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Roshan-Zamir M, Khademolhosseini A, Rajalingam K, Ghaderi A, Rajalingam R. The genomic landscape of the immune system in lung cancer: present insights and continuing investigations. Front Genet 2024; 15:1414487. [PMID: 38983267 PMCID: PMC11231382 DOI: 10.3389/fgene.2024.1414487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 06/07/2024] [Indexed: 07/11/2024] Open
Abstract
Lung cancer is one of the most prevalent malignancies worldwide, contributing to over a million cancer-related deaths annually. Despite extensive research investigating the genetic factors associated with lung cancer susceptibility and prognosis, few studies have explored genetic predispositions regarding the immune system. This review discusses the most recent genomic findings related to the susceptibility to or protection against lung cancer, patient survival, and therapeutic responses. The results demonstrated the effect of immunogenetic variations in immune system-related genes associated with innate and adaptive immune responses, cytokine, and chemokine secretions, and signaling pathways. These genetic diversities may affect the crosstalk between tumor and immune cells within the tumor microenvironment, influencing cancer progression, invasion, and prognosis. Given the considerable variability in the individual immunegenomics profiles, future studies should prioritize large-scale analyses to identify potential genetic variations associated with lung cancer using highthroughput technologies across different populations. This approach will provide further information for predicting response to targeted therapy and promotes the development of new measures for individualized cancer treatment.
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Affiliation(s)
- Mina Roshan-Zamir
- School of Medicine, Shiraz Institute for Cancer Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Khademolhosseini
- School of Medicine, Shiraz Institute for Cancer Research, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Kavi Rajalingam
- Cowell College, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Abbas Ghaderi
- School of Medicine, Shiraz Institute for Cancer Research, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, University of California San Francisco, San Francisco, CA, United States
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Qian W, Yang L, Li T, Li W, Zhou J, Xie S. RNA modifications in pulmonary diseases. MedComm (Beijing) 2024; 5:e546. [PMID: 38706740 PMCID: PMC11068158 DOI: 10.1002/mco2.546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 02/26/2024] [Accepted: 03/14/2024] [Indexed: 05/07/2024] Open
Abstract
Threatening public health, pulmonary disease (PD) encompasses diverse lung injuries like chronic obstructive PD, pulmonary fibrosis, asthma, pulmonary infections due to pathogen invasion, and fatal lung cancer. The crucial involvement of RNA epigenetic modifications in PD pathogenesis is underscored by robust evidence. These modifications not only shape cell fates but also finely modulate the expression of genes linked to disease progression, suggesting their utility as biomarkers and targets for therapeutic strategies. The critical RNA modifications implicated in PDs are summarized in this review, including N6-methylation of adenosine, N1-methylation of adenosine, 5-methylcytosine, pseudouridine (5-ribosyl uracil), 7-methylguanosine, and adenosine to inosine editing, along with relevant regulatory mechanisms. By shedding light on the pathology of PDs, these summaries could spur the identification of new biomarkers and therapeutic strategies, ultimately paving the way for early PD diagnosis and treatment innovation.
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Affiliation(s)
- Weiwei Qian
- Emergency Department of Emergency MedicineLaboratory of Emergency Medicine, West China Hospital, And Disaster Medical, Sichuan UniversityChengduSichuanChina
- Emergency DepartmentShangjinnanfu Hospital, West China Hospital, Sichuan UniversityChengduSichuanChina
| | - Lvying Yang
- The Department of Respiratory and Critical Care MedicineThe First Veterans Hospital of Sichuan ProvinceChengduSichuanChina
| | - Tianlong Li
- Department of Critical Care Medicine Sichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuanChina
| | - Wanlin Li
- National Clinical Research Center for Infectious Disease, Shenzhen Third People's HospitalShenzhenGuangdongChina
| | - Jian Zhou
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National‐Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical SchoolShenzhenChina
- Department of ImmunologyInternational Cancer Center, Shenzhen University Health Science CenterShenzhenGuangdongChina
| | - Shenglong Xie
- Department of Thoracic SurgerySichuan Provincial People's Hospital, University of Electronic Science and Technology of ChinaChengduSichuanChina
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Zhai S, Li X, Lin T. Obese Mouse Fat Cell-derived Extracellular Vesicles Transport miR-99a-5p to Mitigate the Proliferation and Migration of Non-small Cell Lung Cancer Cells. Comb Chem High Throughput Screen 2024; 27:214-226. [PMID: 36927435 DOI: 10.2174/1386207326666230316103604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/29/2022] [Accepted: 01/20/2023] [Indexed: 03/18/2023]
Abstract
OBJECTIVE Fat cells-derived extracellular vesicles (FC-EVs) play a role in regulating the tumor microenvironment in cancers by transporting RNAs. MicroRNAs (miRNAs) are vital regulators of cancer development. This study was conducted to explore the role of FC-EVs in the proliferation and migration of non-small cell lung cancer (NSCLC) cells, providing targets for NSCLC treatment. METHODS The obese mouse model was established via high-fat diet (HFD), followed by separation and characterization of FC-EVs (HFD-EVs). The levels of miR-99a-5p, precursor-miR-99a-5p, and heparan sulfate-glucosamine 3-sulfotransferase 3B1 (HS3ST3B1) were measured by RT-qPCR or Western blot assay. Cell proliferation and migration were evaluated by 3-(4, 5-dimethylthiazol- 2-yl)-2, 5-diphenyltetrazolium bromide and wound healing assays. The expression of Cy3-labeled miR-99a-5p in A549 cells (one NSCLC cell line) was observed via confocal microscopy. The binding of miR-99a-5p to HS3ST3B1 was analyzed by the dual luciferase assay. Rescue experiments were performed to confirm the role of HS3ST3B1 in NSCLC cells. RESULTS miR-99a-5p was upregulated in adipose tissues, FCs, and HFD-EVs. HFD-EVs mitigated the proliferation and migration of NSCLC cells. HFD-EVs transported miR-99a-5p into A549 cells, which upregulated miR-99a-5p expression and inhibited HS3ST3B1 expression in A549 cells. HS3ST3B1 overexpression reversed the inhibition of HFD-EVs on the proliferation and migration of NSCLC cells. CONCLUSION HFD-EVs transported miR-99a-5p into NSCLC cells and inhibited HS3ST3B1, thereby inhibiting proliferation and migration of NSCLC cells.
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Affiliation(s)
- Shengping Zhai
- Department of General Practice, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, 264000, China
| | - Xiaoping Li
- Department of Pulmonary and Critical Care Medicine, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, 264000, China
| | - Tiantian Lin
- Respiratory Intensive Care Unit, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, 264000, China
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Liu T, Yu S, Hu T, Ji W, Cheng X, Lv L, Shi Z. Comprehensive analyses of genome-wide methylation and RNA epigenetics identify prognostic biomarkers, regulating the tumor immune microenvironment in lung adenocarcinoma. Pathol Res Pract 2023; 248:154621. [PMID: 37336075 DOI: 10.1016/j.prp.2023.154621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
The aim of our study was to identify a signature of immune-regulated molecules and reveal its prognostic role in lung adenocarcinoma (LUAD). We downloaded RNA-Sequencing data and DNA methylation data from the Gene Expression Omnibus (GEO) database. GEO2R was used to analyze differentially expressed mRNAs (DEmRNAs). we used "factoextra" R package to do the principal component analysis (PCA) of DEmRNAs. "Limma" R package was used to identify DEmRNAs, differentially expressed miRNAs (DEmiRNAs), differentially expressed lncRNAs (DElncRNAs) from The Cancer Genome Atlas (TCGA) database. Three R packages "org.Hs.eg.db", "clusterProfiler", "ggplot2″ were used to show enrichment results. Considering about methylation and mutation data, TEK and SOX17 mediated cancer signaling pathways. Through tumor-immune system interactions database (TISIDB) and Tumor Immune Estimation Resource (TIMER), higher methylated and lower expressed TEK may act as a prognostic marker, regulating the tumor immunity in LUAD. Through four databases (MEXPRESS, DNMIVD, MethSurv, Firehose), we further verified the methylation (P = 2.33e-23) and mutation about TEK. A signature of immune-associated TEK to predict survival of LUAD patients was validated. Prognostic, methylation, immune microenvironment analysis showed new light on potential novel therapeutic targets in LUAD.
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Affiliation(s)
- Tingting Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuo Yu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.; Department of General Surgery, The Second Affiliated Hospital of Xi'an Jiaotong, University, Xi'an, Shaanxi 710000, China
| | - Tinghua Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Wen Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xue Cheng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Lin Lv
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhihong Shi
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China..
