Significant Differentially Expressed Genes Research Articles

P096 Pathway directionality across different immune cell lineages contributes to methotrexate response in juvenile idiopathic arthritis

Abstract Background/Aims Juvenile idiopathic arthritis (JIA) is the most common autoimmune rheumatic disease in children with methotrexate (MTX) as the first line treatment. However, about 50% of JIA patients will not respond well to MTX yet still experience drug side effects. Early prediction to MTX treatment response would be beneficial for patients and families to avoid incurring unnecessary MTX side effects and ongoing uncontrolled inflammation: such validated tools or biomarkers are currently not available. Methods Transcriptional analysis was performed on peripheral blood mononuclear cells (PBMC) from pre-MTX-treated JIA patients (n = 97) of all ILAR JIA subtypes, excluding systemic JIA. RNAseq was performed on total PBMC and sorted immune cell populations: CD4+ T cells, CD8+ T cells, CD19+ B cells, and CD14+ monocytes. Clinical data collected at the time of sampling (baseline) and at the follow-up time (between 3-12 months) were used to define outcomes, measured as change in active joint count (AJC), change in Physician VAS (PhysVAS), and change in cJADAS10. After batch normalisation with ComBat-seq, differential gene expression (DGE) analysis was performed using limma-voom with age, sex, ethnicity, and steroid status included as covariates. Log2 fold changes were utilised to rank genes to implement gene set enrichment analysis (GSEA) by fgsea. Results DGE analysis showed minimal significant differentially expressed (DE) genes that passed 5% false discovery rate (FDR). The greatest number of significant DE genes were observed in CD14+ monocytes, where baseline expression of 13 genes were significantly associated with change in PhysVAS. As alterations of gene expression for a heterogeneous disease such as JIA can be subtle and correlated between genes, GSEA was performed to investigate expression changes at pathway level. Using MSigDb Hallmark pathways, GSEA showed interferon-related and tumor-necrosis-factor pathways as significantly associated with MTX response in all cell types (5% FDR). However, the directionality (up/down regulation) differed between cell lineages, suggesting pathways divergence between T cell and non-T cell lineages. For example, in interferon gamma pathway, up-regulation associated with poor treatment response in T-cells and down-regulation in non-T cells. Preliminary analysis of the leading edge genes of the interferon gamma pathway in the non-T cell lineages showed that many of the genes are driven by interferon alpha, whilst within CD4+ and CD8+ T cells the majority of the leading edge genes are specific to interferon gamma. Conclusion Different directionality of pathways that might be relevant to JIA response to treatment with MTX is observed in different mononuclear cell lineages. This could potentially explain the difficulties of finding biomarkers which correlate with response to treatment from whole blood or PBMC. Shared genes across different interferon-related pathways also suggest that interaction between interferon pathways might be driving the different direction of interferon pathway expression in different cell lineages. Disclosure M. Kartawinata: None. W. Lin: None. B. Jebson: None. K. O'Brien: None. E. Ralph: None. R. Restuadi: None. G.T. Hall: None. S. Castellano: None. C. Wallace: None. L.R. Wedderburn: Grants/research support; LRW Declares in kind contributions to CLUSTER by AbbVie, GSK, UCB, Sobi and Pfizer inc and non renumerated collaborations with Lilly and Novartis.

The Microglial Transcriptome of Age-Associated Deep Subcortical White Matter Lesions Suggests a Neuroprotective Response to Blood-Brain Barrier Dysfunction.

Age-associated deep-subcortical white matter lesions (DSCLs) are an independent risk factor for dementia, displaying high levels of CD68+ microglia. This study aimed to characterize the transcriptomic profile of microglia in DSCLs and surrounding radiologically normal-appearing white matter (NAWM) compared to non-lesional control white matter. CD68+ microglia were isolated from white matter groups (n = 4 cases per group) from the Cognitive Function and Ageing Study neuropathology cohort using immuno-laser capture microdissection. Microarray gene expression profiling, but not RNA-sequencing, was found to be compatible with immuno-LCM-ed post-mortem material in the CFAS cohort and identified significantly differentially expressed genes (DEGs). Functional grouping and pathway analysis were assessed using the Database for Annotation Visualization and Integrated Discovery (DAVID) software, and immunohistochemistry was performed to validate gene expression changes at the protein level. Transcriptomic profiling of microglia in DSCLs compared to non-lesional control white matter identified 181 significant DEGs (93 upregulated and 88 downregulated). Functional clustering analysis in DAVID revealed dysregulation of haptoglobin-haemoglobin binding (Enrichment score 2.5, p = 0.017), confirmed using CD163 immunostaining, suggesting a neuroprotective microglial response to blood-brain barrier dysfunction in DSCLs. In NAWM versus control white matter, microglia exhibited 347 DEGs (209 upregulated, 138 downregulated), with significant dysregulation of protein de-ubiquitination (Enrichment score 5.14, p < 0.001), implying an inability to maintain protein homeostasis in NAWM that may contribute to lesion spread. These findings enhance understanding of microglial transcriptomic changes in ageing white matter pathology, highlighting a neuroprotective adaptation in DSCLs microglia and a potentially lesion-promoting phenotype in NAWM microglia.

