The prognostic landscape of genes and infiltrating immune cells in cytokine induced killer cell treated-lung squamous cell carcinoma and adenocarcinoma

Objective:Patients with non–small cell lung cancer(NSCLC)respond differently to cytokine-induced killer cell(CIK)treatment.Therefore,potential prognostic markers to identify patients who would benefit from CIK treatment must be elucidated.The current research aimed at identifying predictive prognostic markers for efficient CIK treatment of patients with NSCLC.Methods:Patients histologically diagnosed with NSCLC were enrolled from the Tianjin Medical University Cancer Institute and Hospital.We performed whole-exome sequencing(WES)on the tumor tissues and paired adjacent benign tissues collected from 50 patients with NSCLC,and RNA-seq on tumor tissues of 17 patients with NSCLC before CIK immunotherapy treatment.Multivariate Cox proportional hazard regression analysis was used to analyze the association between clinical parameters and prognostic relevance.WES and RNA-seq data between lung squamous cell carcinoma(SCC)and adenocarcinoma(Aden)were analyzed and compared.Results:The pathology subtype of lung cancer was the most significantly relevant clinical parameter associated with DFS,as analyzed by multivariate Cox proportional hazard regression(P=0.031).The patients with lung SCC showed better CIK treatment efficacy and extended DFS after CIK treatment.Relatively low expression of HLA class II genes and checkpoint molecules,and less immunosuppressive immune cell infiltration were identified in the patients with lung SCC.Conclusions:Coordinated suppression of the expression of HLA class II genes and checkpoint molecules,as well as less immune suppressive cell infiltration together contributed to the better CIK treatment efficacy in lung SCC than lung Aden.

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.

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.

A novel prognostic gene signature,nomogram and immune landscape based on tanshinone IIA drug targets for hepatocellular carcinoma:Comprehensive bioinformatics analysis and in vitro experiments

Tanshinone IIA,one of the main ingredients of Danshen,is used to treat hepatocellular carcinoma(HCC).However,potential targets of the molecule in the therapy of HCC are unknown.Methods:In this study,we collected the tanshinone IIA targets from public databases for investigation.We screened differentially expressed genes(DEGs)across HCC and normal tissues using mRNA expression profiles from The Cancer Genome Atlas(TCGA).Univariate Cox regression analysis and least absolute shrinkage and selection operator(LASSO)Cox regression models were used to identify and construct the prognostic gene signature.Results:Finally,we discovered common genes across tanshinone IIA targets and HCC DEGs.We reported Fatty acid binding protein-6(FABP6),Polo-like Kinase 1(PLK1),deoxythymidylate kinase(DTYMK),Uridine Cytidine Kinase 2(UCK2),Enhancer of Zeste Homolog 2(EZH2),and Cytochrome P4502C9(CYP2C9)as components of a gene signature.The six-gene signature’s prognostic ability was evaluated using the Kaplan-Meier curve,time-dependent receiver operating characteristic(ROC),multivariate Cox regression analysis,and the nomogram.The mRNA level and protein expression of UCK2 were experimentally validated after treatment with different concentrations of tanshinone IIA in HEPG2 cells.CIBERSORTx,TIMER2.0,and GEPIA2 tools were employed to explore the relationship between the prognostic signature and immune cell infiltration.Conclusion:We established a six-gene signature as a reliable model with significant therapeutic possibility for prognosis and overall survival estimation in HCC patients,which might also benefit medical decision-making for appropriate treatment.

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.

Prognostic role of ring finger and WD repeat domain 3 and immune cell infiltration in hepatocellular carcinoma

We have found that the expression of ring finger and WD repeat domain 3(RFWD3)is significantly higher in unpaired and paired hepatocellular carcinoma(HCC)tissues than in normal tissues.Moreover,this expression has a significant correlation with the infiltration level of 14 immune cell types and when the detected RFWD3 expression levels were grouped as high and low,a prominent difference was revealed for overall survival,disease-specific survival,and progression-free interval.Through statistical analysis(univariate Cox),we were also able to identify RFWD3 as an independent prognostic element for HCC,with RFWD3 having an ability to accurately predict HCC prognosis(area under the curve of 0.863).Finally,we have generated prognostic nomograms for probabilities of 1-,3-and 5-year overall survival in HCC via integrating the factors of age,pathologic stage,alpha-fetoprotein level,and RFWD3 expression.

