Significant Changes In Expression Research Articles

(059) Epigenetic Profiles of Men with Peyronie’s Disease

Abstract Introduction Peyronie’s Disease (PD) can significantly impact sexual function. A hereditary predisposition to PD suggests that genetic variants may exist, and gene expression may modulate the penetrance of the disease. Identification of changes in epigenetic or gene expression profiles would facilitate a deeper understanding of the disease and provide insight for more targeted therapies. Objective Our objective is to determine if predisposition to PD is correlated with epigenetic variations and/or gene expression changes, as indicated by DNA methylation assessment and RNA sequencing. Methods Penile tunica albuginea samples were obtained from men with PD undergoing penile prosthesis placement. Penile sample from these men were not from fibrotic plaques. Control samples were collected from men with erectile dysfunction (ED) without PD undergoing penile prosthesis placement. DNA methylation analyses were performed on homogenized penile tissue samples via an Illumina Human MethylationEPIC BeadChip v2 array. Using the minfi package in R, beta values were produced for all 936,990 CpG sites for each sample and SWAN normalization was applied. Differentially methylated regions (DMR) were found via USEQ with a threshold Wilcoxon FDR score of 40. Gene expression levels were examined in PD and ED samples via RNA-sequencing. Gene expression data was compared against epigenetic data to determine if any epigenetics changes identified affected gene expression profiles. Results A total of 24 tissue samples were collected: 12 ED and 12 PD. USEQ yielded 36 total DMRs with a FDR score of 40 or greater (p-value<0.0001). Of these 36 DMRs, a Stanford GREAT analysis revealed 60 total gene-region associations and five implicated biological processes: anterior/posterior pattern specification, chordate embryonic development, embryo development (ending in birth or egg hatching), somitogenesis, and pattern specification process. Furthermore, differential gene expression analysis identified 76 genes with significant expression changes between PD and ED groups, of which 17 genes were upregulated while 59 were downregulated. Long noncoding RNAs and the keratocan gene showed notable expression differences between PD and ED groups. GO enrichment analysis revealed significant terms related to DNA binding and protein binding. None of the differentially regulated genes overlapped with identified DMRs. Conclusions This study identified distinct gene expression and DNA methylation patterns between PD and ED groups, despite PD samples not being taken from plaque regions. Upregulated genes in PD included long noncoding RNAs and the keratocan gene, suggesting their involvement in disease pathogenesis. Long noncoding RNA overexpression may serve a regulatory function in gene expression or cell processes while overexpression of the keratocan gene may promote collagen accumulation and remodeling, leading to fibrous plaque formation in the affected area. Likewise, DMRs and their region-gene associations suggest a role in early embryonic development for pathogenesis. Although RNA-seq did not indicate any significant differentially expressed genes that matched with gene-region associations correlated with DMRs, the significance and quantity of DMRs between ED and PD sample groups is indicative of affected biological processes that manifest in distinct pathophysiologies. Further research is needed to investigate if differentially regulated genes exist in DMRs that exhibited changes but did not meet the criteria threshold for inclusion here. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: Paterna bio, Firmtech, Turtle health, Maximus, Carrot, Contraline, endo pharmaceuticals, inherent biosciences, techfields inc, macro trials, alto neurosciences, curebase, vivify medical.

Type I interferons, inflammation, and fatigue in a longitudinal RNA study of women with breast cancer

BackgroundFatigue is a common side effect of cancer and its treatment and is thought to be driven in part by activation of the proinflammatory cytokine network. However, the cellular and molecular underpinnings of cancer-related fatigue (CRF) have not been determined, nor have immune pathways beyond inflammation been carefully investigated. The goal of this study was to examine the association between CRF and activation of canonical proinflammatory gene regulation pathways and Type I interferon (IFN) signaling pathways in breast cancer patients during and after treatment. MethodsWomen diagnosed with early-stage breast cancer (n = 181) completed assessments before and after treatment with radiation and/or chemotherapy and at 6, 12, and 18-month post-treatment follow-ups. Assessments included self-reported fatigue (Multidimensional Fatigue Symptom Inventory – Short Form) and expression of pre-specified sets of Type I IFN and pro-inflammatory immune response genes determined from mRNA sequencing of PBMCs. Mixed effect linear models examined changes in fatigue and immune gene expression over time and tested the hypothesis that fatigue would be associated with increased expression of Type I IFN and inflammatory response genes. ResultsThere were significant changes in fatigue and immune gene expression across the assessment period; all measures increased from pre- to post-treatment but showed diverging patterns over the follow-up, with declines in fatigue and persistent elevations in Type I IFN and proinflammatory gene expression. In mixed effect linear models, expression of Type I IFN response genes was elevated in association with fatigue across the assessment period, from pre-treatment to 18-month follow-up. In contrast, pro-inflammatory gene expression was associated with fatigue only at 6, 12, and 18-month follow-ups. Analyses controlling for changes in leukocyte subsets continued to show a significant association between fatigue and Type I IFN gene expression but reduced the time-dependent association with pro-inflammatory gene expression to non-significant. ConclusionsResults revealed unexpected complexity in the immune underpinnings of CRF and identify a novel role for IFN signaling as a robust contributor to this symptom before, during, and after treatment. Pro-inflammatory gene expression emerged as a predictor of fatigue later in the cancer trajectory, and that effect was primarily accounted for by a concurrent increase in monocyte prevalence.