Transcriptome data reveal beneficial effects of Rickettsia (Rickettsiales: Rickettsiaceae) on Bemisia tabaci (Hemiptera: Aleyrodidae) through nutritional factors and defense mechanisms.

Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) is a destructive insect pest of many crops. Rickettsia infection in different cryptic species of B. tabaci has been observed worldwide. Understanding the interactions between these 2 organisms is critical to developing Rickettsia-based strategies to control B. tabaci and thereby reduce the transmission of related vector-borne viruses. In this study, we investigated the effects of Rickettsia infection on the biological characteristics of the Middle East Asia Minor 1 (MEAM1) strain of B. tabaci through biological analysis of infected and uninfected individuals. The results of this study suggest that Rickettsia may confer fitness benefits. These benefits include increased fertility, improved survival rates, accelerated development, and resulted in female bias. We also investigated the transcriptomicsimpact of Rickettsia infection on B. tabaci by performing a comparative RNA-seq analysis of nymphs and adult females, both with and without the infection. Our analysis revealed 218 significant differentially expressed genes (DEGs) in infected nymphs compared to uninfected ones and 748 significant DEGs in infected female adults compared to their uninfected whiteflies. Pathway analysis further revealed that Rickettsia can affect many important metabolic pathways in whiteflies. The results suggest that Rickettsia plays an essential role in energy metabolism, and nutrient synthesis in the B. tabaci MEAM1, and depends on metabolites obtained from the host to ensure its survival. Overall, our findings suggest that Rickettsia has beneficial effects on B. tabaci and offered insights into the potential molecular mechanisms governing the interactions between Rickettsia and B. tabaci MEAM1.

Abstract 5978: Therapeutic targeting of MELK using a drug repurposing approach to combat TNBC cells

Abstract Background: Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer linked to high chemo-resistant metastatic cases and limited therapeutic options due to the absence of conventional bioreceptors. Therefore, to treat TNBC, it is imperative to identify promising druggable biological targets. Experimental Procedures: An integrated bioinformatic analysis of microarray datasets was performed to identify significantly differentially expressed genes (DEGs) in TNBC. For selecting a potent therapeutic target, the function and significance of the upregulated DEGs in TNBC was investigated by an in silico study employing the UALCAN portal, String database, KM plotter, and Enrichr tools. This analysis included gene expression validation, insights into protein-protein interactions, survival analysis, and pathway mapping of the genes. To obtain potent drugs binding to the selected target MELK (maternal embryonic leucine zipper kinase), a drug repurposing approach was employed starting with virtual screening followed by molecular dynamic simulation (MDS) using GROMACS. Further, the anti-cancer activity of the top two drugs was validated by live-dead imaging, gene expression analyses, MTT-based cell viability and ROS detection assays. Results: Based on a stringent criterion for significant DEG identification (log2|FC|&amp;gt;1 &amp; adjust P-value &amp;lt; 0.05), 25 overlapping upregulated genes were obtained from three selected datasets. Further, in silico analysis revealed that MELK is significantly upregulated across the four stages and subtypes of breast cancer, including TNBC. Higher MELK expression and its oncogenic interactions correlated with poor overall survival of TNBC patients. Evidence suggests that the existing inhibitor for MELK (OTSSP167) has shown poor specificity. Therefore, to block its activity, a library of 1293 FDA-approved drugs was screened against the kinase domain of MELK. MDS study and analysis using parameters like RMSD, RMSF and pair distance revealed that the top 10 drugs were strongly stabilized by H-bonds in the binding pocket of MELK, with minimal deviation and reduced fluctuations of MELK upon drug binding. Binding free energy calculation of drug-MELK interaction using the MM-PBSA method revealed that nine drugs possessed higher binding energy than the inhibitor. The top two drugs obtained from the study (originally kinase and reductase inhibitors respectively) were further validated for their in vitro anti-cancer efficacy in MDA-MB-231 and MDA-MB-468 cells. Treatment with these drugs exhibited (a) a dose-dependent decrease in proliferation, (b) significant cell death, (c) a marked increase in the cellular ROS levels, and (d) a decrease in the expression of MELK and its downstream targets in TNBC cell lines. Conclusion: The present study opens the avenue for using repurposed drugs as potential therapeutic molecules against MELK activity to combat TNBC progression. Citation Format: Arisha Arora, Shilpi Sarkar, Siddhartha S. Ghosh. Therapeutic targeting of MELK using a drug repurposing approach to combat TNBC cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5978.

PMAIP1, a novel diagnostic and potential therapeutic biomarker in osteoporosis.