Integrated bioinformatics analysis identifies immune-related epithelial-mesenchymal transition prognostic biomarkers and immune infiltrates in patients with lung adenocarcinoma

Background:Lung cancer,particularly lung adenocarcinoma(LUAD),is highly lethal.Understanding the critical interaction between epithelial-mesenchymal transition(EMT)and the immune status of patients is imperative for clinical assessment.Methods:We conducted bioinformatics analysis to identify potential immune-related EMT(iEMT)prognostic genes and explored the immune status in LUAD.Using data from The CancerGenome Atlas andGSE68465,differentially expressed genes,were identified,and a risk modelwas constructed.Cluster analysis was conducted using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways.Results:Our findings revealed 69 differentially expressed iEMT genes,with risk values demonstrating independent prognostic significance for both The Cancer Genome Atlas and GSE68465 samples.The risk value was positively correlated with tumor stage.Immune cell infiltration analysis showed a significant decrease in resting dendritic cells and an increase in CD4 memory T cells in high-risk groups with poor survival prognoses.The immunotherapy analysis revealed weak immunotherapeutic effects in the high-risk group.Conclusions:This study provides insights into potential aberrant differential iEMT genes and risk models and explores immune landscapes that inform personalized immunotherapy in patients with LUAD.

A prognosis model for predicting immunotherapy response of esophageal cancer based on oxidative stress-related signatures

Oxidative stress(OS)is intimately associated with tumorigenesis and has been considered a potential therapeutic strategy.However,the OS-associated therapeutic target for esophageal squamous cell carcinoma(ESCC)remains unconfirmed.In our study,gene expression data of ESCC and clinical information from public databases were downloaded.Through LASSO-Cox regression analysis,a risk score(RS)signature map of prognosis was constructed and performed external verification with the GSE53625 cohort.The ESTIMATE,xCell,CIBERSORT,TIMER,and ImmuCellAI algorithms were employed to analyze infiltrating immune cells and generate an immune microenvironment(IM).Afterward,functional enrichment analysis clarified the underlying mechanism of the model.Nomogram was utilized for forecasting the survival rate of individual ESCC cases.As a result,we successfully constructed an OS-related genes(OSRGs)model and found that the survival rate of high-risk groups was lower than that of low-risk groups.The AUC of the ROC verified the strong prediction performance of the signal in these two cohorts further.According to independent prognostic analysis,the RS was identified as an independent risk factor for ESCC.The nomogram and follow-up data revealed that the RS possesses favorable predictive value for the prognosis of ESCC patients.qRT-PCR detection demonstrated increased expression of MPC1,COX6C,CYB5R3,CASP7,and CYCS in esophageal cancer patients.In conclusion,we have constructed an OSRGs model for ESCC to predict patients’prognosis,offering a novel insight into the potential application of the OSRGs model in ESCC.

Comprehensive analysis of clinical and biological value of ING family genes in liver cancer

