1
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Gilyazova I, Enikeeva K, Rafikova G, Kagirova E, Sharifyanova Y, Asadullina D, Pavlov V. Epigenetic and Immunological Features of Bladder Cancer. Int J Mol Sci 2023; 24:9854. [PMID: 37373000 DOI: 10.3390/ijms24129854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Bladder cancer (BLCA) is one of the most common types of malignant tumors of the urogenital system in adults. Globally, the incidence of BLCA is more than 500,000 new cases worldwide annually, and every year, the number of registered cases of BLCA increases noticeably. Currently, the diagnosis of BLCA is based on cystoscopy and cytological examination of urine and additional laboratory and instrumental studies. However, cystoscopy is an invasive study, and voided urine cytology has a low level of sensitivity, so there is a clear need to develop more reliable markers and test systems for detecting the disease with high sensitivity and specificity. Human body fluids (urine, serum, and plasma) are known to contain significant amounts of tumorigenic nucleic acids, circulating immune cells and proinflammatory mediators that can serve as noninvasive biomarkers, particularly useful for early cancer detection, follow-up of patients, and personalization of their treatment. The review describes the most significant advances in epigenetics of BLCA.
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Affiliation(s)
- Irina Gilyazova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Kadriia Enikeeva
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Guzel Rafikova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Evelina Kagirova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Yuliya Sharifyanova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Dilara Asadullina
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, 450008 Ufa, Russia
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2
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Wang T, Li F, Lu Z. Ultra-conserved RNA: a novel biological tool with diagnostic and therapeutic potential. Discov Oncol 2023; 14:41. [PMID: 37036543 PMCID: PMC10086085 DOI: 10.1007/s12672-023-00650-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/03/2023] [Indexed: 04/11/2023] Open
Abstract
Ultra-conserved RNA (ucRNA) is a subset of long non-coding RNA, that is highly conserved among mice, rats and humans. UcRNA has attracted extensive attention in recent years for its potential biological significance in normal physiological function and diseases. However, due to the instability of RNA and the technical limitation, the function and mechanism of ucRNAs are largely unknown. Over the last two decades, researchers have made a lot of efforts to try to lift the veil of ucRNA in nervous, cardiovascular system and other systems as well as cancers. Since the concept of the glymphatic system is relatively new, we summarized here recent findings on the functions, regulation and the underlying mechanisms of ucRNAs in physiology and pathology. Meanwhile, pathology in some diseases is likely to contribute to abnormal expression of ucRNA in turn. We also discuss the technical challenges and bright prospects for future applications of ucRNAs in the diagnosis and treatment of diseases.
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Affiliation(s)
- Tingye Wang
- Department of Basic Medicine and Medical Technology, Medical College, Yangzhou University, Yangzhou, Jiangsu, China
| | - Feng Li
- Department of Basic Medicine and Medical Technology, Medical College, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou, Jiangsu, China
| | - Zhanping Lu
- Department of Basic Medicine and Medical Technology, Medical College, Yangzhou University, Yangzhou, Jiangsu, China.
- Jiangsu Key Laboratory of Experimental & Translational Non-Coding RNA Research, Yangzhou, Jiangsu, China.