Transcriptome analysis in mouse skin after exposure to ultraviolet radiation from a canopy sunbed.

Exposure to ultraviolet radiation (UV-R), from both natural and artificial tanning, heightens the risk of skin cancer by inducing molecular changes in cells and tissues. Despite established transcriptional alterations at a molecular level due to UV-R exposure, uncertainties persist regarding UV radiation characterization and subsequent genomic changes. Our study aimed to mechanistically explore dose- and time-dependent gene expression changes, that may drive short-term (e.g., sunburn) and long-term actinic (e.g., skin cancer) consequences. Using C57BL/6N mouse skin, we analyzed transcriptomic expression following exposure to five erythemally weighted UV-R doses (0, 5, 10, 20, and 40 mJ/cm2) emitted by a UV-R tanning device. At 96 h post-exposure, 5 mJ/cm2 induced 116 statistically significant differentially expressed genes (DEGs) associated with structural changes from UV-R damage. The highest number of significant gene expression changes occurred at 6 and 48 h post-exposure in the 20 and 40 mJ/cm2 dose groups. Notably, at 40 mJ/cm2, 13 DEGs related to skin barrier homeostasis were consistently perturbed across all timepoints. UV-R exposure activated pathways involving oxidative stress, P53 signaling, inflammation, biotransformation, skin barrier maintenance, and innate immunity. This invivo study's transcriptional data offers mechanistic insights into both short-term and potential non-threshold-dependent long-term health effects of UV-R tanning.

Response of soil microbial glycoside hydrolase family 6 cellulolytic population to lignocellulosic biochar reveals biochar stability toward microbial degradation.

Biochar produced from lignocellulosic biomass offers an opportunity to recycle waste into a valuable soil amendment. The application of biochar has been proposed to mitigate climate change by sequestering carbon in the soil. However, the field impact of biochar treatment on the cellulolytic microbial populations involved in the earlier steps of cellulose degradation is poorly understood. A field trial spanning three consecutive crop cycles of Zea mays was conducted in a degraded tropical Ultisol of Peninsular Malaysia. The soil was amended with two contrasting biochar made from oil palm kernel shells (pyrolyzed at 400°C) and rice husks (gasified at 800°C) with or without fertilizer supplementation. Soil samples were taken at each harvesting stage and analyzed for total organic carbon, labile active organic carbon, total cellulase, and β-glucosidase. Microbial glycoside hydrolase family 6 (GH6) cellulase genes and transcripts, involved in the early steps of cellulose degradation, were quantified from the extracted soil deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), respectively. Total organic carbon, labile active organic carbon, and β-glucosidase activity were significantly increased, while no effect on total cellulase activity was found. Both biochars stimulated the total population (DNA-derived) abundance of soil microorganisms harboring the GH6 cellulase genes. The biochar amendment did not affect the active population (RNA-derived) of the GH6 cellulolytic community, showing no significant changes in transcript expression. This indirectly corroborates the role of biochar as a potential carbon sequester in the soil.

Degrees of macrophage-facilitated healing in aneurysm occlusion devices.

