Comparative Gene Expression Analysis Research Articles

MitoPADdb: A database of mitochondrial proteins associated with diseases

Mitochondrial protein/gene mutations and expression variations contribute to the pathogenesis of various diseases, such as neurodegenerative and metabolic diseases. Detailed studies on mitochondrial protein-encoding (MPE) genes across diseases can provide clues for novel therapeutic strategies. Here, we collected, compiled, and manually curated the MPE gene mutation and expression variations data and their association with diseases in a single platform named mitoPADdb. The database contains 810 genes with 18,356 mutations and 1284 qualitative expression variations associated with 1793 diseases, grouped into 15 categories. It allows users to perform a comparative quantitative gene expression analysis for 317 transcriptomic studies across disease categories. Further, it provides information on MPE genes-associated molecular pathways. The mitoPADdb is a valuable resource for investigating mitochondrial dysfunction-related diseases. It can be accessed via http://bicresources.jcbose.ac.in/ssaha4/mitopaddb/index.html.

Transcriptomic Analysis Reveals Sex-Based Differences in The Prefrontal Cortex of Autism Spectrum Disorder Patients.

The prevalence of neurological disorders often varies by sex, with conditions such as Alzheimer's disease and autism spectrum disorder (ASD) demonstrating notable differences in incidence. The aim of this study is to understand the molecular basis for these divergences in order to facilitate the creation of sex-specific therapeutic strategies. This study is a bioinformatic analysis of publicly available RNA sequencing datasets involving autism patients. The study utilized RNA sequencing data from postmortem human brains' prefrontal cortex, including 38 neurotypical controls and 34 individuals with ASD. The sequencing data was obtained from previously published papers, and we downloaded the raw data from SRA. We investigated the molecular basis of sex-biased presentation in ASD through comprehensive transcriptomic analysis. Comparative analysis of gene expression between male and female subjects, both autistic and unaffected, was conducted, using a significance level of ≤0.01. In autistic individuals, 136 genes demonstrated differential expression between sexes, predominantly upregulated in males, indicating a bias in male gene expression. Among these, 12 genes were identified as risk factors in the SFARI dataset. While most sex-biased genes were autosomal, expression differences on sex chromosomes were also observed in neurotypical subjects. Notable genes included TCF7L2, collagen family genes, and solute carrier family genes. In ASD males, extracellular matrix (ECM) organization emerged as a significant pathway, while immune-related processes were prominent in unaffected individuals. Our study highlights the impact of the ECM pathway in ASD, with notable differences between sexes, particularly in males. MIR424 shows promise as a potential biomarker for ASD in males. Recognizing the importance of sex differences in ASD transcriptomic research is crucial, as these variances provide insights into the disorder's pathophysiology and may guide the development of more personalized treatments for both sexes.

Engineered uterine primary myometrial cells with high-mobility group AT-hook 2 overexpression display a leiomyoma-like transcriptional and epigenomic phenotype

