Gene Expression Research Articles

CXCL12 is a potential therapeutic target for type 2 diabetes mellitus complicated by chronic obstructive pulmonary disease.

To identify the key genes and immunological pathways shared by type 2 diabetes mellitus (T2DM) and chronic obstructive pulmonary disease (COPD) and explore the potential therapeutic targets of T2DM complicated by COPD. GEO database was used for analyzing the gene expression profiles in T2DM and COPD to identify the common differentially expressed genes (DEGs) in the two diseases. A protein-protein interaction network was constructed to identify the candidate hub genes, which were validated in datasets and disease sets to obtain the target genes. The diagnostic accuracy of these target genes was assessed with ROC analysis, and their expression levels and association with pulmonary functions were investigated using clinical data and blood samples of patients with T2DM and COPD. The abundance of 22 immune cells was analyzed with CIBERSORT algorithm, and their relationship with the target genes was examined using correlation analysis. DGIdb database was used for analyzing the drug-gene interactions and the druggable genes followed by gene set enrichment analysis. We identified a total of 175 common DEGs in T2DM and COPD, mainly enriched in immune- and inflammation-related pathways. Among these genes, CXCL12 was identified as the final target gene, whose expression was elevated in both T2DM and COPD (P<0.05) and showed good diagnostic efficacy. Immune cell infiltration correlation analysis showed significant correlations of CXCL12 with various immune cells (P<0.01). GESA analysis showed that high CXCL12 expression was significantly correlated with "cytokine-cytokine receptor interaction". Drug-gene analysis showed that most of CXCL12-related drugs were not targeted drugs with significant cytotoxicity. CXCL12 is a potential common key pathogenic gene of COPD and T2DM, and small-molecule targeted drugs against CXCL12 can provide a new strategy for treatment T2DM complicated by COPD.

Drought Response in the Transcriptome and Ionome of Wild and Domesticated Lablab purpureus L. Sweet, an Underutilized Legume

ABSTRACTHunger remains a prevalent issue worldwide, and with a changing climate, it is expected to become an even greater problem that our food systems are not adapted to. There is therefore a need to investigate strategies to fortify our foods and food systems. Underutilized crops are farmed regionally, are often adapted to stresses, including droughts, and have great nutritional profiles, potentially being key for food security. One of these crops, Lablab purpureus L Sweet, or lablab, is a legume grown for humans or as fodder and shows remarkable drought tolerance. Understanding of lablab's molecular responses to drought and drought's effects on its nutritional qualities is limited and affects breeding potential. Using transcriptomics at three time points, changes in gene expression in response to drought were investigated in wild and domesticated lablab. The effect of drought on the elemental profile of lablab leaves was investigated using ionomics to assess drought's impact on nutritional quality. Differences in drought response between wild and domesticated lablab accessions were revealed, which were mainly due to differences in the expression of genes related to phosphorus metabolic response, cell wall organization, and cellular signaling. The leaves of wild and domesticated lablab accessions differed significantly in their elemental concentrations, with wild accessions having higher protein, zinc, and iron concentrations. Drought affected the concentration of some elements, with potential implications for the use of lablab under different environments. Overall, this study is an important first step in understanding drought response in lablab with implications for breeding and improvement of drought‐tolerant lablab.

Naturally russeted and wound russeted skins of mango (cv. ‘Apple’) show no differences in anatomy, chemical composition or gene expression

The mango cultivar ‘Apple’ is commercially important in Kenya but highly susceptible to russeting. Russeting refers to an area of fruit skin where the primary (epidermal) surface has been replaced by a secondary (peridermal) surface. The objective was to establish histologies, gene expressions and chemical compositions of a natural periderm, a wound-induced periderm and of cuticles of an un-russeted skin. Fluorescence microscopy revealed a suberized phellem in natural and wound-induced periderms. Wound-induced periderms had more cell layers and a higher mass than natural periderms. Compared with cuticles, periderms showed decreased expressions of cuticle-related genes (MiSHN1, MiGPAT6, MiCUS1, MiCER1, MiWCB11) and increased expressions of periderm-related genes (MiMYB93, MiNAC058, MiCYP86A1, MiCYP86B1, MiGPAT5, MiABCG20). Natural periderms and wound-induced periderms contained cutin and suberin monomers (C16-C28), including carboxylic, dicarboxylic, and ω-hydroxy acids and primary alcohols. Cuticles of the primary skin contained cutin monomers of similar chemistry but shorter chain lengths (C16-C22). The wax composition in natural and wound-induced periderms was similar to that in cuticles. Lignin monomers in natural and wound-induced periderms contained p-hydroxyphenyl, guaiacyl and syringyl units, but only traces of these occurred in cuticles. In ‘Apple’ mango, the histologies, gene expressions and compositions of natural and wound-induced periderms are largely the same.

