Biomarker For Lung Adenocarcinoma Research Articles

Deciphering the Role of Shugoshin-Like Protein 1 in Lung Adenocarcinoma: A Comprehensive Analysis and In Vitro Study.

Shugoshin-like protein 1 (SGO1) has been characterized in its function in correct cell division and its role in centrosome cohesion in the nucleus. However, the underlying biological function and potential mechanisms of SGO1 driving the progression of lung adenocarcinoma remain unclear. In this study, we found that SGO1 was increased in LUAD tissues and cell lines. Upregulation of SGO1 expression was correlated with poor overall survival (OS), disease-free survival (DSS), and progression-free survival (PFS) in patients with LUAD. ROC curve analysis suggested that the AUC value of SGO1 was 0.983. Correlation analysis showed that SGO1 expression was related to immune infiltration in LUAD. Meanwhile, a potential ceRNA network was constructed to identify the lncRNA-MIR4435-2HG/miR-125a-5p/SGO1 regulatory axis in LUAD. Finally, we determine that SGO1 regulated the cell proliferation and cell apoptosis of lung adenocarcinoma in vitro. In conclusion, our data suggested that SGO1 could be a novel prognostic biomarker for lung adenocarcinoma.

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.

Identification and Characterization of Extrachromosomal Circular DNA in Plasma of Lung Adenocarcinoma Patients.

BackgroundChromosome is the basic framework for eukaryotic cells to store genetic information, but certain genes exist in circulation, such as extrachromosomal circular DNA (eccDNA). The unique genetic characteristics and structure of eccDNA provide a new vision on the early diagnosis of cancer; however, whether eccDNA contributes to the early diagnosis and progression of lung cancer remains unclear.MethodsWe performed next-generation sequencing (NGS) analysis of eccDNA from the plasma of 6 lung adenocarcinoma (LUAD) patients. The data of plasma eccDNA of healthy people were obtained from public available database. We compared size distribution, chromosome origin, formation and expression patterns of eccDNA between LUAD patients and those of 6 healthy people and 4 healthy gravidas.ResultsA total number of 716,059 eccDNA ranging from 22 bp to 3,297,519 bp were detected with an average size less than 800bp and distinctive bimodality in size around 191 bp and 320 bp. After comparison of eccDNA abundance in each sequencing sample, nine eccDNA were ranked on top with higher frequency in lung adenocarcinoma patients than healthy people. Among them, four eccDNA (DOCK1, PPIC, TBC1D16, and RP11-370A5.1) were uniquely expressed in lung adenocarcinoma patients, which may serve as potential biomarkers for early diagnosis LUAD.ConclusionCancer-specific eccDNA was presented in LUAD compared to normal people, which might serve as a promising biomarker in LUAD.

A Comprehensive Prognostic and Immune Analysis of Ferroptosis-Related Genes Identifies SLC7A11 as a Novel Prognostic Biomarker in Lung Adenocarcinoma.

Lung adenocarcinoma (LUAD) is still one of the illnesses with the greatest mortality and morbidity. As a recently identified mode of cellular death, the activation of ferroptosis may promote the effectiveness of antitumor therapies in several types of tumors. However, the expression and clinical significance of Ferroptosis-associated genes in LUAD are still elusive. The RNA sequencing data of LUAD and relevant clinical data were downloaded from The Cancer Genome Atlas (TCGA) datasets. Subsequently, potential prognostic biomarkers were determined by the use of biological information technology. The R software package “ggalluvial” was applied to structure Sanguini diagram. Herein, our team screened 14 dysregulated ferroptosis-associated genes in LUAD. Among them, only four genes were associated with clinical outcome of LUAD patients, including ATP5MC3, FANCD2, GLS2, and SLC7A11. In addition, we found that high SLC7A11 expression predicted an advanced clinical progression in LUAD patients. Additionally, 8 immune checkpoint genes and 7 immune cells for LUAD were recognized to be related to the expression of SLC7A11. KEGG assays indicated that high expression of SLC7A11 might participate in the modulation of intestinal immune network for IgA generation and Staphylococcus aureus infection. Overall, our findings revealed that SLC7A11 might become a potentially diagnostic biomarker and SLC7A11 might serve as an independent prognosis indicator for LUAD.