Insufficient healing of aneurysms following treatment with vascular occlusion devices put patients at severe risk of fatal rupture. Therefore, promoting healing and not just occlusion is vital to enhance aneurysm healing. Following occlusion device implantation, healing is primarily orchestrated by macrophage immune cells, ending with fibroblasts depositing collagen to stabilize the aneurysm neck and dome, preventing rupture. Several modified occlusion devices are available currently on-market. Previous in vivo work demonstrated that modifications of occlusion devices with a shape memory polymer foam had enhanced aneurysm healing outcomes. To better understand cellular response to occlusion devices and improve aneurysm occlusion device design variables, we developed an in vitro assay to isolate prominent interactions between devices and key healing players: macrophages and fibroblasts. We used THP-1 monocyte derived macrophages and human dermal fibroblasts in our cell culture models. Macrophages were allowed device contact with on-market competitor aneurysm occlusion devices for up to 96 h, to allow for any spontaneous device-driven macrophage activation. Macrophage secreted factors were captured in the culture media, in response to device-specific activation. Fibroblasts were then exposed to device-conditioned macrophage media (with secreted factors alone), to determine if there were any device-induced changes in collagen secretion. Our in vitro studies were designed to test the direct effect of devices on macrophage activation, and the indirect effect of devices on collagen secretion by fibroblasts to promote aneurysm healing and stabilization. Over 96 h, macrophages displayed significant migration toward and interaction with all tested devices. As compared to other devices, shape memory polymer foams (SMM, Shape Memory Medical) induced significant changes in gene expression indicating a shift toward an anti-inflammatory pro-healing M2-like phenotype. Similarly, macrophages in contact with SMM devices secreted more vascular endothelial growth factor (VEGF) compared with other devices. Macrophage conditioned media from SMM-contacted macrophages actively promoted fibroblast secretion of collagen, comparable to amounts observed with exogenous stimulation via VEGF supplementation. Our data indicate that SMM devices may promote good aneurysm healing outcomes, because collagen production is an essential step to ultimately stabilize an aneurysm.

Molecular Analysis of Pseudomonas aeruginosa Isolates with Mutant gyrA Gene and Development of a New Ciprofloxacin Derivative for Antimicrobial Therapy.

This study focuses on the prevalence of Pseudomonas aeruginosa in various medical specimens. In addition, the investigates of this research shows the genetic analysis of pathogen-resistant isolates and chemical modifications to ciprofloxacin. A total of 225 specimens from men and women aged 30 to 60 were carefully collected and examined, including samples from wound, burn, urine, sputum, and ear samples. The data were obtained from AL Muthanna hospitals. PCR-RFLP and gene expression analysis were used to identify resistant strains and explore the genetic basis of antibiotic resistance. A ciprofloxacin derivative was synthesized and confirmed through FT-IR, 1H-NMR, and mass spectroscopy techniques then it was tested as antibacterial agent. Also, molecular docking study was conducted to predict the mechanism of action for the synthesized derivative. The results demonstrated that wound samples had the highest positive rate (33.7%) of P. aeruginosa isolates. The PCR-RFLP testing correlated ciprofloxacin resistance with gyrA gene mutation. Gene expression analysis revealed significant changes in the gyrA gene expression in comparison to the reference rpsL gene subsequent to exposure to the synthesized derivative. Furthermore, the molecular docking investigation illustrated the strategic positioning of the ciprofloxacin derivative within the DNA-binding site of the gyrA enzyme. The examination of genetic expression patterns manifested diverse effects attributed to the CIP derivative on P. aeruginosa, thus portraying it as a viable candidate in the quest for the development of novel antimicrobial agents. Ciprofloxacin derivative may offer new antimicrobial therapeutic options for treating Pseudomonas aeruginosa infections in wound specimens, addressing resistance and gyrA gene mutations.

Mutation of conserved histidine residues of dengue virus envelope protein impairs viral like particle maturation and secretion

Dengue virus (DENV) envelope protein plays crucial role in virus entry and maturation of virus during infection. Maturation of DENV occurs in the trans Golgi network at slightly acidic pH which is close to pKa of histidine. When exposed to the acidic environment of the late secretory pathway, dengue virus particles go through a significant conformational change, whereby interactions of structural proteins envelope (E) and prM proteins are reorganised and enable furin protease to cleave prM resulting in mature virus. In order to study the role of histidine of E protein in DENV maturation, we mutated 7 conserved histidine residues of envelope protein and assessed the percent of budding using viral like particle (VLP) system. Histidine mutants; H144A, H244A, H261A and H282A severely disrupted VLP formation without any significant change in expression in cell and its oligomerization ability. Treatment with acidotropic amine reversed the defect for all 4 mutants suggesting that these histidines could be involved in maturation and release. Over expression of capsid protein slightly enhanced VLP release of H244A and H261A. Similarly, furin over expression increased VLP release of these mutants. Co-immunoprecipitation studies revealed that prM and E interaction is lost for H244A, H261A and H282A mutants at acidic pH but not at neutral pH indicating that they could be involved in histidine switch during maturation at acidic pH. Detailed analysis of the mutants could provide novel insights on the interplay of envelop protein during maturation and aid in target for drug development.

E3 Ubiquitin Ligase Uhrf2 Knockout Reveals a Critical Role in Social Behavior and Synaptic Plasticity in the Hippocampus.

