Immune Infiltration In Lung Adenocarcinoma Research Articles

Integrative Multi-Omics Analysis of Identified SKA3 as a Candidate Oncogene Correlates with Poor Prognosis and Immune Infiltration in Lung Adenocarcinoma.

BackgroundSpindle and kinetochore-associated complex subunit 3 (SKA3) plays important roles in promoting the migration and the invasion of various human cancer cells. There are a few studies on SKA3 in lung adenocarcinoma (LUAD), but the in-depth analysis of the expression of SKA3 and the correlated possible immune mechanism of SKA3 in LUAD are not clear.MethodsIn our study, the expression and survival data of SKA3 were analyzed in LUAD using TIMER, Oncomine, UALCAN, cBioPortal, LinkedOmics, Human Protein Atlas, and Kaplan–Meier plotter. Then, quantitative PCR was used to verify the expression differences of SKA3 between LUAD tissues of mice and the normal tissues.ResultsWe established that the expression of SKA3 in the LUAD group was remarkably higher than that in the normal group. Additionally, high SKA3 expression was linked to poorer survival in LUAD. Moreover, SKA3 expression had a remarkable negative correlation with the immune infiltration of B cells, macrophages, and CD4+ T cells. SKA3 was markedly negatively related to the immune type biomarkers of T cells and B cells in LUAD. The elevated expression of SKA3 with LUAD in enriched B cells, CD4+ T cells, CD8+ T cells, macrophages and Treg cells had worse prognosis, respectively. Functional network analysis showed that SKA3 regulated the mitotic cell cycle, mitosis, chromosome segregation and cell division via pathways.ConclusionIn summary, our study suggested that SKA3 was highly expressed in LUAD and SKA3 might function as a prognostic biomarker in LUAD. Besides, SKA3 may be a candidate oncogene, which correlates with poor prognosis and immune infiltration in lung adenocarcinoma.

CSF2RB Is a Unique Biomarker and Correlated With Immune Infiltrates in Lung Adenocarcinoma.

BackgroundThe tumor microenvironment plays an important role in the occurrence and development of tumors. However, there are gaps in understanding the molecular and cellular interactions between tumor cells and the immune tumor microenvironment (TME). The aim of this study was to identify a novel gene that played an important role in the tumor microenvironment of lung adenocarcinoma (LUAD).MethodsThe gene expression profile and clinical data for LUAD were downloaded from TCGA database. First, we used the ESTIMATE algorithm to evaluate the immune and stromal scores accordingly. Also, we analyzed differentially expressed immune-related genes (IRGs) in the high and low immune/stromal score groups. Then, we used the protein–protein interaction network (PPI network) and a univariate Cox regression analysis to identify the hub gene. After that, we analyzed the relationship between CSF2RB expression and TNM stage/prognosis. Furthermore, gene set enrichment analysis (GSEA) was used to analyze the pathway regulated by CSF2RB and the Pearson correlation analysis method was used to analyze the correlation between the CSF2RB and immune cells. Finally, we used Western blot, real-time quantitative PCR (RT-qPCR), and immunohistochemistry (IHC) to validate CSF2RB expression in cancer and para-cancerous tissues.ResultsWe identified that CSF2RB played an important role in the tumor microenvironment of LUAD. The expression of CSF2RB in tumor tissues was lower than that in normal tissues. Furthermore, the Kaplan–Meier plotter showed that a low CSF2RB expression was associated with poor survival and multivariate COX regression analysis revealed that the CSF2RB gene was an independent risk factor for prognosis, independent of whether patients received chemotherapy or radiotherapy. More importantly, a high expression of CSF2RB was related to early T, N, and clinical stages. GSEA analysis revealed that CSF2RB associated with diverse immune-related pathways, including T-cell receptor signaling pathway, Toll-like receptor signaling pathway, and B-cell receptor signaling pathway. CSF2RB expression levels were also positively related with the levels of infiltrating CD4+ T cells, macrophages, NK cells, and monocytes in LUAD. Finally, tumor tissues from LUAD patients were used for the assessment of CSF2RB expression. It was significantly lower in tumor sites than in adjacent normal tissues, which was consistent with data analysis.ConclusionCSF2RB effectively predicted the prognosis of patients with lung adenocarcinoma which could also be a potential target for cancer treatment and prevention. However, further studies are required to elucidate the function and regulatory mechanisms of CSF2RB and to develop some novel treatment strategies.

Identification of Novel Prognostic Biomarkers Relevant to Immune Infiltration in Lung Adenocarcinoma.