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Wang X, Guo Z, Yan F. RNA Epigenetics in Chronic Lung Diseases. Genes (Basel) 2022; 13:genes13122381. [PMID: 36553648 PMCID: PMC9777603 DOI: 10.3390/genes13122381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including N6 methylation of adenosine (m6A), N1 methylation of adenosine (m1A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), 2'O-methylation (2'-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.
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Affiliation(s)
- Xiaorui Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Zhihou Guo
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Furong Yan
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
- Correspondence:
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del Valle-Morales D, Le P, Saviana M, Romano G, Nigita G, Nana-Sinkam P, Acunzo M. The Epitranscriptome in miRNAs: Crosstalk, Detection, and Function in Cancer. Genes (Basel) 2022; 13:genes13071289. [PMID: 35886072 PMCID: PMC9316458 DOI: 10.3390/genes13071289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
The epitranscriptome encompasses all post-transcriptional modifications that occur on RNAs. These modifications can alter the function and regulation of their RNA targets, which, if dysregulated, result in various diseases and cancers. As with other RNAs, miRNAs are highly modified by epitranscriptomic modifications such as m6A methylation, 2′-O-methylation, m5C methylation, m7G methylation, polyuridine, and A-to-I editing. miRNAs are a class of small non-coding RNAs that regulates gene expression at the post-transcriptional level. miRNAs have gathered high clinical interest due to their role in disease, development, and cancer progression. Epitranscriptomic modifications alter the targeting, regulation, and biogenesis of miRNAs, increasing the complexity of miRNA regulation. In addition, emerging studies have revealed crosstalk between these modifications. In this review, we will summarize the epitranscriptomic modifications—focusing on those relevant to miRNAs—examine the recent crosstalk between these modifications, and give a perspective on how this crosstalk expands the complexity of miRNA biology.
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Affiliation(s)
- Daniel del Valle-Morales
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Michela Saviana
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giovanni Nigita
- Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
- Correspondence:
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Jiang M, Qi F, Zhang K, Zhang X, Ma J, Xia S, Chen L, Yu Z, Chen J, Chen D. MARCKSL1-2 reverses docetaxel-resistance of lung adenocarcinoma cells by recruiting SUZ12 to suppress HDAC1 and elevate miR-200b. Mol Cancer 2022; 21:150. [PMID: 35864549 PMCID: PMC9306054 DOI: 10.1186/s12943-022-01605-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are implicated in the development of multiple cancers. In our previous study, we demonstrated that HDAC1/4-mediated silencing of microRNA-200b (miR-200b) enhances docetaxel (DTX)-resistance of human lung adenocarcinoma (LAD) cells. Methods and results Herein, we probed the function of LncRNA MARCKSL1–2 (MARCKSL1-transcript variant 2, NR_052852.1) in DTX resistance of LAD cells. It was found that MARCKSL1–2 expression was markedly reduced in DTX-resistant LAD cells. Through gain- or loss- of function assays, colony formation assay, EdU assay, TUNEL assay, and flow cytometry analysis, we found that MARCKSL1–2 suppressed the growth and DTX resistance of both parental and DTX-resistant LAD cells. Moreover, we found that MARCKSL1–2 functioned in LAD through increasing miR-200b expression and repressing HDAC1. Mechanistically, MARCKSL1–2 recruited the suppressor of zeste 12 (SUZ12) to the promoter of histone deacetylase 1 (HDAC1) to strengthen histone H3 lysine 27 trimethylation (H3K27me3) of HDAC1 promoter, thereby reducing HDAC1 expression. MARCKSL1–2 up-regulated miR-200b by blocking the suppressive effect of HDAC1 on the histone acetylation modification at miR-200b promoter. Furthermore, in vivo analysis using mouse xenograft tumor model supported that overexpression of MARCKSL1–2 attenuated the DTX resistance in LAD tumors. Conclusions We confirmed that MARCKSL1–2 alleviated DTX resistance in LAD cells by abolishing the inhibitory effect of HDAC1 on miR-200b via the recruitment of SUZ12. MARCKSL1–2 could be a promising target to improve the chemotherapy of LAD. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01605-w.
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Affiliation(s)
- Min Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China
| | - Feng Qi
- Department of Pharmacy, The Fourth Affiliated Hospital of Nantong University, Yancheng, 224005, Jiangsu, China
| | - Kai Zhang
- Department of Respiratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, 210006, Jiangsu, China
| | - Xiaofei Zhang
- Department of Medical Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Pudong New District, Shanghai, 200127, China
| | - Jingjing Ma
- Department of Pharmacy, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China
| | - Suhua Xia
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China
| | - Longbang Chen
- Department of Medical Oncology, Nanjing Jinling Hospital, School of Medicine, Nanjing University, Nanjing, 210008, Jiangsu, China
| | - Zhengyuan Yu
- Department of Medical Oncology, The First Affiliated Hospital of Soochow University, No.188 Shizi Street, Gusu District, Suzhou, 215006, Jiangsu, China.
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, No.138 Xianlin Avenue, Nanjing, 210023, Jiangsu, China.
| | - Dongqin Chen
- Department of Medical Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Pudong New District, Shanghai, 200127, China. .,Department of Medical Oncology, Baoshan Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.1058 Huanzhen North Road, Baoshan District, Shanghai, 200444, China. .,Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, No.42 Baiziting Road, Xuanwu District, Nanjing, 210009, Jiangsu, China.
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Sun B, Zhao H. Bioinformatics Analysis of Differential Gene and MicroRNA Expression in Lung Adenocarcinoma: Genetic Effects on Patient Prognosis, as Indicated by the TCGA Database. Cancer Inform 2022; 21:11769351221082020. [PMID: 35342284 PMCID: PMC8943533 DOI: 10.1177/11769351221082020] [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: 11/06/2021] [Accepted: 01/26/2022] [Indexed: 12/24/2022] Open
Abstract
Objective: To investigate the differential expression of genes and microRNAs (miRNAs) in patients with lung adenocarcinoma and the relationship between such changes and patient prognosis. Methods: We analyzed the expression levels of genes and miRNAs in lung adenocarcinoma tissues and adjacent normal tissues using The Cancer Genome Atlas database (TCGA). We analyzed the function of the differentially expressed genes and miRNAs in a co-expression network. Finally, we performed survival analysis of differential genes and miRNAs in the co-expression network using clinical data from the TCGA database. Results: We successfully identified 6064 differentially expressed genes: 5324 upregulated genes and 740 downregulated genes. And we identified 161 differentially expressed miRNAs: 126 upregulated miRNAs and 35 downregulated miRNAs. We identified several genes that were related to each other in the co-expression network. Further analysis revealed that the high expression levels of G6PC, APOB, F2, PAQR9, and PAQR9-AS1 genes were associated with poor prognosis. However, there was no significant correlation between the expression of hsa-mir-122 with regards to patient prognosis. Conclusions: Our data showed that hsa-mir-122 and a number of related genes may affect the prognosis of patients with lung adenocarcinoma by regulating the cytoskeleton, thus promoting tumor angiogenesis and the metastasis of tumor cells. The high expression levels of some differentially expressed genes was associated with the low survival rate in patients with lung adenocarcinoma. However, the levels of hsa-mir-122 were not correlated with patient prognosis.
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Affiliation(s)
- Bingqing Sun
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Hongwen Zhao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of China Medical University, Shenyang, China
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RNA Modifications and Epigenetics in Modulation of Lung Cancer and Pulmonary Diseases. Int J Mol Sci 2021; 22:ijms221910592. [PMID: 34638933 PMCID: PMC8508636 DOI: 10.3390/ijms221910592] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/18/2021] [Accepted: 09/20/2021] [Indexed: 11/21/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide, and its tumorigenesis involves the accumulation of genetic and epigenetic events in the respiratory epithelium. Epigenetic modifications, such as DNA methylation, RNA modification, and histone modifications, have been widely reported to play an important role in lung cancer development and in other pulmonary diseases. Whereas the functionality of DNA and chromatin modifications referred to as epigenetics is widely characterized, various modifications of RNA nucleotides have recently come into prominence as functionally important. N6-methyladosine (m6A) is the most prevalent internal modification in mRNAs, and its machinery of writers, erasers, and readers is well-characterized. However, several other nucleotide modifications of mRNAs and various noncoding RNAs have also been shown to play an important role in the regulation of biological processes and pathology. Such epitranscriptomic modifications play an important role in regulating various aspects of RNA metabolism, including transcription, translation, splicing, and stability. The dysregulation of epitranscriptomic machinery has been implicated in the pathological processes associated with carcinogenesis including uncontrolled cell proliferation, migration, invasion, and epithelial-mesenchymal transition. In recent years, with the advancement of RNA sequencing technology, high-resolution maps of different modifications in various tissues, organs, or disease models are being constantly reported at a dramatic speed. This facilitates further understanding of the relationship between disease development and epitranscriptomics, shedding light on new therapeutic possibilities. In this review, we summarize the basic information on RNA modifications, including m6A, m1A, m5C, m7G, pseudouridine, and A-to-I editing. We then demonstrate their relation to different kinds of lung diseases, especially lung cancer. By comparing the different roles RNA modifications play in the development processes of different diseases, this review may provide some new insights and offer a better understanding of RNA epigenetics and its involvement in pulmonary diseases.
