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Ghafouri-Fard S, Askari A, Hussen BM, Rasul MF, Taheri M, Ayatollahi SA. A review on the role of LINC00472 in malignant and non-malignant disorders. Pathol Res Pract 2023; 247:154549. [PMID: 37235910 DOI: 10.1016/j.prp.2023.154549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023]
Abstract
Long intergenic non-protein coding RNA 472 (LINC00472) has been shown to regulate diverse cellular functions and contribute to the etiology of human disorders. LINC00472 gene is located on 6q13 and has different alternatively spliced transcripts. Expression pattern and function of LINC00472 have been evaluated in different types of cancers and some other disorders, including atherosclerosis, sepsis-induced acute hepatic injury, atrial fibrillation, neuropathic pain, primary biliary cholangitis and sepsis-induced cardiac dysfunction. This lincRNA can serve as a sponge for miR-24-3p, miR-196b-5p, miR-23a-3p, miR-93-5p, miR-4311, miR-455-3p and a number of other miRNAs. LINC00472 is able to regulate several pathways, including MEK/ERK, NF-kB, PTEN/PI3K/AKT, and STAT3 signaling pathways. This raises some concerning aspects that need to be investigated further and clarified in relation to diseases. Increasing our understanding of LINC00472's crucial roles will open new doors for creating effective therapeutic approaches against cancer and related diseases. The current study aims at providing an overview of functions of LINC00472 in malignant and non-malignant disorders.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arian Askari
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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LINC00472 inhibits cell migration by enhancing intercellular adhesion and regulates H3K27ac level via interacting with P300 in renal clear cell carcinoma. Cell Death Dis 2022; 8:454. [PMID: 36371410 PMCID: PMC9653443 DOI: 10.1038/s41420-022-01243-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/14/2022]
Abstract
Renal clear cell carcinoma (RCCC) is the most common type of renal cell carcinoma, which is also difficult to diagnose and easy to metastasize. Currently, there is still a lack of effective clinical diagnostic indicators and treatment targets. This study aims to find effective diagnostic markers and therapeutic targets from the perspective of noncoding RNA. In this study, we found that the expression of Long noncoding RNA LINC00472 was significantly decreased in RCCC and showed a downward trend with the progression of cancer stage. Patients with low LINC00472 expression have poor prognosis. Inhibition of LINC00472 significantly increased cell proliferation and migration, while overexpression of LINC00472 obviously inhibited cell proliferation and enhanced intercellular adhesion. Transcriptome sequencing analysis demonstrated that LINC00472 was highly correlated with extracellular matrix and cell metastasis-related pathways, and the consistent results were obtained by The Cancer Genome Atlas (TCGA) data analysis. Additionally, we discovered that the integrin family protein ITGB8 is a potential target gene of LINC00472. Mechanistically, we found that the change of LINC00472 affected the acetylation level of H3K27 site in cells, and we speculate that this effect is likely to be generated through the interaction with acetyltransferase P300. In conclusion, LINC00472 has an important impact on the proliferation and metastasis of renal clear cells, and probably participate in the regulation of histone modification, and it may be used as a potential diagnostic marker of RCCC.
