LncRNA ADAMTS9-AS2 is a Prognostic Biomarker and Correlated with Immune Infiltrates in Lung Adenocarcinoma

Lin, Zhichao; Huang, Wenhai; Yi, Yongsheng; Li, Dongbing; Xie, Zehua; Li, Zumei; Ye, Min

doi:10.2147/ijgm.s340683

Cited by 36 publications

(27 citation statements)

References 32 publications

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“…Unlike protein-coding genes, most pentose phosphate-related lncRNAs are negatively associated with pentose phosphate activity ( 13 , 22 ). As a majority of them are localized to the nucleus, they are likely to suppress the expression of pentose phosphate by directly binding to the target genes ( 10 , 11 , 16 , 35 ). For lncRNA-mediated regulation, we identified significantly differentially expressed TFs.…”

Section: Discussionmentioning

confidence: 99%

Identification of Two Subtypes and Prognostic Characteristics of Lung Adenocarcinoma Based on Pentose Phosphate Metabolic Pathway-Related Long Non-coding RNAs

Liu

Wang

2022

Front. Public Health

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This study analyzed the differences in subtypes and characteristics of advanced lung adenocarcinoma (LUAD) patients based on the pentose phosphate metabolic pathway-related long non-coding RNAs (lncRNAs), along with their potential regulatory mechanisms. Using the expression profiling and corresponding clinical information of LUAD patients from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA). Differential pathway scores between normal and tumor samples from TCGA were identified by rank-sum tests. Pearson correlation coefficients between pentose phosphate scores of the pentose phosphate samples and lncRNAs of the corresponding datasets were calculated. Next, the clusterProfiler software package was used for functional annotation. Clustering of pentose phosphate-related lncRNAs from LUAD samples categorized two molecular subtypes (C1, and C2). C1 was associated with a lower pentose phosphate score and a good prognosis; the C2 showed a higher pentose phosphate score and was related to poorer prognoses. The C2 was markedly associated with energy metabolic pathways. The expression of most immune cells were markedly higher in C1 subtype. Some crucial immune checkpoints, including CTLA4, CD274, and CD47, were also significantly upregulated in C1 subtype, leading to a higher score of clinical effect on the C1 subtype. Finally, one TF, BACH1, was found to be significantly upregulated in C1 subtypes; the pathways activated by this TF may be associated with tumor progression and poor prognoses. LUAD typing based on pentose phosphate metabolic pathway-related lncRNAs was confirmed. Differences in characteristics between C1 and C2 subtypes improved the current LUAD detection and treatment.

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Section: Discussionmentioning

confidence: 99%

Identification of Two Subtypes and Prognostic Characteristics of Lung Adenocarcinoma Based on Pentose Phosphate Metabolic Pathway-Related Long Non-coding RNAs

Liu

Wang

2022

Front. Public Health

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“…All the three ir-lncRNA pairs were markers of poor prognosis with worse overall survival for ESCC. A previous research showed that ADAMTS9-AS2 is a prognostic biomarker correlated with immune infiltrates and predicted a poorer overall survival when it was low expressed in lung adenocarcinoma ( Lin et al, 2021 ). Li W. et al (2020) had identified the expression levels of eight lncRNAs to establish a signature for predicting the survival of patients with ESCC.…”

Section: Discussionmentioning

confidence: 99%

A novel immune-related radioresistant lncRNAs signature based model for risk stratification and prognosis prediction in esophageal squamous cell carcinoma

Zheng

Chen

Huang³

et al. 2022

Front. Genet.

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Background and purpose: Radioresistance remains a major reason of radiotherapeutic failure in esophageal squamous cell carcinoma (ESCC). Our study is to screen the immune-related long non-coding RNA (ir-lncRNAs) of radiation-resistant ESCC (rr-ESCC) via Gene Expression Omnibus (GEO) database and to construct a prognostic risk model.Methods: Microarray data (GSE45670) related to radioresistance of ESCC was downloaded from GEO. Based on pathologic responses after chemoradiotherapy, patients were divided into a non-responder (17 samples) and responder group (11 samples), and the difference in expression profiles of ir-lncRNAs were compared therein. Ir-lncRNA pairs were constructed for the differentially expressed lncRNAs as prognostic variables, and the microarray dataset (GSE53625) was downloaded from GEO to verify the effect of ir-lncRNA pairs on the long-term survival of ESCC. After modelling, patients are divided into high- and low-risk groups according to prognostic risk scores, and the outcomes were compared within groups based on the COX proportional hazards model. The different expression of ir-lncRNAs were validated using ECA 109 and ECA 109R cell lines via RT-qPCR.Results: 26 ir-lncRNA genes were screened in the GSE45670 dataset with differential expression, and 180 ir-lncRNA pairs were constructed. After matching with ir-lncRNA pairs constructed by GSE53625, six ir-lncRNA pairs had a significant impact on the prognosis of ESCC from univariate analysis model, of which three ir-lncRNA pairs were significantly associated with prognosis in multivariate COX analysis. These three lncRNA pairs were used as prognostic indicators to construct a prognostic risk model, and the predicted risk scores were calculated. With a median value of 2.371, the patients were divided into two groups. The overall survival (OS) in the high-risk group was significantly worse than that in the low-risk group (p < 0.001). The 1-, 2-, and 3-year prediction performance of this risk-model was 0.666, 0.702, and 0.686, respectively. In the validation setting, three ir-lncRNAs were significantly up-regulated, while two ir-lncRNAs were obviouly down-regulated in the responder group.Conclusion: Ir-lncRNAs may be involved in the biological regulation of radioresistance in patients with ESCC; and the prognostic risk-model, established by three ir-lncRNAs pairs has important clinical value in predicting the prognosis of patients with rr-ESCC.

