Prognostic Biomarker In Lung Adenocarcinoma Research Articles

The bioinformatics analysis of RIOX2 gene in lung adenocarcinoma and squamous cell carcinoma

Lung cancer is characterized by high morbidity and mortality rates, and it has become an important public health issue worldwide. The occurrence and development of tumors is a multi-gene and multi-stage complex process. As an oncogene, ribosomal oxygenase 2 (RIOX2) has been associated with a variety of cancers. In this article, we analyzed the correlation between RIOX2 expression and methylation in lung cancer based on the databases including the cancer genome atlas (TCGA) (https://portal.gdc.cancer.gov/) and the gene expression omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). It was found that RIOX2 is highly expressed in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) tissues, whose expression is negatively correlated with its methylation level. In this regard, methylation at cg09716038, cg14773523, cg14941179, and cg22299097 had a significant negative correlation with RIOX2 expression in LUAD, whereas in LUSC, methylation at cg09716038, cg14773523, cg14941179, cg22299097, cg05451573, cg10779801, and cg23629183 is negatively correlated with RIOX2 expression. According to the analysis based on the databases, RIOX2 gene could not be considered as the independent prognostic biomarker in lung adenocarcinoma or squamous cell lung cancer. However, the molecular mechanism of RIOX2 gene in the development of lung cancer may be helpful in improving lung cancer therapy.

CBX7, a Potential Prognostic Biomarker in Lung Adenocarcinoma.

BackgroundLung adenocarcinoma (LUAD) is a major type of NSCLC and has high morbidity and mortality. The identification of useful prognostic biomarkers for LUAD is important. CBX7 has been reported in various cancers yet its expression level and potential roles have not been fully understood.MethodsGEPIA, Oncomine, TCGA, KM plotter and OSluca databases were used to explore the expression profile and prognostic effects of CBX7 mRNA expression in patients with LUAD. TIMER was used to explore the relationship between CBX7 and immune infiltrating cells. GSEA was used to further explore the potential biological process and pathways regulated by CBX7 in LUAD. Lastly, IHC detection of CBX7 in 95 samples was used to validate the result.ResultsWe found CBX7 was downregulated in LUAD in GEPIA, Oncomine and TCGA databases. TCGA, KM plotter and OSluca databases suggested that CBX7 was associated with poor clinical outcomes and low survival rate. Using TIMER, we found that CBX7 might be associated with immune infiltration. Via gene set enrichment analysis, we found that tumor-associated biological processes and signaling pathways were enriched in the CBX7 downregulated group. Using clinical samples, we found that CBX7 protein has low expression in LUAD and was associated with poor survival.ConclusionCBX7 might serve as a promising biomarker and potential molecular target in LUAD.

Development and validation of a tumor microenvironment-related prognostic signature in lung adenocarcinoma and immune infiltration analysis*

Abstract Objective Tumor-infiltrating immune cells and stromal cells in the tumor microenvironment (TME) significantly affect the prognosis of and immune response to lung adenocarcinoma (LUAD). In this study, we aimed to develop a novel TME-related prognostic model based on immune and stromal genes in LUAD. Methods LUAD data from the TCGA database were used as the training cohort, and three Gene Expression Omnibus (GEO) datasets were used as the testing cohort. The Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data algorithm was used to analyze the immune and stromal genes involved in the TME. Kaplan-Meier and Cox regression analyses were used to identify prognostic genes and construct a TME-related prognostic model. Gene set enrichment analysis and TIMER were used to analyze the immune features and signaling pathways of the model. Results A TME-related prognostic model based on six hub genes was generated that significantly stratified patients into the high- and low-risk groups in terms of overall survival. The model had strong predictive ability in both the training (TCGA) and testing (GEO) datasets and could serve as an independent prognostic factor for LUAD. Moreover, the low-risk group was characterized by greater immune cell infiltration and antitumor immune activity than the high-risk group. Importantly, the signature was closely associated with immune checkpoint molecules, which may serve as a predictor of patient response to immunotherapy. Finally, the hub genes BTK, CD28, INHA, PIK3CG, TLR4, and VEGFD were considered novel prognostic biomarkers for LUAD and were significantly correlated with immune cells. Conclusion The TME-related prognostic model could effectively predict the prognosis and reflect the TME status of LUAD. These six hub genes provided novel insights into the development of new therapeutic strategies.