Chemical complementarity between immune receptor CDR3s and candidate cancer antigens correlating with reduced survival: evidence for outcome mitigation with corticosteroid treatments

The evaluation of physicochemical characteristics of extensive adaptive immune receptor (IR) recombination sequence collections has led to the discovery of many correlations of those sequences and a variety of diseases, including cancer. In the cancer setting, these evaluations have recently focused on the adaptive IR, complementarity determining region-3 (CDR3) amino acid (AA) sequences, which play a major role in antigen binding. For example, the chemical complementarities of the tumor resident, CDR3 AA sequences and the BRAFV600E mutant, common in melanoma, have proved informative with regard to outcomes. Many of these evaluations led to the conclusion that a high affinity match, efficiently, algorithmically designated as a high chemical complementarity score (CS) for the patient specific, IR CDR3 AA sequences and the cancer antigens, correlated with improved survival outcomes. In this report, the complementarity scoring algorithms were used to investigate the opposite phenomenon, high complementarity chemistry between CRD3 AAs and cancer antigens that correlated with a worse survival, an approach that revealed potential risk stratification biomarkers for lung adenocarcinoma, lung squamous carcinoma, and likely other cancer types. Most importantly, analyses suggested that high IR CDR3 AA-candidate antigen CS, low overall survival results for low grade glioma were mitigated by neoadjuvant corticosteroid treatments. Overall, the analyses of this report, coupled with earlier work establishing the CS approach for identifying likely good outcomes, have the potential to distinguish patients who will benefit from (i) immune activating or (ii) immune augmenting or (iii) even immunosuppressive treatment strategies. Communicated by Ramaswamy H. Sarma

Differential expression and analysis of extrachromosomal circular DNAs as serum biomarkers in lung adenocarcinoma.

BackgroundExtrachromosomal circular DNAs (eccDNAs) increase the number of proto‐oncogenes by enhancing oncogene expression to promote tumorigenesis. However, there are limited reports on differential eccDNA expression and analysis in lung cancer, especially in lung adenocarcinoma (LAD).MethodsThree LAD and three corresponding NT tissues samples were used for eccDNA next‐generation sequencing analysis, and an additional 20 were used for quantitative PCR (qPCR) evaluations. We further performed qPCR amplification using serum samples from LAD patients and healthy medical examiners.ResultseccDNAs from LAD samples were mainly 200–1000 bp in length. Gene annotation analysis revealed that most eccDNAs were derived from chromosomes 1 and 2. The top‐ten increased and top‐ten decreased eccDNAs in LAD tissues were CircD‐ARPC1B, CircD‐ARPC1A, CircD‐FAM49B, CircD‐SDK1, CircD‐KCNG1, CircD‐POLR2F, CircD‐SS18L1, CircD‐SLC16A3, CircD‐CSNK1D, CircD‐KCTD1, and CircD‐TMIGD2, CircD‐PDIA5, CircD‐VAV2, CircD‐GATAD2A, CircD‐CAB39L, CircD‐KHDC1, CircD‐FOXN3, CircD‐SULT2B1, CircD‐DPP9, and CircD‐CSNK1D. qPCR demonstrated that the expression of CircD‐DZRN3 was higher in LAD tissues than in normal lung tissues, whereas CircD‐LGR6 and CircD‐UMODL1 expression levels were lower in LAD than in normal lung tissues. Furthermore, the serum CircD‐PDZRN3 level increased, while CircD‐LGR6 decreased in LAD. Receiver operating characteristic (ROC) analysis showed that area under curve (AUC) of serum CircD‐PDZRN3 (0.991), CircD‐LGR6 (0.916) was higher than that of serum carcinoembryonic antigen (CEA) (0.825), CY211 (cytokeratin 19 fragment) (0.842), SCCA(squamous cell carcinoma antigen) (0.857) for the diagnosis of LAD.ConclusionsOur study first showed that several eccDNAs were aberrantly expressed in LAD, among which CircD‐PDZRN3 and CircD‐LGR6 clearly distinguished LAD patients from healthy controls, indicating their potential as biomarkers.

SNCA correlates with immune infiltration and serves as a prognostic biomarker in lung adenocarcinoma