To determine if engineered HMGA2 overexpressing uterine primary myometrial cells recapitulate the transcriptional and epigenomic features of HMGA2-subtype leiomyomas. Isolated primary, "normal" myometrial cells from 3 patients were engineered to overexpress HMGA2 to determine how HMGA2 establishes transcriptomic and epigenomic features of HMGA2-overexpressing leiomyoma. Academic research laboratory PATIENTS: Primary myometrial cells were isolated from normal myometrium obtained from three patients undergoing hysterectomy. Not applicable MAIN OUTCOME MEASURES: Determined genome-wide transcriptomic and epigenomic features of engineered HMGA2-overexpressing uterine primary myometrial cells. Engineered HMGA2-V5-overexpressing primary myometrial cells approximated the HMGA2 expression level observed in HMGA2-overexpression subtype leiomyoma. HMGA2-V5 expression resulted in differential expression of 1612 genes (FDR < 0.05) which were found to be enriched in pathways associated with leiomyoma formation, including extracellular matrix organization. Comparative gene expression analysis between HMGA2-V5 engineered primary cells and HMGA2-overexpression subtype leiomyoma revealed significant overlap of differentially expressed genes. Mechanistically, HMGA2-V5 overexpression resulted in 41,323 regions with differential H3K27ac deposition (FDR < 0.05) and 205,605 regions of altered chromatin accessibility (FDR < 0.05). Transcription factor binding site analysis implicated the AP-1 family of transcription factors. • What clinical problem is addressed by these studies? About 10-15% of the uterine leiomyoma cases exhibit increased expression of HMGA2; our study addresses the primary role of HMGA2 overexpression in the pathogenesis of leiomyoma. • What are the key findings? Ectopic expression of HMGA2 in primary myometrial cells transforms transcriptional and epigenomic machinery in these cells which to some extent resemble features of leiomyoma. • How do these findings apply to human fertility or the reproductive process? Our study provides a comprehensive analysis into the changes occurring in epigenome of myometrial cells when HMGA2 is overexpressed. Because epigenome can be targeted with drugs, therefore understanding alterations in epigenome provides new avenues for treating leiomyoma which affects reproductive age women.

Comparative Cytological and Gene Expression Analysis Reveals That a Common Wild Rice Inbred Line Showed Stronger Drought Tolerance Compared with the Cultivar Rice.

Common wild rice (Oryza rufipogon Griff.) is an important germplasm resource containing valuable genes. Our previous analysis reported a stable wild rice inbred line, Huaye3, which derives from the common wild rice of Guangdong Province. However, there was no information about its drought tolerance ability. Here, we assessed the germination characteristics and seedling growth between the Dawennuo and Huaye3 under five concentrations of PEG6000 treatment (0, 5%, 10%, 15%, and 20%). Huaye3 showed a stronger drought tolerance ability, and its seed germination rate still reached more than 52.50% compared with Dawennuo, which was only 25.83% under the 20% PEG6000 treatment. Cytological observations between the Dawennuo and Huaye3 indicated the root tip elongation zone and buds of Huaye3 were less affected by the PEG6000 treatment, resulting in a lower percentage of abnormalities of cortical cells, stele, and shrinkage of epidermal cells. Using the re-sequencing analysis, we detected 13,909 genes that existed in the genetic variation compared with Dawennuo. Of these genes, 39 were annotated as drought stress-related genes and their variance existed in the CDS region. Our study proved the strong drought stress tolerance ability of Huaye3, which provides the theoretical basis for the drought resistance germplasm selection in rice.

Single-neuron analysis of aging-associated changes in learning reveals impairments in transcriptional plasticity.

The molecular mechanisms underlying age-related declines in learning and long-term memory are still not fully understood. To address this gap, our study focused on investigating the transcriptional landscape of a singularly identified motor neuron L7 in Aplysia, which is pivotal in a specific type of nonassociative learning known as sensitization of the siphon-withdraw reflex. Employing total RNAseq analysis on a single isolated L7 motor neuron after short-term or long-term sensitization (LTS) training of Aplysia at 8, 10, and 12 months (representing mature, late mature, and senescent stages), we uncovered aberrant changes in transcriptional plasticity during the aging process. Our findings specifically highlight changes in the expression of messenger RNAs (mRNAs) that encode transcription factors, translation regulators, RNA methylation participants, and contributors to cytoskeletal rearrangements during learning and long noncoding RNAs (lncRNAs). Furthermore, our comparative gene expression analysis identified distinct transcriptional alterations in two other neurons, namely the motor neuron L11 and the giant cholinergic neuron R2, whose roles in LTS are not yet fully elucidated. Taken together, our analyses underscore cell type-specific impairments in the expression of key components related to learning and memory within the transcriptome as organisms age, shedding light on the complex molecular mechanisms driving cognitive decline during aging.