Correlation of ARNTL2 with Immune Infiltration and Its Role as a Potential Prognostic Biomarker in Lung Adenocarcinoma

ARNTL2 is a core component of the circadian clock genes and plays regulatory roles in the cell cycle and immune infiltration, but its mechanism in lung cancer (LC) remains unclear. To investigate the clinical and therapeutic value of ARNTL2 in LC. The Oncomine and Cancer Cell Line Encyclopedia (CCLE) databases were adopted for assessing the ARNTL2 expression, after which the Kaplan-Meier plotter and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) databases were used to assess the correlation of ARNTL2 with prognosis. The univariate and multivariate Cox regression analyses were utilized to identify independent prognostic factors. Also, we explored how ARNTL2 expression is related to immune infiltration, and immunomodulators in non-small lung cancer (NSCLC) using the Tumor Immune Estimation Resource (TIMER) database, TISIDB database and Gene Set Enrichment Analysis (GSEA). Finally, coexpression of ARNTL2 and PD-L1 in lung adenocarcinoma (LUAD) was verified via immunofluorescence staining and COXPRESdb v7 database. Our study demonstrated a remarkable upregulated expression of ARNTL2 in multiple cell lines and cancers, including NSCLC. Prognostic analysis displayed a remarkable correlation between high ARNTL2 expression and unfavorable overall survival (OS) and first progressive (FP) survival among patients ailing from LUAD, and ARNTL2 was an independent predictor of prognosis for LUAD patients. GSEA analysis showed that overexpression of ARNTL2 was significantly linked with cell cycle and immunity. Furthermore, we reported a correlation of ARNTL2 expression with immunomodulators and lymphocytes. Immunofluorescence staining revealed that ARNTL2 and PD-L1 were elevated relative to normal tissue for LUAD, and colocalization of them was observed. Elevated ARNTL2 expression in LUAD revealed the prognostic values and its prospective role as a target for cell cycle and immune therapy.

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.

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.

LncRNA NFYC-AS1 promotes the development of lung adenocarcinomas through autophagy, apoptosis, and MET/c-Myc oncogenic proteins.

BackgroundNuclear transcription factor Y subunit C antisense RNA 1 (NFYC-AS1) was revealed to be a potential prognostic biomarker in lung adenocarcinoma (LAUD) by analyzing The Cancer Genome Atlas (TCGA) database. However, the function of NFYC-AS1 has not been verified in cancers, including LAUD. We plan to verify the function of NFYC-AS1 in LAUD through this study.MethodsWe determined NFYC-AS1 expression in 4 LAUD cell lines, and 1 normal lung cell line (HBE) by quantitative real-time reverse transcription PCR (qRT-PCR). small interfering RNA (siRNA) was employed to specifically knockdown NFYC-AS1 in H1299 and PC9 cell lines. Cell growth and invasion activity of LAUD cells was assessed by WST-1, colony formation and transwell assay, respectively. The effect of NFYC-AS1 expression on cell apoptosis was then assessed by flow cytometry assay. Furthermore, the expression of downstream proteins of NFYC-AS1 was investigated by Western blot.ResultsThe proliferation, migration, and invasion of cells were inhibited and apoptosis was increased after NFYC-AS1 knockdown in LAUD cells. The cells transfected with NFYC-AS1 siRNA had a higher rate of apoptosis compared with that in control cells. The apoptosis-related proteins p53 and PARP were upregulated. These suggested NFYC-AS1 could inhibit the apoptosis of LAUD cells. In terms of the expression of major autophagy proteins, p62 was downregulated while Beclin 1 was upregulated after NFYC-AS1 knockdown, which suggested that autophagy was activated. The expression of oncogenic proteins MET and c-Myc was downregulated.ConclusionsIn summary, the above results suggest that NFYC-AS1 may promote the proliferation of LAUD through autophagy and apoptosis.