Osteoporosis is a common endocrine metabolic bone disease, which may lead to severe consequences. However, the unknown molecular mechanism of osteoporosis, the observable side effects of present treatments and the inability to fundamentally improve bone metabolism seriously restrict the impact of prevention and treatment. The study aims to identify potential biomarkers from osteoclast progenitors, specifically peripheral blood monocytes on predicting the osteoporotic phenotype. Datasets were obtained from Gene Expression Omnibus (GEO). Based on the differentially expressed genes (DEGs) and GSEA results, GO and KEGG analyses were performed using the DAVID database and Metascape database. PPI network, TF network, drug-gene interaction network, and ceRNA network were established to determine the hub genes. Its osteogenesis, migration, and proliferation abilities in bone marrow mesenchymal stem cells (BMSCs) were validated through RT-qPCR, WB, ALP staining, VK staining, wound healing assay, transwell assay, and CCK-8 assay. A total of 63 significant DEGs were screened. Functional and pathway enrichment analysis discovered that the functions of the significant DEGs (SDEGs) are mainly related to immunity and metal ions. A comprehensive evaluation of all the network analyses, PMAIP1 was defined as osteoporosis's core gene. This conclusion was further confirmed in clinical cohort data. A series of experiments demonstrated that the PMAIP1 gene can promote the osteogenesis, migration and proliferation of BMSC cells. All of these outcomes showed a new theoretical basis for further research in the treatment of osteoporosis, and PMAIP1 was identified as a potential biomarker for osteoporosis diagnosis and treatment.

The Main Targets of Okadaic Acid Toxin in Human Intestinal Caco-2 Cells: An Investigation of Biological Systems

Background: Okadaic acid (OA) is a toxin of polluted shellfish. Consuming the contaminated shellfish is accompanied by diarrhea and paralytic and amnesic disorders. There is a correlation between diarrhea and the consumed OA. Determining the critical targeted genes by OA was the aim of this study. Methods: The transcriptomic data about the effect of OA on human intestinal caco-2 cells were extracted from gene expression omnibus (GEO) and evaluated via the GEO2R program. The significant differentially expressed genes (DEGs) were included in a protein-protein interaction (PPI) network and the central nodes were enriched via gene ontology to find the crucial affected biological terms. Results: Among the 178 significant DEGs plus 50 added first neighbors, four hub-bottleneck genes (ALB, FOS, JUN, and MYC) were determined. Twenty-eight critical biological terms were identified as the dysregulated individuals in response to the presence of OA. “ERK1/2-activator protein-1 (AP-1) complex binds KDM6B promoter” was highlighted as the major class of biological terms. Conclusion: It can be concluded that down-regulation of ALB as a potent central gene leads to impairment of blood homeostasis in the presence of OA. Up-regulation of the other three central genes (JUN, FOS, and MYC) grossly affects the vital pathways in the human body.

Efficacy Evaluation of Human Skin Treatment with Photodynamic Therapy in Actinic Keratoses Patients.

Introduction: Photodynamic therapy (PDT) is a combined method of light and light-activated chemicals that are called photosensitizers (PSs). PDT is recommended as a high cure rate method with fewer side effects and a noninvasive tool to treat cancer. This study aimed to evaluate PDT efficacy as a therapeutic method against actinic keratoses in patients via protein-protein interaction (PPI) network analysis by using the gene expression profiles of Gene Expression Omnibus (GEO). Methods: Twenty-one gene expression profiles were extracted from GEO and analyzed by GEO2R to determine the significant differentially expressed genes (DEGs). The significant DEGs were included in PPI networks via Cytoscape software. The networks were analyzed by the "Network Analyzer", and the elements of the main connected components were assessed. Results: There were three main connected components for the compared sets of the gene expression profiles including the lesional region of skin before (Before set) and after (After set) PDT versus healthy (healthy set) skin and before versus after. The before-health comparison showed a partial similarity with the After-Healthy assessment. The before-after evaluation indicated that there were not considerable differences between the gene expression profile of the lesional region before and after PDT. Conclusion: In conclusion, PDT was unable to return the gene expression pattern of the actinic keratoses skin to a healthy condition completely.

Spatial transcriptomics reveal basal sex differences in supraoptic nucleus gene expression of adult rats related to cell signaling and ribosomal pathways

BackgroundThe supraoptic nucleus (SON) of the hypothalamus contains magnocellular neurosecretory cells that secrete the hormones vasopressin and oxytocin. Sex differences in SON gene expression have been relatively unexplored. Our study used spatially resolved transcriptomics to visualize gene expression profiles in the SON of adult male (n = 4) and female (n = 4) Sprague-Dawley rats using Visium Spatial Gene Expression (10x Genomics).MethodsBriefly, 10-μm coronal sections (~ 4 × 4 mm) containing the SON were collected from each rat and processed using Visium slides and recommended protocols. Data were analyzed using 10x Genomics’ Space Ranger and Loupe Browser applications and other bioinformatic tools. Two unique differential expression (DE) analysis methods, Loupe Browser and DESeq2, were used.ResultsLoupe Browser DE analysis of the SON identified 116 significant differentially expressed genes (DEGs) common to both sexes (e.g., Avp and Oxt), 31 significant DEGs unique to the males, and 73 significant DEGs unique to the females. DESeq2 analysis revealed 183 significant DEGs between the two groups. Gene Ontology (GO) enrichment and pathway analyses using significant genes identified via Loupe Browser revealed GO terms and pathways related to (1) neurohypophyseal hormone activity, regulation of peptide hormone secretion, and regulation of ion transport for the significant genes common to both males and females, (2) Gi signaling/G-protein mediated events for the significant genes unique to males, and (3) potassium ion transport/voltage-gated potassium channels for the significant genes unique to females, as some examples. GO/pathway analyses using significant genes identified via DESeq2 comparing female vs. male groups revealed GO terms/pathways related to ribosomal structure/function. Ingenuity Pathway Analysis (IPA) identified additional sex differences in canonical pathways (e.g., ‘Mitochondrial Dysfunction’, ‘Oxidative Phosphorylation’) and upstream regulators (e.g., CSF3, NFKB complex, TNF, GRIN3A).ConclusionThere was little overlap in the IPA results for the two different DE methods. These results suggest sex differences in SON gene expression that are associated with cell signaling and ribosomal pathways.

