Differences In Gene Expression Research Articles

Transcriptome Analysis Reveals the Impact of Arbuscular Mycorrhizal Symbiosis on Toona ciliata var. pubescens Seedlings

Toona ciliata var. pubescens, known as “Chinese mahogany”, has high commercial value and is classified as a level II priority protected wild plant in China. However, due to overexploitation and its poor natural regeneration capacity, natural T. ciliata var. pubescens forests show varying degrees of decline in habitat adaptability. Arbuscular mycorrhizal fungi (AMF) symbiosis presents a potential strategy to enhance its regeneration. In this study, T. ciliata var. pubescens seedlings were inoculated with Septoglomus viscosum, followed by RNA-Seq analysis to compare gene expression differences between AMF-inoculated (AMI) and non-mycorrhizal (NM) treatments three months post-inoculation. A total of 16,163 differentially expressed genes (DEGs) were upregulated by AMF colonization, constituting 96.46% of the total DEGs. Specifically, 14,420 DEGs were exclusively expressed in the AMI treatment, while 35 DEGs were completely silenced. Most of the upregulated DEGs were located on the cell membrane, nucleus, and cytoskeleton and functioned in protein binding, S-adenosylmethionine-dependent methyltransferase activity, and lipid binding during cellular/macromolecule/protein localization, intracellular/protein transport, the cell cycle, and signal transduction. Additionally, lots of key genes related to oxidative stress responses, nutrient transport, and small GTPase-mediated signal transduction were found to be upregulated. These results suggest that AMF inoculation may enhance root cell growth by activating genes involved in nutrient uptake, stress responses, signal transduction, and substance transportation. This study elucidates the molecular mechanisms underlying the growth promotion of T. ciliata var. pubescens through AMF symbiosis, laying a foundation for the future application of AMF in its natural forest regeneration.

The role of circulating neutrophils in the progression of kidney cancer

Introduction. Currently, the question of the role of neutrophils in the progression of kidney cancer remains relevant. Neutrophils are capable of exhibiting protumor properties through the secretion of cytokines, chemokines, and growth factors, which is determined by the expression of genes for these molecules. And the functional heterogeneity of neutrophils is characterized by differences in gene expression patterns.Aim. To assess the role of circulating neutrophils in the progression of kidney cancer.Materials and methods. In circulating neutrophils of patients with verified clear cell kidney cancer at stages I–III according to Tumor, Nodus and Metastasis (TNM) (n = 88) before surgical treatment and conditionally healthy donors (control group) (n = 20), the expression of NGAL genes was determined using quantitative reverse transcription polymerase chain reaction, MMP-13 and VEGF-A.Results. There was an increase in NGAL gene expression in circulating neutrophils (p = 0.05) at the initial stage and a decrease in it at advanced stages of kidney cancer (p = 0.03). High expression of the MMP-13 gene by circulating neutrophils was detected at all stages of kidney cancer relative to control values (at stage I p = 0.005; at stage II p = 0.003; at stage III p = 0.0008). A significant direct correlation was observed between the expression of the NGAL and MMP-13 genes in neutrophils at stage I kidney cancer (r = 0.696; p = 0.003). In the group of patients with kidney cancer, a direct correlation was found between the expression of the NGAL and VEGF-A genes (r = 0.322; p = 0.049). A multivariable Cox regression model for disease-free survival revealed the predictive value of VEGF-A and NGAL genes expression in circulating neutrophils. With an increase in the expression of the VEGF-A and NGAL genes in neutrophils by 1 unit, the risk of metastases increases by 0.80 (0.65–0.99; p = 0.043) and 1.42 (1.01–2.00; p = 0.046) times, respectively. The Kaplan–Meier analysis of disease-free survival in patients with kidney cancer showed the influence of NGAL expression in circulating neutrophils on progression-free time. In the group of patients with high NGAL expression, the median follow-up was 31.7 months, and in the group with low NGAL expression – more than 36 months (log-rank-test; p = 0.017).Conclusion. Thus, the data obtained suggest that circulating neutrophils play a leading role in the progression of kidney cancer. The level of expression of NGAL in circulating neutrophils can be used to predict the relapse-free period in patients with kidney cancer.

