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Shu Q, Liu X, Yang J, Mou T, Xie F. The clinical prognostic value of lncRNA FOXP4-AS1 in cancer patients: A meta-analysis and bioinformatics analysis based on TCGA datasets. Medicine (Baltimore) 2022; 101:e31439. [PMID: 36281152 PMCID: PMC9592412 DOI: 10.1097/md.0000000000031439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The mortality and recurrence of patients with cancer is of high prevalence. Long non-coding RNA (lncRNA) forkhead box P4 antisense RNA 1 (FOXP4-AS1) is a promising lncRNA. There is increasing evidence that lncRNA FOXP4-AS1 is abnormally expressed in various tumors and is associated with cancer prognosis. This study was designed to identify the prognostic value of lncRNA FOXP4-AS1 in human malignancies. METHODS We searched electronic databases up to April 29, 2022, including PubMed, Cochrane Library, Embase, MEDLINE, and Web of Science. Eligible studies that evaluated the clinicopathological and prognostic role of lncRNA FOXP4-AS1 in patients with malignant tumors were included. The pooled odds ratios (ORs) and the hazard ratios (HRs) were calculated to assess the role of lncRNA FOXP4-AS1 using Stata/SE 16.1 software. RESULTS A total of 6 studies on cancer patients were included in the present meta-analysis. The combined results revealed that high expression of lncRNA FOXP4-AS1 was significantly associated with unfavorable overall survival (OS) (HR = 1.99, 95% confidence interval [CI]: 1.65-2.39, P < .00001), and poor disease-free survival (DFS) (HR = 1.81, 95% CI: 1.54-2.13, P < .00001) in a variety of cancers. In additional, the increase in lncRNA FOXP4-AS1 expression was also correlated with tumor size ((larger vs smaller) (OR = 3.16, 95% CI: 2.12-4.71, P < .00001), alpha-fetoprotein (≥400 vs <400) (OR = 3.81, 95%CI: 2.38-6.11, P = .83), lymph node metastasis (positive vs negative) (OR = 2.93, 95%CI: 1.51-5.68, P = .001), and age (younger vs older) (OR = 2.06, 95% CI: 1.41-3.00, P = .00002) in patients with cancer. Furthermore, analysis results using The Cancer Genome Atlas (TCGA) dataset showed that the expression level of lncRNA FOXP4-AS1 was higher in most tumor tissues than in the corresponding normal tissues, which predicted a worse prognosis. CONCLUSIONS In this meta-analysis, we demonstrate that high lncRNA FOXP4-AS1 expression may become a potential marker to predict cancer prognosis.
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Affiliation(s)
- Qiang Shu
- Department of Hepatic-Biliary-Pancreatic Surgery, The Neijiang First People’s Hospital affiliated to Chongqing Medical University, Neijiang City, Sichuan Province, China
| | - Xiaoling Liu
- Department of Hospital Infection Management, The Neijiang Hospital of Traditional Chinese Medicine, Neijiang City, Sichuan Province, China
| | - Jushu Yang
- Department of Hepatic-Biliary-Pancreatic Surgery, The Neijiang First People’s Hospital affiliated to Chongqing Medical University, Neijiang City, Sichuan Province, China
| | - Tinggang Mou
- Department of Hepatic-Biliary-Pancreatic Surgery, The Neijiang First People’s Hospital affiliated to Chongqing Medical University, Neijiang City, Sichuan Province, China
| | - Fei Xie
- Department of Hepatic-Biliary-Pancreatic Surgery, The Neijiang First People’s Hospital affiliated to Chongqing Medical University, Neijiang City, Sichuan Province, China
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Zhang G, Wang Y, Han X, Lu T, Fu L, Jin H, Yang K, Cai H. FOXP4-AS1 May be a Potential Prognostic Biomarker in Human Cancers: A Meta-Analysis and Bioinformatics Analysis. Front Oncol 2022; 12:799265. [PMID: 35719909 PMCID: PMC9204280 DOI: 10.3389/fonc.2022.799265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 05/04/2022] [Indexed: 12/26/2022] Open
Abstract
Background Cancer is one of the leading causes of death worldwide. Early diagnosis can significantly lower cancer-related mortality. Studies have shown that the lncRNA Forkhead box P4 antisense RNA 1 (FOXP4-AS1) is aberrantly expressed in various solid tumors. A meta-analysis was performed to evaluate the correlation of FOXP4-AS1 with the prognosis of cancer patients and determine the clinical value of FOXP4-AS1 as a potential diagnostic marker. Methods Correlational studies from the Web of Science, Embase, OVID, Cochrane and PubMed databases were screened (up to April 1, 2021). Meta-analysis was performed using Stata SE12.0 software. Results Eleven original studies with 1,332 patients who were diagnosed with a solid cancer (nasopharyngeal carcinoma, hepatocellular carcinoma, colorectal cancer, gastric cancer, osteosarcoma, mantle cell lymphoma, prostate cancer, and pancreatic ductal adenocarcinoma) were included in the meta-analysis. High expression of FOXP4-AS1 was correlated with poor overall survival (OS) (HR = 