Downregulation Of Genes Research Articles

Altered expression of Csnk1a1p in Autism Spectrum Disorder in Iranian population: case-control study.

Over the past decade, substantial scientific evidence has showed that long non-coding RNAs (lncRNAs) are extensively expressed and play a crucial role in gene modulation through a diverse range of transcriptional, and post-transcriptional mechanisms. Recent discoveries have emphasized the involvement of lncRNAs in maintaining cellular homeostasis and neurogenesis in the brain. Accumulating reports identified dysregulated lncRNAs associated with psychiatric disorders, including autism. In this study, we examined the expression levels of DISC2, Linc00945, Foxg1-as1, Csnk1a1p, and Evf2 lncRNAs in blood samples from 21 clinically diagnosed autistic patients based on the Diagnostic and Statistical Manual of Mental Disorders criteria-5th edition (DSM-5), compared to age, sex, and ethnically-matched 25 healthy individuals. RNA extraction and cDNA synthesis were performed, followed by real-time PCR for quantification of lncRNAs expression levels. Receiver operating characteristic (ROC) curve analysis was used to evaluate biomarker potential. Additionally, we investigated the correlation between gene expression levels and autism comorbidities. Our results showed a significant decrease in Csnk1a1p expression in patients with autism spectrum disorder (ASD) compared to healthy children (P value = 0.0008). ROC curve analysis indicated that Csnk1a1p expression levels could effectively discriminate patients from healthy controls (AUC = 0.837, P value = 0.000284). No significant differences were observed between Csnk1a1p expression levels and comorbidity with ADHD or intellectual disability (p-value > 0.05). Based on these findings, Csnk1a1p may play a significant role in autistic patients and could serve as a potential biomarker for diagnostic and predictive purposes, as well as a therapeutic target.

Single-cell expression and immune infiltration analysis of polyamine metabolism in breast cancer.

Breast cancer is one of the most threatening women health diseases worldwide and its molecular heterogeneity offers a range of response to therapy. The role of polyamine metabolism is receiving increasing attention. Polyamine metabolism not only plays an important role in the occurrence and development of breast cancer, but also interacts with tumor immune microenvironment. In this work, we applied single-cell RNA-sequencing (scRNA-seq) and systems immunological approaches to interrogate immune cell infiltration gene-to-gene co-expressions in the bulk tumor transcriptomes of breast cancer. We acquired breast cancer sample data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), evaluated the infiltration status of 22 immune cell types using CIBERSORTx tool, respectively. By leveraging the Retrospective Breast sample of various technologies including gene expression and methylation, we identified 46 breast cancer proliferation-associated co-expression modules using weighted gene coexpression network analysis (WGCNA) approach along with machine learning models which in turn delineated single cell level expressions features that these selected module possessed. We observed substantial cellular heterogeneity in the breast cancer microenvironment, where lineage-specific gene expression patterns were highly associated with tumor progression. Moreover, we also identified the gene modules correlated with immune cell infiltration level that could function as regulators in response to tumors for immune therapy. Moreover, risk scores were correlated with immune cell function in different patient groups defined by high- and low-risk. The findings of this study shed a new light upon molecular classification prognostic assessment and personalized treatment in breast cancer.

ABA and Melatonin: Players on the Same Field?

In plants, abscisic acid (ABA) and melatonin (MT) are conventionally treated as molecules mitigating stress responses. To understand the mechanisms of ABA–MT interplay, we examined the effects of ABA and MT treatment in ABA and MT loss-of-function mutants of Arabidopsis thaliana exposed to high light (HL) stress. ABA constantly suppressed ASMT encoding N-acetylserotonin methyltransferase in the context of differential responses of other MT biosynthesis genes in both the wild type (WT) and mutants. However, this response was absent in the mutant with the disrupted ABI4. Given that the ASMT promoter region contains several potential ABI4-binding elements, these data suggest that ASMT can be a potential target gene for ABI4. A role for ABI4 in the interactions between ABA and MT is supported by the finding that ABI4 is constitutively derepressed in the MT signaling mutants cand2 and gpa1, which exhibited elevated steady state levels of ABI4 transcripts and were not regulated by either stress or melatonin. In addition, the abi4 mutant showed increased modulations in the expression of the MT catabolic genes M2H and M3H in response to ABA treatment, inferring that this transcription factor is a negative regulator of ABA-dependent changes in MT content. Furthermore, all tested mutants with impaired ABA synthesis or signaling displayed elevated steady state MT levels compared to WT, while MT treatment contributed to the downregulation of key ABA synthesis and signaling genes. Collectively, our results suggest that ABA and melatonin act antagonistically, modulating the expression of ABA and MT signaling and metabolism genes. To understand the mechanisms of ABA–MT interactions, we studied the effects of ABA and MT treatment in ABA and MT loss-of-function mutants of Arabidopsis thaliana exposed to severe light stress (SLS).