Novel insights into drought-induced regulation of ribosomal genes through DNA methylation in chickpea

Modifications within the epigenome of an organism in response to external environmental conditions allow it to withstand the hostile stress factors. Drought in chickpea is a severely limiting abiotic stress factor which is known to cause huge yield loss. To analyse the methylome of chickpea in response to drought stress conditions and how it affects gene expression, we performed whole-genome bisulfite sequencing (WGBS) and RNA-seq of two chickpea genotypes which contrast for drought tolerance. It was observed that the mCHH was most variable under drought stress and the drought tolerant (DT) genotype exhibited substantial genome-wide hypomethylation as compared to the drought sensitive (DS) genotype. Specifically, there was substantial difference in gene expression and methylation for the ribosomal genes for the tolerant and sensitive genotypes. The differential expression of these genes was in complete agreement with earlier reported transcriptomes in chickpea. Many of these genes were hypomethylated (q < 0.01) and downregulated under drought stress (p < 0.01) in the sensitive genotype. The gene RPS6 (ribosomal protein small subunit) was found to be downregulated and hypomethylated in the drought sensitive genotype which could possibly lead to reduced ribosomal biosynthesis. This study provides novel insights into regulation of drought-responsive genes in chickpea.

GTADC: A Graph-Based Method for Inferring Cell Spatial Distribution in Cancer Tissues.

The heterogeneity of tumors poses a challenge for understanding cell interactions and constructing complex ecosystems within cancer tissues. Current research strategies integrate spatial transcriptomics (ST) and single-cell sequencing (scRNA-seq) data to thoroughly analyze this intricate system. However, traditional deep learning methods using scRNA-seq data tend to filter differentially expressed genes through statistical methods. In the context of cancer tissues, where cancer cells exhibit significant differences in gene expression compared to normal cells, this heterogeneity renders traditional analysis methods incapable of accurately capturing differences between cell types. Therefore, we propose a graph-based deep learning method, GTADC, which utilizes Silhouette scores to precisely capture genes with significant expression differences within each cell type, enhancing the accuracy of gene selection. Compared to traditional methods, GTADC not only considers the expression similarity of genes within their respective clusters but also comprehensively leverages information from the overall clustering structure. The introduction of graph structure effectively captures spatial relationships and topological structures between the two types of data, enabling GTADC to more accurately and comprehensively resolve the spatial composition of different cell types within tissues. This refinement allows GTADC to intricately reconstruct the cellular spatial composition, offering a precise solution for inferring cell spatial composition. This method allows for early detection of potential cancer cell regions within tissues, assessing their quantity and spatial information in cell populations. We aim to achieve a preliminary estimation of cancer occurrence and development, contributing to a deeper understanding of early-stage cancer and providing potential support for early cancer diagnosis.

Transcriptome Sequencing Provides Insights into High-Temperature-Induced Leaf Senescence in Herbaceous Peony

Global warming causes frequent high temperatures in summer; which negatively impacts herbaceous peonies (Paeonia lactiflora Pall.) by accelerating leaf senescence and reducing biomass accumulation, leading to reduced flower quality in the subsequent year. Our findings revealed that as heat stress progressed, the high-temperature-sensitive cultivar ‘Meigui Zi’ (MGZ) exhibited a higher rate of chlorophyll content reduction and more pronounced premature aging symptoms than the high-temperature-tolerant cultivar ‘Chi Fen’ (CF). To investigate gene expression differences between CF and MGZ under high-temperature stress, we combined PacBio Iso-Seq sequencing (Iso-Seq) with next-generation sequencing (RNA-seq). Iso-seq yielded 352,891 full-length transcripts ranging from 61 bp to 49,022 bp in length. RNA-seq generated 257,562 transcripts across all samples. Further analysis revealed that differentially expressed genes (DEGs) between CF and MGZ were primarily enriched in “Photosynthesis”, with most photosynthesis-related DEGs highly expressed in CF. This indicates that CF has higher stability in its photosystem compared with MGZ, which is crucial for mitigating leaf senescence caused by high temperatures. Additionally, the highly expressed chlorophyll degradation genes stay-green (SGR) and stay-green-like (SGRL) in MGZ may be involved in chlorophyll content reduction induced by high temperature. This study preliminarily revealed the molecular mechanism of high-temperature-induced leaf senescence of in herbaceous peony and provided candidate genes for further studies of the regulation mechanism of high -temperature-induced leaf senescence.

