Immune-related Signaling Pathways Research Articles

Homologous recombination deficiency serves as a prognostic biomarker in clear cell renal cell carcinoma.

Kidney renal clear cell carcinoma (KIRC) is a frequent malignant tumor characterized by a high degree of heterogeneity and genetic instability. DNA double-strand breaks generated by homologous recombination deficit (HRD) are a well-known contributor to genomic instability, which can encourage tumor development. It is not known, however, whether the molecular characteristics linked with HRD have a predictive role in KIRC. The discovery cohort comprised 501 KIRC patients from The Cancer Genome Atlas database. Genome and transcriptome data of HRD patients were used for comprehensive analysis. Single cell RNA sequencing (scRNA-seq) was used to verify the test results of bulk RNA-seq. In the present study, patients with a high HRD score had a worse prognosis compared with those with a low HRD score. The DNA damage response signaling pathways and immune-related signaling pathways were notably enriched in the HRD-positive subgroup. Further comprehensive analysis of the tumor microenvironment (TME) revealed that the signal of exhausted CD8+ T cells was enriched in the HRD-positive subgroup. Finally, scRNA-seq analyses confirmed that the immune-related signaling pathways were upregulated in HRD-positive patients. In conclusion, the present study not only demonstrated that a high HRD score is a valid prognostic biomarker in KIRC patients, but also revealed the TME in HRD-positive tumors.

Chlorogenic Acid Alleviates LPS-Induced Inflammation and Oxidative Stress by Modulating CD36/AMPK/PGC-1α in RAW264.7 Macrophages.

Chlorogenic acid (CGA) is a bioactive substance with anti-inflammatory activities. Clusters of CD36 have been suggested to be widely involved in inflammatory damage. However, the mechanism of CGA protecting against LPS-induced inflammation involving the CD36 regulation is unclear. Here, we demonstrated that CGA protected against LPS-induced cell death and decreased the production of ROS. Moreover, the SOD, CAT, and GSH-Px activities were also upregulated in CGA-treated cells during LPS stimulation. CGA reduced COX-2 and iNOS expression and IL-1β, IL-6, and TNF-α secretion in LPS-stimulated RAW264.7 macrophages. In addition, CGA treatment widely involved in immune-related signaling pathways, including NF-κB signaling, NOD-like receptor signaling, and IL-17 signaling using transcriptomic analysis and CD36 also markedly reduced during CGA pretreatment in LPS-induced RAW264.7 cells. Furthermore, the CD36 inhibitor SSO attenuated inflammation and oxidative stress by enabling activation of the AMPK/PGC-1α cascade. These results indicate that CGA might provide benefits for the regulation of inflammatory diseases by modulating CD36/AMPK/PGC-1α to alleviate oxidative stress.

FoxO signaling and mitochondria-related apoptosis pathways mediate tsinling lenok trout (Brachymystax lenok tsinlingensis) liver injury under high temperature stress

Tsinling lenok trout (Brachymystax lenok tsinlingensis) is a typical cold water fish. High temperature has been shown to damage the liver of fish. However, few studies have investigated the liver apoptosis induced by high temperature stress in fish from the perspective of gene expression and metabolic function. Therefore, we investigated the changes caused by high temperature stress (24 °C) on the liver tissue structure, antioxidant capacity, liver gene expression, and the metabolome of tsinling lenok trout. The transcriptomic results showed that genes associated with apoptosis, such as CASP8, CASP3, PERK, Bcl-6 and TRAIL, were upregulated under high temperature stress. Metabolomic analysis showed that the metabolic pathway of nucleotide synthesis was significantly downregulated, while that of oxygen radical synthesis was significantly upregulated. Integrated analysis showed that after high temperature stress, immune-related signaling pathways in trout were activated and their apoptosis level increased, which might be related to hepatopancreas injury. In addition, abnormalities in the tricarboxylic acid cycle and mitochondrial function were observed, suggesting that functional hypoxia caused by high temperature might be involved fish cell apoptosis. These results provide new insights into the process of cell apoptosis in fish under high temperature stress.

Transcriptome analysis of Fenneropenaeus merguiensis in response to Vibrio proteolyticus infection.

