Infiltration Scores Research Articles

Cuproptosis gene characterizes the immune microenvironment of diabetic nephropathy.

The cuproptosis is an intracellular copper (Cu) accumulation triggering the aggregation of mitochondrial lipoylated proteins and destabilization of iron‑sulfur (FeS) cluster proteins, leading to cell death. This copper-triggered modality of mitochondrial cell death has been associated with cuproptosis-related signature key genes (CRGs). Our study focused on the relationship between the cuproptosis CRGs and diabetic nephropathy (DN) to understand how such immune microenvironment may influence DN. We downloaded and compared RNA sequencing data sets of DN glomerular tissue samples vs. normal renal tissue samples (GSE142025, GSE30528, and GSE96804) from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between DN and control samples were screened. Immune cell subtypes infiltration and immune score were figured out via different algorithms. Consensus clustering was performed by the Ward's method to determine different phenotypes of DN. CRG key genes between two phenotypes were identified via machine learning algorithm. Logistic regression analysis was applied to establish a nomogram for assessing the risk of DN. In DN samples, two genes NLRP3 and CDKN2A were positively correlated to the immune score. In contrast, six genes NFE2L2, LIAS, LIPT1, DLD, DBT and DLST were negatively correlated to the immune score. Via Consensus clustering based on cuproptosis CRG key genes, the DN samples were divided into cluster C1 and cluster C2. The cluster C1 was characterized by low cuproptosis CRG genes expression, high immune cell subtypes infiltration, and high enrichment of immune-related pathways. Cluster C2 was on the contrary, the Dicarbonyl/l-xylulose reductase (DCXR) and heat-responsive protein 12 (HRSP12) genes were related to clinical traits and the immune microenvironment, negatively correlated with most immune cell subtypes. The nomogram was constructed based on DCXR and HRSP12 showing good efficiency for the DN diagnosis. We conclude that the immune microenvironment imbalance and metabolic disorders lead to the occurrence of DN. The signature cuproptosis genes, regulating the immune microenvironment and metabolism, represented the DN disease clustering to describe the heterogeneity and characterize immune microenvironment. Both HRSP12 and DCXR key genes are related to DN disease phenotypes and immune microenvironment characteristic and may help in DN diagnosis.

Identification of the clinical and genetic characteristics of gliomas with gene fusions by integrated genomic and transcriptomic analysis

The identification of oncogenic gene fusions in diffuse gliomas may serve as potential therapeutic targets and prognostic indicators, representing a novel strategy for treating gliomas consistent with the principles of personalized medicine. This study identified detectable oncogene fusions in glioma patients through an integrated analysis of genomic and transcriptomic data, which encompassed whole exon sequencing and next-generation RNA sequencing. In addition, this study also conducted a comparison of the genetic characteristics, tumor microenvironment, mutation burden and survival between glioma patients with or without gene fusions. A total of 68 glioma patients were enrolled in this study, including glioblastoma (GBM), low grade glioma (LGG) and diffuse midline glioma (DMG). 14 cases of GBM patients (51.9%, 14/27) were found to harbor the following 70 oncogenic gene fusions: ROS1 (n = 8), NTRK (n = 5), KIF5 (n = 5), RET (n = 3) and other infrequent gene fusions (n = 49). A total of 11 gene fusions were identified in 8 LGG patients (32.0%, 8/25) and seven gene fusions were identified in one DMG patient (16.7%, 1/6). In GBM patient group, five genes including HOXA3, ACTB, CDK5, GNA12 and CARD11 exhibited a statistically significant higher copy number amplification frequency in the GBM group without gene fusions compared to that in the GBM group with gene fusions. In LGG patient group, CDK5 gene was also found to exhibit a statistically significant higher amplification frequency in the LGG group without gene fusions. In addition, KMT2D exhibited a statistically significant higher mutation frequency in the LGG group with gene fusions compared to that in the LGG group without gene fusions. Comparison of the other genetic characteristics including immune cell infiltration score, tumor mutation burden (TMB), and microsatellite instability (MSI). The results showed no statistically significant differences were observed between fusion and non-fusion group of GBM and LGG. The survival analysis revealed that GBM patients without gene fusions exhibited a longer median survival (737 days) compared to GBM patients with gene fusions (642 days), but without a statistical significancy. Our study has identified a set of gene fusions present in gliomas, including a number of novel gene fusions that have not been previously reported. We have also elucidated the underlying genetic characteristics of glioma with gene fusions. Collectively, our findings have the potential to inform future clinical treatment strategies for patients with glioma.

Establishment of a Prognostic Necroptosis-Related lncRNA Signature in Ovarian Cancer.