BACKGROUND Liver cancer(LIHC)is a malignant tumor that occurs in the liver and has a high mortality in cancer.The ING family genes were identified as tumor suppressor genes.Dysregulated expression of these genes can lead to cell cycle arrest,senescence and/or apoptosis.ING family genes are promising targets for anticancer therapy.However,their role in LIHC is still not well understood.AIM To have a better understanding of the important roles of ING family members in LIHC.METHODS A series of bioinformatics approaches(including gene expression analysis,genetic alteration analysis,survival analysis,immune infiltration analysis,prediction of upstream microRNAs(miRNAs)and long noncoding RNAs(lncRNAs)of ING1,and ING1-related gene functional enrichment analysis)was applied to study the expression profile,clinical relationship,prognostic significance and immune infiltration of ING in LIHC.The relationship between ING family genes expression and tumor associated immune checkpoints was investigated in LIHC.The molecular mechanism of ING1 mediated hepatocarcinogenesis was preliminarily discussed.RESULTS mRNA/protein expression of different ING family genes in LIHC was analyzed in different databases,showing that ING family genes were highly expressed in LIHC.In 47 samples from 366 LIHC patients,the ING family genes were altered at a rate of 13%.By comprehensively analyzing the expression,clinical pathological parameters and prognostic value of ING family genes,ING1/5 was identified.ING1/5 was related to poor prognosis of LIHC,suggesting that they may play key roles in LIHC tumorigenesis and progression.One of the target miRNAs of ING1 was identified as hsa-miR-214-3p.Two upstream lncRNAs of hsa-miR-214-3p,U91328.1,and HCG17,were identified.At the same time,we found that the expression of ING family genes was correlated with immune cell infiltration and immune checkpoint genes.CONCLUSION This study lays a foundation for further research on the potential mechanism and clinical value of ING family genes in the treatment and prognosis of LIHC.

Hub genes associated with immune cell infiltration in breast cancer, identified through bioinformatic analyses of multiple datasets

Objective:The aim of this study was to identify hub genes associated with immune cell infiltration in breast cancer through bioinformatic analyses of multiple datasets.Methods:Nonparametric(NOISeq)and robust rank aggregation-ranked parametric(EdgeR)methods were used to assess robust differentially expressed genes across multiple datasets.Protein-protein interaction network,GO,KEGG enrichment,and subnetwork analyses were performed to identify immune-associated hub genes in breast cancer.Immune cell infiltration was evaluated with the CIBERSORT,XCELL,and TIMER methods.The association between the hub gene-based risk signature and survival was determined through Kaplan–Meier survival analysis,multivariate Cox analysis,and a nomogram with external verification.Results:We identified 163 robust differentially expressed genes in breast cancer through applying both nonparametric and parametric methods to multiple GEO(n=2,212)and TCGA(n=1,045)datasets.Integrated bioinformatic analyses further identified 10 hub genes:CXCL10,CXCL9,CXCL11,SPP1,POSTN,MMP9,DPT,COL1A1,ADAMDEC1,and RGS1.The 10 hub-gene-based risk signature significantly correlated with the prognosis of patients with breast cancer.Moreover,these hub genes were strongly associated with the extent of infiltration of CD4+T cells,CD8+T cells,neutrophils,macrophages,and myeloid dendritic cells into breast tumors.Conclusions:Integrated analyses of multiple databases led to the discovery of 10 robust hub genes that together may serve as a risk factor characteristic of the immune microenvironment in breast cancer.

Study on the relationship between immune cell infiltration pattern and clinical characteristics and prognosis of cervical cancer based on TCGA database

Objective:To investigate the correlation between immune cell infiltration pattern and clinical features and prognosis of cervical carcinoma.Methods:All cervical cancer transcript data and related clinical data were downloaded from the public database Cancer Genome Atlas(TCGA),and the relative proportions of 22 invasive immune cell types were calculated by Cibersort software.Perl was used to assess the correlation between the pattern of immune cell invasion and clinical characteristics(age,clinical stage,tumor grade)in cervical cancer,and the correlation between the pattern of immune cell invasion and survival in cervical cancer was calculated by the K-M Log-Rank method.Result:The distribution of immune cells in 306 cases of cervical cancer and 3 cases of normal tissues was assessed using Cibersort.Compared with normal tissues,the contents of resting dendritic cells,activated dendritic cells,M1 macrophages and activated CD4+memory T cells were higher;the contents of M2 macrophages,neutrophils,regulatory T cells and activated mast cells were lower in cervical cancer tissues.The contents of M1 macrophages,unactivated CD4+memory T cells,andγδT cells were positively correlated with patient age(P<0.05).The contents of follicular helper T cells,activated and unactivated natural killer(NK)cells,and naive CD4 T cells were negatively correlated with patient age(P<0.05).Those with high resting dendritic cell composition had shorter overall survival,while those with high follicular helper T cell composition had longer overall survival(P<0.05).Conclusion:Compared with normal tissues,the composition of immune cells in cervical cancer tissues has certain specificity,which can provide reference for the early screening and diagnosis of the disease.Patients in different age groups may have different immune cell infiltration patterns,which can be used as a basis to explore drug targets in clinical practice.Resting dendritic cells and follicular helper T cells in cervical cancer can be used as possible efficacy predictors of clinical immunotherapy for cervical cancer.

