicopathologic examinations from single centers revealed left-sided and rectal enrichment, poorly differentiated, and higher stage at presentation. Genomic studies examining the potential germline mutations/variants for EOCRC demonstrated mixed results. Transcriptomic analysis of the EOCRC compared to LOCRC remains limited. We hypothesized that EOCRC present with enrichment in aggressive molecular signatures consisting of CMS4 and iCMS3 signatures. To understand the mechanism behind EOCRC, we performed an unbiased RNA-Seq analysis in age groups of 32-82 in 95 patients. Methods: We utilized RNA-Seq data from the Orien Network, a collaborative between 19 NCI/NCCN cancer centers. We identified 95 patients diagnosed with colorectal cancer ranging in age from 32-82 and undergone RNA-sequencing of their primary tumors. Clinicopathologic assessment were analogously performed. We collected unnormalized raw-count RNA-Seq data from these patients. To account for differences in sequencing depth across samples, raw counts were scaled using the Reads Per Million (RPM) formula. The scaled reads in RPM were then utilized to assess the Consensus Molecular Subtypes (CMS) classification through two distinct approaches: the R package CMScaller and a deconvolution analysis using the R package SpatialDecon with the iCMS gene signature. Differences in age at the sample collection across patients with different CMS classifications were assessed by performing two-tailed unpaired T-tests. Additionally, differential expression analysis between EOCRC and LOCRC patients, defined by the upper and lower quartiles of the patients’ ages at the sample collection, was conducted using the LIMMA R package. Results: Clinicopathologic assessment of the primary tumors revealed left-sided tumors with poorly differentiated phenotype. Differential gene expression analysis between EOCRC and LOCRC demonstrated no significant differences. Stratification of transcriptomic data by decades also did not reveal any significant differences. Furthermore, there were no differences in CMS or iCMS classifications between different age groups. Conclusions: The RNA-Seq analysis comparing EOCRC and LOCRC did not identify any differential gene expression patterns. There was no significant differences were observed in CMS or iCMS classifications. These findings suggest that EOCRC and LOCRC share similar tumor biology based on molecular phenotypes. This implies that the initiating events for the disease may occur earlier in life while triggering a same disease process. As such, the findings underscores the importance of considering preventive measures, including earlier colonoscopy screenings.

Quantification of heavy metal exposure in a British population cohort links total mercury levels in plasma with skin tissue-specific changes in mitochondrial-related gene expression.

Heavy metals in our direct environment have profound effects on human health and while some are essential for life, others can be toxic. In vivo studies often focus on clinical features caused by overexposure to, or by deprivation of a heavy metal. However, to understand the cellular impact of heavy metals on health, studies in healthy volunteers before symptom onset are needed. Here, we explored the impact of mercury, lead and selenium in over 800 British female twins on multi-tissue gene expression levels as an intermediate phenotype. Total mercury, lead and selenium concentrations were determined in plasma as a proxy for heavy metal exposure. We identified significant associations between total mercury levels measured in plasma, that fall within normal ranges, and expression of 873 genes within skin tissue, including PUSL1, SAMD10, ERCC1, MRPL17, NDUFB8, SELENOH, SEC31A, and KAT7P1. Functional analysis of genes associated with total mercury levels in plasma show a strong link to the mitochondrial oxidative phosphorylation pathway (p-value=3.02×10-10). Analysis of mitochondrial-specific gene expression supported involvement of genes of oxidative phosphorylation complexes (MT-ND4L, and MT-ND5), which are encoded in mitochondrial DNA. These results suggest that mercury is likely detrimental to the energy metabolism of mitochondria. We also tested for associations between total mercury levels in plasma and gene expression in adipose and whole blood samples, but did not identify significant associations in these tissues, nor with lead or selenium in any tissue. Our results demonstrate that subtoxic mercury exposure leaves a clear molecular signature. It also underscores the necessity of conducting tissue-specific association studies to accurately capture the molecular impact of environmental exposures, as only relevant tissues will manifest a response to environmental exposures.

BTN1A1 expression in colon cancer: Implications for immunotherapy and patient stratification.