Transcriptomics Meta-Analysis Reveals Phagosome and Innate Immune System Dysfunction as Potential Mechanisms in the Cortex of Alzheimer's Disease Mouse Strains.

Immune-related pathways can affect the immune system directly, such as the chemokine signaling pathway, or indirectly, such as the phagosome pathway. Alzheimer's disease (AD) is reportedly associated with several immune-related pathways. However, exploring its underlying mechanism is challenging in animal studies because AD mouse strains differentially express immune-related pathway characteristics. To overcome this problem, we performed a meta-analysis to identify significant and consistent immune-related AD pathways that are expressed in different AD mouse strains. Next-generation RNA sequencing (RNA-seq) and microarray datasets for the cortex of AD mice from different strains such as APP/PSEN1, APP/PS2, 3xTg, TREM, and 5xFAD were collected from the NCBI GEO database. Each dataset's quality control and normalization were already processed from each original study source using various methods depending on the high-throughput analysis platform (FastQC, median of ratios, RMA, between array normalization). Datasets were analyzed using DESeq2 for RNA-seq and GEO2R for microarray to identify differentially expressed (DE) genes. Significantly DE genes were meta-analyzed using Stouffer's method, with significant genes further analyzed for functional enrichment. Ten datasets representing 20 conditions were obtained from the NCBI GEO database, comprising 116 control and 120 AD samples. The DE analysis identified 284 significant DE genes. The meta-analysis identified three significantly enriched immune-related AD pathways: phagosome, the complement and coagulation cascade, and chemokine signaling. Phagosomes-related genes correlated with complement and immune system. Meanwhile, phagosomes and chemokine signaling genes overlapped with B cells receptors pathway genes indicating potential correlation between phagosome, chemokines, and adaptive immune system as well. The transcriptomic meta-analysis showed that AD is associated with immune-related pathways in the brain's cortex through the phagosome, complement and coagulation cascade, and chemokine signaling pathways. Interestingly, phagosome and chemokine signaling pathways had potential correlation with B cells receptors pathway.

Transcriptomic Response of Differentiating Porcine Myotubes to Thermal Stress and Donor Piglet Age.

Climate change is a current concern that directly and indirectly affects agriculture, especially the livestock sector. Neonatal piglets have a limited thermoregulatory capacity and are particularly stressed by ambient temperatures outside their optimal physiological range, which has a major impact on their survival rate. In this study, we focused on the effects of thermal stress (35 °C, 39 °C, and 41 °C compared to 37 °C) on differentiating myotubes derived from the satellite cells of Musculus rhomboideus, isolated from two different developmental stages of thermolabile 5-day-old (p5) and thermostable 20-day-old piglets (p20). Analysis revealed statistically significant differential expression genes (DEGs) between the different cultivation temperatures, with a higher number of genes responding to cold treatment. These DEGs were involved in the macromolecule degradation and actin kinase cytoskeleton categories and were observed at lower temperatures (35 °C), whereas at higher temperatures (39 °C and 41 °C), the protein transport system, endoplasmic reticulum system, and ATP activity were more pronounced. Gene expression profiling of HSP and RBM gene families, which are commonly associated with cold and heat responses, exhibited a pattern dependent on temperature variability. Moreover, thermal stress exhibited an inhibitory effect on cell cycle, with a more pronounced downregulation during cold stress driven by ADGR genes. Additionally, our analysis revealed DEGs from donors with an undeveloped thermoregulation capacity (p5) and those with a fully developed thermoregulation capacity (p20) under various cultivation temperature. The highest number of DEGs and significant GO terms was observed under temperatures of 35 °C and 37 °C. In particular, under 35 °C, the DEGs were enriched in insulin, thyroid hormone, and calcium signaling pathways. This result suggests that the different thermoregulatory capacities of the donor piglets determined the ability of the primary muscle cell culture to differentiate into myotubes at different temperatures. This work sheds new light on the underlying molecular mechanisms that govern piglet differentiating myotube response to thermal stress and can be leveraged to develop effective thermal management strategies to enhance skeletal muscle growth.