In recent years, due to the destruction of the culture environment and serious ecological pressure, especially in the process of culture, residual bait, faeces and fishery drug abuse will lead to the accumulation of harmful metabolites such as ammonia nitrogen and nitrite, and biological denitrification is the most economical and effective method to remove the single. Therefore, in this study, a nitrite removal strain XA19 was isolated and screened from a shrimp biofloc culture pond. This strain was identified as a clade of Vibrio proteolyticus because the homology between XA19 and V. proteolyticus WDVP was as high as 99.86% by using 16S rDNA gene sequence analysis and NCBI database comparison. Scanning electron microscopy images showed that V. proteolyticus is short-rod-shaped with a curved body and no budding spores, pods and flagella. Antimicrobial susceptibility test proved that V. proteolyticus was resistant to ampicillin, oxacillin, penicillin, vancomycin and clindamycin. In the median lethal concentration 50 (LC50 ) test, at 7-day post-infection (dpi), LC50 of V. proteolyticus for Fenneropenaeus merguiensis was 1.69 × 104 CFU/mL. Transcriptome sequencing analysis was carried out on hepatopancreas of F. merguiensis at 24 and 48 hpi. A total of 176 differentially expressed genes (DEGs) were screened at 24 hpi, including 104 up-regulated DEGs and 72 down-regulated DEGs, and a total of 52 DEGs were screened at 48 hpi, including 32 up-regulated DEGs and 20 down-regulated DEGs. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs, many immune-related signalling pathways were significantly enriched, including Hippo signalling pathway, phagosome, Toll and Imd signalling pathways and Wnt signalling pathway. In addition, some pathways related to Warburg effect were also enriched, including Glycolysis/Gluconeogenesis, Biosynthesis of amino acids, amino sugar and nucleotide sugar metabolism and so on. In this study, the toxicity and drug sensitivity of V. proteolyticus were systematically studied, and the immune response of hepatopancreas of F. merguiensis to V. proteolyticus infection was preliminarily revealed from the molecular level. The results may provide a reference for the prevention and control of V. proteolyticus.

MMP12 serves as an immune cell-related marker of disease status and prognosis in lung squamous cell carcinoma.

Worldwide, lung squamous cell carcinoma (LUSC) has wreaked havoc on humanity. Matrix metallopeptidase 12 (MMP12) plays an essential role in a variety of cancers. This study aimed to reveal the expression, clinical significance, and potential molecular mechanisms of MMP12 in LUSC. There were 2,738 messenger RNA (mRNA) samples from several multicenter databases used to detect MMP12 expression in LUSC, and 125 tissue samples were validated by immunohistochemistry (IHC) experiments. Receiver operator characteristic (ROC) curves, Kaplan-Meier curves, and univariate and multivariate Cox regression analyses were used to assess the clinical value of MMP12 in LUSC. The potential molecular mechanisms of MMP12 were explored by gene enrichment analysis and immune correlation analysis. Furthermore, single-cell sequencing was used to determine the distribution of MMP12 in multiple tumor microenvironment cells. MMP12 was significantly overexpressed at the mRNA level (p<0.05, SMD = 3.13, 95% CI [2.51-3.75]), which was verified at the protein level (p<0.001) by internal IHC experiments. MMP12 expression could be used to differentiate LUSC samples from normal samples, and overexpression of MMP12 itself implied a worse clinical prognosis and higher levels of immune cell infiltration in LUSC patients. MMP12 was involved in cancer development and progression through two immune-related signaling pathways. The high expression of MMP12 in LUSC might act as an antigen-presenting cell-associated tumor neoantigen and activate the body's immune response. MMP12 expression is upregulated in LUSC and high expression of MMP12 serves as a risk factor for LUSC patients. MMP12 may be involved in cancer development by participating in immune-related signaling pathways and elevating the level of immune cell infiltration.

Identification of a glycolysis-related miRNA Signature for Predicting Breast cancer Survival.

Breast cancer (BC) is a common type of cancer and has a poor prognosis. In this study, we collected the mRNA and miRNA expression profiles of BC patients were obtained from The Cancer Genome Atlas (TCGA) to explore a novel prognostic strategy for BC patients using bioinformatics tools. We found that six glycolysis-related miRNAs (GRmiRs, including hsa-mir-1247, hsa-mir148b, hsa-mir-133a-2, has-mir-1307, hsa-mir-195 and hsa-mir-1258) were correlated with prognosis of BC samples. The risk score model was established based on 6 prognosis-associated GRmiRs. The outcome of high risk group was significantly poorer. Cox regression analysis showed that risk score was an independent prognostic factor. Differentially expressed genes identified between high and low risk groups were mainly enriched in inflammation and immune-related signaling pathways. The proportion of infiltration of 12 kinds of immune cells in high and low risk groups were significantly different. Risk score was closely associated with many immune indexes. Multiple DEGRGs and miRNAs were associated with drugs. In conclusion, glycolysis-related miRNA signature effectively predicts BC prognosis.

Multi-omics analysis of LAMB3 as a potential immunological and biomarker in pan-cancer.