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Magnaye KM, Naughton KA, Huffman J, Hogarth DK, Naureckas ET, White SR, Ober C. A-to-I editing of miR-200b-3p in airway cells is associated with moderate-to-severe asthma. Eur Respir J 2021; 58:13993003.03862-2020. [PMID: 33446603 DOI: 10.1183/13993003.03862-2020] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/19/2020] [Indexed: 11/05/2022]
Abstract
BACKGROUND Asthma is a chronic lung disease characterised by persistent airway inflammation. Altered microRNA (miRNA)-mediated gene silencing in bronchial epithelial cells (BECs) has been reported in asthma, yet adenosine deaminase acting on RNA (ADAR)-mediated miRNA editing in asthma remains unexplored. METHODS We first identified adenosine to inosine (A-to-I) edited sites in miRNAs in BECs from 142 adult asthma cases and controls. A-to-I edited sites were tested for associations with asthma severity and clinical measures of asthma. Paired RNA sequencing data were used to perform pathway enrichments and test for associations with bioinformatically predicted target genes of the unedited and edited miRNAs. RESULTS Of 19 A-to-I edited sites detected in these miRNAs, one site at position 5 of miR-200b-3p was edited less frequently in cases compared with controls (pcorrected=0.013), and especially compared with cases with moderate (pcorrected=0.029) and severe (pcorrected=3.9×10-4), but not mild (pcorrected=0.38), asthma. Bioinformatic prediction revealed 232 target genes of the edited miR-200b-3p, which were enriched for both interleukin-4 and interferon-γ signalling pathways, and included the SOCS1 (suppressor of cytokine signalling 1) gene. SOCS1 was more highly expressed in moderate (pcorrected=0.017) and severe (pcorrected=5.4×10-3) asthma cases compared with controls. Moreover, both miR-200b-3p editing and SOCS1 were associated with bronchoalveolar lavage eosinophil levels. CONCLUSIONS Reduced A-to-I editing of position 5 of miR-200b-3p in lower airway cells from moderate-to-severe asthmatic subjects may lead to overexpression of SOCS1 and impaired cytokine signalling. We propose ADAR-mediated editing as an epigenetic mechanism contributing to features of moderate-to-severe asthma in adulthood.
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Affiliation(s)
- Kevin M Magnaye
- Dept of Human Genetics, University of Chicago, Chicago, IL, USA.,These two authors contributed equally to this article as lead authors and supervised the work
| | | | - Janel Huffman
- Dept of Human Genetics, University of Chicago, Chicago, IL, USA
| | - D Kyle Hogarth
- Dept of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Steven R White
- Dept of Medicine, University of Chicago, Chicago, IL, USA
| | - Carole Ober
- Dept of Human Genetics, University of Chicago, Chicago, IL, USA .,These two authors contributed equally to this article as lead authors and supervised the work
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Yang D, He Y, Wu B, Liu R, Wang N, Wang T, Luo Y, Li Y, Liu Y. Predictions of the dysregulated competing endogenous RNA signature involved in the progression of human lung adenocarcinoma. Cancer Biomark 2021; 29:399-416. [PMID: 32741804 DOI: 10.3233/cbm-200133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer worldwide. Until now, the molecular mechanisms underlying LUAD progression have not been fully explained. This study aimed to construct a competing endogenous RNA (ceRNA) network to predict the progression in LUAD. METHODS Differentially expressed lncRNAs (DELs), miRNAs (DEMs), and mRNAs (DEGs) were identified from The Cancer Genome Atlas (TCGA) database with a |log2FC|> 1.0 and a false discovery rate (FDR) < 0.05. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI) network, and survival analyses were performed to analyse these DEGs involved in the ceRNA network. Subsequently, the drug-gene interaction database (DGIdb) was utilized to select candidate LUAD drugs interacting with significant DEGs. Then, lasso-penalized Cox regression and multivariate Cox regression models were used to construct the risk score system. Finally, based on the correlations between DELs and DEGs involved in the risk score system, the final ceRNA network was identified. Meanwhile, the GEPIA2 database and immunohistochemical (IHC) results were utilized to validate the expression levels of selected DEGs. RESULTS A total of 340 DELs, 29 DEMs, and 218 DEGs were selected to construct the initial ceRNA network. Functional enrichment analyses indicated that 218 DEGs were associated with the KEGG pathway terms "microRNAs in cancer", "pathways in cancer", "cell cycle", "HTLV-1 infection", and the "PI3K-Akt signalling pathway". K-M survival analysis of all differentially expressed genes involved in the ceRNA network identified 24 DELs, 4 DEMs, and 29 DEGs, all of which were significantly correlated with LUAD progression (P< 0.05). Furthermore, 15 LUAD drugs interacting with 29 significant DEGs were selected. After lasso-penalized Cox regression and multivariate Cox regression modelling, PRKCE, DLC1, LATS2, and DPY19L1 were incorporated into the risk score system, and the results suggested that LUAD patients who had the high-risk score always suffered from a poorer overall survival. Additionally, the correlation coefficients between these 4 DEGs and their corresponding DELs involved in the ceRNA network suggested that there were 2 significant DEL-DEG pairs, NAV2-AS2 - PRKCE (r= 0.430, P< 0.001) and NAV2-AS2 - LATS2 (r= 0.338, P< 0.001). And NAV2-AS2 - mir-31 - PRKCE and NAV2-SA2 - mir-31 - LATS2 were finally identified as ceRNA network involved in the progression of LUAD. CONCLUSIONS The lncRNA-miRNA-mRNA ceRNA network plays an essential role in predicting the progression of LUAD. These results may improve our understanding and provide novel mechanistic insights to explore prognosis and therapeutic drugs for LUAD patients.
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Affiliation(s)
- Dan Yang
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China.,Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yang He
- Molecular Oncology Laboratory of Cancer Research Institute, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China.,Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Bo Wu
- Department of Anus and Intestine Surgery, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Ruxi Liu
- Department of Rheumatology and Immunology, The First Affiliated Hospital, China Medical University, Shenyang, Liaoning, China
| | - Nan Wang
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Tieting Wang
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yannan Luo
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yunda Li
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Yang Liu
- Department of Environmental Health, School of Public Health, China Medical University, Shenyang, Liaoning, China
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12
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MiR-379-5p targets microsomal glutathione transferase 1 (MGST1) to regulate human glioma in cell proliferation, migration and invasion and epithelial-mesenchymal transition (EMT). Biochem Biophys Res Commun 2021; 568:8-14. [PMID: 34171541 DOI: 10.1016/j.bbrc.2021.05.099] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 05/29/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Glioma is one of the most malignant tumors worldwide. This study was aimed to study the effect of miR-379-5p/MGST1 on cell proliferation, migration, invasion and EMT in glioma. METHODS RT-qPCR detected the expression of miR-379-5p and MGST1 in RNA level in glioma cell lines. Bioinformatic analysis was made to explore the associations between miR-379-5p and MGST1 while survival analysis was made with regards to MGST1 expression in glioma patients. Western blot analysis was applied to measure the EMT changes. MTT examined the cell viability. Transwell was used to detect the cellular invasion and migration. The binding sites between miR-379-5p and MGST1 were validated by luciferase reporter assays. RESULTS miR-379-5p expression was lower in glioma cells. MiR-379-5p increase inhibited the viability, migration, invasion and EMT while inhibition of miR-379-5p showed a reverse effect. MGST1 inhibition curbed the cell functions. MiR-379-5p targeted and regulated MGST1 expression. Lower MGST1 is related to higher survival rate. CONCLUSION miR-379-5p could regulate glioma cell viability, migration, invasion and EMT through MGST1, suggesting that miR-379-5p/MGST1 axis might function in the regulation of glioma progression.
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13
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Le P, Romano G, Nana-Sinkam P, Acunzo M. Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer. Cancers (Basel) 2021; 13:cancers13061372. [PMID: 33803619 PMCID: PMC8003033 DOI: 10.3390/cancers13061372] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer.
