GEO Data Research Articles

Abstract 2789: NCAPG promotes triple-negative breast cancer stemness by a positive feedback loop with HIF-1α

Abstract Objective: Triple-negative breast cancer (TNBC) is life-threatening because of limited therapies and lack of effective therapeutic targets. NCAPG, an oncogenic marker, might be served as a new target for TNBC treatment. Here, we aimed to elucidate the role of NCAPG played in TNBC and the underlying mechanism. Design: GEO data was used to investigate the potential targets for TNBC. Patient samples and TCGA data were used to demonstrate the clinical significance. Cell migration, self-renewal ability, chemoresistance and expression of pluripotency factors were tested to detect the stemness of TNBC cells. Immunoprecipitation, ubiquitination assay and chromatin immunoprecipitation assay were utilized to investigate the mutual regulation mechanism of NCAPG and HIF-1α. Results: NCAPG was significantly overexpressed in TNBC compared with other subtypes of breast cancer and was positively correlated with poor overall survival. Elevated NCAPG expression could enhance cancer stem-like cell properties of TNBC cells. Mechanically, NCAPG positively regulated HIF-1α protein stability by interacting with HIF-1α and competitively abrogating the E3 ligase FBXW7-mediated ubiquitination and degradation towards HIF-1α. NCAPG, as a direct target gene of HIF-1α, could be in turn transcriptionally upregulated by HIF-1α. Conclusion: NCAPG promotes TNBC stemness by a HIF-1α/NCAPG positive feedback loop. NCAPG is a promising target for TNBC treatment. Citation Format: Huimin Zhang, Peiling Xie, Rui An. NCAPG promotes triple-negative breast cancer stemness by a positive feedback loop with HIF-1α [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 2789.

Abstract 6274: Integrated multi-omics revealed the involvement of MYC and mTOR pathways in radiation resistance of adrenocortical cancer

Abstract The morbidity and mortality of patients with adrenocortical cancer (ACC) are commonly due to locoregional postoperative recurrence and progressive systemic metastasis. Surgical resection remains the only curative treatment option, but even with complete resection, locoregional recurrence rates remain high. Adjuvant radiation therapy (RT) has been shown to reduce recurrence rates and may improve overall survival in selected patients. However, half of the patients receiving postoperative RT still develop locoregional recurrence, clearly demonstrating the heterogeneous nature of ACC. Minimal investigation into the mechanisms underlying radiation response and resistance in ACC has been performed, but elucidating this information is critical to improving outcomes. To address this knowledge gap, NCI-H295R cells were treated with fractionated radiation at 1 Gray (Gy) per day for 5 consecutive days for two consecutive weeks, cumulating in a total radiation dose of 10 Gy. Treated and control ACC cells were harvested on days 7 and 14 for bulk RNA-sequencing (RNA-Seq) and total proteomics by liquid chromatography and tandem mass spectrometry. Significantly differentially expressed genes (DEGs) and proteomes (adj. p. value <0.05) that overlapped between day 7 and day 14 were selected for further analysis and comparison with publicly available gene expression data sets in ACC (The Cancer Genome Atlas (TCGA); Gene Expression Omnibus: GSE12368, GSE33371, GSE75415, GSE90713). There were 3993 DEGs and 423 proteomes identified, respectively. Of these, there were 139 overlapping DEGs with respective proteomes found, 72 of which were differentially expressed in the 4 GEO data sets comparing normal adrenal cortex to ACC. RNA-Seq pathway analysis demonstrated enrichment of E2F targets, G2M checkpoint, mTORC1 signaling, and MYC targets v1, while total proteomics pathway analysis revealed enrichment of cell cycle, transcriptional regulation, cellular stress and injury, alterations of RNA metabolism, and metabolism proteomes. Given that MYC and mTOR are both involved in transcriptional regulation and cell cycle regulation, and mTORC1 in particular is associated with cellular metabolism, the RNA-Seq and proteomics pathway analyses show general consistency with each other. TCGA gene expression analysis showed that overexpression of MYC or mTOR was correlated with shorter overall survival (OS) and disease-free survival (DFS) in the entire ACC cohort (p<0.05). Together, the combination of in vitro pathway analysis and TCGA analysis suggests a potential involvement of the MYC and mTOR pathways in radiation resistance in ACC. Further in vitro and in vivo studies are warranted to identify specific molecular compounds that target MYC and mTOR pathways and improve radiation response in ACC. Citation Format: Bhavishya Ramamoorthy, Prachi Mishra, Myriem Boufraqech, Nicholas Michael, Margaret Cam, Richard Finney, Thomas Meyer, Ronald Holewinski, Thorkell Andresson, Madeline Wong, Steven Shema, Desiree Tillo, Naris Nilubol. Integrated multi-omics revealed the involvement of MYC and mTOR pathways in radiation resistance of adrenocortical cancer [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 6274.