Unveiling the Anticancer Potential of a New Ciprofloxacin-Chalcone Hybrid as an Inhibitor of Topoisomerases I & II and Apoptotic Inducer

The current study has yielded promising results in the evaluation of a new ciprofloxacin-chalcone hybrid (CP derivative) for its anticancer activity as potential Topoisomerases (Topo) I and II inhibitors. The in vitro results showed that the CP derivative significantly suppressed the growth of HCT-116 and LOX IMVI cells, with IC50 values of 5.0 μM and 1.3 μM, respectively, outperforming Staurosporine, which had IC50 values of 8.4 μM and 1.6 μM, respectively. Flow cytometry analysis revealed that the new CP derivative triggered apoptosis and cell cycle arrest at the G2/M phase, associated with the up-regulation of pro-apoptotic genes (Bax and Caspase 9) and downregulation of the anti-apoptotic gene (Bcl-2). Further investigations showed that the CP derivative inhibited Topo I and II enzymes, as expected molecular targets; docking studies further supported its dual inhibitory action on Topo I and II. These findings suggest that the ciprofloxacin-chalcone hybrid could be a promising lead compound for developing new anticancer therapy.

The H3K27me3 histone mark correlates with repression of colour and aroma development post-harvest in strawberry fruit.

Strawberry ripening is non-climacteric, and post-harvest fruit enter senescence and deteriorate rapidly. Chilled storage induces transcriptome wide changes in gene expression, including the down-regulation of aroma related genes. Histone marks are associated with transcriptional activation or repression; the H3K27me3 mark is mainly associated with repression of gene expression. Here genes associated with H3K27me3 were identified through ChIP-seq in ripe red strawberry fruit at harvest and after 5 days of chilled storage in the dark. The number of ChIP peaks increased with storage time, indicating an increased role for this mark in regulation of gene expression following chilled dark storage. Comparing ChIP-seq data to RNA-seq data from the same material identified 440 genes whose expression correlates with H3K27me3 repression. Abiotic stress genes, especially cold stress response genes, were down-regulated during storage. Increased association with the H3K27me3 mark indicates that they may be repressed via this epigenetic mark. Other functional groups included cell wall and carbohydrate metabolism. The association with the H3K27me3 mark of two transcription factors (FaHY5 and FaTRAB1) and FaADH, involved in ester biosynthesis, was validated by ChIP-PCR. These three genes are all down-regulated during storage and indicate a network of H3K27me3 gene repression affecting both anthocyanin and ester biosynthesis.

Transcriptional Responses of Lacticaseibacillus rhamnosus to TNFα, IL-6, IL-8, and IL-10 Cytokines

The interaction between gut microbiota and the host immune system is a complex and understudied field, with cytokines like TNFα, IL-6, IL-8, and IL-10 playing pivotal roles. Commensal bacteria, including lactobacilli, respond to these cytokines through adaptive mechanisms that support their survival and function within the gut. While the influence of cytokines on pathogenic bacteria is well documented, their impact on commensal bacteria, particularly lactobacilli, remains underexplored. This study investigates the transcriptional responses of Lacticaseibacillus rhamnosus strains K32 and R19-3 to various cytokines using next-generation RNA sequencing (RNA-seq). Our findings reveal that cytokines, especially IL-8 and IL-10, significantly alter the L. rhamnosus transcriptome, affecting genes involved in carbohydrate metabolism, stress response, and transcriptional regulation. Notably, IL-8 and IL-10 induce a significant downregulation of genes related to the phosphotransferase system, suggesting a reduction in metabolic activity in response to inflammatory signals. This study unveils a previously unexplored aspect of L. rhamnosus adaptation, highlighting its intricate response to cytokine signals. By modulating gene expression, L. rhamnosus may mitigate the adverse effects of inflammation and promote gut health. These insights could inform the development of targeted probiotic therapies for inflammatory bowel disease (IBD) and other conditions with altered cytokine levels. Our results suggest that co-evolution between a host and gut microbiota enables bacteria to respond to specific cytokines through gene expression changes, revealing a unique and underexplored facet of the interaction between commensal bacteria and the host organism.

