Changes In Expression Patterns Research Articles

Portulaca oleracea L. (purslane) improves the anti-inflammatory, antioxidant and autophagic actions of metformin in the hippocampus of diabetic demented rats

Great body of evidence links cognitive decline to diabetes/insulin resistance. In this study the effect of Portulaca oleracea (PUR) (100 mg/kg), Metformin (MET) (200 mg/kg), a first line diabetes mellitus type 2 therapy, and their combination on cognitive function and hippocampal markers in diabetic rats were assessed. Male rats were injected with streptozotocin (30 mg/kg on two successive weeks) followed by 4 weeks of treatment. Possible antioxidant, anti-inflammatory, and autophagy enhancing mechanisms of these drugs were investigated in the hippocampal tissue using spectrophotometry, ELISA, and western blotting. Diabetic rats suffered significant cognitive impairment in Morris's water maze, hippocampal TBARS elevation, GSH depletion, and SOD upregulation. In addition, diabetes promoted the secretion of hippocampal inflammatory cytokines, TNF-α and IL-1β, and depleted anti-inflammatory cytokines as IL-10. Such detrimental changes were reversed by MET and/or PUR. Notably, AMPK was upregulated by diabetes, then restored to normal by MET and/or PUR. The pattern of change in AMPK expression was concomitant with changes in oxidative and inflammatory burden. Hence, AMPK is believed to be a key mediator in most of the measured pre-AD markers in this study. However, from our results, PUR is believed to have non-AMPK dependent actions as well.In conclusion, antidiabetic agents as metformin and purslane extract proved to be invaluable in addressing the cognitive decline and hippocampal changes that arise as a complication of diabetes. They mainly acted through AMPK pathway; however, their usefulness was not limited to AMPK pathways since their combination was suggested to have a different mechanism.

Peritoneal Fluid Analysis of Advanced Ovarian Cancers after Hyperthermic Intraperitoneal Chemotherapy.

This study investigated miRNA and cytokine expression changes in peritoneal fluid samples of patients with advanced ovarian cancer (OVCA) after receiving hyperthermic intraperitoneal chemotherapy (HIPEC) during cytoreduction surgery (CRS). We collected samples prior to HIPEC, immediately after HIPEC, and 24/48/72 h after CRS from a total of 6 patients. Cytokine levels were assessed using a multiplex cytokine array, and a miRNA PanelChip Analysis System was used for miRNA detection. Following HIPEC, miR-320a-3p, and miR-663-a were found to be immediately down-regulated but increased after 24 h. Further, significant upregulation post-HIPEC and sustained increases in expression were detected in six other miRNAs, including miR-1290, miR-1972, miR-1254, miR-483-5p, miR-574-3p, and miR-574-5p. We also found significantly increased expression of cytokines, including MCP-1, IL-6, IL-6sR, TIMP-1, RANTES, and G-CSF. The changing expression pattern throughout the study duration included a negative correlation in miR-320a-3p and miR-663-a to cytokines including RANTES, TIMP-1, and IL-6 but a positive correlation in miRNAs to cytokines including MCP-1, IL-6sR, and G-CSF. Our study found miRNAs and cytokines in the peritoneal fluid of OVCA patients demonstrated different expression characteristics following CRS and HIPEC. Both changes in expression demonstrated correlations, but the role of HIPEC remains unknown, prompting the need for research in the future.

Identification of a Comprehensive Gene Co-Expression Network Associated with Autotetraploid Potato (Solanum tuberosum L.) Development Using WGCNA Analysis.

The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. The regulatory mechanisms underlying the growth and development are still unclear. In this work, we aimed to explore the changes in gene expression patterns and genetic characteristics of potato tissues throughout different developmental stages. To achieve this, we used autotetraploid potato JC14 as an experimental subject to analyze the transcriptome of the root, stem, and leaf at the seedling, tuber formation, and tuber expansion stages. The results revealed thousands of differentially expressed genes, predominantly involved in defense response and carbohydrate metabolism according to KEGG pathway enrichment analysis. Weighted gene co-expression network analysis (WGCNA) revealed a total of 12 co-expressed gene modules, with 4 modules showing the highest correlation with potato stem development. By calculating the connectivity of genes within the module, hub genes were identified, and functional annotations were subsequently performed. A total of 40 hub genes from the four modules were identified, and their functions were found to be related to carbohydrate metabolism, defense response, and transcription factors. These findings provide important insights for further understanding of the molecular regulation and genetic mechanisms involved in potato tissue development.