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Qian S, Lin S, Xu X, Bai H, Yeerken A, Ying X, Li Z, Fei X, Yang J, Tang M, Wang J, Jin M, Chen K. Hypermethylation of tumor suppressor lncRNA MEF2C-AS1 frequently happened in patients at all stages of colorectal carcinogenesis. Clin Epigenetics 2022; 14:111. [PMID: 36064442 PMCID: PMC9446566 DOI: 10.1186/s13148-022-01328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Background The novel long noncoding RNA MEF2C-AS1 has been identified to play suppressor roles during tumorigenesis. DNA methylation has a regulatory effect on gene expression in cancer initiation and progression. However, the methylation status of MEF2C-AS1 and its role in colorectal cancer (CRC) development remain unclear. Methods The expression and methylation levels of MEF2C-AS1 were systematically analyzed among 31 cancers with available qualified data in GEPIA and UCSC Xena databases. Then, the MEF2C-AS1 methylation status was firstly examined among 12 CRCs by Illumina Infinium MethylationEPIC BeadChip in in-house step 1 and further quantified among 48 CRCs by the MassARRAY method in in-house step 2. Subsequently, its methylation and expression levels were quantified among 81 non-advanced adenomas (NAAs), 81 advanced adenomas (AAs), and 286 CRCs using the MassARRAY method, and among 34 NAAs, 45 AAs, and 75 CRCs by qRT-PCR, in in-house step 3, respectively. The effect of MEF2C-AS1 methylation on CRC survival was analyzed by the Kaplan–Meier method. Additionally, in vitro cell proliferation, migration and invasion assays, and bioinformatics analysis were performed to explore the role of MEF2C-AS1 in colorectal carcinogenesis. Results Lower expression and higher methylation of MEF2C-AS1 were found in CRC by online databases. In the comparisons of lesion tissues with adjacent normal tissues, MEF2C-AS1 hypermethylation of each individual site and mean level was found among CRC patients in in-house step 1 and step 2, more meaningfully, among NAA patients, AA patients, and CRC patients at all stages during colorectal carcinogenesis in in-house step 3 (all p < 0.05). Further comparisons demonstrated significant differences between CRC and NAA (p = 0.025), AA and NAA (p = 0.020). Moreover, MEF2C-AS1 hypermethylation was associated with poorer disease-specific survival of CRC patients (p = 0.044). In addition, hypermethylation and lower expression of MEF2C-AS1 were verified in RKO cells, and the MEF2C-AS1 overexpression significantly suppressed RKO cell proliferation, migration, and invasion. Conclusions The findings reveal that MEF2C-AS1 hypermethylation might be an early driven event during colorectal carcinogenesis. It might serve as a promising prognostic biomarker for CRC survival. Our study also indicates the potential tumor-suppressing role of MEF2C-AS1 in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01328-1.
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Affiliation(s)
- Sangni Qian
- Department of Public Health, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Shujuan Lin
- Department of Public Health, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xin Xu
- Department of Public Health, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hao Bai
- Department of Public Health, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Aibuta Yeerken
- Department of Public Health, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Xiaojiang Ying
- Department of Anorectal Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Zhenjun Li
- Department of Anorectal Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Xinglin Fei
- Jiashan Institute of Cancer Prevention and Treatment, Jiaxing, 314100, China
| | - Jinhua Yang
- Jiashan Institute of Cancer Prevention and Treatment, Jiaxing, 314100, China
| | - Mengling Tang
- Department of Public Health, Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jianbing Wang
- Department of Public Health, National Clinical Research Center for Child Health of the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mingjuan Jin
- Department of Public Health, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Kun Chen
- Department of Public Health, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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Mao X, Zhou X, Liu J, Mao Y, Zhou H. Retracted: Up-regulated Linc00472 suppresses development of lung cancer cell via inhibition of MiR-196b-5p. Biosci Biotechnol Biochem 2022; 86:e1-e13. [PMID: 31791206 DOI: 10.1080/09168451.2019.1694404] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
The role of linc00472 in lung cancer (LC) has been rarely reported. We aimed to study the role of linc00472 in LC progression. Expressions of linc00472 and miR-196b-5p in LC cell lines were measured by qRT-PCR. The targeting relationship between linc00472 and miR-196b-5p was determined by Starbase and dual-luciferase reporter. The viability, migration, invasion, and apoptosis of LC cells were determined using CCK-8 assay, scratch test, transwell assay, and flow cytometry, respectively. The levels of epithelial-to-mesenchymal transition (EMT)-related proteins and apoptosis-related proteins in LC cells were determined by western blot. Down-regulated linc00472 was observed in five LC cell lines. Linc00472 overexpression suppressed viability, migration, invasion and EMT process, but elevated apoptotic rate in LC cells. MiR-196b-5p mimic promoted viability, migration, invasion, and EMT process, but decreased apoptotic rate, which was reversed by up-regulated linc00472. Linc00472 functioned as a cancer suppressor via negatively regulating miR-196b-5p of LC cells.