Genetic improvement of eating and cooking quality of rice cultivars in southern China.

The genetic improvement of rice eating and cooking quality (ECQ) is an important goal in rice breeding. It is important to understand the genetic regulation of ECQ at the genomic level for effective breeding to improve ECQ. However, the mechanisms underlying the improvement of ECQ of indica and japonica cultivars in southern China remain unclear. In this study, 290 rice cultivars (155 indica and 135 japonica cultivars) bred in southern China in the past 30 years were collected. Physicochemical indicators, namely, apparent amylose content (AAC), protein content (PC), lipid content and taste value, were measured and correlation analysis was performed. Adecrease in AAC and PC was a crucial factor for the ECQ improvement of the rice cultivars in southern China. Genome-wide association analysis and selective domestication analysis preliminarily clarified that the comprehensive utilization of major and minor genes was an important genetic basis for improvement of ECQ. An elite allele, RAmy1AA, with potential application in breeding to improve starch viscosity characteristics and ECQ, was mined. The Wxb/OsmtSSB1LT/OsDML4G/RPBFT/Du3T and Wxb/OsEro1T/Glup3G/OsNAC25G/OsBEIIbC/RAmy1AA/FLO12A gene modules, neither of which have been widely used, are proposed as the optimal allele combinations for ECQ improvement of indica and japonica cultivars in southern China. The results clarify the genetic regulation of rice ECQ improvement in southern China and provide novel genetic resources and breeding strategies for ECQ improvement in rice.

Comprehensive assessment of cellular senescence in intestinal immunity and biologic therapy response in ulcerative colitis.

Ulcerative Colitis (UC) is an inflammatory disorder characterized by chronic intestinal inflammation and immune dysregulation. Despite a clear association between cellular senescence and chronic inflammation and immune dysregulation, the mechanisms underlying cellular senescence in UC remain unclear. We screened differentially expressed genes (DEGs) associated with cellular senescence in multiple UC datasets, performed immune infiltration analysis, and constructed clinical diagnostic models. Additionally, we investigated the relationship between key genes related to cellular senescence and disease remission in UC patients undergoing biologic therapy, validating their expression in a single-cell dataset. We identified six DEGs associated with cellular senescence (TWIST1, IGFBP5, MME, IFNG, ME1, FOS). Immune infiltration results indicated strong correlations of four of these genes with immune cells and pathways. Through WGCNA, GO, and KEGG analyses, we found that gene modules strongly associated with the expression of hub genes in cellular senescence were enriched in inflammation-related pathways. In the single-cell dataset, the expression of these six key genes exhibited similarities with Immune infiltration results. Additionally, we constructed a nomogram using these six genes for diagnosing UC, demonstrating good diagnostic capability and clinical efficacy. Kaplan-Meier survival analysis revealed a significant association between changes in the expression levels of these cell genes and disease remission in UC patients undergoing biologic therapy. This study utilizes bioinformatic analysis and machine learning to identify and analyze features associated with cellular senescence in multiple UC datasets. It provides insights into the role of cellular senescence in the premature onset of intestinal aging in UC and offers new perspectives for exploring novel therapeutic targets.