The hippocampal formation, particularly the CA2 subregion, is critical for social memory formation and memory processing, relying on synaptic plasticity-a fundamental mechanism by which synapses strengthen. Given the role of the ubiquitin-proteasome system (UPS) in various nervous system processes, including learning and memory, we were particularly interested in exploring the involvement of RING-type ubiquitin E3 ligases, such as UHRF2 (NIRF), in social behavior and synaptic plasticity. Our results revealed altered social behavior in mice with systemic Uhrf2 knockout, including changes in nest building, tube dominance, and the three-chamber social novelty test. In Uhrf2 knockout mice, the entorhinal cortex-CA2 circuit showed significant reductions in synaptic plasticity during paired-pulse facilitation and long-term potentiation, while the inability to evoke synaptic plasticity in the Schaffer-collateral CA2 synapses remained unaffected. These changes in synaptic plasticity correlated with significant changes in gene expression including genes related to vesicle trafficking and transcriptional regulation. The effects of Uhrf2 knockout on synaptic plasticity and the observed gene expression changes highlight UHRF2 as a regulator of learning and memory processes at both the cellular and systemic levels. Targeting E3 ubiquitin ligases, such as UHRF2, may hold therapeutic potential for memory-related disorders, warranting further investigation.

Comparative proteomics reveals different protein expression in platelets in patients with alcoholic liver cirrhosis

BackgroundThe role of platelets in disease progression as well as the function of platelets as part of the haemostatic and immunological system in patients with liver cirrhosis is only incompletely understood. This is partly due to difficulties in assessing platelet function. Proteome analyses of platelets have been used to further investigate the role of platelets in other diseases.AimTo assess possible changes in the platelet proteome during different stages of alcohol induced liver cirrhosis compared to healthy donors.Patients and methodsA 45 ml blood sample was drawn from 18 participants aged 18–80 years evenly divided into three groups of healthy donors, patients with less advanced alcohol induced liver cirrhosis (Child-Pugh < 7) and patients with advanced liver cirrhosis (Child-Pugh > 10). The blood was processed to isolate platelets and perform subsequent two-dimensional gel-electrophoresis using a SYPRO™ Ruby dye. After computational analysation significantly in- or decreased protein spots (defined as a two-fold abundance change between different study cohorts and ANOVA < 0.05) were identified via liquid chromatography–mass spectrometry (LCMS) and searching against human protein databases.ResultsThe comparative analysis identified four platelet proteins with progressively decreased protein expression in patients with liver cirrhosis. More specifically Ras-related protein Rab-7a (Rab-7a), Ran-specific binding protein 1 (RANBP1), Rho GDP-dissociation inhibitor 1 (RhoGDI1), and 14–3-3 gamma.ConclusionThere is significant change in protein expression in the platelet proteome throughout the disease progression of alcohol induced liver cirrhosis. The identified proteins are possibly involved in haemostatic and immunoregulatory function of platelets.

Transcriptome analysis reveals the molecular mechanisms of rubber biosynthesis and laticifer differentiation during rubber seed germination.

The molecular mechanisms underlying the initiation of natural rubber synthesis and laticifer differentiation have not been fully elucidated. In this study, we conducted a time-series transcriptome analysis of five rubber tree tissues at four stages of seed germination. A total of 161,199 DEGs were identified between the two groups, including most 16,673 DEGs (A3 vs B3 and A3 vs C3) and lest 1,210 DEGs (C2 vs D2). We found that the maturation of the seed is accompanied by the formation of laticifer cells in cotyledon. Meanwhile, the analysis of hormones related genes expression may provide effective clues for us to promote the differentiation of laticifer cells in seeds by hormones in the future. In this study, hormone-related gene enrichment analyses revealed that IAA, GA, and CTK were activated in laticifer containing tissues. Similarly, GO and GEGG analysis showed that hormone pathways, especially the auxin pathway, are enriched. Gene expression clustering was analyzed using the short time-series expression miner (STEM), and the analysis revealed four distinct trends in the gene expression profiles. Moreover, we enriched transcription factor (TF) enrichment in cotyledon and embryonic axis tissues, and the MYB type exhibited the most significant difference. Furthermore, our findings revealed that genes related to rubber synthesis exhibited tissue-specific expression patterns during seed germination. Notably, key genes associated with rubber biosynthesis, specifically small rubber particle protein (SRPP) and cis-prenyltransferase (CPT), exhibited significant changes in expression in cotyledon and embryonic axis tissues, suggesting synchronous rubber synthesis with seed germination. Our staining results reveled that laticifer cells were exits in the cotyledon before seed imbibition stage. In conclusion, these results lay the foundation for exploring the molecular mechanisms underlying laticifer differentiation and rubber synthesis during seed germination, deepening our understanding of the initiation stages of rubber biosynthesis and laticifer differentiation.