Prognostic value of inflammation and immune-related gene NOD2 in clear cell renal cell carcinoma.

Inflammation and immune responses play important roles in cancer development and prognosis. We identified 59 upregulated inflammation- and immune-related genes (IIRGs) in clear cell renal cell carcinoma (ccRCC) from The Cancer Genome Atlas database. Among the upregulated IIRGs, nucleotide binding oligomerization domain 2 (NOD2), PYD and CARD domain (PYCARD) were also confirmed to be upregulated in the Oncomine database and in three independent GEO data sets. Tumor immune infiltration resource database analysis revealed that NOD2 and PYCARD levels were significantly positively correlated with infiltration levels of B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages and dendritic cells. Multivariate Cox hazards regression analysis indicated that based on clinical variables (age, gender, tumor grade, pathological TNM stage), NOD2, but not PYCARD, was an independent, unfavorable ccRCC prognostic biomarker. Functional enrichment analyses (GSEA) showed that NOD2 was involved in innate immune responses, inflammatory responses, and regulation of cytokine secretion. Meanwhile, mRNA and protein levels of NOD2 were elevated in four ccRCC cell lines (786-O, ACHN, A498 and Caki-1), and its knockdown significantly inhibited IL-8 secretion, thereby inhibiting ccRCC cell proliferation and invasion. Furthermore, results showed that miR-20b-5p targeted NOD2 to alleviate NOD2-mediated IL-8 secretion. In conclusion, NOD2 is a potential prognostic biomarker for ccRCC and the miR-20b-5p/NOD2/IL-8 axis may regulate inflammation- and immune-mediated tumorigenesis in ccRCC.

Allicin treats myocardial infarction in I/R through the promotion of the SHP2 axis to inhibit p-PERK-mediated oxidative stress.

The study attempted to explore how allicin reduces oxidative stress levels by promoting SHP2 expression to inhibit p-PERK in I/R mice. The GEO database and RNA sequencing were used to predict downstream gene. TTC staining was used to visualize the myocardial infarction area. Masson staining was used to assess the level of fibrosis. IF was used to examine the expression of SHP2, CTGF, ROS. RT-PCR analysis was used to quantify the expression of SHP2 mRNA. Western blot was used to detect the protein expression levels of SHP2, p-PERK, MFN1, NLRP3, NOX2, and NOX3. GEO and transcriptomic data revealed low expression of SHP2 in the heart tissues I/R mice. In the I/R mouse model, TTC staining result showed that allicin can reduce the area of myocardial infarction; Masson staining results indicated that allicin can reduce fibrosis; Macrophage transcriptome sequencing found SHP2 is a target gene of allicin; Immunofluorescence showed allicin can increase SHP2; qPCR results showed allicin can raise SHP2 mRNA level; Immunofluorescence indicated that allicin can inhibit ROS in myocardial infarction tissue, but the specific SHP2-KD eliminates changes in ROS. Western blot analysis demonstrated allicin can increase SHP2 protein and reduce the expression of p-PERK, MFN1, NLRP3, NOX2, and NOX3; SHP2-KD eliminates the expression differences in p-PERK, MFN1, NLRP3, NOX2, and NOX3. Allicin can modulate p-PERK activation by enhancing the expression of SHP2, thereby inhibiting myocardial ischemia-reperfusion-induced oxidative stress in mice.

P011 Altered Expression and Enzymatic Activity of Xanthine Oxidase in Inflammatory Bowel Disease