Ovarian Cancer (OC) was known for its high mortality rate among gynecological malignancies, often resulting in a poor prognosis. This study sought to identify prognostic necroptosis-related long non-coding RNAs (lncRNAs) (NRlncRNAs) with prognostic potential and to construct a reliable risk prediction model for OC patients. The transcriptome and clinic data were sourced from TCGA and GTEx databases. Initially, NRlncRNAs were discovered by assessing gene correlations and evaluating differences in gene expression. Subsequently, Cox regression and LASSO methods were employed to develop the NRlncRNAs risk model, which was further validated through survival analysis, ROC curves, Cox regression, and nomograms across both the test and entire datasets. Multivariate Cox analysis revealed that the risk score based on 14 NRlncRNAs can independently predict the prognosis of OC. The low-risk group demonstrated significantly higher immune cell infiltration scores and lower tumor immune dysfunction, exclusion, and TIDE scores, as well as an increased number of neoantigens and higher TMB. Notably, the low-risk group also exhibited an elevated HRD score. The model's predictive accuracy was further substantiated through ROC analysis, showing superior performance compared to many existing models.Finally, the expression levels of 14 NRlncRNAs were confirmed using the qRT-PCR in two OC cell lines. These findings suggested that the NRlncRNAs risk model could serve as a more precise indicator for forecasting immune response and outcomes of targeted treatments in OC.

Genomic, transcriptomic, and T cell receptor profiling in stratifying response to first-line chemoradiotherapy or radiotherapy for esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) accounts for 80% of esophageal cancer (EC) worldwide. The molecular characteristics of locally advanced ESCC have been extensively studied. In this study, we investigate the genomic and transcriptomic characteristics and try to provide the basic T-cell receptors (TCRs) dynamics and its genomic and transcriptome association during the radiochemotherapy of ESCC using multi-omics analysis. A total of 23 patients with pathologic diagnoses of locally advanced ESCC were enrolled. The median tumor mutational burden (TMB) of the 23 ESCC patients were 3.47 mutations/ Mb (mega-base). The TP53, RTK/RAS, and NOTCH pathways were concurrently prevalent in ESCC. Besides, some less prevalent pathways, including WNT and HIPPO pathways also exhibited superior frequencies in ESCC. Meantime, we found the immune-hot tumor had higher immune infiltration scores. The median TMB in the progression-free survival (PFS) low group was significantly higher than that in the PFS-high group. The chromosomal copy number variation (CNV) burden of the neutrophil-to-lymphocyte ratio (NLR)-high group appeared to be higher than that of the NLR-low group, and the StromalScore in the NLR-low group was significantly higher. Clonality score was significantly increased from pre-treat to post-treat and from on-treat to post-treat. Shannon index was significantly decreased from pre-treat to post-treat and from on-treat to posttreat. Richness was significantly decreased from pre-treat to post-treat. Multiomics analysis provided the basic TCRs dynamics and their genomic and transcriptome association during the radio-chemotherapy of 23 locally advanced ESCC in China, and provided a valuable insights into the heterogeneity and the tumor microenvironment and treatment responses. Meantimes, the identification of biomarkers and the exploration of their association with treatment outcomes could have important implications for clinical practice.

Histopathologic evaluation of wooden breast and white striping myopathy in different broiler genotypes using light microscopy and image analysis

Broiler myopathies cause significant economic losses in the poultry industry, adversely affecting meat quality and animal welfare. Cobb 500 and Ross 308 are widely cultivated commercial lines globally; however, Anadolu–T is a newly developed genotype with limited research on the histopathological evaluation of myopathic lesions. This study focuses on the histopathological evaluation of breast muscle myopathies in three different broiler lines (Cobb 500, Anadolu–T, and Ross 308). Additionally, histopathological lesions such as lipidosis, inflammatory cell infiltration, connective tissue formation, and degeneration were compared among genotypes using manual scoring with traditional light microscopy, as well as less commonly utilized digital image analysis software, including ImageJ and QuPath. Macroscopically, the Cobb genotype exhibited the highest WB scores (mean score: 2) (P<0.05), while the Anadolu–T genotype had the highest WS scores (1.11) (P>0.05). In the evaluation of histopathological lesions, the highest fibrosis scores were observed in the Cobb genotype (0.86), the highest mononuclear inflammatory cell infiltration scores in the Ross genotype (2.25), the highest lipidosis scores in the Anadolu–T genotype (3.22), and the highest degeneration scores in the Cobb genotype (3) (P>0.05). In this study, the evaluation of myopathy scores revealed significant differences in myopathy susceptibility among different genotypes. The Anadolu–T genotype was found to be less susceptible to WB myopathy severity (P<0.05) but more prone to WS myopathy severity (P>0.05).

Exploring the heterogeneity of osteosarcoma cell characteristics and metabolic states and their association with clinical prognosis.