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14
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Du H, Bao Y, Liu C, Zhong A, Niu Y, Tang X. miR‑139‑5p enhances cisplatin sensitivity in non‑small cell lung cancer cells by inhibiting cell proliferation and promoting apoptosis via the targeting of Homeobox protein Hox‑B2. Mol Med Rep 2021; 23:104. [PMID: 33300085 PMCID: PMC7723155 DOI: 10.3892/mmr.2020.11743] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/14/2020] [Indexed: 02/07/2023] Open
Abstract
The development of chemotherapeutic dug resistance hinders the clinical treatment of cancer. MicroRNAs (miRNAs/miRs) have been revealed to serve essential roles in the drug resistance of numerous types of cancer. miR‑139‑5p was previously reported to be associated with cisplatin (DDP) sensitivity in human nasopharyngeal carcinoma cells and colorectal cancer cells. However, the effect and underlying mechanism of miR‑139‑5p in DDP sensitivity in non‑small cell lung cancer (NSCLC) cells has not yet been fully elucidated. In the present study, the expression of miR‑139‑5p and Homeobox protein Hox‑B2 (HOXB2) in NSCLC tissues was examined by reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) and western blotting. Subsequently, the effect of miR‑139‑5p on the DDP sensitivity of NSCLC cells in vitro was investigated. Cell proliferation was examined using a Cell Counting Kit‑8 assay. Western blotting was used to evaluate the protein expression of HOXB2, phosphorylated (p)‑PI3K, p‑AKT, caspase‑3 and cleaved‑caspase‑3, and RT‑qPCR was used to evaluate the expression of miR‑139‑5p, and the mRNA expression levels of HOXB2, PI3K, AKT and caspase‑3. The apoptotic rate of the cells was detected using flow cytometry. miR‑139‑5p expression in NSCLC tissues was shown to be significantly lower compared with that in adjacent tissues. Additionally, miR‑139‑5p increased cell apoptosis and inhibited NSCLC cell proliferation induced by DDP in vitro via modulating the PI3K/AKT/caspase‑3 signaling pathway. Furthermore, HOXB2 was identified to be a target of miR‑139‑5p, and miR‑139‑5p was revealed to sensitize NSCLC cells to DDP via the targeting of HOXB2. Taken together, the results of the present study demonstrated that regulating the expression of miR‑139‑5p could provide a novel approach to reverse DDP resistance and increase chemosensitivity in the treatment of NSCLC.
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Affiliation(s)
- Hailian Du
- Department of Respiratory Medicine, Weifang Yidu Central Hospital, Weifang, Shandong 262500, P.R. China
| | - Ya'nan Bao
- Department of Thoracic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650000, P.R. China
| | - Chunying Liu
- Ultrasonic Department, Anqiu People's Hospital, Anqiu, Shandong 262100, P.R. China
| | - Anqiao Zhong
- Department of Respiratory Medicine, Weifang Yidu Central Hospital, Weifang, Shandong 262500, P.R. China
| | - Yikai Niu
- Department of Respiratory Medicine, Weifang Yidu Central Hospital, Weifang, Shandong 262500, P.R. China
| | - Xingping Tang
- Department of Respiratory Medicine, Weifang Yidu Central Hospital, Weifang, Shandong 262500, P.R. China
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Sima M, Rossnerova A, Simova Z, Rossner P. The Impact of Air Pollution Exposure on the MicroRNA Machinery and Lung Cancer Development. J Pers Med 2021; 11:60. [PMID: 33477935 PMCID: PMC7833364 DOI: 10.3390/jpm11010060] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
Small non-coding RNA molecules (miRNAs) play an important role in the epigenetic regulation of gene expression. As these molecules have been repeatedly implicated in human cancers, they have been suggested as biomarkers of the disease. Additionally, miRNA levels have been shown to be affected by environmental pollutants, including airborne contaminants. In this review, we searched the current literature for miRNAs involved in lung cancer, as well as miRNAs deregulated as a result of exposure to air pollutants. We then performed a synthesis of the data and identified those molecules commonly deregulated under both conditions. We detected a total of 25 miRNAs meeting the criteria, among them, miR-222, miR-21, miR-126-3p, miR-155 and miR-425 being the most prominent. We propose these miRNAs as biomarkers of choice for the identification of human populations exposed to air pollution with a significant risk of developing lung cancer.
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Affiliation(s)
- Michal Sima
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (M.S.); (Z.S.)
| | - Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic;
| | - Zuzana Simova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (M.S.); (Z.S.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague, Czech Republic; (M.S.); (Z.S.)
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16
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Katakura S, Kobayashi N, Hashimoto H, Kamimaki C, Tanaka K, Kubo S, Nakashima K, Teranishi S, Manabe S, Watanabe K, Horita N, Hara Y, Yamamoto M, Kudo M, Piao H, Kaneko T. MicroRNA-200b is a potential biomarker of the expression of PD-L1 in patients with lung cancer. Thorac Cancer 2020; 11:2975-2982. [PMID: 32893980 PMCID: PMC7529545 DOI: 10.1111/1759-7714.13653] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 08/19/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Advanced non-small cell lung cancer (NSCLC) has a high mortality rate and poor prognosis. However, outcomes have gradually improved after the introduction of novel immunotherapies, including immune checkpoint inhibitors (ICIs). Although programmed death-ligand 1 (PD-L1) expression in tumor tissues is a known biomarker for guiding ICI treatment of NSCLC, challenges such as difficulty of liquid biopsy and heterogeneous results during treatment persist. This study evaluated the potential of miR200b as a surrogate biomarker for PD-L1 expression. METHODS We used the human lung cancer cell lines H226, H460, H520, A549, and H1975. miR200b expression in blood and bronchoscopy specimens of NSCLC patients was evaluated using reverse-transcription-quantitative PCR. Using flow cytometry, PD-L1 expression in vitro, as well as in tumor tissues, was evaluated after transfection with a mimic miR200b or siRNA. RESULTS miR200b expression negatively correlated with PD-L1 expression in all cell lines. The induction or knockdown of miR200b also altered PD-L1 expression in vitro. The patient group with a PD-L1 tumor proportion score ≥ 50% had significantly lower miR200b expression in the bronchoscopy specimens (P = 0.025) and serum-derived exosomes (P = 0.022) than that with PD-L1 tumor proportion score < 50%. CONCLUSIONS miR200b can regulate PD-L1 expression in lung cancer cells, and miR200b expression in clinical specimens negatively correlated with PD-L1 expression. Thus, miR200b may be a useful surrogate biomarker for PD-L1 expression in lung cancer patients. KEY POINTS SIGNIFICANT FINDINGS OF THE STUDY: High PD-L1 expression was linked to low miR200b expression, whereas low PD-L1 expression was linked to high miR200b expression in human lung cancer patients. Thus, miR200b overexpression or silencing can control PD-L1 expression in cancer cells. What this study adds We demonstrated the potential of miR200b as a surrogate biomarker for PD-L1 expression in lung cancer patients.
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Affiliation(s)
- Seigo Katakura
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuaki Kobayashi
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hisashi Hashimoto
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chisato Kamimaki
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Katsushi Tanaka
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sousuke Kubo
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kentaro Nakashima
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shuhei Teranishi
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Saki Manabe
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Keisuke Watanabe
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuyuki Horita
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yu Hara
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masaki Yamamoto
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Makoto Kudo
- Respiratory Disease Center, Yokohama City University Medical Center, Yokohama, Japan
| | - Hongmei Piao
- Department of Respiratory Medicine, Affiliated Hospital of Yanbian University, Yanji, China
| | - Takeshi Kaneko
- Department of Pulmonology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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17
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Ali J, Liu W, Duan W, Liu C, Song J, Ali S, Li E, Wang Q. METTL7B (methyltransferase-like 7B) identification as a novel biomarker for lung adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1130. [PMID: 33240979 PMCID: PMC7576055 DOI: 10.21037/atm-20-4574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background Lung adenocarcinoma (LUAD) is still one of the major causes of cancer-related mortality across the globe. Therefore, there is a dire need to identify early specific and sensitive biomarkers or drug targets of LUAD for developing improved diagnosis and clinical management. We aimed to investigate the role of methyltransferase-like 7B (METTL7B) on LUAD tumor development and progression in this study. Methods METTL7B’s expression was confirmed in two independent clinical cohort samples, including LUAD tissues microarray (TMA) via immunohistochemistry (IHC) and serum samples via enzyme-linked immunosorbent assay (ELISA). The correlation between METTL7B expression with clinicopathological features and overall survival rate in LUAD patients was then further analyzed. Meanwhile, the messenger ribonucleic acid (mRNA) and protein levels of METTL7B were verified in cell lines and in vitro experiments, including cell proliferation assay, and migration. Invasion assays were conducted to explore the effects of METTL7B on LUAD by silencing the protein expression. Results METTL7B was remarkably overexpressed in clinical LUAD tumor tissues and serum compared to the normal control group and in LUAD cell lines. The expression level of METTL7B was significantly correlated with tumor size, advanced tumor node and metastases (TNM) stages, and lymph node metastasis. The Kaplan-Meier survival curves proved that high METTL7B expression was significantly associated with a reduced survival rate in LUAD patients (P<0.05), and univariate analysis showed that high METTL7B expression was significantly associated with poor overall survival [hazard ratio (HR) =2.220, 95% confidence interval (CI): 1.211–4.086; P=0.010]. In vitro assays showed that METTL7B overexpression augmented cell proliferation, migration, and the invasion in LUAD. Conclusions METTL7B was overexpressed in LUAD and significantly associated with the poor progression, showing that METTL7B may serve as a potential novel biomarker for the diagnosis and prognosis of LUAD. Moreover, METTL7B plays a role in promoting tumor proliferation, migration, and invasion in LUAD.
