1
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Caponnetto A, Ferrara C, Fazzio A, Agosta N, Scribano M, Vento ME, Borzì P, Barbagallo C, Stella M, Ragusa M, Scollo P, Barbagallo D, Purrello M, Di Pietro C, Battaglia R. A Circular RNA Derived from the Pumilio 1 Gene Could Regulate PTEN in Human Cumulus Cells. Genes (Basel) 2024; 15:124. [PMID: 38275605 PMCID: PMC10815046 DOI: 10.3390/genes15010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
CircRNAs are a class of non-coding RNAs able to regulate gene expression at multiple levels. Their involvement in physiological processes, as well as their altered regulation in different human diseases, both tumoral and non-tumoral, is well documented. However, little is known about their involvement in female reproduction. This study aims to identify circRNAs potentially involved in reproductive women's health. Candidate circRNAs expressed in ovary and sponging miRNAs, already known to be expressed in the ovary, were selected by a computational approach. Using real time PCR, we verified their expression and identified circPUM1 as the most interesting candidate circRNA for further analyses. We assessed the expression of circPUM1 and its linear counterpart in all the follicle compartments and, using a computational and experimental approach, identified circPUM1 direct and indirect targets, miRNAs and mRNAs, respectively, in cumulus cells. We found that both circPUM1 and its mRNA host gene are co-expressed in all the follicle compartments and proposed circPUM1 as a potential regulator of PTEN, finding a strong positive correlation between circPUM1 and PTEN mRNA. These results suggest a possible regulation of PTEN by circPUM1 in cumulus cells and point out the important role of circRNA inside the pathways related to follicle growth and oocyte maturation.
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Affiliation(s)
- Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Carmen Ferrara
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Anna Fazzio
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Noemi Agosta
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy; (N.A.); (M.S.)
| | - Marianna Scribano
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy; (N.A.); (M.S.)
| | - Maria Elena Vento
- IVF Unit, Cannizzaro Hospital, 95123 Catania, Italy; (M.E.V.); (P.B.)
| | - Placido Borzì
- IVF Unit, Cannizzaro Hospital, 95123 Catania, Italy; (M.E.V.); (P.B.)
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Paolo Scollo
- Department of Medicine and Surgery, Kore University, 94100 Enna, Italy;
- Maternal and Child Department, Obstetrics and Gynecology Unit, Cannizzaro Hospital, 95123 Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
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2
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Beňačka R, Szabóová D, Guľašová Z, Hertelyová Z, Radoňak J. Non-Coding RNAs in Human Cancer and Other Diseases: Overview of the Diagnostic Potential. Int J Mol Sci 2023; 24:16213. [PMID: 38003403 PMCID: PMC10671391 DOI: 10.3390/ijms242216213] [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: 09/30/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are abundant single-stranded RNA molecules in human cells, involved in various cellular processes ranging from DNA replication and mRNA translation regulation to genome stability defense. MicroRNAs are multifunctional ncRNA molecules of 18-24 nt in length, involved in gene silencing through base-pair complementary binding to target mRNA transcripts. piwi-interacting RNAs are an animal-specific class of small ncRNAs sized 26-31 nt, responsible for the defense of genome stability via the epigenetic and post-transcriptional silencing of transposable elements. Long non-coding RNAs are ncRNA molecules defined as transcripts of more than 200 nucleotides, their function depending on localization, and varying from the regulation of cell differentiation and development to the regulation of telomere-specific heterochromatin modifications. The current review provides recent data on the several forms of small and long non-coding RNA's potential to act as diagnostic, prognostic or therapeutic target for various human diseases.
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Affiliation(s)
- Roman Beňačka
- Department of Pathophysiology, Medical Faculty, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (R.B.); (D.S.)
| | - Daniela Szabóová
- Department of Pathophysiology, Medical Faculty, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (R.B.); (D.S.)
| | - Zuzana Guľašová
- Center of Clinical and Preclinical Research MEDIPARK, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (Z.G.); (Z.H.)
| | - Zdenka Hertelyová
- Center of Clinical and Preclinical Research MEDIPARK, Pavol Jozef Šafarik University, 04011 Košice, Slovakia; (Z.G.); (Z.H.)
| | - Jozef Radoňak
- 1st Department of Surgery, Faculty of Medicine, Louis Pasteur University Hospital (UNLP) and Pavol Jozef Šafarik University, 04011 Košice, Slovakia
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3
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Solati A, Thvimi S, Khatami SH, Shabaninejad Z, Malekzadegan Y, Alizadeh M, Mousavi P, Taheri-Anganeh M, Razmjoue D, Bahmyari S, Ghasemnejad-Berenji H, Vafadar A, Soltani Fard E, Ghasemi H, Movahedpour A. Non-coding RNAs in gynecologic cancer. Clin Chim Acta 2023; 551:117618. [PMID: 38375624 DOI: 10.1016/j.cca.2023.117618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 02/21/2024]
Abstract
The term "gynecologic cancer" pertains to neoplasms impacting the reproductive tissues and organs of women encompassing the endometrium, vagina, cervix, uterus, vulva, and ovaries. The progression of gynecologic cancer is linked to various molecular mechanisms. Historically, cancer research primarily focused on protein-coding genes. However, recent years have unveiled the involvement of non-coding RNAs (ncRNAs), including microRNAs, long non-coding RNAs (LncRNAs), and circular RNAs, in modulating cellular functions within gynecological cancer. Substantial evidence suggests that ncRNAs may wield a dual role in gynecological cancer, acting as either oncogenic or tumor-suppressive agents. Numerous clinical trials are presently investigating the roles of ncRNAs as biomarkers and therapeutic agents. These endeavors may introduce a fresh perspective on the diagnosis and treatment of gynecological cancer. In this overview, we highlight some of the ncRNAs associated with gynecological cancers.
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Affiliation(s)
- Arezoo Solati
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sina Thvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Shabaninejad
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Mehdi Alizadeh
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Damoun Razmjoue
- Medicinal Plants Research Center, Yasuj University of Medical Sciences, Yasuj, Iran; Department of Pharmacognosy, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Sedigheh Bahmyari
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hojat Ghasemnejad-Berenji
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Asma Vafadar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
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4
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Wu S, Wu Y, Deng S, Lei X, Yang X. Emerging roles of noncoding RNAs in human cancers. Discov Oncol 2023; 14:128. [PMID: 37439905 DOI: 10.1007/s12672-023-00728-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023] Open
Abstract
Studies have found that RNA encoding proteins only account for a small part of the total number, most RNA is non-coding RNA, and non-coding RNA may affect the occurrence and development of human cancers by affecting gene expression, therefore play an important role in human pathology. At present, ncRNAs studied include miRNA, circRNA, lncRNA, piRNA, and snoRNA, etc. After decades of research, the basic role of these ncRNAs in many cancers has been clear. As far as we know, the role of miRNAs in cancer is one of the hottest research directions, however, it is also found that the imbalance of ncRNAs will affect the occurrence of gastric cancer, breast cancer, lung cancer, meanwhile, it may also affect the prognosis of these cancers. Therefore, the study of ncRNAs in cancers may help to find new cancer diagnostic and treatment methods. Here, we reviewed the biosynthesis and characteristics of miRNA, cricRNA, and lncRNA etc., their roles in human cancers, as well as the mechanism through which these ncRNAs affect human cancers.
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Affiliation(s)
- Shijie Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Yiwen Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Sijun Deng
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiaoyong Lei
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
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5
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Mohamed AA, Abo–Elmatty DM, Esmail OE, Salim HSM, El Salam SMA, El-Ansary AR, Yacoub MF, Abdelrahman SAI, Saleh OM, Hassan Y, Abdulgawad EA, Sakr Y, Wahba AS. MicroRNA-224 Up-regulation: A Risk for Complications in Type 2 Diabetes Mellitus Egyptian Patients. PHARMACOPHORE 2022; 13:137-145. [DOI: 10.51847/skwtzqgb22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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6
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Zheng BH, He ZX, Zhang J, Ma JJ, Zhang HW, Zhu W, Shao ZM, Ni XJ. The Biological Function of TUSC7/miR-1224-3p Axis in Triple-Negative Breast Cancer. Cancer Manag Res 2021; 13:5763-5774. [PMID: 34305410 PMCID: PMC8296971 DOI: 10.2147/cmar.s305865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022] Open
Abstract
Background Triple-negative breast cancers (TNBC), comprising about 20% of breast cancers, have a poor prognosis. Currently, there is no effective target therapy for TNBC. LncRNA TUSC7 has been identified as a tumor suppressor in osteosarcoma and colorectal cancer. In this study, we investigated the clinical significance and the biological function of TUSC7 in breast cancer. Methods We retrospectively evaluated the expression level and clinical significance of TUSC7 in 90 paired breast cancer tissues and normal tissues. The proliferation, migration, and invasion assays were performed to investigate the biological function of TUSC7 in breast cancer. Finally, microarray, a luciferase reporter assay, and quantitative real-time polymerase chain reaction (qPCR) were used to explore the potential underlying mechanism of tumor suppressor role of TUSC7. Results Low TUSC7 expression was found to be an independent prognostic factor of poor overall survival (OS) in TNBC patients. Ectopic expression of TUSC7 inhibited tumor cell growth both in vitro and in vivo. TUSC7 overexpression significantly promoted the sensitivity of MDA-MB-468 cells to paclitaxel and carboplatin. In terms of the mechanism, TUSC7 might perform its biological function through binding with miR-1224-3P and regulating its expression level. Besides, genes in cell cycle pathways, such as BUB3 (budding uninhibited by benzimidazoles 3) and TGF-ß (targeting transforming growth factor β) pathways were downregulated, and genes involved in the MAPK (mitogen-activated protein kinase) (TGFBR2, transforming growth factor-beta receptor 2), PI3K-AKT (phosphoinositide 3-kinase- AKT serine/threonine kinase 1) and NF-κB (nuclear factor-kappa B subunit) pathways were upregulated in TUSC7 knockdown MDA-MB-231 cells. Conclusion The low TUSC7 expression is an independent prognostic factor of poor OS of TNBC patients. TUSC7 might inhibit breast cancer cell growth and metastasis both in vitro and vivo through binding with miR-1224-3P and regulating MAPK, PI3K/AKT, and NF-κB signaling pathways.