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3
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Ciaramella A, Di Nardo E, Terracciano D, Conte L, Febbraio F, Cimmino A. A new biomarker panel of ultraconserved long non-coding RNAs for bladder cancer prognosis by a machine learning based methodology. BMC Bioinformatics 2023; 23:569. [PMID: 36879192 PMCID: PMC9987036 DOI: 10.1186/s12859-023-05167-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 01/25/2023] [Indexed: 03/08/2023] Open
Abstract
BACKGROUND Recent studies have indicated that a special class of long non-coding RNAs (lncRNAs), namely Transcribed-Ultraconservative Regions are transcribed from specific DNA regions (T-UCRs), 100[Formula: see text] conserved in human, mouse, and rat genomes. This is noticeable, as lncRNAs are usually poorly conserved. Despite their peculiarities, T-UCRs remain very understudied in many diseases, including cancer and, yet, it is known that dysregulation of T-UCRs is associated with cancer as well as with human neurological, cardiovascular, and developmental pathologies. We have recently reported the T-UCR uc.8+ as a potential prognostic biomarker in bladder cancer. RESULTS The aim of this work is to develop a methodology, based on machine learning techniques, for the selection of a predictive signature panel for bladder cancer onset. To this end, we analyzed the expression profiles of T-UCRs from surgically removed normal and bladder cancer tissues, by using custom expression microarray. Bladder tissue samples from 24 bladder cancer patients (12 Low Grade and 12 High Grade), with complete clinical data, and 17 control samples from normal bladder epithelium were analysed. After the selection of preferentially expressed and statistically significant T-UCRs, we adopted an ensemble of statistical and machine learning based approaches (i.e., logistic regression, Random Forest, XGBoost and LASSO) for ranking the most important diagnostic molecules. We identified a signature panel of 13 selected T-UCRs with altered expression profiles in cancer, able to efficiently discriminate between normal and bladder cancer patient samples. Also, using this signature panel, we classified bladder cancer patients in four groups, each characterized by a different survival extent. As expected, the group including only Low Grade bladder cancer patients had greater overall survival than patients with the majority of High Grade bladder cancer. However, a specific signature of deregulated T-UCRs identifies sub-types of bladder cancer patients with different prognosis regardless of the bladder cancer Grade. CONCLUSIONS Here we present the results for the classification of bladder cancer (Low and High Grade) patient samples and normal bladder epithelium controls by using a machine learning application. The T-UCR's panel can be used for learning an eXplainable Artificial Intelligent model and develop a robust decision support system for bladder cancer early diagnosis providing urinary T-UCRs data of new patients. The use of this system instead of the current methodology will result in a non-invasive approach, reducing uncomfortable procedures (such as cystoscopy) for the patients. Overall, these results raise the possibility of new automatic systems, which could help the RNA-based prognosis and/or the cancer therapy in bladder cancer patients, and demonstrate the successful application of Artificial Intelligence to the definition of an independent prognostic biomarker panel.
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Affiliation(s)
- Angelo Ciaramella
- Department of Science and Technology, University of Naples "Parthenope", Centro Direzionale, Isola C4, 80143, Naples, Italy.
| | - Emanuel Di Nardo
- Department of Science and Technology, University of Naples "Parthenope", Centro Direzionale, Isola C4, 80143, Naples, Italy.,Department of Computer Science, University of Milan, Via Celoria, 18, 20133, Milan, Italy
| | - Daniela Terracciano
- Department of Translational Medical Science, University of Naples "Federico II", Via Pansini 5, 80131, Naples, Italy
| | - Lia Conte
- Department of Experimental Urology, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525 GA, Nijmegen, The Netherlands
| | - Ferdinando Febbraio
- Institute of Biochemistry and Cell Biology, CNR, Via Pietro Castellino 111, 80131, Naples, Italy.
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
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4
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Aprile M, Costa V, Cimmino A, Calin GA. Emerging role of oncogenic long noncoding RNA as cancer biomarkers. Int J Cancer 2023; 152:822-834. [PMID: 36082440 DOI: 10.1002/ijc.34282] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 02/05/2023]
Abstract
The view of long noncoding RNAs as nonfunctional "garbage" has been definitely outdated by the large body of evidence indicating this class of ncRNAs as "golden junk", especially in precision oncology. Indeed, in light of their oncogenic role and the higher expression in multiple cancer types compared with paired adjacent tissues, the clinical interest for lncRNAs as diagnostic and/or prognostic biomarkers has been rapidly increasing. The emergence of large-scale sequencing technologies, their subsequent diffusion even in small research and clinical centers, the technological advances for the detection of low-copy lncRNAs in body fluids, coupled to the huge reduction of operating costs, have nowadays made possible to rapidly and comprehensively profile them in multiple tumors and large cohorts. In this review, we first summarize some relevant data about the oncogenic role of well-studied lncRNAs having a clinical relevance. Then, we focus on the description of their potential use as diagnostic/prognostic biomarkers, including an updated overview about licensed patents or clinical trials on lncRNAs in oncology.