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Affiliation(s)
- Jawad Ali
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Wenwen Liu
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Wenzhe Duan
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Chang Liu
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Jing Song
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Sameen Ali
- Dalian Medical University, Dalian, China
| | - Encheng Li
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
| | - Qi Wang
- Department of Respiratory Medicine, The Second Hospital, Dalian Medical University, Dalian, China
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Competitive endogenous network of lncRNA, miRNA, and mRNA in the chemoresistance of gastrointestinal tract adenocarcinomas. Biomed Pharmacother 2020; 130:110570. [PMID: 32763816 DOI: 10.1016/j.biopha.2020.110570] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/17/2020] [Accepted: 07/26/2020] [Indexed: 12/12/2022] Open
Abstract
Chemotherapy is one of the main therapeutic strategies used for gastrointestinal tract adenocarcinomas (GTAs), but resistance to anticancer drugs is a substantial obstacle in successful chemotherapy. Accumulating evidence shows that non-coding RNAs, especially long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), can affect the drug resistance of tumor cells by forming a ceRNA regulatory network with mRNAs. The efficiency of the competing endogenous RNAs (ceRNAs) network can be affected by the number and integrality of miRNA recognition elements (MREs). Dynamic factors such as RNA editing, alternative splicing, single nucleotide polymorphism (SNP), RNA-binding proteins and RNA secondary structure can influence the MRE activity, which may in turn be involved in the regulation of chemoresistance-associated ceRNA network by prospective approaches. Besides activities in a single tumor cell, the components of the tumor micoenvironment (TME) also affect the ceRNA network by regulating the expression of non-coding RNA directly or indirectly. The alternation of the ceRNA network often has an impact on the malignant phenotype of tumor including chemoresistance. In this review, we focused on how MRE-associated dynamic factors and components of TME affected the ceRNA network and speculated the potential association of ceRNA network with chemoresistance. We also summarized the ceRNA network of lncRNAs, miRNAs, and mRNAs which efficiently triggers chemoresistance in the specific types of GTAs and analyzed the role of each RNA as a "promoter" or "suppressor" of chemoresistance.
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Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:cancers12071845. [PMID: 32650588 PMCID: PMC7408896 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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Liu K, Zhang W, Tan J, Ma J, Zhao J. MiR-200b-3p Functions as an Oncogene by Targeting ABCA1 in Lung Adenocarcinoma. Technol Cancer Res Treat 2020; 18:1533033819892590. [PMID: 31795847 PMCID: PMC6893970 DOI: 10.1177/1533033819892590] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Objective: The aim of this study was to investigate the microRNA-200b-3p expression in lung adenocarcinoma and the possible functional associations of microRNA-200b-3p with cell proliferation, migration, and invasion. Methods: Quantitative real-time polymerase chain reaction was used to detect the expression of microRNA-200b-3p in lung adenocarcinoma samples and in the human lung adenocarcinoma cell lines A549 and H1299. A549 and H1299 cells were transfected with either a microRNA-200b-3p mimic or a negative control microRNA or either an empty vector or an adenosine triphosphate-binding cassette transporter A-1 overexpression vector. A Cell Counting Kit-8 assay was employed to assess the ability of cell proliferation. Transwell assays and transwell-Matrigel invasion assay were, respectively, utilized to assess the capacity of migration and invasion in A549 and H1299 cells. Results: The results showed that microRNA-200b-3p expression was significantly upregulated in tumor tissues compared with that in adjacent normal tissues. Overexpression of microRNA-200b-3p promoted lung adenocarcinoma cell proliferation and metastasis. Furthermore, adenosine triphosphate-binding cassette transporter A-1 was a direct target of microRNA-200b-3p, and this binding was verified by luciferase reporter analysis. Overexpression of adenosine triphosphate-binding cassette transporter A-1 obviously suppressed lung adenocarcinoma cell proliferation, migration, and invasion. Lung adenocarcinoma cell phenotypes induced by microRNA-200b-3p overexpression could be partially remitted by the co-overexpression of microRNA-200b-3p and adenosine triphosphate-binding cassette transporter A-1. Conclusion: This study first identified that microRNA-200b-3p is upregulated in lung adenocarcinoma cells and associated with cell proliferation and metastasis. MicroRNA-200b-3p promoted lung adenocarcinoma cell proliferation and metastasis by suppressing adenosine triphosphate-binding cassette transporter A-1. MicroRNA-200b-3p may function as a novel molecular marker and therapeutic target for lung adenocarcinoma treatment.
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Affiliation(s)
- Keqiang Liu
- Department of thoracic surgery, 7th Medical Center of Peoples Liberation Army General Hospital, Beijing, China
| | - Weiqiang Zhang
- Department of thoracic surgery, 7th Medical Center of Peoples Liberation Army General Hospital, Beijing, China
| | - Jian Tan
- Department of thoracic surgery, 7th Medical Center of Peoples Liberation Army General Hospital, Beijing, China
| | - Jingbo Ma
- Department of thoracic surgery, 7th Medical Center of Peoples Liberation Army General Hospital, Beijing, China
| | - Jing Zhao
- Department of thoracic surgery, 7th Medical Center of Peoples Liberation Army General Hospital, Beijing, China
- Jing Zhao, Department of thoracic surgery, 7th Medical Center of Peoples Liberation Army General Hospital, Beijing, 100700, China.
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21
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Guo Q, Ke XX, Liu Z, Gao WL, Fang SX, Chen C, Song YX, Han H, Lu HL, Xu G. Evaluation of the Prognostic Value of STEAP1 in Lung Adenocarcinoma and Insights Into Its Potential Molecular Pathways via Bioinformatic Analysis. Front Genet 2020; 11:242. [PMID: 32265985 PMCID: PMC7099762 DOI: 10.3389/fgene.2020.00242] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/28/2020] [Indexed: 12/19/2022] Open
Abstract
Background Upregulation of the six-transmembrane epithelial antigen of prostate-1 (STEAP1) is closely associated with prognosis of numerous malignant cancers. However, its role in lung adenocarcinoma (LUAD), the most common type of lung cancer, remains unknown. This study aimed to investigate the role of STEAP1 in the occurrence and progression of LUAD and the potential mechanisms underlying its regulatory effects. Methods STEAP1 mRNA and protein expression were analyzed in 40 LUAD patients via real-time PCR and western blotting, respectively. We accessed the clinical data of 522 LUAD patients from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) to investigate the expression and prognostic role of STEAP1 in LUAD. Further, we performed gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) to elucidate the potential mechanism underlying the role of STEAP1 in LUAD. The protein-protein interaction (PPI) network of STEAP1 was analyzed using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and hub genes with significant positive and negative associations with STEAP1 were identified and their role in LUAD prognosis was predicted. Results STEAP1 was significantly upregulated in LUAD patients and associated with LUAD prognosis. Further, TCGA data indicated that STEAP1 upregulation is correlated with the clinical prognosis of LUAD. GO and KEGG analysis revealed that the genes co-expressed with STEAP1 were primarily involved in cell division, DNA replication, cell cycle, apoptosis, cytokine signaling, NF-kB signaling, and TNF signaling. GSEA revealed that homologous recombination, p53 signaling pathway, cell cycle, DNA replication, apoptosis, and toll-like receptor signaling were highly enriched upon STEAP1 upregulation. Gene Expression Profiling Interactive Analysis (GEPIA) analysis revealed that the top 10 hub genes associated with STEAP1 expression were also associated with the LUAD prognosis. Conclusion STEAP1 upregulation potentially influences the occurrence and progression of LUAD and its co-expressed genes via regulation of homologous recombination, p53 signaling, cell cycle, DNA replication, and apoptosis. STEAP1 is a potential prognostic biomarker for LUAD.