Exogenous diethyl aminoethyl hexanoate alleviates the damage caused by low-temperature stress in Phaseolus vulgaris L. seedlings through photosynthetic and antioxidant systems

BackgroundPhaseolus vulgaris is a warm-season crop sensitive to low temperatures, which can adversely affect its growth, yield, and market value. Exogenous growth regulators, such as diethyl aminoethyl hexanoate (DA-6), have shown potential in alleviating stress caused by adverse environmental conditions. However, the effects that DA-6 has on P. vulgaris plants subjected to low-temperature stress are not well understood. This study aimed to investigate the impact DA-6 has on the growth, photosynthesis, antioxidant system, and gene expression in cold-tolerant (YJ009763) and cold-sensitive (Baibulao) P. vulgaris seedlings under low-temperature stress.ResultsTo simulate low-temperature stress, P. vulgaris seedlings were exposed to 5 °C, and 25 mg/L DA-6 solution applied to their leaves. This study revealed that DA-6 significantly enhanced the growth and photosynthetic performance of P. vulgaris seedlings under low-temperature stress. Specifically, DA-6 increased chlorophyll content and photosynthetic rates, reducing stomatal limitation and enhancing carbon assimilation. It also improved the photosynthetic efficiency by boosting electron transport in the reaction center. The antioxidant enzyme activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were markedly increased following DA-6 treatment. After 24 h of low-temperature stress, the cold-tolerant seedlings showed a 68.95% increase in POD activity, whereas the cold-sensitive seedlings displayed a 160.63% increase in SOD activity and an 85.56% increase in CAT activity. In addition, DA-6 significantly reduced the production rate of superoxide anion radical generation, with a 25.24% reduction in cold-tolerant seedlings and a 49.38% reduction in cold-sensitive seedlings. Under low-temperature stress, exogenous DA-6 could upregulate the relative expression of antioxidant enzyme-related genes, such as PvSOD and PvAPX. DA-6 also promoted the expression of key antioxidant genes, including PvMDHAR and PvDHAR2, which accelerated the ascorbate-glutathione cycle and mitigated oxidative stress.ConclusionExogenous application of DA-6 effectively alleviates low-temperature stress in P. vulgaris by enhancing photosynthetic capacity and regulating the antioxidant defense system. Cold-tolerant varieties exhibited a stronger response to DA-6, demonstrating a greater ability to withstand cold stress. These findings suggest that DA-6 treatment could serve as a promising approach for improving the resilience of P. vulgaris to low temperatures.

The Circadian Rhythm Regulates the Hepato-ovarian Axis Linking Polycystic Ovary Syndrome and Non-alcoholic Fatty Liver Disease.

This study aimed to identify shared gene expression related to circadian rhythm disruption in polycystic ovary syndrome (PCOS) and non-alcoholic fatty liver disease (NAFLD) to discover common diagnostic biomarkers. Visceral fat RNA samples were collected from 12 PCOS and 14 non-PCOS patients, a sample size representing the clinical situation and sufficient to capture PCOS gene expression profiles. Along with liver transcriptome profiles from NAFLD patients, these data were analyzed to identify crosstalk circadian rhythm-related genes (CRRGs) between the diseases. Single-sample and single-gene gene set enrichment analyses explored immune infiltration and pathways associated with CRRGs. Diagnostic biomarkers were identified using a random forest algorithm and validated through nomograms and a mouse model. Seven crosstalk CRRGs (FOS, ACHE, FOSB, EGR1, NR4A1, DUSP1, and EGR3) were associated with clinical features, immunoinflammatory microenvironment, and metabolic pathways in both diseases. EGR1, DUSP1, and NR4A1 were identified as diagnostic biomarkers, exhibiting robust diagnostic capacity (AUC = 0.7679 for PCOS, AUG = 0.9981 for NAFLD). Nomogram validation showed excellent calibration, and independent datasets confirmed their discriminatory ability (AUC = 0.6528 for PCOS, AUC = 0.8275 for NAFLD). Additionally, ceRNA networks and androgen receptor binding sites were identified, suggesting their regulatory roles. Mouse model validation confirmed significant downregulation of EGR1, DUSP1, and NR4A1 in liver tissues, consistent with sequencing data. This study identifies crosstalk CRRGs and diagnostic biomarkers shared between PCOS and NAFLD, highlighting their roles in immune and metabolic dysregulation. These biomarkers offer the potential for improving diagnosis and guiding targeted treatments for both diseases.