Osteosarcoma is a malignant tumor originating from mesenchymal bone tissue, characterized by high malignancy and poor prognosis. Despite progress in comprehensive treatment approaches, the five-year survival rate remains largely unchanged, highlighting the need to clarify its underlying mechanisms and discover new therapeutic targets. This study utilized RNA sequencing data from multiple public databases, encompassing osteosarcoma samples and healthy controls, along with single-cell RNA sequencing data. Various methods were utilized, such as differential expression analysis of genes, analysis of metabolic pathways, and weighted gene co-expression network analysis (WGCNA), to pinpoint crucial genes. Using this list of genes, we developed and validated a prognostic model that incorporated risk signatures, and we evaluated the effectiveness of the model through survival analysis, immune cell infiltration examination, and drug sensitivity evaluation. We analyzed gene expression and metabolic pathways in nine samples using single-cell sequencing data. Initially, we performed quality control and clustering, identifying 21 statistically significant cell subpopulations. Metabolic analyses of these subpopulations revealed heterogeneous activation of metabolic pathways. Focusing on the osteoblastic cell subpopulation, we further subdivided it into six groups and examined their gene expression and differentiation capabilities. Differential expression and enrichment analyses indicated that tumor tissues were enriched in cytoskeletal and structural pathways. Through WGCNA, we identified core genes negatively correlated with four highly activated metabolic pathways. Using osteosarcoma patient data, we developed a risk signature model that demonstrated robust prognostic predictions across three independent cohorts. Ultimately, we performed a thorough examination of the model, which encompassed clinical and pathological characteristics, enrichment analysis, pathways associated with cancer markers, and scores of immune infiltration, highlighting notable and complex disparities between high-risk and low-risk populations. This research clarifies the molecular mechanisms and metabolic features associated with osteosarcoma and how they relate to patient outcomes, offering novel perspectives and approaches for targeted therapy and prognostic assessment in osteosarcoma.

Exploring the impact of deubiquitination on melanoma prognosis through single-cell RNA sequencing.

Cutaneous melanoma, characterized by the malignant proliferation of melanocytes, exhibits high invasiveness and metastatic potential. Thus, identifying novel prognostic biomarkers and therapeutic targets is essential. We utilized single-cell RNA sequencing data (GSE215120) from the Gene Expression Omnibus (GEO) database, preprocessing it with the Seurat package. Dimensionality reduction and clustering were executed through Principal Component Analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP). Cell types were annotated based on known marker genes, and the AUCell algorithm assessed the enrichment of deubiquitination-related genes. Cells were categorized into DUB_high and DUB_low groups based on AUCell scores, followed by differential expression analysis. Importantly, we constructed a robust prognostic model utilizing various genes, which was evaluated in the TCGA cohort and an external validation cohort. Our prognostic model, developed using Random Survival Forest (RSF) and Ridge Regression methods, demonstrated excellent predictive performance, evidenced by high C-index and AUC values across multiple cohorts. Furthermore, analyses of immune cell infiltration and tumor microenvironment scores revealed significant differences in immune cell distribution and microenvironment characteristics between high-risk and low-risk groups. Functional experiments indicated that TBC1D16 significantly impacts the migration and proliferation of melanoma cells. This study highlights the critical role of deubiquitination in melanoma and presents a novel prognostic model that effectively stratifies patient risk. The model's strong predictive ability enhances clinical decision-making and provides a framework for future studies on the therapeutic potential of deubiquitination mechanisms in melanoma progression. Further validation and exploration of this model's applicability in clinical settings are warranted.

Comprehensive Analysis Reveals That ISCA1 Is Correlated with Ferroptosis-Related Genes Across Cancers and Is a Biomarker in Thyroid Carcinoma.

ISCA1 (Iron-Sulfur Cluster Assembly 1) is involved in the assembly of iron-sulfur (Fe-S) clusters, which are vital for electron transport and enzyme activity. Some studies suggest the potential involvement of ISCA1 in tumor progression through interactions with ferroptosis-related genes (FRGs) and the tumor immune microenvironment (TME). However, there has been no systematic analysis of its role in FRGs and the TME or its predictive value for prognosis and immunotherapy response across different cancer types. In this study, we analyzed the expression and prognosis of ISCA1 RNA, CNV, methylation, and protein in multiple tumor tissues via data from the TCGA and CPTAC databases and clinical information. We conducted a comprehensive analysis of the correlations between ISCA1 and FRGs, immune-related genes (including immune regulatory genes and immune checkpoint genes), immune cell infiltration, immune infiltration scores, tumor stemness, and genomic heterogeneity. We performed drug prediction and validation through molecular docking and molecular dynamics analysis to identify candidate drugs that could promote or inhibit ISCA1 RNA expression. Our findings revealed that ISCA1 could serve as a biomarker in thyroid carcinoma, play a role with different FRGs in various cell types, and mediate different ligand-receptor pathways for cell-cell communication. Overall, our study highlights the potential of ISCA1 as a novel biomarker for predicting prognosis and immunotherapeutic efficacy in thyroid carcinoma and suggests its potential for developing novel antitumor drugs or improving immunotherapy.