249 Background: Butyrophilin 1A1 (BTN1A1) is a promising immune checkpoint protein offering a novel option for immunotherapy. We discovered that BTN1A1 and PD-L1 expression are mutually exclusive through the JAK/STAT pathway in various tumors. Recently, Nelmastobart, an antibody targeting BTN1A1, successfully completed a Phase 1 clinical trial at three sites in the United States and two in the Republic of Korea, spanning 98 weeks. This abstract focuses on the results from the Phase 1 trial in patients with colorectal cancer (CRC), emphasizing biomarker diagnostics and therapeutics derived from translational research. Methods: We conducted a first-in-human, multicenter, open-label Phase I clinical trial to evaluate the safety, tolerability, pharmacokinetics, and preliminary efficacy of hSTC810 monotherapy in CRC patients. Extensive analyses of BTN1A1 expression were performed using patient specimens through immunohistochemistry and multi-immunofluorescence techniques to identify critical biomarkers and accurately assess nelmastobart's anticancer activity. We then analyzed progression-free survival (PFS), overall survival (OS), objective response rate (ORR), and safety alongside translational research findings using patient tissue samples. Results: A total of 47 patients were enrolled in the study. The median PFS across all cohorts was 1.9 months, while the median Kaplan-Meier estimate for OS was 12.8 months. Among the 16 CRC patients enrolled, tissue samples were obtained and analyzed using IHC in 12 patients and OPAL staining in 7 patients. The objective response rate (ORR) for CRC was 2.3%. The median progression-free survival (PFS) and overall survival (OS) were 3.6 months and 11 months, respectively. Notably, PFS, OS, and ORR strongly correlated with BTN1A1 expression levels in CRC patients. High levels of BTN1A1 expression in colorectal tumor tissues correlated with clinical outcomes, identifying BTN1A1 as a potential biomarker for predicting patient responses to targeted therapies. The mutual exclusivity of BTN1A1 and PD-L1 expression suggests that BTN1A1 could serve as a diagnostic marker to identify patients who may be unresponsive to PD-1/PD-L1 blockade therapy and might benefit from BTN1A1 blockade therapy. Conclusions: This Phase 1 clinical trial demonstrated that antibody-mediated BTN1A1 blockade effectively suppresses tumor growth in patients with BTN1A1-positive CRC. These findings suggest that BTN1A1-targeted therapies could provide a viable treatment option for patients with colon cancers that are refractory or resistant to anti-PD-1/PD-L1 therapies. Clinical trial information: NCT05231746 .

The hematopoietic function, histological characteristics, and transcriptome profiling of Wanxi white geese ovary during nesting and late-laying stages.

Despite several factors influencing reproduction in geese, but the precise molecular mechanisms of egg cessation are not fully understood. In the present study, the hematopoietic parameters and serum hormone levels in Wanxi white geese were analyzed. RNA-Seq was utilized to identify the differentially expressed mRNAs (DEGs) and lncRNAs (DE lncRNAs) in the ovarian tissues associated with nesting in geese during the late-laying and nesting periods. Triglyceride (TG) and alkaline phosphatase (ALP) levels were higher in late-laying geese, while white blood cell (WBC), neutrophil (NEU), hemoglobin (HGB), and hematocrit (HCT) levels were significantly lower in late-laying geese. Serum levels of luteinizing hormone (LH), estrogen (E2), and progesterone (P4) increased significantly during the late-laying period, whereas prolactin (PRL) level was lower in the late-laying period than the nesting period. During the late-laying period, geese had a clear follicular hierarchy, with ovaries exhibiting mature and primary follicles. In the nesting period, the ovaries were degenerated and had many primary follicles without follicular development. Analysis of mRNA-lncRNA expression revealed 1,257 DEGs between the nesting and the late-laying stages, of which 841 were up-regulated and 416 were down-regulated DEGs. A total of 340 DE lncRNAs were identified between the nesting and the late-laying periods, with 113 being up-regulated and 227 down-regulated lncRNAs. DEGs, including TMEM, DRD3, IGFBP7, MAPK13, GnRHR2, HECTD3, KCNU1, OPRD1, and VCAM1, along with DE lncRNAs, including XR_001203613.1, XR_001206155.1, XR_001207759.1, XR_001213571.1 and XR_001214368.1 participate in reproduction in geese. Correlation analysis indicated that the cis-regulation of XR_001213096.1-ITPR3, XR_001203613.1-GALNT15, XR_001206155.1-COL6A3, XR_001207759.1-ANKS1B, and XR_001214368.1-VPS45 participate in the molecular mechanisms underlying nesting in geese. Functional enrichment analysis revealed the DEGs and DE lncRNAs associated with focal adhesion, extracellular matrix (ECM)-receptor interaction, cell adhesion molecules (CAMs), and PI3K-Akt signaling pathways, were responsible for the differences in the ovaries between the nesting and late-laying periods. This study offers valuable information on the roles of genes and lncRNAs, and the mechanisms underlying variations in reproductive performance between the late-laying and nesting periods.