Risk assessment, fitness cost and transcriptome analysis of cyantraniliprole resistance in Spodoptera frugiperda

Spodoptera frugiperda is a notorious invasive pest causing substantial yield losses of crops and has developed resistance to various types of insecticides. In this study, a cyantraniliprole-resistant strain, SfCYAN-R, was obtained from a susceptible strain, SfCYAN-S, after 13 generations of selection with cyantraniliprole. The fitness cost in SfCYAN-R strain was evaluated, and the putative resistance-related genes were explored by RNA-seq analysis. The results showed that SfCYAN-R strain developed 23.97-fold resistance to cyantraniliprole with the realistic heritability of 0.127. The development time of eggs, larvae, prepupae and pupae in SfCYAN-R strain was significantly prolonged than that in SfCYAN-S strain, but no difference in pupation rate, emergence rate and female fecundity was observed between SfCYAN-R and SfCYAN-S strains. Comparative gene expression analysis between SfCYAN-R and SfCYAN-S strains identified 776 significant differentially expressed genes (DEGs), among which several DEGs associated with xenobiotic metabolism were upregulated in SfCYAN-R strain. These results provide insights into the resistance mechanisms of cyantraniliprole and would be helpful for resistance management of S. frugiperda.

Integration of Image Pattern Recognition and Photon Sensor for Analyzing Cytokine Gene Expression Using πCode MicroDisc.

Current quantitative gene expression detection in genomic and transcriptomic research heavily relies on quantitative real-time PCR (qPCR). While existing multiplex gene detection techniques offer simultaneous analysis of multiple targets, we present an alternative assay capable of detecting gene expression simultaneously within a single well. This highly sensitive method utilizes πCode MicroDiscs, featuring unique identification patterns and fluorescent detection. Our study compared this multiplex πCode platform with a qPCR platform for profiling cytokine gene expression. The πCode MicroDisc assay successfully demonstrated the expression of polymerization markers for M1- and M2-like macrophages generated from THP-1-derived macrophages in a qualitative assay. Additionally, our findings suggest a pattern agreement between the πCode assay and the qPCR assay, indicating the potential of the πCode technology for comparative gene expression analysis. Regarding the inherent sensitivity and linearity, the developed πCode assay primarily provides qualitative gene expression to discriminate the polarization of macrophages. This remarkable capability presents substantial advantages for researchers, rendering the technology highly suitable for high-throughput applications in clinical diagnosis and disease monitoring.

Unraveling the influence of metabolic signatures on immune dynamics for predicting immunotherapy response and survival in cancer

AbstractMetabolic reprogramming in cancer significantly impacts immune responses within the tumor microenvironment, but its influence on cancer immunotherapy effectiveness remains uncertain. This study aims to elucidate the prognostic significance of metabolic genes in cancer immunotherapy through a comprehensive analytical approach. Utilizing data from the IMvigor210 trial (n = 348) and validated by retrospective datasets, we performed patient clustering using non‐negative matrix factorization based on metabolism‐related genes. A metabiotic score was developed using a “DeepSurv” neural network to assess correlations with overall survival (OS), progression‐free survival, and immunotherapy response. Validation of the metabolic score and key genes was achieved via comparative gene expression analysis using qPCR. Our analysis identified four distinct metabolic classes with significant variations in OS. Notably, the metabolism‐inactive and hypoxia‐low class demonstrated the most pronounced benefit in terms of OS. The metabolic score predicted immunotherapeutic benefits with high accuracy (AUC: 0.93 at 12 months). SETD3 emerged as a crucial gene, showing strong correlations with improved OS outcomes. This study underscores the importance of metabolic profiling in predicting cancer immunotherapy success. Specifically, patients classified as metabolism‐inactive and hypoxia‐low appear to derive substantial benefits. SETD3 is established as a promising prognostic marker, linking metabolic activity with patient outcomes, advocating for the integration of metabolic profiling into immunotherapy strategies to enhance treatment precision and efficacy.