1.77, 95% CI 1.29-2.44, P < 0.001) and shorter disease-free survival (DFS) (HR = 1.66, 95% CI 1.01-2.72, P = 0.044). Subgroup analysis based on sample size, follow-up time and Newcastle-Ottawa Scale (NOS) score revealed significant differences between FOXP4-AS1 levels and OS (P < 0.05). However, the expression level of FOXP4-AS1 was not significantly correlated with the OS of gastric cancer patients (P = 0.381). High expression of FOXP4-AS1 was predictive of a larger tumor size (OR = 3.82, 95% CI 2.3-6.3, P < 0.001). Conclusions Overexpression of FOXP4-AS1 correlates with poor prognosis of cancer patients, and is a potential prognostic biomarker and therapeutic target. Systematic Review Registration PROSPERO, identifier CRD42021245267.
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Affiliation(s)
- Guangming Zhang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China.,Department of General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China.,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Lanzhou, China.,Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China
| | - Yongfeng Wang
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China.,Department of General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China.,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Lanzhou, China
| | | | - Tingting Lu
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Institution of Clinical Research and Evidence Based Medicine, Gansu Provincial Hospital, Lanzhou, China
| | - Liangyin Fu
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China.,Department of General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China.,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Lanzhou, China
| | - Haojie Jin
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Kehu Yang
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Hui Cai
- The First Clinical Medical College of Gansu University of Chinese Medicine (Gansu Provincial Hospital), Lanzhou, China.,Department of General Surgery Clinical Medical Center, Gansu Provincial Hospital, Lanzhou, China.,Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Lanzhou, China
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Yang J, Wei X, Hu F, Dong W, Sun L. Development and validation of a novel 3-gene prognostic model for pancreatic adenocarcinoma based on ferroptosis-related genes. Cancer Cell Int 2022; 22:21. [PMID: 35033072 PMCID: PMC8760727 DOI: 10.1186/s12935-021-02431-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/25/2021] [Indexed: 12/24/2022] Open
Abstract
Background Molecular markers play an important role in predicting clinical outcomes in pancreatic adenocarcinoma (PAAD) patients. Analysis of the ferroptosis-related genes may provide novel potential targets for the prognosis and treatment of PAAD. Methods RNA-sequence and clinical data of PAAD was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public databases. The PAAD samples were clustered by a non-negative matrix factorization (NMF) algorithm. The differentially expressed genes (DEGs) between different subtypes were used by “limma_3.42.2” package. The R software package clusterProfiler was used for functional enrichment analysis. Then, a multivariate Cox proportional and LASSO regression were used to develop a ferroptosis-related gene signature for pancreatic adenocarcinoma. A nomogram and corrected curves were constructed. Finally, the expression and function of these signature genes were explored by qRT-PCR, immunohistochemistry (IHC) and proliferation, migration and invasion assays. Results The 173 samples were divided into 3 categories (C1, C2, and C3) and a 3-gene signature model (ALOX5, ALOX12, and CISD1) was constructed. The prognostic model showed good independent prognostic ability in PAAD. In the GSE62452 external validation set, the molecular model also showed good risk prediction. KM-curve analysis showed that there were significant differences between the high and low-risk groups, samples with a high-risk score had a worse prognosis. The predictive efficiency of the 3-gene signature-based nomogram was significantly better than that of traditional clinical features. For comparison with other models, that our model, with a reasonable number of genes, yields a more effective result. The results obtained with qPCR and IHC assays showed that ALOX5 was highly expressed, whether ALOX12 and CISD1 were expressed at low levels in tissue samples. Finally, function assays results suggested that ALOX5 may be an oncogene and ALOX12 and CISD1 may be tumor suppressor genes. Conclusions We present a novel prognostic molecular model for PAAD based on ferroptosis-related genes, which serves as a potentially effective tool for prognostic differentiation in pancreatic cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02431-8.