Background: Programmed death ligand-1 (PD-L1) is a biomarker for assessing the immune microenvironment, prognosis, and response to immune checkpoint inhibitors in the clinical treatment of lung adenocarcinoma (LUAD), but it does not work for all patients. This study aims to discover alternative biomarkers. Methods: Public data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) were used to determine the gene modules relevant to tumor immunity. Protein–protein interaction (PPI) network and GO semantic similarity analyses were applied to identify the module hub genes with functional similarities to PD-L1, and we assessed their correlations with immune infiltration, patient prognosis, and immunotherapy response. Immunohistochemistry (IHC) and hematoxylin and eosin (H&E) staining were used to validate the outcome at the protein level. Results: We identified an immune response–related module, and two hub genes (PSTPIP1 and PILRA) were selected as potential biomarkers with functional similarities to PD-L1. High expression levels of PSTPIP1 and PILRA were associated with longer overall survival and rich immune infiltration in LUAD patients, and both were significantly high in patients who responded to anti–PD-L1 treatment. Compared to PD-L1–negative LUAD tissues, the protein levels of PSTPIP1 and PILRA were relatively increased in the PD-L1–positive tissues, and the expression of PSTPIP1 and PILRA positively correlated with the tumor-infiltrating lymphocytes. Conclusion: We identified PSTPIP1 and PILRA as prognostic biomarkers relevant to immune infiltration in LUAD, and both are associated with the response to anti–PD-L1 treatment.

ADAM12as a Clinical Prognostic Indicator Associated with Tumor Immune Infiltration in Lung Adenocarcinoma

Twenty-two functional α-disintegrin and metalloproteinases (ADAMs) have been identified in humans, 12 of which have proteolytic activity. The role of ADAMs in cancer has attracted increasing attention. However, the expression and significance of ADAMs in lung adenocarcinoma (LUAD) remain unclear. Most recently, we investigated the transcriptional data of ADAMs and related overall survival in patients with LUAD based on several databases, including TCGA, cBioPortal, Kaplan-Meier Plotter, LinkedOmics, KEGG, TIMER, and TISIDB. Knockdown of ADAM12 was performed in vitro to verify its biological function. According to our findings, 10 ADAMs exhibited significant differential expression in LUAD compared with cancer-adjacent normal tissues. ADAM12 expression was significantly higher in LUAD tissues than in paracancerous tissues, and lower ADAM12 expression was associated with better survival. Genetic alterations of ADAM12 mainly included missense mutations, amplifications, and deep deletions. ADAM12 and positively correlated genes were mainly enriched in protein digestion and absorption, extracellular matrix-receptor interaction, and adhesion plaques. ADAM12 had a moderate correlation with immune cell markers EBIP1, CCNB1, EXO1, KNTC1, PRC1, and FAM198B. Prognostic model was established based on ADAM12 and immune-related genes. In vitro experiments revealed that knocking down ADAM12 inhibited cell proliferation, migration, and invasion. ADAM12 potentially plays an important role in the occurrence of LUAD and may be utilized as an immunotherapy target and a valuable prognostic biomarker for LUAD.

CD1B is a Potential Prognostic Biomarker Associated with Tumor Mutation Burden and Promotes Antitumor Immunity in Lung Adenocarcinoma.

PurposeTumor mutation burden (TMB) and tumor-infiltrating lymphocytes (TILs) have been well recognized as molecular determinants of immunotherapy responsiveness. In this study, we aimed to construct a TMB prognostic model and explore biomarkers that have predictive potential for prognosis and therapeutic effect in lung adenocarcinoma (LUAD).Patients and MethodsThe TCGA, GEO and Immport databases were used to analyze the mutation profiles and immune infiltration of LUAD. TMB scores were calculated and differential analysis was conducted to identify TMB-related genes. Then, Cox regression model and survival analysis were applied to identify the prognostic genes and construct a TMB prognostic model. The expression and prognostic value of CD1B were further verified by immunohistochemistry (IHC) in 92 patient tissue samples. GSEA was performed to analyze the signaling pathways associated with CD1B expression.ResultsHigh-TMB samples exhibited higher infiltration of CD8+ T cells, CD4+ memory T cells, and M1 macrophages. A total of 397 TMB-related differentially expressed genes were identified, of which 47 were immune-related genes. Cox regression analyses determined 3 hub TMB-related immune genes (CD1B, SCGB3A1, and VEGFD) with prognostic effects, and a TMB prognostic model was constructed. The model demonstrated robust predictive ability in both the training (TCGA) and testing (GEO) datasets. Notably, CD1B was identified as an independent prognostic factor. IHC of clinical samples showed that low expression of CD1B was related to poor overall survival and advanced pathological stages. In addition, there was a strong positive correlation between CD1B and most immune checkpoint molecules, including PD-L1. CD1B expression was associated with immune cell infiltration and immune activation in LUAD.ConclusionOur study constructed a TMB prognostic model that effectively predicted the prognosis of LUAD patients. CD1B expression is correlated with better prognosis and promotes antitumor immunity in LUAD, which may serve as a potential prognostic biomarker and immune-related therapeutic target for LUAD.