LncRNA NEAT1-miR-101-3p/miR-335-5p/miR-374a-3p/miR-628-5p-TRIM6 axis identified as the prognostic biomarker for lung adenocarcinoma via bioinformatics and meta-analysis.

BackgroundOverexpression of the tripartite motif containing 6 (TRIM6) is associated with dismal prognosis in cancer patients, but its exact roles in lung adenocarcinoma (LUAD) have not been reported.MethodsThe roles of TRIM6 are identified by using The Cancer Genome Atlas (TCGA), TIMER2, Gene Expression Omnibus (GEO), etc., and the regulatory networks and related-prognostic biomarkers of TRIM6 are identified via the ENCORI and LNCAR databases in the LUAD progression.ResultsTRIM6 expression level in LUAD tissues was significantly increased. TRIM6 over-expression level in LUAD patients was associated with smoking, clinical stage, histological type, lymph node metastasis, TP53 mutation and dismal prognosis, and related to prognosis-related age, race, sex, clinical stage and tumor purity of LUAD patients. TRIM6 overexpression was associated with the levels of CD8+ T cells, macrophages, neutrophils and myeloid dendritic cells, and correlated with the levels of LUAD immune cell markers CD8A, IRF5, CD163, VSIG4, MS4A4A, ITGAM, HLA-DPA1, NRP1, ITGAX, etc. TRIM6 might influence the progression of LUAD by regulating homologous recombination, oocyte meiosis, and ubiquitin-mediated proteolysis. LUAD patients with overexpression of miR-101-3p, miR-335-5p, miR-374a-3p, miR-628-5p, and NEAT1 had a poor prognosis.ConclusionsNEAT1-miR-101-3p/335-5p/374a-3p/628-5p-TRIM6 network, which we constructed from our results, might be an important factor in the dismal prognosis of LUAD patients.

Pan-Cancer Analysis Reveals FH as a Potential Prognostic and Immunological Biomarker in Lung Adenocarcinoma.

Fumarate hydratase (FH) is an important enzymatic component in the tricarboxylic acid cycle. Studies have reported that FH plays an important role in hereditary leiomyomatosis and renal cell cancer (HLRCC). However, the role of FH in human different cancers remains unknown. This study is aimed at analyzing the prognostic value of FH and demonstrating the correlation between FH expression and tumor immunity. Results showed that FH was mutated or copy number varied in 27 types of cancer. FH mRNA was abnormally upregulated across various cancers. Survival analysis suggested high expression of FH was associated with poor prognosis in many cancer types, including lung adenocarcinoma (LUAD). Additionally, FH expression was associated with immune infiltration, including B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells, especially in liver hepatocellular carcinoma (LIHC), LUAD, and lung squamous cell carcinoma (LUSC). Moreover, FH expression showed a strong correlation with immune checkpoint markers in LUAD and testicular germ cell tumors (TGCT). These results indicate that FH is an immunotherapeutic target and a potential prognostic biomarker in LUAD.

IRF4 Correlated With Immune Cells Infiltration Could Predict Prognosis for Patients With Lung Adenocarcinoma