Transcriptomic profiling of human granulosa cells between women with advanced maternal age with different ovarian reserve

BackgroundAge-related diminished ovarian reserve (DOR) is not absolute. Some advanced maternal age (AMA) still have normal ovarian reserve (NOR) and often show better pregnancy outcomes. Exploring the transcriptomic profile of granulosa cells (GCs) in AMA could lead to new ideas for mitigating age-related diminished ovarian reserve.AimThis study aimed to analyze the transcriptomic profile of GCs in AMA with different ovarian reserve.ResultsIn total, 6273 statistically significant differential expression genes (DEGs) (|log2fc|> 1, q < 0.05) were screened from the two groups, among which 3436 genes were upregulated, and 2837 genes were downregulated in the DOR group. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, the potential functions of dysregulated genes in AMA with DOR or NOR were predicted. The GO enrichment analysis revealed that the DEGs were mainly enriched in obsolete oxidation–reduction process, mitochondrion, metal ion binding, ATP binding, etc. The KEGG pathway enrichment analysis revealed that the above-mentioned DEGs were mainly enriched in ferroptosis, regulation of actin cytoskeleton, oxidative phosphorylation, etc. Meanwhile, verification of the mRNA expression levels of DEGs revealed the possible involvement of “ferroptosis” in age-related diminished ovarian reserve.ConclusionsFrom a new clinical perspective, we presented the first data showing the transcriptomic profile in GCs between AMA with different ovarian reserve. At the same time, we identified the role of ferroptosis in the GCs of AMA, providing a new biological basis for studying ovarian aging and improving pregnancy outcomes of AMA.

Identification of ATP6V0A4 as a potential biomarker in renal cell carcinoma using integrated bioinformatics analysis.

Clear cell renal cell carcinoma (ccRCC) is the most common pathological type of renal cancer, and is associated with a high mortality rate, which is related to high rates of tumor recurrence and metastasis. The aim of the present study was to identify reliable molecular biomarkers with high specificity and sensitivity for ccRCC. A total of eight ccRCC-related expression profiles were downloaded from Gene Expression Omnibus for integrated bioinformatics analysis to screen for significantly differentially expressed genes (DEGs). Reverse transcription-quantitative (RT-q)PCR, western blotting and immunohistochemistry staining assays were performed to evaluate the expression levels of candidate biomarkers in ccRCC tissues and cell lines. In total, 255 ccRCC specimens and 165 adjacent normal kidney specimens were analyzed, and 344 significant DEGs, consisting of 115 upregulated DEGs and 229 downregulated DEGs, were identified. The results of Gene Ontology analysis suggested a significant enrichment of DEGs in 'organic anion transport' and 'small molecule catabolic process' in biological processes, in 'apical plasma membrane' and 'apical part of the cell' in cell components, and in 'anion transmembrane transporter activity' and 'active transmembrane transporter activity' in molecular functions. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis indicated that the DEGs were significantly enriched in the 'phagosome', the 'PPAR signaling pathway', 'complement and coagulation cascades', the 'HIF-1 signaling pathway' and 'carbon metabolism'. Next, 7 hub genes (SUCNR1, CXCR4, VCAN, CASR, ATP6V0A4, VEGFA and SERPINE1) were identified and validated using The Cancer Genome Atlas database. Survival analysis showed that low expression of ATP6V0A4 was associated with a poor prognosis in patients with ccRCC. Additionally, received operating characteristic curves indicated that ATP6V0A4 could distinguish ccRCC samples from normal kidney samples. Furthermore, RT-qPCR, western blotting and immunohistochemistry staining results showed that ATP6V0A4 was significantly downregulated in ccRCC tissues and cell lines. In conclusion, ATP6V0A4 may be involved in tumor progression and regarded as a potential therapeutic target for the recurrence and metastasis of ccRCC.

Identification and cross-validation of autophagy-related genes in cardioembolic stroke.

Cardioembolic stroke (CE stroke, also known as cardiogenic cerebral embolism, CCE) has the highest recurrence rate and fatality rate among all subtypes of ischemic stroke, the pathogenesis of which was unclear. Autophagy plays an essential role in the development of CE stroke. We aim to identify the potential autophagy-related molecular markers of CE stroke and uncover the potential therapeutic targets through bioinformatics analysis. The mRNA expression profile dataset GSE58294 was obtained from the GEO database. The potential autophagy-related differentially expressed (DE) genes of CE stroke were screened by R software. Protein-protein interactions (PPIs), correlation analysis, and gene ontology (GO) enrichment analysis were applied to the autophagy-related DE genes. GSE66724, GSE41177, and GSE22255 were introduced for the verification of the autophagy-related DE genes in CE stroke, and the differences in values were re-calculated by Student's t-test. A total of 41 autophagy-related DE genes (37 upregulated genes and four downregulated genes) were identified between 23 cardioembolic stroke patients (≤3 h, prior to treatment) and 23 healthy controls. The KEGG and GO enrichment analysis of autophagy-related DE genes indicated several enriched terms related to autophagy, apoptosis, and ER stress. The PPI results demonstrated the interactions between these autophagy-related genes. Moreover, several hub genes, especially for CE stroke, were identified and re-calculated by Student's t-test. We identified 41 potential autophagy-related genes associated with CE stroke through bioinformatics analysis. SERPINA1, WDFY3, ERN1, RHEB, and BCL2L1 were identified as the most significant DE genes that may affect the development of CE stroke by regulating autophagy. CXCR4 was identified as a hub gene of all types of strokes. ARNT, MAPK1, ATG12, ATG16L2, ATG2B, and BECN1 were identified as particular hub genes for CE stroke. These results may provide insight into the role of autophagy in CE stroke and contribute to the discovery of potential therapeutic targets for CE stroke treatment.