Aspergillus fumigatus is responsible for inflammation in a murine model of chronic obstructive pulmonary disease exacerbation

BackgroundIn patients with chronic obstructive pulmonary disease (COPD), a sensitization to A. fumigatus has been related to a decline in lung function, but the role of fungal agents in the disease pathogenesis remains unclear. The main purpose of the present study was to investigate whether cell inflammation could worsen after exposure to A. fumigatus spores in vitro and then, in mice, following chronic exposure to cigarette smoke mimicking COPD.MethodsThe inflammatory response to cigarette smoke alone or with A. fumigatus was investigated in cell culture models of murine macrophages and alveolar epithelial cells. In an animal model, mice were exposed daily to two cigarettes smoke over 14 weeks, and two intranasal instillations of 105 spores at weeks 7 and 14. Then, their lungs were recovered to perform inflammatory and histopathological analyses.ResultsIn co-cultures of macrophages and epithelial cells treated with both cigarette smoke extracts (CSE) and A. fumigatus compared to CSE alone there were significant inductions in TNF-α (6.2-fold) and CXCL-2 (21.5-fold) gene expression, confirmed by significant increases in the corresponding protein secretion. In the murine model, histological analyses of the lung after chronic smoke exposure showed an increase in airspace enlargement. Moreover, a Bio-Plex approach on bronchoalveolar lavage of cigarette smoke and A. fumigatus-treated mice showed significant increases in multiple inflammatory proteins secreted in the lung.ConclusionsThere was a stronger inflammatory response after cigarette smoke exposure with A. fumigatus compared to cigarette smoke alone. These findings were correlated with histopathological changes in the mouse lung in vivo.

Ion specificity of salt glands in zoysiagrass under different exposures to sodium and potassium

AbstractSalt glands are a notable feature on halophytic turfgrass species from the genus Zoysia. Plants were exposed to differing levels of NaCl and KCl to better understand the specificity of salt glands toward secreting specific ions. Plants were exposed to 75 mM NaCl:225 mM KCl, 150 mM NaCl:150 mM KCl, or 225 mM NaCl:75 mM KCl. Ion secretions were measured via leaf washes and compared to ion contents from whole leaf extractions. Salt glands secreted both potassium and sodium but secreted sodium at relatively greater proportions. Gene expression for several ion transporters including high‐affinity potassium transporter (HKT) and Na+/H+ antiporter (NHX) genes showed that gene expression is highly variable, and further work is needed to understand the regulation of salt gland activity. This study aims to better understand the specificity of zoysiagrass salt glands for specific ions, particularly under saline conditions, even when sodium is not the dominant ion.

Longitudinal association between DNA methylation and type 2 diabetes: findings from the KORA F4/FF4 study