Abstract Background Xanthine oxidase (XO) is involved in the last steps of purine metabolism; indeed, it catalyzes the oxidation of hypoxanthine to xanthine and xanthine to uric acid (UA) with the production of superoxide anion. The accumulation of UA has been shown to initiate the inflammatory process through NLRP3 inflammasome and the production of reactive oxygen species (ROS) contributes to inflammation-related tissue damage. In murine models of colitis, XO inhibitors, allopurinol or febuxostat, reduced the expression of proinflammatory cytokines supporting the involvement of XO in the intestinal inflammatory process. This study aims to conduct a thorough investigation of the role XO plays in IBD pathogenesis and to explore the potential of XO inhibition as a therapeutic strategy. Methods Biopsies from the colon of patients with ulcerative colitis (UC) and Crohn’s disease (CD) were collected at University Hospital of Cagliari. Disease activity was assessed using Mayo and SES-CD scores. XO expression levels were evaluated using Real-Time PCR, validated by GEO database (GSE11223, GSE117993). XO enzymatic activity was quantified spectrophotometrically in protein extracts from the biopsies. XO and NLRP3 inflammasome activation pathway, including NLRP3, ASC, and CASPASE1, was investigated using immunohistochemistry (IHC). In vitro, Caco2, HT29, SW480 cells were treated with xanthine, XO inhibitors (allopurinol, febuxostat) to assess XO inhibition on NLRP3 activation, analyzed by immunocytochemistry (ICC). Results Biopsies from the sigmoid colon of 15 HC, 20 UC, and 15 CD patients, as well as from the ileum of 10 HC and 10 CD, were analyzed. Increased XO expression was found in UC and CD sigmoid mucosa (Relative Quantification [RQ]: 1.93 vs. 0.99, p=0.004), and CD ileum (RQ: 2.72 vs. 1.26, p=0.004), confirmed by GEO data. XO activity was higher in UC and CD sigmoid (3.86 nmol UA/min/mg in UC, 4.82 in CD vs. 1.03 in HC, p<0.001) and CD ileum (8.41 vs. 1.83 in HC, p<0.001). IHC confirmed that XO and the NLRP3 inflammasome pathway are more highly expressed in IBD patients than HC, predominantly within epithelial cells. In vitro studies on Caco2, HT29, and SW480 cells demonstrated that suppressing XO activity with XO inhibitors leads to the inhibition of the NLRP3 pathway. Conclusion XO expression was higher in IBD pts than in HC individuals. Alongside this increase in XO activity, there was a concurrent hyperactivation of the NLRP3 inflammasome. The inhibition of XO activity in cell lines resulted in reduced activation of the NLRP3 inflammasome pathway. These findings support the hypothesis that XO plays a critical role in the pathogenesis of IBD and highlight its potential as a therapeutic target.

Small Cajal Body-Specific RNA12 Promotes Carcinogenesis through Modulating Extracellular Matrix Signaling in Bladder Cancer

Background: Small Cajal body-specific RNAs (scaRNAs) are a specific subset of small nucleolar RNAs (snoRNAs) that have recently emerged as pivotal contributors in diverse physiological and pathological processes. However, their defined roles in carcinogenesis remain largely elusive. This study aims to explore the potential function and mechanism of SCARNA12 in bladder cancer (BLCA) and to provide a theoretical basis for further investigations into the biological functionalities of scaRNAs. Materials and Methods: TCGA, GEO and GTEx data sets were used to analyze the expression of SCARNA12 and its clinicopathological significance in BLCA. Quantitative real-time PCR (qPCR) and in situ hybridization were applied to validate the expression of SCARNA12 in both BLCA cell lines and tissues. RNA sequencing (RNA-seq) combined with bioinformatics analyses were conducted to reveal the changes in gene expression patterns and functional pathways in BLCA patients with different expressions of SCARNA12 and T24 cell lines upon SCARNA12 knockdown. Single-cell mass cytometry (CyTOF) was then used to evaluate the tumor-related cell cluster affected by SCARNA12. Moreover, SCARNA12 was stably knocked down in T24 and UMUC3 cell lines by lentivirus-mediated CRISPR/Cas9 approach. The biological effects of SCARNA12 on the proliferation, clonogenic, migration, invasion, cell apoptosis, cell cycle, and tumor growth were assessed by in vitro MTT, colony formation, wound healing, transwell, flow cytometry assays, and in vivo nude mice xenograft models, respectively. Finally, a chromatin isolation by RNA purification (ChIRP) experiment was further conducted to delineate the potential mechanisms of SCARNA12 in BLCA. Results: The expression of SCARNA12 was significantly up-regulated in both BLCA tissues and cell lines. RNA-seq data elucidated that SCARAN12 may play a potential role in cell adhesion and extracellular matrix (ECM) related signaling pathways. CyTOF results further showed that an ECM-related cell cluster with vimentin+, CD13+, CD44+, and CD47+ was enriched in BLCA patients with high SCARNA12 expression. Additionally, SCARNA12 knockdown significantly inhibited the proliferation, colony formation, migration, and invasion abilities in T24 and UMUC3 cell lines. SCARNA12 knockdown prompted cell arrest in the G0/G1 and G2/M phase and promoted apoptosis in T24 and UMUC3 cell lines. Furthermore, SCARNA12 knockdown could suppress the in vivo tumor growth in nude mice. A ChIRP experiment further suggested that SCARNA12 may combine transcription factors H2AFZ to modulate the transcription program and then affect BLCA progression. Conclusions: Our study is the first to propose aberrant alteration of SCARNA12 and elucidate its potential oncogenic roles in BLCA via the modulation of ECM signaling. The interaction of SCARNA12 with the transcriptional factor H2AFZ emerges as a key contributor to the carcinogenesis and progression of BLCA. These findings suggest SCARNA12 may serve as a diagnostic biomarker and potential therapeutic target for the treatment of BLCA.

