Integrated analysis of lncRNA–mRNA co-expression networks in the α-particle induced carcinogenesis of human branchial epithelial cells

Liu, Xiaodan; Xie, Dafei; Wang, Yilong; Guan, Hua; Huang, Ruixue; Zhou, Ping‐Kun

doi:10.1080/09553002.2019.1539880

Cited by 26 publications

(16 citation statements)

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“…From this, a prognostic prediction model was constructed, the RiskScore of patients was calculated, and prediction and verification were also carried out. Among all 14 prognosis-specific immunerelated genes, 9 (e.g., PSMD11, PPIA, MIF, BMP5, DKK1, PDGFB, ANGPTL4, IL1R2, and THRB) (26)(27)(28)(29)(30)(31)(32)(33)(34) have been reported to be involved in the immune microenvironmentassociated pathogenesis of lung adenocarcinoma or suggested to be significant predictors of recurrence-free or overall survival. This implies that our bioinformatics analysis using TCGA and ImmPort cohorts has prognostic value.…”

Section: Discussionmentioning

confidence: 99%

An Immune-Related Signature Predicts Survival in Patients With Lung Adenocarcinoma

et al. 2019

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We investigated the local immune status and its prognostic value in lung adenocarcinoma. In total, 513 lung adenocarcinoma samples from TCGA and ImmPort databases were collected and analyzed. The R package coxph was employed to mine immune-related genes that were significant prognostic indicators using both univariate and multivariate analyses. The R software package glmnet was then used for Lasso Cox regression analysis, and a prognosis prediction model was constructed for lung adenocarcinoma; clusterProfiler was selected for functional gene annotations and KEGG enrichment analysis. Finally, correlations between the RiskScore and clinical features or signaling pathways were established. Sixty-four immune-related genes remarkably correlated with patient prognosis and were further applied. Samples were hierarchically clustered into two subgroups. Accordingly, the LASSO regression algorithm was employed to screen the 14 most representative immune-related genes (PSMD11,

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Section: Discussionmentioning

confidence: 99%

An Immune-Related Signature Predicts Survival in Patients With Lung Adenocarcinoma

et al. 2019

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“…The GeneChip Fluidics Station 450, GeneChip Hybridization Oven 645, and GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA, USA) were used to detect mRNA changes in the HBE p53-wt and HBE p53-/-groups after exposure to 4 Gy radiation. In our laboratory, we previously conducted integrated analysis of lncRNA-mRNA co-expression networks in α lung bronchial epithelial cells with -particle-induced carcinogenesis [31]. Fold changes greater than 2 and p-values less than 0.05 were considered to represent significant changes in mRNA levels.…”

Section: Transcriptome Detection Through Microarray Analysis and Valimentioning

confidence: 99%

“…To ascertain whether p53 deficiency affected mRNA expression post-radiation, we compared mRNA expression levels between the p53-/-HBE and p53-wt HBE cells. We conducted this analysis 24 h after 4 Gy γ radiation exposure, because human lung branchial epithelial cells exhibit 4 Gy-induced radiation injury (i.e., significant DNA damage) at this timepoint, based on our previous studies [31,33,[41][42][43]. According to the transcriptomic data, 326 mRNAs showed significantly altered expression in HBE p53-/-cells postradiation, of which 269 were upregulated and 57 were downregulated ( Fig.…”

Section: Loss Of P53 Significantly Alters Mrna Expressionmentioning

confidence: 99%

Integrated analysis of transcriptomic and metabolomic profiling reveal the p53 associated pathways underlying the response to ionizing radiation in HBE cells

Huang

Liu

et al. 2020

Cell Biosci

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Background: Radiation damage to normal tissues is a serious concern. P53 is a well-known transcription factor which is closely associated with radiation-induced cell damage. Increasing evidence has indicated that regulation of metabolism by p53 represents a reviving mechanism vital to protect cell survival. We aimed to explore the interactions of radiation-induced transcripts with the cellular metabolism regulated by p53.Methods: Human bronchial epithelial (HBE) cell line was used to knockout p53 using CRISPR/cas9. Transcriptomic analysis was conducted by microarray and metabolomic analysis was conducted by GC-MS. Integrative omics was performed using MetaboAnalyst.Results: 326 mRNAs showed significantly altered expression in HBE p53-/-cells post-radiation, of which 269 were upregulated and 57 were downregulated. A total of 147 metabolites were altered, including 45 that increased and 102 that decreased. By integrated analysis of both omic data, we found that in response to radiation insult, nitrogen metabolism, glutathione metabolism, arachidonic acid metabolism, and glycolysis or gluconeogenesis may be dysregulated due to p53. Conclusions:Our study provided a pilot comprehensive view of the metabolism regulated by p53 in response to radiation exposure. Detailed evaluation of these important p53-regulated metabolic pathways, including their roles in the response to radiation of cells, is essential to elucidate the molecular mechanisms of radiation-induced damage.

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“…Heat shock cognate 71 kDa protein HSPA8 A Involved in CFTR biogenesis and trafficking [20] Regulated by corticoid in cell lysate of sputum of COPD patients [21] Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform* PPP2R5E* A Genetically associated with lung cancer [22] PP2A activity was strongly enhanced in NSCLC [23] TBC1 domain family member 5 TBC1D5 A Induced by smoking and ozone (murine COPD model) [24] Filamin-B FLNB C No 14-3-3 protein beta/alpha YWHAB C Interact with and regulate surfactant protein A2 [25] Involved in lung cancer [26] Enhancer of mRNA-decapping protein 4 EDC4 C No 14-3-3 protein zeta/delta YWHAZ E Identified as a metastasis enhancer gene in lung cancer [32] Upregulated in lung cancer [33] Differentially expressed in malignant bronchial epithelial cell line compared to control cell line [34] More frequent increased expression in patients with resectable lung adenocarcinoma with an improved prognosis [35] 26S proteasome non-ATPase regulatory subunit 11 PSMD11 F Differentially expressed in malignant bronchial epithelial cell line compared to control cell line [34] Fig . 1 Diagram of the proteins identified in the two-hybrid screening and their interaction domains Fig.…”

Section: Cilia-and Flagella-associated Protein 97 Cfap97 a Nomentioning

confidence: 99%

Two-hybrid screening of FAM13A protein partners in lung epithelial cells

2019

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Objectives: Family with sequence similarity 13 member A (FAM13A) genetic variants have been associated with several chronic respiratory diseases including chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), idiopathic pulmonary fibrosis (IPF) and lung cancer. The FAM13A protein includes a RhoGTPase activating protein (RhoGAP) domain known to participate in various cellular mechanisms including cell proliferation. While intensive genomic studies have been performed to reveal its involvement in lung diseases, the biological role of FAM13A protein is still not completely elucidated. Results: We therefore performed a two-hybrid screening to identify protein partners of FAM13A using a human lung cancer cDNA library. We identified several protein partners with a high confidence score. Researchers in the field of chronic lung diseases may benefit from this two-hybrid screening data which may reveal new research pathways to decipher.

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Integrated analysis of lncRNA–mRNA co-expression networks in the α-particle induced carcinogenesis of human branchial epithelial cells

Cited by 26 publications

References 50 publications

An Immune-Related Signature Predicts Survival in Patients With Lung Adenocarcinoma

An Immune-Related Signature Predicts Survival in Patients With Lung Adenocarcinoma

Integrated analysis of transcriptomic and metabolomic profiling reveal the p53 associated pathways underlying the response to ionizing radiation in HBE cells

Two-hybrid screening of FAM13A protein partners in lung epithelial cells

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