Metadherin promotes stem cell phenotypes and correlated with immune infiltration in hepatocellular carcinoma

BACKGROUND Metadherin(MTDH)is a key oncogene in most cancer types,including hepato-cellular carcinoma(HCC).Notably,MTDH does not affect the stemness pheno-type or immune infiltration of HCC.AIM To explore the role of MTDH on stemness and immune infiltration in HCC.METHODS MTDH expression in HCC tissues was detected using TCGA and GEO databases.Immunohistochemistry was used to analyze the tissue samples.MTDH was stably knocked down or overexpressed by lentiviral transfection in the two HCC cell lines.The invasion and migration abilities of HCC cells were evaluated using Matrigel invasion and wound healing assays.Next,we obtained liver cancer stem cells from the spheroids by culturing them in a serum-free medium.Gene expression was determined by western blotting and quantitative reverse transcri-ption PCR.Flow cytometry,immunofluorescence,and tumor sphere formation assays were used to characterize stem-like cells.The effects of MTDH inhibition on tumor growth were evaluated in vivo.The correlation of MTDH with immune cells,immunomodulators,and chemokines was analyzed using ssGSEA and TISIDB databases.RESULTS HCC tissues expressed higher levels of MTDH than normal liver tissues.High MTDH expression was associated with a poor prognosis.HCC cells overex-pressing MTDH exhibited stronger invasion and migration abilities,exhibited a stem cell-like phenotype,and formed spheres;however,MTDH inhibition attenuated these effects.MTDH inhibition suppressed HCC progression and CD133 expression in vivo.MTDH was positively correlated with immature dendritic,T helper 2 cells,central memory CD8^(+)T,memory B,activated dendritic,natural killer(NK)T,NK,activated CD4^(+)T,and central memory CD4^(+)T cells.MTDH was negatively correlated with activated CD8^(+)T cells,eosinophils,activated B cells,monocytes,macrophages,and mast cells.A positive correlation was observed between the MTDH level and CXCL2 expression,whereas a negative correlation was observed between the MTDH level and CX3CL1 and CXCL12 expression.CONCLUSION High levels of MTDH expression in patients with HCC are associated with poor prognosis,promoting tumor stemness,immune infiltration,and HCC progression.

Screening and immune infiltration analysis of ferroptosis-related genes in pancreatic cancer with predictions for traditional Chinese medicine treatments

Background:This study aims to explore the involvement of ferroptosis-related genes and pathogenesis in pancreatic cancer and predict potential therapeutic interventions using Traditional Chinese Medicine(TCM).Methods:We utilized gene expression datasets,ferroptosis upregulated genes and applied machine learning algorithms,including LASSO and SVM-RFE,to identify key ferroptosis-related genes in pancreatic cancer.Perform Gene Ontology,Kyoto Encyclopedia of Genes and Genomes,and Disease Ontology enrichment analysis,immune infiltration analysis and correlation analysis between immune infiltrating cells and characteristic genes on differentially expressed genes using the R software package.Retrieve potential traditional Chinese medicine for targeted ferroptosis gene therapy for pancreatic cancer through Coremine and Herb databases.Results:Seventeen feature genes were identified,with significant implications for immune cell infiltration in pancreatic cancer.The results of immune cell infiltration analysis showed that B cells naive,B cells memory,T cells regulatory,and M0 macrophages were significantly upregulated in pancreatic cancer patients;Mast cells resting were significantly downregulated.Chinese herbal medicines such as ginkgo,turmeric,ginseng,Codonopsis pilosula,Zedoary turmeric,deer tendons,senna leaves,Guanmu Tong,Huangqi,and Banzhilian are potential drugs for targeted ferroptosis gene therapy for pancreatic cancer.Conclusion:TIMP1 emerged as a key gene,with several TCM herbs predicted to modulate its expression,offering new avenues for treatment.

Cervical cancer with transferrin receptor has a poor prognosis and is associated with immune infiltration, according to a comprehensive bioinformatics study

Background:The molecular mechanism underlying the involvement of the Transferrin receptor(TFRC)in cervical cancer remains poorly understood.This study aims to elucidate the role of TFRC in cervical cancer by analyzing data from The Cancer Genome Atlas(TCGA)and Genotype-Tissue Expression(GTEx)databases.Methods:TFRC protein expression was obtained from Human Protein Altas(HPA).All datas were collected from TCGA and GTEx.In this study,we analyzed the expression of TFRC in cervical cancer and its clinical significance.Through Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene set enrichment analyses(GSEA),investigated the related molecular pathways of TFRC.The relationship between TFRC and immune infiltration was then examined.The prognosis of different immune cell subsets was then analyzed after dividing cervical cancer patients into high and low expression of TFRC groups.Results:TFRC is highly expressed in various tumor tissues compared to control normal tissues,including cervical cancer.An increased expression of TFRC was associated with higher Tumor(T)and Node(N)stage,as well as a higher clinical stage.Kaplan–Meier(KM)survival analysis investigated that higher TFRC expression patients have a poor overall survival(OS),disease specific survival(DSS)and progress free interval(PFI).Both KEGG and GSEA enriched signaling pathway by high TFRC and low TFRC groups.There was a significant negative linear correlation between TFRC expression and immune infiltration.TFRC affects the prognosis of cervical cancer patients through immune pathway.Conclusions:Cervical cancer patients with TFRC expression may have a worse prognosis.