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Affiliation(s)
- Marianna Aprile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - George Adrian Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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5
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Emerging RNA-Based Therapeutic and Diagnostic Options: Recent Advances and Future Challenges in Genitourinary Cancers. Int J Mol Sci 2023; 24:ijms24054601. [PMID: 36902032 PMCID: PMC10003365 DOI: 10.3390/ijms24054601] [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: 12/01/2022] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Renal cell carcinoma, bladder cancer, and prostate cancer are the most widespread genitourinary tumors. Their treatment and diagnosis have significantly evolved over recent years, due to an increasing understanding of oncogenic factors and the molecular mechanisms involved. Using sophisticated genome sequencing technologies, the non-coding RNAs, such as microRNAs, long non-coding RNAs, and circular RNAs, have all been implicated in the occurrence and progression of genitourinary cancers. Interestingly, DNA, protein, and RNA interactions with lncRNAs and other biological macromolecules drive some of these cancer phenotypes. Studies on the molecular mechanisms of lncRNAs have identified new functional markers that could be potentially useful as biomarkers for effective diagnosis and/or as targets for therapeutic intervention. This review focuses on the mechanisms underlying abnormal lncRNA expression in genitourinary tumors and discusses their role in diagnostics, prognosis, and treatment.
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6
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de Oliveira JC. Transcribed Ultraconserved Regions: New regulators in cancer signaling and potential biomarkers. Genet Mol Biol 2023; 46:e20220125. [PMID: 36622962 PMCID: PMC9829027 DOI: 10.1590/1678-4685-gmb-2022-0125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 11/06/2022] [Indexed: 01/11/2023] Open
Abstract
The ultraconserved regions (UCRs) are 481 genomic elements, longer than 200 bp, 100% conserved in human, mouse, and rat genomes. Usually, coding regions are more conserved, but more than 80% of UCRs are either intergenic or intronic, and many of them produce long non-coding RNAs (lncRNAs). Recently, the deregulated expression of transcribed UCRs (T-UCRs) has been associated with pathological conditions. But, differently from many lncRNAs with recognized crucial effects on malignant cell processes, the role of T-UCRs in the control of cancer cell networks is understudied. Furthermore, the potential utility of these molecules as molecular markers is not clear. Based on this information, the present review aims to organize information about T-UCRs with either oncogenic or tumor suppressor role associated with cancer cell signaling, and better describe T-UCRs with potential utility as prognosis markers. Out of 481 T-UCRs, 297 present differential expression in cancer samples, 23 molecules are associated with tumorigenesis processes, and 12 have more clear potential utility as prognosis markers. In conclusion, T-UCRs are deregulated in several tumor types, highlighted as important molecules in cancer networks, and with potential utility as prognosis markers, although further investigation for translational medicine is still needed.
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7
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Yu TX, Kalakonda S, Liu X, Han N, Chung HK, Xiao L, Rao JN, He TC, Raufman JP, Wang JY. Long noncoding RNA uc.230/CUG-binding protein 1 axis sustains intestinal epithelial homeostasis and response to tissue injury. JCI Insight 2022; 7:156612. [PMID: 36214222 PMCID: PMC9675575 DOI: 10.1172/jci.insight.156612] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/31/2022] [Indexed: 01/16/2023] Open
Abstract
Intestinal epithelial integrity is commonly disrupted in patients with critical disorders, but the exact underlying mechanisms are unclear. Long noncoding RNAs transcribed from ultraconserved regions (T-UCRs) control different cell functions and are involved in pathologies. Here, we investigated the role of T-UCRs in intestinal epithelial homeostasis and identified T-UCR uc.230 as a major regulator of epithelial renewal, apoptosis, and barrier function. Compared with controls, intestinal mucosal tissues from patients with ulcerative colitis and from mice with colitis or fasted for 48 hours had increased levels of uc.230. Silencing uc.230 inhibited the growth of intestinal epithelial cells (IECs) and organoids and caused epithelial barrier dysfunction. Silencing uc.230 also increased IEC vulnerability to apoptosis, whereas increasing uc.230 levels protected IECs against cell death. In mice with colitis, reduced uc.230 levels enhanced mucosal inflammatory injury and delayed recovery. Mechanistic studies revealed that uc.230 increased CUG-binding protein 1 (CUGBP1) by acting as a natural decoy RNA for miR-503, which interacts with Cugbp1 mRNA and represses its translation. These findings indicate that uc.230 sustains intestinal mucosal homeostasis by promoting epithelial renewal and barrier function and that it protects IECs against apoptosis by serving as a natural sponge for miR-503, thereby preserving CUGBP1 expression.