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Affiliation(s)
- Xiaoming Mao
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Jiangshan, Zhejiang, China
| | - Xiaohu Zhou
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Jiangshan, Zhejiang, China
| | - Jun Liu
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Jiangshan, Zhejiang, China
| | - Yiran Mao
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Jiangshan, Zhejiang, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang, China
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Seo D, Roh J, Chae Y, Kim W. Gene expression profiling after LINC00472 overexpression in an NSCLC cell line. Cancer Biomark 2021; 32:175-188. [PMID: 34397405 DOI: 10.3233/cbm-210242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lung cancer accounts for a large proportion of cancer-related deaths worldwide. Personalized therapeutic medicine based on the genetic characteristics of non-small cell lung cancer (NSCLC) is a promising field, and discovering clinically applicable biomarkers of NSCLC is required. LINC00472 is a long non-coding RNA and has been recently suggested to be a biomarker of NSCLC, but little is known of its mechanism in NSCLC. Thus, the current study was performed to document changes in gene expression after LINC00472 overexpression in NSCLC cells. As a result of cell viability and migration assay, LINC00472 downregulated cell survival, proliferation, and motility. Transcriptome sequencing analysis showed 3,782 genes expression were changed in LINC00472 overexpressing cells. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed most genes were associated with intracellular metabolism. The PPP1R12B, RGS5, RBM5, RBL2, LDLR and PTPRM genes were upregulated by LINC00472 overexpression and these genes functioned as tumor suppressors in several cancers. In contrast, SPSB1, PCNA, CD24, CDK5, CDC25A, and EIF4EBP1 were downregulated by LINC00472, and they functioned as oncogenes in various cancers. Consequently, the function of LINC00472 in tumorigenesis might be related to changes in the expressions of other oncogenes and tumor suppressors.
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Affiliation(s)
- Danbi Seo
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Jungwook Roh
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Yeonsoo Chae
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
| | - Wanyeon Kim
- Department of Science Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea.,Department of Biology Education, Korea National University of Education, Cheongju-si, Chungbuk, Republic of Korea
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Yu Y, Zhao Y, Wang C, Zhang X, Liu X. Long noncoding RNAs as diagnostic biomarkers for the early detection of digestive tract cancers: a systematic review and meta-analysis. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2021; 112:797-804. [PMID: 32338027 DOI: 10.17235/reed.2020.5450/2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND long noncoding RNAs (lncRNAs) have attracted attention recently. However, many inconsistencies frequently appeared for the early diagnosis of digestive tract cancers (DTCs). We performed this meta-analysis to describe the diagnostic performance of lncRNAs in the discrimination of DTCs. METHODS data were extracted from PubMed, Web of Science, Embase, and Cochrane Library. Their quality was evaluated using the revised Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2). Such parameters as sensitivity and specificity were included for pooled analyses. The STATA 12.0 and Meta-Disc 1.4 software packages were used to perform the statistical analysis. RESULTS sixty-nine papers were included in this meta-analysis. The pooled analysis of DTCs showed that lncRNAs had a sensitivity of 0.78 and a specificity of 0.80. The area under the summary ROC curve (AUC) was 0.86. For gastric cancer (GC), the pooled sensitivity and specificity were 0.77 (95 % CI: 0.72-0.81) and 0.75 (95 % CI: 0.71-0.79), respectively, and the AUC was 0.83. For colorectal cancer (CRC), these three parameters were 0.82 (95 % CI: 0.76-0.86), 0.84 (95 % CI: 0.79-0.88), and 0.90, respectively. For esophageal cancer (EC) sensitivity was 0.74 (95 % CI: 0.67-0.80) and specificity reached 0.86 (95 % CI: 0.72-0.93), with an AUC of 0.82. CONCLUSIONS LncRNAs show potential diagnostic value for discrimination between DTCs.