BackgroundType 2 diabetes (T2D) has been linked to changes in DNA methylation levels, which can, in turn, alter transcriptional activity. However, most studies for epigenome-wide associations between T2D and DNA methylation comes from cross-sectional design. Few large-scale investigations have explored these associations longitudinally over multiple time-points.MethodsIn this longitudinal study, we examined data from the Cooperative Health Research in the Region of Augsburg (KORA) F4 and FF4 studies, conducted approximately seven years apart. Leucocyte DNA methylation was assessed using the Illumina EPIC and 450K arrays. Linear mixed-effects models were employed to identify significant associations between methylation sites and diabetes status, as well as with fasting plasma glucose (FPG), hemoglobin A1c (HbA1c), homoeostasis model assessment of beta cell function (HOMA-B), and homoeostasis model assessment of insulin resistance (HOMA-IR). Interaction effects between diabetes status and follow-up time were also examined. Additionally, we explored CpG sites associated with persistent prediabetes or T2D, as well as the progression from normal glucose tolerance (NGT) to prediabetes or T2D. Finally, we assessed the associations between the identified CpG sites and their corresponding gene expression levels.ResultsA total of 3,501 observations from 2,556 participants, with methylation measured at least once across two visits, were included in the analyses. We identified 64 sites associated with T2D including 15 novel sites as well as known associations like those with the thioredoxin-interacting protein (TXNIP) and ATP-binding cassette sub-family G member 1 (ABCG1) genes. Of these, eight CpG sites exhibited different rates of annual methylation change between the NGT and T2D groups, and seven CpG sites were linked to the progression from NGT to prediabetes or T2D, including those annotated to mannosidase alpha class 2a member 2 (MAN2A2) and carnitine palmitoyl transferase 1 A (CPT1A). Longitudinal analysis revealed significant associations between methylation and FPG at 128 sites, HbA1c at 41 sites, and HOMA-IR at 57 sites. Additionally, we identified 104 CpG-transcript pairs in whole blood, comprising 40 unique CpG sites and 96 unique gene transcripts.ConclusionsOur study identified novel differentially methylated loci linked to T2D as well as to changes in diabetes status through a longitudinal approach. We report CpG sites with different rates of annual methylation change and demonstrate that DNA methylation associated with T2D is linked to following transcriptional differences. These findings provide new insights into the molecular mechanisms of diabetes development.Graphical abstract

Exercise induces dynamic changes in intra-articular metabolism and inflammation associated with remodeling of the infrapatellar fat pad in mice

We hypothesized that daily exercise promotes joint health by upregulating anti-inflammatory mediators via adaptive molecular and metabolic changes in the infrapatellar fat pad (IFP). We tested this hypothesis by conducting time-resolved analyses between 1 and 14 days of voluntary wheel running exercise in C57BL/6J mice. IFP structure and cellularity were evaluated by histomorphology, picrosirius red collagen staining, and flow cytometry analysis of stromal vascular fraction cells. Joint inflammation and metabolism were evaluated by multiplex gene expression analysis of synovium-IFP tissue and synovial fluid metabolomics, respectively. Exercise transiently increased cytokine and chemokine gene expression in synovium-IFP tissue, resolving within the first 5 days of exercise. The acute inflammatory response was associated with decreased adipocyte size and elevated CD45+Gr1+ myeloid cells, increased collagen content, and oxidized phospholipids. Exercise acutely altered synovial fluid metabolites, characterized by increased amino acids, peptides, bile acids, sphingolipids, dicarboxylic acids, and straight medium chain fatty acids and decreased hydroxy fatty acids and diacylglycerols. Between 5 and 14 days of exercise, inflammation, collagen, and adipocyte size returned to pre-exercise levels, and CD206+ immuno-regulatory macrophages increased. Thus, although the onset of new daily exercise transiently induced synovium-IFP inflammation and altered tissue structure, sustained daily exercise promoted IFP homeostasis.

Enhancement of adipose stem cell quality via Cu‐MON: Transcriptome and bioinformatics analysis of normal and diabetic stem cells

AbstractTransplanted adipose stem cells (ASC) have a low survival rate in the body, and there are not many ASC that can be effectively used, which weakens their tissue repair function. Based on this status quo, a new type of copper‐based metal–organic network (Cu‐MON) was used to pretreat cells to regulate cell activity in order to improve the efficacy of cell therapy or reduce the number of cells used, thus reducing the cost of clinical treatment. Gene expression changes before and after Cu‐MON treatment of normal donor adipose stem cells (ND‐ASC) and type 2 diabetes mellitus adipose stem cells (T2DM‐ASC) were evaluated through RNA sequencing, KEGG and GO enrichment analysis. The results showed that Cu‐MON improved ASC cell quality by regulating immune response and promoting paracrine secretion. IL‐17 signaling pathway and IL‐6, CXCL8, and MMP‐9 were key pathways and necessary genes that affected the ability of stem cells. In addition, Cu‐MON also improved stem cell antiviral ability through Type I interferon signaling pathway. Our research showed that Cu‐MON had improved the cell quality of ASC by regulating immune response, promoting paracrine secretion, and improving antiviral capabilities. This approach to biomaterial pretreatment is fast, convenient, and relatively safe, and provides new strategies for improving the efficiency of cell therapies.