P078 Inflammatory transcriptomic signatures and cell type compositions in colonic mucosa of ulcerative colitis

Abstract Background Previous studies have explored transcriptomic profiles associated with active inflammation in patients with IBD patients, but consistent characteristics of gene expression and enriched pathways, particularly in Asian patients with UC, remain unconfirmed. Here, we aimed to assess distinctive transcriptomic changes associated with persistent active mucosal inflammation in Asian patients with UC despite of medical treatment. Methods We obtained colonic mucosa biopsies of inflamed and noninflamed tissue from 15 patients with UC and 15 healthy controls and performed RNA sequencing analysis. Utilizing publicly available single cell RNA sequencing (scRNAseq) data, we also identified cell types expressing differentially expressed genes from RNAseq data and performed data deconvolution using CIBERSORTx. Results Transcriptomics profiling revealed that the inflammatory transcriptomic signature was highly enriched in the colonic mucosa of UC-active compared to UC-inactive and controls. By incorporating scRNAseq data, the genes upregulated in UC-active were highly expressed in M cells, inflammatory monocytes, and inflammatory fibroblasts, while downregulated genes were prominent in BEST4+ enterocytes and WNT5B+ fibroblasts. Notably, a sub-cluster of enterocytes associated with SAA1, SLC6A14, and DUOXA2 genes exhibited high expression in UC-active. Deconvolution analysis using CIBERSORTx identified significant enrichment of natural killer cells, inflammatory monocytes, Tuft cells, inflammatory fibroblast, WNT2B+Fos-lo1, and pericytes in UC-active. Conclusion Our RNAseq analysis not only identified significant gene expression changes but also revealed shifts in cell type proportions associated with persistent inflammation. These findings offer valuable insights for developing novel treatment strategies for UC.

Effects of Alkalinity Exposure on Antioxidant Status, Metabolic Function, and Immune Response in the Hepatopancreas of Macrobrachium nipponense.

The oriental river prawn Macrobrachium nipponense is an important freshwater economic species in China, producing huge economic benefits. However, M. nipponense shows lower alkali tolerance than fish species, thus genetic selection is urgently needed in order to improve alkali tolerance in this species. In the present study, the effects of alkalinity exposure on the hepatopancreas of M. nipponense were measured under the alkali concentrations of 0 (control), 4, 8, and 12 mmol/L with the exposure time of 96 h through histological observations, measurement of antioxidant enzymes, metabolic profiling analysis, and transcriptome profiling analysis. The present study identified that the low concentration of alkali treatment (<4 mmol/L) did not result in morphological changes in the hepatopancreas and activity changes in antioxidant enzymes, while high-alkali treatment (>8 mmol/L) damaged the normal structures of the lumen and vacuoles and significantly stimulated the levels of superoxide dismutase, catalase, and total antioxidant capacity, indicating these antioxidant enzymes play essential roles in the protection of the body from the damage caused by the alkali treatment. Metabolic profiling analysis revealed that the main enriched metabolic pathways of differentially expressed metabolites in the present study were consistent with the metabolic pathways caused by environmental stress in plants and other aquatic animals. Transcriptome profiling analysis revealed that the alkali concentration of <8 mmol/L did not lead to significant changes in gene expression. The main enriched metabolic pathways were selected from the comparison between 0 mmol/L vs. 12 mmol/L, and some significantly up-regulated genes were selected from these metabolic pathways, predicting these selected metabolic pathways and genes are involved in the adaptation to alkali treatment in M. nipponense. The expressions of Ras-like GTP-binding protein, Doublesex and mab-3 related transcription factor 1a, and Hypothetical protein JAY84 are sensitive to changes in alkali concentrations, suggesting these three genes participated in the process of alkali adaptation in M. nipponense. The present study identified the effects of alkalinity exposure on the hepatopancreas of M. nipponense, including the changes in antioxidant status and the expressions of metabolites and genes, contributing to further studies of alkali tolerance in this species.

MicroRNA-194 regulates parasitic load and IL-1β-dependent nitric oxide production in the peripheral blood mononuclear cells of dogs with leishmaniasis.