Analysis of low expression of ferroptosis-related gene DECR1 on poor prognosis and immune cell defects of bladder urothelial carcinoma

Background:Ferroptosis is an iron dependent form of cell death,which plays an important role in the pathogenesis of a variety of urinary malignancies.The down-regulation of DECR1 gene causes the accumulation of polyunsaturated fatty acids(PUFAs),increases the susceptibility to lipid peroxidation,and finally leads to cell death.Methods:We first searched the data to find reductase 1(DECR1)expression in bladder uroepithelial carcinoma and healthy surrounding tissues in the Cancer Genome Atlas(TCGA),and we then confirmed DECR1 expression with additional independent cohorts in the Gene Expression Omnibus(GEO)database and the Human Protein Atlas(HPA).In order to determine the link between DECR1 expression and clinical traits and overall survival(OS),as well as to create nomograms,multivariate analysis and Kaplan Meier survival curves were utilized.Through the use of an online string website,the network of proteins that interact with DECR1 was created.Through an online string website,the protein network interacting with DECR1 was built.Finally,we looked at the association between aggressive immune cells and the marker genes that belong to them and DECR1 expression.Results:When compared to normal tissues,bladder tumor tissues had higher DECR1 expression(P=0.002).Low DECR1 expression was linked with tumor grade and stage in tumor cells.BLCA patients with low DECR1 expression had a lower overall survival than BLCA patients with high DECR1 expression,according to a survival study(P=0.008).The protein network’s HSD17B4 and DECR1 connections are crucial.The expression of regulatory T cells,regulatory B cells,and their markers were decreased when DECR1 was missing in bladder cancer.Conclusion:Decreased DECR1 expression was associated with BLCA progression,poor prognosis and impaired infiltration of some immune cells.

Prognostic prediction and expression validation of NSD3 in pan-cancer analyses

Background:Nuclear receptor binding SET domain protein-3(NSD3)is a histone lysine methyltransferase and a crucial regulator of carcinogenesis in several cancers.We aimed to investigate the prognostic value and potential function of NSD3 in 33 types of human cancer.Methods:The data were obtained from The Cancer Genome Atlas.Kaplan-Meier analysis,CIBERSORT,gene set enrichment analysis,and gene set variation analysis were performed.The expression of NSD3 was measured using quantitative real-time polymerase chain reaction and western blot.Results:The expression of NSD3 was altered in pan-cancer samples.Patients with higher levels of NDS3 generally had shorter overall survival and disease-specific survival.Levels of NSD3 were positively correlated with DNA copy number variation(CNV)in pan-cancer.NSD3 expression was also associated with tumor mutation burden and microsatellite instability.The levels of immune-cell infiltration differed significantly between high and low NSD3 expression.NSD3 negatively correlated with levels of CD8+T cells.Functional enrichment analysis showed that while NSD3 expression was positively associated with several immune cell-related and histone methylation-related pathways,it was negatively correlated with cell metabolism-related,drug transport-related,and drug metabolismrelated pathways.NSD3 levels in the cell lines tested were significantly different.In U251 and NCI-H23 cells,silencing NSD3 inhibited cell proliferation and promoted apoptosis.Conclusions:NSD3 expression was changed in pan-cancer samples that was also verified in cell lines.NSD3 was associated with CNV and immune-cell infiltration.A poor prognosis was predicted in patients with high expression of NSD3.NSD3 might hence be a potential marker for predicting tumor prognosis.