298 Differential Gene Expression Underlying Glioma Related Epilepsy

INTRODUCTION: Seizures are a common sequalae for patients suffering from gliomas. There are several factors, such as molecular characteristics, known to influence the initiation of seizures that may ultimately drive tumor growth. However, different levels of gene expression associated with seizures for gliomas remain unclear. Here, we review current literature and analyze RNA sequencing of gliomas to further probe these differences. METHODS: Utilizing total RNA sequencing obtained from The Cancer Genome Atlas - Lower Grade Glioma to identify and characterize differential expression in patients that do and do not experience seizures. Utilizing QIAGEN Ingenuity Pathways Analysis (IPA), we identified canonical and functional pathways to further characterize differential expression. RESULTS: From 289 patients with gliomas, 83 (28.7%) had available information regarding seizures and other variables of interest. Of these, 50 (60.2%) were allocated to the seizure group and the remaining 33 (39.8%) to the non-seizure group. There were no statistically significant differences in age (p = 0.4661), sex (p = -0.1338), race/ethnicity (p = 0.7331), molecular subtype (0.8656), tumor grade (p = 0.2260), or anatomical location. When comparing the level of RNA expression from these tumors between the seizure and non-seizure groups, we identified 52 genes that were significantly differentially regulated. Critical canonical pathways were identified, most significantly RHOGDI and Semaphorin Neuronal Repulsive signaling.Finally, in the functional analysis, tumors that promoted seizures had gene sets that were significantly increased involving neuronal differentiation and synaptogenesis. CONCLUSIONS: In the setting of gliomas, differences in tumor gene expression exist between individuals with seizures and without seizures despite similarities in patient demographics and other tumor characteristics. There was significant difference in gene expression that were most associated with neuron development and synaptogenesis, ultimately suggesting a mechanistic role of a tumor-neuron synapse in seizure initiation and potentially tumor growth.

High-Throughput Transcriptomics of Nontumorigenic Breast Cells Exposed to Environmentally Relevant Chemicals.

There is a suite of chemicals, including metals, pesticides, and personal care product compounds, which are commonly detected at high levels in US Center for Disease Control's National Health and Nutrition Examination Survey (NHANES) chemical biomarker screens. Whether these chemicals influence development of breast cancer is not well understood. The objectives were to perform an unbiased concentration-dependent assessment of these chemicals, to quantify differences in cancer-specific genes and pathways, to describe if these differences occur at human population-relevant concentrations, and to specifically test for differences in markers of stemness and cellular plasticity. We treated nontumorigenic mammary epithelial cells, MCF10A, with 21 chemicals at four concentrations (, , , and ) for 48 h. We conducted RNA-sequencing for these 408 samples, adapting the plexWell plate-based RNA-sequencing method to analyze differences in gene expression. We calculated gene and biological pathway-specific benchmark concentrations (BMCs) using BMDExpress3, identifying differentially expressed genes and generating the best fit benchmark concentration models for each chemical across all genes. We identified enriched biological processes and pathways for each chemical and tested whether chemical exposures change predicted cell type distributions. We contextualized benchmark concentrations relative to human population biomarker concentrations in NHANES. We detected chemical concentration-dependent differences in gene expression for thousands of genes. Enrichment and cell type distribution analyses showed benchmark concentration responses correlated with differences in breast cancer-related pathways, including induction of basal-like characteristics for some chemicals, including arsenic, lead, copper, and methyl paraben. Comparison of benchmark data to NHANES chemical biomarker (urine or blood) concentrations indicated an overlap between exposure levels and levels sufficient to cause a gene expression response. These analyses revealed that many of these 21 chemicals resulted in differences in genes and pathways involved in breast cancer in vitro at human exposure-relevant concentrations. https://doi.org/10.1289/EHP12886.

Analysis of network expression and immune infiltration of disulfidptosis-related genes in chronic obstructive pulmonary disease.

Chronic obstructive pulmonary disease (COPD) is a globally prevalent respiratory disease, and programmed cell death plays a pivotal role in the development of COPD. Disulfidptosis is a newly discovered type of cell death that may be associated with the progression of COPD. However, the expression and role of disulfidptosis-related genes (DRGs) in COPD remain unclear. The expression of DRGs was identified by analyzing RNA sequencing (RNA-seq) data in COPD. Further, COPD patients were classified into two subtypes by unsupervised cluster analysis to reveal their differences in gene expression and immune infiltration. Meanwhile, hub genes associated with disulfidptosis were screened by weighted gene co-expression network analysis. Subsequently, the hub genes were validated experimentally in cells and animals. In addition, we screened potential therapeutic drugs through the hub genes. We identified two distinct molecular clusters and observed significant differences in immune cell populations between them. In addition, we screened nine hub genes, and experimental validation showed that CDC71, DOHH, PDAP1, and SLC25A39 were significantly upregulated in cigarette smoke-induced COPD mouse lung tissues and bronchial epithelial cells (BEAS-2B) treated with cigarette smoke extract. Finally, we predicted 10 potential small molecule drugs such as Atovaquone, Taurocholic acid, Latamoxef, and Methotrexate. We highlighted the strong association between COPD and disulfidptosis, with DRGs demonstrating a discriminative capacity for COPD. Additionally, the expression of certain novel genes, including CDC71, DOHH, PDAP1, and SLC25A39, is linked to COPD and may aid in the diagnosis and assessment of this condition.