Whole genome resequencing reveals the genetic basis of albino phenotype in an ornamental fish, Channa asiatica

Body color is one of the most noticeable phenotypic and economic characteristics in fish. Fish exhibit a diverse array of body color mutations influenced by factors such as artificial selection and natural mutations. Elucidating the genetic mechanisms of these color variants in fish is crucial for developing new breeds with higher ornamental value. In this study, we identified a nonsense mutation in csf1ra (c. 1249 C>T) with whole genome resequencing technology, and which may potentially contribute to the albino phenotype in Channa asiatica. The albino individuals exhibited a substantial decrease in the expression level of csf1ra compared to that of the wild individuals. To unravel the underlying mechanism of csf1ra, we delved into comparative transcriptomic and gene expression analyses. Our findings suggest that csf1ra may impact tyrosine kinase activity. Furthermore, csf1ra may not only regulate the expression levels of genes (sox9, ephb6, and wnt9) involved in melanin-based pigmentation but also influence genes (ampd3, ak1, and bco1) associated with non-melanin-based pigmentation. Our study investigated the genetic basis of the albino mutant of C. asiatica and provided new insights into the function of csf1ra in fish pigmentation.

Genome-Wide Transcriptomic and Metabolomic Analyses Unveiling the Defence Mechanisms of Populus tremula against Sucking and Chewing Insect Herbivores.

Plants and insects coevolved as an evolutionarily successful and enduring association. The molecular arms race led to evolutionary novelties regarding unique mechanisms of defence and detoxification in plants and insects. While insects adopt mechanisms to conquer host defence, trees develop well-orchestrated and species-specific defence strategies against insect herbivory. However, current knowledge on the molecular underpinnings of fine-tuned tree defence responses against different herbivore insects is still restricted. In the current study, using a multi-omics approach, we unveiled the defence response of Populus tremula against aphids (Chaitophorus populialbae) and spongy moths (Lymantria dispar) herbivory. Comparative differential gene expression (DGE) analyses revealed that around 272 and 1203 transcripts were differentially regulated in P. tremula after moth and aphid herbivory compared to uninfested controls. Interestingly, 5716 transcripts were differentially regulated in P. tremula between aphids and moth infestation. Further investigation showed that defence-related stress hormones and their lipid precursors, transcription factors, and signalling molecules were over-expressed, whereas the growth-related counterparts were suppressed in P. tremula after aphid and moth herbivory. Metabolomics analysis documented that around 37% of all significantly abundant metabolites were associated with biochemical pathways related to tree growth and defence. However, the metabolic profiles of aphid and moth-fed trees were quite distinct, indicating species-specific response optimization. After identifying the suitable reference genes in P. tremula, the omics data were further validated using RT-qPCR. Nevertheless, our findings documented species-specific fine-tuning of the defence response of P. tremula, showing conservation on resource allocation for defence overgrowth under aphid and moth herbivory. Such findings can be exploited to enhance our current understanding of molecular orchestration of tree responses against herbivory and aid in developing insect pest resistance P. tremula varieties.

Identification and validation of potential diagnostic signature and immune cell infiltration for HIRI based on cuproptosis-related genes through bioinformatics analysis and machine learning.