Nucleotide sequence variants, gene expression and serum profile of immune and antioxidant markers associated with brucellosis resistance/susceptibility in Shami goat

Brucellosis is a highly contagious zoonotic bacterial disease. It has considerable negative consequences on the animal production industry worldwide. The objective of this study was to investigate the genetic and molecular variations in Shami goat susceptible to Brucella infection. Blood samples were collected from fifty mature Shami goats (30 Brucella-infected does and 20 non-infection). DNA was extracted and selected parts the immunity; solute carrier family 11 member 1 (SLC11A1), toll-like receptor 1 (TLR1), toll-like receptor 9 (TLR9), SP110 nuclear body protein (SP110), the adenosine A3 receptor (ADORA3), caspase activating recruitment domain 15 (CARD15) and interferon regulatory factor 3 (IRF3), antioxidant glutathione peroxidase 1 (GPX1), nitric oxide synthase (NOS), NAD(P)H dehydrogenase [quinone] 1 (NQO1) and transcription factor NF-E2-related factor 2 (Nrf2) and erythritol related transketolase (TKT), ribose 5-phosphate isomerase (RPIA) and Adenosine monophosphate deaminase (AMPD) genes were sequenced. Likewise, the levels of gene expressions were investigated. The results identified polymorphic variants between healthy and infected does. Levels of gene expression of SLC11A1, TLR1, TLR9, SP110, ADORA3, CARD15, IRF3, HMOX1, TKT, RPIA and AMPD were significantly (P < 0.05) up regulated in the infected compared to the non-infected ones. On the other hand, GPX1, NOS, NQO1 and Nrf2 genes were significantly (P < 0.05) downregulated in the infected compared to the non-infected does. The results of serum profile indicated that there is a significant (P < 0.05) increase in the activities of AST, ALT, GGT, LDH, ALP as well as serum level of globulin, triglycerides, cholesterol, MDA, NO, IL-1β, TNF-α, IgM, IgG, haptoglobin and amyloid A. On the other hand, there were significant reductions in the glucose, total protein albumin, urea, calcium, inorganic phosphorus, sodium, copper, zinc, iron, TAC, GSH, SOD, GPx, IL-10 and fibrinogen in the infected compared to the non-infected does. Our results provide valuable information about the serum profile variations and putative genetic markers for Brucella infection in goats. This could be utilized in controlling goat brucellosis through selective breeding of natural resistant animals.

Analyzing the relationship between gene expression and phenotype in space-flown mice using a causal inference machine learning ensemble

Spaceflight has several detrimental effects on human and rodent health. For example, liver dysfunction is a common phenotype observed in space-flown rodents, and this dysfunction is partially reflected in transcriptomic changes. Studies linking transcriptomics with liver dysfunction rely on tools which exploit correlation, but these tools make no attempt to disambiguate true correlations from spurious ones. In this work, we use a machine learning ensemble of causal inference methods called the Causal Research and Inference Search Platform (CRISP) which was developed to predict causal features of a binary response variable from high-dimensional input. We used CRISP to identify genes robustly correlated with a lipid density phenotype using transcriptomic and histological data from the NASA Open Science Data Repository (OSDR). Our approach identified genes and molecular targets not predicted by previous traditional differential gene expression analyses. These genes are likely to play a pivotal role in the liver dysfunction observed in space-flown rodents, and this work opens the door to identifying novel countermeasures for space travel.