Molecular Profiling to Understand Treatment Resistance and Response in Glioblastoma

INTRODUCTION: Patients with glioblastoma experience a wide variation in response to standard treatment, with nearly 30% experiencing tumour progression during treatment, and nearly 6% surviving more than 5 years. To date, there are few non-invasive clinical biomarkers to predict response to firstline treatment. Chemical exchange saturation transfer (CEST) MRI may have the potential to fill this gap. CEST MRI is sensitive to treatment-induced changes and changes in tumor metabolism1. Our team has obtained CEST data for patients before, during and after standard chemoradiation treatment, and found that CEST provides markers of early response and can identify early, standard and late progressors before treatment initiation.2 METHODS: Patients (n = 104) with primary, IDH wild-type glioblastoma were imaged with CEST-MRI at multiple time points throughout standard chemoradiation treatment. DNA and RNA were co-extracted from matched normal and tumour pairs and processed for whole genome sequencing and gene expression analysis using Nanostring. Clinical variables such as age, extent of resection, sex, ECOG status and MGMT promoter methylated were also collected. A survival analysis was conducted using the Kaplan-Meier method with log-rank tests. Univariate and multi-variate hazard ratios for clinical variables were calculated by fitting Cox Proportional Hazards Models. RESULTS: Early progressors reported a median progression-free survival (PFS) of 142 days compared to 296.5 in standard and 832 days in late progressors (p &lt; 0.0001). Early progressors also harbored distinct and statistically significant differences in gene expression and genomic alterations, namely in DNA damage repair, glucose transport and arginine metabolism pathways. A gene signature was prognostic of PFS and overall survival in a Cox proportional hazards model. CONCLUSIONS: This data may serve as a radiogenomic biomarker to assess treatment response within early phases of treatment and allow for a personalized treatment plan.

Identification of Drug Targets and Agents Associated with Ferroptosis-related Osteoporosis through Integrated Network Pharmacology and Molecular Docking Technology.

Osteoporosis is a systemic bone disease characterized by progressive reduction of bone mineral density and degradation of trabecular bone microstructure. Iron metabolism plays an important role in bone; its imbalance leads to abnormal lipid oxidation in cells, hence ferroptosis. In osteoporosis, however, the exact mechanism of ferroptosis has not been fully elucidated. The main objective of this project was to identify potential drug target proteins and agents for the treatment of ferroptosis-related osteoporosis. In the current study, we investigated the differences in gene expression of bone marrow mesenchymal stem cells between osteoporosis patients and normal individuals using bioinformatics methods to obtain ferroptosis-related genes. We could predict their protein structure based on the artificial intelligence database of AlphaFold, and their target drugs and binding sites with the network pharmacology and molecular docking technology. We identified five genes that were highly associated with osteoporosis, such as TP53, EGFR, TGFB1, SOX2 and MAPK14, which, we believe, can be taken as the potential markers and targets for the diagnosis and treatment of osteoporosis. Furthermore, we observed that these five genes were highly targeted by resveratrol to exert a therapeutic effect on ferroptosis-related osteoporosis. We examined the relationship between ferroptosis and osteoporosis based on bioinformatics and network pharmacology, presenting a promising direction to the pursuit of the exact molecular mechanism of osteoporosis so that a new target can be discovered for the treatment of osteoporosis.