Cuproptosis has emerged as a significant contributor in the progression of various diseases. This study aimed to assess the potential impact of cuproptosis-related genes (CRGs) on the development of hepatic ischemia and reperfusion injury (HIRI). The datasets related to HIRI were sourced from the Gene Expression Omnibus database. The comparative analysis of differential gene expression involving CRGs was performed between HIRI and normal liver samples. Correlation analysis, function enrichment analyses, and protein-protein interactions were employed to understand the interactions and roles of these genes. Machine learning techniques were used to identify hub genes. Additionally, differences in immune cell infiltration between HIRI patients and controls were analyzed. Quantitative real-time PCR and western blotting were used to verify the expression of the hub genes. Seventy-five HIRI and 80 control samples from three databases were included in the bioinformatics analysis. Three hub CRGs (NLRP3, ATP7B and NFE2L2) were identified using three machine learning models. Diagnostic accuracy was assessed using a receiver operating characteristic (ROC) curve for the hub genes, which yielded an area under the ROC curve (AUC) of 0.832. Remarkably, in the validation datasets GSE15480 and GSE228782, the three hub genes had AUC reached 0.904. Additional analyses, including nomograms, decision curves, and calibration curves, supported their predictive power for diagnosis. Enrichment analyses indicated the involvement of these genes in multiple pathways associated with HIRI progression. Comparative assessments using CIBERSORT and gene set enrichment analysis suggested elevated expression of these hub genes in activated dendritic cells, neutrophils, activated CD4 memory T cells, and activated mast cells in HIRI samples versus controls. A ceRNA network underscored a complex regulatory interplay among genes. The genes mRNA and protein levels were also verified in HIRI-affected mouse liver tissues. Our findings have provided a comprehensive understanding of the association between cuproptosis and HIRI, establishing a promising diagnostic pattern and identifying latent therapeutic targets for HIRI treatment. Additionally, our study offers novel insights to delve deeper into the underlying mechanisms of HIRI.

Expression and clinical significance of pattern recognition receptor-associated genes in hand, foot and mouth disease

Objective: To explore which pattern recognition receptors (PRRs) play a key role in the development of hand, foot, and mouth disease (HFMD) by analyzing PRR-associated genes. Methods: We conducted a comparative analysis of PRR-associated gene expression in human peripheral blood mononuclear cells (PBMCs) infected with enterovirus 71 (EV-A71) which were derived from patients with HFMD of different severities and at different stages. A total of 30 PRR-associated genes were identified as significantly upregulated both over time and across different EV-A71 isolates. Subsequently, ELISA was employed to quantify the expression of the six most prominent genes among these 30 identified genes, specifically, BST2, IRF7, 1FI16, TRIM21, MX1, and DDX58. Results: Compared with those at the recovery stage, the expression levels of BST2 (P=0.027), IFI16 (P=0.016), MX1 (P=0.046) and DDX58 (P=0.008) in the acute stage of infection were significantly upregulated, while no significant difference in the expression levels of IRF7 (P=0.495) and TRIM21 (P=0.071) was found between different stages of the disease. The expression levels of BST2, IRF7, IFI16 and MX1 were significantly higher in children infected with single pathogen than those infected with mixed pathogens, and BST2, IRF7, IFI16 and MX1 expression levels were significantly lower in coxsackie B virus (COXB) positive patients than the negative patients. Expression levels of one or more of BST2, IRF7, IFI16, TRIM21, MX1 and DDX58 genes were correlated with PCT levels, various white blood cell counts, and serum antibody levels that reflect disease course of HFMD. Aspartate aminotransferase was correlated with BST2, MX1 and DDX58 expression levels. Conclusions: PRR-associated genes likely initiate the immune response in patients at the acute stage of HFMD.

Comparative analysis of gene expression between mice and humans in acetaminophen-induced liver injury by integrating bioinformatics analysis

