Identification of lncRNA biomarkers in lung squamous cell carcinoma using comprehensive analysis of lncRNA mediated ceRNA network

Li, Rui; Yang, Yie; Jin, Jia; Zhang, Mengyu; Liu, Xiao; Liu, Xiaoxia; Yin, Yunhong; Qu, Yi

doi:10.1080/21691401.2019.1647225

Cited by 25 publications

(19 citation statements)

References 48 publications

(52 reference statements)

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“…Current prognostic biomarkers for LUSC included prognostic alternative mRNA splicing signature, lncRNA signatures, and microRNA signatures [9,[11][12][13]. However, these studies [9,[11][12][13] only included LUSC data from the TCGA database. In this study, we built IRGPI based on 13 immune-related gene pairs from the training cohort and explored the prognostic value of IRGPI in the testing and validation cohorts.…”

Section: Discussionmentioning

confidence: 99%

“…We summarized current biomarkers for LUSC and compared the biomarkers in Table 4. Li et al constructed a model with 6 lncRNAs from the TCGA LUSC cohort and the area under the curve (AUC) of the 6-lncRNA signature associated with 3-year survival was 0.672 in the training cohort [11]. Hu et al constructed a 3-lncRNA signature for LUSC and the AUC of this model associated with 3-year survival was 0.629 in the training cohort [12].…”

Section: Comparison Of Biomarkers For Luscmentioning

confidence: 99%

“…Previous studies associated with prognosis of lung squamous cell carcinoma (LUSC) patients mainly concentrated on the alternative mRNA splicing signatures, lncRNA signatures, and other transcriptome signatures [8][9][10][11][12][13]. As the component of the tumor microenvironment, tumor-in ltrating immune cells (TIICs) revealed promising value for providing prognostic biomarkers [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

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Validation of an Immune-Related Gene Pair Index as a Prognostic Marker of Lung Squamous Cell Carcinoma

Wang

Xuan

Wei

et al. 2020

Preprint

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Abstract Background: Lung squamous cell carcinoma (LUSC) is one of the subtypes of non-small-cell lung cancer (NSCLC) and accounts for approximately 20 to 30% of all lung cancers. Methods: In this study, we developed an immune-related gene pair index (IRGPI) for LUSC from 8 public LUSC data sets, including The Cancer Genome Atlas LUSC cohort and Gene Expression Omnibus data sets, and explored the prognostic value of IRGPI for patients with LUSC. Results: IRGPI was constructed by 13 gene pairs consisting of 25 unique immune-related genes from the training cohort. Multivariate cox regression analysis showed that high risk based on IRGPI was an independent risk factor for poor prognosis of patients with LUSC in the training cohort (230 patients; HR= 3.40; 95%CI [2.34-4.94]; p<0.001), the testing cohort (228 patients; HR=2.11; 95%CI [1.48-3.01]; p<0.001) and the validation cohort (472 patients; HR=1.99; 95%CI [1.5-2.63]; p<0.001). The infiltrations of naïve B cells, plasma cells, CD8+ T cells, activated memory CD4+ T cells, gamma delta (γδ) T cells, M1 macrophages, and activated dendritic cells were lower in the high-risk group, as compared with the low-risk group in the TCGA cohort. The infiltrations of neutrophils, activated mast cells, and monocytes were higher in the high-risk group. Conclusions: IRGPI is a significant prognostic biomarker for predicting overall survival in LUSC patients. Combining clinical features with IRGPI will improve prognostic accuracy.

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Section: Discussionmentioning

confidence: 99%

Section: Comparison Of Biomarkers For Luscmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Validation of an Immune-Related Gene Pair Index as a Prognostic Marker of Lung Squamous Cell Carcinoma

Wang

Xuan

Wei

et al. 2020

Preprint

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“…We summarized current biomarkers for LUSC and compared the biomarkers in Table 3. Li et al constructed a model with 6 lncRNAs from TCGA LUSC cohort and the area under the curve (AUC) of the 6-lncRNA signature associated with 3-year survival was 0.672 in the training cohort [11]. Hu et al…”

Section: Comparison Of Biomarkers For Luscmentioning

confidence: 99%

“…Previous studies associated with prognosis of LUSC patients mainly concentrated on the alternative mRNA splicing signatures, lncRNA signatures, and other transcriptome signatures [8][9][10][11][12][13]. As the component of the tumor microenvironment, tumor-in ltrating lymphocytes (TIL) revealed promising value for providing prognostic biomarkers [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Validation of an Immune-related Gene Pair Index as a Prognostic Marker of Early-Stage Lung Squamous Cell Carcinoma