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Affiliation(s)
- Bo-Hao Zheng
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Zhi-Xian He
- Department of General Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, People's Republic of China
| | - Juan Zhang
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, People's Republic of China
| | - Jing-Jing Ma
- State Key Laboratory of Reproductive Medicine, Department of Breast Surgery, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing, 210004, People's Republic of China
| | - Hong-Wei Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Wei Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
| | - Zhi-Min Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Cancer Center and Cancer Institute, Fudan University, Shanghai, 200032, People's Republic of China
| | - Xiao-Jian Ni
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China.,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, People's Republic of China
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7
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Comprehensive Analysis of Differentially Expressed circRNAs Reveals a Colorectal Cancer-Related ceRNA Network. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:7159340. [PMID: 32952599 PMCID: PMC7481959 DOI: 10.1155/2020/7159340] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/25/2020] [Indexed: 12/15/2022]
Abstract
The morbidity and mortality of colorectal cancer (CRC) remained to be very high worldwide. Recently, circRNAs had been revealed to have a crucial role in cancer prognosis and progression. Numerous researches have shown that RNA sequencing technology and in silico method were widely used to identify pathogenic mechanisms and uncover promising targets for diagnosis and therapy. In this study, these methods were analyzed to obtain differentially expressed circRNAs (DECs). We identified upregulated 316 circRNAs and reduced 76 circRNAs in CRC samples, in comparison with those in normal tissues. In addition, a competitive endogenous network of circRNA-miRNA-mRNA was established to predict the mechanisms of circRNAs. Bioinformatics analysis revealed that these circRNAs participated in metabolism regulation and cell cycle progression. Of note, we observed the hub genes and miRNAs in this ceRNA network were associated with the survival time in CRC. We think this study could provide potential prognostic biomarkers and targets for CRC.
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8
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Shen H, Mo Q, Xu X, Liu B. The prognostic value of lncRNA SNHG6 in cancer patients. Cancer Cell Int 2020; 20:286. [PMID: 32655318 PMCID: PMC7339569 DOI: 10.1186/s12935-020-01383-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 06/26/2020] [Indexed: 01/01/2023] Open
Abstract
Background Although tremendous improvement has been seen in cancer diagnosis and treatment, its morbidity and mortality is still high due to lack of ideal biomarkers. An increasing number of studies have demonstrated that the expression of lncRNA small nucleolar RNA host gene 6 (SNHG6) has significantly negative correlation with various cancer prognosis. The present meta-analysis was aimed to clarify the potential of clinical application of SNHG6 in cancers. Methods A detailed literature review was conducted by searching through PubMed and Web of Science databases. The expression level of SNHG6, clinicopathological features and survival outcomes were extracted from eligible studies. Pooled analysis was performed with a DerSimonian-Laird random-effect model. The results were further validated through the Cancer Genome Atlas (TCGA) dataset. Results Five studies with a total of 487 cases were finally included in this meta-analysis. The results demonstrated that a high expression of SNHG6 was significantly associated with an increased risk of poor overall survival (OS) in cancer patients (HR = 2.06, 95% CI 1.56–2.73). Similar results from the TCGA dataset further confirmed our findings. Conclusions Overexpressed SNHG6 was significantly associated with poor prognosis in various cancers. Therefore, SNHG6 may become a novel molecular target for treatment and prognostic evaluation.
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Affiliation(s)
- Haixiang Shen
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Qingchun Road 79, Hangzhou, 310003 Zhejiang China
| | - Qiwang Mo
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Qingchun Road 79, Hangzhou, 310003 Zhejiang China.,Department of Urology, Shengzhou People's Hospital, Shengzhou, 312400 Zhejiang China
| | - Xin Xu
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Qingchun Road 79, Hangzhou, 310003 Zhejiang China
| | - Ben Liu
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Qingchun Road 79, Hangzhou, 310003 Zhejiang China
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9
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Lopez-Rincon A, Mendoza-Maldonado L, Martinez-Archundia M, Schönhuth A, Kraneveld AD, Garssen J, Tonda A. Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. Cancers (Basel) 2020; 12:cancers12071785. [PMID: 32635415 PMCID: PMC7407482 DOI: 10.3390/cancers12071785] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating microRNAs (miRNA) are small noncoding RNA molecules that can be detected in bodily fluids without the need for major invasive procedures on patients. miRNAs have shown great promise as biomarkers for tumors to both assess their presence and to predict their type and subtype. Recently, thanks to the availability of miRNAs datasets, machine learning techniques have been successfully applied to tumor classification. The results, however, are difficult to assess and interpret by medical experts because the algorithms exploit information from thousands of miRNAs. In this work, we propose a novel technique that aims at reducing the necessary information to the smallest possible set of circulating miRNAs. The dimensionality reduction achieved reflects a very important first step in a potential, clinically actionable, circulating miRNA-based precision medicine pipeline. While it is currently under discussion whether this first step can be taken, we demonstrate here that it is possible to perform classification tasks by exploiting a recursive feature elimination procedure that integrates a heterogeneous ensemble of high-quality, state-of-the-art classifiers on circulating miRNAs. Heterogeneous ensembles can compensate inherent biases of classifiers by using different classification algorithms. Selecting features then further eliminates biases emerging from using data from different studies or batches, yielding more robust and reliable outcomes. The proposed approach is first tested on a tumor classification problem in order to separate 10 different types of cancer, with samples collected over 10 different clinical trials, and later is assessed on a cancer subtype classification task, with the aim to distinguish triple negative breast cancer from other subtypes of breast cancer. Overall, the presented methodology proves to be effective and compares favorably to other state-of-the-art feature selection methods.
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Affiliation(s)
- Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands; (A.D.K.); (J.G.)
- Correspondence:
| | - Lucero Mendoza-Maldonado
- Nuevo Hospital Civil de Guadalajara “Dr. Juan I. Menchaca”, Salvador Quevedo y Zubieta 750, Independencia Oriente, Guadalajara C.P. 44340, Jalisco, Mexico;
| | - Marlet Martinez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y Diseno de farmacos, Seccion de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Alexander Schönhuth
- Life Sciences and Health, Centrum Wiskunde & Informatica, Science Park 123, 1098 XG Amsterdam, The Netherlands;
- Genome Data Science, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Aletta D. Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands; (A.D.K.); (J.G.)
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands; (A.D.K.); (J.G.)
- Global Centre of Excellence Immunology Danone Nutricia Research, Uppsalaan 12, 3584 CT Utrecht, The Netherlands
| | - Alberto Tonda
- UMR 518 MIA-Paris, INRAE, Université Paris-Saclay, 75013 Paris, France;
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Brownmiller T, Juric JA, Ivey AD, Harvey BM, Westemeier ES, Winters MT, Stevens AM, Stanley AN, Hayes KE, Sprowls SA, Ammer ASG, Walker M, Bey EA, Wu X, Lim ZF, Zhu L, Wen S, Hu G, Ma PC, Martinez I. Y Chromosome LncRNA Are Involved in Radiation Response of Male Non-Small Cell Lung Cancer Cells. Cancer Res 2020; 80:4046-4057. [PMID: 32616503 DOI: 10.1158/0008-5472.can-19-4032] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/01/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022]
Abstract
Numerous studies have implicated changes in the Y chromosome in male cancers, yet few have investigated the biological importance of Y chromosome noncoding RNA. Here we identify a group of Y chromosome-expressed long noncoding RNA (lncRNA) that are involved in male non-small cell lung cancer (NSCLC) radiation sensitivity. Radiosensitive male NSCLC cell lines demonstrated a dose-dependent induction of linc-SPRY3-2/3/4 following irradiation, which was not observed in radioresistant male NSCLC cell lines. Cytogenetics revealed the loss of chromosome Y (LOY) in the radioresistant male NSCLC cell lines. Gain- and loss-of-function experiments indicated that linc-SPRY3-2/3/4 transcripts affect cell viability and apoptosis. Computational prediction of RNA binding proteins (RBP) motifs and UV-cross-linking and immunoprecipitation (CLIP) assays identified IGF2BP3, an RBP involved in mRNA stability, as a binding partner for linc-SPRY3-2/3/4 RNA. The presence of linc-SPRY3-2/3/4 reduced the half-life of known IGF2BP3 binding mRNA, such as the antiapoptotic HMGA2 mRNA, as well as the oncogenic c-MYC mRNA. Assessment of Y chromosome in NSCLC tissue microarrays and expression of linc-SPRY3-2/3/4 in NSCLC RNA-seq and microarray data revealed a negative correlation between the loss of the Y chromosome or linc-SPRY3-2/3/4 and overall survival. Thus, linc-SPRY3-2/3/4 expression and LOY could represent an important marker of radiotherapy in NSCLC. SIGNIFICANCE: This study describes previously unknown Y chromosome-expressed lncRNA regulators of radiation response in male NSCLC and show a correlation between loss of chromosome Y and radioresistance. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/19/4046/F1.large.jpg.
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Affiliation(s)
- Tayvia Brownmiller
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Jamie A Juric
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Abby D Ivey
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Brandon M Harvey
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Emily S Westemeier
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Michael T Winters
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Alyson M Stevens
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Alana N Stanley
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Karen E Hayes
- Modulation Therapeutics, West Virginia University, Morgantown, West Virginia
| | - Samuel A Sprowls
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia
| | - Amanda S Gatesman Ammer
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Mackenzee Walker
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia
| | - Erik A Bey
- Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, Indiana
| | - Xiaoliang Wu
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Zuan-Fu Lim
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania.,Cancer Cell Biology Program, West Virginia University School of Graduate Studies, West Virginia University, Morgantown, West Virginia
| | - Lin Zhu
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Sijin Wen
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, West Virginia
| | - Gangqing Hu
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia.,Bioinformatics Core, West Virginia University, Morgantown, West Virginia
| | - Patrick C Ma
- Penn State Cancer Institute, Penn State Health Milton S. Hershey Medical Center, Pennsylvania State University, Hershey, Pennsylvania
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, West Virginia University Cancer Institute, School of Medicine, West Virginia University, Morgantown, West Virginia.