NADPH oxidase 1 promotes hepatic steatosis in obese mice and is abrogated by augmented skeletal muscle mass.

Exercise as a lifestyle modification is a frontline therapy for nonalcoholic fatty liver disease (NAFLD), but how components of exercise attenuate steatosis is unclear. To uncouple the effect of increased muscle mass from weight loss in obesity, myostatin knockout mice were bred on a lean and obese db/db background. Myostatin deletion increases gastrocnemius (Gastrocn.) mass and reduces hepatic steatosis and hepatic sterol regulatory element binding protein 1 (Srebp1) expression in obese mice, with no impact on adiposity or body weight. Interestingly, hypermuscularity reduces hepatic NADPH oxidase 1 (Nox1) expression but not NADPH oxidase 4 (Nox4) in db/db mice. To evaluate a deterministic function of Nox1 on steatosis, Nox1 knockout mice were bred on a lean and db/db background. NOX1 deletion significantly attenuates hepatic oxidant stress, steatosis, and Srebp1 programming in obese mice to parallel hypermuscularity, with no improvement in adiposity, glucose control, or hypertriglyceridemia to suggest off-target effects. Directly assessing the role of NOX1 on SREBP1, insulin (Ins)-mediated SREBP1 expression was significantly increased in either NOX1, NADPH oxidase organizer 1 (NOXO1), and NADPH oxidase activator 1 (NOXA1) or NOX5-transfected HepG2 cells versus ?-galactosidase control virus, indicating superoxide is the key mechanistic agent for the actions of NOX1 on SREBP1. Metabolic Nox1 regulators were evaluated using physiological, genetic, and diet-induced animal models that modulated upstream glucose and insulin signaling, identifying hyperinsulinemia as the key metabolic derangement explaining Nox1-induced steatosis in obesity. GEO data revealed that hepatic NOX1 predicts steatosis in obese humans with biopsy-proven NAFLD. Taken together, these data suggest that hypermuscularity attenuates Srebp1 expression in db/db mice through a NOX1-dependent mechanism.NEW & NOTEWORTHY This study documents a novel mechanism by which changes in body composition, notably increased muscle mass, protect against fatty liver disease. This mechanism involves NADPH oxidase 1 (NOX1), an enzyme that increases superoxide and increases insulin signaling, leading to increased fat accumulation in the liver. NOX1 may represent a new early target for preventing fatty liver to stave off later liver diseases such as cirrhosis or liver cancer.

Alterations in Alzheimer's disease microglia transcriptome might be involved in bone pathophysiology

Aging is a major risk factor for multiple chronic disorders in the elderly population, including Alzheimer's disease (AD) and Osteoporosis. AD is a progressive neurodegenerative disease characterized by memory loss. In addition to dementia, several studies have shown that AD patients experience an increased rate of musculoskeletal co-morbidities, such as osteoporosis. Since tissue-specific macrophages contribute to both diseases, this study analyzed the microglia transcriptome of AD mice to determine a common gene signature involved in osteoclast biology. After comparing differentially regulated genes from GEO data sets (GSE93824 and GSE212277), there were 35 common upregulated genes and 89 common downregulated genes. Of these common genes, seven genes are known to play an important role in bone homeostasis. CSF1, SPP1, FAM20C, and Cst7 were upregulated and are associated with osteoclastogenesis and inflammation. Among the downregulated genes, LILRA6, MMP9, and COL18A1 are involved in bone formation and osteoclast regulation. We further validated some of these genes (CSF1, Cst7, and SPP1) in the cortex and the bone of AD mice models. The dysregulation of these microglial genes in AD might provide insights into the co-occurrence of AD and osteoporosis and offer potential therapeutic targets to combat disease progression.

CDC6 may serve as an indicator of lung adenocarcinoma prognosis and progression based on TCGA and GEO data mining and experimental analyses.