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Affiliation(s)
- Yinghui Yu
- School of Public Health, Jilin University, China
| | - Yinlong Zhao
- Department of Nuclear Medicine, the 2nd Hospital of Jilin University, China
| | - Chunpeng Wang
- School of Mathematics and Statistics, Northeast Normal University, China
| | | | - Xin Liu
- School of Public Health, Jilin University,
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Gao S, Wang Z. Comprehensive Analysis of Regulatory Network for LINC00472 in Clear Cell Renal Cell Carcinoma. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:3533608. [PMID: 34221297 PMCID: PMC8211516 DOI: 10.1155/2021/3533608] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/13/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022]
Abstract
Renal cell carcinoma (RCC) accounts for about 2% to 3% of adult malignancies, and clear cell renal cell carcinoma (ccRCC) is the most common and aggressive type of kidney cancer. It accounts for 75% of all kidney tumors. Although new targeted drugs continue to appear, they are still not suitable for all patients. Therefore, an in-depth study of the molecular mechanism of the development of ccRCC and exploration of new targets for the treatment of ccRCC will help to achieve precise treatment for ccRCC. With the development of molecular research, the study of long noncoding RNA (LncRNA) has given us a new understanding of tumors. Although LncRNA does not encode proteins, it directly interacts with proteins in various signaling pathways and affects cell functions. Therefore, it is of great significance to study the mechanism of LncRNA in ccRCC. The expression level of Linc00472 in ccRCC tissues is significantly lower than adjacent normal tissues, and its low expression is closely related to Furman's high grade. The low expression of Linc00472 is associated with poor prognosis in patients with ccRCC. The results of protein interaction and functional enrichment analysis indicate that genes upregulated in renal clear cell carcinoma may play a major role. Analysis of target gene prediction results showed that Linc00472 may be used as ceRNA in the miR-24-3p-HLA-DPB1 pathway, miR-24-3p-CXCL9 pathway, miR-221-3p-C3aR1-VEGFR2 pathway, miR-17-5p-HLA-DQA1/HLA-DQB1 pathway, and miR-17-5p-C3aR1/C5aR1-VEGFR2 pathway which play important functions. In addition, the regulatory relationship between miR-24-3p and TNFR2 (TNFRSF1B), CD36, and COL4A1 should also be noted. The value of Linc00472 in the diagnosis and treatment of ccRCC is worthy of further study.
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Affiliation(s)
- Shuoze Gao
- Institute of Gansu Nephro-Urological Clinical Center, Department of Urology, Institute of Urology, Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
| | - Zhiping Wang
- Institute of Gansu Nephro-Urological Clinical Center, Department of Urology, Institute of Urology, Key Laboratory of Urological Disease of Gansu Province, Lanzhou University Second Hospital, Lanzhou, China
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Liao Q, Chen L, Zhang N, Xi Y, Hu S, Ng DM, Ahmed FYH, Zhao G, Fan X, Xie Y, Dai X, Jin Y, Ge J, Dong C, Zhang X, Guo J. Network analysis of KLF5 targets showing the potential oncogenic role of SNHG12 in colorectal cancer. Cancer Cell Int 2020; 20:439. [PMID: 32943987 PMCID: PMC7487661 DOI: 10.1186/s12935-020-01527-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/29/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND KLF5 is a member of the Kruppel-like factor, subfamily of zinc finger proteins that are involved in cancers. KLF5 functions as a transcription factor and regulates the diverse protein-coding genes (PCGs) in colorectal cancer (CRC). However, the long non-coding RNAs (lncRNAs) regulated by KLF5 in CRC are currently unknown. METHODS In this study, we first designed a computational pipeline to determine the PCG and lncRNA targets of KLF5 in CRC. Then we analyzed the motif pattern of the binding regions for the lncRNA targets. The regulatory co-factors of KLF5 were then searched for through bioinformatics analysis. We also constructed a regulatory network for KLF5 and annotated its functions. Finally, one of the KLF5 lncRNA targets, SNHG12, was selected to further explore its expression pattern and functions in CRC. RESULTS We were able to identify 19 lncRNA targets of KLF5 and found that the motifs of the lncRNA binding sites were GC-enriched. Next, we pinpointed the transcription factors AR and HSF1 as the regulatory co-factors of KLF5 through bioinformatics analysis. Then, through the analysis of the regulatory network, we found that KLF5 may be involved in DNA replication, DNA repair, and the cell cycle. Furthermore, in the cell cycle module, the SNHG12 up-regulating expression pattern was verified in the CRC cell lines and tissues, associating it to CRC invasion and distal metastasis. This indicates that SNHG12 may play a critical part in CRC tumorigenesis and progression. Additionally, expression of SNHG12 was found to be down-regulated in CRC cell lines when KLF5 expression was knocked-down by siRNA; and a strong correlation was observed between the expression levels of SNHG12 and KLF5, further alluding to their regulatory relationship. CONCLUSIONS In conclusion, the network analysis of KLF5 targets indicates that SNHG12 may be a significant lncRNA in CRC.