Abstract B004: Ovarian cancer long intergenic noncoding RNA 1 is a potential therapeutic target in advanced ovarian cancer by promoting glycolytic pathway and hypoxic response

Abstract Ovarian cancer (OvC) is often diagnosed as an advanced disease because symptoms do not develop at earlier stages. Besides current treatments, alternative efficient therapies for OvC need to be established. We have previously identified that a novel long intergenic noncoding RNA (lincRNA) originated from chromosome 10q21 was predominantly expressed in clinical ovarian cancer tissues, designated as ovarian cancer lincRNA 1 (OIN1). Silencing of OIN1 in OvC cell lines substantially exhibited the inhibition of in vitro and in vivo cell proliferation, by upregulating apoptosis-related genes. In the present study, we aimed to evaluate whether OIN1 can be a therapeutic target in advanced OvC and how OIN1 drives the progression of OvC. We established long-term culturable spheroid cultures of OvC patient-derived cells (OvC-PDCs) from ascites of OvC patients as an advanced OvC model. The OvC-PDC spheroid cultures abundantly expressed OIN1 and stemness-related genes. OIN1-targeted siRNAs could suppress the spheroid growth and upregulate apoptosis-related genes such as RASSF5 and ADORA1 in OvC-PDC cultures. In a bloody ascites-generating xenograft in vivo model of mice intraperitoneally injected with OvC-PDC, OIN1-targeted siRNA treatment engineered by drug delivery system alleviated ascites production and prolonged the mice survival time. Based on transcriptomic analysis of OIN1 silencing in OvC-PDC cultures, we found that OIN1 inhibition exerts the downregulation of genes involved in glycolytic pathway and hypoxic response. We further demonstrated that OIN1 modulates HIF1a-mediated transcriptional regulation in OvC- PDCs. The present findings provide promising evidence that OIN1 can be a potential therapeutic target for advanced OvC. Citation Format: Kuniko Horie, Wataru Sato, Kazuhiro Ikeda, Satoshi Inoue. Ovarian cancer long intergenic noncoding RNA 1 is a potential therapeutic target in advanced ovarian cancer by promoting glycolytic pathway and hypoxic response [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr B004.

Transcriptome-based network analysis related to regulatory T cells infiltration identified RCN1 as a potential biomarker for prognosis in clear cell renal cell carcinoma.

Regulatory T cells (Tregs) play a critical role in shaping the immunosuppressive microenvironment within tumors. Investigating the role of Tregs in Clear cell renal cell carcinoma (ccRCC) is crucial for identifying prognostic markers and therapeutic targets for ccRCC. Weighted gene co-expression network analysis (WGCNA) was utilized to pinpoint modules related to Treg infiltration in TCGA-KIRC samples. Following this, consensus clustering was employed to derive two clusters associated with Treg infiltration in ccRCC. A prognostic model was then developed using the gene module associated with Treg infiltration. We then evaluated the ability of the prognostic model to predict ccRCC overall survival and demonstrated that RCN1 can be used as a target to predict ccRCC prognosis. We deduce that the two clusters associated with Treg infiltration exhibit distinct compositions of the immune microenvironment, pathway activations, prognosis, and drug sensitivities commonly utilized in ccRCC treatment. Furthermore, a 7-gene model risk score, developed based on ccRCC Treg infiltration, proved to be a reliable prognostic marker in both training and validation cohorts. Additionally, survival analysis indicated that RCN1 serves as a reliable prognostic factor for ccRCC. Single-cell sequencing analysis revealed that RCN1 is predominantly expressed in tumor cells. A pan-cancer analysis highlighted that RCN1 is linked with poor prognosis and the activation of inflammatory response pathways across various cancers. We developed a prognostic model associated with Treg infiltration, which facilitates the clinical categorization of ccRCC progression. Moreover, our findings underscore the significant potential of RCN1 as a ccRCC biomarker.