Dawn-to-dusk intermittent fasting is associated with overexpression of autophagy genes: A prospective study on overweight and obese cohort

Aim and BackgroundA growing body of evidence supports the impact of intermittent fasting (IF) on longevity and healthy aging via the modulation of autophagy genes. The activation of the catabolic autophagic machinery (LAMP2, LC3B, ATG5, and ATG4D) has protective effects against degenerative aging and chronic diseases. This research examined the changes in the expression of the aforementioned genes upon the observance of dawn-to-dusk IF among metabolically healthy participants with overweight and obesity. MethodsFifty-one (51) participants (36 males and 15 females, 38.84 ± 11.73 years) with overweight and obesity (BMI = 29.75 ± 5.04 kg/m2) were recruited and monitored before and at the end of the commencement of the four-week IF. Six healthy subjects with normal BMI (21.4±2.20 kg/m2) were recruited only to standardize the reference for normal levels of gene expressions. At the two time points, anthropometric, biochemical, and dietary assessments were performed, and LAMP2, LC3B, ATG5, and ATG4D gene expressions were assessed using qRT-PCR on RNA extracted from whole blood samples. ResultsAt the end of IF, and compared to the pre-fasting levels, the relative gene expressions among participants with overweight/obesity were significantly increased for the three autophagy genes LAMP2, LC3B, and ATG5, with increments of about 4.2 folds, 1.9-fold, and 1.4-fold, respectively. In contrast, the increase in the ATG4D gene was not significant. Concomitantly, significant decreases were found in body weight, BMI, fat mass, body fat percent, hip and waist circumferences, LDL, IL-6, and TNF-a (P <0.05), While HDL, IL-10, and CD163 significantly increased (P <0.05). Binary logistic regression analysis for genetic expressions showed no significant association between high-energy intake, waist circumference, or obesity and the four gene expressions. ConclusionsFour consecutive weeks of dawn-to-dusk IF of Ramadan is associated with the upregulation of autophagy gene expressions in participants with overweight/obesity, and this may explain, at least in part, its favorable short-term temporal metabolic and health-improving effects on early aging-related markers. Hence, IF presumably may entail a protective impact against early markers of aging and metabolic diseases in participants with overweight/obesity.

Biological and therapeutic impact of tumor mutational burden in microsatellite instability/mismatch repair-deficient (MSI/dMMR) metastatic colorectal cancer (mCRC) treated with immune checkpoint inhibitors (ICI).

272 Background: Microsatellite instability (MSI) is linked to hypermutability and response to ICI(s), especially in colorectal cancer. The predictive impact of tumor mutational burden (TMB) in ICI-treated MSI/dMMR metastatic colorectal cancer remains controversial, with some studies suggesting low TMB as a potential biomarker of resistance to ICI(s). We aimed to investigate the biological relevance of TMB in MSI/dMMR mCRC and its impact on survival outcomes in ICI(s)-treated patients (pts). Methods: MSI/dMMR mCRC pts treated with ICI(s) from the NIPICOL trial (NCT03350126) and the immunoMSI prospective monocentric cohort with available data from whole exome sequencing (WES) and RNA-sequencing (RNA-seq) were included. All cases were centrally assessed for MSI and dMMR status. TMB was calculated as described (Dupain et al., BMC, 2024). The search for a cutpoint able to optimize the difference in survival between 2 groups of patients with low and high-TMB was applied. The main endpoint was progression free survival (PFS) by iRECIST criteria. The cohort (NIPICOL, immunoMSI) was included as a covariate in the analysis of differential gene expression and pathway enrichment, with various tumor mutational burden (TMB) thresholds evaluated, specifically 10 and 30 mutations per megabase (mut/Mb). Results: A total of 99 pts were analyzed, with 4 (4%) excluded after central MSI/dMMR status review. Of these, 52 received anti-PD1 plus anti-CTLA4 therapy, while 43 received anti-PD1 alone. Median follow-up was 25 months. Median TMB was 51.8 mut/Mb (IQR: 35.9-74.9). TMB was not predictive of patient PFS, whatever the TMB threshold applied, including cutpoints already reported in the literature, the 2-year PFS rates being 80% versus 80% for TMB ≤ 10 and &gt; 10 mut/Mb, and 79% versus 82% for TMB ≤ 30 and &gt; 30 mut/Mb, respectively. Multivariate analysis including treatment type confirmed no association between TMB and PFS (HR 1.00, 95% CI [0.97–1.04]). TMB levels were not linked with specific signalling pathways related to immune checkpoints or antigen presentation as evaluated by RNA-seq with Gene Set Enrichment Analysis (GSEA) at a TMB threshold of 10 or 30 mut/Mb. However pathways involved in cell proliferation (e.g., “cell cycle”, “DNA replication”) were increased in TMB high (adjusted p-value &lt;0.05). RNA-seq signature quantification and deconvolution analysis revealed similar cell populations (e.g., fibroblasts, B cells, T cells) between high and low TMB groups at a TMB threshold of 10 and 30 mut/Mb. Conclusions: TMB has no survival impact for patients with ICI(s)-treated dMMR/MSI mCRC and does not discriminate two biologically distinct subpopulations. Other biomarkers should be developed for personalized medicine amongst these patients.