BMI1 overexpression is correlated with a poor prognosis and immune infiltration in hepatocellular carcinoma

Background:Owing to the occurrence of primary or secondary tolerance,the efficacy of immunotherapy for hepatocellular carcinoma(HCC)patients is limited.Therefore,the mechanism underlying this tolerance needs to be further investigated.B cell–specific Moloney murine leukemia virus integration site 1(BMI1)is associated with cancer stem cell tumorigenesis,progression,and the maintenance of the self-renewal.However,the effect of BMI1 expression on immune infiltration and prognosis in HCC is still unclear.Methods:To assess the relationship between BMI1 expression and HCC prognosis and immune infiltration,the GEPIA database,TIMER database,and K-M plotter were used.TIMER database was used to determine the levels ofBMI1 in various tumor tissues and corresponding normal tissues,and examine the association between BMI1 expression and tumor-infiltrating immune cells.GEPIA database was applied to determine BMI1 expression in various tumor tissues and corresponding normal tissues.K-M Plotter was used to study the relationships among BMI1 expression,clinicopathological features,and survival rates.Results:BMI1 expression was markedly higher in various solid tumors compared with that in the respective normal tissues,including HCC,and high expression led to poor relapse-free survival and overall survival in HCC patients.BMI1 overexpression was also correlated with the infiltration of immune cells(eg,B cells,CD8+T cells,CD4+T cells,dendritic cells,neutrophils,and macrophages)and positively associated with different subsets of T cells,monocytes,and M1 macrophages,among others.Conclusions:This study demonstrates that high BMI1 expression is strongly correlated with immune infiltration and poor prognosis in HCC.Increased expression of BMI1 might thus be a potential mechanism of immune tolerance in this disease.

A Prognostic Biomarker for Bladder Cancer Correlated with Immune Infiltration Is PAEP

Background: A major cause of cancer death worldwide is bladder cancer, which is the most common malignant tumor of the urinary tract. PAEP is a member of the kernel lipocalin superfamily whose members share relatively low sequence similarity but have highly conserved exon/intron structure and three-dimensional protein folding. Most lipocalins are clustered on the long arm of chromosome 9. The purpose of this study was to clarify the correlation between PAEP expression level and bladder cancer. Methods: In the TCGA database, we obtained clinical and RNA sequencing data of 431 BLCA patients, including 412 BLCA tissues and 19 normal bladder tissues in the study. Analyses of bioinformatics were conducted in this study to determine the role of PAEP in bladder cancer. A quantitative real-time PCR method was used to quantitate the gene expression profile. Additionally, the effect of PAEP on tumor immune infiltration and prognosis was analyzed. Results: PAEP was a poor prognostic biomarker of bladder cancer because it was significantly upregulated. bladder cancer patients with higher PAEP expression had poor outcomes. An AUC of 0.780 was calculated from the area under the ROC curve. PAEP was associated with T stage, pathologic stage, Histologic grade and Subtype of bladder cancer patients, and served as an independent predictor of overall survival in bladder cancer patients. Functional enrichment analysis revealed PAEP was obviously enriched in pathways connected with carcinogenesis and immunosuppression. The expression of PAEP was significantly associated with tumor immune cells and immune checkpoints according to ssGSEA and Spearman correlation analysis. Conclusions: In this study, we screened and detected a mRNA, PAEP is a prognostic and immune-related biomarker in BLCA, which may contribute to the early diagnosis and treatment of BLCA.

Comprehensive bioinformatics analysis of CYB561 expression in breast cancer:Link between prognosis and immune infiltration

Background:Cytochrome b561(CYB561)plays a critical role in neuroendocrine function,cardiovascular regulation,and tumor growth;however,the prognostic value of CYB561 in patients with breast cancer and the relationship between CYB561 expression and immune infiltration in breast cancer remain unclear.Methods:The mRNA expression and clinical data of patients with breast cancer were obtained from The Cancer Genome Atlas database.Functional enrichment analysis was used to explore underlying biological functions associated with CYB561.The methylation status of CYB561 was analyzed using the MethSurv database.The enrichment score of immune cell infiltration for CYB561 in breast cancer was calculated using single-sample gene set enrichment analysis.The prognostic value of CYB561 was evaluated using Kaplan-Meier method and Cox regression analysis.Based on the results of the multivariate Cox analysis,a nomogram was constructed to predict the effect of CYB561 expression on overall survival(OS).Results:The results showed that CYB561 was highly expressed in breast cancer tissues.Hypomethylation of CYB561 is associated with an unfavorable prognosis.In multivariate Cox regression analysis,CYB561 was an independent prognostic factor for OS.Functional enrichment analysis indicated that estrogen signaling pathway,inflammatory response,KRAS signaling pathway,epithelial-mesenchymal transition,leukocyte migration,and regulation of lymphocyte activation were strongly enriched in the low CYB561 expression group.Additionally,CYB561 expression was negatively correlated with immune infiltration of B cells,plasmacytoid dendritic cells,dendritic cells,and neutrophils.Conclusion:CYB561 may serve as a potential biomarker for breast cancer diagnosis and prognosis.