Finding prognostic biomarkers and novel targets to optimize immunotherapy for non-small-cell lung carcinoma (NSCLC) is necessary and urgent. Immune related interferon regulatory factor 4 (IRF4) is a member of the IRF family, whereas the clinical significance and possible role of IRF4 in NSCLC remains unclear.We analyzed the expression levels of IRF4 via Oncomine and Tumor Immune Estimation Resource (TIMER) databases. Additionally, we assessed the correlation between IRF4 and overall survival in Lung adenocarcinoma (LUAD) and Lung squamous cell carcinoma (LUSC) using the Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan Meier plotter databases. We also used the TIMER and TISIDB databases to analyze the correlation between IRF4 expression and immune infiltration level. We further carried out a survival analysis between IRF4 and LUAD based on immune cellular content. Using the UALCAN database, we analyzed the relationship between IRF4 and LUAD with different clinical features.IRF4 was significantly overexpressed in LUAD compared to normal tissues, and high IRF4 predicted better survival in LUAD patients. However, our results showed that IRF4 was not correlated the survival of LUSC patients. Using TIMER and TISIDB databases, we demonstrated that IRF4 was positively correlated with various immune infiltrations including B Cells, CD8+ T Cells, CD4+ T Cells, Neutrophil and Dendritic Cells in both LUAD and LUSC. Additionally, we found that the prognostic value of IRF4 diminished in LUAD with decreasing levels of B cells, but not other immune cellular contents. Correspondingly, we found that the prognostic ability of tumor-infiltrating B lymphocyte (TIL-B) in LUAD was depended on the contribution of high IRF4 expression. Besides, we found that IRF4 expression level was significantly higher in the early stage of LUAD compared to advanced stage.Our results suggested that IRF4 is associated with higher immune infiltration levels especially for TIL-B and is a potential favorable prognostic biomarker in LUAD.

TPD52L2 Is a Prognostic Biomarker and Correlated With Immune Infiltration in Lung Adenocarcinoma.

Tumor protein D52-like 2 (TPD52L2) belongs to the members of the TPD52 family. TPD52L2 was reported to regulate proliferation and apoptosis in cancer cells. However, its role in lung adenocarcinoma (LUAD) was uncertain. We evaluated the expression, methylation, copy number alteration, and prognostic significance of TPD52L2 using RNA-seq data from The Cancer Genome Atlas (TCGA). Enrichment analysis of TPD52L2 was conducted using the R package “clusterProfiler.” We further assessed the association between TPD52L2 and immune cell infiltration level, immunosuppressive genes, and tumor mutational burden (TMB). The difference of gene mutant frequency in high- and low-TPD52L2 groups was also analyzed. The results showed that TPD52L2 was over-expressed and predicted worse survival status in LUAD. We also found that TPD52L2 expression was positively associated with the infiltration levels of immunosuppressive cells, such as regulatory T cells (Tregs) and tumor-associated macrophages (TAMs), and negatively correlated with immune killer cells, such as CD8+ T and NK cells in pan-cancer, including LUAD. In addition, TPD52L2 expression was associated with immunosuppressive genes and TMB. High expression of TPD52L2 was with more mutant frequency of TP53. In summary, our results show that TPD52L2 is an oncogene and a potential prognostic biomarker in LUAD. High TPD52L2 expression is a possible indicator of immune infiltration and associated with tumor immunosuppressive status in LUAD.

P57.14 LRMP Associates With Immune Infiltrates and Acts as a Prognostic Biomarker in Lung Adenocarcinoma

Lymphoid-restricted membrane protein (LRMP), also known as Jaw1, is an endoplasmic reticulum-associated protein that is expressed in a developmentally regulated fashion in both the B and T cell lineages. However, the relationship between LRMP and prognosis of lung adenocarcinoma (LUAD) and tumor-infiltrating lymphocytes remains unclear. The expression levels of LRMP mRNA in tumor and normal tissues were analyzed via Tumor Immune Estimation Resource2.0 (TIMER2.0) and Gene Expression Profiling Interactive Analysis2 (GEPIA2). LRMP protein expression was examined in The Human Protein Atlas (HPA). The association between LRMP expression and clinicopathological variables was analyzed using Pearson chi-squared test. GEPIA2 and Kaplan–Meier plotter databases were used to analyzed the clinical prognostic significance of LRMP. To further confirm the underlying function of LRMP, the data were analyzed by gene set enrichment analysis. In addition, Tumor Immune single-cell Hub (TISCH) 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 with TIMER 2.0. The expression of LRMP was significantly low in LUAD, and correlated with vital status, age, gender, TNM stage, new tumor event type of LUAD patients. High LRMP expression was related to a better prognosis in patients with LUAD. GSEA results showed that immuno-related and cell adhesion pathways were enriched in samples with high LRMP expression. In LUAD tumor immune microenvironment, LRMP was mainly distributed in tumor infiltrating immune cells. TIMER and CIBERSORT results showed that LRMP and its co-expressed genes were positively correlated with various tumor infiltrating immune cells and their markers. In addition, LRMP was positively correlated with immune checkpoints. In conclusion, LRMP expression was significantly reduced in LUAD patients, which indicated a poor prognosis. The expression of LRMP was significantly associated to the levels of immune cell infiltration and immune checkpoints expression. Therefore, LRMP may be used as a prognostic biomarker and as an indicator of immunotherapy response. Further studies need to validate our findings.