Ulp1 Regulates Cell Proliferation Through INO1 in Pichia pastoris

Background/Objectives: Ulp1 is a vital regulator of the cell cycle, with its absence leading to G2/M phase arrest in Saccharomyces cerevisiae. This study aims to investigate the role of Ulp1 in cell cycle regulation in Pichia pastoris and to elucidate its mechanisms of action, particularly through the modulation of the gene INO1. Methods: We generated Ulp1 knockout strains in Pichia pastoris using the FLP-FRT system and performed RNA sequencing (RNA-seq) to analyze gene expression changes. We assessed cell proliferation in Ulp1 knockout and INO1 overexpressing strains, as well as the effects of inositol supplementation. Results: Our findings revealed significant downregulation of INO1 and other genes in Ulp1 knockout strains. Importantly, overexpression of INO1 restored cell proliferation, indicating that Ulp1 regulates this process via INO1. Notably, supplementation with exogenous inositol did not rescue cell proliferation, suggesting that the enzymatic activity of INO1 is not required for Ulp1’s regulatory function. Conclusions: This study demonstrates that Ulp1 modulates cell proliferation in Pichia pastoris through INO1, independent of its enzymatic activity. These insights enhance our understanding of Ulp1’s role in cell cycle regulation and open new avenues for exploring the molecular mechanisms governing yeast cell division. Further investigations are warranted to delineate the intricate regulatory pathways involved in this process.

Synergistic Effects of Dietary Tryptophan and Dip Vaccination in the Immune Response of European Seabass Juveniles

Vaccination is an effective, cost-efficient method to preventing disease outbreaks. However, vaccine procedures can induce adverse reactions due to stress, increasing plasma cortisol in the short term. In this context, tryptophan may prove to be fundamental as it has been demonstrated to have various desirable neuroendocrine attributes in different fish species. Therefore, this study aimed to evaluate both short-term (3 days) and long-term (21 days) effects of dietary tryptophan supplementation on European seabass juveniles’ (26.23 ± 7.22 g) response to vaccination and disease resistance to Tenacibaculum maritimum. The short-term tryptophan-fed fish exhibited increased hepatic superoxide dismutase and plasma cortisol levels, along with the downregulation of immune-related genes. Despite these changes, disease resistance was unaffected. When fish were later dip vaccinated, tryptophan prevented the stress-induced plasma cortisol increase and upregulated the gene expression of igm, suggesting tryptophan’s role in enhancing vaccination efficiency by counteracting stress-associated effects. In the long term, the lowest supplementation dose counteracted vaccine-mediated reduced gene expression, and fish fed this diet showed a more modest molecular response. Overall, the findings suggest a complex interplay between tryptophan supplementation, immune responses, and vaccine efficiency in fish. Further research is necessary to clarify how tryptophan could consistently improve vaccine efficiency in aquaculture.

Stable self-assembled oral metformin-bridged nanocochleates against hepatocellular carcinoma.

Despite its established anti-diabetic activity, Metformin hydrochloride (MET) has been repurposed for the management of hepatocellular carcinoma (HCC). Owing to MET high aqueous solubility and poor oral permeability, a novel nanoplatform is sought to overcome the current challenges of traditional formulations. In this study, we developed MET-bridged nanocochleates (MET-CO) using a direct bridging method followed by optimization and assessment using various in-vitro and in-vivo pharmacokinetic methods. The optimized nanocochleates MET-CODCP 19, containing dicetyl phosphate (DCP), displayed uniform snail-shaped nano-rolls measuring 136.41 ± 2.11nm with a PDI of 0.241 ± 0.005 and a highly negative ζ-potential of -61.93 ± 2.57 mV. With an impressive MET encochleation efficiency (> 75%), MET-CODCP 19 exhibited a controlled biphasic release profile, with minimal initial burst followed by prolonged release for 24h. Importantly, they showed significant MET permeation in both in-vitro Caco-2 and ex-vivo intestinal models compared to non-DCP containing formula or MET solution. The in-vivo oral bioavailability study demonstrated pronounced improvements in the pharmacokinetic parameters with a 5.5 relative bioavailability compared to MET solution. Notably, a significant reduction in IC50 values in HepG2 cells after 24h of treatment was observed. Furthermore, the optimized formulation showed a significant downregulation of anti-apoptotic and cancer stemness genes, with 12- and 2-fold lower expression compared to MET solution. These promising results highlight the efficacy of the novel MET-bridged nanocochleates as a stable nanoplatform for enhancing the oral bioavailability of MET and boosting its anticancer potential against HCC.

Notch signaling mediates between two pattern-forming processes during head regeneration in Hydra.