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Affiliation(s)
- Qi Liao
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Linbo Chen
- Department of Gastroenterology, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040 Zhejiang China
| | - Ning Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080 China
| | - Yang Xi
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Shiyun Hu
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Derry Minyao Ng
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Fatma Yislam Hadi Ahmed
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Guofang Zhao
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Xiaoxiang Fan
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Yangyang Xie
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Xiaoyu Dai
- Hua Mei Hospital, University of Chinese Academy of Science, Ningbo, 315000 China
| | - Yanping Jin
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, 315020 China
| | - Jiaxin Ge
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, 315020 China
| | - Changzheng Dong
- Department of Preventative Medicine, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
| | - Xinjun Zhang
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, 315020 China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211 Zhejiang China
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Liu Y, Wang H, Yang W, Qian Y. Prediction of Specific Subtypes and Common Markers of Non-Small Cell Lung Cancer Based on Competing Endogenous RNA Network. Med Sci Monit 2020; 26:e922280. [PMID: 32703928 PMCID: PMC7377007 DOI: 10.12659/msm.922280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background There are various pathological types of lung cancer, including squamous cell carcinoma and adenocarcinoma. Although both of them are lung cancers, there are significant differences in diagnosis, pathogenesis, location, imaging, metastasis, and treatment. According to the competing endogenous RNA (ceRNA) theory, long non-coding RNAs (lncRNAs) compete with encoding protein genes (mRNAs) to connect with miRNAs, thus affecting the level of mRNA. Material/Methods First, using the t test, we identified mRNAs and lncRNAs that have different expressions (fold change >2, P<0.01) in normal samples and in tumor samples. We calculated the significance of the shared miRNAs for mRNAs and lncRNAs by hypergeometric test (P<0.01). Further, mRNA and lncRNA pairs with co-expression relationships in cancer samples were used to establish ceRNA networks. Then, the random walk algorithm was used to optimize the specific ceRNA networks and identify potential prognostic markers of survival. Finally, we built a common ceRNA network to find markers of non-small-cell lung cancer. Results We identified some potential key markers, such as PVT1, LINC00472, CDKN2A, and FAM83B, in LUSC and HOXA11-AS, HNF1A-AS1, LINC00511, and HOTAIR in LUAD by analyzing the ceRNA networks. Moreover, a number of common ceRNA pairs, such as CDC25C/CDK1/RRM2-LINC00355, have been found, and they are also significant markers for tumor survival and prognosis. Conclusions In summary, the present study provides a comparative analysis in 2 kinds of lung cancer ceRNA networks. Some specific and common markers we predicted that may be of great importance for clinical diagnosis and treatment.