BackgroundThe SNCA gene is a critical gene in Parkinson’s disease (PD) pathology. Accumulating evidence indicates that SNCA is involved in tumorigenesis; however, the role of SNCA in lung adenocarcinoma (LUAD) remains unclear. This study aimed to explore the potential value of SNCA as a prognostic and diagnostic molecular marker in LUAD.MethodsIn this study, we explored the expression pattern, prognostic value, and promoter methylation status of SNCA in LUAD based on Oncomine, UALCAN, and Kaplan–Meier Plotter. Then, using TIMER, we investigated the correlation between SNCA expression and immune infiltration. And cBioPortal were used to analysis the correlation between SNCA expression and immune checkpoint. The transcriptome data of A549 cells overexpressing SNCA were used to further study the potential immune role of SNCA in LUAD. The effect of SNCA on proliferation of A549 cells were evaluated by CCK-8, EdU and colony formation. Finally, LUAD cell lines treated with 5-aza-dC were used to explore the correlation between increased promoter methylation and downregulated mRNA expression of SNCA.ResultsIn general, the expression level of SNCA in LUAD tissue was lower than that in normal tissue, and high expression of SNCA was related to better prognosis.There were significant positive correlations between SNCA expression and immune infiltrations, including CD8+ T cells, macrophages, neutrophils, dendritic cells, B cells, and CD4+ T cells, and immune checkpoints, suggesting that immune infiltration was one of the reasons for the influence of SNCA on prognosis in LUAD. The transcriptome data of A549 cells overexpressing SNCA were further used to screen the relevant immune-related genes regulated by SNCA. Enrichment analysis confirmed that SNCA participates in the PI3K-AKT signaling pathway and other key tumor signaling pathways and regulates the expression of MAPK3, SRC, PLCG1, and SHC1. Cellular proliferation assay showed that SNCA could inhabit the growth of A549 cells via inhibiting activity of PI3K/AKT/ mTOR pathway. Finally, analysis of the methylation level of SNCA promoter showed that the promoter methylation negatively correlated with mRNA level. The expression of SNCA in LUAD cell lines was significantly upregulated by treatment with 5-aza-dC.ConclusionHigh methylation of SNCA promoter in LUAD is one of the reasons for the downregulation of SNCA mRNA level. Given that SNCA could inhibit the proliferation of A549 cells and correlates with immune infiltrates, it may serve as a prognostic biomarker in LUAD.

LncRNA-AC02278.4 Is a Novel Prognostic Biomarker That Promotes Tumor Growth and Metastasis in Lung Adenocarcinoma.

LncRNA-AC02278.4 (ENSG00000248538) is a long non-coding RNA (lncRNA) found to be highly expressed in multiple human cancers including lung adenocarcinoma (LUAD). However, the underlying biological function and potential mechanisms of AC02278.4 driving the progression of LUAD remain unclear. In this study, we investigated the role of AC02278.4 in LUAD and found that AC02278.4 expression was significantly increased in datasets extracted from The Cancer Genome Atlas. Increased expression of lncRNA-AC02278.4 was correlated with advanced clinical parameters. Receiver operating characteristic (ROC) curve analysis revealed the significant diagnostic ability of AC02278.4 [area under the ROC curve (AUC) = 0.882]. In addition, gene set enrichment analysis (GSEA) enrichment showed that AC02278.4 expression was correlated with immune response-related signaling pathways. Finally, we determined that AC02278.4 regulated cell proliferation and migration of LUAD in vitro. Our clinical sample results also confirmed that AC02278.4 was highly expressed in LUAD and correlated with adverse clinical outcomes. In conclusion, our data demonstrated that AC02278.4 was correlated with progression and immune infiltration and could serve as a prognostic biomarker for LUAD.

Comprehensive Analysis of CDK1-Associated ceRNA Network Revealing the Key Pathways LINC00460/LINC00525-Hsa-Mir-338-FAM111/ZWINT as Prognostic Biomarkers in Lung Adenocarcinoma Combined with Experiments.

Lung adenocarcinoma (LUAD) is the leading cause of cancer deaths worldwide, and effective biomarkers are still lacking for early detection and prognosis prediction. Here, based on gene expression profiles of LUAD patients from The Cancer Genome Atlas (TCGA), 806 long non-coding RNAs (lncRNAs), 122 microRNAs (miRNAs) and 1269 mRNAs associated with CDK1 were identified. The regulatory axis of LINC00460/LINC00525-hsa-mir-338-FAM111B/ZWINT was determined according to the correlation between gene expression and patient prognosis. The abnormal up-regulation of FAM111B/ZWINT in LUAD was related to hypomethylation. Furthermore, immune infiltration analysis suggested FAM111B/ZWINT could affect the development and prognosis of cancer by regulating the LUAD immune microenvironment. EMT feature analysis suggested that FAM111B/ZWINT promoted tumor spread through the EMT process. Functional analysis showed FAM111B/ZWINT was involved in cell cycle events such as DNA replication and chromosome separation. We analyzed the HERB and GSCALite databases to identify potential target medicines that may play a role in the treatment of LUAD. Finally, the expression of LINC00460/LINC00525-hsa-mir-338-FAM111B/ZWINT axis was verified in LUAD cells by RT-qPCR, and these results were consistent with bioinformatics analysis. Overall, we constructed a CDK1-related ceRNA network and revealed the LINC00460/LINC00525-hsa-mir-338-FAM111/ZWINT pathways as potential diagnostic biomarkers or therapeutic targets of LUAD.