Characterization of prognosis and immune infiltration by a novel glutamine metabolism-related model in cutaneous melanoma

Glutamine metabolism(GM)plays an important role in tumor growth and proliferation.Skin cutaneous melanoma(SKCM)is a glutamine-dependent cancer.However,the molecular characteristics and action mechanism of GM on SKCM remain unclear.Therefore,we aimed to explore the effects of GM-related genes on survival,clinicopathological characteristics,and the tumor microenvironment in SKCM.In this study,682 SKCM samples were obtained from the Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)databases.Consensus clustering was used to classify SKCM samples into distinct subtypes based on 41 GM-related genes.Differences in survival,immune infiltration,clinical characteristics,and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways as well as differentially expressed genes(DEGs)between subgroups were evaluated.A prognostic model was constructed according to prognostic DEGs.Differential analyses in survival,immune infiltration,tumor microenvironment(TME),tumor mutation burden(TMB),stemness,and drug sensitivity between risk groups were conducted.We identified two distinct GM-related subtypes on SKCM and found that GM-related gene alterations were associated with survival probability,clinical features,biological function,and immune infiltration.Then a risk model based on six DEGs(IL18,SEMA6A,PAEP,TNFRSF17,AIM2,and CXCL10)was constructed and validated for predicting overall survival in SKCM patients.The results showed that the risk score was negatively correlated with CD8+T cells,activated CD4+memory T cells,M1 macrophages,andγδT cells.The group with a low-risk score was accompanied by a better survival rate with higher TME scores and lower stemness index.Moreover,the group with high-and low-risk score had a significant difference with the sensitivity of 75 drugs(p<0.001).Overall,distinct subtypes in SKCM patients based on GM-related genes were identified and the risk model was constructed,which might contribute to prognosis prediction,guide clinical therapy,and develop novel therapeutic strategies.

Assessment of gastric cancer prognosis,immune infiltration based on cuproptosis-related LncRNAs and prediction of traditional Chinese medicine

Objective:Constructing a prognostic model for gastric cancer(GC)based on cuproptosisrelated LncRNAs(CRLs)and predict the traditional Chinese medicine that regulate cuproptosis-related genes(CRGs).Methods:Clinical data and RNA-seq of 443 GC cases were obtained from The Cancer Genome Atlas(TCGA)database,and CRLs were screened by Pearson analysis,Cox regression,and least absolute shrinkage and selection operator(LASSO)regression to construct a risk model to predict GC prognosis,and the nomogram was constructed by combining risk scores and clinical characteristics.The accuracy of the model was validated by the receiver operating characteristic curve,Kaplan-Meier curves and C-index.To assess the correlation of risk scores with immune infiltration,immune checkpoint gene expression and chemotherapy/targeted agents.The Coremine Medical database was applied to predict potential traditional Chinese medicine that regulate CRGs.Results:Risk models for GC were constructed based on the risk scores of seven CRLs(AP001107.9,VCAN-AS1,AC016394.2,LINC02675,AC100814.1,HAGLR,and LINC01094).The AUC of the risk model predicting 1-,3-,and 5-year survival in GC patients was 0.720,0.682,and 0.711,and its prognostic value was better than age,Grade classification,and TNM stage.The AUC of the risk model combining age and TNM stage to predict 1-year survival in GC patients was 0.793.The risk score correlated with the degree of enrichment of immune cells such as tumorinfiltrating lymphocytes and regulatory T cells and the expression of 22 immune checkpoint genes such as LAG3,ICOS,CD28,NRP1 and the sensitivity of 13 chemotherapeutic/targeted agents.There are 58 traditional Chinese medicine with potential regulatory effects on CRGs,mainly for clearing heat and detoxing,promoting blood circulation and relieving pain,which are mainly attributed to the liver,spleen and lung meridians.Spirulina and osthole have potential regulatory effects on FDX1,a key gene in the death mechanism of cuproptosis.Conclusions:A risk signature constructed based on seven CRLs could assess the prognosis and immunity of GC,and Spirulina and Serpentine may have important regulatory efficacy on the mechanism of copper cuproptosis.

High spindle and kinetochore-associated complex subunit-3 expression predicts poor prognosis and correlates with adverse immune infiltration in hepatocellular carcinoma