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Affiliation(s)
- Jihua Yang
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - XiaoHong Wei
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - Fang Hu
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China
| | - Wei Dong
- Department of Pathology, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University, Shanghai, China.
| | - Liao Sun
- Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, 519000, China.
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Long non-coding RNA FOXP4-AS1 facilitates the biological functions of hepatocellular carcinoma cells via downregulating ZC3H12D by mediating H3K27me3 through recruitment of EZH2. Cell Biol Toxicol 2022; 38:1047-1062. [PMID: 34545456 PMCID: PMC9750913 DOI: 10.1007/s10565-021-09642-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/09/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND Some studies have reported the effect of long non-coding RNA forkhead box P4 antisense RNA 1 (lncRNA FOXP4-AS1) on hepatocellular carcinoma (HCC). Here, we aimed to discuss the effects of FOXP4-AS1/enhancer of zeste homolog 2 (EZH2)/trimethylation of lysine 27 on histone H3 (H3K27me3)/zinc finger CCCH-type containing 12D (ZC3H12D) axis on HCC. METHODS The expression of FOXP4-AS1, EZH2, and ZC3H12D, and abundance of H3K27me3 in HCC tissues and cells were tested. The relationship between FOXP4-AS1 expression and prognosis of HCC patients was analyzed. The biological functions of HCC cells were detected via loss- and gain-of-function assays. The tumor weight and volume in vivo were tested. The interaction between FOXP4-AS1 and EZH2 as well as that between EZH2 and H3K27me3 was verified. RESULTS FOXP4-AS1 and EZH2 expression and H3K27me3 abundance were enhanced while ZC3H12D expression was depressed in HCC tissues and cells. Knockdown of FOXP4-AS1 suppressed biological functions of HCC cells as well as the weight and volume of HCC transplanted tumor. Depleting ZC3H12D reversed the effect of downregulated FOXP4-AS1 on HCC cells. FOXP4-AS1 suppressed ZC3H12D expression via mediating H3K27me3 by recruitment of EZH2. CONCLUSION The key findings of the present study demonstrate that FOXP4-AS1 suppresses ZC3H12D expression via mediating H3K27me3 by recruitment of EZH2, thus promoting the progression of HCC.
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Niu Y, Wang G, Li Y, Guo W, Guo Y, Dong Z. LncRNA FOXP4-AS1 Promotes the Progression of Esophageal Squamous Cell Carcinoma by Interacting With MLL2/H3K4me3 to Upregulate FOXP4. Front Oncol 2022; 11:773864. [PMID: 34970490 PMCID: PMC8712759 DOI: 10.3389/fonc.2021.773864] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/19/2021] [Indexed: 01/16/2023] Open
Abstract
Malignant tumors are a grave threat to human health. Esophageal squamous cell carcinoma (ESCC) is a common gastrointestinal malignant tumor. China has a high incidence of ESCC, and its morbidity and mortality are higher than the global average. Increasingly, studies have shown that long noncoding RNAs (lncRNAs) play a vital function in the occurrence and development of tumors. Although the biological function of FOXP4-AS1 has been demonstrated in various tumors, the potential molecular mechanism of FOXP4-AS1 in ESCC is still poorly understood. The expression of FOXP4 and FOXP4-AS1 was detected in ESCC by quantitative real-time PCR (qRT–PCR) or SP immunohistochemistry (IHC). shRNA was used to silence gene expression. Apoptosis, cell cycle, MTS, colony formation, invasion and migration assays were employed to explore the biological functions of FOXP4 and FOXP4-AS1. The potential molecular mechanism of FOXP4-AS1 in ESCC was determined by dual-luciferase reporter, RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP). Here, we demonstrated that FOXP4-AS1 was significantly increased in ESCC tissues and cell lines, associated with lymph node metastasis and TNM staging. Cell function experiments showed that FOXP4-AS1 promoted the proliferation, invasion and migration ability of ESCC cells. The expression of FOXP4-AS1 and FOXP4 in ESCC tissues was positively correlated. Further research found that FOXP4-AS1, upregulated in ESCC, promotes FOXP4 expression by enriching MLL2 and H3K4me3 in the FOXP4 promoter through a “molecular scaffold”. Moreover, FOXP4, a transcription factor of β-catenin, promotes the transcription of β-catenin and ultimately leads to the malignant progression of ESCC. Finally, FOXP4-AS1 may be a new therapeutic target for ESCC.