Domestic dogs are the primary urban reservoirs of Leishmania infantum, the causative agent of visceral leishmaniasis. In Canine Leishmaniasis (CanL), modulation of the host's immune response may be associated with the expression of small non-coding RNAs called microRNA (miR). miR-194 expression increases in peripheral blood mononuclear cells (PBMCs) of dogs with leishmaniasis with a positive correlation with the parasite load and in silico analysis demonstrated that the TRAF6 gene is the target of miR-194 in PBMCs from diseased dogs. Here, we isolated PBMCs from 5 healthy dogs and 28 dogs with leishmaniasis, naturally infected with L. infantum. To confirm changes in miR-194 and TRAF6 expression, basal expression of miR-194 and gene expression of TRAF6 was measured using qPCR. PBMCs from healthy dogs and dogs with leishmaniasis were transfected with miR-194 scramble, mimic, and inhibitor and cultured at 37° C, 5% CO2 for 48 hours. The expression of possible targets was measured: iNOS, NO, T-bet, GATA3, and FoxP3 were measured using flow cytometry; the production of cytokines IL-1β, IL-4, IL-6, IL-10, TNF-α, IFN-γ, and TGF-β in cell culture supernatants was measured using capture enzyme-linked immunosorbent assays (ELISA). Parasite load was measured using cytometry and qPCR. Functional assays followed by miR-194 inhibitor and IL-1β blockade and assessment of NO production were also performed. Basal miR-194 expression was increased in PBMC from dogs with Leishmaniasis and was negatively correlated with TRAF6 expression. The mimic of miR-194 promoted an increase in parasite load. There were no significant changes in T-bet, GATA3, or FoxP3 expression with miR-194 enhancement or inhibition. Inhibition of miR-194 increased IL-1β and NO in PBMCs from diseased dogs, and blockade of IL-1β following miR-194 inhibition decreased NO levels. These findings suggest that miR-194 is upregulated in PBMCs from dogs with leishmaniasis and increases parasite load, possibly decreasing NO production via IL-1β. These results increase our understanding of the mechanisms of evasion of the immune response by the parasite and the identification of possible therapeutic targets.

Abscisic Acid Affects Phenolic Acid Content to Increase Tolerance to UV-B Stress in Rhododendron chrysanthum Pall.

The presence of the ozone hole increases the amount of UV radiation reaching a plant's surface, and UV-B radiation is an abiotic stress capable of affecting plant growth. Rhododendron chrysanthum Pall. (R. chrysanthum) grows in alpine regions, where strong UV-B radiation is present, and has been able to adapt to strong UV-B radiation over a long period of evolution. We investigated the response of R. chrysanthum leaves to UV-B radiation using widely targeted metabolomics and transcriptomics. Although phytohormones have been studied for many years in plant growth and development and adaptation to environmental stresses, this paper is innovative in terms of the species studied and the methods used. Using unique species and the latest research methods, this paper was able to add information to this topic for the species R. chrysanthum. We treated R. chrysanthum grown in a simulated alpine environment, with group M receiving no UV-B radiation and groups N and Q (externally applied abscisic acid treatment) receiving UV-B radiation for 2 days (8 h per day). The results of the MN group showed significant changes in phenolic acid accumulation and differential expression of genes related to phenolic acid synthesis in leaves of R. chrysanthum after UV-B radiation. We combined transcriptomics and metabolomics data to map the metabolic regulatory network of phenolic acids under UV-B stress in order to investigate the response of such secondary metabolites to stress. L-phenylalanine, L-tyrosine and phenylpyruvic acid contents in R. chrysanthum were significantly increased after UV-B radiation. Simultaneously, the levels of 3-hydroxyphenylacetic acid, 2-phenylethanol, anthranilate, 2-hydroxycinnamic acid, 3-hydroxycinnamic acid, α-hydroxycinnamic acid and 2-hydroxy-3-phenylpropanoic acid in this pathway were elevated in response to UV-B stress. In contrast, the study in the NQ group found that externally applied abscisic acid (ABA) in R. chrysanthum had greater tolerance to UV-B radiation, and phenolic acid accumulation under the influence of ABA also showed greater differences. The contents of 2-phenylethanol, 1-o-p-coumaroyl-β-d-glucose, 2-hydroxy-3-phenylpropanoic acid, 3-(4-hydroxyphenyl)-propionic acid and 3-o-feruloylquinic ac-id-o-glucoside were significantly elevated in R. chrysanthum after external application of ABA to protect against UV-B stress. Taken together, these studies of the three groups indicated that ABA can influence phenolic acid production to promote the response of R. chrysanthum to UV-B stress, which provided a theoretical reference for the study of its complex molecular regulatory mechanism.

Transcriptomic evaluation of N6-methyladenosine modification can be used to identify differentially gene and immune-related biological processes in TX mice with liver fibrosis.

N6-methyladenosine (m6A) modification controls the stability, splicing, and translation of mRNA, which is important in the development of illnesses. Wilson's disease (WD) is an autosomal recessive liver copper metabolic disorder that causes liver fibrosis. The role of m6A methylation in WD-induced liver fibrosis development is still unclear. Thus, the goal of this study was to examine the scope of m6A methylation and further explore the potential targets related to WD-induced liver fibrosis. A total of 1930 significantly different m6A peaks were found on 1737 mRNAs, of which 993 were hypermethylated and 744 were hypomethylated when comparing normal and WD-induced liver fibrosis mice (n = 3). In parallel, 1261 differentially expressed mRNAs, comprising 557 upregulated and 704 downregulated mRNAs, were found. Overall, 114 mRNAs with significant changes in m6A levels and RNA expression were identified via joint analysis. Then, through PPI network construction and functional enrichment analysis, 12 hub genes were identified, these genes were mainly enriched in the inflammatory response and immunomodulation, and they are associated with immune cell infiltration. The significant difference in the amount of mRNA m6A modifications indicates that m6A modification is involved in the progression of WD-induced liver fibrosis, and theidentified hub genes are involved in inflammation and immune infiltration. These results may provide insights for subsequent studies on potential regulatory mechanisms.