A model based on eight iron metabolism-related genes accurately predicts acute myeloid leukemia prognosis

Purpose:Iron metabolism maintains the balance between iron absorption and excretion.Abnormal iron metabolism can cause numerous diseases,including tumor.This study determined the iron metabolism-related genes(IMRGs)signature that can predict the prognosis of acute myeloid leukemia(AML).The roles of these genes in the immune microenvironment were also explored.Methods:A total of 514 IMRGs were downloaded from the Molecular Characteristics Database(MSigDB).IMRGs related to AML prognosis were identified using Cox regression and LASSO analyses and were used to construct the risk score model.AML patients were stratified into high-risk groups(cluster 1)and low-risk groups(cluster 2)based on the mean value of the risk score.The accuracy and prognosis prediction potential of the risk-score model was evaluated using Kaplan-Meier and receiver operating characteristics analysis.The stromal score,immune scores,and immune cells infiltrated in AML samples were estimated using CIBERSORT,MCPcountre,and Xcell algorithms.The role of immune checkpoint genes in the AML microenvironment and the prognostic value of the IMRGs were also evaluated.Results:An AML prognosis prediction model was established based on the eight most critical IMRGs.Further analyses revealed that the model could accurately predict AML prognosis.The expression of IMRGs correlated with the infiltration of several immune cells and could influence response to certain chemotherapy drugs and immunotherapy.Conclusion:A model based on IMRGs can accurately predict the overall survival and disease-free survival of AML patients.

Apolipoprotein C1 promotes tumor progression in gastric cancer

Background:Gastric cancer(GC)is a malignancy with the worst prognosis that seriously threatens human health,especially in East Asia.Apolipoprotein C1(apoc1)belongs to the apolipoprotein family.In addition,apoc1 has been associated with various tumors.However,its role in GC remains unclear.Methods:Firstly,we quantified its expression in GC and adjacent tumor tissues,using The Cancer Genome Atlas(TCGA).Next,we assessed cell invasion and migration abilities.Finally,we revealed the role of apoc1 in the tumor microenvironment(TME),immune cell infiltration and drug sensitivity.Results:Firstly,in TCGA database,it has been shown that elevated expression of apoc1 was identified in various cancers,including GC,then we found that high expression of apoc1 was significantly correlated with poor prognosis in GC.Histologically,apoc1 expression is proportional to grade,cancer stage,and T stage.The experimental results showed that apoc1 promoted cell invasion and migration.Then GO,KEGG,and GSEA pathway analyses indicated that apoc1 may be involved in the WNT pathway and immune regulation.Furthermore,we found out the tumor-infiltrating immune cells related to apoc1 in the tumor microenvironment(TME)using TIMER.Finally,we investigated the correlation between apoc1 expression and drug sensitivity,PD-1 and CTLA-4 therapy.Conclusions:These results suggest that apoc1 participates in the evolution of GC,and may represent a potential target for detection and immunotherapy in GC.

Immunohistochemical analysis of PD-L1 and tumor-infiltrating immune cells expression in the tumor microenvironment of primary signet ring cell carcinoma of the prostate