H2A Histone Family Member Z (H2AFZ) Serves as a Prognostic Biomarker in Lung Adenocarcinoma: Bioinformatic Analysis and Experimental Validation.

BackgroundH2A histone family member Z (H2AFZ) is a special subtype in the H2A histone family, which participates in the regulation of gene transcription. Nevertheless, little is known about the role of H2AFZ in the tumor microenvironment and genetic factors associated with lung cancer.Material/MethodsThe expression of H2AFZ in LUAD was analyzed via Tumor Immune Estimation Resource (TIMER), the Cancer Genome Atlas (TCGA), and Gene Expression Omnibus (GEO) databases at the mRNA level. To detect the protein expression level of H2AFZ, immunohistochemistry (IHC) was performed using LUAD tissues and non-tumor lung tissues. Kaplan-Meier survival analysis and Cox regression analysis were conducted to identify the effect of H2AFZ expression on overall survival (OS) based on TCGA-LUAD and the GEO dataset GSE68465 cohorts, and our LUAD patient cohort was used for validation. Identification of signaling pathways associated with the expression of H2AFZ was performed using Gene Set Enrichment Analysis (GSEA). The influences of expression of H2AFZ on tumor immune-infiltrating cell (TIICs) were assessed via TIMER and CIBERSORT.ResultsThe expression of H2AFZ was increased in LUAD tissues at both mRNA and protein levels. In addition, high expression of H2AFZ predicted poor OS and might be an independent prognostic predictor in LUAD patients. Moreover, H2AFZ affected the relative proportion of TIICs and was positively associated with Myeloid-derived suppressor cells (MDSC) infiltration level in LUAD.ConclusionsH2AFZ was upregulated in LUAD and related to poor prognosis of LUAD patients; thus, it could be an underlying prognostic biomarker correlated with immune infiltration in LUAD.

Identification of Key Genes Related to CD8+ T-Cell Infiltration as Prognostic Biomarkers for Lung Adenocarcinoma.

BackgroundCD8+ T cells are one of the central effector cells in the immune microenvironment. CD8+ T cells play a vital role in the development and progression of lung adenocarcinoma (LUAD). This study aimed to explore the key genes related to CD8+ T-cell infiltration in LUAD and to develop a novel prognosis model based on these genes.MethodsWith the use of the LUAD dataset from The Cancer Genome Atlas (TCGA), the differentially expressed genes (DEGs) were analyzed, and a co-expression network was constructed by weighted gene co-expression network analysis (WGCNA). Combined with the CIBERSORT algorithm, the gene module in WGCNA, which was the most significantly correlated with CD8+ T cells, was selected for the subsequent analyses. Key genes were then identified by co-expression network analysis, protein–protein interactions network analysis, and least absolute shrinkage and selection operator (Lasso)-penalized Cox regression analysis. A risk assessment model was built based on these key genes and then validated by the dataset from the Gene Expression Omnibus (GEO) database and multiple fluorescence in situ hybridization experiments of a tissue microarray.ResultsFive key genes (MZT2A, ALG3, ATIC, GPI, and GAPDH) related to prognosis and CD8+ T-cell infiltration were identified, and a risk assessment model was established based on them. We found that the risk score could well predict the prognosis of LUAD, and the risk score was negatively related to CD8+ T-cell infiltration and correlated with the advanced tumor stage. The results of the GEO database and tissue microarray were consistent with those of TCGA. Furthermore, the risk score was higher significantly in tumor tissues than in adjacent lung tissues and was correlated with the advanced tumor stage.ConclusionsThis study may provide a novel risk assessment model for prognosis prediction and a new perspective to explore the mechanism of tumor immune microenvironment related to CD8+ T-cell infiltration in LUAD.