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Affiliation(s)
- Yunfeng Niu
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Gaoyan Wang
- Experimental Center, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Yan Li
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wei Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yanli Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhiming Dong
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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Liao C, Wang A, Ma Y, Liu H. Long non-coding RNA FOXP4-AS1 is a prognostic biomarker and associated with immune infiltrates in ovarian serous cystadenocarcinoma. Medicine (Baltimore) 2021; 100:e27473. [PMID: 34622876 PMCID: PMC8500601 DOI: 10.1097/md.0000000000027473] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/21/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND FOXP4-AS1 expression participates in multiple signal pathways and has been previously reported in colorectal cancer, cervical cancer, and other cancer cells. However, its role on prognosis and immune infiltrates in ovarian serous cystadenocarcinoma (OVs) remains unclear. The purpose of our study was to investigate the expression of FOXP4-AS1 in OVs and its association with immune infiltrates, and determined its prognostic roles in OVs. METHODS Using The Cancer Genome Atlas (TCGA) database, we retrieved FOXP4-AS1 expression and clinical information for 376 patients with OVs. Wilcoxon rank sum test was used to compare the expression of FOXP4-AS1 in OVs and normal ovarian tissue. Logistic regression was used to analyze the relationship between clinicopathologic features and FOXP4-AS1. Gene Set Enrichment Analysis (GSEA), and single sample Gene Set Enrichment Analysis (ssGSEA) was conducted to investigate the enrich pathways and functions and quantify the extent of immune cells infiltration for FOXP4-AS1. Kaplan-Meier method was used to generate survival curves, and Cox regression was used to analyze the relationship between FOXP4-AS1 and survival rate. RESULTS High FOXP4-AS1 expression was significantly correlated with tumor FIGO stage (P = .026). Multivariate survival analysis showed that FOXP4-AS1was an independent prognostic marker for overall survival (OS; hazard ratio [HR]: 0.638; 95% confidence interval [CI]:0.467-0.871; P = .001) and disease-specific survival (DSS; HR: 0.649; CI: 0.476-0.885; P = .006). GSEA showed that High FOXP4-AS1 expression may active programmed cell death 1 (PD-1) signaling, the cytotoxic T lymphocyte-associated antigen-4 (CTLA4) pathway, the B cell receptor signaling pathway, apoptosis, fibroblast growth factor receptor (FGFR) signaling, and the Janus-activated kinase signal transducers and activators of transcription (JAK-STAT) signaling pathway. FOXP4-AS1 expression was negatively correlated with markers of immune cells, including aDC, cytotoxic cells and neutrophils. CONCLUSION High FOXP4-AS1 expression has the potential to be a prognostic molecular marker of favorable survival in OVs.
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Affiliation(s)
- Cheng Liao
- Department of Anesthesiology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, P. R. China
| | - Ao Wang
- Department of Gynecology and Obstetrics, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, P. R. China
| | - Yushan Ma
- Department of Anesthesiology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, P. R. China
| | - Hui Liu
- Department of Anesthesiology, West China Second University Hospital, Sichuan University, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, Sichuan, P. R. China
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Seyed Hosseini E, Nikkhah A, Sotudeh A, Alizadeh Zarei M, Izadpanah F, Nikzad H, Haddad Kashani H. The impact of LncRNA dysregulation on clinicopathology and survival of pancreatic cancer: a systematic review and meta-analysis (PRISMA compliant). Cancer Cell Int 2021; 21:447. [PMID: 34425840 PMCID: PMC8383355 DOI: 10.1186/s12935-021-02125-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 07/30/2021] [Indexed: 12/26/2022] Open
Abstract
Purpose An increasing number of studies have reported a significant association between long non-coding RNAs (lncRNAs) dysregulation and pancreatic cancers. In the present study, we aimed to gather articles to evaluate the prognostic value of long non coding RNA in pancreatic cancer. Experimental design We systematically searched all eligible articles from databases of PubMed, Web of Science, and Scopus to meta-analysis of published articles and screen association of multiple lncRNAs expression with clinicopathology and/or survival of pancreatic cancer. The pooled hazard ratios (HRs) and their 95% confidence intervals (95% CIs) were used to analysis of overall survival, disease-free survival and progression-free survival were measured with a fixed or random effects model. Results A total of 39 articles were included in the present meta-analysis. Our results showed that dysregulation of lncRNAs were linked to overall survival (39 studies, 4736 patients HR = 0.41, 95% CI 0.25 ± 0.58, random-effects in pancreatic cancer. Moreover, altered lncRNAs were also contributed to progression-free survival (8 studies, 1180 patients HR: 1.88, 95% CI (1.35–2.62) and disease-free survival (2 studies, 285 patients, HR: 6.07, 95% CI 1.28–28.78). In addition, our findings revealed the association between dysregulated RNAs and clinicopathological features in this type of cancer. Conclusions In conclusion, dysregulated lncRNAs could be served as promising biomarkers for diagnosis and prognosis of pancreatic cancer.