BACKGROUND Spindle and kinetochore-associated complex subunit 3(SKA3)is a malignancyassociated gene that plays a critical role in the regulation of chromosome separation and cell division.However,the molecular mechanism through which SKA3 regulates tumor cell proliferation in hepatocellular carcinoma(HCC)has not been fully elucidated.AIM To investigate the molecular mechanisms underlying the role of SKA3 in HCC.METHODS SKA3 expression,clinicopathological,and survival analyses were performed using multiple public database platforms,and the results were verified by Western blot and immunohistochemistry staining using collected clinical samples.Functional enrichment analyses were performed to evaluate the biological functions and molecular mechanisms of SKA3 in HCC.Furthermore,the Tumor Immune Estimation Resource and single-sample Gene Set Enrichment Analysis(ssGSEA)algorithms were utilized to investigate the abundance of tumor-infiltrating immune cells in HCC.The response to chemotherapeutic drugs was evaluated by the R package“pRRophetic”.RESULTS We found that upregulated SKA3 expression was significantly correlated with poor prognosis in patients with HCC.Multivariable Cox regression analysis indicated that SKA3 was an independent risk factor for survival.GSEA revealed that SKA3 expression may facilitate proliferation and migratory processes by regulating the cell cycle and DNA repair.Moreover,patients with high SKA3 expression had significantly decreased ratios of CD8+T cells,natural killer cells,and dendritic cells.Drug sensitivity analysis showed that the high SKA3 group was more sensitive to sorafenib,sunitinib,paclitaxel,doxorubicin,gemcitabine,and vx-680.CONCLUSION High SKA3 expression led to poor prognosis in patients with HCC by enhancing HCC proliferation and repressing immune cell infiltration surrounding HCC.SKA3 may be used as a biomarker for poor prognosis and as a therapeutic target in HCC.

Solute carrier family 2 members 1 and 2 as prognostic biomarkers in hepatocellular carcinoma associated with immune infiltration

BACKGROUND Metabolic reprogramming has been identified as a core hallmark of cancer.Solute carrier family 2 is a major glucose carrier family.It consists of 14 members,and we mainly study solute carrier family 2 member 1(SLC2A1)and solute carrier family 2 member 2(SLC2A2)here.SLC2A1,mainly existing in human erythrocytes,brain endothelial cells,and normal placenta,was found to be increased in hepatocellular carcinoma(HCC),while SLC2A2,the major transporter of the normal liver,was decreased in HCC.AIM To identify if SLC2A1 and SLC2A2 were associated with immune infiltration in addition to participating in the metabolic reprogramming in HCC.METHODS The expression levels of SLC2A1 and SLC2A2 were tested in HepG2 cells,HepG215 cells,and multiple databases.The clinical characteristics and survival data of SLC2A1 and SLC2A2 were examined by multiple databases.The correlation between SLC2A1 and SLC2A2 was analyzed by multiple databases.The functions and pathways in which SLC2A1,SLC2A2,and frequently altered neighbor genes were involved were discussed in String.Immune infiltration levels and immune marker genes associated with SLC2A1 and SLC2A2 were discussed from multiple databases.RESULTS The expression level of SLC2A1 was up-regulated,but the expression level of SLC2A2 was down-regulated in HepG2 cells,HepG215 cells,and liver cancer patients.The expression levels of SLC2A1 and SLC2A2 were related to tumor volume,grade,and stage in HCC.Interestingly,the expression levels of SLC2A1 and SLC2A2 were negatively correlated.Further,high SLC2A1 expression and low SLC2A2 expression were linked to poor overall survival and relapse-free survival.SLC2A1,SLC2A2,and frequently altered neighbor genes played a major role in the occurrence and development of tumors.Notably,SLC2A1 was positively correlated with tumor immune infiltration,while SLC2A2 was negatively correlated with tumor immune infiltration.Particularly,SLC2A2 methylation was positively correlated with lymphocytes.CONCLUSION SLC2A1 and SLC2A2 are independent therapeutic targets for HCC,and they are quintessential marker molecules for predicting and regulating the number and status of immune cells in HCC.

Prognostic tumor microenvironment gene and the relationship with immune infiltration characteristics in metastatic breast cancer

The aim of this study was to reveal genes associated with breast cancer metastasis,to investigate their intrinsic relationship with immune cell infiltration in the tumor microenvironment,and to screen for prognostic biomarkers.Gene expression data of breast cancer patients and their metastases were downloaded from the GEO,TCGA database.R language package was used to screen for differentially expressed genes,enrichment analysis of genes,PPI network construction,and also to elucidate key genes for diagnostic and prognostic survival.Spearman’s r correlation was used to analyze the correlation between key genes and infiltrating immune cells.We screened 25 hub genes,FN1,CLEC5A,ATP8B4,TLR7,LY86,PTGER3 and other genes were differentially expressed in cancer and paraneoplastic tissues.However,patients with higher expression of CD1C,IL-18 breast cancer had a better prognosis in the 10 years survival period,while patients with high expression of FN1,EIF4EBP1 tumors had a worse prognosis.In addition,TP53 and HIF1 genes are closely related to the signaling pathway of breast cancer metastasis.In this study,gene expression of ATP8B4 and CD1C were correlated with cancer tissue infiltration of CD8^(+)T lymphocytes,while GSE43816,GSE62327 and TCGA databases showed that CD8^(+)T lymphocytes were closely associated with breast cancer progression.Functional enrichment analysis of genes based on expression differences yielded key genes of prognostic value in the breast cancer microenvironment.