Epigenetic regulation of human-specific gene expression in the prefrontal cortex

BackgroundChanges in gene expression levels during brain development are thought to have played an important role in the evolution of human cognition. With the advent of high-throughput sequencing technologies, changes in brain developmental expression patterns, as well as human-specific brain gene expression, have been characterized. However, interpreting the origin of evolutionarily advanced cognition in human brains requires a deeper understanding of the regulation of gene expression, including the epigenomic context, along the primate genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) to measure the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), both of which are associated with transcriptional activation in the prefrontal cortex of humans, chimpanzees, and rhesus macaques.ResultsWe found a discrete functional association, in which H3K4me3HP gain was significantly associated with myelination assembly and signaling transmission, while H3K4me3HP loss played a vital role in synaptic activity. Moreover, H3K27acHP gain was enriched in interneuron and oligodendrocyte markers, and H3K27acHP loss was enriched in CA1 pyramidal neuron markers. Using strand-specific RNA sequencing (ssRNA-seq), we first demonstrated that approximately 7 and 2% of human-specific expressed genes were epigenetically marked by H3K4me3HP and H3K27acHP, respectively, providing robust support for causal involvement of histones in gene expression. We also revealed the co-activation role of epigenetic modification and transcription factors in human-specific transcriptome evolution. Mechanistically, histone-modifying enzymes at least partially contribute to an epigenetic disturbance among primates, especially for the H3K27ac epigenomic marker. In line with this, peaks enriched in the macaque lineage were found to be driven by upregulated acetyl enzymes.ConclusionsOur results comprehensively elucidated a causal species-specific gene-histone-enzyme landscape in the prefrontal cortex and highlighted the regulatory interaction that drove transcriptional activation.

Cell-specific transcriptome changes in the hypothalamic arcuate nucleus in a mouse deoxycorticosterone acetate-salt model of hypertension.

A common preclinical model of hypertension characterized by low circulating renin is the "deoxycorticosterone acetate (DOCA)-salt" model, which influences blood pressure and metabolism through mechanisms involving the angiotensin II type 1 receptor (AT1R) in the brain. More specifically, AT1R within Agouti-related peptide (AgRP) neurons of the arcuate nucleus of the hypothalamus (ARC) has been implicated in selected effects of DOCA-salt. In addition, microglia have been implicated in the cerebrovascular effects of DOCA-salt and angiotensin II. To characterize DOCA-salt effects upon the transcriptomes of individual cell types within the ARC, we used single-nucleus RNA sequencing (snRNAseq) to examine this region from male C57BL/6J mice that underwent sham or DOCA-salt treatment. Thirty-two unique primary cell type clusters were identified. Sub-clustering of neuropeptide-related clusters resulted in identification of three distinct AgRP subclusters. DOCA-salt treatment caused subtype-specific changes in gene expression patterns associated with AT1R and G protein signaling, neurotransmitter uptake, synapse functions, and hormone secretion. In addition, two primary cell type clusters were identified as resting versus activated microglia, and multiple distinct subtypes of activated microglia were suggested by sub-cluster analysis. While DOCA-salt had no overall effect on total microglial density within the ARC, DOCA-salt appeared to cause a redistribution of the relative abundance of activated microglia subtypes. These data provide novel insights into cell-specific molecular changes occurring within the ARC during DOCA-salt treatment, and prompt increased investigation of the physiological and pathophysiological significance of distinct subtypes of neuronal and glial cell types.

Cis-regulatory evolution underlying the changes in wingless expression pattern associated with wing pigmentation of Drosophila.

The co-option of regulatory genes has the potential to play an important role in the evolutionary gain of new traits. However, the changes at the sequence level that underlie such a co-option event are still elusive. We identified the changes in the cis-regulatory sequence of wingless that caused co-option of wingless and led to its expression in new places in Drosophila guttifera, which has unique pigmentation patterns on its wings. The newly gained function of gene expression activation was acquired evolutionarily via a combination of pre-existing sequences containing a putative binding site for SMAD transcription factors that exhibit an ancestral function in driving expression at crossveins, and a sequence that is specific to the lineage leading to D. guttifera.