Hydra head regeneration consists of hypostome/organizer and tentacle development, and involves Notch and Wnt/β-catenin signaling. Notch inhibition blocks hypostome/organizer regeneration, but not the appearance of the tentacle tissue. β-Catenin inhibition blocks tentacle, but not hypostome/organizer regeneration. Gene expression analyses during head regeneration revealed the Notch-promoting expression of HyWnt3, HyBMP2/4, and the transcriptional repressor genes CnGsc, Sp5, and HyHes, while blocking HyBMP5/8b and the c-fos-related gene HyKayak β-Catenin promotes the expression of the tentacle specification factor HyAlx, but not of HyWnt3 This suggests HyWnt3 and HyBMP4 as parts of a hypostome/organizer gene module, and BMP5/8, HyAlx, and β-catenin as parts of a tentacle gene module. Notch then functions as an inhibitor of tentacle production to allow regeneration of a hypostome/head organizer. HyKayak is a candidate target gene for HvNotch-induced repressor genes. Inhibiting HyKayak attenuated the expression of HyWnt3 Polyps of Craspedacusta do not have tentacles and thus after head removal only regenerate a hypostome structure. Notch signaling was not needed for head regeneration in Craspedacusta, corroborating the idea of its requirement during Hydra head regeneration to harmonize two co-operating pattern-forming processes.

Mechanistic Insight into the Anti-Bacterial/Anti-Biofilm Effects of Low Chlorhexidine Concentrations on Enterococcus faecalis—In Vitro Study

Background: Endodontic treatment failures are often linked to the persistence of Enterococcus faecalis in the root canal system. This study aimed to investigate the antibacterial/antibiofilm mechanism of chlorhexidine (CHX), particularly at low concentrations, against E. faecalis, to improve endodontic treatment protocols. Methods: The antibacterial activity of CHX (0.125–20 μg/mL) was evaluated against E. faecalis ATCC 29212 using various assays, including planktonic growth inhibition, colony-forming units (CFUs), membrane permeability and potential assays, high-resolution scanning electron microscopy (HR-SEM), confocal laser scanning microscopy of biofilms, biomass and metabolic activity assays on matured biofilm, and quantitative real-time PCR for gene expression. Statistical analysis was performed using Student’s t-test and ANOVA. Results: CHX demonstrated concentration-dependent inhibition of E. faecalis, significantly reducing planktonic growth and CFUs. Membrane assays showed increased permeability and depolarization, indicating damage. HR-SEM revealed morphological changes, such as pore formation, while confocal microscopy showed a reduction in biofilm mass and extracellular substances. Gene expression analysis indicated the downregulation of virulence genes and upregulation of stress response genes. Conclusions: CHX at low concentrations disrupts E. faecalis at multiple levels, from membrane disruption to gene expression modulation, affecting mature biofilm. These findings support the refinement of endodontic disinfection protocols to reduce microbial persistence.

Abstract 4117767: Interplay Between ST2 Gene Downregulation and Inflammatory Processes in Hypertrophic Cardiomyopathy

Introduction: Hypertrophic Cardiomyopathy (HCM) is an inherited heart disease and the pathogenesis of HCM involves genetic mutations, hemodynamic stress, and metabolic factors, with myocardial fibrosis playing a crucial role in severe clinical events. IL-33/ST2 signaling pathway known for its roles in immune response and tissue repair, participates in cardiac protection and anti-cardiac fibrosis in heart failure. The role of ST2 in HCM remains unclear, and IL-33/ST2 pathway and broader inflammatory responses may be critical in HCM. Hypothesis: ST2 gene downregulation and dysregulation of inflammatory pathways represent a novel mechanism in HCM. Methods: We re-analyzed the raw whole transcriptome sequencing data using a comprehensive bioinformatics pipeline from 9 GEO datasets. After removing low-quality samples, myocardial tissue samples from 109 HCM patients and 210 non-HCM controls were included. HTSeq-count was used to obtain the read count of each gene. Differential expression analyses were conducted using DESeq2. Spearman correlation analysis was performed for ST2 with all other protein-coding genes. Gene set enrichment analysis (GSEA) was performed to explore the biological significance of ST2 related genes. CIBERSORTx was used to estimate the immune cell composition of heart tissues. Additionally, network analyses and statistical correlations were conducted. Results: Our analysis identified significant downregulation of the ST2 gene in HCM patients compared to controls (log2FC = -5.0, p = 2.7E-147). In total, 5,180 upregulated and 741 downregulated genes were detected. Additionally, 208 genes were significantly correlated with the expression of ST2. GSEA based on the correlation coefficients revealed a significant increase in immune response, inflammation, and IFN-γ pathway activity, along with a decrease in the expression of genes related to sarcomeric function, cardiac morphogenesis, and metabolism in HCM. Notably, the significant inverse correlation between ST2 expression and regulatory T cells (r = -0.34) and a positive correlation with neutrophils (r = 0.39) suggest that ST2 may modulate immune cell populations in HCM. Pathway analysis indicated ST2's central role in networks involving inflammatory and fibrotic responses. Conclusion: The interplay between ST2 and inflammatory pathways may drive myocardial remodeling and fibrosis in HCM. This study paves a new way for investigating pathogenic mechanisms and therapeutic strategies for HCM.