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Affiliation(s)
- Yao Liu
- Department of Thoracic Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China (mainland)
| | - Hao Wang
- Department of Thoracic Surgery, Mingzhou Hospital, Ningbo, Zhejiang, China (mainland)
| | - Wenhan Yang
- School of Basic Medicine, Shenzhen University Health Science Center, Shenzhen, Guangdong, China (mainland)
| | - Youhui Qian
- Department of Thoracic Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China (mainland)
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Ashrafizadeh M, Najafi M, Mohammadinejad R, Farkhondeh T, Samarghandian S. Flaming the fight against cancer cells: the role of microRNA-93. Cancer Cell Int 2020; 20:277. [PMID: 32612456 PMCID: PMC7325196 DOI: 10.1186/s12935-020-01349-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 06/15/2020] [Indexed: 12/14/2022] Open
Abstract
There have been attempts to develop novel anti-tumor drugs in cancer therapy. Although satisfying results have been observed at a consequence of application of chemotherapeutic agents, the cancer cells are capable of making resistance into these agents. This has forced scientists into genetic manipulation as genetic alterations are responsible for generation of a high number of cancer cells. MicroRNAs (miRs) are endogenous, short non-coding RNAs that affect target genes at the post-transcriptional level. Increasing evidence reveals the potential role of miRs in regulation of biological processes including angiogenesis, metabolism, cell proliferation, cell division, and cell differentiation. Abnormal expression of miRs is associated with development of a number of pathologic events, particularly cancer. MiR-93 plays a significant role in both physiological and pathological mechanisms. At the present review, we show how this miR dually affects the proliferation and invasion of cancer cells. Besides, we elucidate the oncogenesis or oncosuppressor function of miR-93.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Mohammadinejad
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Tahereh Farkhondeh
- Cardiovascular Diseases Research Center, Birjand University of Medical Sciences, Birjand, Iran
| | - Saeed Samarghandian
- Healthy Ageing Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
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11
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Xu X, Gong C, Wang Y, Hu Y, Liu H, Fang Z. Multi-omics analysis to identify driving factors in colorectal cancer. Epigenomics 2020; 12:1633-1650. [PMID: 32573269 DOI: 10.2217/epi-2020-0073] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: We aim to identify driving genes of colorectal cancer (CRC) through multi-omics analysis. Materials & methods: We downloaded multi-omics data of CRC from The Cancer Genome Atlas dataset. Integrative analysis of single-nucleotide variants, copy number variations, DNA methylation and differentially expressed genes identified candidate genes that carry CRC risk. Kernal genes were extracted from the weighted gene co-expression network analysis. A competing endogenous RNA network composed of CRC-related genes was constructed. Biological roles of genes were further investigated in vitro. Results: We identified LRRC26 and REP15 as novel prognosis-related driving genes for CRC. LRRC26 hindered tumorigenesis of CRC in vitro. Conclusion: Our study identified novel driving genes and may provide new insights into the molecular mechanisms of CRC.
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Affiliation(s)
- Xi Xu
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China
| | - Chaoju Gong
- Central Laboratory, The Municipal Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221106, PR China
| | - Yunfeng Wang
- Institute for Integrative Biology of the Cell, UMR 9198, CNRS, Commissariat à l'Energie Atomique et aux Énergies Alternatives (CEA), Université Paris-Sud, 91198 Gif-sur-Yvette, Palaiseau, 91120, France
| | - Yanyan Hu
- Central Laboratory, Sanmen People's Hospital of Zhejiang Province, Sanmen, 317100, PR China
| | - Hong Liu
- Zhejiang Normal University - Jinhua People's Hospital Joint Center for Biomedical Research, Jinhua, 321004, PR China.,The Affiliated Hospital of Jinhua Polytechnic College, Jinhua, 321000, PR China
| | - Zejun Fang
- Central Laboratory, Sanmen People's Hospital of Zhejiang Province, Sanmen, 317100, PR China.,Central Laboratory, Sanmenwan Branch, The First Affiliated Hospital, College of Medicine, Zhejiang University, Sanmen, 317100, PR China
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12