Primary signet ring cell carcinoma(SRCC)of the prostate is a rare neoplasm.However,its potential tumorigenic mechanism,clinicopathological features,and prognostic outcome have not been systematically described.To determine the pathogenic mechanism,we detected distributions of programmed cell death-ligand 1(PD-L1),programmed death 1(PD-1),and cellular components in the tumor microenvironment,including tumor-infiltrating lymphocytes(CD4 and CD8),tumor-associated macrophages(TAMs;CD163 and CD68),and tumor-associated fibroblasts(vimentin and alpha-smooth muscle actin[α-SMA]),in tumor tissues from four patients with primary prostatic SRCC compared with corresponding adjacent tissues and tumor tissues from 30 patients with prostate adenocarcinoma(PCa)by immunohistochemical staining.We found higher expression of PD-L1,CD163,and CD68 in primary SRCC specimens than that in both corresponding adjacent nontumor specimens and PCa specimens with different Gleason scores,indicating that TAMs may participate in the malignant biological behavior of primary SRCC of the prostate.For further analysis,we searched electronic journal databases and Surveillance,Epidemiology,and End Results(SEER)to identify 200 eligible patients including our four cases.According to Kaplan–Meier survival curve analysis,patients<68 years old,with radical prostatectomy(RP),Gleason score of 7–8,and lower clinical stage had longer overall survival(OS).Moreover,Cox multivariate analysis indicated that race(hazard ratio[HR]=1.422),surgical approach(HR=1.654),and Gleason score(HR=2.162)were independent prognostic factors for OS.Therefore,primary SRCC of the prostate represents a distinct and aggressive subtype of prostate cancer associated with a higher distribution of PD-L1 and TAMs,which warrants further clinical investigation.

Prognostic potential of the small GTPase Ran and its methylation in hepatocellular carcinoma

Background: Hepatocellular carcinoma(HCC) is a common malignant tumor with high mortality. The prognostic significance of Ran, a member of Ras superfamily, remains unclear in HCC patients. Methods: Based on The Cancer Genome Atlas(TCGA) database and Tumor Immune Estimation Resource(TIMER), we analyzed the correlations among Ran expression, promoter methylation and immune cell infiltration. We also investigated the Ran expression levels in HCC tissues and normal tissues by using quantitative real-time PCR. Results: Ran m RNA expression was significantly increased in HCC tissues compared with the normal tissues( P < 0.001). Time-dependent receiver operating characteristic(ROC) curves showed that Ran expression had predictive value of the 1-, 3-and 5-year overall survival for HCC patients, and the areas under the curves(AUC) were 0.747, 0.634 and 0.704, respectively. Cox regression analysis showed that Ran expression was an independent prognostic factor for HCC patients(HR = 1.492, 95% CI: 1.129-1.971, P = 0.005). We also found a negative relationship between Ran m RNA expression and its promoter methylation( r =-0.36, P < 0.001). High Ran expression and promoter hypomethylation predicted worse overall survival and progression-free survival( P < 0.05) and were involved in the progression of HCC. Ran expression exhibited significant correlations with immune infiltrates and prognostic immune-related genes. Conclusions: The present study provides further insight into the prognosis of HCC, and Ran could serve as a biomarker for predicting the survival of HCC patients.

Immune cells in alcohol-related liver disease

Alcohol-related liver disease(ALD),which is caused by excessive alcohol consumption,is one of the most common types of liver disease and a primary cause of hepatic injury,with a disease spectrum that in-cludes steatosis,steatohepatitis,fibrosis,cirrhosis,and hepatocellular carcinoma.Various lines of evi-dence have indicated that immune cells play a significant role in the inflammatory processes of ALD.On the one hand,the liver contains various resident immune cells that have been proven to perform different functions in ALD.For example,in the progression of the disease,Kupffer cells(KCs)are activated by lipopolysaccharide-Toll-like receptor 4 signaling and release various proinflammatory cytokines.Moreover,alcohol intake has been shown to depress the function of natural killer cells.Additionally,two types of unconventional T cells(natural killer T cells and mucosal-associated invariant T cells)are involved in the development of ALD.On the other hand,alcohol and many different cytokines stimulate the recruitment and infiltration of circulating immune cells(neutrophils,T cells,macrophages,and mast cells)into the liver.The neutrophils can produce proinflammatory mediators and cause the dysfunction of anti-infection processes.Additionally,alcohol intake can change the phenotype of T cells,resulting in their increased production of interleukin-17.Aside from KCs,infiltrating macrophages have also been observed in patients with ALD,but the roles of all of these cells in the progression of the disease have shown both similarities and differences.Additionally,the activated mast cells are also associated with the development of ALD.Herein,we review the diverse roles of the various immune cells in the progression of ALD.