Identification of a novel Carassius amphitetraploid clone and its transcriptomic responses to herpesvirus infection

A major threat to gibel carp aquaculture is an epizootic disease caused by C. auratus herpesvirus (CaHV). Therefore, breeding of disease resistant strain is one of significant needs for the industry. Polyploids often show enhanced tolerance to abiotic or biotic stress. However, the effects of WGD are complex and the underlying mechanisms remain elusive. In this study, we first synthesized a group of novel amphitetraploids via crossing the eggs of gynogenetic C. gibelio clone A+ with the trypsin-treated sperm of sexual C. cuvieri and then established three gynogenetic amphitetraploid clones with different transferrin phenotypes. They all showed intermediate resistance to CaHV in relative to their parents. Subsequently, we uncovered distinct transcriptomic response to CaHV infection in the one amphitetraploid clone (CaA4n-I) compared with their parents. Interestingly, the coexpression gene network analysis showed that amphitetraploid CaA4n-I and their paternal C. cuvieri adopted different anti-viral strategies via up-regulating the expression of positive factors or down-regulating the expression of negative factors in immune response respectively. Moreover, we revealed the complicated changes of expression patterns, including additivity, maternal expression level dominance, paternal expression level dominance, transgressive up-regulation, and transgressive down-regulation, in the amphitetraploid CaA4n-I. After CaHV infection, the proportions of maternal expression level dominance and transgressive up-regulation increased and more C. cuvieri-derived homeologous genes altered expression patterns in the amphitetraploid CaA4n-I. The current study not only produces a candidate strain for C. auratus aquaculture, but also provides a transcriptomic picture how a newly synthetic animal allopolyploid to response to virus infection.

Gene expression and expression quantitative trait locianalyses uncover natural variations underlying the improvement of important agronomic traits during modern maize breeding.

Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding, cultivars with increased tolerance to high-density planting and higher yield per plant have contributed significantly to the increased yield per unit land area. Systematically identifying key agronomic traits and their associated genomic changes during modern maize breeding remains a significant challenge because of the complexity of genetic regulation and the interactions of the various agronomic traits, with most of them being controlled by numerous small-effect quantitative trait loci (QTLs). Here, we performed phenotypic and gene expression analyses for a set of 137 elite inbred lines of maize from different breeding eras in China. We found four yield-related traits are significantly improved during modern maize breeding. Through gene-clustering analyses, we identified four groups of expressed genes with distinct trends of expression pattern change across the historical breeding eras. In combination with weighted gene co-expression network analysis, we identified several candidate genes regulating various plant architecture- and yield-related agronomic traits, such as ZmARF16, ZmARF34, ZmTCP40, ZmPIN7, ZmPYL10, ZmJMJ10, ZmARF1, ZmSWEET15b, ZmGLN6 and Zm00001d019150. Further, by combining expression quantitative trait loci (eQTLs) analyses, correlation coefficient analyses and population genetics, we identified a set of candidate genes that might have been under selection and contributed to the genetic improvement of various agronomic traits during modern maize breeding, including a number of known key regulators of plant architecture, flowering time and yield-related traits, such as ZmPIF3.3, ZAG1, ZFL2 and ZmBES1. Lastly, we validated the functional variations in GL15, ZmPHYB2 and ZmPYL10 that influence kernel row number, flowering time, plant height and ear height, respectively. Our results demonstrates the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding, and provide a valuable genetic resource for the molecular breeding of maize cultivars with tolerance for high-density planting.

Guidelines for the flow cytometric minimal residual disease monitoring in B-lineage acute lymphoblastic leukemia after CD19-directed immunotherapy

Multicolor flow cytometry is now routinely used in laboratory practice for the minimal residual disease (MRD) monitoring in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). Wide application of CD19-directed immunotherapy leads to frequent loss of CD19 expression, that hampers significantly the flow cytometric MRD detection methodology. We developed an antibody panel and data analysis algorithm for multicolor flow cytometry, which is a reliable method for MRD detection in patients with BCP-ALL treated with CD19-directed therapy. We recommend a single-tube 11-color panel for MRD detection, which is adapted for the case of possible CD19 loss. Based on patterns of antigen expression changes and the relative expansion of normal CD19-negative BCPs, guidelines for multicolored flow cytometry data analysis and interpretation are established. The recommended approach is reliable tool for therapy response monitoring displaying the same effectiveness with the more laborious and costly molecular techniques.