METTL2B m3C RNA transferase: oncogenic role in ovarian cancer progression via regulation of the mTOR/AKT pathway and its link to the tumor immune microenvironment

BackgroundAberrant expression of N3-methylcytidine methyltransferase 2B (METTL2B) has been observed in various human malignancies, including those of the prostate, liver, breasts, and bladder. However, its role in ovarian cancer (OC) remains largely unexplored. This research preliminarily investigated METTL2B expression in OC and elucidated the associated molecular mechanisms.MethodsWe utilized three publicly available cancer-related databases (Genotype-Tissue Expression, Gene Expression Omnibus, and The Cancer Genome Atlas) to identify gene signatures in patients with OC and normal individuals with a specific focus on METTL2B. The role of METTL2B in OC was evaluated using patient survival data, and its impact on oncogenic behaviors in both cell and animal models, including growth potential, migration, invasion, and the tumor microenvironment, was examined. This assessment was conducted using bioinformatics tools such as Gene Set Cancer Analysis, GeneMANIA, and Tumor Immune Single-cell Hub 2. Additionally, the association between drug sensitivity and METTL2B expression was analyzed using CellMiner.ResultsMETTL2B expression was significantly elevated in OC, highlighting its potential clinical value in the diagnosis and prognosis of OC. Patients with lower METTL2B expression exhibited favorable survival. Furthermore, METTL2B knockdown significantly disrupted oncogenic behaviors in OC cell lines by suppressing the mTOR/AKT signaling pathway. Additionally, bioinformatics-based Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses suggested a close correlation between METTL2B and immune responses.ConclusionsOur research confirmed the upregulation of METTL2B in OC, suggesting its oncogenic function. However, METTL2B expression was negatively correlated with the infiltration scores of multiple immune cells, including cytotoxic cells and T cells, indicating its complex role in the tumor immune microenvironment. These findings highlight the significant clinical value of METTL2B in the diagnosis and prognosis of OC.

Regenerative endodontic therapy in immature teeth using photobiomodulation and photodynamic therapy; a histomorphological study in canine model

BackgroundRegenerative endodontic therapy (RET) is still coming up short to demonstrate histological evidence for true regeneration with clinically feasible protocol of cell homing in single visit approach.AimThe aim of the present study is to evaluate the regenerative potential of photobiomodulation (PBM) on RET in immature roots when photodynamic therapy (PDT) protocol is implemented for root canal disinfection in canine model.Materials and methodsSeventy-two root canals were recruited, with sixty assigned to experimental groups and twelve to positive and negative controls. Following the induction of pulp necrosis and apical periodontitis, the roots were divided into two experimental groups: Group I received RET followed by PBM (seven sessions with an 808 nm diode laser at 300 mW for 90 s), and Group II received RET without PBM. Follow-ups were conducted at 1, 2, and 3 months (subgroups A, B, and C respectively). Qualitative and quantitative assessment was carried out histologically. All data were statistically analyzed with the Mann-Whitney U test and Bonferroni’s adjustment, as well as Chi square test.ResultsThe newly formed hard tissue highly resembled true dentine where the dentinal tubules looked well organized lined by poly layers palisading pattern of rounded odontoblast-like cells with cytoplasmic processes extending through the predentine layer. GI exhibited statistically significantly higher scores of vital tissue infiltration and hard tissue deposition in subgroups A and B (P ≤ 0.05). The inflammatory cells scores were significantly lower in GI than in GII at all time intervals. However, no significance could be detected regarding apical closure.ConclusionThe disinfection protocol of PDT and subsequent irradiation with low power laser in PBM protocol pose a promising potential for regenerative endodontics in immature teeth.

Association Between the Expression of T Helper Type 17 Cell-Related Cytokines and Valve Damage in Rheumatic Heart Disease.

The study aimed to clarify the association between Th17 cell-related cytokine expressions and valve damage in rheumatic heart disease (RHD). Twenty RHD patients undergoing mitral valve replacement surgery were selected as the observation group (Group O), and 20 non-rheumatic valve disease patients undergoing mitral valve replacement surgery (degenerative mitral valve prolapse) were recruited as the control group (Group C). Histopathological examination with hematoxylin and eosin (H&E) staining was conducted to observe inflammatory cell infiltration, fibrosis, and neovascularization. Immunohistochemical staining was performed to analyze Th17 cell-related cytokines (interleukin (IL)-17, IL-6, IL-23, IL-21) in patients' cardiac valve tissues. Spearman correlation analysis was employed to investigate the correlation between Th17-related cytokines and inflammatory cell infiltration, fibrosis, and neovascularization. compared to the Group C, the Group O exhibited significantly higher proportions of IL-17, IL-21, IL-6, and IL-23 positive cells and immunohistochemical scores in valve tissues (P < 0.05). Additionally, inflammatory cell infiltration scores, tissue fibrosis scores, and neovascularization scores in valve tissues were significantly higher in the Group O compared to the Group C (P < 0.05). The expression of Th17-related cytokines IL-17, IL-21, IL-6, and IL-23 in valve tissues showed a positive correlation with inflammatory cell infiltration, fibrosis, and neovascularization (P < 0.05). Conclusion: The results demonstrate a notable association between Th17 cell-related cytokine expressions in the heart valves of RHD patients and valve damage, providing a potential target for the treatment and prevention of RHD.