Laminin Subunit Beta 3 (LAMB3) is a transcription factor and participates in the coding of laminin. It plays an important role in cell proliferation, adhesion, and transfer by regulating various target genes and signaling pathways. However, the role of LAMB3 in human pan-cancer immunology and prognosis is still poorly understood. The TCGA, GTEx, CCLE, and HPA databases were utilized for the analysis of LAMB mRNA and protein expression. The expression of LAMB3 in various immune and molecular subtypes of human cancer was examined using the TISIDB database. The prognostic significance of LAMB3 in various cancers and clinical subtypes was investigated using Kaplan-Meier and Cox regression analysis. The relationship between LAMB3 expression, various immune cell infiltration, immune checkpoints, tumor mutational load, microsatellite instability, and DNA methylation was examined using the TCGA database. Clinical samples of four lung cancer cell lines and eight lung cancer cases were collected to confirm the expression of mRNA in lung cancer. In 17 cancers, the mRNA for LAMB3 is expressed differently and has good diagnostic and prognostic value in 22 cancers. Cox regression and Nomogram analysis show that LAMB3 is an independent risk factor for 15 cancers. LAMB3 is implicated in a variety of tumorigenesis and immune-related signaling pathways, according to GO, KEGG, and GSEA results. LAMB3 expression was associated with TMB in 33 cancer types and MSI in 32 cancer types, while in lung cancer LAMB3 expression was strongly associated with immune cell infiltration and negatively correlated with all seven methylated CpG islands. Cellular experiments demonstrated that LAMB3 promotes malignant behavior of tumor cells. Preliminary mechanistic exploration revealed its close association with PD-L1, CTLA4, cell stemness gene CD133 and β-catenin-related signaling pathways. Based on these findings, it appears that LAMB3 could be a potential therapeutic target for immunotherapy and tumor prognosis. Our findings reveal an important role for LAMB3 in different cancer types.

Aerosolization inhalation of non-typeable Haemophilus influenzae outer membrane vesicles contributing to neutrophilic asthma.

Neutrophilic asthma is poorly responsive to corticosteroids, and the mechanism underlying its pathogenesis remains unclear. Non-typeable Haemophilus influenzae (NTHi) is the most common bacterium found in induced sputum from patients with neutrophilic asthma. NTHi can release outer membrane vesicles (OMVs), which transfer biomolecules to host cells and the external environment. However, the role and mechanisms of NTHi OMVs in the pathogenesis of neutrophilic asthma remain unclear. We conducted assays to investigate whether NTHi OMVs can induce neutrophilic asthma when inhaled. We isolated and purified NTHi OMVs and administered them via a nebulizer to ovalbumin (OVA)-sensitized mice. We collected and sequenced serum, blood, bronchoalveolar lavage fluid, and lung tissue from each group and gathered lung function data. Inhaled NTHi OMVs-induced neutrophilic asthma in OVA-sensitized mice. High-throughput sequencing revealed that NTHi OMV inhalation in OVA-sensitized mice significantly enriched inflammatory and immune-related signaling pathways. We found increased transcription and secretion of interleukin (IL)-1β and IL-17, which may contribute to neutrophilic asthma. Furthermore, we discovered that airway epithelium is the first receptor cell of NTHi OMVs and releases IL-1β. These findings suggest that NTHi OMVs could be a potential target for neutrophilic asthma therapy.

Affecting mechanism of Chlorella sorokiniana meal replacing fish meal on growth and immunity of Litopenaeus vannamei based on transcriptome analysis