On the origin and nature of nongenetic information in eumetazoans.

Nongenetic information implies all the forms of biological information not related to genes and DNA in general. Despite the deep scientific relevance of the concept, we currently lack reliable knowledge about its carriers and origins; hence, we still do not understand its true nature. Given that genes are the targets of nongenetic information, it appears that a parsimonious approach to find the ultimate source of that information is to trace back the sequential steps of the causal chain upstream of the target genes up to the ultimate link as the source of the nongenetic information. From this perspective, I examine seven nongenetically determined phenomena: placement of locus-specific epigenetic marks on DNA and histones, changes in snRNA expression patterns, neural induction of gene expression, site-specific alternative gene splicing, predator-induced morphological changes, and cultural inheritance. Based on the available evidence, I propose a general model of the common neural origin of all these forms of nongenetic information in eumetazoans.

Selection and validation of novel stable reference genes for qPCR analysis in EMT and MET

Quantitative real-time polymerase chain reaction is a powerful tool for quantifying gene expression. The relative quantification relies on normalizing the data to reference genes or internal controls not modulated by the experimental conditions. The most widely used internal controls occasionally show changed expression patterns in different experimental settings, such as the mesenchymal to epithelial transition. Thus, identifying appropriate internal controls is of utmost importance. We analyzed multiple RNA-Seq datasets using a combination of statistical approaches such as percent relative range and coefficient of variance to define a list of candidate internal control genes, which was then validated experimentally and by using in silico analyses as well. We identified a group of genes as strong internal control candidates with high stability compared to the classical ones. We also presented evidence for the superiority of the percent relative range method for calculating expression stability in data sets with larger sample sizes. We used multiple methods to analyze data collected from several RNA-Seq datasets; we identified Rbm17 and Katna1 as the most stable reference genes in EMT/MET studies. The percent relative range approach surpasses other methods when analyzing datasets of larger sample sizes.

Sf3b4 regulates chromatin remodeler splicing and Hox expression

SF3B proteins form a heptameric complex in the U2 small nuclear ribonucleoprotein, essential for pre-mRNA splicing. Heterozygous pathogenic variants in human SF3B4 are associated with head, face, limb, and vertebrae defects. Using the CRISPR/Cas9 system, we generated mice with constitutive heterozygous deletion of Sf3b4 and showed that mutant embryos have abnormal vertebral development. Vertebrae abnormalities were accompanied by changes in levels and expression pattern of Hox genes in the somites. RNA sequencing analysis of whole embryos and somites of Sf3b4 mutant and control litter mates revealed increased expression of other Sf3b4 genes. However, the mutants exhibited few differentially expressed genes and a large number of transcripts with differential splicing events (DSE), predominantly increased exon skipping and intron retention. Transcripts with increased DSE included several genes involved in chromatin remodeling that are known to regulate Hox expression. Our study confirms that Sf3b4 is required for normal vertebrae development and shows, for the first time, that like Sf3b1, Sf3b4 also regulates Hox expression. We propose that abnormal splicing of chromatin remodelers is primarily responsible for vertebral defects found in Sf3b4 heterozygous mutant embryos.

Comparison of transcriptome alterations induced by pendimethalin or its commercial formulation Stomp Aqua in human MCF-7, MCF-10 A and MCF-12 A mammary epithelial cells

ObjectiveThe toxicology of herbicides, which are currently in use is under-explored. One highly used but under investigated herbicide is pendimethalin. Here we mined high-throughput data from the US National Toxicology Program (NTP) to identify whether pendimethalin possesses an estrogenic capability in human cells. We also evaluated effects of pendimethalin and its reference commercial formulated herbicide Stomp Aqua on the transcriptome profile of three human mammary epithelial cell lines, cancerous MCF-7 and non-cancerous MCF-10 A and MCF-12 A to see whether this compound could have endocrine disrupting effects and if co-formulants present in the commercial formulation could amplify its toxicity.ResultsThe data mined from the US NTP database suggests that pendimethalin activates estrogen receptors at a concentration of approximately 10?M. MCF-7, MCF-10A and MCF-12A cells were exposed to 10 ?M pendimethalin and Stomp Aqua at an equivalent concentration. Transcriptome analysis showed changes in gene expression patterns implying that pendimethalin affected ubiquitin-mediated proteolysis and the function of the spliceosome. The formulated pendimethalin product Stomp Aqua gave comparable effects suggesting pendimethalin was responsible for the observed transcriptome alterations. Given the lack of information on the exposure to this pesticide, our study prompts the need for biomonitoring studies, especially under occupational use scenarios, to understand if low level exposure to pendimethalin could have endocrine disrupting effects on populations exposed to this compound. A deeper understanding of the exposure and mechanisms of action of this endocrine-disrupting pesticide is needed.