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Affiliation(s)
- Qiang Guo
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xi-Xian Ke
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhou Liu
- Department of Cardiac Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Wei-Long Gao
- Department of Cardiac Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Shi-Xu Fang
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Cheng Chen
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Yong-Xiang Song
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hao Han
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Hong-Ling Lu
- Department of Biochemistry, Zunyi Medical University, Zunyi, China
| | - Gang Xu
- Department of Thoracic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
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22
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Uddin MB, Wang Z, Yang C. Dysregulations of Functional RNA Modifications in Cancer, Cancer Stemness and Cancer Therapeutics. Theranostics 2020; 10:3164-3189. [PMID: 32194861 PMCID: PMC7053189 DOI: 10.7150/thno.41687] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
More than a hundred chemical modifications in coding and non-coding RNAs have been identified so far. Many of the RNA modifications are dynamic and reversible, playing critical roles in gene regulation at the posttranscriptional level. The abundance and functions of RNA modifications are controlled mainly by the modification regulatory proteins: writers, erasers and readers. Modified RNA bases and their regulators form intricate networks which are associated with a vast array of diverse biological functions. RNA modifications are not only essential for maintaining the stability and structural integrity of the RNA molecules themselves, they are also associated with the functional outcomes and phenotypic attributes of cells. In addition to their normal biological roles, many of the RNA modifications also play important roles in various diseases particularly in cancer as evidenced that the modified RNA transcripts and their regulatory proteins are aberrantly expressed in many cancer types. This review will first summarize the most commonly reported RNA modifications and their regulations, followed by discussing recent studies on the roles of RNA modifications in cancer, cancer stemness as wells as functional RNA modification machinery as potential cancer therapeutic targets. It is concluded that, while advanced technologies have uncovered the contributions of many of RNA modifications in cancer, the underlying mechanisms are still poorly understood. Moreover, whether and how environmental pollutants, important cancer etiological factors, trigger abnormal RNA modifications and their roles in environmental carcinogenesis remain largely unknown. Further studies are needed to elucidate the mechanism of how RNA modifications promote cell malignant transformation and generation of cancer stem cells, which will lead to the development of new strategies for cancer prevention and treatment.
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Affiliation(s)
| | | | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536-0305, USA
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23
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Matsuyama H, Suzuki HI. Systems and Synthetic microRNA Biology: From Biogenesis to Disease Pathogenesis. Int J Mol Sci 2019; 21:E132. [PMID: 31878193 PMCID: PMC6981965 DOI: 10.3390/ijms21010132] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/15/2019] [Accepted: 12/20/2019] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are approximately 22-nucleotide-long, small non-coding RNAs that post-transcriptionally regulate gene expression. The biogenesis of miRNAs involves multiple steps, including the transcription of primary miRNAs (pri-miRNAs), nuclear Drosha-mediated processing, cytoplasmic Dicer-mediated processing, and loading onto Argonaute (Ago) proteins. Further, miRNAs control diverse biological and pathological processes via the silencing of target mRNAs. This review summarizes recent findings regarding the quantitative aspects of miRNA homeostasis, including Drosha-mediated pri-miRNA processing, Ago-mediated asymmetric miRNA strand selection, and modifications of miRNA pathway components, as well as the roles of RNA modifications (epitranscriptomics), epigenetics, transcription factor circuits, and super-enhancers in miRNA regulation. These recent advances have facilitated a system-level understanding of miRNA networks, as well as the improvement of RNAi performance for both gene-specific targeting and genome-wide screening. The comprehensive understanding and modeling of miRNA biogenesis and function have been applied to the design of synthetic gene circuits. In addition, the relationships between miRNA genes and super-enhancers provide the molecular basis for the highly biased cell type-specific expression patterns of miRNAs and the evolution of miRNA-target connections, while highlighting the importance of alterations of super-enhancer-associated miRNAs in a variety of human diseases.
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Affiliation(s)
- Hironori Matsuyama
- Fujii Memorial Research Institute, Otsuka Pharmaceutical Co., Ltd., 1-11-1 Karasaki, Otsu-shi, Shiga 520-0106, Japan;
| | - Hiroshi I. Suzuki
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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Correia de Sousa M, Gjorgjieva M, Dolicka D, Sobolewski C, Foti M. Deciphering miRNAs' Action through miRNA Editing. Int J Mol Sci 2019; 20:E6249. [PMID: 31835747 PMCID: PMC6941098 DOI: 10.3390/ijms20246249] [Citation(s) in RCA: 497] [Impact Index Per Article: 99.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with the capability of modulating gene expression at the post-transcriptional level either by inhibiting messenger RNA (mRNA) translation or by promoting mRNA degradation. The outcome of a myriad of physiological processes and pathologies, including cancer, cardiovascular and metabolic diseases, relies highly on miRNAs. However, deciphering the precise roles of specific miRNAs in these pathophysiological contexts is challenging due to the high levels of complexity of their actions. Indeed, regulation of mRNA expression by miRNAs is frequently cell/organ specific; highly dependent on the stress and metabolic status of the organism; and often poorly correlated with miRNA expression levels. Such biological features of miRNAs suggest that various regulatory mechanisms control not only their expression, but also their activity and/or bioavailability. Several mechanisms have been described to modulate miRNA action, including genetic polymorphisms, methylation of miRNA promoters, asymmetric miRNA strand selection, interactions with RNA-binding proteins (RBPs) or other coding/non-coding RNAs. Moreover, nucleotide modifications (A-to-I or C-to-U) within the miRNA sequences at different stages of their maturation are also critical for their functionality. This regulatory mechanism called "RNA editing" involves specific enzymes of the adenosine/cytidine deaminase family, which trigger single nucleotide changes in primary miRNAs. These nucleotide modifications greatly influence a miRNA's stability, maturation and activity by changing its specificity towards target mRNAs. Understanding how editing events impact miRNA's ability to regulate stress responses in cells and organs, or the development of specific pathologies, e.g., metabolic diseases or cancer, should not only deepen our knowledge of molecular mechanisms underlying complex diseases, but can also facilitate the design of new therapeutic approaches based on miRNA targeting. Herein, we will discuss the current knowledge on miRNA editing and how this mechanism regulates miRNA biogenesis and activity.
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Affiliation(s)
| | | | | | | | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (M.C.d.S.); (M.G.); (D.D.); (C.S.)
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25
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Sun D, Han L, Cao R, Wang H, Jiang J, Deng Y, Yu X. Prediction of a miRNA-mRNA functional synergistic network for cervical squamous cell carcinoma. FEBS Open Bio 2019; 9:2080-2092. [PMID: 31642613 PMCID: PMC6886301 DOI: 10.1002/2211-5463.12747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 10/13/2019] [Accepted: 10/22/2019] [Indexed: 01/16/2023] Open
Abstract
Cervical squamous cell carcinoma (CSCC) accounts for a significant proportion of cervical cancer; thus, there is a need for novel and noninvasive diagnostic biomarkers for this malignancy. In this study, we performed integrated analysis of a dataset from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEmiRNAs) between CSCC, cervical intraepithelial neoplasia (CIN) and healthy control subjects. We further established protein-protein interaction and DEmiRNA-target gene interaction networks, and performed functional annotation of the target genes of DEmiRNAs. In total, we identified 1375 DEGs and 19 DEmiRNAs in CIN versus normal control, and 2235 DEGs and 33 DEmiRNAs in CSCC versus CIN by integrated analysis. Our protein-protein interaction network indicates that the common DEGs, Cyclin B/cyclin-dependent kinase 1 (CDK1), CCND1, ESR1 and Aurora kinase A (AURKA), are the top four hub genes. P53 and prostate cancer were identified as significantly enriched signaling pathways of common DEGs and DEmiRNA targets, respectively. We validated that expression levels of three DEGs (TYMS, SASH1 and CDK1) and one DEmiRNA of hsa-miR-99a were altered in blood samples of patients with CSCC. In conclusion, a total of four DEGs (TYMS, SASH1, CDK1 and AURKA) and two DEmiRNAs (hsa-miR-21 and hsa-miR-99a) may be involved in the pathogenesis of CIN and the progression of CIN into CSCC. Of these, TYMS is predicted to be regulated by hsa-miR-99a and SASH1 to be regulated by hsa-miR-21.