453 Ketamine Promotes Sustained Brain-Derived Neurotrophic Factor Levels in the Corticoaccumbens Circuit

OBJECTIVES/GOALS: Neuropsychiatric disorders classified as synaptopathies are marked by a glutamate-associated hypofrontality which impacts decision making and impulsivity. We hypothesized that behavioral efficacy of the psychoplastogen ketamine is mediated in part through lasting promotion of markers of synaptic strength in corticoaccumbens circuit. METHODS/STUDY POPULATION: Male, Sprague-Dawley rats received an intraperitoneal (i.p.) injection of saline, single ketamine (10 mg/kg; 1x/day), or repeated ketamine (10 mg/kg; 1x/day for three days). Twenty-four hrs following the dosing regimen, animals were euthanized, and brains dissected to harvest corticoaccumbens structures including the medial prefrontal cortex (mPFC) and the nucleus accumbens (NAc). mRNA was extracted and converted to cDNA. Levels of brain derived neurotrophic factor (BDNF) exon II mRNA were quantified using reverse transcriptase polymerase chain reaction (RT-PCR); cyclophilin A (PPIA) was used as a loading control. Gene expression differences in ketamine-treated rats were identified versus saline-treated rats. BDNF protein levels were quantified using capillary-electrophoresis immunoblotting. RESULTS/ANTICIPATED RESULTS: Repeated, but not single, ketamine administration decreased mPFC, but increased NAc, BDNF exon II mRNA levels versus saline (p&lt;0.05). Single and repeated ketamine administration increased NAC BDNF protein (p&lt;0.05), while both dosing paradigms induced a trend towards an increase in mPFC BDNF levels. DISCUSSION/SIGNIFICANCE: We discovered a dosing regimen-dependent and sustained effects of ketamine administration on BDNF levels in the rodent brain. Taken together, ketamine-mediated BDNF levels may sustain synaptic strengthening mechanisms supporting future investigation into the utility of ketamine for diseases characterized by synaptopathies.

Transcriptional and functional profiling identifies inflammation and endothelial-to-mesenchymal transition as potential drivers for phenotypic heterogeneity within a cohort of endothelial colony forming cells

BackgroundEndothelial colony-forming cells (ECFCs) derived from patients can be used to investigate pathogenic mechanisms of vascular diseases like von Willebrand disease. Considerable phenotypic heterogeneity has been observed between ECFC clones derived from healthy donors. This heterogeneity needs to be well understood in order to use ECFCs as endothelial models for disease. ObjectivesTherefore, we aimed to determine phenotypic and gene expression differences between control ECFCs. MethodsA total of 34 ECFC clones derived from 16 healthy controls were analyzed. The transcriptome of a selection of ECFC clones (n = 15) was analyzed by bulk RNA sequencing and gene set enrichment analysis. Gene expression was measured in all ECFC clones by quantitative polymerase chain reaction. Phenotypic profiling was performed and migration speed of the ECFCs was measured using confocal microscopy, followed by automated quantification of cell morphometrics and migration speed. ResultsThrough hierarchical clustering of RNA expression profiles, we could distinguish 2 major clusters within the ECFC cohort. Major differences were associated with proliferation and migration in cluster 1 and inflammation and endothelial-to-mesenchymal transition in cluster 2. Phenotypic profiling showed significantly more and smaller ECFCs in cluster 1, which contained more and longer Weibel–Palade bodies. Migration speed in cluster 1 was also significantly higher. ConclusionWe observed a range of different RNA expression patterns between ECFC clones, mostly associated with inflammation and clear differences in Weibel–Palade body count and structure. We developed a quantitative polymerase chain reaction panel that can be used for the characterization of ECFC clones, which is essential for the correct analysis of pathogenic mechanisms in vascular disorders.

A novel anoikis-related gene signature can predict the prognosis of hepatocarcinoma patients.

Hepatocellular carcinoma (HCC) is a major health problem with more than 850,000 cases per year worldwide. This cancer is now the third leading cause of cancer-related deaths worldwide, and the number is rising. Cancer cells develop anoikis resistance which is a vital step during cancer progression and metastatic colonization. However, there is not much research that specifically addresses the role of anoikis in HCC, especially in terms of prognosis. This study obtained gene expression data and clinical information from 371 HCC patients through The Cancer Genome Atlas (TCGA) Program and The Gene Expression Omnibus (GEO) databases. A total of 516 anoikis-related genes (ANRGs) were retrieved from GeneCard database and Harmonizome portal. Differential expression analysis identified 219 differentially expressed genes (DEGs), and univariate Cox regression analysis was utilized to select 99 ANRGs associated with the prognosis of HCC patients. A risk scoring model with seven genes was established using the least absolute shrinkage and selection operator (LASSO) regression model, and internal validation of the model was performed. The identified 99 ANRGs are closely associated with the prognosis of HCC patients. The risk scoring model based on seven characteristic genes demonstrates excellent predictive performance, further validated by receiver operating characteristic (ROC) curves and Kaplan-Meier survival curves. The study reveals significant differences in immune cell infiltration, gene expression, and survival status among different risk groups. The prognosis of HCC patients can be predicted using a unique prognostic model built on ANRGs in HCC.

Contribution of sphingomyelin phosphodiesterase acid-like 3B to the proliferation, migration, and invasion of ovarian cancer cells.