Long-term outcome and antitumor immune activation response in prostate cancer treated with low-dose-rate brachytherapy.

To evaluate the long-term clinical outcomes of iodine-125 low dose-rate brachytherapy (LDR-BT)-based treatment approaches for ≤ cT3 prostate cancer (PC) patients in China, as well as the effects on the PC immune microenvironment. Data was retrospectively collected from 237 patients with ≤ cT3 PC who were treated with radical prostatectomy (RP) or LDR-BT alone or in combination with androgen deprivation therapy (ADT), and biochemical progression-free survival (bPFS), prostate cancer-specific survival (PCSS) and overall survival (OS) rates were compared. In 63 cases, PC patients received RP after biopsy, received at least 6 months of ADT before RP, or received LDR-BT and deferred limited transurethral resection of the prostate (TURP). Immunohistological analyses and expression comparisons of programmed death-ligand 1 (PD-L1) and tumor-infiltrating lymphocytes (TILs, expressing CD3, CD4, CD8, and PD-1) on tissue sections from archival prostate biopsy samples with corresponding TURP or RP history were performed by paired t test. The 8-year bPFS, PCSS, and OS rates for LDR-BT and RP were 53.4% and 63.6%, 84.9% and 86.8%, and 63.8% and 70.2%, respectively, although these differences were not statistically significant. PD-L1 was expressed in 35 of 63 cases. The average infiltration scores of TILs (expressing CD3, CD4, and CD8) were 3.6 (1-5), 2.90 (1-5), and 2.46 (1-5), respectively. PD-1 + T cells were seen in 55.6% of cases, with an average score of 0.89 (range: 0-3). In TURP tissue samples from 23 patients, CD3+, CD4+, and CD8 + T cells increased significantly. PD-1 + T cells exhibited a moderate increase, with conversion to positive PD-1 expression in T cells observed in 13 out of 14 cases. The PD-L1 expression score of PC cells was significantly elevated, with conversion to positive in 8 of 9 cases. LDR-BT monotherapy and combination therapy with external beam radiotherapy (EBRT) and ADT are suitable treatment approaches for low-risk and intermediate- or high-risk PC, respectively. Most TILs in PC are not tumor antigen-specific T-cells. LDR-BT can stimulate anti-tumor immunity during a narrow time window and should be combined with immunotherapy as an auxiliary therapy.

Clinicopathological and imaging differences between pediatric and adult patients with anti-hydroxy-3-methyl-glutaryl-coenzyme A reductase necrotizing myopathy.

We aimed to elucidate the clinicopathological and imaging differences between pediatric and adult patients with anti-hydroxy-3-methyl-glutaryl-coenzyme A reductase (anti-HMGCR) myopathy. A series of 111 patients with anti-HMGCR myopathy were divided into pediatric (33 patients, onset age < 18years) and adult (78 patients, onset age ≥ 18years) groups. Clinical, imaging, and pathological characteristics were compared between the groups. Overall median age at onset was 40years. Median duration of disease was 12months. The male:female ratio was 41:70. Prevalence of statin exposure was 0% in the pediatric group and 21% in the adult group (P < 0.001). The prevalence of severe weakness was significantly higher in the pediatric group (63.6% vs. 36.4%; P = 0.008). Myalgia was significantly more frequent in adults (49.3% vs. 20.8%; P = 0.03). The median serum creatine kinase (CK) concentration was significantly higher in the pediatric group (7263.0 vs. 3388.5U/L; P = 0.03). Magnetic resonance imaging of the thigh revealed muscle edema in 82.8% of patients and fatty infiltration in 60.9%. Muscle edema scores in the sartorius (P = 0.02) and gracilis (P = 0.03) were significantly higher in the pediatric group. Fatty infiltration score was significantly correlated with disease duration (r = 0.51; P < 0.001). Dystrophic pathology was significantly more frequent in pediatric patients (47% vs. 8%; P = 0.001). Regeneration score was significantly higher in pediatric group (P = 0.025). Sarcolemmal deposition of membrane attack complex (MAC) was significantly greater in pediatric patients (P = 0.010) and correlated significantly with manual muscle testing-8 score (r = - 0.14; P = 0.04) and serum CK concentration (r = 0.36; P = 0.002). Pediatric patients presented with more severe weakness, higher CK concentration, higher muscle edema score in the sartorius and gracilis, more muscle regeneration, more sarcolemmal MAC deposition, and dystrophic pathology. Adult patients exhibited more myalgia and more minimal changes. Sarcolemmal MAC deposition is a biomarker for disease activity.