Integrated transcriptomic and metabolomic analysis the variation of rice cultivars response to arsenite stress

Arsenic (As) is considered to be a carcinogen that tends to be accumulated in rice. However, the molecular mechanism of crop response to As is not sufficiently understood. In the study, M2 and L5 were screened out from 16 experimental cultivars as sensitive and tolerant ones based on the phenotypic changes between As(III) treated and control group, respectively. A total of 11052 significant differential expression genes (DEGs) and 918 significantly differentially accumulated metabolites (DAMs) were identified by using the comparative transcriptomic and metabolomic analysis. The KEGG pathway analysis suggesting that As(III) stress could effectively induce the production of DEGs related to rice defense function to improve plant tolerance responses to As(III) toxicity. The variation of DEGs metabolic pathways between two comparison groups was mainly concerning plant growth. The metabolomic analysis demonstrated that DAMs detected in M2 and L5 were principally enriched in the pathway related to plant growth, development and stress tolerance. The dermatan L-iduronate was the largest contributors of the two pairwise groups to separating metabolites in As(III) treated to control group. The combined transcriptome and metabolome analysis revealed that changes of the DAMs in M2 and L5 comparison groups regulated by DEGs resulted in variation in phenotype and arsenic accumulation between the two cultivars. This study provides insight into the molecular mechanisms related to the response and processes involved in toxic effects and adaptive strategies to As(III) stress.

Prognostic model development for classification of colorectal adenocarcinoma by using machine learning model based on feature selection technique boruta

Colorectal cancer (CRC) is the third most prevalent cancer type and accounts for nearly one million deaths worldwide. The CRC mRNA gene expression datasets from TCGA and GEO (GSE144259, GSE50760, and GSE87096) were analyzed to find the significant differentially expressed genes (DEGs). These significant genes were further processed for feature selection through boruta and the confirmed features of importance (genes) were subsequently used for ML-based prognostic classification model development. These genes were analyzed for survival and correlation analysis between final genes and infiltrated immunocytes. A total of 770 CRC samples were included having 78 normal and 692 tumor tissue samples. 170 significant DEGs were identified after DESeq2 analysis along with the topconfects R package. The 33 confirmed features of importance-based RF prognostic classification model have given accuracy, precision, recall, and f1-score of 100% with 0% standard deviation. The overall survival analysis had finalized GLP2R and VSTM2A genes that were significantly downregulated in tumor samples and had a strong correlation with immunocyte infiltration. The involvement of these genes in CRC prognosis was further confirmed on the basis of their biological function and literature analysis. The current findings indicate that GLP2R and VSTM2A may play a significant role in CRC progression and immune response suppression.

Abstract 3901: Identification of genomic pathways associated with resistance of NSCLC to immunotherapies containing granzyme B

Abstract Immuno-oncologic (IO) approaches have completely transformed lung cancer treatment. Unfortunately, most patients with NSCLC develop primary resistance during IO and less than 20% achieve partial or complete response. Understanding the pathways to resistance is a significant challenge that requires a focused approach combining both clinical and basic research. Because resistance to IO is complex and likely multimodal, it is vital to find alternative strategies to overcome these challenges. IO generally employs cellular-mediated delivery of granzyme (GrB) as the final toxic payload and fusion proteins containing GrB serve as a targeted therapeutic with an identical mechanism of cytotoxic action. Subsequent development of resistance to GrB-based fusions may provide a look into the intrinsic mechanism of resistance related to cell signaling and gene expression for IO agents. The human fusion protein GrB-Fc-IT4 contains a single chain variable fragment targeting the Fn14 (fibroblast growth factor-inducible 14) receptor for TWEAK that is overexpressed in several tumor types, including NSCLC. GrB-Fc-IT4 exhibits high affinity and selective cytotoxicity within the nanomolar range when tested against a large panel of Fn14+ human cancer cell lines including NSCLC. We generated 3 resistant clones from a NSCLC GrB-sensitive cell line (A549) by exposing the cells to increasing concentrations of GrB-Fc-IT4. We then conducted a comprehensive genomic characterization of the GrB-sensitive A549 and compared to the GrB-Fc-IT4 resistant clones (A549R-F5, A549R-F7 and A549R-F8) to identify significant differentially expressed genes (DEGs) and pathways involved in GrB-resistance mechanisms. By mapping gene expression changes we have established that clones A549R-F5 and A549R-F7 have a very similar genomic profile, while the clone A549R-F8 displays a distinctive genomic profile. These results suggest that clones A549R-F5 and A549R-F7 shared a similar mechanism of resistance whereas clone A549R-F8 mechanism of resistance might be different. Comparison of the GrB-resistant clones with 7 NSCLC cell lines sensitive to GrB-Fc-IT4 revealed 43 significant DEGs (padj&amp;lt;0.05), suggesting these genes could be involved in the GrB response. From these DEGs, 34 genes had a higher basal expression in the GrB-resistant clonal cell lines while 9 DEGs were downregulated. Significantly, sensitivity of GrB-resistant cell lines to the chemotherapy agent cisplatin showed that the GrB-resistant clones were 6-fold more resistant than the parental cell line. We found that 13 DEGs of the 43 DEGS have also been described to be involved with cisplatin- or damage-response. These novel candidates for GrB resistance could prove to be important prognostic markers or targets for tailored combined therapy in the future. Research conducted, in part, by the Clayton Foundation for Research and Lung Spore (P50CA070907). Citation Format: Ana Alvarez-Cienfuegos, Lawrence H. Cheung, Khalid A. Mohamedali, Ganiraju C. Manyam, Jing Wang, John V. Heymach, Michael G. Rosenblum. Identification of genomic pathways associated with resistance of NSCLC to immunotherapies containing granzyme B. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3901.