Analysis and validation of diagnostic biomarkers and immune cell infiltration characteristics in pediatric sepsis by integrating bioinformatics and machine learning

Background Pediatric sepsis is a complicated condition characterized by life-threatening organ failure resulting from a dysregulated host response to infection in children.It is associated with high rates of morbidity and mortality,and rapid detection and administration of antimicrobials have been emphasized.The objective of this study was to evaluate the diagnostic biomarkers of pediatric sepsis and the function of immune cell infiltration in the development of this illness.Methods Three gene expression datasets were available from the Gene Expression Omnibus collection.First,the differentially expressed genes(DEGs)were found with the use of the R program,and then gene set enrichment analysis was carried out.Subsequently,the DEGs were combined with the major module genes chosen using the weighted gene co-expression network.The hub genes were identified by the use of three machine-learning algorithms:random forest,support vector machine-recursive feature elimination,and least absolute shrinkage and selection operator.The receiver operating characteristic curve and nomogram model were used to verify the discrimination and efficacy of the hub genes.In addition,the inflammatory and immune status of pediatric sepsis was assessed using cell-type identification by estimating relative subsets of RNA transcripts(CIBERSORT).The relationship between the diagnostic markers and infiltrating immune cells was further studied.Results Overall,after overlapping key module genes and DEGs,we detected 402 overlapping genes.As pediatric sepsis diagnostic indicators,CYSTM1(AUC=0.988),MMP8(AUC=0.973),and CD177(AUC=0.986)were investigated and demonstrated statistically significant differences(P<0.05)and diagnostic efficacy in the validation set.As indicated by the immune cell infiltration analysis,multiple immune cells may be involved in the development of pediatric sepsis.Additionally,all diagnostic characteristics may correlate with immune cells to varying degrees.Conclusions The candidate hub genes(CD177,CYSTM1,and MMP8)were identified,and the nomogram was constructed for pediatric sepsis diagnosis.Our study could provide potential peripheral blood diagnostic candidate genes for pediatric sepsis patients.

Identification of immune cell infiltration landscape for predicting prognosis of colorectal cancer

Background:The tumor microenvironment plays an essential role in the therapeutic response to immunotherapy.It is necessary to identify immune cell infiltration(ICI)subtypes for evaluating prognosis and therapeutic benefits.This study aimed to evaluate the ICI score as an effective prognostic biomarker for immune response.Methods:The cell-type identification by estimating relative subsets of RNA transcripts and the estimation of stromal and immune cells in malignant tumors using expression methods were used to analyse ICI landscapes in 161 colorectal cancer(CRC)samples with patients’clinical and prognostic data,RNA sequencing data,and whole-exome sequencing data from the Sixth Affiliated Hospital,Sun Yat-sen University(Guangzhou,China).Statistical analysis and data processing were conducted to calculate ICI scores,and to analyse the prognosis of CRC patients with different ICI scores and other features.A similar analysis with RNA sequencing and clinical data of colon adenocarcinoma(COAD)samples from The Cancer Genome Atlas(TCGA)database was conducted to confirm the correctness of the findings.Results:The high-ICI score group with a better prognosis(hazard ratio[HR],2.19;95%confidence interval[CI],1.03–4.64;logrank test,P=0.036)was characterized by the increased tumor mutational burden and interleukin-17(IL-17)signaling pathway.Significant differences in the prognosis and the expression levels of immune checkpoints and chemokine marker genes were found between the two ICI score groups.For COAD samples from TCGA,the results also showed a significant difference in patients’prognosis between the two ICI score groups(HR,1.72;95%CI,1.00–2.96;log-rank test,P=0.047).Conclusions:Tumor heterogeneity induced differences in identifying ICI subtypes of CRC patients.The ICI score may serve as an effective biomarker for predicting prognosis,help identify new therapeutic markers for CRC,and develop novel effective immune checkpoint blockade therapies.