The purpose of this study was to analyze the affecting mechanism of Chlorella sorokiniana meal replacing fish meal on the growth performance and immune function of Pacific white shrimp, Litopenaeus vannamei by transcriptomics analysis. In a control diet containing 560 g % /kg fish meal, chlorella was used to replace 0 %, 20 %, 40 %, 60 %, 80 % and 100 % of dietary fish meal to form six iso-nitrogenous and iso-lipidic diets (C0, C20, C40, C60, C80, C100). The six diets were fed to white shrimp (1.37 ± 0.02 g) for 8 weeks. Compared to the control group, the final body weight (FBW), specific growth rate (SGR) and feed efficiency (FE) of the C20 group were significantly improved (P < 0.05). There was no significant difference in growth performance between the C40 group and the C0 group (P > 0.05). When the replacement level of fish meal by chlorella was ≥ 60 %, the FBW, SGR and FE of shrimp were significantly decreased (P < 0.05). In the analysis of the hepatopancreatic transcriptome, the amount of differentially expressed genes (DEGs) in C20, C40, C60, C80 and C100 groups were 322 (176 up and 146 down), 482 (246 up and 236 down), 804 (487 up and 317 down), 1080 (684 up and 396 down) and 1262 (827 up and 435 down), respectively, when compared to the C0 group. GO Term and KEGG pathway enrichment analysis of DEGs showed that DEGs between the C20 and C0 groups were significantly enriched in chitin binding and inositol metabolism processes. Several immune-related signaling pathways were also enriched, including the C-type lectin receptor pathway, complement and coagulation cascades, the B-cell receptor pathway, and most of these genes were up-regulated in the C20 group. Compared to the C0 group, DEGs in C40, C60, C80 and C100 groups were significantly enriched in lysosomal, protein digestion, and absorption pathways. In addition, in the C80 and C100 groups, the DEGs were also significantly enriched in lipid catabolism process. The high replacement of fish meal with chlorella meal affected the absorption and utilization of nutrients by regulating the signaling pathways related to protein digestion and absorption, and aggravated lipid catabolism of the body, thereby affecting the growth of shrimp. The high replacement of fish meal might also affect the homeostasis of shrimp cells and reduce immunity through the lysosomal signaling pathway. In summary, the low replacement of fish meal (20 %) with chlorella meal significantly improved the growth performance of Litopenaeus vannamei, which might be realized through activating the C-type lectin receptor signaling pathway to regulate immune function of the body, but the high substitution of fish meal (≥ 60 %) reduced the growth performance and immunity by affecting the lysosomal signaling pathway.

TMEM200A is a potential prognostic biomarker and correlated with immune infiltrates in gastric cancer.

Gastric cancer (GC) is one of the most common malignant tumors in the digestive system. Several transmembrane (TMEM) proteins are defined as tumor suppressors or oncogenes. However, the role and underlying mechanism of TMEM200A in GC remain unclear. We analyzed the expression of TMEM200A in GC. Furthermore, the influence of TMEM200A on survival of GC patients was evaluated. The correlations between the clinical information and TMEM200A expression were analyzed using chi-square test and logistic regression. Relevant prognostic factors were identified performing univariate and multivariate analysis. Gene set enrichment analysis (GSEA) was performed based on the TCGA dataset. Finally, we explore the relationship between TMEM200A expression and cancer immune infiltrates using CIBERSORT. TMEM200A was up-regulated in GC tissues than that in adjacent non-tumor tissues based on TCGA database. Meta-analysis and RT-qPCR validated the difference in TMEM200A expression. Kaplan-Meier curves suggested the increased TMEM200A had a poor prognosis in GC patients. The chi-square test and logistic regression analyses showed that the TMEM200A expression correlates significantly with T stage. Multivariate analysis showed that TMEM200A expression might be an important independent predictor of poor overall survival in GC patients. GSEA identified five immune-related signaling pathways and five tumor-related signaling pathways significantly enriched in the high TMEM200A expression phenotype pathway. Finally, we found CD8+ T cells is apparently decreased in high TMEM200A expression group. Conversely, eosinophils is increased in high expression group compared with low expression group. TMEM200A is a potential prognostic biomarker and correlated with immune infiltrates in GC.

A novel signature of aging-related genes associated with lymphatic metastasis for survival prediction in patients with bladder cancer.

The predominant and most prevalent form of metastatic bladder cancer (BCa) is lymphatic metastasis, which is associated with a highly dismal prognosis for patients. Aging-related genes (ARGs) are believed to contribute significantly to tumor development. However, the effect of ARGs on lymphatic metastasis of BCa is unclear. This research sought to establish a prognosis model based on ARGs associated with lymphatic metastasis in BCa. We downloaded BCa data from the TCGA and GEO databases and ARGs from the Aging Atlas database. The least absolute shrinkage and selection operator (LASSO) approach was applied to obtain the characteristic ARGs of risk signature in the TCGA cohort. Verification was done using the GSE13507 dataset. The R package 'ConsensusClusterPlus' was employed to identify the molecular subtypes based on the characteristic ARGs. Protein-Protein interaction network, MCODE analysis, enrichment analysis (KEGG, GO, GSEA), and immune infiltration analysis were performed to investigate underlying mechanisms. EdU, migration and invasion assays, wound healing assays, immunofluorescence staining, and quantitative polymerase chain reaction were conducted to evaluate the impact of ELN on the proliferative, migratory, and invasive capacities of BCa cells. We identified 20 differently expressed ARGs. A four ARGs risk signature (EFEMP1, UCHL1, TP63, ELN) was constructed in the TCGA cohort. The high-risk group (category) recorded a reduced overall survival (OS) rate relative to the low-risk category (hazard ratio, 2.15; P <0.001). The risk score could predict lymphatic metastasis in TCGA cohort (AUC=0.67). The GSE13507 dataset was employed to verify the validity of this risk score. Based on the four ARGs, two distinct aging profiles (Cluster 1 and Cluster 2) were discovered utilizing the ConsensusClusterPlus, and Cluster 2 possessed a favorable OS in contrast with Cluster 1 (hazard ratio, 0.69; P =0.02). Classical tumor signaling pathways, ECM-associated signaling pathways, and immune-related signaling pathways participate in BCa progression. ELN recombinant protein affected the expression of collagen and increased migration and invasiveness in BCa cells. We constructed a four-ARG risk signature and identified two aging molecular subtypes. This signature could serve as an effective survival predictor for patients with BCa.