Life-history adaptation under climate warming magnifies the agricultural footprint of a cosmopolitan insect pest

Climate change is affecting population growth rates of ectothermic pests with potentially dire consequences for agriculture and global food security. However, current projection models of pest impact typically overlook the potential for rapid genetic adaptation, making current forecasts uncertain. Here, we predict how climate change adaptation in life-history traits of insect pests affects their growth rates and impact on agricultural yields by unifying thermodynamics with classic theory on resource acquisition and allocation trade-offs between foraging, reproduction, and maintenance. Our model predicts that warming temperatures will favour resource allocation towards maintenance coupled with increased resource acquisition through larval foraging, and the evolution of this life-history strategy results in both increased population growth rates and per capita host consumption, causing a double-blow on agricultural yields. We find support for these predictions by studying thermal adaptation in life-history traits and gene expression in the wide-spread insect pest, Callosobruchus maculatus; with 5 years of evolution under experimental warming causing an almost two-fold increase in its predicted agricultural footprint. These results show that pest adaptation can offset current projections of agricultural impact and emphasize the need for integrating a mechanistic understanding of life-history evolution into forecasts of pest impact under climate change.

TRPV4 as a Novel Regulator of Ferroptosis in Colon Adenocarcinoma: Implications for Prognosis and Therapeutic Targeting.

Colon adenocarcinoma (COAD) is a leading cause of cancer-related mortality worldwide. Transient receptor potential vanilloid 4 (TRPV4), a calcium-permeable non-selective cation channel, has been implicated in various cancers, including COAD. This study investigates the role of TRPV4 in colon adenocarcinoma and elucidates its potential mechanism via the ferroptosis pathway. Gene expression profiles and clinical data were obtained from The Cancer Genome Atlas (TCGA), encompassing 647 colon adenocarcinoma tissue samples and 51 normal colorectal tissue samples. Ferroptosis-related genes were retrieved from the FerrDb database. Differential expression analysis, survival analysis, and Cox proportional hazards regression were performed to assess the prognostic significance of TRPV4. Protein-protein interaction networks and gene enrichment analyses (GO and KEGG) were conducted to explore functional associations. In vitro experiments were carried out using HT-29 and SW480 colon cancer cell lines. TRPV4 was knocked down using siRNA, and cell viability was assessed via hematoxylin and eosin (HE) staining. Immunofluorescence assays evaluated the expression of ferroptosis-related proteins (SLC3A2, GPX4) and proliferation markers (KI67, SRC, CTNNB1, COL1). TRPV4 expression was significantly elevated in colon adenocarcinoma tissues compared to normal tissues (p < 0.05), demonstrating high diagnostic accuracy (AUC = 0.848). High TRPV4 expression correlated with poorer overall survival (OS) and disease-specific survival (DSS), particularly in patients over 65years old and those in clinical stage II. Cox regression analysis confirmed TRPV4 as an independent prognostic factor (HR = 1.395, p = 0.074). Bioinformatics analyses revealed that TRPV4 is closely associated with ferroptosis-related genes, participating in key biological processes such as responses to external stimuli, oxidative stress, and cell adhesion. In vitro, TRPV4 knockdown significantly reduced cell viability (p < 0.05) and decreased expression levels of SLC3A2, GPX4, KI67, SRC, and COL1 (p < 0.05). The addition of the ferroptosis inhibitor FER-1 did not restore cell viability in TRPV4 knockdown cells, suggesting that TRPV4 modulates cell survival through the ferroptosis pathway. The bioinformation and in vitro experiments inTRPV4 and ferroptosis-related genes support the hypothesis that TRPV4 influences tumor cell survival via the ferroptosis pathway. The inability of FER-1 to rescue viability in TRPV4-deficient cells further confirms this mechanism. These findings provide novel insights into the molecular mechanisms of COAD and highlight TRPV4 as a potential therapeutic target. TRPV4 is significantly upregulated in COAD and is associated with unfavorable patient outcomes. It appears to promote tumor progression by regulating the ferroptosis pathway, affecting the expression of key ferroptosis-related genes and proliferation markers. Targeting TRPV4 may offer a new therapeutic approach for COAD, and further research is warranted to explore its role in other cancers and to develop TRPV4-based therapies.