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11
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Zhang Y, Lin X, Geng X, Shi L, Li Q, Liu F, Fang C, Wang H. Advances in circular RNAs and their role in glioma (Review). Int J Oncol 2020; 57:67-79. [PMID: 32319596 PMCID: PMC7252450 DOI: 10.3892/ijo.2020.5049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Glioma is the most common primary tumour of the central nervous system, and is associated with a high postoperative recurrence rate and resistance to chemotherapy. High‑grade glioblastoma in particular has a very poor prognosis and poses a serious threat to human health. Related studies have confirmed that the occurrence and development of gliomas are closely associated with the abnormal expression and regulation of genes. Moreover, the number of studies on the association of the expression of non‑coding RNAs [linear RNAs, microRNAs and circular RNAs (circRNAs)] in human cells with glioma has been gradually increasing in recent years. Among those, circRNAs, previously considered to be 'splicing errors', have been shown to be highly expressed in eukaryotic cells and regulate the biological behaviour of gliomas. circRNAs are highly abundant and stable, and have become a research hotspot in the field of glioma molecular biology. The aim of the present review was to focus on the research progress regarding the association between circRNA expression and gliomas, and to provide a theoretical basis according to the currently available literature for further exploring this association. The present study may be of value for the early diagnosis, pathological grading, targeted therapy and prognostic evaluation of gliomas.
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Affiliation(s)
- Yuhao Zhang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Xiaomeng Lin
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Xiuchao Geng
- Hebei University of Chinese Medicine, Faculty of Integrated Traditional Chinese and Western Medicine, Shijiazhuang, Hebei 050091, P.R. China
| | - Liang Shi
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Qiang Li
- Hebei University of Chinese Medicine, Faculty of Acupuncture‑Moxibustion and Tuina, Shijiazhuang, Hebei 050200, P.R. China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Hong Wang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
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12
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Shih JH, Chen HY, Lin SC, Yeh YC, Shen R, Lang YD, Wu DC, Chen CY, Chen RH, Chou TY, Jou YS. Integrative analyses of noncoding RNAs reveal the potential mechanisms augmenting tumor malignancy in lung adenocarcinoma. Nucleic Acids Res 2020; 48:1175-1191. [PMID: 31853539 PMCID: PMC7026595 DOI: 10.1093/nar/gkz1149] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 07/06/2019] [Accepted: 12/01/2019] [Indexed: 01/12/2023] Open
Abstract
Precise noncoding RNA (ncRNA)-based network prediction is necessary to reveal ncRNA functions and pathological mechanisms. Here, we established a systemic pipeline to identify prognostic ncRNAs, predict their functions and explore their pathological mechanisms in lung adenocarcinoma (LUAD). After in silico and experimental validation based on evaluations of prognostic value in multiple LUAD cohorts, we selected the PTTG3P pseudogene from among other prognostic ncRNAs (MIR497HG, HSP078, TBX5-AS1, LOC100506990 and C14orf64) for mechanistic studies. PTTG3P upregulation in LUAD cells shortens the metaphase to anaphase transition in mitosis, increases cell viability after cisplatin or paclitaxel treatment, facilitates tumor growth that leads to poor survival in orthotopic lung models, and is associated with a poor survival rate in LUAD patients in the TCGA cohort who received chemotherapy. Mechanistically, PTTG3P acts as an ncRNA that interacts with the transcription factor FOXM1 to regulate the transcriptional activation of the mitotic checkpoint kinase BUB1B, which augments tumor growth and chemoresistance and leads to poor outcomes for LUAD patients. Overall, we established a systematic strategy to uncover prognostic ncRNAs with functional prediction methods suitable for pan-cancer studies. Moreover, we revealed that PTTG3P, due to its upregulation of the PTTG3P/FOXM1/BUB1B axis, could be a therapeutic target for LUAD patients.
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Affiliation(s)
- Jou-Ho Shih
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology & Drug Discovery, College of Medical Science & Technology, Taipei Medical University, Taipei 11221, Taiwan
| | - Shin-Chih Lin
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.,Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan
| | - Yi-Chen Yeh
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan
| | - Roger Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan
| | - Yaw-Dong Lang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Dung-Chi Wu
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yu Chen
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Teh-Ying Chou
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan.,Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11221, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan
| | - Yuh-Shan Jou
- Genome and Systems Biology Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 11221, Taiwan
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13
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Weng NQ, Chi J, Wen J, Mai SJ, Zhang MY, Huang L, Liu J, Yang XZ, Xu GL, Fu JH, Wang HY. The prognostic value of a seven-lncRNA signature in patients with esophageal squamous cell carcinoma: a lncRNA expression analysis. J Transl Med 2020; 18:47. [PMID: 32005248 PMCID: PMC6995134 DOI: 10.1186/s12967-020-02224-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/10/2020] [Indexed: 12/15/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) have been reported to be prognostic biomarkers in many types of cancer. We aimed to identify a lncRNA signature that can predict the prognosis in patients with esophageal squamous cell carcinoma (ESCC). Methods Using a custom microarray, we retrospectively analyzed lncRNA expression profiles in 141 samples of ESCC and 81 paired non-cancer specimens from Sun Yat-Sen University Cancer Center (Guangzhou, China), which were used as a training cohort to identify a signature associated with clinical outcomes. Then we conducted quantitative RT-PCR in another 103 samples of ESCC from the same cancer center as an independent cohort to verify the signature. Results Microarray analysis showed that there were 338 lncRNAs significantly differentially expressed between ESCC and non-cancer esophagus tissues in the training cohort. From these differentially expressed lncRNAs, we found 16 lncRNAs associated with overall survival (OS) of ESCC patients using Cox regression analysis. Then a 7-lncRNA signature for predicting survival was identified from the 16 lncRNAs, which classified ESCC patients into high-risk and low-risk groups. Patients with high-risk have shorter OS (HR: 3.555, 95% CI 2.195–5.757, p < 0.001) and disease-free survival (DFS) (HR: 2.537, 95% CI 1.646–3.909, p < 0.001) when compared with patients with low-risk in the training cohort. In the independent cohort, the 7 lncRNAs were detected by qRT-PCR and used to compute risk score for the patients. The result indicates that patients with high risk also have significantly worse OS (HR = 2.662, 95% CI 1.588–4.464, p < 0.001) and DFS (HR 2.389, 95% CI 1.447–3.946, p < 0.001). The univariate and multivariate Cox regression analyses indicate that the signature is an independent factor for predicting survival of patients with ESCC. Combination of the signature and TNM staging was more powerful in predicting OS than TNM staging alone in both the training (AUC: 0.772 vs 0.681, p = 0.002) and independent cohorts (AUC: 0.772 vs 0.660, p = 0.003). Conclusions The 7-lncRNA signature is a potential prognostic biomarker in patients with ESCC and may help in treatment decision when combined with the TNM staging system.
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Affiliation(s)
- Nuo-Qing Weng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Jun Chi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China.,Department of Endoscopy and Laser, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Jing Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China.,Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China
| | - Shi-Juan Mai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Mei-Yin Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Long Huang
- Department of Oncology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ji Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Xian-Zi Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China.,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China
| | - Guo-Liang Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China. .,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China. .,Department of Endoscopy and Laser, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Jian-Hua Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China. .,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China. .,Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, 510060, China.
| | - Hui-Yun Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Building 2, Room 704, Guzngzhou, 510060, China. .,Guangdong Esophageal Cancer Institute, Guangzhou, 510060, China.
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14
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Huang L, Tang X, Shi X, Su L. miR-532-5p promotes breast cancer proliferation and migration by targeting RERG. Exp Ther Med 2019; 19:400-408. [PMID: 31853317 DOI: 10.3892/etm.2019.8186] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/04/2019] [Indexed: 02/06/2023] Open
Abstract
Aberrant expression of microRNAs (miRNAs/miRs) mediates the initiation and progression of breast cancer. Therefore, it is important to investigate the molecular mechanisms of miRNAs and their effects on breast cancer progression. In the present study, miR-532-5p was highly expressed in breast cancer tissues compared with normal tissues. In addition, expression of ras-related and estrogen-regulated growth inhibitor (RERG), a tumor suppressor in breast cancer, was negatively correlated with miR-532-5p expression. Inhibition of miR-532-5p significantly elevated RERG at both mRNA and protein levels and inactivated the mitogen-activated protein kinase (MAPK)/ERK signaling pathway. Overexpression of miR-532-5p decreased RERG expression and activated the MAPK/ERK signaling in breast cancer cell line MDA-MB-231. Bioinformatic analysis indicated that RERG 3'-untraslated region contained a putative binding site for miR-532-5p. Dual luciferase assay further validated RERG as a target gene of miR-532-5p. Notably, downregulation of miR-532-5p inhibited MDA-MB-231 cell proliferation and migration, which was partially attenuated upon RERG knockdown. In conclusion, the current study revealed an oncogenic role of miR-532-5p in breast cancer cells via direct targeting of RERG expression.
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Affiliation(s)
- Lei Huang
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Xiaoqiao Tang
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Xianbiao Shi
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Lei Su
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
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15
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Talotta R, Sarzi-Puttini P, Laska MJ, Atzeni F. Retrotransposons shuttling genetic and epigenetic information from the nuclear to the mitochondrial compartment: Do they play a pathogenetic role in scleroderma? Cytokine Growth Factor Rev 2019; 49:42-58. [PMID: 31677967 DOI: 10.1016/j.cytogfr.2019.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 10/25/2022]
Abstract
Endogenous retroelements are a class of ancient defective viral insertions contained in the genome of host cells, where they account for up to 40% of all DNA. Centuries of co-existence in host genome have led to the development of immunotolerance to endogenous retroelements, most of which are defective and unable to replicate or transcribe functional proteins. However, given their capacity to move across the nuclear and mitochondrial genome and recombine, they could mix phenotypes and give rise to infections that may trigger innate and adaptive immune responses by sensing receptors capable of recognising foreign nucleic acids and proteins. It has recently been suggested that they play a role in the pathogenesis of autoimmune diseases on the grounds of their partial reactivation or the epigenetic control of host gene transcription. A number of studies have confirmed their contribution to the development of rheumatoid arthritis, multiple sclerosis and systemic lupus erythematosus, but there is still a lack of data concerning systemic sclerosis (SSc). Their role in the pathogenesis of SSc can be hypothesised on the basis of mitochondrial and nuclear chromatinic damage, and hyper-activation of the immune pathway involved in antiviral defense. SSc is characterised by genetic and immunological evidence of a viral infection but, as no viral agent has yet been isolated from SSc patients, the hypothesis that partial reactivation of endogenous retroviruses may trigger the disease cannot be excluded and deserves further investigation.