Blood transcriptome analysis suggests an indirect molecular association of early life adversities and adult social anxiety disorder by immune-related signal transduction.

Social anxiety disorder (SAD) is a psychiatric disorder characterized by severe fear in social situations and avoidance of these. Multiple genetic as well as environmental factors contribute to the etiopathology of SAD. One of the main risk factors for SAD is stress, especially during early periods of life (early life adversity; ELA). ELA leads to structural and regulatory alterations contributing to disease vulnerability. This includes the dysregulation of the immune response. However, the molecular link between ELA and the risk for SAD in adulthood remains largely unclear. Evidence is emerging that long-lasting changes of gene expression patterns play an important role in the biological mechanisms linking ELA and SAD. Therefore, we conducted a transcriptome study of SAD and ELA performing RNA sequencing in peripheral blood samples. Analyzing differential gene expression between individuals suffering from SAD with high or low levels of ELA and healthy individuals with high or low levels of ELA, 13 significantly differentially expressed genes (DEGs) were identified with respect to SAD while no significant differences in expression were identified with respect to ELA. The most significantly expressed gene was MAPK3 (p = 0.003) being upregulated in the SAD group compared to control individuals. In contrary, weighted gene co-expression network analysis (WGCNA) identified only modules significantly associated with ELA (p ≤ 0.05), not with SAD. Furthermore, analyzing interaction networks of the genes from the ELA-associated modules and the SAD-related MAPK3 revealed complex interactions of those genes. Gene functional enrichment analyses indicate a role of signal transduction pathways as well as inflammatory responses supporting an involvement of the immune system in the association of ELA and SAD. In conclusion, we did not identify a direct molecular link between ELA and adult SAD by transcriptional changes. However, our data indicate an indirect association of ELA and SAD mediated by the interaction of genes involved in immune-related signal transduction.

Abstract LB283: ARC2-001 inhibits cancer-associated fibroblast-dependent cancer stem cell populations by disrupting cancer-stroma interactions

Abstract ARC2-001, a natural product and FDA-approved anti-leukemic drug, has shown anticancer effects in hematological malignancies. This study investigates the inhibitory effect of ARC2-001 on cancer-associated fibroblasts (CAFs). CAFs promote cancer progression and directly stimulate cancer cell proliferation. In addition, CAFs act as therapeutic barriers to prevent the penetration of anticancer drugs and immune cells in the treatment of solid tumors such as colorectal cancer. In our previous study, we found a master transcription factor PRRX1 of stromal fibroblasts for myofibroblastic lineage progression in the cancer microenvironment. After deleting the expression of PRRX1 in various CAFs using the CRISPR-CAS9-sgRNA system, we confirmed changes in gene expression patterns and performed in silico screening to derive drugs showing similar gene expression patterns. These drugs were investigated through a gel contraction assay and indirect co-culture/direct 3D spheroid co-culture systems using various cancer cells and CAFs. Among them, ARC2-001 treatment not only significantly reduced the ECM remodeling ability of CAFs but also showed strong anticancer effects in the co-culture systems. In addition, the response to ARC2-001 was much more sensitive in CAFs than in cancer cells: the IC50 values in cancer cells were30-50nM, and the IC50 values in CAFs were 10-20nM. We produced HCT116 (colon cancer cell)-Colon CAFs spheroids, treated them with ARC2-001at low concentrations that could only affect CAFs, and analyzed RNA transcriptome changes by RNA-SEQ. We confirmed that HCT116 cells underwent EMT as well as observed an increase in the cancer stem cell (CSC) population by CAFs through co-culture of HCT116-CAFs spheroids. Interestingly, treatment with a concentration of ARC2-001 sufficient to inhibit only CAFs had no significant effect on HCT116-only spheroids, and little change occurred in gene expression patterns, but in HCT116 cells in spheroid co-culture with CAFs, the aforementioned changes (EMT and CSC population increase) all collapsed. This indicates that ARC2-001 interferes with the interactions between cancer cells and CAFs. ARC2-001 damages the cancer stem cell population of HCT116 through CAFs inhibition, indicating that the CSC subpopulation of HCT116 cells is dependent on CAFs. We further hypothesized that co-administration of ARC2-001 and commonly used anticancer drugs could be a very effective strategy, considering the ineffectiveness of commonly used anticancer drugs on the CSC subpopulation. Thus, we transplanted colon CAFs together with HCT116 cells into NOD/SCID mice and then administered 5FU, an existing anticancer drug, together with ARC2-001. For the combined treatment in the in vivo experiment, we treated ARC2-001 and 5FU at half of the commonly used concentrations. Surprisingly, we observed that both tumor growth and cancer metastasis were suppressed in the combination treatment group. This indicates that ARC2-001 dramatically increases the effectiveness of existing anticancer drugs and can be used as an additional combination therapy for colorectal cancer chemotherapy. Citation Format: Keun-Woo Lee, So-Young Yeo, InSuk Sohn, Seok-Hyung Kim. ARC2-001 inhibits cancer-associated fibroblast-dependent cancer stem cell populations by disrupting cancer-stroma interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB283.