Identification of WWTR1 as an immune infiltration-correlated prognostic biomarker in colon cancer

WWTR1,a gene related to the TGF-βsignaling pathway,has been elucidated to be involved in oncogenesis in multiple studies.There is,however,no research on its link to immune infiltration in colon cancer.The TCGA database has identified WWTR1,a gene related to the TGF-βsignaling pathway,which is lowly expressed in colon cancer patients compared to normal subjects.Meanwhile,we produced the Kapan-Meier curve with GEO and the TCGA database,which revealed that colon cancer patients with high WWTR1 expression had a poor prognosis.We discovered that high expression of WWTR1 in colon cancer was associated with clinical stage,pathological T-stage,and lymphatic metastasis after examining the clinical characteristics of colon cancer patients.WWTR1 was found to be an independent predictive factor for colon cancer in a multivariate Cox regression study.Infiltration of immunological cells(B cells,CD8^(+)T cells,CD4^(+)T cells,Macrophage,Neutrophil,Dendritic cells)was linked to WWTR1 expression.In colon cancer,WWTR1 expression was also found to be favorably linked with major immune cell markers.According to an analysis of WWTR1 DCGs,GO,and KEGG enrichment analysis,WWTR1 expression levels were associated with ameboidal-type cell migration,focal adhesion,actin binding,Chemical carcinogenesis-reactive oxygen species,Non-alcoholic fatty liver disease,and Alzheimer disease.These findings imply that WWTR1 is a prognostically valuable and important biomarker for colon cancer,and imply that its expression is strongly linked to colon cancer immune infiltration,making it a potential new target for colon cancer biotherapy.

WGCNA and LASSO algorithm constructed an immune infiltration-related 5-gene signature and nomogram to improve prognosis prediction of hepatocellular carcinoma

Hepatocellular carcinoma(HCC)is a common immunogenic malignant tumor.Although the new strategies of immunotherapy and targeted therapy have made considerable progress in the treatment of HCC,the 5-year survival rate of patients is still very low.The identification of new prognostic signatures and the exploration of the immune microenvironment are crucial to the optimization and improvement of molecular therapy strategies.We studied the potential clinical benefits of the inflammation regulator miR-93-3p and mined its target genes.Weighted gene coexpression network analysis(WGCNA),univariate and multivariate COX regression and the LASSO COX algorithm are employed to identify prognostic-related genes and construct multi-gene signature-based risk model and nomogram for survival prediction.Support vector machine(SVM)based Cibersort’s deconvolution algorithm and gene set enrichment analysis(GSEA)is used to evaluate the changes in tumor immune microenvironment and pathway differences.The study found the favorable prognostic performance of miR-93-3p and identified 389 prognostic-related target genes.The risk model based on a novel 5-gene signature(cct5,cdk4,cenpa,dtnbp1 and flvcr1)was developed and has prominent prognostic significance in the training cohort(P<0.0001)and validation cohort(P=0.0016).The nomogram constructed by combining the gene signature and the AJCC stage further improves the survival prediction ability of the gene signature.The infiltration level of multiple immune cells(especially T cells,B cells and macrophages)were positively correlated with the expression of prognostic signature.In addition,we found that gene markers of T cells and B cells is monitored and regulated by prognostic signature.Meanwhile,several GSEA pathways related to the immune system are enriched in the high-risk group.In general,we integrated the WGCNA,LASSO COX and SVM algorithms to develop and verify 5-gene signatures and nomograms related to immune infiltration to improve the survival prediction of patients.

An integrated bioinformatics analysis and experimental study identified key biomarkers CD300A or CXCL1,pathways and immune infiltration in diabetic nephropathy mice

Diabetic nephropathy(DN)is a common microvascular complication that easily leads to end-stage renal disease.It is important to explore the key biomarkers andmolecular mechanisms relevant to diabetic nephropathy(DN).We used highthroughput RNA sequencing to obtain the genes related to DN glomerular tissues and healthy glomerular tissues of mice.Then we used LIMMA to analyze differentially expressed genes(DEGs)between DN and non-diabetic glomerular samples.And we performed KEGG,gene ontology functional(GO)enrichment,and gene set enrichment analysis to reveal the signaling pathway of the disease.The CIBERSORT algorithm based on support vector machine was used to determine the immune infiltration score.Random forest algorithm and Cytoscape obtained hub genes.Finally,we applied co-staining,immunohistochemical staining,RT-qPCR and western blotting to validate the protein and mRNA expression of both hub genes.We obtained 913 DEGs mainly related to inflammatory factors and immunity.GSEA results showed that differential genes were mainly enriched in IL-17 signaling pathway,lipid and atherosclerosis,rheumatoid arthritis,TNF signaling pathway,neutrophil extracellular trap formation,Staphylococcus aureus infection and other pathways.The intersection of the random forest algorithm and Cytoscape revealed both hub genes of CD300A and CXCL1.Experiments have shown that the both key genes of CD300A and CXCL1 shown increased expression in glomerular podocytes,and are related to the inflammation of diabetic nephropathy.And immunohistochemical staining and RT-qPCR further confirmed that the protein and mRNA expression level of CD300A or CXCL1 in glomeruli tissue in DN mice were increased.The expression levels of CD300A and CXCL1 increased significantly under HG(high glucose)stimulation,further confirming that diabetes can lead to increased levels of CD300A and CXCL1 at the cellular level.Through bioinformatics analysis,machine learning algorithms,and experimental research,CD300A and CXCL1 are confirmed as both potential biomarkers in diabetic nephropathy.And we further revealed the main pathways of differential genes and the differentially distributed immune infiltrating cells in diabetic nephropathy.