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“…In accordance with the reference, we conducted the analysis. 13 , 14 Molecule: hsa-miR-3940-5p. In the TCGA LUAD project, miRNAseq data were collected from the level 3 BCGSC miRNA profiling.…”

Section: Methodsmentioning

confidence: 99%

“…In accordance with the reference, we conducted the analysis. 14 , 19 , 22 , 23 Target molecule: hsa-miR-3940-5p.…”

Section: Methodsmentioning

confidence: 99%

Expression, Clinical Significance, Immune Infiltration, and Regulation Network of miR-3940-5p in Lung Adenocarcinoma Based on Bioinformatic Analysis and Experimental Validation

Lin¹,

Huang²,

Xie³

et al. 2022

IJGM

Self Cite

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Background Based on bioinformatics analysis and experimental validation, we investigated the expression, clinical significance, immune infiltration, and potential signaling pathways of miR-3940-5p in lung adenocarcinoma (LUAD). Methods 521 LUAD tissue samples and 46 normal lung tissue samples from The Cancer Genome Atlas (TCGA) database. We evaluated the relationship between clinical features and miR-3940-5p expression using Kruskal–Wallis, Wilcoxon sign-rank, and logistic regression, explored the relationship between miR-3940-5p expression and the prognosis of LUAD patients using Kaplan–Meier survival curve analysis. Several databases were used to identify miRNA targets. MiR-3940-5p target genes were analyzed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The significant role of miR-3940-5p in function was evaluated using immune infiltration analysis. LUAD cell lines were tested for miR-3940-5p expression using QRT-PCR. Results There was a significant association between high miR-3940-5p expression in LUAD and T stage (P=0.005), pathologic stage (P=0.047), race (White vs Asian & Black or African American) (P=0.041), residual tumor (P=0.043), and anatomic neoplasm subdivision2 (P=0.030). MiR-3940-5p expression predicted poor overall survival (HR: 1.35; 95% CI: 1.01–1.81; P=0.045), disease-specific survival (HR: 1.53; 95% CI: 1.05–2.23; P=0.026), and progression-free survival (HR: 1.35; 95% CI: 1.03–1.77; P=0.032). BAP1, BBS1, CCR2, KCNE3, PEBP1, and RABL2A were all associated with poor OS in LUAD patients with low miR-3940-5p expression levels. According to GO and KEGG analyses, miR-3940-5p may play a role in LUAD development by regulating pathways such as measles, PI3K-Akt signaling pathway, and p53 signaling pathway. There was a correlation between the expression level of miR-3940-5p and immune infiltration. LUAD cell lines showed significantly higher levels of miR-3940-5p than Beas-2B cells. Conclusion A high expression of miR-3940-5p is significantly associated with a poor prognosis in patients with LUAD, suggesting that it could be used as a prognostic biomarker.

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LncRNA ADAMTS9-AS2 is a Prognostic Biomarker and Correlated with Immune Infiltrates in Lung Adenocarcinoma

Cited by 36 publications

References 32 publications

Identification of Two Subtypes and Prognostic Characteristics of Lung Adenocarcinoma Based on Pentose Phosphate Metabolic Pathway-Related Long Non-coding RNAs

Identification of Two Subtypes and Prognostic Characteristics of Lung Adenocarcinoma Based on Pentose Phosphate Metabolic Pathway-Related Long Non-coding RNAs

A novel immune-related radioresistant lncRNAs signature based model for risk stratification and prognosis prediction in esophageal squamous cell carcinoma

Expression, Clinical Significance, Immune Infiltration, and Regulation Network of miR-3940-5p in Lung Adenocarcinoma Based on Bioinformatic Analysis and Experimental Validation

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