Development of Virus-Like Particles (VLPs) for Hepatitis C Virus genotype 4: a novel approach for vaccine development in Egypt

BackgroundEgypt has the highest global prevalence of Hepatitis C Virus (HCV) infection, particularly of genotype 4. The development of a prophylactic vaccine remains crucial for HCV eradication, yet no such vaccine currently exists due to the vaccine development challenges. The ability of Virus-Like Particles (VLPs) to mimic the native virus and incorporate neutralizing and conformational epitopes, while effectively engaging both humoral and cellular immune responses, makes them a promising approach to addressing the challenges in HCV vaccine development.MethodsLentiviral-based vectors were constructed and employed to integrate the full-length sequence of Core, E1, E2, and P7 genes of HCV genotype 4 into the genome of Human Embryonic Kidney cells (HEK293T). Upon the expression, HCV structural proteins can oligomerize and self-assemble into VLPs mimicking the structure of HCV native virus. VLPs were purified and characterized for the development of a potential VLPs-based vaccine.ResultsIn this study, mammalian cells were successfully engineered to stably express HCV structural proteins and generate non-infectious VLPs for HCV genotype 4. The expression of HCV-integrated genes resulted in a successful production of HCV structural proteins, which oligomerized and self-assembled into two layers enveloped VLPs. Electron microscopy analysis of purified VLPs revealed spherical particles with an average diameter of 60–65 nm, closely resembling mature HCV virions. These results highlighted the potential of these VLPs as a vaccine candidate for HCV genotype 4.ConclusionsHCV genotype 4 remains an underexplored target in vaccine development, despite its significant public health burden, especially in Egypt. The successful generation of VLPs for this genotype represents a promising avenue for further vaccine development. The established system provides a robust platform for the production and study of VLP-based vaccines targeting HCV genotype 4.

Expression and prognostic value of ferritinophagy-related NCOA4 gene in low-grade glioma: integration of bioinformatics and experimental validation

BackgroundLow-grade glioma (LGG) is a primary brain tumor with relatively low malignancy. NCOA4 is a key regulator of ferritinophagy-related processes and is involved in the occurrence and development of many cancers. However, the role of NCOA4 in LGG remains poorly understood.MethodsThis study comprehensively analyzed several mainstream bioinformatics databases to explore the expression, diagnostic efficacy, clinical pathological features, immune infiltration, prognostic value, and biological functions of NCOA4 in LGG. Immunohistochemistry experiments were conducted using LGG tissue samples collected from our hospital to validate the bioinformatics analysis results.ResultsNCOA4 expression was significantly elevated in LGG (p < 0.05), with an Area Under the Receiver Operating Characteristic Curve (AUC) of 0.973, suggesting it as a potential diagnostic marker. High NCOA4 expression was associated with younger age (21–40 years), lower malignancy (oligodendroglioma), and better prognosis (IDHmut-non-codel and IDHmut-codel subtypes) (all p < 0.05) in LGG. Kaplan-Meier survival curves from three databases showed that high NCOA4-expressing LGG patients had better prognosis (all p < 0.05). NCOA4 correlated weakly with B cells, CD8 + T cells, macrophages, and dendritic cells infiltration (all with correlation coefficients r < 0.3, and p < 0.05) in LGG. Multivariate Cox regression identified NCOA4, age, CD8 T cells, and macrophages as LGG independent prognostic factors (all p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that NCOA4’s primary function in LGG is related to autophagy processes (all p < 0.05).ConclusionOur findings suggest that NCOA4 could be a potential prognostic marker and therapeutic target in LGG.

Recombinant Expression of a New Antimicrobial Peptide Composed of hBD-3 and hBD-4 in Escherichia coli and Investigation of Its Activity Against Multidrug-Resistant Bacteria.

Human β-defensin (HBD) has been recognized as a promising antimicrobial agent due to its broad-spectrum antimicrobial activity against various pathogens. In our previous work, we engineered a chimeric human β-defensin, designated H4, by fusing human β-defensin 3 and human β-defensin 4, resulting in enhanced antimicrobial activity and salt stability. However, the high cost of chemical synthesis due to the relatively large number of amino acids in H4 has limited its applications. To reduce production costs, we aimed to develop an alternative method using a prokaryotic expression system. We first optimized the codon usage of the H4 gene for prokaryotic expression and then cloned it into the pET32a vector, incorporating thioredoxin and enterokinase cleavage sites to minimize toxicity in host cells. The resulting plasmid was transformed into E. coli BL21, yielding a fusion protein (TrxA-EK-H4). Correct cleavage of TrxA-EK-H4 required the addition of urea as a denaturant in the dialysis buffer. However, on-column enzymatic cleavage obviated the need for denaturants and yielded higher-purity rH4. The antibacterial activity of rH4 against multidrug-resistant Acinetobacter baumannii was comparable to that of chemically synthesized H4. This study demonstrates a valuable strategy for efficient purification of challenging proteins and has significant implications for future biotechnological applications.