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Affiliation(s)
- Rossella Talotta
- Rheumatology Unit, University of Messina, Azienda Ospedaliera Gaetano Martino, Via Consolare Valeria 1, 98100 Messina, Italy.
| | - Piercarlo Sarzi-Puttini
- Rheumatology Unit, University Hospital ASST-Fatebenefratelli-Sacco, Via G.B Grassi 74, 20157 Milan, Italy.
| | | | - Fabiola Atzeni
- Rheumatology Unit, University of Messina, Azienda Ospedaliera Gaetano Martino, Via Consolare Valeria 1, 98100 Messina, Italy.
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16
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Deocesano-Pereira C, Machado RAC, De Jesus-Ferreira HC, Marchini T, Pereira TF, Carreira ACO, Sogayar MC. Functional impact of the long non-coding RNA MEG3 deletion by CRISPR/Cas9 in the human triple negative metastatic Hs578T cancer cell line. Oncol Lett 2019; 18:5941-5951. [PMID: 31788068 PMCID: PMC6865607 DOI: 10.3892/ol.2019.10969] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/26/2019] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) serve critical roles in regulating cellular homeostasis, and their deregulated expression/activity is associated with neoplastic transformation. The maternally expressed gene 3 (MEG3) has been extensively described as a tumor suppressor gene in different types of cancer, including breast cancer. Interestingly, using a panel of seven different breast cancer cell lines, the present study revealed that MEG3 is highly expressed in the triple negative metastatic human Hs578T breast cancer cell line, which is refractory to different therapeutic approaches. Therefore, the present study aimed to investigate the phenotypic impact of MEG3 deletion in this cell line. Using the CRISPR/Cas9 system, complete knockout (KO) of MEG3 was achieved. Deletion was confirmed by genomic PCR and reverse transcription-quantitative PCR. The MEG3_KO cell population displaying the highest efficiency of genomic editing was selected for phenotypic in vitro assays, including wound scratch and Transwell assays, flow cytometry and immunofluorescence. The results demonstrated that MEG3 deletion increased cell proliferation, anchorage-independent cell growth and cell motility, which was consistent with its well-known tumor suppressor function. However, the present study revealed that MEG3_KO also lead to decreased cell invasiveness ability, supporting previous evidence that MEG3 modulates epithelial-to-mesenchymal inducing factors. The present study demonstrated that deletion of MEG3 promoted an increase in transforming growth factor β and N-cadherin protein levels and significant reduction in matrix metallopeptidase 2, zinc-finger E-box binding homeobox 1 and collagen type III α1 chain gene expression levels. Additionally, MEG3_KO cells displayed significant resistance to doxorubicin treatment, demonstrating the role of this lncRNA in cancer cell survival by regulating apoptosis. The present study highlighted the utility of CRISPR/Cas9 for anticancer studies of intergenic lncRNAs and demonstrated that, although Hs578T cells express MEG3 at high levels, these cells display mechanisms to escape the growth suppression effects of this lncRNA. Notably, the detailed pathological mechanisms of MEG3 concerning tumor metastasis remain to be elucidated prior to applying MEG3 expression/activation in future therapeutic approaches for breast cancer treatment.
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Affiliation(s)
- Carlos Deocesano-Pereira
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
| | - Raquel Arminda Carvalho Machado
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.,Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil
| | - Henrique Cesar De Jesus-Ferreira
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.,Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil
| | - Thiago Marchini
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
| | - Tulio Felipe Pereira
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.,Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil
| | | | - Mari Cleide Sogayar
- Cell and Molecular Therapy Center, School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil.,Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo 05508-000 SP, Brazil
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17
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Lopez-Rincon A, Martinez-Archundia M, Martinez-Ruiz GU, Schoenhuth A, Tonda A. Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection. BMC Bioinformatics 2019; 20:480. [PMID: 31533612 PMCID: PMC6751684 DOI: 10.1186/s12859-019-3050-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/22/2019] [Indexed: 12/16/2022] Open
Abstract
Background MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entities to be measured for discriminating both different types of cancer and normal tissues, is of utmost importance. Feature selection techniques applied in machine learning can help however they often provide naive or biased results. Results An ensemble feature selection strategy for miRNA signatures is proposed. miRNAs are chosen based on consensus on feature relevance from high-accuracy classifiers of different typologies. This methodology aims to identify signatures that are considerably more robust and reliable when used in clinically relevant prediction tasks. Using the proposed method, a 100-miRNA signature is identified in a dataset of 8023 samples, extracted from TCGA. When running eight-state-of-the-art classifiers along with the 100-miRNA signature against the original 1046 features, it could be detected that global accuracy differs only by 1.4%. Importantly, this 100-miRNA signature is sufficient to distinguish between tumor and normal tissues. The approach is then compared against other feature selection methods, such as UFS, RFE, EN, LASSO, Genetic Algorithms, and EFS-CLA. The proposed approach provides better accuracy when tested on a 10-fold cross-validation with different classifiers and it is applied to several GEO datasets across different platforms with some classifiers showing more than 90% classification accuracy, which proves its cross-platform applicability. Conclusions The 100-miRNA signature is sufficiently stable to provide almost the same classification accuracy as the complete TCGA dataset, and it is further validated on several GEO datasets, across different types of cancer and platforms. Furthermore, a bibliographic analysis confirms that 77 out of the 100 miRNAs in the signature appear in lists of circulating miRNAs used in cancer studies, in stem-loop or mature-sequence form. The remaining 23 miRNAs offer potentially promising avenues for future research. Electronic supplementary material The online version of this article (10.1186/s12859-019-3050-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandro Lopez-Rincon
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, David de Wied building,Universiteitsweg 99, Utrecht, 3584 CG, The Netherlands.
| | - Marlet Martinez-Archundia
- Laboratorio de Modelado Molecular, Bioinformática y diseño de fármacos. Departamento de Posgrado. Escuela Superior de Medicina del Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Gustavo U Martinez-Ruiz
- Faculty of Medicine, National Autonomous University of Mexico; Federico Gomez Children's Hospital of Mexico, Mexico City, Mexico
| | | | - Alberto Tonda
- UMR 782 GMPA, Université Paris-Saclay, INRA, AgroParisTech, Thiverval-Grignon, France
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18
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Qiu J, Pan G, Li M. Decreased expression of long non-coding LOC285194 predicts tumour progression and poor prognosis of hepatocellular carcinoma after curative hepatectomy. Postgrad Med J 2019; 96:79-83. [PMID: 31494574 DOI: 10.1136/postgradmedj-2019-136905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) have been recently implicated as having oncogenic and tumour suppressor roles. LncRNA LOC285194 (LOC285194) expression was significantly reduced in a variety of tumour tissues and cell lines, which promotes cell proliferation and migration. The aim of the present study is to examine the expression pattern of LOC285194 and its clinical significance in hepatocellular carcinoma (HCC) patients after curative liver resection. MATERIALS AND METHODS We examined the expression of LOC285194 in 120 HCC samples and controls from adjacent non-tumour tissues using real-time quantitative reverse transcription-PCR and analysed its correlation with clinical parameters and prognosis in these patients who have undergone curative hepatic resection with a median follow-up of 3.5 years. RESULTS The expression level of LOC285194 was significantly lower in tumour tissues and four liver cancer cell lines compared with adjacent normal tissues and normal liver cell line. Furthermore, a low expression of LOC285194 was significantly correlated with advanced tumour stage, microvascular invasion, tumour number and differentiation. Additionally, survival analysis showed that patients with low LOC285194 expression had a significantly worse overall and disease-free survival. Moreover, univariate and multivariate analyses showed that decreased expression of LOC285194 was an independent predictor of long-term survival. CONCLUSIONS The low expression level of LOC285194 might be a novel candidate biomarker for predicting tumour progression and poor prognosis in HCC patients who have undergone hepatectomy and might be a potential target for gene therapy.
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Affiliation(s)
- Jianguo Qiu
- Department of Hepatobiliary surgery, The First Affiliated Hospital of Chonqing Medical University, Chongqing, China
| | - Gang Pan
- Department of General surgery, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China
| | - Ming Li
- Hepatobiliary surgery, Chongqing Medical University, Chongqing, China
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19
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Moscetti I, Cannistraro S, Bizzarri AR. Probing direct interaction of oncomiR-21-3p with the tumor suppressor p53 by fluorescence, FRET and atomic force spectroscopy. Arch Biochem Biophys 2019; 671:35-41. [PMID: 31181181 DOI: 10.1016/j.abb.2019.05.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 11/30/2022]
Abstract
miRNA-21-3p is overexpressed in a number of cancers and contributes to their development with a concomitant inhibition of the p53 onco-suppressive function. While a direct interaction of p53 with some miRNA precursors (namely pri-miRNAs and pre-miRNAs) was found, no interaction with mature micro RNA has been so far evidenced. It could therefore be very interesting to investigate if a direct interaction of miR-21-3p and p53 is occurring with possible impairment of the p53 onco-suppressive function. Fluorescence and Atomic Force Spectroscopy (AFS) were applied to study the interaction of p53 DNA Binding Domain (DBD) and miRNA-21-3p. Förster resonance energy transfer (FRET) was used to measure the distance between the DBD lone tryptophan (FRET donor) and a dye (FRET acceptor) bound to miRNA-21-3p. AFS and Fluorescence evidenced a direct interaction between miRNA-21-3p and DBD; with the formed complex being characterized by an affinity of 105 M, with a lifetime in the order of seconds. FRET allowed to determine an average distance of 4.0 nm between the DBD lone Trp146 and miRNA-21-3p; consistently with the involvement of the DBD L3 loop and/or the H1 helix in the complex formation, directly involved in the oligomerization and DNA binding. This may suggest that a functional inhibition of p53 could arise from its interaction with the oncogenic miRNA. Evidence of DBD-miRNA-21-3p complex formation may deserve some interest for inspiring novel therapeutic strategies.