TCN1 is a potential prognostic biomarker and correlates with immune infiltrates in lung adenocarcinoma

BackgroundAround the world, lung cancer is the leading cause of cancer-related death. Lung adenocarcinomas are among the most common diagnosed forms of lung cancer, whose overall survival has not improved significantly, which makes finding an effective therapeutic target vital. Transcobalamin (TCN1) is a vitamin B12-binding protein which regulates cobalamin homeostasis. In tumor tissues, TCN1 is expressed highly, and its expression is correlated with cancer aggressiveness and poor prognosis according to recent studies and bioinformatic analyses. However, its effect on lung adenocarcinoma (LUAD) is unknown.MethodsWe evaluated whether TCN1 shows diagnostic and prognostic value in LUAD using bioinformatic analysis. In particular, various databases and analysis tools were used to determine TCN1’s relationship with LUAD, including TCGA, GTEx, GEO, STRING, and TISIDB.ResultsAs compared to normal lung tissue, the level of TCN1 expression in LUAD tissues was significantly higher (P < 0.001). TCN1 also had a good ability to distinguish lung adenocarcinoma from non-lung adenocarcinoma samples [area under the curve (AUC) = 0.788]. According to univariate Cox statistics, high expression levels of TCN1 correlate with poor overall survival (OS) in LUAD (P < 0.001). Moreover, based on a multivariate Cox analysis, TCN1 expression was independently correlated with OS (P = 0.011). GO/KEGG and GSEA indicated enrichment in epidermal cell differentiation (P < 0.0005), keratinocyte differentiation (P < 0.0005), neuroactive ligand–receptor interaction (P < 0.0005), epithelial–mesenchymal transition (P = 0.029, FDR = 0.023) and TNFA signaling via NFKB (P = 0.029, FDR = 0.023). Furthermore, TCN1 is associated with immune infiltration based on an analysis of immune cell infiltration.ConclusionsIn summary, TCN1 could be used as a prognostic and diagnostic biomarker and provide deeper perspectives for the development of therapies and prognostic markers in LUAD.

BOLA3 is a prognostic-related biomarker and correlated with immune infiltrates in lung adenocarcinoma

BackgroudBolA gene family contains three members, high expression of BolA family member 2 (BOLA2) has been reported to be associated with prognosis of several cancers. However, the relationship between BOLA3 and lung adenocarcinoma (LUAD) remains unclear. MethodsExpression of BOLA3 was analyzed by online database. Co-expressed genes and gene set enrichment analysis (GSEA) were performed using LinkedOmics. Diagnostic value was assessed using receiver operating characteristic (ROC) curves. The prognostic value of BOLA3 was analyzed using Prognoscan and Kaplan-Meier Plotter. The Tumor Immune Estimation Resource (TIMER) and Single-sample Gene Set Enrichment Analysis (ssGSEA) were used to explore the relationship between BOLA3 and tumor immune infiltration. ResultsThe results showed that the expression of BOLA3 was significantly higher in LUAD than in normal tissues. High expression of BOLA3 was associated with T stage, N stage, pathologic stage (all P < 0.001). In addition, elevated expression of BOLA3 was associated with overall survival (OS) and progression-free survival (PFS) in LUAD ((OS:HR = 2.58, log-rank P = 1.3e − 11; PFS:HR = 2.36, log-rank P = 4.1e − 05). BOLA3 expression level has negative correlations with infiltrating levels of B cells, CD4 +T cells, macrophages, neutrophils, and dendritic cells (DCs). GSEA analysis showed BOLA3 joined mainly in mitochondrial respiratory chain complex assembly, translational initiation, etc. ConclusionsThese results showed up-regulated in BOLA3 was correlated with poor prognosis and immune infiltrates in LUAD, BOLA3 can be served as a potential immunotherapy target.