SLC2A5 Correlated with Immune Infiltration: A Candidate Diagnostic and Prognostic Biomarker for Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) is a major subtype of lung cancer with a relatively poor prognosis, requiring novel therapeutic approaches. Great advances in new immunotherapy strategies have shown encouraging results in lung cancer patients. This study is aimed at elucidating the function of SLC2A5 in the prognosis and pathogenesis of LUAD by analyzing public databases. The differential expression of SLC2A5 in various tissues from Oncomine, GEPIA, and other databases was obtained, and SLC2A5 expression at the protein level in normal and tumor tissues was detected with the use of the HPA database. Then, we used the UALCAN database to analyze the expression of SLC2A5 in different clinical feature subgroups. Notably, in both PrognoScan and Kaplan-Meier plotter databases, we found a certain association between SLC2A5 and poor OS outcomes in LUAD patients. Studies based on the TIMER database show a strong correlation between SLC2A5 expression and various immune cell infiltrates and markers. The data analysis in the UALCAN database showed that the decreased promoter methylation level of SLC2A5 in LUAD may lead to the high expression of SLC2A5. Finally, we used the LinkedOmics database to evaluate the SLC2A5-related coexpression and functional networks in LUAD and to investigate their role in tumor immunity. These findings suggest that SLC2A5 correlated with immune infiltration can be used as a candidate diagnostic and prognostic biomarker in LUAD patients.

CCR2 and PTPRC are regulators of tumor microenvironment and potential prognostic biomarkers of lung adenocarcinoma.

BackgroundTumor microenvironment (TME) plays an essential role in lung adenocarcinoma (LUAD) development and metastasis. With the development of TME research, it has been proved that differences in tumor-infiltrating immune cells (TICs) and gene expression profile are related to the prognosis of cancer. The aim of our study was to identify key genes affecting immune state in TME of LUAD.MethodsThe RNA-seq data and clinical characteristics of 594 LUAD patients were downloaded from the TCGA database. ImmuneScore, StromalScore and ESTIMATEScore of each LUAD sample were calculated using ESTIMATE algorithm. Based on the median of different scores, LUAD samples were divided into high and low score groups. Differentially expressed genes (DEGs) between groups were obtained, and univariate Cox regression analysis and protein-protein interaction (PPI) network were used to screen the shared DEGs generating in the intersection analysis. Finally, the CIBORSORT algorithm was performed to calculate the relative contents of TICs for each LUAD sample, and the correlation analysis between TICs and key genes was used to determine the influence of key genes to the TME.ResultsIn the presented study, we found that three different scores were positively correlated with the prognosis of LUAD patients, and correlation analysis showed the different scores were closely related to tumor progression and metastasis. After performing the intersection analysis, a total of 585 up-regulated and 107 down-regulated DEGs between the high and low score groups were obtained, all of which were enriched in immune-related functions. Having used univariate COX regression analysis and PPI network, the key genes, CCR2 and PTPRC, affecting the immune status of TME and the prognosis of LUAD were acquired. Analysis based on the CIBERSORT algorithm suggested that CCR2 and PTPRC were correlated with a variety of TICs, and closely related to the clinical characteristics of the LUAD patients.ConclusionsOur research showed that CCR2 and PTPRC may be potential prognostic markers in LUAD, which may affect the function of γδT cells and other immune cells by participating in the regulation of TME immune state.