Analysis of Lipid Metabolism in Adipose Tissue and Liver of Chinese Soft-Shelled Turtle Pelodiscus sinensis During Hibernation

Hibernation serves as an energy-conserving strategy that enables animals to withstand harsh environments by reducing their metabolic rate significantly. However, the mechanisms underlying energy adaptation in hibernating ectotherms, such as Pelodiscus sinensis, remain contentious. This paper first reports the decrease in lipid levels and the expression of metabolism-related genes in P. sinensis during hibernation. The results of physiological and biochemical analysis showed that adipocyte cell size was reduced and liver lipid droplet (LD) contents were decreased during hibernation in P. sinensis. Concurrently, serum levels of triglycerides (TGs), total cholesterol (TC), non-esterified fatty acids (NEFAs), high-density lipoprotein cholesterol (HDLC), and low-density lipoprotein cholesterol (LDLC) were diminished (n = 8, p < 0.01), while an increase in serum glucose (Glu) (n = 8, p < 0.01) was noted among hibernating P. sinensis. These observations suggest a shift in energy metabolism during hibernation. To gain insights into the molecular mechanisms, we performed integrated transcriptomic and lipidomic analyses of adipose tissue and livers from summer-active versus overwintering P. sinensis, which revealed downregulation of free fatty acids (FFAs), triglycerides (TGs), diglycerides (DGs), and ceramides (Cers) during hibernation. The results of GSEA analysis showed that metabolic pathways associated with lipid metabolism, including glycerolipid metabolism and regulation of lipolysis in adipocytes, were suppressed significantly. Notably, acute cold exposure induced significant downregulation of genes related to lipolysis such as PNPLA2, ABHD5, LPL, CPT1A, and PPARα. The results indicate that lipolysis is suppressed during hibernation in P. sinensis. Collectively, these findings deepen our understanding of survival mechanisms and elucidate the unique energy adaptation strategies employed by hibernating ectotherms. Future research should explore the implications of these findings for the conservation of ectotherms and the applications for artificially inducing hibernation.

TMIC-13. INTEGRATING SNRNASEQ AND SPATIAL TRANSCRIPTOME (ST) SHOWS DIVERSE TRANSCRIPTOMIC LANDSCAPE FOR TUMOR MICROENVIRONMENT (TME) IN INTRACRANIAL GERMINOMAS

Abstract The incidence of intracranial germ cell tumors is 5-8 times higher in East Asia and histologically, germinoma is well known to show intense lymphocytic infiltrates. In spite of germinoma’s well known immune infiltration, there have only been a few studies on its tumor micro-environment (TME). There has been no study using the recent and comprehensive techniques of single nucleus sequencing or spatial transcriptomics to study its TME. In this study, we studied snRNAseq (Chromium 10X) of FFPE tissues of 24 intracranial germinomas, and spatial transcriptomes (STs) (Visium Spatial) from fresh tissues from ten matched cases. For the TME, in contrast to common belief, macrophages and fibroblasts were equally represented as T- and NK-cells as immune cells. Clinical stage correlated with a lesser proportion of fibroblasts and T- and NK-cells. There was no correlation with proportion of tumor cells with either focal vs bifocal disease or clinical stage. Common gene modules (non-negative matrix factorization) were epithelial-mesenchymal transition (complete and partial), cell cycle and immune cells. Cell interaction analysis showed strong interaction between germ cells and macrophages involving CXCL, MIF and MK pathways. By ligand-receptor analysis, MIF combined with CD74 might promote tumor development. For ten cases, we studied STs with fresh tissues and integrated the results with snRNSeq, deconvoluting the spots for ST using snRNAseq cell types as reference (SPOTight) and achieved integrated single cell expression atlases of the STs (Seurat package). STs revealed a similar CNV plot pattern as those derived from snRNAseqs. Multimodal Intersection Analysis integrated significant genes based on snRNAseq and different regions’ significant genes based on STs. There was correlation between the expression of the four gene modules for tumor and immune cells for cell neighborhood. In conclusion, we showed in details the heterogenous expression landscape of TME of germinomas.