Hyperuricemia Induces Reproductive Damage in Male Rats through Zinc Homeostasis Imbalance and Oxidative Stress

Studies have reported the adverse effects of hyperuricemia on male reproduction, but the mechanism is still unclear. The purpose of this study is to explore the mechanism of hyperuricemia on reproductive system damage in male rats. The rats were divided into a control group and a model group. Rats were given hypoxanthine and potassium oxonate dissolved in 0.5% (w/v) sodium carboxymethyl cellulose solution to induce the hyperuricemia (HUA) model. After 6 weeks, the blood, testis, and epididymis tissues of the anesthetized rats were collected for further experiments and analysis. Compared with the control rats, the serum uric acid of HUA rats was significantly increased, and the serum testosterone, sperm count, and motility were significantly decreased. The protein expression of testosterone-related molecules CYP11A1, 3β-HSD, and StAR was downregulated in the testis of HUA rats. The protein expression of blood–testis barrier (BTB) related molecules ZO-1 and Connexin43 was downregulated in the testis of HUA rats. Compared with the control group, the zinc content and zinc-containing enzymes (ALP and LDH) were decreased, and the mRNA and protein expression of zinc transporters (ZnT4 and ZIP7) were downregulated in the testis of HUA rats. Furthermore, the level of MDA increased and the activities of CAT, GSH-PX, and SOD decreased in the testicular tissue of HUA rats. The PI3K/AKT/mTOR pathway in the testis of HUA rats was activated. However, there was no significant change in the protein expression of autophagy associated molecules LC3, Beclin1, and ATG5 in the testis of HUA rats. Thus, the conclusion is that hyperuricemia can lead to the destruction of BTB, impaired testosterone synthesis, and decreased sperm count and motility in male rats, mainly by inducing zinc homeostasis imbalance and oxidative stress, rather than autophagy.

Spatial Transcriptomic Profiling of Tetraspanins in Stage 4 Colon Cancer from Primary Tumor and Liver Metastasis.

Stage 4 colon cancer (CC) presents a significant global health challenge due to its poor prognosis and limited treatment options. Tetraspanins, the transmembrane proteins involved in crucial cancer processes, have recently gained attention as diagnostic markers and therapeutic targets. However, their spatial expression and potential roles in stage 4 CC tissues remain unknown. Using the GeoMx digital spatial profiler, we profiled all 33 human tetraspanin genes in 48 areas within stage 4 CC tissues, segmented into immune, fibroblast, and tumor compartments. Our results unveiled diverse gene expression patterns across different primary tumor sub-regions. CD53 exhibited distinct overexpression in the immune compartment, hinting at a potential role in immune modulation. TSPAN9 was specifically overexpressed in the fibroblast compartment, suggesting involvement in tumor invasion and metastasis. CD9, CD151, TSPAN1, TSPAN3, TSPAN8, and TSPAN13 displayed specific overexpression in the tumor compartment, indicating potential roles in tumor growth. Furthermore, our differential analysis revealed significant spatial changes in tetraspanin expression between patient-matched stage 4 primary CC and metastatic liver tissues. These findings provide spatially resolved insights into the expression and potential roles of tetraspanins in stage 4 CC progression, proposing their utility as diagnostic markers and therapeutic targets. Understanding this landscape is beneficial for tailoring therapeutic strategies to specific sub-tumor regions in the context of stage 4 CC and liver metastasis.

Reduced surface pH and upregulated AE2 anion exchange in SLC26A3-deleted polarized intestinal epithelial cells.