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Affiliation(s)
- Dan Sun
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Lu Han
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Rui Cao
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Huali Wang
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Jiyong Jiang
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Yanjie Deng
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
| | - Xiaohui Yu
- Obstetrics and Gynecology, Dalian Maternity and Child Health Care Hospital, China
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26
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Guo T, Ma H, Zhou Y. Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma. PeerJ 2019; 7:e7313. [PMID: 31333911 PMCID: PMC6626531 DOI: 10.7717/peerj.7313] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the major subtype of lung cancer and the most lethal malignant disease worldwide. However, the molecular mechanisms underlying LUAD are not fully understood. Methods Four datasets (GSE118370, GSE85841, GSE43458 and GSE32863) were obtained from the gene expression omnibus (GEO). Identification of differentially expressed genes (DEGs) and functional enrichment analysis were performed using the limma and clusterProfiler packages, respectively. A protein–protein interaction (PPI) network was constructed via Search Tool for the Retrieval of Interacting Genes (STRING) database, and the module analysis was performed by Cytoscape. Then, overall survival analysis was performed using the Kaplan–Meier curve, and prognostic candidate biomarkers were further analyzed using the Oncomine database. Results Totally, 349 DEGs were identified, including 275 downregulated and 74 upregulated genes which were significantly enriched in the biological process of extracellular structure organization, leukocyte migration and response to peptide. The mainly enriched pathways were complement and coagulation cascades, malaria and prion diseases. By extracting key modules from the PPI network, 11 hub genes were screened out. Survival analysis showed that except VSIG4, other hub genes may be involved in the development of LUAD, in which MYH10, METTL7A, FCER1G and TMOD1 have not been reported previously to correlated with LUAD. Briefly, novel hub genes identified in this study will help to deepen our understanding of the molecular mechanisms of LUAD carcinogenesis and progression, and to discover candidate targets for early detection and treatment of LUAD.
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Affiliation(s)
- Tingting Guo
- Department of Biotechnology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing, China
| | - Hongtao Ma
- Department of Biotechnology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing, China
| | - Yubai Zhou
- Department of Biotechnology, College of Life Science & Bioengineering, Beijing University of Technology, Beijing, China
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27
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Moore S, Alsop E, Lorenzini I, Starr A, Rabichow BE, Mendez E, Levy JL, Burciu C, Reiman R, Chew J, Belzil VV, W. Dickson D, Robertson J, Staats KA, Ichida JK, Petrucelli L, Van Keuren-Jensen K, Sattler R. ADAR2 mislocalization and widespread RNA editing aberrations in C9orf72-mediated ALS/FTD. Acta Neuropathol 2019; 138:49-65. [PMID: 30945056 DOI: 10.1007/s00401-019-01999-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 12/12/2022]
Abstract
The hexanucleotide repeat expansion GGGGCC (G4C2)n in the C9orf72 gene is the most common genetic abnormality associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Recent findings suggest that dysfunction of nuclear-cytoplasmic trafficking could affect the transport of RNA binding proteins in C9orf72 ALS/FTD. Here, we provide evidence that the RNA editing enzyme adenosine deaminase acting on RNA 2 (ADAR2) is mislocalized in C9orf72 repeat expansion mediated ALS/FTD. ADAR2 is responsible for adenosine (A) to inosine (I) editing of double-stranded RNA, and its function has been shown to be essential for survival. Here we show the mislocalization of ADAR2 in human induced pluripotent stem cell-derived motor neurons (hiPSC-MNs) from C9orf72 patients, in mice expressing (G4C2)149, and in C9orf72 ALS/FTD patient postmortem tissue. As a consequence of this mislocalization we observe alterations in RNA editing in our model systems and across multiple brain regions. Analysis of editing at 408,580 known RNA editing sites indicates that there are vast RNA A to I editing aberrations in C9orf72-mediated ALS/FTD. These RNA editing aberrations are found in many cellular pathways, such as the ALS pathway and the crucial EIF2 signaling pathway. Our findings suggest that the mislocalization of ADAR2 in C9orf72 mediated ALS/FTD is responsible for the alteration of RNA processing events that may impact vast cellular functions, including the integrated stress response (ISR) and protein translation.
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28
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Yang Q, Li J, Hu Y, Tang X, Yu L, Dong L, Chen D. MiR-218-5p Suppresses the Killing Effect of Natural Killer Cell to Lung Adenocarcinoma by Targeting SHMT1. Yonsei Med J 2019; 60:500-508. [PMID: 31124332 PMCID: PMC6536398 DOI: 10.3349/ymj.2019.60.6.500] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Lung adenocarcinoma (LA) is one of the major types of lung cancer. MicroRNAs (miRNAs) play an essential role in regulating responses of natural killer (NK) cells to cancer malignancy. However, the mechanism of miR-218-5p involved in the killing effect of NK cells to LA cells remains poorly understood. MATERIALS AND METHODS The expression of miR-218-5p was examined by quantitative real-time polymerase chain reaction (qRT-PCR). Serine hydroxymethyl transferase 1 (SHMT1) level was detected by qRT-PCR or western blots. Cytokines production of interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) were detected by ELISA. The killing effect of NK cells to LA cells was investigated using lactate dehydrogenase cytotoxicity assay kit. The interaction of miR-218-5p and SHMT1 was probed by luciferase activity assay. Xenograft model was established to investigate the killing effect of NK cells in vivo. RESULTS miR-218-5p was enhanced and SHMT1 was inhibited in NK cells of LA patients, whereas stimulation of interleukin-2 (IL-2) reversed their abundances. Addition of miR-218-5p reduced IL-2-induced cytokines expression and cytotoxicity in NK-92 against LA cells. Moreover, SHMT1 was negatively regulated by miR-218-5p and attenuated miR-218-5p-mediated effect on cytotoxicity, IFN-γ and TNF-α secretion in IL-2-activated NK cells. In addition, miR-218-5p exhaustion inhibited tumor growth by promoting killing effect of NK cells. CONCLUSION miR-218-5p suppresses the killing effect of NK cells to LA cells by targeting SHMT1, providing a potential target for LA treatment by ameliorating NK cells function.
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Affiliation(s)
- Quanjun Yang
- Department of Oncology, The Affiliated Renhe Hospital of China Three Gorges University, Yichang, China
| | - Jingjing Li
- Department One of Medical Oncology, Jing Men No.2 People's Hospital, Jing Men, China.
| | - Yili Hu
- Department of Oncology, The Affiliated Renhe Hospital of China Three Gorges University, Yichang, China
| | - Xiaofei Tang
- Internal Medicine, Changyang Tujia Autonomous District People's Hospital, Yichang, China
| | - Lili Yu
- Department of Oncology, The Affiliated Renhe Hospital of China Three Gorges University, Yichang, China
| | - Lihua Dong
- Department of Oncology, The Affiliated Renhe Hospital of China Three Gorges University, Yichang, China
| | - Diandian Chen
- Department of Oncology, The Affiliated Renhe Hospital of China Three Gorges University, Yichang, China
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29
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Jin H, Liu P, Kong L, Fei X, Gao Y, Wu T, Sun D, Tan X. Identification of RE1-Silencing Transcription Factor as a Promoter of Metastasis in Pancreatic Cancer. Front Oncol 2019; 9:291. [PMID: 31041193 PMCID: PMC6476950 DOI: 10.3389/fonc.2019.00291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/29/2019] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer is characterized by its rapid progression and early metastasis. This requires further elucidation of the key promoters for its progression and metastasis. In this study, we identified REST as the hub gene of a gene module which is closely associated with cancer stage by weighted gene correlation network analysis. Validation with the TCGA database, western blot analysis of human pancreatic cancer cell lines (AsPC-1, Capan-2, SW-1990, and PANC-1) and immunohistochemical analysis of paraffin-embedded pancreatic cancer tissue sections showed that REST was enriched in tissue samples of advanced stage and metastatic phenotype cell lines. Survival analysis with the TCGA database and our own follow-up data suggested that patients with higher expression level of REST showed worse overall survival rate. In vitro functional experiments suggested that knockdown of REST suppressed proliferation, migration, invasion and epithelial-mesenchymal transition of AsPC-1 and PANC-1 cells. In vivo experiments (a subcutaneous BALB/c nude mouse model and a superior mesenteric vein injection BALB/c nude mouse model) suggested that knockdown of REST suppressed growth and metastasis of xenograft tumor. Finally, we investigated the underlying molecular mechanism of REST and identified REST as a potential downstream target of MAPK signaling pathway. In conclusion, our results of bioinformatic analysis, in vitro and in vivo functional analysis suggested that REST may serve as a promoter of metastasis in pancreatic cancer.