Lung adenocarcinoma (LUAD) is one of the most lethal types of cancer worldwide, and accurately predicting patient prognosis is an important challenge. Gene prediction models, which are known for their simplicity and efficiency, have the potential to be used for prognostic predictions. However, the availability of models with true clinical value is limited. The present study integrated tissue sequencing and the clinical information of patients with LUAD from The Cancer Genome Atlas and Gene Expression Omnibus databases using bioinformatics. This comprehensive approach enabled the identification of 252 differentially expressed genes. Subsequently, univariate and multivariate Cox analyses were performed using these genes, and 14 and 3genes [including cell division cycle6 (CDC6), hyaluronan mediated motility receptor and STIL centriolar assembly protein] were selected for the construction of two prognostic models. Notably, the 3‑gene prognostic model exhibited a comparable predictive ability to that of the 14‑gene model. Functionally, pathway enrichment analysis revealed that CDC6 played a role in regulating the cell cycle and promoting tumor staging. To further investigate the relevance of CDC6, invitro experiments involving the downregulation of CDC6 expression were conducted, which resulted in significant inhibition of tumor cell migration, invasion and proliferation. Moreover, invivo experiments demonstrated that downregulating CDC6 expression significantly reduced the burden and metastasis of insitu lung tumors in mice. These findings suggested that CDC6 may be a critical gene involved in the development and prognosis of LUAD. In summary, the present study successfully constructed a simple yet accurate prognostic prediction model consisting of 3genes. Additionally, the functional importance of CDC6 as a key gene in the model was identified. These findings lay a crucial foundation for further exploration of prognostic prediction models and a deeper understanding of the functional mechanisms of CDC6. Notably, these results have potential clinical implications for improving personalized treatment and prognosis evaluation for patients with LUAD.

Integrated whole transcriptome profiling revealed a convoluted circular RNA-based competing endogenous RNAs regulatory network in colorectal cancer

Recently, it has been identified that circRNAs can act as miRNA sponge to regulate gene expression in various types of cancers, associating them with cancer initiation and progression. The present study aims to identify colorectal cancer-related circRNAs and the underpinning mechanisms of circRNA/miRNA/mRNA networks in the development and progress of Colorectal Cancer. Differentially expressed circRNAs, miRNAs, and mRNAs were identified in GEO microarray datasets using the Limma package of R. The analysis of differentially expressed circRNAs resulted in 23 upregulated and 31 downregulated circRNAs. CeRNAs networks were constructed by intersecting the results of predicted and experimentally validated databases, circbank and miRWalk, and by performing DEMs and DEGs analysis using Cytoscape. Next, functional enrichment analysis was performed for DEGs included in ceRNA networks. Followed by survival analysis, expression profile assessment using TCGA and GEO data, and ROC curve analysis we identified a ceRNA sub-networks that revealed the potential regulatory effect of hsa_circ_0001955 and hsa_circ_0071681 on survival-related genes, namely KLF4, MYC, CCNA2, RACGAP1, and CD44. Overall, we constructed a convoluted regulatory network and outlined its likely mechanisms of action in CRC, which may contribute to the development of more effective approaches for early diagnosis, prognosis, and treatment of CRC.

Bioinformatic Analysis and Clinical Case Studies Identify CD276 as a Promising Diagnostic Biomarker for Clear Cell Renal Cell Carcinoma.

This study aimed to explore the relationship between CD276 and clear cell renal carcinoma (ccRCC) and assess the diagnostic value of CD276 in ccRCC. Expression levels of CD276 in ccRCC and para-cancer tissues were compared and analyzed retrospectively using data obtained from TCGA and GEO databases. The clinical data was analyzed prospectively. Immunohistochemistry and RT-PCR analyses were used to analyze the expression of CD276 at the mRNA and protein levels. These analyses compared the expression between ccRCC tissues and para-cancer tissues obtained from 70 patients with ccRCC. Next, ELISA was used to analyze peripheral blood samples from 70 patients with ccRCC and 72 healthy individuals, facilitating the differentiation of ccRCC patients from normal controls. Finally, we utilized the Kaplan-Meier method to generate ROC curves for assessing the diagnostic value of CD276 for ccRCC. Analysis of TCGA and GEO data revealed that the mRNA expression of CD276 was higher in ccRCC tissues than in para-cancer tissues (P < .05). Clinical validation using IHC and RT-PCR confirmed that the expression of CD276 was higher in ccRCC tissues than in para-cancer tissues, both at the mRNA and protein levels (P < .05). ELISA demonstrated that the expression of CD276 was higher in ccRCC patients than in normal individuals, and patients with a higher pathological grade showed higher expression of CD276 in the peripheral blood than those with a lower pathological grade (P < .05). ROC curves drawn from the above three datasets demonstrated that CD276 had a high diagnostic value for ccRCC (AUC = .894, .795, .938, respectively). The expression of CD276 was higher in ccRCC tissues and positively associated with the pathological grade. Therefore, CD276 may serve as a molecular biomarker for ccRCC prediction.

Deep Learning Prediction of Inflammatory Inducing Protein Coding mRNA in P. gingivalis Released Outer Membrane Vesicles.