Influence of MRP4 levels on clinical outcomes in biliary tract cancer.

624 Background: Biliary tract cancer (BTC) are rare tumors with a poor prognosis.Multidrug resistance protein 4 (MRP4) is a transmembrane efflux transporter that influences on cellular growth and differentiation. Recent studies have linked high MRP4 levels to increased aggressiveness in pancreatic cancer and other tumor types. This study aimed to evaluate the role of MRP4 in BTC and its association with clinical outcomes in a real-world cohort from endemic areas in Argentina. Methods: We conducted a retrospective analysis of clinical outcomes and MRP4 expression in paraffin-embedded tissue samples from 78 patients with BTC. Immunohistochemistry staining was performed, and MRP4 expression was scored based on staining intensity and the percentage of positive cells. A score exceeding 100 was classified as high MRP4 levels. Statistical analyses included Chi-square, Kaplan-Meier survival curves, and log-rank tests, with significance set as p &lt;0.05 (two-tailed). Results: High MRP4 levels were observed in 46 out of the 78 samples (59%). Patients with gallbladder cancer (n=64) and elevated MRP4 levels had significantly poorer overall survival (OS) compared to those with low MRP4 levels (median 11.3 and 14.5 months, high and low, p =0.038). In the broader BTC cohort evaluable for survival (n=73; 64 gallbladder, 7 cholangiocarcinoma, 1 ampulla of Vater, and 1 biliary undefined) patients with elevated MRP4 levels had non-significant shorter OS (median 12.4 and 13.5 months, high and low, p =0.17). Poorly differentiated tumors were more likely to express high MRP4 levels ( p =0.06). High MRP4 expression was found in 59% of localized stages (0-II) and in 57% of advanced stages (III, IV and relapsed). Conclusions: High MRP4 expression is common in BTC, particularly gallbladder cancer, and could be a marker of poor prognosis. MRP4 levels appear more elevated in poorly differentiated tumors, and are similar in both, early and advanced stages, suggesting its involvement in early tumor progression. Further prospective studies are needed to confirm MRP4 as a biomarker. If MRP4 is a driver gene, targeting with inhibitors could represent a promising therapeutic strategy for these challenging tumors.

A psychologically interpretable artificial intelligence framework for the screening of loneliness, depression, and anxiety.

Negative emotions such as loneliness, depression, and anxiety (LDA) are prevalent and pose significant challenges to emotional well-being. Traditional methods of assessing LDA, reliant on questionnaires, often face limitations because of participants' inability or potential bias. This study introduces emoLDAnet, an artificial intelligence (AI)-driven psychological framework that leverages video-recorded conversations to detect negative emotions through the analysis of facial expressions and physiological signals. We recruited 50 participants to undergo questionnaires and interviews, with their responses recorded on video. The emoLDAnet employs a combination of deep learning (e.g., VGG11) and machine learning (e.g., decision trees [DTs]) to identify emotional states. The emoLDAnet incorporates the OCC-PAD-LDA psychological transformation model, enhancing the interpretability of AI decisions by translating facial expressions into psychologically meaningful data. Results indicate that emoLDAnet achieves high detection rates for loneliness, depression, and anxiety, with F1-scores exceeding 80% and Kendall's correlation coefficients above 0.5, demonstrating strong agreement with traditional scales. The study underscores the importance of the OCC-PAD-LDA model in improving screening accuracy and the significant impact of machine learning classifiers on the framework's performance. The emoLDAnet has the potential to support large-scale emotional well-being early screening and contribute to the advancement of mental health care.