Cancer has the highest mortality rate among gynecological cancers and poses a serious threat to women's lives. However, the treatment options for ovarian cancer are still limited, and exploring effective targeted biomarkers is particularly important for predicting and treating ovarian cancer. Therefore, it is necessary to explore the molecular mechanisms of the occurrence and development of ovarian cancer. This investigation encompassed the analysis of gene expression profiles, measurement of transcription levels of potential target genes in peripheral blood samples from ovarian cancer patients and characterization of the ovarian cancer-related secretory protein sphingomyelin phosphodiesterase acid-like 3B (SMPDL3B). Through bioinformatics analysis, potential target genes were identified, and their association with overall survival (OS) and progression-free survival (PFS) in ovarian cancer patients was assessed utilizing relevant databases. Subsequently, differences in target gene expression in ovarian cancer tissue samples were validated through protein blotting and quantitative real-time PCR (qRT-qPCR). Cell proliferation assays using the cell count kit-8 (CCK-8) method, as well as transwell chamber assay and pre coated matrix gel chamber assay were employed to elucidate the role of SMPDL3B in ovarian cancer cell migration and invasion. This study revealed a substantial upregulation of SMPDL3B in the serum of ovarian cancer patients, correlating with an unfavorable prognosis. High SMPDL3B expression was linked not only to increased proliferation of ovarian cancer cells, but also enhanced migration and invasion. Remarkably, the knockdown the human alkaline ceramidase 2 (ACER2) gene in cancer cells with heightened SMPDL3B expression significantly inhibited cell proliferation, migration, and invasion induced by SMPDL3B activation (P<0.05), highlighting the functional interplay between ACER2 and SMPDL3B in ovarian cancer. In summary, this study proposes SMPDL3B as a prognostic marker for ovarian cancer, with implications for potential therapeutic intervention targeting the ACER2-SMPDL3B axis.

Identification and Verification of Potential Ferroptosis-Related Biomarkers in Cervical Cancer

This study screened important genes contributing to morbidity from differential ferroptosis-related genes (FRGs) in cervical cancer and to establish a risk assessment model with ferroptosis-related LncRNAs. Total RNA sequencing data were extracted from The cancer genome atlas (TCGA), Gene Expression Omnibus (GEO) and Genotype-Tissue Expression (GTEx). By differential analysis, we identified ferroptosis-related hub genes close to prevalence of cervical cancer. According to receiver operator curves (ROC) curves, hub genes have good diagnostic performance. The diagnostic potential of hub genes for occurrence of the disease was further assessed and verified. Further, a risk-assessing model based on ferroptosis-related LncRNAs was established. Finally, the differential expressions of hub genes were verified through qRT-PCR. Five hub genes were identified, and we found through GO, KEGG and immune infiltration, that the hub genes are connection with cervical cancer. The Area Under Curve (AUC) values were all greater than 0.8 in ROC curve, and the hub genes presented differences between disease and control groups in validation set GSE29570. We created a risk assessment model with 16 ferroptosis-related LncRNAs. There was a difference in survival between high-risk and low-risk groups. The AUC result for risk assessment model reached 0.792, and there were significant expression differences of Hub genes in Huvec and Hela cells. The study screened 5 hub genes and constructed the risk-assessment model based on 16 LncRNAs associated with ferroptosis genes.

Difference of effective component content and key enzyme gene expression of biosynthesis in Atractylodes chinensis with different leaf shapes