Mining of clinical and prognosis related genes in the tumor microenvironment of endometrial cancer: A field synopsis of observational study.

Endometrial cancer (EC) is the sixth most common malignant tumor in women worldwide, and its morbidity and mortality are on the rise. The purpose of this study was to explore potential tumor microenvironment (TME)-related biomarkers associated with the clinical features and prognosis of EC. The Estimating Stromal and Immune Cells in Malignancy Using Expression Data (ESTIMATE) algorithm was used to calculate TME immune and stromal scores of EC samples and to analyze the relationship between immune/stromal scores, clinical features, and prognosis. Heat maps and Venn maps were used to screen for differentially expressed genes (DEGs). The ESTIMATE algorithm revealed immune score was significantly correlated with overall survival and tumor grade in patients with EC. A total of 1448 DEGs were screened, of which 387 were intersecting genes. Gene Ontology (GO) analysis revealed that the biological processes (BP) related to intersecting genes mainly included T cell activation and regulation of lymphocyte activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the intersecting genes were closely related to immune-related signaling pathways. Thirty core genes with more than 7 nodes were identified using protein-protein interaction (PPI) analysis. Six independent prognostic genes of EC were identified using Kaplan-Meier survival analysis and multivariate Cox analysis, namely CD5, BATF, CACNA2D2, LTA, CD52, and NOL4, which are all immune-infiltrating genes that are closely related to clinical features. The current study identified 6 key genes closely related to immune infiltration in the TME of EC that predict clinical outcomes, which may provide new insights into novel prognostic biomarkers and immunotherapy for patients with EC.

Comprehensive analysis to identify a novel diagnostic marker of lung adenocarcinoma and its immune infiltration landscape.

Lung cancer continues to be a problem faced by all of humanity. It is the cancer with the highest morbidity and mortality in the world, and the most common histological type of lung cancer is lung adenocarcinoma (LUAD), accounting for about 40% of lung malignant tumors. This study was conducted to discuss and explore the immune-related biomarkers and pathways during the development and progression of LUAD and their relationship with immunocyte infiltration. The cohorts of data used in this study were downloaded from the Gene Expression Complex (GEO) database and the Cancer Genome Atlas Program (TCGA) database. Through the analysis of differential expression analysis, weighted gene co-expression network analysis (WGCNA), and least absolute shrinkage and selection operator(LASSO), selecting the module with the highest correlation with LUAD progression, and then the HUB gene was further determined. The Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) were then used to study the function of these genes. Single-sample GSEA (ssGSEA) analysis was used to investigate the penetration of 28 immunocytes and their relationship with HUB genes. Finally, the receiver operating characteristic curve (ROC) was used to evaluate these HUB genes accurately to diagnose LUAD. In addition, additional cohorts were used for external validation. Based on the TCGA database, the effect of the HUB genes on the prognosis of LUAD patients was assessed using the Kaplan-Meier curve. The mRNA levels of some HUB genes in cancer cells and normal cells were analyzed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The turquoise module with the highest correlation with LUAD was identified among the seven modules obtained with WGCNA. Three hundred fifty-four differential genes were chosen. After LASSO analysis, 12 HUB genes were chosen as candidate biomarkers for LUAD expression. According to the immune infiltration results, CD4 + T cells, B cells, and NK cells were high in LUAD sample tissue. The ROC curve showed that all 12 HUB genes had a high diagnostic value. Finally, the functional enrichment analysis suggested that the HUB gene is mainly related to inflammatory and immune responses. According to the RT-qPCR study, we found that the expression of DPYSL2, OCIAD2, and FABP4 in A549 was higher than BEAS-2B. The expression content of DPYSL2 was lower in H1299 than in BEAS-2B. However, the expression difference of FABP4 and OCIAD2 genes in H1299 lung cancer cells was insignificant, but both showed a trend of increase. The mechanism of LUAD pathogenesis and progression is closely linked to T cells, B cells, and monocytes. 12 HUB genes(ADAMTS8, CD36, DPYSL2, FABP4, FGFR4, HBA2, OCIAD2, PARP1, PLEKHH2, STX11, TCF21, TNNC1) may participate in the progression of LUAD via immune-related signaling pathways.