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Affiliation(s)
- Haoyi Jin
- Department of Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Peng Liu
- Thyroid and Pancreatic Surgery Ward, Shengjing Hospital of China Medical University, Shenyang, China
| | - Lingming Kong
- Department of Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiang Fei
- Department of Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yang Gao
- Department of Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tianyu Wu
- Department of Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Defeng Sun
- Department of Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaodong Tan
- Thyroid and Pancreatic Surgery Ward, Shengjing Hospital of China Medical University, Shenyang, China
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30
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Fang H, Liu Y, He Y, Jiang Y, Wei Y, Liu H, Gong Y, An G. Extracellular vesicle‑delivered miR‑505‑5p, as a diagnostic biomarker of early lung adenocarcinoma, inhibits cell apoptosis by targeting TP53AIP1. Int J Oncol 2019; 54:1821-1832. [PMID: 30864684 DOI: 10.3892/ijo.2019.4738] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/25/2019] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LA) is the most commonly occurring histological type of non‑small cell lung cancer. Diagnosis and treatment of LA remain a major clinical challenge. In the present study, to identify early LA biomarkers, extracellular vesicles (EVs) were separated from the plasma samples from 153 patients with LA and 75 healthy controls. microRNA (miRNA) expression profiling was performed at the screening stage (5 patients with LA vs. 5 controls), followed by verification at the validation stage (40 patients with LA vs. 20 controls) using reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). The four disordered miRNAs (miR‑505‑5p, miR‑486‑3p, miR‑486‑3p and miR‑382‑3p) identified in the plasma EVs were further evaluated at the testing stage (108 patients with LA vs. 50 controls) by RT‑qPCR. It was revealed that miR‑505‑5p was upregulated, whereas miR‑382‑3p was downregulated, in the EVs from patients with LA. Furthermore, miR‑505‑5p was also upregulated in tumor tissues, compared with adjacent non‑tumor control tissues. Subsequently, the direct targets of miR‑505‑5p were predicted using bioinformatics analyses, and verified by luciferase assay and immunoblotting. The present study determined that miR‑505‑5p functions as an oncogene, promoting lung cancer cell proliferation and inhibiting cancer cell apoptosis via the targeting of tumor protein P53‑regulated apoptosis‑inducing protein 1 (TP53AIP1). Finally, it was confirmed that miR‑505‑5p in plasma EVs could be delivered to lung cancer cells, inhibiting cell apoptosis and promoting cell proliferation by targeting TP53AIP1. In conclusion, the present study indicated that miRNA‑505‑5p functions as an oncogene that may be used as a novel biomarker for the diagnosis and treatment of LA.
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Affiliation(s)
- Hua Fang
- Department of Oncology, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
| | - Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Yaohong He
- Department of Respiratory Medicine, Fuxing Hospital, The Eighth Clinical Medical College, Capital Medical University, Beijing 100038, P.R. China
| | - Yang Jiang
- Department of Thoracic Surgery, Fuxing Hospital, The Eighth Clinical Medical College, Capital Medical University, Beijing 100038, P.R. China
| | - Yaping Wei
- Department of Oncology, Capital Medical University, Beijing 100038, P.R. China
| | - Han Liu
- Department of Oncology, Capital Medical University, Beijing 100038, P.R. China
| | - Yueqing Gong
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, P.R. China
| | - Guangyu An
- Department of Oncology, Beijing Chao‑Yang Hospital, Capital Medical University, Beijing 100020, P.R. China
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31
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Siriwardhana C, Khadka VS, Chen JJ, Deng Y. Development of a miRNA-seq based prognostic signature in lung adenocarcinoma. BMC Cancer 2019; 19:34. [PMID: 30621620 PMCID: PMC6325795 DOI: 10.1186/s12885-018-5206-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
Background We utilized miRNAs expression and clinical data to develop a prognostic signature for patients with lung adenocarcinoma, with respect to their overall survival, to identify high-risk subjects based on their miRNA genomic profile. Methods MiRNA expressions based on miRNA sequencing and clinical data of lung adenocarcinoma patients (n = 479) from the Cancer Genome Atlas were randomly partitioned into non-overlapping Model (n = 320) and Test (n = 159) sets, respectively, for model estimation and validation. Results Among the ten miRNAs identified using the univariate Cox analysis, six from miR-8, miR-181, miR-326, miR-375, miR-99a, and miR-10, families showed improvement of the overall survival chance, while two miRNAs from miR-582 and miR-584 families showed a worsening of survival chances. The final prognostic signature was developed with five miRNAs—miR-375, miR-582-3p, miR-326, miR-181c-5p, and miR-99a-5p—utilizing a stepwise variable selection procedure. Using the KEGG pathway analysis, we found potential evidence supporting their significance in multiple cancer pathways, including non-small cell lung cancer. We defined two risk groups with a score calculated using the Cox regression coefficients. The five-year survival rates for the low-risk group was approximately 48.76% (95% CI = (36.15, 63.93)); however, it was as low as 7.50% (95% CI = (2.34, 24.01)) for the high-risk group. Furthermore, we demonstrated the effect of the genomic profile using the miRNA signature, quantifying survival rates for hypothetical subjects in different pathological stages of cancer. Conclusions The proposed prognostic signature can be used as a reliable tool for identifying high-risk subjects regarding survival based on their miRNA genomic profile. Electronic supplementary material The online version of this article (10.1186/s12885-018-5206-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chathura Siriwardhana
- Bioinformatics and Biostatistics Cores, Department of Complementary and Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Vedbar S Khadka
- Bioinformatics and Biostatistics Cores, Department of Complementary and Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - John J Chen
- Bioinformatics and Biostatistics Cores, Department of Complementary and Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Youping Deng
- Bioinformatics and Biostatistics Cores, Department of Complementary and Integrative Medicine, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
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Tassinari V, Cesarini V, Silvestris DA, Gallo A. The adaptive potential of RNA editing-mediated miRNA-retargeting in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:291-300. [PMID: 30605729 DOI: 10.1016/j.bbagrm.2018.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/20/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
Abstract
A-to-I RNA editing is a post-transcriptional mechanism that converts the genomically coded Adenosine (A) into Inosine (I) at the RNA level. This type of RNA editing is the most frequent in humans and is mediated by the ADAR enzymes. RNA editing can alter the genetic code of mRNAs, but also affect the functions of noncoding RNAs such as miRNAs. Recent studies have identified thousands of microRNA editing events in different cancer types. However, the important role played by miRNA-editing in cancer has been reported for just a few microRNAs. Herein, we recapitulate the current studies on cancer-related microRNA editing and discuss their importance in tumor growth and progression. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Valentina Tassinari
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Valeriana Cesarini
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Domenico Alessandro Silvestris
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy
| | - Angela Gallo
- RNA Editing Laboratory, Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù (OPBG), Viale di San Paolo, 15, 00146 Rome, Italy.
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Maemura K, Watanabe K, Ando T, Hiyama N, Sakatani T, Amano Y, Kage H, Nakajima J, Yatomi Y, Nagase T, Takai D. Altered editing level of microRNAs is a potential biomarker in lung adenocarcinoma. Cancer Sci 2018; 109:3326-3335. [PMID: 30022565 PMCID: PMC6172074 DOI: 10.1111/cas.13742] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/10/2018] [Indexed: 01/16/2023] Open
Abstract
Adenosine‐to‐inosine (A‐to‐I) microRNA editing is associated with tumor phenotypes in various cancer types. Recent analyses of The Cancer Genome Atlas (TCGA) dataset have shown several microRNAs that undergo A‐to‐I editing in human cancers, some of which have been reported to be associated with prognosis. Herein, we examined published small RNA deep sequencing data of 74 cases of lung adenocarcinoma (AD) and the corresponding normal counterpart (NC) specimen in silico in order to identify A‐to‐I microRNA editing events. Editing levels of miR‐379‐5p, miR‐99a‐5p, and miR‐497‐5p were lower in AD than in NC and, in a large number of cases, the editing level of miR‐200b‐3p was higher in AD than in NC. Difference in the editing level between AD and NC was largest for miR‐99a‐5p. Then, we examined the editing level of miR‐99a‐5p in 50 surgically resected lung adenocarcinoma cases at our institution by a conventional sequence‐based method, and its association with clinical outcomes. The editing level of miR‐99a‐5p was significantly lower in 19 cases of AD (38%) than in corresponding NC. These cases showed a shorter overall survival as assessed using the log‐rank test (P = .047). This trend was consistent with previous analyses of TCGA dataset. The altered editing level of microRNAs in lung adenocarcinoma could serve as a potential biomarker.
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Affiliation(s)
- Keita Maemura
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Kousuke Watanabe
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Takahiro Ando
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Noriko Hiyama
- Department of Thoracic Surgery, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Toshio Sakatani
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yosuke Amano
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Hidenori Kage
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Jun Nakajima
- Department of Thoracic Surgery, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Takahide Nagase
- Department of Respiratory Medicine, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Daiya Takai
- Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
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