In this study, four Atractylodes chinensis(A. chinensis) with different leaf shapes, such as the split leaf, long and narrow leaf, oval leaf, and large round leaf, were used as experimental materials to establish a method for simultaneously determining atractylodin, atractylenolide Ⅰ, β-eudesmol, and atractylon in the rhizome of A. chinensis. The expression of key enzyme genes for biosynthesis of acetyl-CoA carboxylase(ACC), 3-hydroxy-3-methylglutaryl-CoA reductase(HMGR), and farnesyl pyrophosphate synthase(FPPS) was detected by real-time fluorescence quantitative polymerase chain reaction(qRT-PCR). High performance liquid chromatography(HPLC) was used to compare the difference in the content of four active components in A. chinensis with different leaf shapes, and the correlation between the content of active components and the expression of key enzyme genes in biosynthesis was discussed. The results show that there was good linearity among atractylodin, atractylenolide Ⅰ, β-eudesmol, and atractylon in the range of 3.30-33.00 μg·mL~(-1)(r =0.999 7), 12.04-120.40 μg·mL~(-1)(r =0.999 5), 29.16-291.60 μg·mL~(-1)(r =0.999 5), and 14.20-142.00 μg·mL~(-1)(r =0.999 5), respectively. The average recoveries were 99.77%(RSD=2.1%), 98.56%(RSD=1.2%), 103.0%(RSD=1.2%), and 100.6%(RSD=1.5%), respectively. The method was accurate and had good reproducibility, which could be used to simultaneously detect atractylodin, atractylenolide Ⅰ, β-eudesmol, and atractylon. The results showed that there were significant differences in the content of four active components in A. chinensis with different leaf shapes. The content of atractylodin, atractylenolide Ⅰ, and β-eudesmol in A. chinensis with split leaves was the highest, which were 1.341 9, 5.237 2, and 12.084 3 mg·g~(-1), respectively. The content of atractylon in A. chinensis with long and narrow leaves was the highest(5.470 1 mg·g~(-1)). The content of atractylodin, atractylenolide Ⅰ, β-eudesmol, and atractylon in A. chinensis with oval leaves was the lowest. The total content of the four effective components in descending order was A. chinensis with split leaves &gt; A. chinensis with long and narrow leaves &gt; A. chinensis with large round leaves &gt; A. chinensis with oval leaves. The gene expression levels of key enzymes ACC, HMGR, and FPPS in A. chinensis with split leaves were the highest(P &lt; 0.05), and the gene expression levels of key enzymes ACC and HMGR in A. chinensis with oval leaves were the lowest(P &lt; 0.05). The gene expression level of key enzyme FPPS in A. chinensis with large round leaves was the lowest. In A. chinensis with different leaf shapes, the key enzyme gene ACC was significantly positively correlated with the polyacetylene component, namely atractylodin(P &lt; 0.01), and the key enzyme genes HMGR and FPPS were positively correlated with the sesquiterpene components, namely atractylenolide Ⅰ, β-eudesmol, and atractylon. In summary, the quality of A. chinensis with split leaves is the best, and the biosynthesis of atractylodin is significantly correlated with the gene expression of key enzyme ACC, which provides a theoretical basis for screening and optimizing the germplasm resources of A. chinensis and improving the quality of medicinal materials.

458 Influence of a Gastrointestinal Infection on Lung Immunity

OBJECTIVES/GOALS: We aim to characterize how Heligmosomoides polygyrus bakeri (H. poly) alleviates murine allergic asthma which shares many characteristics of human asthma. This approach of has already identified helminth-produced human immune cell ligand “mimics” that hold great potential for next-generation clinical biologics METHODS/STUDY POPULATION: We examined the lung tissue of C57BL/6 mice infected with H. poly for changes in the pulmonary microenvironment. At ten days post infection, four infected mice and two co-housed uninfected mice were sacrificed, and their lung tissue harvested for examination of RNA via RT-qPCR. This design allows for the comparison between the lung microenvironments of infected and naīve mice. In future experiments, we intend to characterize what small molecules produced by the helminth drive changes in the lung using germ-free models of H. poly infection. RESULTS/ANTICIPATED RESULTS: We found key differences in lung chemokines between mice infected with H. poly and naīve mice. Using a student t-test with naīve correction for variance, we were able to show significant differences in the expression of E cadherin (p = 0.0355), CXCL10 (p = 0.0025), CX3CL1 (p = 0.0029), CCR2 (p = 0.017), and IDO1 (0.0078). We also found that differences in the expression of CCL5 bordered on significant with a p-value of 0.066. The expression of most of these markers (CXCL10, CCR2, CCL5, and IDO1) was elevated in the lungs of infected mice compared to naīve controls. In contrast, E cadherin and CX3CL1 showed the opposite trend with naīve mice showing greater expression. These clear differences in lung tissue gene expression underscore the connection between the gastrointestinal and pulmonary mucosal immune compartments. DISCUSSION/SIGNIFICANCE: The changes are unexpected for an infection that has been shown to attenuate allergic inflammation in the lung with increases in the IFN-Y responsive genes IDO1 and CXCL10 and inflammatory lung markers, CCL5 and CCR2. In contrast, there were decreases in inflammatory lung marker CX3CL1 and the tight junction protein E cadherin in infected mice.