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Affiliation(s)
- Ilaria Moscetti
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
| | | | - Anna Rita Bizzarri
- Biophysics and Nanoscience Centre, DEB, Università della Tuscia, Viterbo, Italy
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20
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Promoter hypermethylation-mediated downregulation of tumor suppressor gene SEMA3B and lncRNA SEMA3B-AS1 correlates with progression and prognosis of esophageal squamous cell carcinoma. Clin Exp Metastasis 2019; 36:225-241. [PMID: 30915595 DOI: 10.1007/s10585-019-09964-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/22/2019] [Indexed: 02/01/2023]
Abstract
Frequent deletions of tumor-suppressor genes at chromosome 3p21.3 have been detected in esophageal squamous cell carcinoma (ESCC). As a candidate tumor suppressor gene, semaphorin 3B (SEMA3B) is located at 3p21.3 and is frequently inactivated in several tumors. However, the role and inactivation mechanisms of SEMA3B and its antisense long non-coding RNA (lncRNA) SEMA3B-AS1 in the carcinogenesis of ESCC have not been fully elucidated. The present study was conducted to investigate the role, epigenetic inactivation mechanisms, and prognostic value of SEMA3B and SEMA3B-AS1 in ESCC tumorigenesis and prognosis. Frequent downregulation of SEMA3B and SEMA3B-AS1 was detected in esophageal cancer cells and ESCC tissues, and the expression level of SEMA3B and SEMA3B-AS1 in ESCC tissues was correlated with TNM stage and lymph node metastasis. SEMA3B and SEMA3B-AS1 shared the same CpG island in the promoter region and the expression of both genes might be regulated by the promoter methylation status. Furthermore, transcription factor Sp1 activated SEMA3B or SEMA3B-AS1 transcription and the promoter hypermethylation of SEMA3B and SEMA3B-AS1 influenced Sp1 binding ability. Moreover, over-expression of SEMA3B and SEMA3B-AS1 suppressed the viability and invasion of esophageal cancer cells in vitro. SEMA3B-AS1 influenced the protein expression of SEMA3B. SEMA3B or SEMA3B-AS1 expression and promoter methylation status were correlated with ESCC patients' survival. Thus, these findings suggest that SEMA3B and SEMA3B-AS1 may act as tumor suppressors and may serve as potential targets for antitumor therapy.
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21
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Jafari-Oliayi A, Asadi MH. SNHG6 is upregulated in primary breast cancers and promotes cell cycle progression in breast cancer-derived cell lines. Cell Oncol (Dordr) 2019; 42:211-221. [PMID: 30826970 DOI: 10.1007/s13402-019-00422-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are known as RNAs that do not encode proteins and that are more than 200 nucleotides in size. Previously, it has been found that LncRNAs play crucial roles in normal cellular processes, including proliferation and apoptosis. A growing body of evidence suggests that lncRNAs may also play regulatory roles in the initiation, progression and metastasis of various malignancies, including breast cancer. SNHG6 is a lncRNA that has previously been found to contribute to the initiation and progression of hepatocellular and gastric carcinomas. In this study, the clinical significance of SNHG6 expression in breast cancer was investigated. METHODS SNHG6 expression in primary breast cancer tissues was assessed using RT-qPCR. The functional role of SNHG6 was investigated using RNAi-mediated silencing and exogenous overexpression in breast cancer-derived cells. MTT, colony formation, cell cycle, apoptosis and senescence assays were used to determine the impact of SNHG6 expression on breast cancer-derived cells. The effect of SNHG6 on the migration and epithelial-to-mesenchymal transition (EMT) of breast cancer-derived cells was determined using scratch wound healing and immunofluorescence assays, respectively. RESULTS We found that the expression of SNHG6 was significantly upregulated in primary high-grade and progesterone receptor (PR)-positive breast tumours. Additional siRNA-based experiments revealed that SNHG6 silencing led to G1 cell cycle arrest in SK-BR-3 and MDA-MB-231 breast cancer-derived cells. Moreover, we found that SNHG6 silencing led to suppressed breast cancer cell proliferation by inducing apoptosis and senescence. Our data also indicate that SNHG6 may contribute to the migration and EMT of breast cancer cells. CONCLUSIONS Our results indicate that lncRNA SNHG6 is involved in breast cancer development and may be considered as a potential biomarker for the diagnosis, prognosis and treatment of breast cancer.
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Affiliation(s)
- Amin Jafari-Oliayi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Malek Hossein Asadi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
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22
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New Insights into Connection of Nucleolar Functions and Cancer. TANAFFOS 2019; 18:173-179. [PMID: 32411258 PMCID: PMC7210567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The nucleolus is an intranuclear membrane-less organelle. It is involved in ribosome biogenesis and protein synthesis. When the demand for protein synthesis increases in cell growth and proliferation (e.g., tumors), the cell upregulates ribosome biogenesis. Changes in nucleolar size and number have been recognized as known features of many tumor types. Recent evidence suggests that overproduction of ribosome, decreased ribosome biogenesis, and quantitative and qualitative changes in the nucleolus function, may result in oncogenesis. Today, it is clear that the nucleolus is involved in processes other than ribosome biogenesis. Other functions of the nucleolus include detecting and responding to endogenous and exogenous stress, maintaining genome stability, and regulating cell cycle progression, telomere function, cellular senescence, gene expression, and chromatin structure. Alterations in many of these fundamental nucleolar processes may contribute to the formation of cancer cell phenotypes. This phenomenon suggests that normal nucleolar functions are a safeguard against the development of malignancies and have potential therapeutic effects, as reported in non-small-cell lung carcinoma and other malignancies.
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23
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Expanding the miRNA Transcriptome of Human Kidney and Renal Cell Carcinoma. Int J Genomics 2018; 2018:6972397. [PMID: 30057905 PMCID: PMC6051088 DOI: 10.1155/2018/6972397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/15/2018] [Accepted: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Despite advancements in therapeutic strategies, diagnostic and prognostic molecular markers of kidney cancer remain scarce, particularly in patients who do not harbour well-defined driver mutations. Recent evidence suggests that a large proportion of the human noncoding transcriptome has escaped detection in early genomic explorations. Here, we undertake a large-scale analysis of small RNA-sequencing data from both clear cell renal cell carcinoma (ccRCC) and nonmalignant samples to generate a robust set of miRNAs that remain unannotated in kidney tissues. We find that these novel kidney miRNAs are also expressed in renal cancer cell lines. Moreover, these sequences are differentially expressed between ccRCC and matched nonmalignant tissues, implicating their involvement in ccRCC biology and potential utility as tumour-specific markers of disease. Indeed, we find some of these miRNAs to be significantly associated with patient survival. Finally, target prediction and subsequent pathway analysis reveals that miRNAs previously unannotated in kidney tissues may target genes involved in ccRCC tumourigenesis and disease biology. Taken together, our results represent a new resource for the study of kidney cancer and underscore the need to characterize the unexplored areas of the transcriptome.
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Guo W, Liu S, Dong Z, Guo Y, Ding C, Shen S, Liang J, Shan B. Aberrant methylation-mediated silencing of lncRNA CTC-276P9.1 is associated with malignant progression of esophageal squamous cell carcinoma. Clin Exp Metastasis 2018. [PMID: 29524086 DOI: 10.1007/s10585-018-9881-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Downregulation and aberrant hypermethylation of long non-coding RNA CTC-276P9.1 have been detected in limited tumors. However, the distribution of methylated CpG sites and biological role of CTC-276P9.1 in esophageal squamous cell carcinoma (ESCC) progression and prognosis have not been fully clarified. The present study was to investigate the expression status and the distribution of methylated CpG sites within the three CpG islands of CTC-276P9.1, further to clarify its functional role and prognostic value in ESCC development and prognosis. Significant downregulation of CTC-276P9.1 was detected in esophageal cancer cells and ESCC tissues, and the expression of CTC-276P9.1 in ESCC tissues was associated with TNM stage, pathological differentiation, lymph node metastasis, and distant metastasis or recurrence. The expression level of CTC-276P9.1 in esophageal cancer cells was significantly reversed by treatment with 5-Aza-dC and TSA. The aberrant hypermethylation of the regions around the transcription start site was more tumor specific and associated with the expression levels of CTC-276P9.1. Moreover, histone modification may also participate in the regulation of CTC-276P9.1. Furthermore, over-expression of CTC-276P9.1 inhibited esophageal cancer cells proliferation and invasion in vitro, decreased the expression of proliferative markers and inhibited esophageal cancer cells invasion probably by regulating EMT. In addition, the dysregulation and hypermethylation of the regions around the transcription start site of CTC-276P9.1 were associated with poorer ESCC patients' survival. These findings suggest that CTC-276P9.1 may act as a tumor suppressor and may be employed as a new prognostic factor and therapeutic target for ESCC.
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Affiliation(s)
- Wei Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shengnan Liu
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhiming Dong
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanli Guo
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Chunyan Ding
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Supeng Shen
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jia Liang
- Laboratory of Pathology, Hebei Cancer Institute, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Baoen Shan
- Research Center, The Fourth Hospital of Hebei Medical University, Jiankang Road 12, Shijiazhuang, 050011, Hebei, China.
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25
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Krishnan AR, Qu Y, Li PX, Zou AE, Califano JA, Wang-Rodriguez J, Ongkeko WM. Computational methods reveal novel functionalities of PIWI-interacting RNAs in human papillomavirus-induced head and neck squamous cell carcinoma. Oncotarget 2017; 9:4614-4624. [PMID: 29435129 PMCID: PMC5797000 DOI: 10.18632/oncotarget.23464] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022] Open
Abstract
Human papillomavirus (HPV) infection is the fastest growing cause of head and neck squamous cell carcinoma (HNSCC) today, but its role in malignant transformation remains unclear. This study aimed to conduct a comprehensive investigation of PIWI-interacting RNA (piRNA) alterations and functionalities in HPV-induced HNSCC. Using 77 RNA-sequencing datasets from TCGA, we examined differential expression of piRNAs between HPV16(+) HNSCC and HPV(–) Normal samples, identifying a panel of 30 HPV-dysregulated piRNAs. We then computationally investigated the potential mechanistic significances of these transcripts in HPV-induced HNSCC, identifying our panel of piRNAs to associate with the protein PIWIL4 as well as the RTL family of retrotransposon-like genes, possibly through direct binding interactions. We also recognized several HPV-dysregulated transcripts for their correlations with well-documented mutations and copy number variations in HNSCC as well as HNSCC clinical variables, demonstrating the potential ability of our piRNAs to play important roles in large-scale modulation of HNSCC in addition to their direct, smaller-scale interactions in this malignancy. The differential expression of key piRNAs, including NONHSAT077364, NONHSAT102574, and NONHSAT128479, was verified in vitro by evaluating endogenous expression in HPV(+) cancer vs. HPV(–) normal cell lines. Overall, our novel study provides a rigorous investigation of piRNA dysregulation in HPV-related HNSCC, and lends critical insight into the idea that these small regulatory transcripts may play crucial and previously unidentified roles in tumor pathogenesis and progression.