Wang¹,

Xuan²,

Wei³

et al. 2020

Preprint

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Background. Lung squamous cell carcinoma (LUSC) is one of the subtypes of non-small-cell lung cancer (NSCLC) and accounts for approximately 20 to 30% of all lung cancers.Methods. In this study, we developed an immune-related gene pair index (IRGPI) for early-stage LUSC from 3 public LUSC data sets, including The Cancer Genome Atlas LUSC cohort and Gene Expression Omnibus data sets, and explored whether IRGPI could act as a prognostic marker to identify patients with early-stage LUSC at high risk.Results. IRGPI was constructed by 68 gene pairs consisting of 123 unique immune-related genes from TCGA LUSC cohort. In the derivation cohort, the hazard of death among high-risk group was 10.51 times that of the low-risk group (HR, 10.51; 95%CI, 6.96-15.86; p<0.001). The hazard of death among the high-risk group was 2.26 times that of the low-risk group (HR, 2.26; 95%CI, 1.2-4.25; p=0.009) in the GSE37745 validation cohort and was 3.2 times that of low-risk group (HR, 3.2; 95%CI, 0.98-10.4; p=0.042) in the GSE41271 validation cohort. The infiltrations of CD8+ T cells and T follicular helper cells were lower in the high-risk group, as compared with the low-risk group in the TCGA cohort (6.94% vs 9.63%, p=0.004; 2.15% vs 3%, p=0.002, respectively). The infiltrations of neutrophils, activated mast cells and monocytes were higher in the high-risk group, as compared with the low-risk group in the TCGA cohort (1.63% vs 0.72%, p=0.001; 1.64% vs 1.02%, p=0.007; 0.57% vs 0.35%, p=0.041, respectively).Conclusions. IRGPI is a significant prognostic biomarker for predicting overall survival in early-stage LUSC patients.

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LncRNA PITPNA‐AS1/miR‐223‐3p/PTN axis regulates malignant progression and stemness in lung squamous cell carcinoma

Peng

Qiu

2022

Clinical Laboratory Analysis

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Background: Long noncoding RNAs (lncRNAs) are a kind of molecule that cannot code proteins, and their expression is dysregulated in diversified cancers. LncRNA PITPNA-AS1 has been shown to act as a tumor promoter in a variety of malignancies, but its function and regulatory mechanisms in lung squamous cell carcinoma (LUSC) are yet unknown. Methods:The mRNA and protein expression of genes were examined by RT-qPCR, western blot, and IHC assay. The cell proliferation, migration, invasion, and stemness were detected through CCK-8, colony formation, Transwell and spheroid formation assays. The CD44 + and CD166 + -positive cells were detected through flow cytometry.The binding ability among genes through luciferase reporter and RNA pull-down assays. The tumor growth was detected through in vivo nude mice assay. Results:The lncRNA PITPNA-AS1 had increased expression in LUSC and was linked to a poor prognosis. In LUSC, PITPNA-AS1 also enhanced cell proliferation, migration, invasion, and stemness. This mechanistic investigation showed that PITPNA-AS1 absorbed miR-223-3p and that miR-223-3p targeted PTN. MiR-223-3p inhibition or PTN overexpression might reverse the inhibitory effects of PITPNA-AS1 suppression on LUSC progression, as demonstrated by rescue experiments. In addition, the PITPNA-AS1/miR-223-3p/PTN axis accelerated tumor development in vivo. Conclusions: It is the first time we investigated the potential role and ceRNA regulatory mechanism of PITPNA-AS1 in LUSC. The data disclosed that PITPNA-AS1 upregulated PTN through sponging miR-223-3p to enhance the onset and progression of LUSC. These findings suggested the ceRNA axis may serve as a promising therapeutic biomarker for LUSC patients.

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Identification of lncRNA biomarkers in lung squamous cell carcinoma using comprehensive analysis of lncRNA mediated ceRNA network

Cited by 25 publications

References 48 publications

Validation of an Immune-Related Gene Pair Index as a Prognostic Marker of Lung Squamous Cell Carcinoma

Validation of an Immune-Related Gene Pair Index as a Prognostic Marker of Lung Squamous Cell Carcinoma

Validation of an Immune-related Gene Pair Index as a Prognostic Marker of Early-Stage Lung Squamous Cell Carcinoma

LncRNA PITPNA‐AS1/miR‐223‐3p/PTN axis regulates malignant progression and stemness in lung squamous cell carcinoma

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