RAGE is a potential biomarker implicated in immune infiltrates and cellular senescence in lung adenocarcinoma.

BackgroundReceptor for Advanced Glycation End‐products (RAGE) is an oncogene abnormally expressed in various cancers. However, the clinical value of RAGE and the biological role of RAGE in lung cancer have not been fully investigated.MethodsWe compared the RAGE expression using several public databases. The relationship between RAGE expression and clinicopathological variables was assessed. The R software package was used to carry out enrichment analyses of RAGE co‐expression and gene set enrichment analysis (GSEA). Additionally, we used the TIMER database to assess the association between immune infiltration and RAGE expression. The correlation between RAGE expression and senescence biomarkers in lung adenocarcinoma was analyzed using the TCGA database.ResultsOur findings indicated that the expression of RAGE was downregulated in lung adenocarcinoma, and down‐regulation of RAGE was related to poor overall survival and disease‐free survival. Functional enrichment analysis indicated that RAGE co‐expression genes were mainly associated with neutrophil activation involved in immune response, neutrophil degranulation, and regulation of leukocyte‐mediated immunity. Correlation analysis revealed that RAGE expression was closely related to the purity of the tumor and immune infiltration. GSEA indicated that the RAGE‐related differential genes were mainly enriched in senescence‐related pathways. Besides, the RAGE expression was significantly associated with senescence‐related genes.ConclusionDown‐regulation of RAGE expression was associated with poor prognosis, as well as defective immune infiltration and cellular senescence in lung adenocarcinoma.

Serum exosomal miR-16-5p functions as a tumor inhibitor and a new biomarker for PD-L1 inhibitor-dependent immunotherapy in lung adenocarcinoma by regulating PD-L1 expression.

ObjectivesWe aimed at investigating whether serum exosomal miR‐16‐5p could be utilized as an immunotherapy biomarker in lung adenocarcinoma (LUAD) patients administered by programmed cell death ligand‐1 (PD‐L1) inhibitors, and to evaluate its functions in LUAD progression.MethodsSixty LUAD sufferers and 20 healthy controls (HCs) were covered in this work. We applied both IHC and WB to examine PD‐L1 level in clinical tissue samples and utilized WB to quantify PD‐L1 expression in LUAD cells and LUAD xenograft tissues, respectively. Transmission electron microscopy (TEM), WB, and nanoparticle tracking analysis (NTA) were executed to confirm the exosomes isolated from serum specimens and cell culture media. To quantify of exosomal miR‐16‐5p level from serum and culture medium of cultured cell, qRT‐PCR experiment was utilized. The connection between tissue PD‐L1 level and serum exosomal miR‐16‐5p expression in PD‐L1‐positive sufferers administered by PD‐L1 inhibitors was verified using Spearman correlation coefficient analysis. In addition, the overall survival (OS) and progression‐free survival (PFS) rates among PD‐L1 inhibitor managed sufferers were acquired through a follow‐up visit. Finally, we used a group of assays, including 5‐bromo‐2′‐dexoyuridine (BrdU) and colony formation test, wound healing experiment, flow cytometry, and nude mice xenograft experiment, to explore the functions of circulating exosomal miR‐16‐5p on LUAD cell proliferation, apoptosis, and migration, as well as tumor development, respectively.ResultsPD‐L1 expression was positively related to T stage (tumor size stage), and PD‐L1 inhibitor treatment reduced the PD‐L1 expression and mitigated T stage in PD‐L1‐positive LUAD sufferers. For PD‐L1‐positive LUAD sufferers, elevated PD‐L1 expression or reduced serum exosomal miR‐16‐5p level were linked to longer PFS and OS upon PD‐L1 inhibitor treatment. The number of exosomes in patient's serum was more than that in the serum of healthy individuals, and PD‐L1 inhibitor treatment decreased the number of serum‐derived exosomes in PD‐L1‐positive LUAD sufferers. Exosome‐derived miR‐16‐5p was downregulated in patient's serum and cell culture medium, and this was negatively linked to tumor stage and PD‐L1 expression. Meanwhile, PD‐L1 inhibitor treatment could increase the serum exosomal miR‐16‐5p expression, and the expression change of serum exosomal miR‐16‐5p was diametrically related to PD‐L1 after the treatment. Moreover, the overexpression of PD‐L1 accelerated tumor growth and decreased the exosomal miR‐16‐5p content in cell culture media, while exosomal miR‐16‐5p overexpression in cell culture media inhibited tumor development by decreasing the PD‐L1 expression. Exosomal miR‐16‐5p overexpression in cell culture media also depressed LUAD cell proliferation and migration, and stimulated cell apoptosis, especially in the cells which cultured in the mediums with PD‐L1 inhibitor in vitro.ConclusionsSerum exosomal miR‐16‐5p may be a latent tumor inhibitor and a new biomarker for PD‐L1 inhibitor‐dependent immunotherapy in LUAD by regulating the PD‐L1 expression.