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Affiliation(s)
- Aswini R Krishnan
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Yuanhao Qu
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Pin Xue Li
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Angela E Zou
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
| | - Jessica Wang-Rodriguez
- Veterans Administration San Diego Healthcare System and Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Weg M Ongkeko
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, California, USA
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Meng Y, Li Q, Li L, Ma R. The long non-coding RNA CRNDE promotes cervical cancer cell growth and metastasis. Biol Chem 2017; 399:93-100. [PMID: 29194035 DOI: 10.1515/hsz-2017-0199] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 08/18/2017] [Indexed: 01/20/2023]
Abstract
This study was intended to analyze effects of lncRNA CRNDE on cervical cancer cell growth and metastasis. Fifty pairs of cervical cancer tissues and corresponding adjacent tissues were collected. Expressions of long non-coding RNAs (lncRNAs) in tissue samples were detected by microarray analysis. Expression levels of CRNDE in cervical cancer cells and normal cells were detected by qRT-PCR. Cell-counting kit-8 (CCK-8) assay and clone formation assay were utilized to evaluate cell growth. Wound healing assay and Transwell assay were conducted to detect the migratory and invasive capability of cervical cancer cells. The expressions of CRNDE in cervical cancer tissues and cells were higher than those in normal tissues and cells. CCK-8 assay and clone formation assay showed that the knockdown of CRNDE could inhibit the cell proliferation of HeLa and C-33A cells. Wound healing assay indicated that the downregulation of CRNDE expression could suppress the cell migration. The result of a Transwell assay demonstrated that the number of invasion cells reduced in the CRNDE-si group in comparison with the Mock group. LncRNA CRNDE could promote the cell growth and stimulate the metastasis of cervical cancer cells.
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Affiliation(s)
- Yuanyuan Meng
- Department of Gynaecology, Harbin Medical University Cancer Hospital, 150 HaPing Road, Nangang District, Harbin 150001, Heilongjiang, P.R. China
| | - Qi Li
- Department of Radiotherapy for Gynaecology, Harbin Medical University Cancer Hospital, Harbin 150001, Heilongjiang, P.R. China
| | - Lianwei Li
- Department of Gynaecology, Harbin Medical University Cancer Hospital, 150 HaPing Road, Nangang District, Harbin 150001, Heilongjiang, P.R. China
| | - Rong Ma
- Department of Gynaecology, Harbin Medical University Cancer Hospital, 150 HaPing Road, Nangang District, Harbin 150001, Heilongjiang, P.R. China
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27
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Wang L, Zhu H. Long non‑coding nuclear paraspeckle assembly transcript 1 acts as prognosis biomarker and increases cell growth and invasion in cervical cancer by sequestering microRNA‑101. Mol Med Rep 2017; 17:2771-2777. [PMID: 29207151 DOI: 10.3892/mmr.2017.8186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/09/2017] [Indexed: 11/06/2022] Open
Abstract
Emerging studies have focused on the essential role of long non‑coding RNAs (lncRNAs) in cervical carcinogenesis. A recent study has indicated that nuclear paraspeckle assembly transcript 1 (NEAT1) is highly expressed in the human cervical tissue. However, whether NEAT1 is involved in cervical cancer remains to be elucidated. Reverse transcription‑quantitative polymerase chain reaction results demonstrated that the expression of NEAT1 was higher in cervical cancer cells/tissues compared with that in normal human keratinocytes/tissues. Patients with higher NEAT1 level had poorer clinical characteristics and a shorter survival time compared with those that exhibited lower NEAT1 expression levels. In vitro, flow cytometery analysis revealed that transfection with NEAT1 small interfering RNA retarded cervical cancer cell (Caski and HeLa) growth by decreasing the percentage of S phase in the cell cycle and inducing cell apoptosis. In addition, the colony formation assay, wound healing assay and matrigel invasion assay results indicated that downregulation of NEAT1 inhibited colony formation, cell migration and invasion. Further investigation using the luciferase reporter assay revealed that the expression of mircoRNA‑101 (miR‑101) target gene Fos was positively associated with NEAT1 expression due to NEAT1‑competitive molecular sequestering of miR‑101 via base pairing. Furthermore, reduction of miR‑101 expression by inhibitor transfection reversed the effect of NEAT1 siRNA on cervical cancer cells. To conclude, the present data indicated that NEAT1 promoted cervical cancer progression by targeting miR‑101.
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Affiliation(s)
- Li Wang
- Department of Obstetrics and Gynecology, Xidian Group Hospital, Xi'an, Shaanxi 710077, P.R. China
| | - Hongying Zhu
- Department of Obstetrics and Gynecology, Xianyang Caihong Hospital, Xianyang, Shaanxi 712021, P.R. China
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28
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Wang S, Jiang J, Wang Z, Xie Y, Wu X. Long non-coding RNA SNHG1 is an unfavorable prognostic factor and promotes cell proliferation and migration by Wnt/β-catenin pathway in epithelial ovarian cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:9284-9292. [PMID: 31966800 PMCID: PMC6965897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/23/2017] [Indexed: 06/10/2023]
Abstract
Long non-coding RNAs (lncRNA) have been shown to serve critical roles in human cancers development, including epithelial ovarian cancer (EOC). Here, we identified a novel lncRNA SNHG1, which was markedly upregulated in human EOC tissues and cell lines. High SNHG1 expression was associated with aggressive clinical features and poor prognosis of EOC patients. Moreover, the downregulation of SNHG1 remarkably inhibited the EOC cells proliferation, migration and invasion, suppressed S-phase entry in vitro, and repressed tumor growth in vivo. In contrast, overexpression of SNHG1 could promote the aggressive behaviors of EOC cells. Furthermore, through western blot, we found that SNHG1 enhanced the expression of several downstream genes in Wnt/β-catenin pathway. Our findings demonstrated that the dysregulation of SNHG1 is implicated in EOC tumorigenesis and progression through regulating Wnt/β-catenin pathway.
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Affiliation(s)
- Sie Wang
- Department of Obstetrics and Gynecology, Jinan Central Hospital, Shandong University Jinan, Shandong, China
| | - Jingyan Jiang
- Department of Obstetrics and Gynecology, Jinan Central Hospital, Shandong University Jinan, Shandong, China
| | - Zhanying Wang
- Department of Obstetrics and Gynecology, Jinan Central Hospital, Shandong University Jinan, Shandong, China
| | - Yuanyuan Xie
- Department of Obstetrics and Gynecology, Jinan Central Hospital, Shandong University Jinan, Shandong, China
| | - Xihai Wu
- Department of Obstetrics and Gynecology, Jinan Central Hospital, Shandong University Jinan, Shandong, China
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29
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Downregulation of long noncoding RNA MEG3 is associated with poor prognosis and promoter hypermethylation in cervical cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:5. [PMID: 28057015 PMCID: PMC5216566 DOI: 10.1186/s13046-016-0472-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/11/2016] [Indexed: 12/15/2022]
Abstract
Background Our previous study reported that MEG3 is an important tumor suppressor gene that is inactivated in cervical cancer. However, the diagnostic and prognostic values of MEG3, as well as the molecular mechanism of MEG3 inactivation in cervical cancer, remain unclear. In this study, we aimed to further elucidate the role and potential inactivation mechanism of MEG3 in cervical cancer. Methods ROC curve and Cox regression analyses were used to assess the diagnostic and prognostic value of MEG3 in patients with cervical cancer. The methylation status of the MEG3 promoter in cervical cancer tissue samples was tested using methylation-specific PCR. Furthermore, we altered the methylation status of the MEG3 promoter in two cervical cancer cell lines (HeLa and CaSki) using a DNA methylation transfer enzyme inhibitor (5-Aza-CdR), to investigate whether promoter hypermethylation is a potential cause of MEG3 inactivation. Finally, we used CCK-8 and colony formation assays to evaluate the cell proliferation ability of HeLa and CaSki cells that had been treated with 5-aza-CdR, to investigate whether downregulation of MEG3 caused by promoter hypermethylation had biological effects. Results ROC curve analysis indicated that MEG3 status showed sufficient sensitivity and specificity for prediction of tumor size and lymph node metastasis in patients with cervical cancer. In addition, our follow-up data showed that low MEG3 expression was correlated with recurrence and short overall survival. Moreover, hypermethylation of the MEG3 promoter was observed in most cervical cancer tissue samples, and demethylation of the MEG3 promoter led to re-expression of MEG3 and inhibited proliferation of HeLa and CaSki cells. Conclusions MEG3 is a powerful tool for diagnosis and prognosis of patients with cervical cancer, and low expression of MEG3 is likely to be related to promoter hypermethylation in cervical cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0472-2) contains supplementary material, which is available to authorized users.