Bioinformatics-based analysis of the relationship between core genes and immune infiltration and tumor metastasis in esophageal cancer

We analysed four gene microarray datasets by GEO2R and obtained differential genes expressed in oesophageal cancer.To further elaborate the functions of DGEs,this study performed gene ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)enrichment analysis of DEGs.We constructed protein interaction networks of DGEs through the String database and screened core genes.We used the GEPIA online database with the Kaplan-Meier plotter database to verify the expression of Hub genes in expressed normal versus tumour tissues and the effect of Hub genes on overall and disease-free survival in oesophageal cancer.To further understand the relationship between Hub gene and tumour metastasis,we analysed the difference in Hub gene expression in patients without metastatic oesophageal cancer versus those with metastatic oesophageal cancer with the help of the HCMDB database.The relationship between Hub genes and tumour immune infiltration was analysed by the TIMER database.We obtained a total of 149 DEGs,of which 49 were up-regulated genes and 100 were down-regulated genes.These DGEs were importantly enriched in IL-17 signalling pathway,ECM-receptor interactions,p53 signalling pathway,estrogen signalling pathway,complement and coagulation cascade response.We screened 10 Hub genes,MMP9,CXCL8,COL1A1,TIMP1,POSTN,MMP3,MMP1,COL3A1,SERPINE1,LUM,among 149 DGEs.hub genes were all up-regulated in expression in esophageal cancer tissues,in addition,MMP9,T1MP1,CXCL8,POSTN and The expression of COL3A1,LUM,MMP1,MMP3,MMP9,POSTN,SERPINE1 and TIMP1 was positively correlated with the infiltration of immune cells in the tumor microenvironment.In conclusion,our study identified 10 signature genes for oesophageal cancer.These genes are associated with the development,metastasis,prognosis and immune infiltration of oesophageal cancer and may be markers of development,metastasis and prognosis as well as targets for immunotherapy.

Correlations between P2RX1 Expression and Gastrointestinal Cancers Prognosis and Immune Infiltration Based on Bioinformatics Analysis

This study was conducted to explore the correlations between the expression,methylation,and various clinicopathological factors of purinergic P2X1 receptor(P2RX1)and the prognosis of patients with gastrointestinal tumors.The Cancer Genome Atlas(TCGA)and the Genotype-Tissue Expression(GTEx)databases were used to analyze the expression of P2RX1 in different types of gastrointestinal cancers.Kaplan-Meier analysis and univariate Cox regression analysis were used to analyze the correlations between P2RX1 expression and the prognosis of various gastrointestinal tumors.Correlations between P2RX1 expression and N6 methyladenine(m6A)-related genes as well as immune checkpoint genes were analyzed by R packages(R version:4.0.3)based on TCGA database.The association between P2RX1 methylation level and the prognosis of patients with gastrointestinal cancers was analyzed using the MethSurv database.In order to explore the biological functions of P2RX1 in hepatocellular carcinoma,the Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)enrichment analysis were carried out using R software.In order to evaluate the correlations between P2RX1 and tumor immune infiltration,Spearman correlation test was performed.The correlations between P2RX1 expression and immune score as well as immune checkpoint genes were analyzed based on TCGA and Tumor Immune Estimation Resource(TIMER)databases.The expression of P2RX1 was found to be significantly downregulated in gastrointestinal tumors except in cholangiocarcinoma(P<0.05).High expression of P2RX1 tended to present better prognosis in hepatocellular carcinoma(P<0.05).It was noted that cg06475633 of P2RX1 presented a higher methylation level compared with other CpG sites in hepatocellular carcinoma.Overall,six CpGs of P2RX1 were associated with significant prognosis in patients with hepatocellular carcinoma(P<0.05).Among all the 20 m6A-related genes,Wilms'tumor 1-associating protein(WTAP)was the most strongly correlated with P2RX1 in hepatocellular carcinoma.Gene enrichment analysis showed that P2RX1 is widely involved in the proliferation,activation,organization,and differentiation of various immune cells.After investigating the TIMER database,P2RX1 was found to be tightly correlated with immune infiltrating cells in gastrointestinal tumors,especially with dendritic cells.Moreover,P2RX1 was found to be strongly positively associated with programmed cell death 1(PD1),programmed death-ligand 1(PD-L1),and cytotoxic T-lymphocyte-associated protein 4(CTLA4)in hepatocellular carcinoma(P<0.05).In conclusion,the dual role of P2RX1 in cancers and its involvement in the recruitment as well as regulation of tumor infiltrating cells in gastrointestinal cancers may be appreciated through this study.