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Affiliation(s)
- Ting-Xi Yu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sudhakar Kalakonda
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Xiangzheng Liu
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Naomi Han
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Hee K. Chung
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lan Xiao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA
| | - Jaladanki N. Rao
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA
| | - Tong-Chuan He
- Department of Surgery, The University of Chicago Medical Center, Chicago, Illinois, USA
| | - Jean-Pierre Raufman
- Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA.,Department of Medicine and
| | - Jian-Ying Wang
- Cell Biology Group, Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Baltimore Veterans Affairs Medical Center, Baltimore, Maryland, USA.,Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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8
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Gibert MK, Sarkar A, Chagari B, Roig-Laboy C, Saha S, Bednarek S, Kefas B, Hanif F, Hudson K, Dube C, Zhang Y, Abounader R. Transcribed Ultraconserved Regions in Cancer. Cells 2022; 11:1684. [PMID: 35626721 PMCID: PMC9139194 DOI: 10.3390/cells11101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Transcribed ultraconserved regions are putative lncRNA molecules that are transcribed from DNA that is 100% conserved in human, mouse, and rat genomes. This is notable, as lncRNAs are typically poorly conserved. TUCRs remain very understudied in many diseases, including cancer. In this review, we summarize the current literature on TUCRs in cancer with respect to expression deregulation, functional roles, mechanisms of action, and clinical perspectives.
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Affiliation(s)
- Myron K. Gibert
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Aditya Sarkar
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Bilhan Chagari
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Christian Roig-Laboy
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Shekhar Saha
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Sylwia Bednarek
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Benjamin Kefas
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Farina Hanif
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Kadie Hudson
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Collin Dube
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Ying Zhang
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
| | - Roger Abounader
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA; (M.K.G.J.); (A.S.); (B.C.); (C.R.-L.); (S.S.); (S.B.); (B.K.); (F.H.); (K.H.); (C.D.); (Y.Z.)
- Department of Neurology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- NCI Designated Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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9
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Bozgeyik I. The dark matter of the human genome and its role in human cancers. Gene 2022; 811:146084. [PMID: 34843880 DOI: 10.1016/j.gene.2021.146084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/06/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022]
Abstract
The transcribed ultra-conserved regions (T-UCRs) are a novel family of non-coding RNAs which are absolutely conserved (100%) across orthologous regions of the human, mouse, and rat genomes. T-UCRs represent a small portion of the human genome that is likely to be functional but does not code for proteins and is referred to as the "dark matter" of the human genome. Although T-UCRs are ubiquitously expressed, tissue- and disease-specific expression of T-UCRs have also been observed. Accumulating evidence suggests that T-UCRs are differentially expressed and involved in the malignant transformation of human tumors through various genetic and epigenetic regulatory mechanisms. Therefore, T-UCRs are novel candidate predisposing biomarkers for cancer development. T-UCRs have shown to drive malignant transformation of human cancers through regulating non-coding RNAs and/or protein coding genes. However, the functions and fate of most T-UCRs remain mysterious. Here, we review and highlight the current knowledge on these ultra-conserved elements in the formation and progression of human cancers.
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Affiliation(s)
- Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine, Adiyaman University, Adiyaman, Turkey.