Abstract P5-09-02: Impact of neoadjuvant endocrine therapy on tumor transcriptome in patients with early-stage breast cancer from the FLEX trial

Abstract BACKGROUND: Neoadjuvant Endocrine Therapy (NET) is seldom used in breast cancer management except in patients with several comorbidities or in elderly patients in which chemotherapy is not an option. Clinical response with NET is not typically achieved until after several months of treatment. In the NET setting, reduction of Ki67 (&amp;lt; 10%) after 2-4 weeks has been used as a predictor of positive response, but studies such as ALTERNATE have questioned this association. It remains uncertain whether a single gene or protein can adequately predict outcomes or inform how NET alters a variety of cancer genes and global tumor biology. This study evaluated the effect of short-term NET on the tumor genomics of patients with early-stage breast cancer (EBC) by comparing whole transcriptome gene expression changes in matched pre- and post-NET tumor samples. METHODS: In this single-institution FLEX substudy performed at Johns Hopkins, patients (n=30) with matched pre- and post-treatment specimens who received at least two weeks of NET between 2019 – 2021 were included. Premenopausal and male patients with breast cancer received Tamoxifen (n=10) and postmenopausal women received either Letrozole (n=10) or Exemestane (n=10). Limma R package was used for quantile normalization and differential gene expression analysis. Significant differentially expressed genes (DEGs) had a false discovery rate of &amp;lt; 0.05 and &amp;gt;2-fold change. Pathway enrichment analysis was performed using Reactome. For patients with available clinical information, changes in immunohistochemistry (IHC) between pre- and post-NET were quantified using absolute values, and the median percent change was reported, with significance assessed using the Wilcoxon test. The observational FLEX trial (NCT03053193) enrolls patients with EBC who have MammaPrint (MP) with or without BluePrint testing and consent to clinically annotated full transcriptome data collection. MammaPrint classifies tumors as having a Low Risk (LR) or High Risk (HR) of distant recurrence. BluePrint is a molecular subtyping assay, and together with MammaPrint, tumors are classified as Luminal A-Type (MP LR), Luminal B-Type (MP HR), HER2-Type, or Basal-Type. RESULTS: Transcriptional profiles between pre- and post-NET samples were distinct with short-term NET inducing 774 DEGs. The majority of significant DEGs (n=748) such as MGAT1, IQGAP3, and PRC1, which are associated with tumor aggressiveness and metastasis, were downregulated in post-NET samples. Upregulated genes in post-NET tumors, such as FOS, JUN, and EGR1, are involved in estrogen signaling and NF-κB pathways and are associated with better outcomes. Among the 30 patients, 7 (6 Luminal B and 1 Basal) remained MP HR and 16 remained MP LR (Luminal A) pre- and post-NET, 1 changed from LR (Luminal A) pre-NET to HR (Luminal B) post-NET, and 6 changed from HR (Luminal B) pre-NET to LR post-NET (Luminal A). The median percent change by IHC in matched pre- and post-NET tissue was 2.5% for estrogen receptor (ER) (range: 0-50%; p=0.750), 22% for progesterone receptor (PR) (range: 0-81%; p=0.097), and 9% for Ki67 (range: 0-43%; p=0.026). CONCLUSIONS: In this study, significant gene expression changes were discovered within a shorter timeframe than when clinical responses are usually observed in the NET setting. This could indicate biological complexity and diverse response pathways, which may be more informative when combined with a single IHC biomarker (ER/PR/Ki67). Results from this study should be confirmed using a larger cohort. Future studies will determine the significance of these DEGs and their impact on outcomes, and will further define gene expression changes by endocrine therapy type (tamoxifen versus aromatase inhibitors). ACKNOWLEDGMENTS: We would like to thank Lynn and Robert Downing for their generous support of our study. Citation Format: Mehran Habibi, Danijela Jelovac, Rima Couzi, Cesar Augusto Santa-Maria, Catherine Klein, Marissa White, Nivali Naik, Jennifer Wei, Yen Huynh, Architha Ellappalayam, Lisa E. Blumencranz, Erin B. Yoder, Patricia Dauer, Bas van der Baan, William Audeh. Impact of neoadjuvant endocrine therapy on tumor transcriptome in patients with early-stage breast cancer from the FLEX trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-09-02.