Combination of Metabolomics and Bioinformatics to Reveal the Mechanism of Luteolin in the Treatment of Cervical Cancer.

The incidence of cervical cancer is high among women globally. The potential therapeutic efficacy of luteolin in the treatment of cervical cancer has been identified. Therefore, we aim to elucidate the mechanism of action of luteolin in the treatment of cervical cancer through a comprehensive approach that integrates metabolomics with bioinformatics. The first step involved the identification of differential metabolites through UHPLC-Q-Orbitrap-MS, which were then utilized for enrichment analysis of metabolic pathways and to determine the targets associated with these differential metabolites. Subsequently, the differential analysis and WGCNA were employed to identify DEGs and functional module genes respectively. The common targets were obtained by intersecting the results from the aforementioned three analyses, followed by conducting GO and KEGG pathway enrichment analysis on these targets. Subsequently, PPI networks were constructed using these common targets, and key targets were identified utilizing the MCC, EPC, Degree, Closeness Centrality, Betweenness Centrality, and Bottleneck algorithms in the CytoHubba plug-in. The subsequent steps involved the analysis of key genes for constructing a nomogram, conducting a ROC curve, examining content expression and survival analysis, and ultimately employing molecular docking to investigate the interaction between luteolin and crucial targets. The metabolomics analysis revealed the identification of a total of 45 distinct metabolites in this study, primarily associated with amino acid and nucleotide metabolism. The intersection of 773 differential metabolite targets, 3493 cervical cancer differential genes, and 3245 WGCNA-associated module genes yielded a set of 32 target genes associated with luteolin therapy for cervical cancer. The GO and KEGG pathway enrichment analysis also revealed that these targets were primarily associated with amino acid metabolism and nucleotide metabolism. The CytoHubba plug-in was utilized to identify three key genes (DMNT1, EZH2, and GMPS) through the application of multiple algorithms. Additionally, the datasets GSE63514, GSE67522, and GEPIA2 revealed a significant upregulation of all three genes in tumor tissue. ROC analysis demonstrated the good predictive ability of these three hub genes. Finally, the molecular docking results demonstrated the high binding affinity of luteolin towards DMNT1, EZH2, and GMPS. In conclusion, this study has unveiled the potential of luteolin in modulating amino acid and nucleotide metabolism for the treatment of cervical cancer, thereby providing a theoretical foundation for further investigation into the intricate association between luteolin and cervical cancer.

Immunosuppressive State May Lead to Brain Metastases in Lung Squamous Cell Carcinoma: Gene Expression and Immunohistochemical Analysis.

Brain metastases (BMs) are rare in lung squamous cell carcinoma (LUSC). Therefore, research on biomarkers or mechanisms that can be used to predict them is limited. To verify whether mRNA profiles can accurately predict BMs, we used a machine learning approach on 20 TNM-matched LUSC tissue samples. We conducted pathway and immunohistochemical analyses to investigate the underlying mechanisms of BM. A total of 15 mRNAs linked to BM were identified. The 15-mRNA signature was highly accurate in predicting BM, with an area under the curve and accuracy of 0.940 and 0.9, respectively. The pathway analysis revealed that immune-related pathways (leukocyte transendothelial migration, Fc gamma R-mediated phagocytosis, and natural killer cell-mediated cytotoxicity) were suppressed, suggesting that an immunosuppressive state may be involved in the development of BM. In the validation set confirmed by immunohistochemical staining, the BM group exhibited significantly lower levels of CD4+ T cells or CD8+ T cells than the group without BM. BM in patients with LUSC was associated with an immunosuppressive state. Immunotherapy may be effective in preventing BM in patients with LUSC.

Risk factors for relapse based on the molecular profiling of Japanese patients with stage II colorectal cancer.