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De Luca M, Pels K, Moleirinho S, Curtale G. The epigenetic landscape of innate immunity. AIMS MOLECULAR SCIENCE 2017. [DOI: 10.3934/molsci.2017.1.110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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31
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Krishnan AR, Korrapati A, Zou AE, Qu Y, Wang XQ, Califano JA, Wang-Rodriguez J, Lippman SM, Hovell MF, Ongkeko WM. Smoking status regulates a novel panel of PIWI-interacting RNAs in head and neck squamous cell carcinoma. Oral Oncol 2016; 65:68-75. [PMID: 28109471 DOI: 10.1016/j.oraloncology.2016.12.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 11/30/2016] [Accepted: 12/17/2016] [Indexed: 12/28/2022]
Abstract
OBJECTIVE Smoking remains a primary etiological factor in head and neck squamous cell carcinoma (HNSCC). Given that non-coding RNAs (ncRNAs), including PIWI-interacting RNAs (piRNAs), have emerged as mediators of initiation and progression in head and neck malignancies, we undertook a global study of piRNA expression patterns in smoking-associated HNSCC. MATERIALS AND METHODS Using RNA-sequencing data from 256 current smoker and lifelong nonsmoker samples in The Cancer Genome Atlas (TCGA), we analyzed the differential expression patterns of 27,127 piRNAs across patient cohorts stratified by tobacco use, with HPV16 status and tumor status taken into account. We correlated their expression to clinical characteristics and to smoking-induced alterations of PIWI proteins, the functional counterparts of piRNAs. Finally, we correlated our identified piRNAs and PIWI proteins to known chromosomal aberrations in HNSCC to understand their wider-ranging genomic effects. RESULTS AND CONCLUSION Our analyses implicated a 13-member piRNA panel in smoking-related HNSCC, among which NONHSAT123636 and NONHSAT113708 associated with tumor stage, NONHSAT067200 with patient survival, and NONHSAT081250 with smoking-altered PIWIL1 protein expression. 6 piRNAs as well as PIWIL1 correlated with genomic alterations common to HNSCC, including TP53 mutation, TP53-3p co-occurrence, and 3q26, 8q24, and 11q13 amplification. Collectively, our findings provide novel insights into the etiology-specific piRNA landscape of smoking-induced HNSCC.
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Affiliation(s)
- Aswini R Krishnan
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Avinaash Korrapati
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Angela E Zou
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Yuanhao Qu
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Xiao Qi Wang
- Department of Surgery, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
| | - Jessica Wang-Rodriguez
- Veterans Administration Medical Center and Department of Pathology, University of California, San Diego, La Jolla, CA, United States.
| | - Scott M Lippman
- Department of Medicine and Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States.
| | - Melbourne F Hovell
- Graduate School of Public Health, San Diego State University, San Diego, CA, United States.
| | - Weg M Ongkeko
- Department of Otolaryngology-Head and Neck Surgery, University of California, San Diego, La Jolla, CA, United States.
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Tamoxifen Resistance: Emerging Molecular Targets. Int J Mol Sci 2016; 17:ijms17081357. [PMID: 27548161 PMCID: PMC5000752 DOI: 10.3390/ijms17081357] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022] Open
Abstract
17β-Estradiol (E2) plays a pivotal role in the development and progression of breast cancer. As a result, blockade of the E2 signal through either tamoxifen (TAM) or aromatase inhibitors is an important therapeutic strategy to treat or prevent estrogen receptor (ER) positive breast cancer. However, resistance to TAM is the major obstacle in endocrine therapy. This resistance occurs either de novo or is acquired after an initial beneficial response. The underlying mechanisms for TAM resistance are probably multifactorial and remain largely unknown. Considering that breast cancer is a very heterogeneous disease and patients respond differently to treatment, the molecular analysis of TAM’s biological activity could provide the necessary framework to understand the complex effects of this drug in target cells. Moreover, this could explain, at least in part, the development of resistance and indicate an optimal therapeutic option. This review highlights the implications of TAM in breast cancer as well as the role of receptors/signal pathways recently suggested to be involved in the development of TAM resistance. G protein—coupled estrogen receptor, Androgen Receptor and Hedgehog signaling pathways are emerging as novel therapeutic targets and prognostic indicators for breast cancer, based on their ability to mediate estrogenic signaling in ERα-positive or -negative breast cancer.
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Mazza T, Mazzoccoli G, Fusilli C, Capocefalo D, Panza A, Biagini T, Castellana S, Gentile A, De Cata A, Palumbo O, Stallone R, Rubino R, Carella M, Piepoli A. Multifaceted enrichment analysis of RNA-RNA crosstalk reveals cooperating micro-societies in human colorectal cancer. Nucleic Acids Res 2016; 44:4025-36. [PMID: 27067546 PMCID: PMC4872111 DOI: 10.1093/nar/gkw245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 03/24/2016] [Indexed: 12/16/2022] Open
Abstract
Alterations in the balance of mRNA and microRNA (miRNA) expression profiles contribute to the onset and development of colorectal cancer. The regulatory functions of individual miRNA-gene pairs are widely acknowledged, but group effects are largely unexplored. We performed an integrative analysis of mRNA–miRNA and miRNA–miRNA interactions using high-throughput mRNA and miRNA expression profiles obtained from matched specimens of human colorectal cancer tissue and adjacent non-tumorous mucosa. This investigation resulted in a hypernetwork-based model, whose functional backbone was fulfilled by tight micro-societies of miRNAs. These proved to modulate several genes that are known to control a set of significantly enriched cancer-enhancer and cancer-protection biological processes, and that an array of upstream regulatory analyses demonstrated to be dependent on miR-145, a cell cycle and MAPK signaling cascade master regulator. In conclusion, we reveal miRNA-gene clusters and gene families with close functional relationships and highlight the role of miR-145 as potent upstream regulator of a complex RNA–RNA crosstalk, which mechanistically modulates several signaling pathways and regulatory circuits that when deranged are relevant to the changes occurring in colorectal carcinogenesis.
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Affiliation(s)
- Tommaso Mazza
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Anna Panza
- Department of Medical Sciences, Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Annamaria Gentile
- Department of Medical Sciences, Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Angelo De Cata
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Orazio Palumbo
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Raffaella Stallone
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Rosa Rubino
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Unit, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Medical Genetics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
| | - Ada Piepoli
- Division of Epidemiology and Health Statistics, IRCCS Scientific Institute and Regional General Hospital 'Casa Sollievo della Sofferenza', San Giovanni Rotondo (FG), Italy
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Kan JY, Wu DC, Yu FJ, Wu CY, Ho YW, Chiu YJ, Jian SF, Hung JY, Wang JY, Kuo PL. Chemokine (C-C Motif) Ligand 5 is Involved in Tumor-Associated Dendritic Cell-Mediated Colon Cancer Progression Through Non-Coding RNA MALAT-1. J Cell Physiol 2015; 230:1883-94. [PMID: 25546229 DOI: 10.1002/jcp.24918] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 12/10/2014] [Accepted: 12/18/2014] [Indexed: 12/22/2022]
Abstract
Tumor micro-environment is a critical factor in the development of cancer. The aim of this study was to investigate the inflammatory cytokines secreted by tumor-associated dendritic cells (TADCs) that contribute to enhanced migration, invasion, and epithelial-to-mesenchymal transition (EMT) in colon cancer. The administration of recombinant human chemokine (C-C motif) ligand 5 (CCL5), which is largely expressed by colon cancer surrounding TADCs, mimicked the stimulation of TADC-conditioned medium on migration, invasion, and EMT in colon cancer cells. Blocking CCL5 by neutralizing antibodies or siRNA transfection diminished the promotion of cancer progression by TADCs. Tumor-infiltrating CD11c(+) DCs in human colon cancer specimens were shown to produce CCL5. The stimulation of colon cancer progression by TADC-derived CCL5 was associated with the up-regulation of non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), which subsequently increased the expression of Snail. Blocking MALAT-1 significantly decreased the TADC-conditioned medium and CCL5-mediated migration and invasion by decreasing the enhancement of Snail, suggesting that the MALAT-1/Snail pathway plays a critical role in TADC-mediated cancer progression. In conclusion, the inhibition of CCL5 or CCL5-related signaling may be an attractive therapeutic target in colon cancer patients.
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Affiliation(s)
- Jung-Yu Kan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Gastrointestinal and General Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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Zhang L, Wei P, Shen X, Zhang Y, Xu B, Zhou J, Fan S, Hao Z, Shi H, Zhang X, Kong R, Xu L, Gao J, Zou D, Liang C. MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing. PLoS One 2015; 10:e0131336. [PMID: 26158897 PMCID: PMC4497725 DOI: 10.1371/journal.pone.0131336] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
Abstract
Penile cancer (PeCa) is a relatively rare tumor entity but possesses higher morbidity and mortality rates especially in developing countries. To date, the concrete pathogenic signaling pathways and core machineries involved in tumorigenesis and progression of PeCa remain to be elucidated. Several studies suggested miRNAs, which modulate gene expression at posttranscriptional level, were frequently mis-regulated and aberrantly expressed in human cancers. However, the miRNA profile in human PeCa has not been reported before. In this present study, the miRNA profile was obtained from 10 fresh penile cancerous tissues and matched adjacent non-cancerous tissues via next-generation sequencing. As a result, a total of 751 and 806 annotated miRNAs were identified in normal and cancerous penile tissues, respectively. Among which, 56 miRNAs with significantly different expression levels between paired tissues were identified. Subsequently, several annotated miRNAs were selected randomly and validated using quantitative real-time PCR. Compared with the previous publications regarding to the altered miRNAs expression in various cancers and especially genitourinary (prostate, bladder, kidney, testis) cancers, the most majority of deregulated miRNAs showed the similar expression pattern in penile cancer. Moreover, the bioinformatics analyses suggested that the putative target genes of differentially expressed miRNAs between cancerous and matched normal penile tissues were tightly associated with cell junction, proliferation, growth as well as genomic instability and so on, by modulating Wnt, MAPK, p53, PI3K-Akt, Notch and TGF-β signaling pathways, which were all well-established to participate in cancer initiation and progression. Our work presents a global view of the differentially expressed miRNAs and potentially regulatory networks of their target genes for clarifying the pathogenic transformation of normal penis to PeCa, which research resource also provides new insights into future investigations aimed to explore the in-depth mechanisms of miRNAs and other small RNAs including piRNAs in penile carcinogenesis regulation and effective target-specific theragnosis.