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for lung adenocarcinoma

BackgroundMore and more studies have proven that circular RNAs (circRNAs) play vital roles in cancer development via sponging miRNAs. However, the expression pattern of competing endogenous RNA (ceRNA) in lung adenocarcinoma (LUAD) remains largely unclear. The current study explored functional roles and the regulatory mechanisms of circRNA as ceRNAs in LUAD and their potential impact on LUAD patient prognosis.MethodsIn this study, we systematically screened differential expression circRNAs (DEcircRNAs), miRNAs (DEmiRNAs) and mRNAs (DEGs) associated with LUAD. Then, DEcircRNAs, DEmiRNAs and DEGs were selected to construct a circRNA–miRNA–mRNA prognosis-related regulatory network based on interaction information from the ENCORI database. Subsequently, the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed on the genes in the network to predict the potential underlying mechanisms and functions of circRNAs in LUAD. In addition, Kaplan–Meier survival analysis was performed to evaluate clinical outcomes of LUAD patients, and drug sensitivity analysis was used to screen potential biomarkers for drug treatment of patients with LUAD.ResultsAs a result, 10 circRNAs were aberrantly expressed in LUAD tissues. The ceRNA network was built, which included 3 DEcircRNAs, 6 DEmiRNAs and 157 DEGs. The DEGs in the ceRNA network of hsa_circ_0049271 enriched in biological processes of cell proliferation and the Jak-STAT signaling pathway. We also detected 7 mRNAs in the ceRNA network of hsa_circ_0049271 that were significantly associated with the overall survival of LUAD patients (P < 0.05). Importantly, four genes (PDGFB, CCND2, CTF1, IL7R) identified were strongly associated with STAT3 activation and drugs sensitivity in GDSC.ConclusionsIn summary, a ceRNA network of hsa_circ_0049271 was successfully constructed, which including one circRNA, two miRNAs, and seven mRNAs. Seven mRNAs (PDGFB, TNFRSF19, CCND2, CTF1, IL11RA, IL7R and MAOA) were remarkably associated with the prognosis of LUAD patients. Among seven mRNA species, four genes (PDGFB, CCND2, CTF1, and IL7R) could be considered as drug targets in LUAD. Our research will provide new insights into the prognosis-related ceRNA network in LUAD.

Glycolysis Define Two Prognostic Subgroups of Lung Adenocarcinoma With Different Mutation Characteristics and Immune Infiltration Signatures

Increasing studies have proved that malignant tumors are associated with energy metabolism. This study was aimed to explore biological variables that impact the prognosis of patients in the glycolysis-related subgroups of lung adenocarcinoma (LUAD). The mRNA expression profiling and mutation data in large LUAD samples were collected from the Cancer Genome Atlas (TCGA) database. Then, we identified the expression level and prognostic value of glycolysis-related genes, as well as the fractions of 22 immune cells in the tumor microenvironment. The differences between glycolysis activity, mutation, and immune infiltrates were discussed in these groups, respectively. Two hundred fifty-five glycolysis-related genes were identified from gene set enrichment analysis (GSEA), of which 43 genes had prognostic values (p < 0.05). Next, we constructed a glycolysis-related competing endogenous RNA (ceRNA) network which related to the survival of LUAD. Then, two subgroups of LUAD (clusters 1 and 2) were identified by applying unsupervised consensus clustering to 43 glycolysis-related genes. The survival analysis showed that the cluster 1 patients had a worse prognosis (p < 0.001), and upregulated differentially expressed genes (DEGs) are interestingly enriched in malignancy-related biological processes. The differences between the two subgroups are SPTA1, KEAP1, USH2A, and KRAS among top 10 mutated signatures, which may be the underlying mechanism of grouping. Combined high tumor mutational burden (TMB) with tumor subgroups preferably predicts the prognosis of LUAD patients. The CIBERSORT algorithm results revealed that low TMB samples were concerned with increased infiltration level of memory resting CD4+ T cell (p = 0.03), resting mast cells (p = 0.044), and neutrophils (p = 0.002) in cluster 1 and high TMB samples were concerned with increased infiltration level of memory B cells, plasma cells, CD4 memory-activated T cells, macrophages M1, and activated mast cells in cluster 2, while reduced infiltration of monocytes, resting dendritic cells, and resting mast cells was captured in cluster 2. In conclusion, significant different gene expression characteristics were pooled according to the two subgroups of LUAD. The combination of subgroups, TMB and tumor-infiltrating immune cell signature, might be a novel prognostic biomarker in LUAD.