Comprehensive profiling of T-cell exhaustion signatures and establishment of a prognostic model in lung adenocarcinoma through integrated RNA-sequencing analysis

Background T-cell exhaustion (TEX) in the tumor microenvironment causes immunotherapy resistance and poor prognosis. Objective We used bioinformatics to identify crucial TEX genes associated with the molecular classification and risk stratification of lung adenocarcinoma (LUAD). Methods Bulk RNA sequencing data of patients with LUAD were acquired from open sources. LUAD samples exhibited abnormal TEX gene expression, compared with normal samples. TEX gene-based prognostic signature was established and validated in both TCGA and GSE50081 datasets. Immune correlation and risk group-related functional analyses were also performed. Results Eight optimized TEX genes were identified using the LASSO algorithm: ERG, BTK, IKZF3, DCC, EML4, MET, LATS2, and LOX . Several crucial Kyoto encyclopedia of genes and genomes (KEGG) pathways were identified, such as T-cell receptor signaling, toll-like receptor signaling, leukocytes trans-endothelial migration, Fcγ R-mediated phagocytosis, and GnRH signaling. Eight TEX gene-based risk score models were established and validated. Patients with high-risk scores had worse prognosis (P &lt; 0.001). A nomogram model comprising three independent clinical factors showed good predictive efficacy for survival rate in patients with LUAD. Correlation analysis revealed that the TEX signature significantly correlated with immune cell infiltration, tumor purity, stromal cells, estimate, and immunophenotype score. Conclusion TEX-derived risk score is a promising and effective prognostic factor that is closely correlated with the immune microenvironment and estimated score. TEX signature may be a useful clinical diagnostic tool for evaluating pre-immune efficacy in patients with LUAD.

Cold-Pressed Aristotelia chilensis (Mol.) Stuntz Seed Oil Prevents Metabolic-Dysfunction-Associated Steatotic Liver Disease (MASLD) in a High-Fat-Diet-Induced Obesity Murine Model.

This study evaluated the effects of cold-pressed maqui (Aristotelia chilensis (Mol.) Stuntz) seed oil (MO) on liver metabolism and biochemical markers in a high-fat diet (HFD) murine model. In it, the fatty acid profile, tocopherol and tocotrienol contents, and antioxidant capacity of MO were analyzed. Male C57BL/6 mice were divided into four groups (i.e., a, b, c, and d groups) and supplemented for 12 weeks according to the following distribution: (a) control diet (CD)-sunflower oil (SO), (b) CD+MO, (c) HFD+SO, and (d) HFD+MO. Total body and organ weights, serum markers, and liver fat infiltration were assessed. MO contained 32.31% oleic acid, 46.41% linoleic acid, and 10.83% α-linolenic acid; additionally, α- and γ-tocopherol levels were 339.09 ± 5.15 and 135.52 ± 38.03 mg/kg, respectively, while β-, δ-tocopherol, and α-tocotrienol were present in trace amounts and the antioxidant capacity measured was 6.66 ± 0.19 μmol Trolox equivalent/g. MO supplementation significantly reduced the visceral fat (0.76 ± 0.06 g vs. 1.32 ± 0.04 g) and GPT (glutamate pyruvate transaminase) levels (71.8 ± 5.0 vs. 35.2 ± 2.6 U/L), and the liver fat infiltration score (6 vs. 3) in the HFD+MO group compared to HFD+SO. It is suggested that MO may effectively prevent fatty liver disease, warranting further research on its potential benefits for human health.

IMMU-13. TRANS-SPECIES STUDY OF IDH-MUTANT REPLICATION-REPAIR DEFICIENT HIGH-GRADE GLIOMAS (RRD-HGG) AND RESPONSE TO COMBINED TARGETED AND IMMUNOTHERAPY: AN IRRDC STUDY