Loss of function mutations in the SLC26A3 gene cause chloride-losing diarrhea in mice and humans. Although systemic adaptive changes have been documented in these patients and in the corresponding knockout mice, how colonic enterocytes adapt to loss of this highly expressed and highly regulated luminal membrane anion exchanger remains unclear. To address this question, SLC26A3 was deleted in the self-differentiating Caco2BBe colonic cell line by the CRISPR/Cas9 technique. We selected a clone with loss of SLC26A3 protein expression and morphological features indistinguishable from those of the native cell line. Neither growth curves nor development of transepithelial electrical resistance (TEER) differed between wild-type (WT) and SLC26A3 knockout (KO) cells. Real-time qPCR and Western analysis in SLC26A3-KO cells revealed an increase in AE2 expression without significant change in NHE3 expression or localization. Steady-state pHi and apical and basolateral Cl-/HCO3- exchange activities were assessed fluorometrically in a dual perfusion chamber with independent perfusion of luminal and serosal baths. Apical Cl-/HCO3- exchange rates were strongly reduced in SLC26A3-KO cells, accompanied by a surface pH more acidic than that of WT cells. Steady-state pHi was not significantly different from that of WT cells, but basolateral Cl-/HCO3- exchange rates were higher in SLC26A3-KO than in WT cells. The data show that CRISPR/Cas9-mediated SLC26A3 deletion strongly reduced apical Cl-/HCO3- exchange rate and apical surface pH, but sustained a normal steady-state pHi due to increased expression and function of basolateral AE2. The low apical surface pH resulted in functional inhibition of NHE-mediated fluid absorption despite normal expression of NHE3 polypeptide.NEW & NOTEWORTHY SLC26A3 gene mutations cause chloride-losing diarrhea. To understand how colonic enterocytes adapt, SLC26A3 was deleted in Caco2BBe cells using CRISPR/Cas9. In comparison to the wild-type cells, SLC26A3 knockout cells showed similar growth and transepithelial resistance but substantially reduced apical Cl-/HCO3- exchange rates, and an acidic surface pH. Steady-state intracellular pH was comparable between the WT and KO cells due to increased basolateral AE2 expression and function.

The effect of emulsifier type and oil inclusion on stress-related gene expression of Salmonella typhimurium in oil-in-water emulsion.

Salmonella has been associated with numerous outbreaks from contaminated food products, including emulsions. Emulsions are influenced by emulsifier type and oil presence, which can have varying degrees of stress or protection on bacteria. Although our previous research has shown that emulsifier solutions, rather than emulsions, provide a protective effect on Salmonella typhimurium after thermal treatment, the underlying mechanism remains unclear. This study selected S. typhimurium as the model microorganism and utilized the same emulsifiers (Tween 20, Tween 80, Triton X-100) to create emulsifier solutions and emulsions with the same oil fraction (60% (v/v)) to examine their effect on the expression of nine selected genes (rpoE, rpoH, otsB, proV, fadA, fabA, dnaK, ibpA, ompC) associated with stress response. Specifically, the study observed variations in gene expression under normal and thermal stress at 55°C. After 20-h incubation, Triton X-100 emulsion caused an upregulation of stress-related genes, rpoE, otsB, and fabA, suggesting stressful environment. After thermal treatment, S. typhimurium in Triton X-100 solution showed a longer 5-log reduction time with increased proV and decreased fabA and ompC expression, suggesting enhanced thermal protection compared to its emulsion. Conversely, Tween 80 solution increased fabA and ompC expression, indicating greater membrane fluidity and passive diffusion, potentially reducing thermal resistance. However, according to the upregulation of ibpA, this effect was likely mitigated by the overproduction of heat shock proteins. Notably, Triton X-100 environments exhibited the most significant gene expression changes after heat treatment, whereas Tween 80 without oil was the most inhospitable for bacterial survival. These findings inform bacterial responses under various conditions, aiding food safety strategies.

Structural abnormality of hepatic glycogen in rat liver with diethylnitrosamine-induced carcinogenic injury

Growing evidence confirms associations between glycogen metabolic re-wiring and the development of liver cancer. Previous studies showed that glycogen structure changes abnormally in liver diseases such as cystic fibrosis, diabetes, etc. However, few studies focus on glycogen molecular structural characteristics during liver cancer development, which is worthy of further exploration. In this study, a rat model with carcinogenic liver injury induced by diethylnitrosamine (DEN) was successfully constructed, and hepatic glycogen structure was characterized. Compared with glycogen structure in the healthy rat liver, glycogen chain length distribution (CLD) shifts towards a short region. In contrast, glycogen particles were mainly present in small-sized β particles in DEN-damaged carcinogenic rat liver. Comparative transcriptomic analysis revealed significant expression changes of genes and pathways involved in carcinogenic liver injury. A combination of transcriptomic analysis, RT-qPCR, and western blot showed that the two genes, Gsy1 encoding glycogen synthase and Gbe1 encoding glycogen branching enzyme, were significantly altered and might be responsible for the structural abnormality of hepatic glycogen in carcinogenic liver injury. Taken together, this study confirmed that carcinogenic liver injury led to structural abnormality of hepatic glycogen, which provided clues to the future development of novel drug targets for potential therapeutics of carcinogenic liver injury.