One Ferroptosis-Related Gene-Pair Signature Serves as an Original Prognostic Biomarker in Lung Adenocarcinoma.

Lung adenocarcinoma is the most common histological subtype of lung cancer which causes the largest number of deaths worldwide. Exploring reliable prognostic biomarkers based on biological behaviors and molecular mechanisms is essential for predicting prognosis and individualized treatment strategies. Ferroptosis is a recently discovered type of regulated cell death. We downloaded ferroptosis-related genes from the literature and collected transcriptome profiles of lung adenocarcinoma from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to construct ferroptosis-related gene-pair matrixes. Then, we performed the least absolute shrinkage and selection operator regression to build our prognostic ferroptosis-related gene-pair index (FRGPI) in TCGA training matrix. Our study validated FRGPI through ROC curves, Kaplan–Meier methods, and Cox hazard analyses in TCGA and GEO cohorts. The optimal cut-off 0.081 stratified patients into low- and high-FRGPI groups. Also, the low-FRGPI group had a significantly better prognosis than the high-FRGPI group. For further study, we analyzed differentially expressed ferroptosis-related genes between high- and low-FRGPI groups. Gene set enrichment analysis (GSEA) enrichment maps indicated that “cell cycle,” “DNA replication,” “proteasome,” and “the p53 signaling pathway” were significantly enriched in the high-FRGPI group. The high-FRGPI group also presented higher infiltration of M1 macrophages. Meanwhile, there were few differences in adaptive immune responses between high- and low-FRGPI groups. In conclusion, FRGPI was an independent prognostic biomarker which might be beneficial for guiding individualized tumor therapy.

Identification of potential circular RNA biomarkers in lung adenocarcinoma: A bioinformatics analysis and retrospective clinical study.

Non-small cell lung cancer (NSCLC) is one of the leading causes of cancer-associated mortality. Lung adenocarcinoma (LAC) is the most prevalent pathological subtype of NSCLC and accounts for ~40% of all lung cancer mortalities. There remains an urgent demand for the identification of novel biomarkers for the diagnosis and development of therapeutic strategies for LAC. In the present study, the profiles of the differentially-expressed circular RNAs (circRNAs) in LAC tissues compared with those in their corresponding non-cancerous tissues were obtained after analyzing the circRNA microarray dataset GSE101586. The expression pattern of the indicated circRNAs in the LAC tissues were subsequently verified using reverse transcription-quantitative PCR (RT-qPCR). The potential prognostic significance of these circRNAs in patients with LAC were then analyzed in a retrospective clinical study. A circRNA-microRNA (miR or miRNA)-mRNA regulatory network in LAC was established by using Cytoscape. In addition, a protein-protein interaction (PPI) network was plotted using the Search Tool for the Retrieval of Interacting Genes/Proteins and visualized through Cytoscape. The prognostic value of the hub genes found was then analyzed based on the Gene Expression Profiling Interactive Analysis database. In total, four differentially-expressed circRNAs were obtained from the GSE101586 microarray dataset, three of which (hsa_circ_0006220, hsa_circ_0072088 and hsa_circ_0001666) were confirmed by RT-qPCR to be highly expressed in LAC tissues. This retrospective clinical study revealed that higher expression levels of these three circRNAs were associated with poorer prognoses in patients with LAC. In addition, siRNA-mediated knockdown of these circRNAs was found to inhibit cell proliferation, migration and invasion in LAC cells. Following analysis of the molecular mechanism underlying these circRNAs, eight miRNAs, namely miR-520f, miR-1261, miR-1270, miR-620, miR-188-3p, miR-516b, miR-940 and miR-661, were identified with potential binding sites for these three circRNAs. Subsequently, 232 overlapped genes from the 795 upregulated genes in the LAC samples from The Cancer Genome Atlas database and 7,829 predicted target genes of the list of eight aforementioned miRNAs were obtained. A circRNA-miRNA-mRNA network was then constructed. A PPI network was established, with six hub genes, namely kinesin family member (KIF) 2C, KIF18B, maternal embryonic leucine zipper kinase, baculoviral IAP repeat-containing 5, polo-like kinase 1 and cytoskeleton-associated protein 2-like, determined from this network. Higher expression levels of each of these hub genes were found to be associated with poorer prognoses of patients with LAC. To conclude, data from the present study suggested that circRNAs hsa_circ_0006220, hsa_circ_0072088 and hsa_circ_0001666 have the potential to be viable biomarkers and therapeutic targets for LAC.