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10
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Zambalde EP, Adamoski D, Gradia DF, Rabinovich I, Rodrigues AC, Ivan C, Ribeiro EMSF, Calin GA, Carvalho de Oliveira J. Transcribed Ultraconserved Regions Are Associated with Clinicopathological Features in Breast Cancer. Biomolecules 2022; 12:214. [PMID: 35204715 PMCID: PMC8961524 DOI: 10.3390/biom12020214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 01/27/2023] Open
Abstract
Ultraconserved regions (UCRs) are 481 genome segments, with length longer than 200 bp, that are 100% conserved among humans, mice, and rats. The majority of UCRs are transcriptionally active (T-UCRs) as many of them produce non-coding RNAs. In a previous study, we evaluated the expression level of T-UCRs in breast cancer (BC) patients and found that 63% of transcripts correlated with some clinical and/or molecular parameter of BC. In this study, we delved into the expression levels of 12 T-UCRs and correlated them with clinicopathological parameters, immunohistochemical markers, and overall survival in two breast cancer cohorts: TCGA and Brazilian patients. We found that uc.268 is more expressed in TCGA patients under 40 years of age, associated with progesterone receptor (PR) and estrogen receptor (ER), and its high expression is found in luminal A. Lower uc.84 and uc.376 were respectively observed in metastatic and stage IV tumors associated with good prognostic in luminal B. Moreover, uc.84 was only related to the HER2+, while uc.376 was related to ER+ and PR+, and HER2+. A panel composed of uc.147, uc.271, and uc.427 distinguished luminal A from triple negative patients with an AUC of 0.9531 (sensitivity 92.19% and specificity 86.76%). These results highlight the potential role of T-UCRs in BC and provide insights into the potential application of T-UCRs as biomarkers.
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Affiliation(s)
- Erika Pereira Zambalde
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil;
| | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - Iris Rabinovich
- Hospital Nossa Senhora das Graças, Centro de Doenças da Mama, Curitiba 80810-040, PR, Brazil;
| | - Ana Carolina Rodrigues
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - Cristina Ivan
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, TX 77230, USA; (C.I.); (G.A.C.)
| | - Enilze M. S. F. Ribeiro
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
| | - George Adrian Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, TX 77230, USA; (C.I.); (G.A.C.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA
| | - Jaqueline Carvalho de Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, PR, Brazil; (E.P.Z.); (D.F.G.); (A.C.R.); (E.M.S.F.R.)
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11
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Vannini I, Ferracin M, Fabbri F, Fabbri M. Overexpression of ultraconserved region 83- induces lung cancer tumorigenesis. PLoS One 2022; 17:e0261464. [PMID: 35015757 PMCID: PMC8752010 DOI: 10.1371/journal.pone.0261464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/02/2021] [Indexed: 01/12/2023] Open
Abstract
The expression of non-coding RNAs (ncRNAs) is dysregulated in human cancers. The transcribed ultraconserved regions (T-UCRs) express long ncRNAs involved in human carcinogenesis. T-UCRs are non-coding genomic sequence that are 100% conserved across humans, rats and mice. Conservation of genomic sequences across species intrinsically implies an essential functional role and so we considered the expression of T-UCRs in lung cancer. Using a custom microarray we analyzed the global expression of T-UCRs. Among these T-UCRs, the greatest variation was observed for antisense ultraconserved element 83 (uc.83-), which was upregulated in human lung cancer tissues compared with adjacent non cancerous tissues. Even though uc.83- is located within the long intergenic non-protein coding RNA 1876 (LINC01876) gene, we found that the transcribed uc.83- is expressed independently of LINC01876 and was cloned as a 1143-bp RNA gene. In this study, functional analysis confirmed important effects of uc.83- on genes involved in cell growth of human cells. siRNA against uc.83- decreased the growth of lung cancer cells while the upregulation through a vector overexpressing the uc.83- RNA increased cell proliferation. We also show the oncogenic function of uc.83- is mediated by the phosphorylation of AKT and ERK 1/2, two important biomarkers of lung cancer cell proliferation. Based on our findings, inhibition against uc.83- could be a future therapeutic treatment for NSCLC to achieve simultaneous blockade of pathways involved in lung carcinogenesis.