BTG2 Serves as a Potential Prognostic Marker and Correlates with Immune Infiltration in Lung Adenocarcinoma.

BackgroundB-cell translocation gene 2 (BTG2) has been revealed to be involved in the occurrence and development of multiple cancers. However, the role of BTG2 in lung adenocarcinoma (LUAD) is still ambiguous. Thus, this study aims to investigate the prognostic value of BTG2 and its correlation with immune infiltration in LUAD.MethodsThe expression of BTG2 in LUAD was analyzed using the TIMER and UALCAN databases. The correlations between BTG2 expression and clinicopathological factors were investigated using the UALCAN databases. The Kaplan–Meier plotter, GEPIA, and TCGA databases were employed to assess the prognostic value of BTG2. The STRING database and Cytoscape software were used to construct an interaction network and mine co-expression genes. The TISIDB database was examined for a correlation between BTG2 and driver genes in LUAD. Enrichment analysis of co-expressed genes and BTG2 was performed using the LinkedOmics database. Finally, the correlations between BTG2 and immune infiltrates were investigated using the TIMER, GEO, and TISIDB database.ResultsBTG2 was significantly downregulated in LUAD. The decreased expression of BTG2 in LUAD was significantly correlated with higher cancer stages and shorter duration of overall survival. The expressions of BTG2-related co-expression genes were associated with the prognosis in LUAD. The expression of BTG2 was closely associated with the mutations of TP53 and ROS1. Enrichment analysis revealed that BTG2 was significantly correlated with immune‐associated signaling pathways and function. In addition, the expression of BTG2 was found to be closely related to immune infiltration, multiple gene markers of immune cells, chemokines, and chemokine receptors.ConclusionOur findings have effectively demonstrated that BTG2 expression was downregulated in LUAD, indicating poor prognosis. Closely relating to immune cell infiltration, BTG2 may be a promising immune-related biomarker and molecular target for patients with LUAD.

The downregulation of fibrinogen-like protein 1 inhibits the proliferation of lung adenocarcinoma via regulating MYC-target genes.

BackgroundThe mechanisms involved in the malignant progression of lung adenocarcinoma (LUAD) are still inconclusive. Fibrinogen-like protein 1 (FGL1) and LAG3 are a pair of immune checkpoints that create an inhibitory immune microenvironment in tumors. However, other roles of FGL1 in LUAD have not been extensively studied. Our study aims to explore the role of FGL1 in the malignant progression of LUAD and to provide new therapeutic targets and strategies for LUAD treatment.MethodsDifferential gene expression of FGL1 was analyzed using the Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine, UALCAN, and Gene Expression Omnibus (GEO) databases. A pan-cancer analysis was conducted using the Oncomine, TIMER, and UALCAN databases. A total of 140 tumor tissues and paired normal tissues were collected, IHC and immunofluorescence staining were used to explore the expression of FGL1. GeneMANIA database and STRING database were used to analyze gene-gene interaction and protein-protein interaction, respectively. A mutation analysis was conducted using the cBioPortal database, and an immune infiltration analysis was conducted using the TIMER database. A survival analysis was carried out using the GEPIA and PrognoScan database. The knockdown of FGL1 was confirmed by western blot (WB) and immunofluorescence staining. Cell proliferation was tested by cell cycle analysis and real-time cell analysis. RNA sequencing (RNA-seq) was used to explore the differential genes of FGL1 knockdown in LUAD cells.ResultsMultiple databases showed that FGL1 was highly expressed in LUAD. The results of IHC indicated that FGL1 was highly expressed in the cytoplasm of LUAD cells. FGL1 was negatively associated with immune infiltration in LUAD. The main mutation of FGL1 is deep deletion, the altered group and high expression group indicated poor prognosis. The downregulation of FGL1 lead to a significantly decreased percentage of PC9 cells in S phase, but had little effect on the proliferation of Jurkat T cells. RNA-seq and GSEA analysis indicated that the differential genes were mainly enriched in MYC-target genes, which suggested that the downregulation of FGL1 inhibited cell proliferation by regulating MYC-target genes.ConclusionsFGL1 exerts in LUAD proliferation in addition to immune regulation. The downregulation of FGL1 inhibits the proliferation of LUAD cells by regulating MYC-target genes. Thus, FGL1 may be a novel therapeutic target in LUAD.

MECOM/PRDM3 and PRDM16 Serve as Prognostic-Related Biomarkers and Are Correlated With Immune Cell Infiltration in Lung Adenocarcinoma.