Histone Deacetylation in Alzheimer's Diseases (AD); Hope or Hype.

Histone acetylation is the process by which histone acetyltransferases (HATs) add an acetyl group to the N-terminal lysine residues of histones, resulting in a more open chromatin structure. Histone acetylation tends to increase gene expression more than methylation does. In the central nervous system (CNS), histone acetylation is essential for controlling the expression of genes linked to cognition and learning. Histone deacetylases (HDACs), "writing" enzymes (HATs), and "reading" enzymes with bromodomains that identify and localize to acetylated lysine residues are responsible for maintaining histone acetylation. By giving animals HDAC inhibitors (HDACis), it is possible to intentionally control the ratios of "writer" and "eraser" activity, which will change the acetylation of histones. In addition to making the chromatin more accessible, these histone acetylation alterations re-allocate the targeting of "readers," including the transcriptional co-activators, cAMP response element-binding protein (CBP), and bromodomain-containing protein 4 (Brd4) in the CNS. Conclusive evidence has shown that HDACs slow down the progression of Alzheimer's disease (AD) by reducing the amount of histone acetylation, decreasing the activity of genes linked to memory, supporting cognitive decline and Amyloid beta (Aβ) protein accumulation, influencing aberrant tau phosphorylation, and promoting the emergence of neurofibrillary tangles (NFTs). In this review, we have covered the therapeutic targets and functions of HDACs that might be useful in treating AD.

Untargeted metabolomics and functional analyses reveal that the secondary metabolite quinic acid associates with Angelica sinensis flowering

Flowering is a critical step in the plant life cycle. Angelica sinensis (Oliv.) Diels is a medicinal crop whose root is a well-known herbal medicine used in Asia. Early flowering causes changes in secondary metabolic flow and results in the loss of medicinal quality. Based on untargeted metabolomics studies, quinic acid was identified as a metabolite present in significantly higher concentrations during the early-flowering stage in A. sinensis leaves. This metabolite was subsequently investigated as a potential marker for early bolting in A. sinensis under field conditions. Moreover, quinic acid was found to accelerate flowering in the model plant Arabidopsis thaliana. Importantly, the flowering time was delayed in the quinate dehydrogenase At mutant, and this delay was reversed by quinic acid. Quinic acid upregulated the expression of the GA20OX and GID1 receptors and downregulated the expression of the inhibitor DELLA, thereby affecting the levels of FT and LFY and accelerating plant flowering. Quinic acid also significantly changed the expression of genes such as LOX, JAZ1, MYC2 and MYC3 in the jasmonic acid pathway. The trends of GID1, DELLA (GAI) and LOX2 protein expression were essentially consistent with those at the transcription level. These results suggest that quinic acid may promote plant flowering primarily by regulating the expression of genes and proteins in the gibberellin and jasmonic acid pathways.

Neurobehavioral plasticity in the rodent gustatory system induced by regular consumption of a low-calorie sweetener during adolescence

Habitual consumption of low-calorie sweeteners (LCS) during juvenile-adolescence can lead to greater sugar intake later in life. Here, we investigated if exposure to the LCS Acesulfame Potassium (Ace-K) during this critical period of development reprograms the taste system in a way that would alter hedonic responding for common dietary compounds. Results revealed that early-life LCS intake not only enhanced the avidity for a caloric sugar (fructose) when rats were in a state of caloric need, it increased acceptance of a bitterant (quinine) in Ace-K-exposed rats tested when middle-aged. These behavior shifts, which endured months after the end of Ace-K exposure, were accompanied by widespread changes in the peripheral taste system. The anterior tongue had fewer fungiform taste papillae, and the circumvallate papillae had a reduced anterior to posterior span and diminished expression of genes involved in sweet reception, sweet and bitter intracellular signaling, fructose transport, and cellular progeneration in the Ace-K-exposed rats. Ace-K exposure also led to a significant reduction in dopamine-producing cells of the ventral tegmental area. The collective findings reveal that LCS intake early in life alters the taste-brain axis and the behavioral responsiveness to both positive and negative tastants that are important determinants of dietary preferences.