Effect of Pseudostellaria heterophylla polysaccharide on the growth and liver metabolism of chicks.

In this study, the effects of Pseudostellaria heterophylla polysaccharide (PHP) on the growth, development, and liver metabolism of chicks were investigated by feeding chicks diets. Four hundred 7-d-old Gushi roosters were selected and randomly divided into four groups, labeled A, B, C, and D. Group A was fed the basal diet, and Groups B, C, and D were fed 100, 200, and 400 mg PHP per kilogram of basal diet, respectively. At 14, 21, 28 and 35 d of age, five chicks were randomly selected from each group to collect samples for index detection. The results showed that compared with Group A, there were significant reduction in average daily feed intake (ADFI) and feed-to-weight ratio (F/G) at 14, 21, and 28 d (P < 0.05), significant increase in average daily gain (ADG) at 21, 28 d (P < 0.05), significantly increased levels of total protein (TP), albumin (ALB), insulin (INS), thyroxine (T3), growth hormone (GH) at 14, 28 d (P < 0.05), significantly decreased levels of glucose (GLU), total cholesterol (TC), glucagon (GC), and triglyceride (TG) at 28 d in Group C (P < 0.05). There were significantly increased levels of TP, ALB at 14, 21 d (P < 0.05), significantly increased level of TP at 35 d (P < 0.05), significantly increased level of GH at 28 d (P < 0.05), significantly decreased levels of GLU, GC at 28 d (P < 0.05), significant reduction in F/G at 14, 21 d in Groups B and D (P < 0.05). Based on the above results, the livers from chicks in Groups A and C at 28 d were selected for transcriptome sequencing. The sequencing results showed that significantly differentially expressed genes (SDEGs) were enriched in growth and development, oxidative phosphorylation, the PPAR signaling pathway and the lipid metabolism pathway. All these results revealed that the addition of 200 mg/kg PHP in the diet promoted the growth and development, lipid metabolism and energy metabolism of chicks, inhibit inflammation and tumor development, and improve the function of the liver.

The Caribbean-Hispanic Alzheimer's disease brain transcriptome reveals ancestry-specific disease mechanisms

Identifying ancestry-specific molecular profiles of late-onset Alzheimer's Disease (LOAD) in brain tissue is crucial to understand novel mechanisms and develop effective interventions in non-European, high-risk populations. We performed gene differential expression (DE) and consensus network-based analyses in RNA-sequencing data of postmortem brain tissue from 39 Caribbean Hispanics (CH). To identify ancestry-concordant and -discordant expression profiles, we compared our results to those from two independent non-Hispanic White (NHW) samples (n = 731). In CH, we identified 2802 significant DE genes, including several LOAD known-loci. DE effects were highly concordant across ethnicities, with 373 genes transcriptome-wide significant in all three cohorts. Cross-ancestry meta-analysis found NPNT to be the top DE gene. We replicated over 82% of meta-analyses genome-wide signals in single-nucleus RNA-seq data (including NPNT and LOAD known-genes SORL1, FBXL7, CLU, ABCA7). Increasing representation in genetic studies will allow for deeper understanding of ancestry-specific mechanisms and improving precision treatment options in understudied groups.

Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B

BackgroundChrysanthemum virus B (CVB), a key member of the genus Carlavirus, family Betaflexiviridae, causes severe viral diseases in chrysanthemum (Chrysanthemum morifolium) plants worldwide. However, information on the mechanisms underlying the response of chrysanthemum plants to CVB is scant.MethodsHere, an integrated next-generation sequencing and comparative transcriptomic analysis of chrysanthemum leaves was conducted to explore the molecular response mechanisms of plants to a Chinese isolate of CVB (CVB-CN) at the molecular level.ResultsIn total, 4934 significant differentially expressed genes (SDEGs) were identified to respond to CVB-CN, of which 4097 were upregulated and 837 were downregulated. Gene ontology and functional classification showed that the majority of upregulated SDEGs were categorized into gene cohorts involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, and ribosome metabolism. Enrichment analysis demonstrated that ethylene pathway-related genes were significantly upregulated following CVB-CN infection, indicating a strong promotion of ethylene biosynthesis and signaling. Furthermore, disruption of the ethylene pathway in Nicotiana benthamiana, a model plant, using virus-induced gene silencing technology rendered them more susceptible to cysteine-rich protein of CVB-CN induced hypersensitive response, suggesting a crucial role of this pathway in response to CVB-CN infection.ConclusionThis study provides evidence that ethylene pathway has an essential role of plant in response to CVB and offers valuable insights into the defense mechanisms of chrysanthemum against Carlavirus.