BackgroundThe MDS1 and EVI1 complex locus (MECOM, also called PRDM3) and PR domain containing 16 (PRDM16) are two highly related zinc finger transcription factors associated with many malignancies. However, the mechanisms of MECOM and PRDM16 in prognosis and tumor immune infiltration in lung adenocarcinoma (LUAD) remain uncertain.MethodsThe Cancer Genome Atlas (TCGA), Oncomine, UALCAN, GEPIA, and TIMER databases were searched to determine the relationship between the expression of MECOM and PRDM16, clinicopathological features, immune infiltration, and prognosis in LUAD. Coexpressed genes of the two genes were investigated by CBioPortal, and the potential mechanism of MECOM- and PRDM16-related genes was elucidated by GO and KEGG analyses. STRING database was utilized to further construct the protein-protein interaction network of the coexpressed genes, and the hub genes were identified by Cytoscape. Finally, qRT-PCR was performed to identify the mRNA levels of the target genes in LUAD.ResultsmRNA levels of MECOM and PRDM16 were downregulated in LUAD (p < 0.05), and the low expression of the two genes was associated with the age, gender, smoking duration, tissue subtype, poor stage, nodal metastasis status, TP53 mutation, and prognosis in LUAD (p < 0.05). MECOM and PRDM16 were also found to be correlated with the expression of a variety of immune cell subsets and their markers. KEGG analysis showed that both of them were mainly enriched in the cell cycle, cellular senescence, DNA replication, and p53 signaling pathway. Importantly, the mRNA levels of the two genes were also found to be decreased in the clinical samples of LUAD by qRT-PCR.ConclusionMECOM and PRDM16 may serve as potential prognostic biomarkers which govern immune cell recruitment to LUAD.

RNA-Binding Protein IGF2BP1 Associated With Prognosis and Immunotherapy Response in Lung Adenocarcinoma.

N6-methyladenosine (m6A) is the most common modification in eukaryotic RNAs and plays a vital role in the tumorigenesis and metastasis of various cancers. However, a comprehensive study of m6A methylation regulators in lung adenocarcinoma (LUAD) is still lacking. The present study aimed to systematically explore the role of m6A methylation regulators in LUAD. RNA sequencing data of 20 m6A methylation regulators and clinical data of LUAD patients were downloaded from The Cancer Genome Atlas (TCGA) database. The prognosis value of m6A methylation regulators in LUAD was evaluated using the Gene Expression Profiling Interactive Analysis (GEPIA) and PrognoScan database. The correlation between IGF2BP1 and immune infiltrates in LUAD was investigated via CIBERSORT and Tumor Immune Estimation Resource (TIMER). A total of 15 m6A modification regulators were significantly abnormally expressed in LUAD tissues. Survival analysis revealed that four genes (HNRNPC, HNRNPA2B1, IGF2BP1, and IGF2BP3) were significantly associated with poor prognosis in LUAD. Multivariate Cox regression analysis showed that only IGF2BP1 was an independent predictor of LUAD after adjusting common clinical parameters. The mutation rates of m6A modification regulators in LUAD were less than 10%. Further analysis revealed that IGF2BP1 expression was significantly correlated with immune infiltration, the expression of immune checkpoints, and tumor mutational burden (TMB) in LUAD. Our findings suggest that IGF2BP1 is an independent predictor and related to immunotherapy response in LUAD, which maybe a potential novel biomarker for LUAD prognosis and the status of tumor immunity.

High Expression of PTGES3 is an Independent Predictive Poor Prognostic Biomarker and Correlates with Immune Infiltrates in Lung Adenocarcinoma

High Expression of PTGES3 is an Independent Predictive Poor Prognostic Biomarker and Correlates with Immune Infiltrates in Lung Adenocarcinoma

Lower Manic Fringe Expression as an Independent Prognostic Biomarker and Correlated with Immune Suppression of Tumor Microenvironment in Lung Adenocarcinoma