Antibody Profile, Gene Expression and Serum Cytokines in At-Risk Infants before the Onset of Celiac Disease

Immunological events that precede the development of villous atrophy in celiac disease (CeD) are still not completely understood. We aimed to explore CeD-associated antibody production (anti-native gliadin (AGA), anti-deamidated gliadin (DGP) and anti-tissue transglutaminase (anti-tTG)) in infants at genetic risk for CeD from the Italian cohorts of the PREVENT-CD and Neocel projects, as well as the relationship between antibody production and systemic inflammation. HLA DQ2 and/or DQ8 infants from families with a CeD case were followed from birth. Out of 220 at-risk children, 182 had not developed CeD by 6 years of age (CTRLs), and 38 developed celiac disease (CeD). The profiles of serum cytokines (INFγ, IL1β, IL2, IL4, IL6, IL10, IL12p70, IL17A and TNFα) and the expression of selected genes (FoxP3, IL10, TGFβ, INFγ, IL4 and IL2) were evaluated in 46 children (20 CeD and 26 CTRLs). Among the 182 healthy CTRLs, 28 (15.3%) produced high levels of AGA-IgA (AGA+CTRLs), and none developed anti-tTG-IgA or DGP-IgA, compared to 2/38 (5.3%) CeD infants (Chi Sq. 5.97, p = 0.0014). AGAs appeared earlier in CTRLs than in those who developed CeD (19 vs. 28 months). Additionally, the production of AGAs in CeD overlapped with the production of DGP and anti-tTG. In addition, gene expression as well as serum cytokine levels discriminated children who developed CeD from CTRLs. In conclusion, these findings suggest that the early and isolated production of AGA-IgA antibodies is a CeD-tolerogenic marker and that changes in gene expression and cytokine patterns precede the appearance of anti-tTG antibodies.

Changes in gene expression and neuroinflammation in the hippocampus of rats with poststroke cognitive impairment.

Poststroke cognitive impairment (PSCI) often occurs during the stroke recovery period and greatly increases the difficulty of rehabilitation. Activation of neuroinflammation and long-term changes in gene expression patterns in the hippocampus could be essential in the development of PSCI. Therefore, this study aimed to identify neuroinflammation and changes in gene expression patterns in the hippocampus in rats with PSCI. Rats underwent transient middle cerebral artery occlusion (tMCAO) or sham surgery. The infarct volume was measured on day 3 after surgery. The Morris water maze (MWM) test was used to assess cognitive function. Microglial activation and white matter (WM) lesions in the hippocampus were evaluated on day 28 after surgery. In addition, we compared differentially expressed genes (DEGs) in the hippocampus between tMCAO group rats and sham group rats by RNA sequencing. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction (PPI) network analyses were conducted to investigate these DEGs. The results showed that the tMCAO group rats showed extensive infarction and cognitive dysfunction compared with the sham group rats. Microglial activation and WM damage were obvious in the hippocampus of tMCAO group rats. We found 43 DEGs by RNA sequencing: 29 genes with upregulated expression and 14 genes with downregulated expression. The GO analysis indicated that DEGs were mainly involved in cell proliferation and differentiation, cholesterol synthesis, and metabolism. The KEGG pathway analysis suggested that the DEGs were significantly enriched in intestinal immune network for IgA production and steroid biosynthesis. Acta2, Calb2, and Cxcl12 were notable in the PPI analysis. Our results suggest that microglial activation and WM damage are maintained in rats with PSCI. The mechanism may be related to the regulation of steroid biosynthesis, intestinal immunity, and potential key genes such as Acta2, Calb2, and Cxcl12 in the hippocampus.