The Insilco study uses deep learning algorithms to predict the protein-coding pg m RNA sequences. The NCBI GEO DATA SET GSE218606's GEO R tool discovered P.G's outer membrane vesicles' most differentially expressed mRNA. Genemania analyzed differentially expressed gene networks. Transcriptomics data were collected and labeled on P. gingivalis protein-coding mRNA sequence and pseudogene, lincRNA, and bidirectional promoter lincRNA. Orange, a machine learning tool, analyzed and predicted data after preprocessing. Naïve Bayes, neural networks, and gradient descent partition data into training and testing sets, yielding accurate results. Cross-validation, model accuracy, and ROC curve were evaluated after model validation. Three models, Neural Networks, Naive Bayes, and Gradient Boosting, were evaluated using metrics like Area Under the Curve (AUC), Classification Accuracy (CA), F1 Score, Precision, Recall, and Specificity. Gradient Boosting achieved a balanced performance (AUC: 0.72, CA: 0.41, F1: 0.32) compared to Neural Networks (AUC: 0.721, CA: 0.391, F1: 0.314) and Naive Bayes (AUC: 0.701, CA: 0.172, F1: 0.114). While statistical tests revealed no significant differences between the models, Gradient Boosting exhibited a more balanced precision-recall relationship. In silico analysis using machine learning techniques successfully predicted protein-coding mRNA sequences within Porphyromonas gingivalis OMVs. Gradient Boosting outperformed other models (Neural Networks, Naive Bayes) by achieving a balanced performance across metrics like AUC, classification accuracy, and precision-recall, suggests its potential as a reliable tool for protein-coding mRNA prediction in P. gingivalis OMVs.

Deep Learning Based Micro-RNA Analysis of Lipopolysaccharide Exposed Periodontal Ligament Stem Cells Exosomes Reveal Apoptotic and Inflammasome Derived Pathway Activation.

The production of inflammatory factors in periodontium is increased by LPS, particularly from P. gingivalis, and the damage to periodontal tissues is exacerbated. Exosomes from periodontal ligament stem cells change regeneration and repair brought on by bacterial LPS. MiRNAs are carried by exosomes to recipient cells to affect epigenetic functions. Thus, this study aims to utilize deep learning algorithms to uncover novel micro-RNA biomarkers in bacterial LPS-exposed PDLSC stem cells to understand the activation pathway. Using NCBI GEO DATA SET GSE163489, the most differentially expressed micro RNAs were found to differ between healthy and LPS-induced PDLSC cells. Deep learning analysis, employing a Random Forest, Artificial Neural Network c, a Support Vector Machine (SVM), and a Linear Regression model implemented within the orange data mining toolkit, identified novel microRNA biomarkers. The orange data mining toolkit was utilized for deep learning analysis of microRNA expression data, providing a user-friendly environment for machine learning tasks like classification, regression, and clustering. Random Forest emerged as the superior model, achieving the highest R 2 score (.985) and the lowest RMSE (0.189) compared to Neural Networks (R 2 = .952, RMSE = 0.332), Linear Regression (R 2 = .949, RMSE = 0.343), and SVM (R 2 = .931, RMSE = 0.398). This suggests its superior ability to capture the underlying patterns in the microRNA expression data. Given its robust performance, Random Forest holds promise for identifying novel biomarkers, developing more accurate diagnostic tools, and potentially guiding the stratification of patients for targeted therapeutic interventions in periodontal disease. The current study utilizes deep learning analysis of microRNA expression data to identify novel biomarkers associated with inflammasome activation and anti-apoptotic pathways. These findings hold promise for guiding the development of novel therapeutic strategies for periodontal disease. However, future studies are warranted to validate these biomarkers using independent datasets and experimental methods.

Roles of RNA m5C modification patterns in prognosis and tumor microenvironment infiltration of diffuse large B-cell lymphoma.

Genetic and epigenetic aberrations display an essential role in the initiation and progression of diffuse large B-cell lymphoma (DLBCL). 5-methylcytosine (m5C), a common RNA modification, regulates various cellular processes and contributes to tumorigenesis and cancer progression. However, m5C alterations in DLBCL remain unclear. Our research constructed an m5C prognostic model utilizing GEO data sets, which can efficiently predict the prognosis of patients with DLBCL, and verified the m5C prognostic model genes by immunohistochemistry analysis. This model was constructed using unsupervised consensus clustering analyses, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses. Based on the expression of m5C genes in the model, patients with DLBCL could be effectively divided into groups with significant survival time differences. The m5C risk-score signature demonstrated a highly significant independent prognostic value. Results from tumor microenvironment analyses revealed that m5C genes altered the infiltration of eosinophils, Tregs, and M2 macrophages. Additionally, they regulated T cell activation by modulating the expression of CTLA4, PDL1, B2M, CD8A, ICOS, and other relevant immune checkpoint expressions. In conclusion, our study presents a robust m5C prognostic model that effectively predicts prognosis in DLBCL. This model may offer a new approach for prognostic stratification and potential therapeutic interventions for patients with DLBCL.