Abstract BACKGROUND AND AIMS IDH-mutant gliomas comprise &amp;lt;10% of HGG in children. RRD-HGG comprise 5-10% of childhood HGG, demonstrate high mutation burden (TMB) and respond to immune-checkpoint inhibition (ICI). The impact of RRD within childhood IDH-mutant gliomas, and effective therapeutic options for these patients are not well-established. METHODS Clinical and multi-omic analyses were performed on IDH mut -RRD-HGG registered to the IRRDC and the Toronto glioma taskforce. Tumor development and genomic data were studied from a novel IDH mut -RRD-HGG immunocompetent mouse model. Outcome following ICI and targeted therapy were evaluated. RESULTS RRD was detected in &amp;gt;60% of childhood IDH mut -HGG. IDH1-mutations were detected in 20% of RRD-HGG. All patients with IDH mut -RRD-HGG (n=49) harboured germline variants in MMR genes (CMMRD: 65%, Lynch: 35%). Contrary to sporadic IDH mut -gliomas, &amp;gt;91% were WHO-grades 3/4. Diffuse/multifocal disease involving the frontal lobe was frequent. TMB (median: 28 mutations/Mb) was lower than IDH-wildtype RRD-HGG (p&amp;lt;0.05). POLE/POLD1 mutations were absent. TP53 and ATRX were frequent somatic hits. Copy number changes, particularly CDKN2A/2B loss, were common. IDH-mutation contributed to an immune-suppressed microenvironment, with lower CD8-T-cell infiltration (immunohistochemistry) and tumor-inflammation scores (transcriptome; p&amp;lt;0.05). A novel mouse model (Olig2-Cre+/Msh2LoxP/LoxP/LSL-Idh1R132H/+) demonstrated similar TMB, diffuse cerebral involvement, slower growth, and lesser immune infiltrates as compared with IDH-wildtype RRD-HGG models, and provided opportunity for therapeutic testing. RRD contributed to poor survival in IDHmut-gliomas (p&amp;lt;0.001). Despite hypermutation, ICI monotherapy resulted in inferior survival in IDH mut -RRD-HGG vs IDH-wildtype RRD-HGG (p&amp;lt;0.05). Five patients developed metachronous IDH mut -RRD-HGG while on anti-PD1 treatment for IDH-wildtype RRD-HGG, suggesting intrinsic ICI-resistance. Ivosidenib (IDH-inhibitor) demonstrated objective response in 4/8 IDH mut -RRD-HGG. Furthermore, for IDH mut -RRD-HGG on ICI treatment, the addition of ivosidenib prolonged survival at 12-months in comparison to those without IDH-inhibition (p=0.01) CONCLUSIONS Hypermutant RRD-HGG with IDH1;p.R132H harbour unique immuno-biology and do not respond to anti-PD1 monotherapy. The addition of IDH-inhibition demonstrated favourable responses, supporting need for evaluation of the combination in clinical trials.

Immune-based subgroups uncover diverse tumor immunogenicity and implications for prognosis and precision therapy in acute myeloid leukemia.

Although a considerable proportion of acute myeloid leukemia (AML) patients achieve remission through chemotherapy, relapse remains a recurring and significant event leading to treatment failure. This study aims to investigate the immune landscape in AML and its potential implications for prognosis and chemo-/immune-therapy. Integrated analyses based on multiple sequencing datasets of AML were performed. Various algorithms estimated immune infiltration in AML samples. A subgroup prediction model was developed, and comprehensive bioinformatics and machine learning algorithms were applied to compare immune-based subgroups in relation to clinical features, mutational landscapes, immune characterizations, drug sensitivities, and cellular hierarchies at the single-cell level. Two immune-based AML subgroups, G1 and G2, were identified. G1 demonstrated higher immune infiltration, a more monocytic phenotype, increased proportions of monocytes/macrophages, and higher FLT3, DNMT3A, and NPM1 mutation frequencies. It was associated with a poorer prognosis, lower proportions of various immune cell types and a lower T cell infiltration score (TIS). AML T-cell-based immunotherapy target antigens, including CLEC12A, Folate receptor β, IL1RAP and TIM3, showed higher expression levels in G1, while CD117, CD244, CD96, WT and TERT exhibited higher expression levels in G2. G1 samples demonstrated higher sensitivity to elesclomol and panobinostat but increased resistance to venetoclax compared to G2 samples. Moreover, we observed a positive correlation between sample immune infiltration and sample resistance to elesclomol and panobinostat, whereas a negative correlation was found with venetoclax resistance. Our study enriches the current AML risk stratification and provides guidance for precision medicine in AML.

Immune Microenvironment Alterations and Identification of Key Diagnostic Biomarkers in Chronic Kidney Disease Using Integrated Bioinformatics and Machine Learning.

Chronic kidney disease (CKD) involves complex immune dysregulation and altered gene expression profiles. This study investigates immune cell infiltration, differential gene expression, and pathway enrichment in CKD patients to identify key diagnostic biomarkers through machine learning methods. We assessed immune cell infiltration and immune microenvironment scores using the xCell algorithm. Differentially expressed genes (DEGs) were identified using the limma package. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed to evaluate pathway enrichment. Machine learning techniques (LASSO and Random Forest) pinpointed diagnostic genes. A nomogram model was constructed and validated for diagnostic prediction. Spearman correlation explored associations between key genes and immune cell recruitment. The CKD group exhibited significantly altered immune cell infiltration and increased immune microenvironment scores compared to the normal group. We identified 2335 DEGs, including 124 differentially expressed immune-related genes. GSEA highlighted significant enrichment of inflammatory and immune pathways in the high immune score (HIS) subgroup, while GSVA indicated upregulation of immune responses and metabolic processes in HIS. Machine learning identified four key diagnostic genes: RGS1, IL4I1, NR4A3, and SOCS3. Validation in an independent dataset (GSE96804) and clinical samples confirmed their diagnostic potential. The nomogram model integrating these genes demonstrated high predictive accuracy. Spearman correlation revealed positive associations between the key genes and various immune cells, indicating their roles in immune modulation and CKD pathogenesis. This study provides a comprehensive analysis of immune alterations and gene expression profiles in CKD. The identified diagnostic genes and the constructed nomogram model offer potent tools for CKD diagnosis. The immunomodulatory roles of RGS1, IL4I1, NR4A3, and SOCS3 warrant further investigation as potential therapeutic targets in CKD.