Non-small cell lung cancer is the leading cause of cancer-associated mortality worldwide and lung adenocarcinoma is its most common type. The fringe protein family can modulate the Notch receptors to regulate pathways and affect a variety of physiological processes, such as embryo development and tumor formation. To investigate the influence of manic fringe expression on the prognosis of lung adenocarcinoma patients and evaluate its correlation with immune suppression of tumor microenvironment is the objective of the study. Wilcoxon rank test and logistic regression were used to analyze the relationship between manic fringe expression and clinical characteristics of patients with lung adenocarcinoma. The influence of manic fringe expression on the prognosis of lung adenocarcinoma patients was analyzed using Kaplan- Meier plotter analysis and Cox regression, and a receiver operating characteristic curve and nomogram were constructed. Single sample gene set enrichment analysis was used to analyze the correlation between manic fringe expression and immune infiltration. The expression of manic fringe in lung adenocarcinoma was verified using the Oncomine and tumor immune estimation resource database. Manic fringe expression in lung adenocarcinoma patients was significantly lower than that in normal lung tissues. Kaplan-Meier plotter analysis revealed that the overall survival and disease-specific survival of lung adenocarcinoma patients with low manic fringe expression were shorter (p<0.05) than those of patients with high expression. Multivariate Cox analysis further confirmed that high manic fringe expression was an independent predictor of longer overall survival in patients with lung adenocarcinoma. Furthermore, the other clinicopathological features, such as tumour and lymph nodes classification and residual tumor R classification, were correlated with worse prognosis. Single sample gene set enrichment analysis showed that manic fringe expression was correlated with infiltration of interdigitating dendritic cells and tumor cells. Manic fringe may be used as an independent prognostic biomarker and is associated with immune infiltration in lung adenocarcinoma.

P4HA1, a Prognostic Biomarker that Correlates With Immune Infiltrates in Lung Adenocarcinoma and Pan-Cancer.

Objective: Prolyl 4-hydroxylase, alpha polypeptide I (P4HA1), a key enzyme in collagen synthesis, comprises two identical alpha subunits and two beta subunits. However, the immunomodulatory role of P4HA1 in tumor immune microenvironment (TIME) remains unclear. This study aimed to evaluate the prognostic value of P4HA1 in pan-cancer and explore the relationship between P4HA1 expression and TIME. Methods: P4HA1 expression, clinical features, mutations, DNA methylation, copy number alteration, and prognostic value in pan-cancer were investigated using the Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression data. Pathway enrichment analysis of P4HA1 was performed using R package “clusterProfiler.” The correlation between immune cell infiltration level and P4HA1 expression was analyzed using three sources of immune cell infiltration data, including ImmuCellAI database, TIMER2 database, and a published work. Results: P4HA1 was substantially overexpressed in most cancer types. P4HA1 overexpression was associated with poor survival in patients. Additionally, we discovered that P4HA1 expression was positively associated with infiltration levels of immunosuppressive cells, such as tumor-associated macrophages, cancer-associated fibroblasts, nTregs, and iTregs, and negatively correlated with CD8+ T and NK cells in pan-cancer. Conclusions: Our results highlighted that P4HA1 might serve as a potential prognostic biomarker in pan-cancer. P4HA1 overexpression is indicative of an immunosuppressive microenvironment. P4HA1 may be a potential target of immunotherapy.

GPI Is a Prognostic Biomarker and Correlates With Immune Infiltrates in Lung Adenocarcinoma.

BackgroundGlucose-6-phosphate isomerase (GPI) plays an important role in glycolysis and gluconeogenesis. However, the role of GPI in lung adenocarcinoma (LUAD) remains unclear.MethodsAll original data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases and integrated via R 3.2.2. GPI expression was explored with TCGA, GEO, and Oncomine databases. Immunohistochemistry staining was used to analyze GPI expression in clinical specimens. The correlations between GPI and cancer immune characteristics were analyzed via the TIMER and TISIDB databases. GPI-specific siRNAs were used to verify the role of GPI expression on cell proliferation and cell cycle distribution.ResultsIn general, GPI is predominantly overexpressed and has reference value in the diagnosis and prognostic estimation of LUAD. Upregulated GPI was associated with poorer overall survival, clinical stage, N stage, and primary therapy outcome in LUAD. Mechanistically, we identified a hub gene that included a total of 56 GPI-related genes, which were tightly associated with the cell cycle pathway in LUAD patients. Knockdown of GPI induced cell proliferation inhibition and cell cycle arrest. GPI expression was positively correlated with infiltrating levels of Th2 cells and regulatory T cells (Tregs); in contrast, GPI expression was negatively correlated with infiltrating levels of CD8+ T cells, central memory T cells, dendritic cells, macrophages, mast cells, and eosinophils. GPI was negatively correlated with the expression of immunostimulators, such as CD40L, IL6R, and TMEM173, in LUAD.ConclusionGPI may play an important role in the cell cycle and can be used as a prognostic biomarker for determining the prognosis and immune infiltration in LUAD.

LRMP Associates With Immune Infiltrates and Acts as a Prognostic Biomarker in Lung Adenocarcinoma.