SNRPD1/E/F/G Serve as Potential Prognostic Biomarkers in Lung Adenocarcinoma.

Objectives: Sm proteins (SNRPB/D1/D2/D3/E/F/G), involved in pre-mRNA splicing, were previously reported in the tumorigenesis of several cancers. However, their specific role in lung adenocarcinoma (LUAD) remains obscure. Our study aims to feature abnormal expressions and mutations of genes for Sm proteins and assess their potential as therapeutic targets via integrated bioinformatics analysis. Methods: In this research, we explored the expression pattern and prognostic worth of genes for Sm proteins in LUAD across TCGA, GEO, UALCAN, Oncomine, Metascape, David 6.8, and Kaplan-Meier Plotter, and confirmed its independent prognostic value via univariate and multivariate cox regression analysis. Meanwhile, their expression patterns were validated by RT-qPCR. Gene mutations and co-expression of genes for Sm proteins were analyzed by the cBioPortal database. The PPI network for Sm proteins in LUAD was visualized by the STRING and Cytoscape. The correlations between genes for Sm proteins and immune infiltration were analyzed by using the “GSVA” R package. Results: Sm proteins genes were found upregulated expression in both LUAD tissues and LUAD cell lines. Moreover, highly expressed mRNA levels for Sm proteins were strongly associated with short survival time in LUAD. Genes for Sm proteins were positively connected with the infiltration of Th2 cells, but negatively connected with the infiltration of mast cells, Th1 cells, and NK cells. Importantly, Cox regression analysis showed that high SNRPD1/E/F/G expression were independent risk factors for the overall survival of LUAD. Conclusion: Our study showed that SNRPD1/E/F/G could independently predict the prognostic outcome of LUAD and was correlated with immune infiltration. Also, this report laid the foundation for additional exploration on the potential treatment target’s role of SNRPD1/E/F/G in LUAD.

CircP4HB regulates ferroptosis via SLC7A11-mediated glutathione synthesis in lung adenocarcinoma.

BackgroundCircular ribonucleic acids (circRNAs) play a key role in the development of different types of cancer. Ferroptosis is a type of programmed cell death that contributes to cancer progression. However, the role of circRNAs in lung adenocarcinoma (LUAD) ferroptosis remains unclear.MethodsThe gene expression levels of circRNA P4HB (circP4HB), microRNA-1184 (miR-1184) and Solute carrier family 7 member 11 (Slc7a11), also known as Xct were detected using quantitative real-time polymerase chain reaction (qRT-PCR). Ferroptosis of established LUAD cells was induced by erastin. Cell viability was examined via Cell Counting Kit 8 assays. Ferroptosis was evaluated by malondialdehyde (MDA), Prostaglandin-endoperoxide Synthase 2 (Ptgs2), lipid reactive oxygen species (lipid ROS), and JC-1 detection. The mechanism of circP4HB/miR-1184/SLC7A11 was investigated by luciferase reporter assays, RNA immunoprecipitation, RNA pull-down, and western blot assays. A functional for circP4HB in vivo was determined using xenograft nude mice models.ResultsCircP4HB expression levels were increased in LUAD. It triggered glutathione (GSH) synthesis and, therefore protected LUAD cells from ferroptosis induced by erastin. CircP4HB may function as a competing endogenous RNA by modulating miR-1184 to regulate SLC7A11. CircP4HB inhibited ferroptosis by regulating miR-1184/ SLC7A11-mediated GSH synthesis. In vivo, overexpression of circP4HB promoted tumor growth and inhibited ferroptosis.ConclusionsThe circRNA, circP4HB acts as a novel ferroptosis suppressor in LUAD. Furthermore, circP4HB protects LUAD from ferroptosis via modulation of the miR-1184/SLC7A11 axis. Our findings identified circP4HB as a novel biomarker in LUAD and warrants further investigation in the early diagnosis and treatment of LUAD.