IMMU-59. AN IMMUNOSUPPRESSIVE PROGRAM ENCOMPASSING MULTIPLE IMMUNE CELL TYPES IN GBM TYPIFIED BY NOVEL MARKER LRRC25 ASSOCIATED WITH TYROBP SIGNALING

Abstract Immunosuppression in glioblastoma is a powerful impediment to effective immunotherapy. We used maximal tumor sampling and genome-wide coexpression analysis of RNA sequencing, on 69 samples from 8 patients, to identify a module of 270 genes marked by LRRC25, determined by top fidelity score, that covaries with many immunosuppressive molecules. An immunosuppressive module was independently derived from an expanded cohort of 319 samples from 28 GBM also marked by LRRC25 by top fidelity score. Within the gene module, we observed strong co-variation of markers for monocytes, neutrophils, and NK cells with LRRC25. In published single-cell RNA-seq from glioma, we determined that LRRC25 is expressed by neutrophils and myeloid cells while absent from NK-cells. LRRC25 is also constitutively expressed in monocytes and neutrophils while being upregulated by microglia and DCs in the tumor core and necrotic regions. In addition to covariation with multiple cell-type specific markers we also discovered that LRRC25 expression is tightly associated with several members of the TYROBP causal signaling network in microglia. Thus, LRRC25 may play a novel role in TYROBP signaling which may, in turn, represent a novel mechanism of NK cell and neutrophil immunosuppression in glioma. We confirmed LRRC25 RNA expression in patient samples by RNAscope co-stained with an anti-CD163 antibody indicating myeloid expression, as well as tumor cell expression determined by histopathology. Although LRRC25 is known to mediate IFN and NFKb signaling in myeloid cells in-vitro, its function in glioma remains understudied. While significant efforts have focused on mechanisms of myeloid to T-cell immunosuppression, less focus has been given to mechanisms of myeloid to NK-cell and neutrophil immunosuppression, despite the fact they exist at levels comparable to T-cells in the tumor microenvironment. This work will be followed up with antibody validation as well as genetic manipulation of LRRC25 in-vitro and in-vivo.

FDA-approved disulfiram induces ferroptosis via alteration of redox balance and lipid peroxidation and overcomes carfilzomib resistance in multiple myeloma

Multiple myeloma (MM), a malignant plasma cell disorder, remains incurable due to inevitable chemo-resistance development, including carfilzomib (CFZ) leading to relapse and poor patient outcomes. Therefore, new treatment strategies, including using FDA-approved alcohol deterrent disulfiram (DSF) are under investigation. The present study investigated the effect of DSF on ferroptosis and CFZ resistance in MM cells. Our findings indicate that DSF increases the production of cytosolic and mitochondrial reactive oxygen species, and causes a loss of mitochondrial Δψ and an elevation in lipid peroxidation in MM cells. DSF treatment in MM cell lines led to the significant downregulation of ferroptotic genes, including glutathione peroxidase 4. Moreover, ferroptosis inhibitor liproxstatin-1rescued DSF-induced ferroptosis by promoting glutathione peroxidase 4 upregulation. DSF alone overcomes CFZ resistance through lipid peroxidation elevation and acts synergistically with CFZ in CFZ-resistant MM cell lines. Our results suggest that DSF is a promising anti-myeloma agent for overcoming CFZ resistance in MM through ferroptosisinduction.