ObjectiveMice are routinely utilized as animal models of drug-induced liver injury (DILI), however, there are significant differences in the pathogenesis between mice and humans. This study aimed to compare gene expression between humans and mice in acetaminophen (APAP)-induced liver injury (AILI), and investigate the similarities and differences in biological processes between the two species.MethodsA pair of public datasets (GSE218879 and GSE120652) obtained from GEO were analyzed using “Limma” package in R language, and differentially expressed genes (DEGs) were identified, including co-expressed DEGs (co-DEGs) and specific-expressed DEGS (specific-DEGs). Analysis of Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed analyses for specific-DEGs and co-DEGs. The co-DEGs were also used to construct transcription factor (TF)-gene network, gene-miRNA interactions network and protein-protein interaction (PPI) network for analyzing hub genes.ResultsMouse samples contained 1052 up-regulated genes and 1064 down-regulated genes, while human samples contained 1156 up-regulated genes and 1557 down-regulated genes. After taking the intersection between the DEGs, only 154 co-down-regulated and 89 co-up-regulated DEGs were identified, with a proportion of less than 10%. It was suggested that significant differences in gene expression between mice and humans in drug-induced liver injury. Mouse-specific-DEGs predominantly engaged in processes related to apoptosis and endoplasmic reticulum stress, while human-specific-DEGs were concentrated around catabolic process. Analysis of co-regulated genes reveals showed that they were mainly enriched in biosynthetic and metabolism-related processes. Then a PPI network which contains 189 nodes and 380 edges was constructed from the co-DEGs and two modules were obtained by Mcode. We screened out 10 hub genes by three algorithms of Degree, MCC and MNC, including CYP7A1, LSS, SREBF1, FASN, CD44, SPP1, ITGAV, ANXA5, LGALS3 and PDGFRA. Besides, TFs such as FOXC1, HINFP, NFKB1, miRNAs like mir-744-5p, mir-335-5p, mir-149-3p, mir-218-5p, mir-10a-5p may be the key regulatory factors of hub genes.ConclusionsThe DEGs of AILI mice models and those of patients were compared, and common biological processes were identified. The signaling pathways and hub genes in co-expression were identified between mice and humans through a series of bioinformatics analyses, which may be more valuable to reveal molecular mechanisms of AILI.

Abstract 876: spatialGE: Empowering researchers to study the tumor microenvironment leveraging spatial transcriptomics

Abstract The use of single-cell RNA-seq (scRNA-seq) to understand the complexity of the tumor microenvironment (TME) has been pivotal in advancing cancer research and treatment strategies. Nevertheless, locating the individual TME components in their spatial contexts is essential to understanding the complexity of the TME, tumorigenesis, metastasis, and drug response. The recent popularity of spatially resolved transcriptomics (SRT) allows researchers to describe the TME and their spatial neighborhoods; however, SRT data analysis can be challenging for non-data scientists. Thus, we have developed spatialGE, a point-and-click web application designed to empower researchers in the analysis of SRT data. Our application offers a suite of functionalities, including the visualization of spatial gene expression activity maps, quantification of the spatial heterogeneity, testing of pathway-level spatial aggregation, tissue domain/niche detection, detection of spatial gradients in expression patterns, and differential expression analysis. Furthermore, spatialGE allows direct comparative analysis of gene expression with the morphology in tissue images, as well as methods for cell/domain phenotyping. Data input has been streamlined and made flexible to receive outputs from multiple SRT platforms. Analyses and results are stored within user-defined projects to facilitate accessibility at any time. We demonstrate the usefulness of spatialGE through its application to leptomeningeal metastatic melanoma (LMM) tissues assayed with the Visium platform. The gene expression tissue domain detection and gradient analysis in spatialGE indicated that SERPINA3 expression is higher in tumor regions closer to stroma. This finding led to cell culture experiments indicating that knocking down SERPINA3 results in the sensitization of tumors to MAPK-targeting therapy. These results highlight the utility of spatialGE for exploring SRT data and the empowerment of cancer researchers to explore the spatial architecture of the TME. Citation Format: Oscar Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Tsai, Joseph Markowitz, Anders Berglund, Xiaoqing Yu, Brooke L. Fridley. spatialGE: Empowering researchers to study the tumor microenvironment leveraging spatial transcriptomics [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 876.

Comparative analysis of differential gene expression reveals novel insights into the heteroblastic foliage functional traits of Pinus massoniana seedlings