PD35-11 EPITHELIAL DIFFERENTIATION IS ALTERED IN URETHRAL LICHEN SCLEROSUS

You have accessJournal of UrologyCME1 Apr 2023PD35-11 EPITHELIAL DIFFERENTIATION IS ALTERED IN URETHRAL LICHEN SCLEROSUS Ethan Richmond, Caleb Sokovich, Wei Huang, Chad Vezina, and Matthew D Grimes Ethan RichmondEthan Richmond More articles by this author , Caleb SokovichCaleb Sokovich More articles by this author , Wei HuangWei Huang More articles by this author , Chad VezinaChad Vezina More articles by this author , and Matthew D GrimesMatthew D Grimes More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003333.11AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Lichen sclerosus (LS) is an idiopathic chronic inflammatory disease of the genital epithelium resulting in fibrosis and severe urethral stricture disease in affected men. Epithelia are subdivided into basal, intermediate, and superficial cell layers which are defined by protein expression patterns. Loss of basal cell differentiation is a feature of other fibrotic disorders but have not been studied in the urethra or LS. The proteins keratin 5 (KRT5) and p63 have been reliably established as basal cell markers in urothelium. Therefore, we hypothesized that urethral epithelium affected by LS would have decreased basal expression of KRT5 and p63. METHODS: Urethral tissue after urethral biopsy or urethroplasty was examined by a genitourinary pathologist to determine LS status. Using multiplexed fluorescent immunohistochemistry, KRT 5, CD45, p63, and DAPI were stained and three epithelial regions imaged per specimen. Using QuPath analysis software, the epithelium was segmented into basal and luminal compartments and relative abundance (RA) of each primary antibody was measured (number of positive cells/number of nucleated cells). RA was compared with respect to LS status and basal/luminal compartment using a Mann-Whitney U test. RESULTS: We analyzed 14 slides (n=7 LS, n=7 non-LS). The RA of KRT5 and p63 positive cells were similar with respect to epithelial versus basal compartment and LS status. However, we noted a change in patterning such that LS tissues displayed a shift of KRT5 and p63 expression from the basal to the luminal epithelium. To quantify this, we compared the ratio of basal to luminal KRT5 and p63 expression and dichotomized this as “basal predominant” (>1) or “luminal predominant” (<1). LS urethra were significantly more likely to have luminal predominant expression of p63 and KRT5 compared to non-LS (p=0.03, p=0.03) (Figure 1). CONCLUSIONS: We identified a change in expression pattern of basal epithelial markers (KRT5 and p63) in LS urethra. Altered epithelial differentiation is seen in other inflammatory diseases and may be implicated in the pathogenesis of LS. Source of Funding: K12DK100022NIH/NIDDK © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e978 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Ethan Richmond More articles by this author Caleb Sokovich More articles by this author Wei Huang More articles by this author Chad Vezina More articles by this author Matthew D Grimes More articles by this author Expand All Advertisement PDF downloadLoading ...

Adeno-associated virus vector system controlling capsid expression improves viral quantity and quality.

Adeno-associated virus (AAV) vectors are promising tools for gene therapy. The current AAV vector system produces an abundance of empty capsids that are eliminated before clinical use, leading to increased costs for gene therapy. In the present study, we established an AAV production system that regulates the timing of capsid expression using a tetracycline-dependent promoter. Tetracycline-regulating capsid expression increased viral yield and reduced empty capsids in various serotypes without altering AAV vector infectivity invitro and invivo. The replicase expression pattern change observed in the developed AAV vector system improved viral quantity and quality, whereas timing control of capsid expression reduced empty capsids. These findings provide a new perspective on the development of AAV vector production systems in gene therapy.

Evolutionary relevance of single nucleotide variants within the forebrain exclusive human accelerated enhancer regions

BackgroundHuman accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation.ResultsTo start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele.ConclusionThese results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution.MethodsThe present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.