249 Defining the Role of Hedgehog Signaling in Breast Cancer Risk of non-Hispanic Black Women

OBJECTIVES/GOALS: The molecular basis of increased risk of triple negative breast cancer in non-Hispanic Black women represents a critical knowledge gap that this research is designed to address; successful completion of this work could lead to better prevention, earlier stage diagnoses, and possible discovery of novel therapeutic strategies for this population. METHODS/STUDY POPULATION: We have recently generated a living tissue cohort of 11 non-Hispanic Black and 25 non-Hispanic White women who underwent breast surgery at Mayo Clinic. Gene expression profiling of normal breast tissue from this cohort has identified a pattern of gene expression differences that have been associated with the development of basal breast cancer and are also reflective of Hedgehog (Hh) signaling. We will identify protein-based biomarkers for Hedgehog signaling within normal breast tissue using immunohistochemistry methods. We will culture primary human mammary epithelial cells and further separate luminal and myoepithelial cells using flow cytometry to then decipher Hedgehog signaling. RESULTS/ANTICIPATED RESULTS: We anticipate identifying and localizing protein-based biomarkers for Hedgehog signaling within myoepithelial cells of non-Hispanic Black women. Using our findings, we aim to create a biomarker risk model for triple negative breast cancer and validate this model within a separate and larger cohort of women to predict breast cancer risk. DISCUSSION/SIGNIFICANCE: In addition to immediate benefits from improved risk prediction, the proposed work has the potential to provide new insight into the driving forces underlying basal breast carcinogenesis and the distinct biological differences that distinguish non-Hispanic Black women from non-Hispanic White women.

Human Plasma-Like Medium Activates Immune Elements in Glioma

INTRODUCTION: Glioma Surgically eXplanted Organoids (SXOs) are ex vivo three-dimensional models demonstrated to recapitulate the parental tumor microenvironment (TME). Human plasma-like medium (HPLM), a culture medium that mirrors physiologic nutrient conditions, has been found in other cancer subtypes to induce transcriptional differences in T-lymphocyte activation. We hypothesized that SXO culture in HPLM would maintain immune cell populations and induce physiologically relevant immune-modulatory pathways. METHODS: SXOs were established and cultured in conventional Glioma Organoid Complete medium (GOC) and transitioned to HPLM for 24 or 120 hours. Formalin-fixed paraffin-embedded samples were stained for tumor cells (GFAP), immune cells (CD45), and nucleic acid (SYTO-13) and analyzed using the Nanostring GeoMx™ Digital Spatial Profiler for spatial transcriptomics. Gene expression clustering profiles were conducted using GSEA and CIBERSORT. The gene expression differences of SXOs cultured in HPLM for 24 and 120 hours compared to those in GOC were analyzed by unpaired t-tests. RESULTS: Glioma SXOs retain diverse cell populations, with 20-30% of cells belonging to the TME. CD4+ T-cells were the most common (9.7 ± 1.0), followed by CD8+ T-cells (4.4 ± 0.6) and macrophages (3.1 ± 1.2). Following the transition to HPLM for 24 or 120 hours, there were no significant differences in tumor, immune, and stromal cell fractions. HPLM culture upregulated the immune response in SXOs, encompassing enhanced cytokine secretion, as well as improved adaptive and innate immune pathways. We particularly highlighted CD4+ T-cell activation (CD69+), Treg, and TGF-β signaling pathways as significantly increased. CONCLUSIONS: Here, we present that the culture of SXOs in physiologically similar media retains the heterogeneous TME and activates innate and adaptive immune signaling pathways. Culture in HPLM enables investigation of the glioma immune microenvironment, expanding the biological relevance of experimental results from in vitro SXO models.

Humic Acid Mitigates Drought Stress in Tomato

Drought stress, one of the most important abiotic stresses, severely limits global crop production. To increase tolerance to this stress, environmentally friendly practices are emphasised. Humic acid, one of the most important natural biostimulants, has positive effects on plant growth and yield. Recently, it has also been reported to play an important role in resistance to various abiotic stresses. However, many physiological and molecular mechanisms by which humic acid confers drought resistance have not been fully elucidated. Therefore, the effects of humic acid application on different morphological and physiological stress indicators and some antioxidative enzyme gene expressions of tomato seedlings under drought stress conditions were investigated in this study. It was found that drought stress decreased shoot fresh/dry weight, root fresh/dry weight, shoot and root length, chlorophyll and relative water content of plants by 67%, 56%, 31%, 38%, 22%, 20%, 15% and 25%, respectively. Humic acid application significantly increased these parameters, while reducing ion leakage, MDA and proline levels. The antioxidant enzyme gene expression of tomato seedlings under drought conditions showed no significant difference in SOD and APX gene expression, whereas CAT gene expression increased and GR gene expression decreased with humic acid application. Our results showed that humic acid application interacted with stress-related antioxidant enzyme gene expression and may be effective in reducing drought stress.