Pinus massoniana needles, rich in medicinal polysaccharides and flavonoids, undergo heteroblastic foliage, transitioning from primary needles (PN) to secondary needles (SN) during growth, resulting in altered functional traits. Despite its significance, the molecular regulatory mechanisms governing these traits remain unclear. This study employs Iso-Seq and RNA-Seq analyses to explore differentially expressed genes (DEGs) associated with functional traits throughout the main growth season of heteroblastic foliage. Co-expression network analysis identified 34 hub genes and 17 key transcription factors (TFs) influencing light-harvesting antenna, photosystem I and II, crucial in photosynthesis regulation. Additionally, 14 genes involved in polysaccharide metabolism pathways, synthesizing sucrose, glucose, UDP sugars, and xylan, along with four genes in flavonoid biosynthesis pathways, regulating p-coumaroyl-CoA, quercetin, galangin, and myricetin production, exhibited differential expression between PN and SN. Further analysis unveils a highly interconnected network among these genes, forming a pivotal cascade of TFs and DEGs. Therefore, heteroblastic changes significantly impact needle functional traits, potentially affecting the pharmacological properties of PN and SN. Thus, these genomic insights into understanding the molecular-level differences of heteroblastic foliage, thereby establishing a foundation for advancements in the pharmaceutical industry related to needle-derived products.

Genetic diversity promotes resilience in a mouse model of Alzheimer's disease.

Alzheimer's disease (AD) is a neurodegenerative disorder with multifactorial etiology, including genetic factors that play a significant role in disease risk and resilience. However, the role of genetic diversity in preclinical AD studies has received limited attention. We crossed five Collaborative Cross strains with 5xFAD C57BL/6J female mice to generate F1 mice with and without the 5xFAD transgene. Amyloid plaque pathology, microglial and astrocytic responses, neurofilament light chain levels, and gene expression were assessed at various ages. Genetic diversity significantly impacts AD-related pathology. Hybrid strains showed resistance to amyloid plaque formation and neuronal damage. Transcriptome diversity was maintained across ages and sexes, with observable strain-specific variations in AD-related phenotypes. Comparative gene expression analysis indicated correlations between mouse strains and human AD. Increasing genetic diversity promotes resilience to AD-related pathogenesis, relative to an inbred C57BL/6J background, reinforcing the importance of genetic diversity in uncovering resilience in the development of AD. Genetic diversity's impact on AD in mice was explored. Diverse F1 mouse strains were used for AD study, via the Collaborative Cross. Strain-specific variations in AD pathology, glia, and transcription were found. Strains resilient to plaque formation and plasma neurofilament light chain (NfL) increases were identified. Correlations with human AD transcriptomics were observed.

Abstract 1676 Comparative Analysis of Differential Gene Expression of Cultured Cell Lines Exposed to Bisphenol-A and Taxol

Abstract 1676 Comparative Analysis of Differential Gene Expression of Cultured Cell Lines Exposed to Bisphenol-A and Taxol

Comparative Analysis of Quantitative Gene Expression of TGF-β in Patients with Recurrent Vulvovaginal Candidiasis and the Normal Population

Background: Recurrent vulvovaginal candidiasis (RVVC) is a widespread opportunistic gynecological condition resulting from infections by Candida albicans and non-C. albicans (NAC) species. Transforming growth factor-beta (TGF-β), a significant cytokine involved in cell-mediated immunity (CMI), plays a crucial role in vaginal infections. Objectives: The current study was conducted to evaluate the differences in TGF-β gene expression between patients with RVVC and healthy individuals using real-time polymerase chain reaction (PCR). Methods: This case-control study involved 124 patients diagnosed with RVVC and 225 age-matched healthy individuals as controls. The mRNA expression of the TGF-β gene was measured using quantitative real-time PCR (QRT-PCR). Data analysis and the creation of graphs were carried out using SPSS and GraphPad PRISM software. Results: The QRT-PCR findings showed higher TGF-β expression in RVVC patients compared to the control group, though the difference was not statistically significant (P = 0.2538). Conclusions: Our study revealed that the expression of the TGF-β1 isoform was elevated in patients with clinical manifestations in the vagina, although the increase was not statistically significant. Based on this outcome, further in vivo studies are necessary to elucidate the precise role of TGF-β isoforms in the vaginal tract of patients with RVVC.

Functional Analysis of Genes Specifically Expressed during Aerial Hyphae Collapse as a Potential Signal for Perithecium Formation Induction in Fusarium graminearum.