Expression and Gene Regulation Network of Adenosine Receptor A2B in Lung Adenocarcinoma: A Potential Diagnostic and Prognostic Biomarker

Adenosine receptor A2B (ADORA2B) encodes a protein belonging to the G protein–coupled receptor superfamily. Abnormal expression of ADORA2B may play a pathophysiological role in some human cancers. We investigated whether ADORA2B is a potential diagnostic and prognostic biomarker for lung adenocarcinoma (LUAD). The expression, various mutations, copy number variations, mRNA expression levels, and related network signaling pathways of ADORA2B were analyzed using bioinformatics-related websites, including Oncomine, UALCAN, cBioPortal, GeneMANIA, LinkedOmics, KM Plotter, and TIMER. We found that ADORA2B was overexpressed and amplified in LUAD, and a high ADORA2B expression predicted a poor prognosis for LUAD patients. Pathway analyses of ADORA2B in LUAD revealed ADORA2B-correlated signaling pathways, and the expression level of ADORA2B was associated with immune cell infiltration. Furthermore, ADORA2B mRNA and protein levels were significantly higher in human LUAD cell lines (A549 cells and NCl-H1299 cells) than in normal human bronchial epithelial (HBE) cells, and the transcript levels of genes positively or negatively correlated with ADORA2B were consistent and statistically significant. siRNA transfection experiments and functional experiments further confirmed these results. In vitro results were also consistent with those of bioinformatics analysis. Our findings provide a foundation for studying the role of ADORA2B in tumorigenesis and support the development of new drug targets for LUAD.

TBX5-AS1, an enhancer RNA, is a potential novel prognostic biomarker for lung adenocarcinoma

BackgroundEnhancer RNAs (eRNAs) are demonstrated to be closely associated with tumourigenesis and cancer progression. However, the role of eRNAs in lung adenocarcinoma (LUAD) remains largely unclear. Thus, a comprehensive analysis was constructed to identify the key eRNAs, and to explore the clinical utility of the identified eRNAs in LUAD.MethodsFirst, LUAD expression profile data from the Cancer Genome Atlas (TCGA) dataset and eRNA-relevant information were integrated for Kaplan-Meier survival analysis and Spearman’s correlation analysis to filtered the key candidate eRNAs that was associated with survival rate and their target genes in LUAD. Then, the key eRNA was selected for subsequent clinical correlation analysis. KEGG pathway enrichment analyses were undertaken to explore the potential signaling pathways of the key eRNA. Data from the human protein atlas (HPA) database were used to validate the outcomes and the quantitative real time-polymerase chain reaction (qRT-PCR) analysis was conducted to measure eRNA expression levels in tumor tissues and paired normal adjacent tissues from LUAD patients. Finally, the eRNAs were validated in pan-cancer.ResultsAs a result, TBX5-AS1 was identified as the key eRNA, which has T-box transcription factor 5 (TBX5) as its regulatory target. KEGG analysis indicated that TBX5-AS1 may exert a vital role via the PI3K/AKT pathway, Ras signaling pathway, etc. Additionally, the qRT-PCR results and the HPA database indicated that TBX5-AS1 and TBX5 were significantly downregulated in tumour samples compared to matched-adjacent pairs. The pan-cancer validation results showed that TBX5-AS1 was associated with survival in four tumors, namely, adrenocortical carcinoma (ACC), LUAD, lung squamous cell carcinoma (LUSC), and uterine corpus endometrial carcinoma (UCEC). Correlations were found between TBX5-AS1 and its target gene, TBX5, in 26 tumor types.ConclusionCollectively, our results indicated that TBX5-AS1 may be a potential prognostic biomarker for LUAD patients and promote the targeted therapy of LUAD.