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Li L, Qi F, Wang K. Matrine Restrains Cell Growth and Metastasis by Up-Regulating LINC00472 in Bladder Carcinoma. Cancer Manag Res 2020; 12:1241-1251. [PMID: 32110098 PMCID: PMC7035902 DOI: 10.2147/cmar.s224701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/08/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose Bladder Carcinoma (BC) is a malignant carcinoma with a high incidence in masculinity. We preliminarily researched the efficacy and mechanism of matrine (MAT) in T24 and 5637 cells. Patients and Methods CCK-8, flow cytometry, migration and invasion means were adopted to detect cell viability, apoptosis, migratory and invasive potentials. Moreover, LINC00472 expression was changed via transfection assays and was tested by RT-qPCR. Western blot was used for investigating the levels of CyclinD1, p53, Bcl-2, Bax, pro-Caspase-3, Cleaved-Caspase-3, β-actin, programmed cell death protein 4 (PDCD4) and relate-proteins of cell pathways. Tumor volume and weight were tested via animal experiments. Results MAT could not affect the growth of SV-HUC-1 cell but MAT promoted tumor cell apoptosis but restrained viability, invasion and migration. Furthermore, LINC00472 was prominently low expressed in BC tissues. MAT positively regulated LINC00472 and transfection with si-00472 could partly reverse the efficacies of MAT. Moreover, MAT enhanced PDCD4 expression by up-regulating LINC00472. Besides, we discovered MAT elevated PTEN but restrained PI3K/AKT proteins. Finally, tumor volume and weight were declined by MAT in vivo via up-regulating LINC00472. Conclusion MAT restrained cell growth and metastasis but promoted PDCD4 expression by up-regulating LINC00472 via restraining PTEN/PI3K/AKT pathway in BC.
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Affiliation(s)
- Linlin Li
- Department of Operating Room, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, People's Republic of China
| | - Fei Qi
- Department of Operating Room, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, People's Republic of China
| | - Kaichen Wang
- Department of Urinary Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, Jilin, People's Republic of China
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13
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Wang LY, Shen H, Yang Q, Min J, Wang Q, Xi W, Yin L, Le SG, Zhang YF, Xiao J, Wang ZN, Ji GY. LncRNA-LINC00472 contributes to the pathogenesis of atrial fibrillation (Af) by reducing expression of JP2 and RyR2 via miR-24. Biomed Pharmacother 2019; 120:109364. [DOI: 10.1016/j.biopha.2019.109364] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/31/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
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14
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Chen C, Zheng Q, Kang W, Yu C. Long non-coding RNA LINC00472 suppresses hepatocellular carcinoma cell proliferation, migration and invasion through miR-93-5p/PDCD4 pathway. Clin Res Hepatol Gastroenterol 2019; 43:436-445. [PMID: 30522853 DOI: 10.1016/j.clinre.2018.11.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 10/10/2018] [Accepted: 11/14/2018] [Indexed: 02/04/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most prevalent cancer and the second leading cause of cancer-related deaths. In the present study, we have demonstrated that long non-coding RNA (lncRNA) LINC00472 was low expressed in human HCC tissues and cell lines compared with adjacent non-tumor liver tissues and normal liver cell lines respectively. LINC00472 was also low expressed in HCC tissues from patients with metastasis compared with tissues from patients without metastasis. Expression level of LINC00472 was positively correlated with patient overall survival (OS) rate. Forced expression of LINC00472 suppressed cell proliferation, migration, invasion and promoted cell apoptosis in HCC cells Huh-7 and SMMC-7721. MiR-93-5p was a direct target of LINC00472, and miR-93-5p directly targeted PDCD4. The miR-93-5p/PDCD4 pathway mediated the suppressing role of LINC00472 in HCC cells. Therefore, LINC00472 was an important tumor suppressor in human HCC, which could be used as a bio-marker for HCC therapy.
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Affiliation(s)
- Changyu Chen
- Department of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital of Anhui Medical University, 218, Jixi avenue, Hefei 230022, Anhui, PR China
| | - Qiang Zheng
- Department of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital of Anhui Medical University, 218, Jixi avenue, Hefei 230022, Anhui, PR China
| | - Weibiao Kang
- Department of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital of Anhui Medical University, 218, Jixi avenue, Hefei 230022, Anhui, PR China
| | - Changjun Yu
- Department of Gastrointestinal Surgery, Department of General Surgery, First Affiliated Hospital of Anhui Medical University, 218, Jixi avenue, Hefei 230022, Anhui, PR China.