215 Background: The association between the molecular profiles and prognosis of Stage II colorectal cancer (CRC) remains unclear. This study aimed to evaluate the long-term outcomes of Stage II CRC based on the molecular profiling and to examine the risk factors for relapse. Methods: We retrospectively enrolled Japanese patients with pStage II CRC without pre- and/or postoperative adjuvant therapy and whose surgically resected specimens were evaluated using gene expression and whole exome analyses from January 2014 to December 2018. We evaluated the 5-year overall survival (OS) and relapse-free survival (RFS), and examined the risk factors for RFS. Results: We evaluated 322 patients with pStage II CRC, including 126 (39.1%) with right colon cancer, 133 (41.3%) with left colon cancer and 63 (19.6%) with rectal cancer. There were 87 patients (27.0%) with pT4, 175 (54.3%) with venous invasion, 120 (37.3%) with lymphatic invasion, and 68 (21.1%) with perineural invasion. Whole exome analyses revealed that there were 48 patients (14.9%) with MSI-High, and the presence of mutations in key genes for colorectal cancer development was as follows: APC , 245 (76.1%); TP53 , 208 (64.6%); KRAS , 134 (6.5%); PIK3CA , 64 (19.9%); FBXW7 , 27 (8.4%); and BRAF , 21 (6.5%). The 5-year OS and RFS rates were 98.0% and 90.7%, respectively. According to the consensus molecular subtype (CMS) classification based on gene expression, 76 patients (23.6%) had CMS4 and a significantly lower RFS than the other patients (5-year RFS: 83.8% vs. 92.9%, p=0.017). The independent risk factors for RFS were perineural invasion (Hazard ratio [HR] 5.316, p&lt;0.001) and CMS4 (HR 2.399, p=0.020). Conclusions: Molecular profiling of Stage II CRC to assess the risk factors for relapse may contribute to the indication and drug selection for postoperative adjuvant chemotherapy and lead to personalized treatment to improve prognosis.

690 Differential gene expression and pathway analysis in eosinophillic and reflux esophagitis

690 Differential gene expression and pathway analysis in eosinophillic and reflux esophagitis

Expression, optimization and biological activity analysis of recombinant type III collagen in Komagataella phaffii.

Type III collagen, a fundamental constituent of the extracellular matrix (ECM), is extensively utilized across the biomedicine, tissue engineering, and cosmetic industries because of its exceptional biocompatibility and biodegradability. Despite its widespread application, traditional methods of collagen production are often hindered by the limit yield, potential immunogenicity, and batch-to-batch variability. In the present study, we describe a synthetic biological approach for expressing full-length recombinant type III collagen (RCIII) in the Komagataella phaffii system. Furthermore, the protein expression level was effectively increased by co-expression of the MPR1 gene, which improved the intrinsic antioxidant defenses of yeast cells, thereby reducing oxidative stress damage. The resulting RCIII maintains its native secondary structure and exhibits robust biological activities, including the promotion of platelet coagulation, enhancement of cell migration, and anti-inflammatory efficacy. Our findings suggest a viable pathway for large-scale, industrial production of type III collagen, offering a promising biomaterial for advanced biomedical applications, and contributing to the circular economy of the biomedical sector.

Exploring the anti‑inflammatory activity of boron compounds through the miR‑21/PTEN/AKT pathway in cecal ligation and puncture‑induced sepsis.

The present study investigated the impact of boric acid (BA) and borax (BX) on markers of inflammation and modifications in miR‑21/PTEN/AKT pathway genes in the liver and kidney tissues of Sprague Dawley male rats with sepsis induced by cecal ligation and puncture (CLP). A total of 60 male Sprague Dawley rats were randomly divided into 6 groups, each containing 10 animals as follows: Control, CLP (where the model was created), 20 mg/kg BX (CLP + BX1), 40 mg/kg BX (CLP + BX2), 20 mg/kg BA (CLP + BA1) and 40 mg/kg BA (CLP + BA2). Liver and kidney tissues were analyzed for histopathological changes, immunopositivity for tumor necrosis factor‑α, interleukin (IL)‑6 and IL‑10, and gene expression of microRNA‑21 (miR‑21), phosphatase and tensin homolog (PTEN) and AKT. Gene expression analysis in the liver tissues revealed a significant decrease in miR‑21, and a marked but not significant decrease in PTEN levels in the CLP group, while AKT expression was significantly increased in the CLP group, and was significantly decreased in CLP + BA1 group compared with in the CLP group. In the kidney tissues, miR‑21 levels were significantly decreased in the CLP group, but the CLP + BA2 group showed a significant increase compared with in the CLP group. These results suggest the potential therapeutic benefits of low‑dose BA and BX in ameliorating sepsis‑induced tissue damage, emphasizing the need for further exploration of their mechanisms of action.