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Affiliation(s)
- Ivan Vannini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine—DIMES, University of Bologna, Bologna, Italy
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Muller Fabbri
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC, United States of America
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12
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Pereira Zambalde E, Bayraktar R, Schultz Jucoski T, Ivan C, Rodrigues AC, Mathias C, knutsen E, Silveira de Lima R, Fiori Gradia D, de Souza Fonseca Ribeiro EM, Hannash S, Adrian Calin G, Carvalhode Oliveira J. A novel lncRNA derived from an ultraconserved region: lnc- uc.147, a potential biomarker in luminal A breast cancer. RNA Biol 2021; 18:416-429. [PMID: 34387142 PMCID: PMC8677017 DOI: 10.1080/15476286.2021.1952757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/02/2021] [Accepted: 07/04/2021] [Indexed: 02/06/2023] Open
Abstract
The human genome contains 481 ultraconserved regions (UCRs), which are genomic stretches of over 200 base pairs conserved among human, rat, and mouse. The majority of these regions are transcriptionally active (T-UCRs), and several have been found to be differentially expressed in tumours. Some T-UCRs have been functionally characterized, but of those few have been associated to breast cancer (BC). Using TCGA data, we found 302 T-UCRs related to clinical features in BC: 43% were associated with molecular subtypes, 36% with oestrogen-receptor positivity, 17% with HER2 expression, 12% with stage, and 10% with overall survival. The expression levels of 12 T-UCRs were further analysed in a cohort of 82 Brazilian BC patients using RT-qPCR. We found that uc.147 is high expressed in luminal A and B patients. For luminal A, a subtype usually associated with better prognosis, high uc.147 expression was associated with a poor prognosis and suggested as an independent prognostic factor. The lncRNA from uc.147 (lnc-uc.147) is located in the nucleus. Northern blotting results show that uc.147 is a 2,8 kb monoexonic trancript, and its sequence was confirmed by RACE. The silencing of uc.147 increases apoptosis, arrests cell cycle, and reduces cell viability and colony formation in BC cell lines. Additionally, we identifed 19 proteins that interact with lnc-uc.147 through mass spectrometry and demonstrated a high correlation of lnc-uc.147 with the neighbour gene expression and miR-18 and miR-190b. This is the first study to analyse the expression of all T-UCRs in BC and to functionally assess the lnc-uc.147.
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Affiliation(s)
- Erika Pereira Zambalde
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
| | - Tayana Schultz Jucoski
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Cristina Ivan
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Carolina Rodrigues
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Carolina Mathias
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | - Erik knutsen
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Department of Medical Biology, Faculty of Health Sciences, UiT - the Arctic University of Norway, Tromsø, Norway
| | | | - Daniela Fiori Gradia
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
| | | | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George Adrian Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, TX, USA
- Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaqueline Carvalhode Oliveira
- Laboratory of Human Cytogenetics and Oncogenetics, Department of Genetics, Universidade Federal Do Paraná, Curitiba, PR, Brazil
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13
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The Role of lncRNA in the Development of Tumors, including Breast Cancer. Int J Mol Sci 2021; 22:ijms22168427. [PMID: 34445129 PMCID: PMC8395147 DOI: 10.3390/ijms22168427] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/28/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are the largest groups of ribonucleic acids, but, despite the increasing amount of literature data, the least understood. Given the involvement of lncRNA in basic cellular processes, especially in the regulation of transcription, the role of these noncoding molecules seems to be of great importance for the proper functioning of the organism. Studies have shown a relationship between disturbed lncRNA expression and the pathogenesis of many diseases, including cancer. The present article presents a detailed review of the latest reports and data regarding the importance of lncRNA in the development of cancers, including breast carcinoma.
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14
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Ding Z, Yan Y, Guo YL, Wang C. Esophageal carcinoma cell-excreted exosomal uc.189 promotes lymphatic metastasis. Aging (Albany NY) 2021; 13:13846-13858. [PMID: 34024769 PMCID: PMC8202844 DOI: 10.18632/aging.202979] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/16/2021] [Indexed: 04/12/2023]
Abstract
Most cancers are old age-related diseases. Patients with lymphatic metastasis have an extremely poor prognosis in esophageal cancers (ECs). Previous studies showed ultraconserved RNAs are involved in tumorigenesis and ultraconserved RNA 189 (uc.189) served as an oncogene in cervical cancer, but the effect of exosomal uc.189 in esophageal squamous cell carcinoma (ESCC) remains undefined. This study revealed that uc.189 is closely correlated with lymph node (LN) metastasis and the number of lymphatic vessels in ESCC. ESCC-secreted exosomal uc.189 is transferred into human lymphatic endothelial cells (HLECs) to promote its proliferation, migration and tube formation to facilitate lymph node metastasis. Mechanistically, uc.189 regulated EPHA2 expression by directly binding to its 3'UTR region through dual-luciferase reporter assay. Over-expression and knockdown of EPHA2 could respectively rescue and simulate the effects induced by exosomal uc.189. Especially, the uc.189-EPHA2 axis activates the P38MAPK/VEGF-C pathway in HLECs. Finally, ESCC-secreted exosomal of uc.189 promotes HLECs sprouting in vitro, migration, and lymphangiogenesis. Thus, these findings suggested that exosomal uc.189 targets the EPHA2 of HLECs to promote lymphangiogenesis, and may represent a novel marker of diagnosis and treatment for ESCC patients in early stages.