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15
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Cai J, Zuo X, Chen Z, Zhang Y, Wang J, Wang J, Ye X, Zhao W. Long Noncoding RNAs Serve as Potential Diagnostic Biomarkers for Colorectal Cancer. J Cancer 2019; 10:611-619. [PMID: 30719158 PMCID: PMC6360435 DOI: 10.7150/jca.28780] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/08/2018] [Indexed: 12/24/2022] Open
Abstract
Background: Mounting evidence has indicated that long noncoding RNAs (lncRNAs) are promising candidates for tumor diagnosis and prognosis. Nonetheless, the significance of lncRNAs in colorectal cancer (CRC) diagnosis remains to be clarified. Here, we performed a comprehensive meta-analysis to evaluate the utility of lncRNAs as diagnostic indicators for CRC. Materials and Methods: Pertinent studies were searched using PubMed, PMC, Web of Science, Cochrane, and EMBASE database up to September 2018. Study quality was assessed with the Quality Assessment for Studies of Diagnostic Accuracy-2. Subgroup analyses by sample size and publication year were conducted. Threshold effect and meta-regression were performed to find the origin of heterogeneity. Statistical analyses were conducted using Stata and Meta-Disc. Results: A total of 19 studies with 3,114 individuals were enrolled in the current analysis. The overall sensitivity and specificity of lncRNAs in the diagnosis of CRC were 0.83 [95% confidence interval (CI): 0.76-0.87] and 0.84 (95% CI: 0.77-0.89), respectively. The pooled positive likelihood ratio was 5.11 (95% CI: 3.57-7.31), and the pooled negative likelihood ratio was 0.21 (95% CI: 0.15-0.28). The overall area under the curve was 0.90 (95% CI: 0.87-0.92), with a diagnostic odds ratio of 24.57 (95% CI: 14.67-41.17). Conclusions: The accuracy of lncRNAs for CRC diagnosis is high, and lncRNAs could be functioned as promising candidates for CRC diagnosis.
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Affiliation(s)
- Juan Cai
- Department of Oncology, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
| | - Xueliang Zuo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China.,Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing 210029, China
| | - Zhiqiang Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing 210029, China
| | - Yao Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing 210029, China
| | - Jinguo Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
| | - Junfeng Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
| | - Xiaobing Ye
- Department of Oncology, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
| | - Wenying Zhao
- Department of Oncology, The First Affiliated Hospital, Yijishan Hospital of Wannan Medical College, Wuhu 241000, China
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16
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Ye Y, Yang S, Han Y, Sun J, Xv L, Wu L, Wang Y, Ming L. Linc00472 suppresses proliferation and promotes apoptosis through elevating PDCD4 expression by sponging miR-196a in colorectal cancer. Aging (Albany NY) 2018; 10:1523-1533. [PMID: 29930217 PMCID: PMC6046238 DOI: 10.18632/aging.101488] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/16/2018] [Indexed: 12/19/2022]
Abstract
Long intergenic non-coding RNA Linc00472 has been considered as a tumor suppressor in some cancers. However, the function and mechanism of Linc00472 in colorectal cancer has not been well elucidated. In this study, we found that Linc00472 was down-regulated in colorectal cancer tissues and cells. Elevated Linc00472 expression suppressed proliferation and induced apoptosis in colorectal cancer cells. Moreover, Linc00472 acted as a competing endogenous RNA (ceRNA) of miR-196a to release programmed cell death 4 (PDCD4). Furthermore, miR-196a overexpression or PDCD4 knockdown reversed Linc00472-mediated proliferation inhibition and apoptosis induction in colorectal cancer cells. Ectopic Linc00472 expression hindered tumor growth in vivo. Our study demonstrated that Linc00472 suppressed proliferation and induced apoptosis through up-regulating PDCD4 by decoying miR-196a, which may be an effective therapeutic target for colorectal cancer.
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Affiliation(s)
- Yafei Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Shengnan Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Yanping Han
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Jingjing Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Lijuan Xv
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Lina Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Yongfeng Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Henan, Zhengzhou 450000, China
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