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Affiliation(s)
- Elahe Seyed Hosseini
- Gametogenesis Research Center, Kashan University of Medical Science, Kashan, Iran.,Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Ali Nikkhah
- Student Research Committee, Kashan University of Medical Science, Kashan, Iran
| | - Amir Sotudeh
- Student Research Committee, Kashan University of Medical Science, Kashan, Iran
| | - Marziyeh Alizadeh Zarei
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Izadpanah
- Food and Drug Laboratory Research Center and Food and Drug Reference Control Laboratories Center, Food & Drug Administration of Iran, MOH & ME, Tehran, Iran
| | - Hossein Nikzad
- Gametogenesis Research Center, Kashan University of Medical Science, Kashan, Iran.,Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Haddad Kashani
- Gametogenesis Research Center, Kashan University of Medical Science, Kashan, Iran. .,Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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FOXP4-AS1 is a favorable prognostic-related enhancer RNA in ovarian cancer. Biosci Rep 2021; 41:228414. [PMID: 33870423 PMCID: PMC8150160 DOI: 10.1042/bsr20204008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/22/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Ovarian cancer (OV) is the main cause of deaths worldwide in female reproductive system malignancies. Enhancer RNAs (eRNAs) are derived from the transcription of enhancers and has attracted increasing attention in cancers recently. However, the biological functions and clinical significance of eRNAs in OV have not been well described presently. We used an integrated data analysis to identify prognostic-related eRNAs in OV. Tissue-specific enhancer-derived RNAs and their regulating genes were considered as putative eRNA–target pairs using the computational pipeline PreSTIGE. Gene expression profiles and clinical data of OV and 32 other cancer types were obtained from the UCSC Xena platform. Altogether, 71 eRNAs candidates showed significant correlation with overall survival (OS) of OV samples (Kaplan–Meier log-rank test, P<0.05). Among which, 23 were determined to be correlated with their potential target genes (Spearman’s r > 0.3, P<0.001). It was found that among the 23 prognostic-related eRNAs, the expression of forkhead box P4 antisense RNA 1 (FOXP4-AS1) had the highest positive correlation with its predicted target gene FOXP4 (Spearman’s r = 0.61). Moreover, the results were further validated by RT-qPCR analysis in an independent OV cohort. Our results suggested the eRNA FOXP4-AS1 expression index may be a favorable independent prognostic biomarker candidate in OV.
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Chen X, Wang J, Xie F, Mou T, Zhong P, Hua H, Liu P, Yang Q. Long noncoding RNA LINC01559 promotes pancreatic cancer progression by acting as a competing endogenous RNA of miR-1343-3p to upregulate RAF1 expression. Aging (Albany NY) 2020; 12:14452-14466. [PMID: 32678071 PMCID: PMC7425501 DOI: 10.18632/aging.103487] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/27/2020] [Indexed: 12/17/2022]
Abstract
Background: An increasing number of studies have shown that lncRNAs are involved in the biological processes of pancreatic cancer (PC). Hence, we investigated the role of a novel noncoding RNA, LINC01559, involved in PC progression. Results: LINC01559 and RAF1 were highly expressed in PC, while miR-1343-3p had low expression. High expression of LINC01559 was significantly associated with large tumors, lymph node metastasis, and poor prognosis. Functional experiment results revealed that silencing of LINC01559 significantly suppressed PC cell proliferation and metastasis. Meanwhile, LINC01559 could act as a ceRNA to competitively sponge miR-1343-3p to up-regulate RAF1 and activate its downstream ERK pathway Conclusions: LINC01559 functions as an oncogene in PC progression through acting as a ceRNA of miR-1343-3p. Hence, LINC01559 is a potential diagnostic and therapeutic target. Methods: RT-qPCR was performed to determine the expression of LINC01559 and miR-1343-3p in PC. Individual patient data were collected to investigate the correlation between clinicopathological features and LINC01559 expression. Subsequently, the expression of LINC01559, miR-1343-3p, and RAF1 was altered using transfection of vectors or inhibitors. Gain- and loss-of-function assays and mechanistic assays were applied to verify the effects of LINC01559, miR-1343-3p, and RAF1 on PC cell proliferation and metastasis in vivo and in vitro.