Ferroptosis-related gene HIC1 in the prediction of the prognosis and immunotherapeutic efficacy with immunological activity.

Hypermethylated in Cancer 1 (HIC1) was originally confirmed as a tumor suppressor and has been found to be hypermethylated in human cancers. Although growing evidence has supported the critical roles of HIC1 in cancer initiation and development, its roles in tumor immune microenvironment and immunotherapy are still unclear, and no comprehensive pan-cancer analysis of HIC1 has been conducted. HIC1 expression in pan-cancer, and differential HIC1 expression between tumor and normal samples were investigated. Immunohistochemistry (IHC) was employed to validate HIC1 expression in different cancers by our clinical cohorts, including lung cancer, sarcoma (SARC), breast cancer, and kidney renal clear cell carcinoma (KIRC). The prognostic value of HIC1 was illustrated by Kaplan-Meier curves and univariate Cox analysis, followed by the genetic alteration analysis of HIC1 in pan-cancer. Gene Set Enrichment Analysis (GSEA) was conducted to illustrate the signaling pathways and biological functions of HIC1. The correlations between HIC1 and tumor mutation burden (TMB), microsatellite instability (MSI), and the immunotherapy efficacy of PD-1/PD-L1 inhibitors were analyzed by Spearman correlation analysis. Drug sensitivity analysis of HIC1 was performed by extracting data from the CellMiner™ database. HIC1 expression was abnormally expressed in most cancers, and remarkable associations between HIC1 expression and prognostic outcomes of patients in pan-cancer were detected. HIC1 was significantly correlated with T cells, macrophages, and mast cell infiltration in different cancers. Moreover, GSEA revealed that HIC1 was significantly involved in immune-related biological functions and signaling pathways. There was a close relationship of HIC1 with TMB and MSI in different cancers. Furthermore, the most exciting finding was that HIC1 expression was significantly correlated with the response to PD-1/PD-L1 inhibitors in cancer treatment. We also found that HIC1 was significantly correlated with the sensitivity of several anti-cancer drugs, such as axitinib, batracylin, and nelarabine. Finally, our clinical cohorts further validated the expression pattern of HIC1 in cancers. Our investigation provided an integrative understanding of the clinicopathological significance and functional roles of HIC1 in pan-cancer. Our findings suggested that HIC1 can function as a potential biomarker for predicting the prognosis, immunotherapy efficacy, and drug sensitivity with immunological activity in cancers.

Comprehensive analysis identifies CLEC1B as a potential prognostic biomarker in hepatocellular carcinoma

BackgroundC-type lectin domain family 1 member B (CLEC1B, encoding the CLEC-2 protein), a member of the C-type lectin superfamily, is a type II transmembrane receptor involved in platelet activation, angiogenesis, and immune and inflammatory responses. However, data regarding its function and clinical prognostic value in hepatocellular carcinoma (HCC) remain scarce.MethodsThe expression of CLEC1B was explored using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. RT-qPCR, western blot, and immunohistochemistry assays were employed to validate the downregulation of CLEC1B. Univariate Cox regression and survival analyses were used to evaluate the prognostic value of CLEC1B. Gene Set Enrichment Analysis (GSEA) was conducted to investigate the potential association between cancer hallmarks and CLEC1B expression. The TISIDB database was applied to search for the correlation between immune cell infiltration levels and CLEC1B expression. The association between CLEC1B and immunomodulators was conducted by Spearman correlation analysis based on the Sangerbox platform. Annexin V-FITC/PI apoptosis kit was used for the detection of cell apoptosis.ResultsThe expression of CLEC1B was low in various tumors and exhibited a promising clinical prognostic value for HCC patients. The expression level of CLEC1B was tightly associated with the infiltration of various immune cells in the HCC tumor microenvironment (TME) and positively correlated with a bulk of immunomodulators. In addition, CLEC1B and its related genes or interacting proteins are implicated in multiple immune-related processes and signaling pathways. Moreover, overexpression of CLEC1B significantly influenced the treatment effects of sorafenib on HCC cells.ConclusionsOur results reveal that CLEC1B could serve as a potential prognostic biomarker and may be a novel immunoregulator for HCC. However, its function in immune regulation should be further explored.