MiR-873 and miR-105-2 May Affect the Tumour Microenvironment and are Potential Biomarkers for Lung Adenocarcinoma

BackgroundLung adenocarcinoma (LUAD) accounts for approximately 40% of all lung cancer cases. The tumour microenvironment (TME) and microRNAs affect the occurrence, metastasis, recurrence and treatment of tumours. However, the role of microRNAs in the TME and LUAD still needs to be further investigated.MethodsRNA-seq and microRNA-seq data of LUAD and NSCLC samples were downloaded from the TCGA and GEO database. The immune and stromal components in the TME and the abundance of tumour-infiltrating immune cells (TICs) were calculated by the ESTIMATE and CIBERSORT algorithms, respectively. The differentially expressed microRNAs (DEMs) between different StromalScore and ImmuneScore groups were screened out by the edgeR package. Bioinformatics analysis was performed to screen out important DEMs and explore their functional effect.ResultsOur results revealed that a low StromalScore, ImmuneScore and ESTIMATEScore led to poor prognosis of LUAD. Then, 62 DEMs were screened out as downregulated in both the high StromalScore and ImmuneScore groups. Among these DEMs, elevated expression levels of miR-873, miR-105-2 and miR-516a-2 significantly shortened the survival time of LUAD patients. Subsequent analysis revealed that the expression levels of miR-873 and miR-105-2 were increased significantly in tumour tissues. The expression patterns of these 2 microRNAs were confirmed by GSE102286, implying the important roles of these 2 microRNAs in LUAD. Further analysis showed that miR-873 and miR-105-2 were mainly involved in immune-related pathways and that high expression levels of miR-873 and miR-105-2 decreased the abundance of monocytes and resting dendritic cells in the TME.ConclusionAlthough further exploration is still needed, our results revealed that miR-873 and miR-105-2 were closely related to the TME and affected the prognosis of LUAD by altering the abundance of TICs.

Long non-coding RNA FAM230B is a novel prognostic and diagnostic biomarker for lung adenocarcinoma

ABSTRACT Long non-coding RNA (lncRNA) FAM230B has been reported to participate in gastric cancer and papillary thyroid cancer, while its role in other cancers has not been reported. We then explored the role of FAM230B in lung adenocarcinoma (LA). This study enrolled a total of 60 LA patients, 60 patients with gastric reflux disease (GRD), 60 cases of chronic obstructive pulmonary disease (COPD), 60 cases of asthma and 60 cases of healthy controls. LA and paired non-tumor tissues were donated by all LA patients. Plasma samples were donated by all participants. Expression of FAM230B in these samples was determined by RT-qPCR. The 60 LA patients were followed up for 5 years to evaluate the prognostic value of plasma FAM230B for LA. Diagnostic value of FAM230B for LA was analyzed with ROC curve analysis. FAM230B was highly expressed in LA tissues compared to that in non-tumor samples. In addition, plasma FAM230B was specifically upregulated in LA patients, but not in GRD, COPD and asthma patients. High expression levels of FAM230B in plasma samples were closely correlated with poor survival. Plasma FAM230B effectively separated LA patients from GRD, COPD, asthma and control groups. Plasma FAM230B was closely correlated with tumor size, but not other clinical factors of LA patients. Therefore, FAM230B is highly upregulated in LA and may serve as a potential diagnostic and prognostic biomarker for LA.

Circular RNA–microRNA–mRNA network identified circ_0007618 and circ_0029426 as new valuable biomarkers for lung adenocarcinoma

ABSTRACT Circular RNAs (circRNAs) are involved in multiple physiological processes. However, whether circRNAs function as the indicators of lung adenocarcinoma (LUAD) remains unclear. Three LUAD-related microarray datasets were downloaded from the Gene Expression Omnibus database, and overlapping differentially expressed circRNAs (DECs) in LUAD were identified. circ_0007618 and circ_0029426 were revealed to be significantly dysregulated in LUAD and verified in LUAD tissues and serum obtained in this study. Subsequently, the overall survival curve and receiver operating characteristics curve analyses were performed to evaluate the prognosis, sensitivity, and specificity of circ_0007618 and circ_0029426 for LUAD diagnosis. The results indicate that the combination of circ_0007618 and circ_0029426 is a potential biomarker for LUAD diagnosis and prognosis. TargetScan and miRDB were used to predict interactions between microRNAs (miRNAs) and circRNAs/mRNAs. A circRNA–miRNA–mRNA network was established for LUAD diagnosis. The Kyoto Encyclopedia of Genes and Genomes and protein–protein interaction network identified four hub genes. In conclusion, circ_0007618 and circ_0029426 may be novel biomarkers for LUAD diagnosis and prognosis. For LUAD diagnosis, PIK3CA and NRAS, and KRAS and ETS1, were targeted by circ_0007618 and circ_0029426, respectively.