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Affiliation(s)
- Xiao Chen
- Department of Osteology, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Jie Wang
- Department of Hepatic-Biliary-Pancreatic Surgery, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Fei Xie
- Department of Hepatic-Biliary-Pancreatic Surgery, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Tinggang Mou
- Department of Hepatic-Biliary-Pancreatic Surgery, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Pingyong Zhong
- Department of Hepatic-Biliary-Pancreatic Surgery, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Hao Hua
- Department of Hepatic-Biliary-Pancreatic Surgery, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Pan Liu
- Department of Hepatic-Biliary-Pancreatic Surgery, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
| | - Qin Yang
- Department of Gastroenterology, The First Peoples Hospital of Neijiang, Neijiang, Sichuan, China
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10
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Liu XG, Xu H, Chen M, Tan XY, Chen XF, Yang YG, Lin MZ, Liu GH, Liang XL, Qian YB, Yuan GJ, Chen MQ, Li WT, Miao HL, Li MY, Liao XW, Dai W, Chen NP. Identify potential clinical significance of long noncoding RNA forkhead box P4 antisense RNA 1 in patients with early stage pancreatic ductal adenocarcinoma. Cancer Med 2020; 9:2062-2076. [PMID: 31991068 PMCID: PMC7064149 DOI: 10.1002/cam4.2818] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/04/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Previous studies have shown that forkhead box P4 antisense RNA 1 (FOXP4‐AS1) is dysregulated in tumor tissues and can serve as a prognostic indicator for multiple cancers. However, the clinical significance of FOXP4‐AS1 in pancreatic ductal adenocarcinoma (PDAC) remains unclear. The goal of this study is to recognize the possible clinical significance of long noncoding RNA FOXP4‐AS1 in patients with early stage PDAC. A total of 112 patients from The Cancer Genome Atlas (TCGA) PDAC cohort, receiving RNA sequencing, were involved in the study. Survival analysis, functional mechanism, and potential small molecule drugs of target therapy of FOXP4‐AS1 were performed in this study. Survival analysis in TCGA PDAC cohort suggested that patients with high FOXP4‐AS1 expression had significantly augmented possibility of death than in PDAC patients with lower FOXP4‐AS1 expression (adjusted P = .008; adjusted HR = 2.143, 95% CI = 1.221‐3.760). In this study, a genome‐wide RNA sequencing dataset was used to identify 927 genes co‐expressing with FOXP4‐AS1 in PDAC tumor tissues. A total of 676 differentially expressed genes were identified between different FOXP4‐AS1 expression groups. Functional enrichment analysis of these genes and gene set enrichment analysis for PDAC genome‐wide RNA sequencing dataset was done. We have found that FOXP4‐AS1 may function in PDAC by participating in biological processes and pathways including oxidative phosphorylation, tricarboxylic acid cycle, classical tumor‐related pathways such as NF‐kappaB as well as Janus kinase/signal transducers in addition to activators of transcription, cell proliferation, and adhesion. In addition, we also screened two potential targeted therapeutic small molecule drugs (dimenhydrinate and metanephrine) for FOXP4‐AS1 in PDAC. In conclusion, our present study demonstrated that higher expression of FOXP4‐AS1 in PDAC tumor tissues were related with an inferior medical outcome. Through multiple genome‐wide approaches, we identified the potential molecular mechanisms of FOXP4‐AS1 in PDAC and two targeted therapeutic drugs for it.
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Affiliation(s)
- Xiao-Guang Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Hao Xu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Ming Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Xiao-Yu Tan
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Xiao-Feng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Yong-Guang Yang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Man-Zhou Lin
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Guo-Hua Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Xiao-Lu Liang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Yi-Bin Qian
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Guo-Jia Yuan
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Min-Qiang Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Wen-Tao Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Hui-Lai Miao
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Ming-Yi Li
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Xi-Wen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei Dai
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
| | - Nian-Ping Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong Province, People's Republic of China
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