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Affiliation(s)
- Zhiyan Ding
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, PR China
| | - Yun Yan
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou 225009, PR China
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, PR China
| | - Yu Lian Guo
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, PR China
| | - Chenghai Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, PR China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou 225001, PR China
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15
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Zheng Z, Hong D, Zhang X, Chang Y, Sun N, Lin Z, Li H, Huang S, Zhang R, Xie Q, Huang H, Jin H. uc.77- Downregulation Promotes Colorectal Cancer Cell Proliferation by Inhibiting FBXW8-Mediated CDK4 Protein Degradation. Front Oncol 2021; 11:673223. [PMID: 34094975 PMCID: PMC8172171 DOI: 10.3389/fonc.2021.673223] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 01/15/2023] Open
Abstract
Transcribed ultraconserved regions (T-UCRs) are a new type of long non-coding RNA, and the UCR has 481 segments longer than 200 base pairs that are 100% conserved between humans, rats, and mice. T-UCRs involved in colorectal cancer (CRC) have not been studied in detail. We performed T-UCR microarray analysis and found that uc.77- was significantly downregulated in CRC tissues and cell lines. Ectopic expression of uc.77- significantly inhibited the proliferation of CRC cells in vitro and the growth of xenograft tumors in nude mice in vivo. Mechanistic studies showed that uc.77- competed with FBXW8 mRNA for binding to microRNA (miR)-4676-5p through a competing endogenous RNA mechanism and inhibited the proliferation of CRC cells by negatively regulating CDK4. The present findings highlight the role of the uc.77-/miR-4676-5p/FBXW8 axis in CRC and identify uc.77- as a potential novel target for the treatment of CRC.
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Affiliation(s)
- Zhijian Zheng
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dan Hong
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Xiaodong Zhang
- Department of Colorectal Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yixin Chang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ning Sun
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhenni Lin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Hongyan Li
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Shirui Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruirui Zhang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Qipeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Haishan Huang
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Honglei Jin
- Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
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16
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Huang Y, Wang ZG, Tang L, Gong SG, Sun YY, Wang L, Jiang R, Wu WH, Luo CJ, Zhang J, Yang XJ, Li JL, Yuan XT, Zhao QH, Yuan P. Plasma exosomal miR-596: a novel biomarker predicts survival in patients with idiopathic pulmonary artery hypertension. J Int Med Res 2021; 49:3000605211002379. [PMID: 33788649 PMCID: PMC8020249 DOI: 10.1177/03000605211002379] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Objective To determine if plasma exosomal microRNAs (miRNAs) can predict survival in
patients with idiopathic pulmonary arterial hypertension (IPAH). Methods The study enrolled patients with IPAH that underwent right heart
catheterization. Plasma was collected and exosomal miRNAs were extracted.
Exosomes were evaluated using transmission electron microscopy, Western blot
analysis and particle size distribution analysis. MiRNAs were evaluated
using a miRNA microarray and validated using real-time polymerase chain
reaction. Results This study included 12 patients with IPAH in the study group and 48 patients
with IPAH in the validation group. The mean ± SD follow-up duration was
60.3 ± 35.4 months in the overall cohort. The levels of miR-596 were higher
in the nonsurvivors compared with the survivors. The levels of miR-596
significantly correlated with survival time, mean right atrial pressure,
pulmonary vascular resistance (PVR) and cardiac index. High levels of
miR-596 and PVR were significantly associated with poor overall survival.
Multivariate analysis demonstrated that exosomal miR-596 (hazard ratio
[HR] = 2.119; 95% confidence interval [CI] 1.402, 3.203) and PVR
(HR = 1.146; 95% CI 1.010, 1.300) were independent predictors of
survival. Conclusions High levels of plasma exosomal miR-596 were significantly associated with
disease severity and poor prognosis of patients with IPAH.