Ultrasonography of the salivary glands in Sjögren's disease: own data analysis

Objective: to investigate feasibility of using ultrasonography (US) to evaluate structural changes of salivary glands (SG) in patients with Sjögren's disease (SD).Material and methods. The study included 159 patients who were examined in V.A. Nasonova Research Institute of Rheumatology from 2016 to 2022 who met V.A. Nasonova Research Institute of Rheumatology 2001, and/or ACR 2012, and/or ACR/EULAR 2016 criteria for SD, and who had not previously received immunosuppressive therapy. All patients underwent a comprehensive classical examination (ophthalmological, dental, immunological) to diagnose SD. Disease activity was determined using ESSDAI index. US of the parotid gland (PG) and submandibular SGs was performed using a GE LOGIQ 9 device, and the images obtained were scored according to the OMERACT SGUS scoring system (SGUS SS).Results and discussion. All SGUS SS scores statistically significantly correlated (p&lt;0.05) with mouth sicca symptoms, enlargement of PG, ESSDAI activity index, presence of lymphohistiocytic infiltrate and focus score in labial SG biopsy, and parenchymatous parotitis according to sialography. No significant correlation was found with the results of sialometry. There was a significant correlation between the changes detected by US and sialography (r=0.422; p=0.001). Considering the data obtained, the consistency of the results of the different examination methods was analyzed. Bland-Altman diagrams were created to reflect the dependence of the differences between the results of US and sialography. At various stages of the comparison, not all data points were within the standardized range. In addition, 5% of the parameters were not within the interval of two standard deviations. The Bland-Altman analysis revealed a systematic discrepancy indicating a low degree of agreement between the two methods for determining structural changes in SG. According to the ROC analysis, sensitivity of ultrasound was 94% and specificity 51%. The area under the curve (AUC) was 0.787 (95% confidence interval 0.700–0.875).Conclusion. SG US and sialography are not interchangeable, but complement each other in the assessment of SG structure. SG US is a safer and non-invasive method of SG examination that does not require contrast agent administration and is likely to play an important role in the dynamic monitoring of patients during the therapy. However, sialography is a more accurate method of diagnostics and assessment of the extent of SG lesions.

Integrative analysis of single-cell and bulk multi-omics data to reveal subtype-specific characteristics and therapeutic strategies in clear cell renal cell carcinoma patients.

Background: Kidney renal clear cell carcinoma (KIRC) is the most prevalent subtype of malignant renal cell carcinoma and is well known as a common genitourinary cancer. Stratifying tumors based on heterogeneity is essential for better treatment options. Methods: In this study, consensus clusters were constructed based on gene expression, DNA methylation, and gene mutation data, which were combined with multiple clustering algorithms. After identifying two heterogeneous subtypes, we analyzed the molecular characteristics, immunotherapy response, and drug sensitivity differences of each subtype. And we further integrated bulk data and single-cell RNA sequencing (scRNA-Seq) data to infer the immune cell composition and malignant tumor cell proportion of subtype-related cell subpopulations. Results: Among the two identified consensus subtypes (CS1 and CS2), CS1 was enriched in more inflammation-related and oncogenic pathways than CS2. Simultaneously, CS1 showed a worse prognosis and we found more copy number variations and BAP1 mutations in CS1. Although CS1 had a high immune infiltration score, it exhibited high expression of suppressive immune features. Based on the prediction of immunotherapy and drug sensitivity, we inferred that CS1 may respond poorly to immunotherapy and be less sensitive to targeted drugs. The analysis of bulk data integrated with single-cell data further reflected the high expression of inhibitory immune features in CS1 and the high proportion of malignant tumor cells. And CS2 contained a large number of plasmacytoid B cells, presenting an activated immune microenvironment. Finally, the robustness of our subtypes was successfully validated in four external datasets. Conclusion: In summary, we conducted a comprehensive analysis of multi-omics data with 10 clustering algorithms to reveal the molecular characteristics of KIRC patients and validated the relevant conclusions by single-cell analysis and external data. Our findings discovered new KIRC subtypes and may further guide personalized and precision treatments.