Background: Lymphoid-restricted membrane protein (LRMP) is an endoplasmic reticulum-associated protein that is expressed in a developmentally regulated manner in both B and T cell lineages. However, the role of LRMP in the growth, prognosis and immune infiltration in lung adenocarcinoma (LUAD) remains unclear. Method: The expression levels of LRMP mRNA in tumor and normal tissues were analyzed using Tumor Immune Estimation Resource 2.0 (TIMER 2.0) and Gene Expression Profiling Interactive Analysis 2 (GEPIA 2). LRMP protein expression was examined using the Human Protein Atlas. In vitro experiments, including qRT-PCR Western blot and immunohistochemistry staining were also performed to investigate LRMP expression. GEPIA2 and Kaplan-Meier plotter databases were used to analyze the clinical prognostic significance of LRMP. To further confirm the underlying function of LRMP, the data were analyzed using gene set enrichment analysis. Moreover, we also constructed plasmids to overexpress LRMP and explored the effect of LRMP in A549 cell line. Additionally, Tumor Immune single-cell Hub was used to investigate the distribution of LRMP in the LUAD immune microenvironment; TIMER and CIBERSORT were used to investigate the relationships among LRMP, LRMP co-expressed genes, and tumor-infiltrating immune cells; Finally, the correlations between LRMP and immune checkpoints were analyzed using TIMER 2.0. Results: The expression of LRMP was significantly lower in LUAD tissues and cell lines. High LRMP expression is associated with a better prognosis in patients with LUAD. In vitro experimental studies demonstrated that overexpression of LRMP could decrease the proliferation, migration and invasion in A549 cells, and downregulated multiple oncogenic signaling pathways, including p-STAT3, p-PI3K-p-AKT, p-MEK and EMT pathways. GSEA results showed that immuno-related and cell adhesion pathways were enriched in samples with high LRMP expression. LRMP and its co-expressed genes were positively correlated with various tumor-infiltrating immune cells and their markers. Additionally, LRMP positively correlated with immune checkpoints. Conclusions: Our data suggest that LRMP may act as a tumor suppressor gene and indicates a better prognosis. Moreover, LRMP is associated with immune infiltrates which may be involved in immunotherapy response in LUAD. Further studies are needed to validate these findings.

Alternative Splicing Events in Immune Infiltration of Lung Adenocarcinoma

BackgroundThe exact mechanisms of lung adenocarcinoma (LUAD) etiology and pathogenesis remain unclear.Material/MethodsIn this study, we evaluated alternative splicing (AS) events in LUAD. We separately analyzed LUAD data from The Cancer Genome Atlas (TCGA) database and AS-related feature lists from SpliceSeq to develop risk models for AS events and further validated risk models for AS events. The association between immune-related features and the risk model of AS events was evaluated.ResultsWe found that exon skip (ES) and mutually exclusive exons (ME) exhibited the most and least AS events, respectively. The risk score and stage of LUAD patients were strongly associated with prognosis and were independent influences on the prognosis of LUAD. The pathological stage (stage, T, N) and risk model were incorporated to construct a column line graph with better predictive ability. Risk models were associated with tumor microenvironment, and higher risk score values were associated with higher M2 macrophage content and lower M0 macrophage and helper T lymphocyte content. The correlation between core genes and immunity was further assessed by analyzing differentially-expressed genes between risk models. These results suggest an association between the level of risk for AS events and the density of immune cell infiltration.ConclusionsOur findings suggest a clear association between AS risk model and patient prognosis, and was performed to confirm the biological relationship between AS and immunity.

The construction and analysis of ceRNA network and patterns of immune infiltration in lung adenocarcinoma