Screening of Postpartum Depression Diagnostic Markers Based on Immune-Related Genes and Immune Infiltration

Background:Postpartum depression(PPD)is a mild to severe non-psychotic depressive episode,one of the main factors leading to pregnancy-related morbidity and mortality,and a mental disorder that has not been fully diagnosed and treated.Compared with women without polycystic ovary syndrome,women with polycystic ovary syndrome are more likely to have a variety of pregnancy complications,including PPD.However,there is currently limited research on whether polycystic ovary syndrome is related to anxiety and depression during pregnancy,and whether this increases the risk of postpartum depression in women.Study design:The GSE10558 data set gene expression profile matrix was used for PPD expression profiles from Gene Expression Synthesis(GEO).The differentially expressed genes were selected and analyzed.Perform gene ontology(GO)enrichment and gene set variation analysis(GSVA)for annotation,visualization,and integrated discovery.At the same time,CIBERSORT and ESTIMATE were used to analyze the immune infiltration situation of the GSE10558 expression profile matrix,including the immune infiltration pattern of ovarian samples,and construct the immune cell infiltration(ICI)score.Then we screened the differentially expressed genes(DEGs)clustered with three groups of immune subtypes,and constructed a protein-protein interaction(PPI)and mRNA-miRNA-TF molecular interaction network.And further predicted the drug target of the hub gene and the target of small molecule compounds,and constructed a network.Based on the intersection of the phenotypic gene set,the pivot gene was identified.Finally,evaluate the expression differences of Hub genes between the data set groups,and generate receiver operating characteristic(ROC)curves to verify the diagnostic value of differentially expressed genes(DEG).Finally,genes with high area under the curve(AUC)values are validated.Results:We analyzed 222 DEGs with statistically significant differences in the GSE10558 data set by bioinformatics methods,of which 18 DEGs have significant differences.GO analysis showed that most of the 18 significantly differentially expressed genes were rich in receptor ligand activity and cytokine receptor binding.It is worth noting that these genes are also enriched in functional areas related to immune inflammatory response and immune cell regulation.The GSVA package was used for GSVA analysis,and the results showed that it was significantly enriched in growth factor binding and other aspects.And according to the ssGSEA analysis to obtain immune clustering groupings,the DEGs found in the high,medium,and low immune score groups are mainly enriched in immune inflammatory response and immune cell regulation through GO analysis.CIBERSORT analysis found that there are significant differences in memory B cells of 22 types of immune cells in ovarian samples.By mining the phenotypic gene set,the DEGs that are significantly related to PPD are intersected respectively,and four overlapping genes APOA1,PLN,PRKCZ,and TRPV2 are obtained as the most important pivot genes.We also use box plots to show the expression differences between tissue samples.The results show that there are significant differences in expression of these genes between groups,which may serve as new potential targets for the diagnosis and treatment of PPD.Subsequently,the ROC curve analysis of the four APOA1,PLN,PRKCZ,and TRPV2 that are significantly related to PPD showed significant prediction accuracy,and all AUCs were above 0.9,indicating that these new biomarkers can be further developed in PPD Research.Conclusion:The molecular markers APOA1,PLN,PRKCZ and TRPV2,which are closely related to immune cell function,can efficiently identify PPD.A diagnostic prediction model composed of these four immune function-related genes can distinguish PPD patients with different immune status.This discovery contributes to a more comprehensive understanding of the molecular mechanisms driving the occurrence and development of PPD,which is critical for improving the diagnosis,prognosis and treatment of this disease.

Highly expression of MYBL2 is correlated with a poor prognosis and immune infiltration in clear cell renal carcinoma

Background:Clear cell renal carcinoma(ccRCC)is notorious for its highly unfavorable prognosis,closely related to immune cell infiltration(ICI).MYB Proto-Oncogene Like 2(MYBL2)is elevated in multiple types of human cancer and is recognized as a crucial role in tumorigenesis.In the present study,we aimed to determine the roles of MYBL2 in the prognostic outcomes of ccRCC.Methods:We analyzed the GSE100666 dataset from the Gene Expression Omnibus(GEO)database and found that the expression of MYBL2 was significantly higher in ccRCC subjects than in normal controls.Next,RNA sequencing data related to ccRCC were retrieved from The Cancer Genome Atlas(TCGA)database and the levels of MYBL2 were compared between tumor and peri-tumor tissues.The correlation between MYBL2 and clinicopathological parameters was assessed by logistic analysis.The Kaplan-Meier method,Cox-regression analysis,and nomograms,were applied to investigate the potential clinical benefits of MYBL2 in ccRCC.We also evaluated the correlation between MYBL2 and immune cell infiltration with a single-sample gene set enrichment analysis(ssGSEA).The association between MYBL2 and immune checkpoints was determined via the TIMER and TISIDB databases.Finally,correlation analysis was conducted to predict upstream non-coding RNAs(ncRNAs)regulating MYBL2,and a completing endogenous RNA(ceRNA)network was constructed to visualize the long non-coding RNAs(lncRNAs)-microRNAs(miRNAs)-MYBL2 axis in ccRCC.Finally,further analysis of upstream lncRNAs was carried out to validate the accuracy of the network.Results:MYBL2 was significantly over-expressed in ccRCC(P<0.001).High levels of MYBL2 expression in ccRCC correlated with a worse T stage,a more advanced N stage,a higher M stage,a more deleterious pathological stage,and higher histological grades.MYBL2 was identified as a risk factor for disease-specific survival(hazard ratio(HR)=2.73,P<0.001),overall survival(HR=1.91,P<0.001),and progression-free interval(HR=2.03,P<0.001).MYBL2 also positively associated with multiple types of immune cells and checkpoints.Finally,two ceRNA axes,PVT1-miR-30e-5p-MYBL2 and LINC00511-miR-29c-3p-MYBL2 were detected as the most promising upstream ncRNAs regulating MYBL2 in ccRCC,and we also validated the expression of MYBL2 and PVT1 by launching qRT-PCR.We found that the expression of MYBL2 was significantly higher in 786-O than in human kidney-2 cell line HK-2(P<0.001)and the expression of PVT1 was significantly higher in Caki-1 than in HK-2(P<0.001).Conclusion:Our study revealed that ncRNAs might upregulated the expression of MYBL2 in ccRCC and that this was associated with an unfavorable prognosis and immune infiltration.