High expression of GPR176 predicts poor prognosis of gastric cancer patients and promotes the proliferation, migration, and invasion of gastric cancer cells

G-protein-coupled receptors (GPCRs) are the most prominent family of cell surface receptors, which can regulate various biological functions and play an essential role in many diseases. GPR176 is a member of the GPCRs family and has been rarely studied in cancer. We aim to investigate the diagnostic and prognostic value of GPR176 in gastric cancer (GC) and explore its potential mechanism. Through the TCGA database and real-time quantitative PCR, we found that the expression level of GPR176 was significantly increased in GC and had good value in the diagnosis and prognosis of GC. Vitro experiments revealed that GPR176 could promote the proliferation, migration, and invasion of GC cells and may be involved in regulating multiple tumors and immune-related signaling pathways. In addition, we found that GPR176 is associated with GC immune infiltration and may affect the immune efficacy of GC patients. In summary, the high GPR176 expression level was associated with poor prognosis, more robust immune infiltration, and worse immunotherapy efficacy in GC patients, suggesting that GPR176 may be an immune-related biomarker for GC that can promote the proliferation, migration, and invasion of GC cells.

Repair of dysfunctional bone marrow endothelial cells alleviates aplastic anemia.

Aplastic anemia (AA) is a life-threatening disease characterized by bone marrow (BM) failure and pancytopenia. As an important component of the BM microenvironment, endothelial cells (ECs) play a crucial role in supporting hematopoiesis and regulating immunity. However, whether impaired BM ECs are involved in the occurrence of AA and whether repairing BM ECs could improve hematopoiesis and immune status in AA remain unknown. In this study, a classical AA mouse model and VE-cadherin blocking antibody that could antagonize the function of ECs were used to validate the role of BM ECs in the occurrence of AA. N-acetyl-L-cysteine (NAC, a reactive oxygen species scavenger) or exogenous EC infusion was administered to AA mice. Furthermore, the frequency and functions of BM ECs from AA patients and healthy donors were evaluated. BM ECs from AA patients were treated with NAC in vitro, and then the functions of BM ECs were evaluated. We found that BM ECs were significantly decreased and damaged in AA mice. Hematopoietic failure and immune imbalance became more severe when the function of BM ECs was antagonized, whereas NAC or EC infusion improved hematopoietic and immunological status by repairing BM ECs in AA mice. Consistently, BM ECs in AA patients were decreased and dysfunctional. Furthermore, dysfunctional BM ECs in AA patients led to their impaired ability to support hematopoiesis and dysregulate T cell differentiation toward proinflammatory phenotypes, which could be repaired by NAC in vitro. The reactive oxygen species pathway was activated, and hematopoiesis- and immune-related signaling pathways were enriched in BM ECs of AA patients. In conclusion, our data indicate that dysfunctional BM ECs with impaired hematopoiesis-supporting and immunomodulatory abilities are involved in the occurrence of AA, suggesting that repairing dysfunctional BM ECs may be a potential therapeutic approach for AA patients.

Stimulator of interferon gene (STING) expression as a biomarker for overall survival in PDL1-negative, TMB-low non-small cell lung cancer (NSCLC) treated with immune checkpoint inhibitors (ICIs).

9120 Background: cGAS-STING (CGS) is an intracellular DNA sensing pathway that when activated, stimulates interferon and other immune-related signaling pathways. While increased expression of CGS-related genes has been associated with better survival in NSCLC, studies investigating this phenomenon in tumors less likely to respond to ICIs such as PDL1-negative, TMB-Low NSCLC are lacking. Here we report the role of CGS pathway in NSCLC tumors that are both PDL1-negative and TMB-Low. Methods: DNA (592-gene or whole exome) and RNA sequencing (whole transcriptome) was performed for NSCLC specimens (n=7264) submitted to Caris Life Sciences (Phoenix, AZ). PDL1 negativity was defined as &lt;1% TPS score (22C3) &amp; TMB-Low as &lt;10 mutations/Mb. Hierarchical Agglomerative Clustering (HAC) was performed on STING pathway genes (CXCL10, CCL5 and GZB) and tumors were grouped into STING-high (n=3070), STING-intermediate (n=1609) and STING-low (n=2585) groups. Microenvironmental cell populations (MCP)-counter analysis was used to estimate cellular composition of immune cells. Statistical significance was determined using chi-square/Fisher’s exact/Mann-Whitney U tests and adjusted for multiple comparisons (q&lt;0.05). Kaplan Meier method was used to estimate the overall survival (OS) derived from insurance claims of IO treated pts with NSCLC (n=400). Pts were stratified into groups above or below the median expression of the STING gene ( TMEM173). Results: Compared to STING-low, tumors that were STING-high had enrichment in immune cell infiltrates including CD8+ T cells (4.4-fold) and B-cells (5.9-fold); Additionally, STING-high cohort had significantly higher expression of immune checkpoint (IC) genes including CD274(2.5-fold), CD80 (2.7-fold, all q&lt;0.05). STING-high tumors also had a higher prevalence of TP53 mutations (mts) and a lower prevalence of STK11 and KEAP1 mts (Table). Median overall survival (OS) was 21.1 months in the STING-high cohort (n=200) vs 11.9 months in the STING-low cohort (n=199) in IO treated pts (HR = 0.62, p&lt;0.000.1) Conclusions: To our knowledge this is the largest real-world dataset indicating that enrichment of both the STING gene, and gene signatures associated with the STING pathway represent valuable transcriptomic biomarkers to stratify pts with PDL1-negative and TMB-Low NSCLC who benefit more from IO therapies. Conversely, novel IO combination strategies need to be employed in STING-low tumors to enhance outcomes. [Table: see text]