BackgroundCompetitive Endogenous RNA (ceRNA) may be closely associated with tumor progression. However, studies on ceRNAs and immune cells in LUAD are scarce.MethodThe profiles of gene expression and clinical data of LUAD patients were extracted from the TCGA database. Bioinformatics methods were used to evaluate differentially-expressed genes (DEGs) and to form a ceRNA network. Preliminary verification of clinical specimens was utilized to detect the expressions of key biomarkers at the tissues. Cox and Lasso regressions were used to identify key genes, and prognosis prediction nomograms were formed. The mRNA levels of 9 genes in the risk score model in independent clinical LUAD samples were detected by qRT-PCR. The interconnection between the risk of cancer and immune cells was evaluated using the CIBERSORT algorithm, while the conformation of notable tumor-infiltrating immune cells (TIICs) in the LUAD tissues of the high and low risk groups was assessed using the RNA transcript subgroup in order to identify tissue types. Finally, co-expression study was used to examine the interconnection between the key genes in the ceRNA networks and the immune cells.ResultA ceRNA network of 115 RNAs was established, and nine key genes were identified to construct a Cox proportional-hazard model and create a prognostic nomogram. This risk-assessment model might serve as an independent factor to forecast the prognosis of LUAD, and it was consistent with the preliminary verification of clinical specimens. Survival analysis of clinical samples further validated the potential value of high risk groups in predicting LUAD prognosis. Five immune cells were identified with significant differences in the LUAD tissues of the high and low risk groups. Besides, two pairs of biomarkers associated with the growth of LUAD were found, i.e., E2F7 and macrophage M1 (R = 0.419, p = 1.4e− 08) and DBF4 and macrophage M1 (R = 0.282, p < 2.2 e− 16).ConclusionThis study identified several important ceRNAs, i.e. (E2F7 and BNF4) and TIICs (macrophage M1), which might be related to the development and prognosis of LUAD. The established risk-assessment model might be a potential tool in predicting LUAD of prognosis.

DNASE1L3 as a Novel Diagnostic and Prognostic Biomarker for Lung Adenocarcinoma Based on Data Mining.

Previous researches have highlighted that low-expressing deoxyribonuclease1-like 3 (DNASE1L3) may play a role as a potential prognostic biomarker in several cancers. However, the diagnosis and prognosis roles of DNASE1L3 gene in lung adenocarcinoma (LUAD) remain largely unknown. This research aimed to explore the diagnosis value, prognostic value, and potential oncogenic roles of DNASE1L3 in LUAD. We performed bioinformatics analysis on LUAD datasets downloaded from TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus), and jointly analyzed with various online databases. We found that both the mRNA and protein levels of DNASE1L3 in patients with LUAD were noticeably lower than that in normal tissues. Low DNASE1L3 expression was significantly associated with higher pathological stages, T stages, and poor prognosis in LUAD cohorts. Multivariate analysis revealed that DNASE1L3 was an independent factor affecting overall survival (HR = 0.680, p = 0.027). Moreover, decreased DNASE1L3 showed strong diagnostic efficiency for LUAD. Results indicated that the mRNA level of DNASE1L3 was positively correlated with the infiltration of various immune cells, immune checkpoints in LUAD, especially with some m6A methylation regulators. In addition, enrichment function analysis revealed that the co-expressed genes may participate in the process of intercellular signal transduction and transmission. GSEA indicated that DNASE1L3 was positively related to G protein-coupled receptor ligand biding (NES = 1.738; P adjust = 0.044; FDR = 0.033) and G alpha (i) signaling events (NES = 1.635; P adjust = 0.044; FDR = 0.033). Our results demonstrated that decreased DNASE1L3 may serve as a novel diagnostic and prognostic biomarker associating with immune infiltrates in lung adenocarcinoma.

Tumor stemness and immune infiltration synergistically predict response of radiotherapy or immunotherapy and relapse in lung adenocarcinoma.

Cancer stem cells (CSCs) have been shown to accelerate tumor recurrence, radiotherapy, and chemotherapy resistance. Immunotherapy is a powerful anticancer treatment that can significantly prolong the overall survival of patients with lung adenocarcinoma (LUAD). However, little is known about the function of genes related to tumor stemness and immune infiltration in LUAD. After integrating the tumor stemness index based on mRNA expression (mRNAsi), immune score, mRNA expression, and clinical information from the TCGA database, we screened 380 tumor stemness and immune (TSI)‐related genes and constructed a five TSI‐specific‐gene (CPS1, CCR2, NT5E, ANLN, and ABCC2) signature (TSISig) using a machine learning method. Survival analysis indicated that TSISig could stably predict the prognosis of patients with LUAD. Comparison of mRNAsi and immune score between high‐ and low‐TSISig groups suggested that TSISig characterized tumor stemness and immune infiltration. In addition, enrichment of immune subpopulations showed that the low‐TSISig group held more immune subpopulations. GSEA revealed that TSISig had a strong association with the cell cycle and human immune response. Further analysis revealed that TSISig not only had a good predictive ability for prognosis but could also serve as an excellent predictor of tumor recurrence and response to radiotherapy and immunotherapy in LUAD patients. TSISig might regulate the development of LUAD by coordinating tumor stemness and immune infiltration. Finally, a connectivity map (CMap) analysis demonstrated that the HDAC inhibitor could target TSISig.