CRABP2 regulates infiltration of cancer-associated fibroblasts and immune response in melanoma

Finding biomarkers for immunotherapy is an urgent issue in cancer treatment.Cellular retinoic acid-binding protein 2(CRABP2)is a controversial factor in the occurrence and development of human tumors.However,there is limited research on the relationship between CRABP2 and immunotherapy response.This study found that negative correlations of CRABP2 and immune checkpoint markers(PD-1,PD-L1,and CTLA-4)were observed in breast invasive carcinoma(BRCA),skin cutaneous melanoma(SKCM),stomach adenocarcinoma(STAD)and testicular germ cell tumors(TGCT).In particular,in SKCM patients who were treated with PD-1 inhibitors,high levels of CRABP2 predicted poor prognosis.Additionally,CRABP2 expression was elevated in cancer-associated fibroblasts(CAFs)at the single-cell level.The expression of CRABP2 was positively correlated with markers of CAFs,such as MFAP5,PDPN,ITGA11,PDGFRα/βand THY1 in SKCM.To validate the tumor-promoting effect of CRABP2 in vivo,SKCM xenograft mice models with CRABP2 overexpression have been constructed.These models showed an increase in tumor weight and volume.Enrichment analysis indicated that CRABP2 may be involved in immunerelated pathways of SKCM,such as extracellular matrix(ECM)receptor interaction and epithelial-mesenchymal transition(EMT).The study suggests that CRABP2 may regulate immunotherapy in SKCM patients by influencing infiltration of CAFs.In conclusion,this study provides new insights into the role of CRABP2 in immunotherapy response.The findings suggest that CRABP2 may be a promising biomarker for PD-1 inhibitors in SKCM patients.Further research is needed to confirm these findings and to explore the clinical implications of CRABP2 in immunotherapy.

Transcriptome sequencing reveals novel biomarkers and immune cell infiltration in esophageal tumorigenesis

BACKGROUND Esophageal squamous cell carcinoma(ESCC)is one of the most common malignancies worldwide,and its development comprises a multistep process from intraepithelial neoplasia(IN)to carcinoma(CA).However,the critical regulators and underlying molecular mechanisms remain largely unknown.AIM To explore the genes and infiltrating immune cells in the microenvironment that are associated with the multistage progression of ESCC to facilitate diagnosis and early intervention.METHODS A mouse model mimicking the multistage development of ESCC was established by providing warter containing 4-nitroquinoline 1-oxide(4NQO)to C57BL/6 mice.Moreover,we established a control group without 4NQO treatment of mice.Then,transcriptome sequencing was performed for esophageal tissues from patients with different pathological statuses,including low-grade IN(LGIN),high-grade IN(HGIN),and CA,and controlled normal tissue(NOR)samples.Differentially expressed genes(DEGs)were identified in the LGIN,HGIN,and CA groups,and the biological functions of the DEGs were analyzed via Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses.The CIBERSORT algorithm was used to detect the pattern of immune cell infilt-ration.Immunohistochemistry(IHC)was also conducted to validate our results.Finally,the Luminex multiplex cytokine analysis was utilized to measure the serum cytokine levels in the mice.RESULTS Compared with those in the NOR group,a total of 681541,and 840 DEGs were obtained in the LGIN,HGIN,and CA groups,respectively.Using the intersection of the three sets of DEGs,we identified 86 genes as key genes involved in the development of ESCC.Enrichment analysis revealed that these genes were enriched mainly in the keratinization,epidermal cell differentiation,and interleukin(IL)-17 signaling pathways.CIBERSORT analysis revealed that,compared with those in the NOR group,M0 and M1 macrophages in the 4NQO group showed stronger infiltration,which was validated by IHC.Serum cytokine analysis revealed that,compared with those in the NOR group,IL-1βand IL-6 were upregulated,while IL-10 was downregulated in the LGIN,HGIN,and CA groups.Moreover,the expression of the representative key genes,such as S100a8 and Krt6b,was verified in external human samples,and the results of immunohistochemical staining were consistent with the findings in mice.CONCLUSION We identified a set of key genes represented by S100a8 and Krt6b and investigated their potential biological functions.In addition,we found that macrophage infiltration and abnormal alterations in the levels of inflam-mation-associated cytokines,such as IL-1β,IL-6,and IL-10,in the peripheral blood may be closely associated with the development of ESCC.