Fusarium graminearum, the causal agent of Fusarium head blight (FHB) in cereal crops, employs the production of sexual fruiting bodies (perithecia) on plant debris as a strategy for overwintering and dissemination. In an artificial condition (e.g., carrot agar medium), the F. graminearum Z3643 strain was capable of producing perithecia predominantly in the central region of the fungal culture where aerial hyphae naturally collapsed. To unravel the intricate relationship between natural aerial hyphae collapse and sexual development in this fungus, we focused on 699 genes differentially expressed during aerial hyphae collapse, with 26 selected for further analysis. Targeted gene deletion and quantitative real-time PCR analyses elucidated the functions of specific genes during natural aerial hyphae collapse and perithecium formation. Furthermore, comparative gene expression analyses between natural collapse and artificial removal conditions reveal distinct temporal profiles, with the latter inducing a more rapid and pronounced response, particularly in MAT gene expression. Notably, FGSG_09210 and FGSG_09896 play crucial roles in sexual development and aerial hyphae growth, respectively. Taken together, it is plausible that if aerial hyphae collapse occurs on plant debris, it may serve as a physical cue for inducing perithecium formation in crop fields, representing a survival strategy for F. graminearum during winter. Insights into the molecular mechanisms underlying aerial hyphae collapse provides offer potential strategies for disease control against FHB caused by F. graminearum.

OP21 Spatial Transcriptomics of Pre-treatment Biopsies Revealing Molecular Maturation State and Chronic Crypt Damage, Reflecting Histological Severity, as Predictors of Primary Responsiveness to TNF-α Inhibitors in Bio-naive Ulcerative Colitis Patients

Abstract Background Biologic therapies, particularly tumor necrosis factor-alpha inhibitors (TNFi), have greatly advanced the treatment of ulcerative colitis (UC), yet significant number of patients still do not respond to these treatments. For UC management, achieving both histologic and molecular healing is crucial, highlighting the need for more comprehensive therapeutic strategies. Despite extensive research, there is a significant gap in studies that simultaneously assess histologic and molecular changes at both the crypt and lamina propria (LP) levels. Our study addresses this gap by investigating TNFi-resistant UC patients, utilizing spatial transcriptomics to discern specific cell types within histologic sections and integrating these insights to enhance understanding of UC treatment responses. Methods We evaluated 56 patients categorized into test (n=23), validation (n=31), and healthy control groups (n=2). Each underwent biopsies at the same sites before (preTx) and after treatment (postTx), as shown in Figure 1A. This study focused on a 3-month follow-up of patients who were administered TNFi as a primary biologic therapy following resistance to conventional treatments. We used digital spatial profiling to analyze gene expression in the crypt and LP, as seen in Figures 1B and 1C. We then correlated molecular data with morphological characteristics and quantitatively evaluated histologic factors, especially crypt distortion and atrophy, reported as percentages (%). Results Among the study participants, 29 were classified as responders (R) to TNFi, while 25 were non-responders (non-R). A comparative analysis of gene expression between R and non-R groups revealed a differential expression pattern: 72 genes in the crypt and 105 genes in the LP across varying histologies, as shown in Figure 1D and 1E. Notably, in the preTx samples of non-R, crypts displayed significantly lower expression of genes associated with the maturation of colonocytes, including BEST4, C10orf99, CA2, CA4, CA7, PHGR1, SLC26A2, SLC26A3, LYPD8, CLCA1, and SCNN1, compared to the R group (Figure 1F). Furthermore, when correlating spatial transcriptomic data with histomorphological features, we observed that crypt distortion and atrophy were significantly more pronounced in the non-R group than in the R group in the preTx biopsy samples (Figures 1G and 1H). Conclusion Our study's spatial profiling unveils distinct molecular and histologic features between R and non-R to TNFi among bio-naive UC patients. The evaluation of chronic histological features such as crypt distortion, and molecular maturation status, in predicting TNFi response highlights the potential of early histologic assessment in guiding biologic therapy in the UC treatment pathway.