Comprehensive multi-omics analysis of pyroptosis for optimizing neoadjuvant immunotherapy in patients with gastric cancer.

Background: Pyroptosis plays a crucial role in immune responses. However, the effects of pyroptosis on tumor microenvironment remodeling and immunotherapy in gastric cancer (GC) remain unclear. Patients and Methods: Large-sample GEO data (GSE15459, GSE54129, and GSE62254) were used to explore the immunoregulatory roles of pyroptosis. TCGA cohort was used to elucidate multiple molecular events associated with pyroptosis, and a pyroptosis risk score (PRS) was constructed. The prognostic performance of the PRS was validated using postoperative GC samples from three public databases (n=925) and four independent Chinese medical cohorts (n=978). Single-cell sequencing and multiplex immunofluorescence were used to elucidate the immune cell infiltration landscape associated with PRS. Patients with GC who received neoadjuvant immunotherapy (n=48) and those with GC who received neoadjuvant chemotherapy (n=49) were enrolled to explore the value of PRS in neoadjuvant immunotherapy. Results: GC pyroptosis participates in immune activation in the tumor microenvironment and plays a powerful role in immune regulation. PRS, composed of four pyroptosis-related differentially expressed genes (BATF2, PTPRJ, RGS1, and VCAN), is a reliable and independent biomarker for GC. PRSlow is associated with an activated pyroptosis pathway and greater infiltration of anti-tumor immune cells, including more effector and CD4+ T cells, and with the polarization of tumor-associated macrophages in the tumor center. Importantly, PRSlow marks the effectiveness of neoadjuvant immunotherapy and enables screening of GC patients with combined positive score ≥1 who benefit from neoadjuvant immunotherapy. Conclusion: Our study demonstrated that pyroptosis activates immune processes in the tumor microenvironment. A low PRS correlates with enhanced infiltration of anti-tumor immune cells at the tumor site, increased pyroptotic activity, and improved patient outcomes. The constructed PRS can be used as an effective quantitative tool for pyroptosis analysis to guide more effective immunotherapeutic strategies for patients with GC.

도시 기능지역 추출을 위한 Geo Data Cube 모델 기반 계층적 격자 분할 기법

도시 기능지역 추출을 위한 Geo Data Cube 모델 기반 계층적 격자 분할 기법

Potential impact of cuproptosis-related genes on tumor immunity in esophageal carcinoma.

Cuproptosis involves a direct interaction with the tricarboxylic acid (TCA) lipid acylation components. This process intricately intersects with post-transcriptional lipid acylation (LA) and is linked to mitochondrial respiration and LA metabolism. Copper ions form direct bonds with acylated DLAT, promoting DLAT oligomerization, reducing Fe-S cluster proteins, and inducing a protein-triggered toxic stress response that culminates in cell demise. Simultaneously, the importance of immune contexture in cancer progression and treatment has significantly increased. We assessed the expression of cuproptosis-related genes (CRGs) across TCGA and validated our findings using the GEO data. Consensus clustering divided esophageal cancer (ESCA) patients into two clusters based on the expression of 7 CRGs. We evaluated the expression of immune checkpoint inhibitor (ICI) targets and calculated the elevated tumor mutational burden (TMB). Weighted gene co-expression network analysis (WGCNA) identified genes associated with the expression of CRGs and immunity. Cluster 1 exhibited increased immune infiltration, higher expression of ICI targets, higher TMB, and a higher incidence of deficiency in mismatch repair-microsatellite instability-high status. WGCNA analysis identified 14 genes associated with the expression of CRGs and immune scores. ROC analysis revealed specific hub genes with strong predictive capabilities. The expression levels of SLC6A3, MITD1, and PDHA1 varied across different pathological stages; CCS, LIPT2, PDHB, and PDHA1 showed variation in response to radiation therapy; MITD1 and PDHA1 exhibited differences related to the pathological M stages of ESCA. CRGs influence the immune contexture and can potentially transform cold tumors into hot tumors in ESCA patients.