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Affiliation(s)
- Li Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Pengfei Wei
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xudong Shen
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Yuanwei Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Bo Xu
- Center for Reproductive Medicine, Anhui Provincial Hospital Affiliated to Anhui Medical University, Hefei, Anhui, China
| | - Jun Zhou
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Song Fan
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Zongyao Hao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Haoqiang Shi
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Xiansheng Zhang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Rui Kong
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Lingfan Xu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Jingjing Gao
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
| | - Duohong Zou
- Key Laboratory of Oral Diseases Research of Anhui Province, Stomatologic College, Anhui Medical University, Hefei, Anhui, China
- * E-mail: (CZL); (DHZ)
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Institute of Urology, Anhui Medical University, Hefei, Anhui, China
- * E-mail: (CZL); (DHZ)
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36
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Altered MicroRNA Expression in Folliculotropic and Transformed Mycosis Fungoides. Pathol Oncol Res 2015; 21:821-5. [DOI: 10.1007/s12253-015-9897-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/06/2015] [Indexed: 10/24/2022]
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Wang J, Song YX, Wang ZN. Non-coding RNAs in gastric cancer. Gene 2015; 560:1-8. [PMID: 25659765 DOI: 10.1016/j.gene.2015.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/31/2015] [Accepted: 02/04/2015] [Indexed: 12/12/2022]
Abstract
Non-coding RNAs (ncRNAs) have recently become increasingly important in the study of cellular metabolism and regulation such as development, proliferation, differentiation and apoptosis. However, the functions of most ncRNAs have remained largely unknown. Recently, studies have begun to characterize the aberrant regulation of ncRNAs in gastric cancer (GC) cells and tissues. These ncRNAs have a close relationship with drug resistance, and with the occurrence, development, invasion and metastasis of tumors, so they could possibly become new therapeutic targets and treatment tools for GC in the future. The present review summarized current advances in our knowledge of the roles of ncRNAs in GC.
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Affiliation(s)
- Jun Wang
- Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang City 110001, China.
| | - Yong-Xi Song
- Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang City 110001, China.
| | - Zhen-Ning Wang
- Department of Surgical Oncology and General Surgery, First Hospital of China Medical University, 155 North Nanjing Street, Heping District, Shenyang City 110001, China.
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Abstract
Epigenetic and genetic alterations contribute to cancer initiation and progression. Epigenetics refers to the study of heritable changes in gene expression without alterations in DNA sequences. Epigenetic changes are reversible and include key processes of DNA methylation, chromatin modifications, nucleosome positioning, and alterations in noncoding RNA profiles. Disruptions in epigenetic processes can lead to altered gene function and cellular neoplastic transformation. Epigenetic modifications precede genetic changes and usually occur at an early stage in neoplastic development. Recent technological advances offer a better understanding of the underlying epigenetic alterations during carcinogenesis and provide insight into the discovery of putative epigenetic biomarkers for detection, prognosis, risk assessment, and disease monitoring. In this chapter we provide information on various epigenetic mechanisms and their role in carcinogenesis, in particular, epigenetic modifications causing genetic changes and the potential clinical impact of epigenetic research in the future.
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Affiliation(s)
- Rajnee Kanwal
- Department of Urology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
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Ricciuti B, Mecca C, Crinò L, Baglivo S, Cenci M, Metro G. Non-coding RNAs in lung cancer. Oncoscience 2014; 1:674-705. [PMID: 25593996 PMCID: PMC4278269 DOI: 10.18632/oncoscience.98] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 11/15/2014] [Indexed: 12/14/2022] Open
Abstract
The discovery that protein-coding genes represent less than 2% of all human genome, and the evidence that more than 90% of it is actively transcribed, changed the classical point of view of the central dogma of molecular biology, which was always based on the assumption that RNA functions mainly as an intermediate bridge between DNA sequences and protein synthesis machinery. Accumulating data indicates that non-coding RNAs are involved in different physiological processes, providing for the maintenance of cellular homeostasis. They are important regulators of gene expression, cellular differentiation, proliferation, migration, apoptosis, and stem cell maintenance. Alterations and disruptions of their expression or activity have increasingly been associated with pathological changes of cancer cells, this evidence and the prospect of using these molecules as diagnostic markers and therapeutic targets, make currently non-coding RNAs among the most relevant molecules in cancer research. In this paper we will provide an overview of non-coding RNA function and disruption in lung cancer biology, also focusing on their potential as diagnostic, prognostic and predictive biomarkers.
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Affiliation(s)
- Biagio Ricciuti
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | | | - Lucio Crinò
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Sara Baglivo
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Matteo Cenci
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Giulio Metro
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
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40
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Yapijakis C, Serefoglou Z, Papadimitriou K, Makrinou E. High frequency of TTTY2-like gene-related deletions in patients with idiopathic oligozoospermia and azoospermia. Andrologia 2014; 47:536-44. [PMID: 24919818 DOI: 10.1111/and.12300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2014] [Indexed: 11/30/2022] Open
Abstract
Genes located on Y chromosome and expressed in testis are likely to be involved in spermatogenesis. TTTY2 is a Y-linked multicopy gene family of unknown function that includes TTTY2L2A and TTTY2L12A at Yq11 and Yp11 loci respectively. Using PCR amplification, we screened for TTTY2L2A- and TTTY2L12A-associated deletions, in 94 Greek men with fertility problems. Patients were divided into three groups as following: group A (n = 28) included men with idiopathic moderate oligozoospermia, group B (n = 34) with idiopathic severe oligozoospermia and azoospermia, and group C (n = 32) with oligo- and azoospermia of various known etiologies. No deletions were detected in group C patients and 50 fertile controls. However, two patients from group A had deletions in TTTY2L2A (7.1%) and six in TTTY2L12A (21.4%), whereas from group B, four patients had deletions in TTTY2L2A (11.8%) and 10 in TTTY2L12A (29.4%). In addition, five patients from both groups A and B (8%) appeared to have deletions in both studied TTTY2 genes, although these are located very far apart. These results indicate that the TTTY2 gene family may play a significant role in spermatogenesis and suggest a possible mechanism of nonhomologous recombinational events that may cause genomic instability and ultimately lead to male infertility.
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Affiliation(s)
- C Yapijakis
- Department of Neurology, University of Athens Medical School, Eginition Hospital, Athens, Greece; Department of Molecular Genetics, "Cephalogenetics" Diagnostic Center, Athens, Greece
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Gajadhar AS, White FM. System level dynamics of post-translational modifications. Curr Opin Biotechnol 2014; 28:83-7. [PMID: 24441143 DOI: 10.1016/j.copbio.2013.12.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 12/24/2013] [Indexed: 11/20/2022]
Abstract
Attempts to characterize cellular behaviors with static, univariate measurements cannot fully capture biological complexity and lead to an inadequate interpretation of cellular processes. Significant biological insight can be gleaned by considering the contribution of dynamic protein post-translational modifications (PTMs) utilizing systems-level quantitative analysis. High-resolution mass spectrometry coupled with computational modeling of dynamic signal-response relationships is a powerful tool to reveal PTM-mediated regulatory networks. Recent advances using this approach have defined network kinetics of growth factor signaling pathways, identified systems level responses to cytotoxic perturbations, elucidated kinase-substrate relationships, and unraveled the dynamics of PTM cross-talk. Innovations in multiplex measurement capacity, PTM annotation accuracy, and computational integration of datasets promise enhanced resolution of dynamic PTM networks and further insight into biological intricacies.
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Affiliation(s)
- Aaron S Gajadhar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Teixeira AL, Ferreira M, Silva J, Gomes M, Dias F, Santos JI, Maurício J, Lobo F, Medeiros R. Higher circulating expression levels of miR-221 associated with poor overall survival in renal cell carcinoma patients. Tumour Biol 2013; 35:4057-66. [PMID: 24379138 DOI: 10.1007/s13277-013-1531-3] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/11/2013] [Indexed: 01/18/2023] Open
Abstract
The mechanisms involved in renal cell carcinoma (RCC) development and progression remain unclear, and new biomarkers for early detection, follow-up of the disease and prognosis are needed in routine practice to improve the diagnostic and/or prognostic accuracy. There is increasing evidence that microRNAs (miRNAs) are involved in cancer development and progression. The up-regulation of miR-221/222 has been described in several human cancers, and during RCC development, this up-regulation can modulate the metastatic process. Our purpose was to investigate the circulating expression levels of miR-221/222 as potential biomarkers for RCC detection and their influence in patients' overall survival. The circulating miR-221/222 was studied by relative quantification in 77 plasma samples. A follow-up study was undertaken to evaluate the overall survival. We observed that RCC patients presented higher circulating expression levels of miR-221 and miR-222 than healthy individuals (2(-ΔΔCt) = 2.8, P = 0.028; 2(-ΔΔCt) = 2.2, P = 0.044, respectively). The RCC patients with metastasis at diagnosis also presented higher circulating expression levels of miR-221 than patients with no metastasis (2(-ΔΔCt) = 10.9, P = 0.001). We also observed a significantly lower overall survival in patients with higher expression levels of miR-221 (48 vs 116 months, respectively; P = 0.024). Furthermore, multivariate Cox regression analysis using the tumour, nodes and metastasis stage (TNM stage); Fuhrman nuclear grade and age (≥60 years) as covariants demonstrated a higher risk of specific death by cancer in patients who presented higher expression levels of miR-221 (hazard ratio (HR) = 10.7, 95% confidence interval 1.33-85.65, P = 0.026). The concordance (c) index showed that the definition of profiles that contain information regarding tumour characteristics associated with circulating miR-221 expression information presents an increased capacity to predict the risk of death by RCC (c index model 1, 0.800 vs model 2, 0.961). Our results, which identified the plasma miR-221/222 at variable levels during RCC development, suggest that these miRNAs may have a potential as noninvasive biomarkers of RCC development.
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Affiliation(s)
- Ana L Teixeira
- Molecular Oncology Group, Portuguese Institute of Oncology of Porto, Rua Dr. António Bernardino de Almeida, 4200-072,, Porto, Portugal,
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Delihas N. Editorial on the Special Issue: Regulation by non-coding RNAs. Int J Mol Sci 2013; 14:21960-4. [PMID: 24201126 PMCID: PMC3856044 DOI: 10.3390/ijms141121960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Accepted: 10/31/2013] [Indexed: 12/13/2022] Open
Abstract
This Special Issue of IJMS is devoted to regulation by non-coding RNAs and contains both original research and review articles. An attempt is made to provide an up-to-date analysis of this very fast moving field and cover regulatory roles of both microRNAs and long non-coding RNAs. Multifaceted functions of these RNAs in normal cellular processes, as well as in disease progression, are highlighted.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, NY 11794-5222 USA.
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Levenson VV, Melnikov AA. Molecular biomarkers in 2013. Expert Rev Mol Diagn 2013; 13:773-6. [PMID: 24151845 DOI: 10.1586/14737159.2013.850419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Victor V Levenson
- US Biomarkers, Inc., 2201 W. Campbell Park Drive, Ste. 118, Chicago, IL 60612, USA +1 312 626 2886
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