MicroRNA miR-3646 promotes malignancy of lung adenocarcinoma cells by suppressing sorbin and SH3 domain-containing protein 1 via the c-Jun NH2-terminal kinase signaling pathway

ABSTRACT Lung adenocarcinoma (LUAD) is a highly malignant tumor. In this study, we examined the role of miR-3646 and its underlying mechanism in the progression of LUAD. The expression of miR-3646 and sorbin and SH3 domain-containing protein 1 (SORBS1) in LUAD tissues and cells was evaluated by quantitative reverse transcription-polymerase chain reaction. LUAD cell adhesion, proliferation, apoptosis was determined. The targeting relationship between SORBS1 and miR-3646 was verified by dual luciferase and RNA pull-down assays. In vivo assays were performed to verify the in vitro results. The expression of miR-3646 was found to be upregulated in LUAD tissues and cells. MiR-3646 overexpression stimulated the proliferation and adhesion of LUAD cells but inhibited apoptosis, whereas a miR-3646 inhibitor produced the opposite results. Furthermore, the inhibitory effect of miR-3646 inhibitor was verified in vivo. SORBS1, a target gene identified downstream of miR-3646, was downregulated in LUAD tissues and cells. Additionally, increased SORBS1 inhibited the malignant phenotypes of LUAD cells, which was restored by miR-3646 upregulation. Additionally, western blot analysis revealed that SORBS1 ectopic expression disrupted the JNK signaling pathway, and this effect was restored by miR-3646 overexpression. Thus, this study revealed that miR-3646 promotes LUAD cell proliferation and adhesion, and reduces apoptosis by directly downregulating SORBS1 via the JNK signaling pathway. Investigation of the molecular mechanism of LUAD carcinogenesis revealed that miR-3646 may serve as a biomarker for LUAD treatment.in vivo

Plasma tRNA-derived small RNAs signature as a predictive and prognostic biomarker in lung adenocarcinoma

BackgroundThe prevalence of lung adenocarcinoma (LUAD) has increased, thus novel biomarkers for its early diagnosis is becoming more important than ever. tRNA-derived small RNA (tsRNA) is a new class of non-coding RNA which has important regulatory roles in cancer biology. This study was designed to identify novel predictive and prognostic tsRNA biomarkers.MethodstsRNAs were identified and performed differential expression analysis from 10 plasma samples (6 LUAD and 4 normal, SRP266333) and 96 tissue samples (48 LUAD and 48 normal, SRP133217). Then a tsRNA-mRNA regulatory network was constructed to find hub tsRNAs. Functional enrichment analysis was performed to infer the potential pathways associated with tsRNAs. Afterwards, a Support Vector Machine (SVM) algorithm was used to explore the potential biomarkers for diagnosing LUAD. Lastly, the function of tRF-21-RK9P4P9L0 was explored in A549 and H1299 cell lines.ResultsA significant difference of read distribution was observed between normal people and LUAD patients whether in plasma or tissue. A tsRNA-mRNA regulatory network consisting of 155 DEtsRNAs (differential expression tsRNAs) and 406 DEmRNAs (differential expression mRNAs) was established. Three tsRNAs (tRF-16-L85J3KE, tRF-21-RK9P4P9L0 and tRF-16-PSQP4PE) were identified as hub genes with degree > 100. We found Co-DEmRNAs (intersection of DEtsRNAs target mRNAs and differentially expressed mRNAs in LUAD) were engaged in a number of cancer pathways. The AUC of the three hub tsRNAs’ expression for diagnosing LUAD reached 0.92. Furthermore, the qPCR validation of the three hub tsRNAs in 37 paired normal and LUAD tissues was consistent with the RNA-Seq results. In addition, tRF-21-RK9P4P9L0 was negatively associated with LUAD prognosis. Inhibition of tRF-21-RK9P4P9L0 expression reduced the proliferation, migration and invasion ability of A549 and H1299 cell lines.ConclusionThese findings will help us further understand the molecular mechanisms of LUAD and contribute to novel diagnostic biomarkers and therapeutic target discovery.