A comprehensive evaluation of circ_0065214/ miR-188-3p/GPNMB axis in breast cancer

CircRNAs are involved in multiple aspects during carcinogenesis, including tumorigenesis, vascularization, apoptosis and others. Exploring the role of circRNAs in breast cancer (BC) enables us to understand the development mechanism of BC more comprehensively. Here, we screened out and verified an up-regulated circRNA in BC from GEO data. Quantitative Real-time PCR (qRT-PCR) showed that circ_0065214 had a high expression level in BC patients. Besides, circ_0065214 had good diagnostic value in BC serum, and the area under the diagnostic curve, sensitivity and specificity were 0.78, 0.63 and 0.85, respectively. The combined application of circ_0065214 with CEA and CA-153 can further improve the diagnostic efficiency. The knockdown of circ_0065214 in vivo and in vitro inhibited the proliferation, migration and invasion of BC, but promoted autophagy. At last, dual-luciferase reporter assay and rescue assays revealed that circ_0065214 acted as a decoy to adsorb miR-188-3p, and then relieved the repressive effect of miR-188-3p on its target GPNMB. Our results demonstrated that circ_0065214 regulated the expression of GPNMB by competitively binding to miR-188-3p, thus promoting the proliferation, migration and invasion of breast cancer cells and inhibiting autophagy. These findings provided an original therapeutic strategy for BC.

ROLE OF THE METHYLTRANSFERASE METTL21C IN DRIVING MUSCLE ATROPHY WITH AGING AND HIV INFECTION

Abstract Osteoporosis and sarcopenia are both frequently observed in older people living with HIV. We developed an animal model to investigate the cellular and molecular mechanisms underlying accelerated muscle aging in the setting of HIV infection. Wild-type C57BL/6 mice received bone marrow from Tg26 HIV-1 transgenic mice at 8 weeks of age and tissues were collected 8 weeks later. Tg26 mice express 7 of 9 HIV proteins but lack gag and pol so are non-infectious. RNA was isolated from the tibialis anterior and microarray was performed using the Clariom S Mouse array that contains more than 22,100 well-annotated genes and 150,300 transcripts. Differential expressions were calculated using ANOVA and filtered with a p-value cutoff of 0.05. Results show that the methyltransferase Mettl21c, a methyltransferase previously shown to stimulate muscle protein synthesis and suppress muscle degradation, is one of the most highly downregulated (more than two-fold) genes in muscle from mice receiving Tg26 bone marrow. We then analyzed GEO data sets to identify changes in muscle Mettl21c expression in various disease settings. These data sets reveal that Mettl21c is consistently downregulated in skeletal muscle with inflammatory conditions such as cancer cachexia and sepsis. In addition, GWAS studies have previously shown Mettl21c deficiency in patients with sarcopenia and osteoporosis. Our data suggest that HIV proteins may produce epigenetic modifications in skeletal muscle leading to muscle loss, and that therapies restoring expression of methyltransferases such as Mettl21c might improve muscle health in patients living with HIV.

Association of MIR4435-2HG Expression with TP53 Mutation, Estrogen Receptor Activity, and Poor Prognosis in Breast Cancer

Background: The roles of many long noncoding RNAs (lncRNAs) in breast cancer (BC) are unclear, and the medications that affect them have attracted less attention. Objectives: This study aimed to identify lncRNAs that have the highest association with poor prognosis in BC. Moreover, the relationship between the expression of identified lncRNA and conventional chemotherapy agents was investigated. Methods: The cancer genome atlas data were used to identify lncRNA with the most significant impact on BC survival. The relation of identified lncRNA levels with different subtypes of BC and mutation was assessed. PharmacoGX data and the GEO database were used to evaluate the association of identified lncRNA levels with drug sensitivity and find appropriate medications to reduce its expression, respectively. To assess the effect of the identified drug on the level of lncRNA expression, MCF7, and MDA-MB-468 cell lines were used, and the expression level of target genes was assessed by quantitative reverse transcription polymerase chain reaction. Results: The expression level of lncRNA MIR4435-2HG was most associated with the poor survival of BC patients, and its expression level can be related to TP53 mutation and estrogen and progesterone receptors. Increased expression of MIR4435-2HG was observed in cancer samples, and MIR4435-2HG level was correlated with metastasis pathway genes. Drug sensitivity to epirubicin, irinotecan, and lestaurtinib correlated with MIR4435-2HG levels. Furthermore, GEO data showed that the expression level of MIR4435-2HG could decrease under estrogen receptor (ER) activity. Finally, in vitro, results showed that MIR4435-2HG expression declined in response to estradiol as an ER-activating ligand in the MCF7 cell line. Conclusions: The expression of MIR4435-2HG can be a powerful biomarker for poor prognosis in BC. The data also suggested that this lncRNA may play an oncogenic role in metastatic pathways, and ER activity could regulate its expression.