Genomic and molecular landscape of homologous recombination deficiency across multiple cancer types

Homologous recombination deficiency (HRD) causes faulty double-strand break repair and is a prevalent cause of tumorigenesis. However, the incidence of HRD and its clinical significance in pan-cancer patients remain unknown. Using computational analysis of Single-nucleotide polymorphism array data from 10,619 cancer patients, we demonstrate that HRD frequently occurs across multiple cancer types. Analysis of the pan-cancer cohort revealed that HRD is not only a biomarker for ovarian cancer and triple-negative breast cancer, but also has clinical prognostic value in numerous cancer types, including adrenocortical cancer and thymoma. We discovered that homologous recombination–related genes have a high mutation or deletion frequency. Pathway analysis shows HRD is positively correlated with the DNA damage response and the immune-related signaling pathways. Single cell RNA sequencing of tumor-infiltrating lymphocytes reveals a significantly higher proportion of exhausted T cells in HRD patients, indicating pre-existing immunity. Finally, HRD could be utilized to predict pan-cancer patients’ responses to Programmed cell death protein 1 immunotherapy. In summary, our work establishes a comprehensive map of HRD in pan-cancer. The findings have significant implications for expanding the scope of Poly ADP-ribose polymerase inhibitor therapy and, possibly, immunotherapy.

Screening of novel biomarkers for breast cancer based on WGCNA and multiple machine learning algorithms.

Breast cancer (BC) ranks first in incidence among women, with approximately 2 million new cases per year. Therefore, it is essential to investigate emerging targets for BC patients' diagnosis and prognosis. We analyzed gene expression data from 99 normal and 1,081 BC tissues in The Cancer Genome Atlas (TCGA) database. Differentially expressed genes (DEGs) were identified using "limma" R package, and relevant modules were chosen through Weighted Gene Coexpression Network Analysis (WGCNA). Intersection genes were obtained by matching DEGs to WGCNA module genes. Functional enrichment studies were performed on these genes using Gene Ontology (GO), Disease Ontology (DO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Biomarkers were screened via Protein-Protein Interaction (PPI) networks and multiple machine-learning algorithms. The Gene Expression Profiling Interactive Analysis (GEPIA), The University of ALabama at Birmingham CANcer (UALCAN), and Human Protein Atlas (HPA) databases were employed to examine mRNA and protein expression of eight biomarkers. Kaplan-Meier mapper tool assessed their prognostic capabilities. Key biomarkers were analyzed via single-cell sequencing, and their relationship with immune infiltration was examined using Tumor Immune Estimation Resource (TIMER) database and "xCell" R package. Lastly, drug prediction was conducted based on the identified biomarkers. We identified 1,673 DEGs and 542 important genes through differential analysis and WGCNA, respectively. Intersection analysis revealed 76 genes, which play significant roles in immune-related viral infection and IL-17 signaling pathways. DIX domain containing 1 (DIXDC1), Dual specificity phosphatase 6 (DUSP6), Pyruvate dehydrogenase kinase 4 (PDK4), C-X-C motif chemokine ligand 12 (CXCL12), Interferon regulatory factor 7 (IRF7), Integrin subunit alpha 7 (ITGA7), NIMA related kinase 2 (NEK2), and Nuclear receptor subfamily 3 group C member 1 (NR3C1) were selected as BC biomarkers using machine-learning algorithms. NEK2 was the most critical gene for diagnosis. Prospective drugs targeting NEK2 include etoposide and lukasunone. Our study identified DIXDC1, DUSP6, PDK4, CXCL12, IRF7, ITGA7, NEK2, and NR3C1 as potential diagnostic biomarkers for BC, with NEK2 having the highest potential to aid in diagnosis and prognosis in clinical settings.