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Affiliation(s)
- Yang Huang
- Department of Cardiosurgery, Weifang Traditional Chinese Hospital, Weifang, Shandong Province, China
| | - Zuo-Gang Wang
- Department of Cardiosurgery, Weifang Traditional Chinese Hospital, Weifang, Shandong Province, China
| | - Liang Tang
- Department of Central Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Su-Gang Gong
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Yuan-Yuan Sun
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Lan Wang
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Rong Jiang
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Wen-Hui Wu
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Ci-Jun Luo
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Jie Zhang
- Department of Central Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Xiao-Jun Yang
- Department of Central Laboratory, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Jin-Ling Li
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Xun-Tao Yuan
- Department of Gastroenterology, Weifang Traditional Chinese Hospital, Weifang, Shandong Province, China
| | - Qin-Hua Zhao
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Ping Yuan
- Department of Cardio-Pulmonary Circulation, Shanghai Pulmonary Hospital, Tongji University, School of Medicine, Shanghai, China
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17
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Ferro M, La Civita E, Liotti A, Cennamo M, Tortora F, Buonerba C, Crocetto F, Lucarelli G, Busetto GM, Del Giudice F, de Cobelli O, Carrieri G, Porreca A, Cimmino A, Terracciano D. Liquid Biopsy Biomarkers in Urine: A Route towards Molecular Diagnosis and Personalized Medicine of Bladder Cancer. J Pers Med 2021; 11:jpm11030237. [PMID: 33806972 PMCID: PMC8004687 DOI: 10.3390/jpm11030237] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/10/2021] [Accepted: 03/19/2021] [Indexed: 12/11/2022] Open
Abstract
Bladder cancer (BC) is characterized by high incidence and recurrence rates together with genomic instability and elevated mutation degree. Currently, cystoscopy combined with cytology is routinely used for diagnosis, prognosis and disease surveillance. Such an approach is often associated with several side effects, discomfort for the patient and high economic burden. Thus, there is an essential demand of non-invasive, sensitive, fast and inexpensive biomarkers for clinical management of BC patients. In this context, liquid biopsy represents a very promising tool that has been widely investigated over the last decade. Liquid biopsy will likely be at the basis of patient selection for precision medicine, both in terms of treatment choice and real-time monitoring of therapeutic effects. Several different urinary biomarkers have been proposed for liquid biopsy in BC, including DNA methylation and mutations, protein-based assays, non-coding RNAs and mRNA signatures. In this review, we summarized the state of the art on different available tests concerning their potential clinical applications for BC detection, prognosis, surveillance and response to therapy.
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Affiliation(s)
- Matteo Ferro
- Department of Urology of European Institute of Oncology (IEO), IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (M.F.); (O.d.C.)
| | - Evelina La Civita
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
| | - Antonietta Liotti
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
| | - Michele Cennamo
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
| | - Fabiana Tortora
- Institute of Protein Biochemistry, National Research Council, 80131 Naples, Italy;
| | - Carlo Buonerba
- CRTR Rare Tumors Reference Center, AOU Federico II, 80131 Naples, Italy;
- Environment & Health Operational Unit, Zoo-Prophylactic Institute of Southern Italy, 80055 Portici, Italy
| | - Felice Crocetto
- Department of Neurosciences, Sciences of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy;
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation, Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy;
| | - Gian Maria Busetto
- Department of Urology and Organ Transplantation, University of Foggia, 71122 Foggia, Italy;
| | - Francesco Del Giudice
- Department of Urology, Sapienza University of Rome, 00185 Rome, Italy; (F.D.G.); (G.C.)
| | - Ottavio de Cobelli
- Department of Urology of European Institute of Oncology (IEO), IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (M.F.); (O.d.C.)
- Dipartimento di Oncologia ed Ematoncologia-DIPO-Università degli Studi di Milano, 20122 Milan, Italy
| | - Giuseppe Carrieri
- Department of Urology, Sapienza University of Rome, 00185 Rome, Italy; (F.D.G.); (G.C.)
| | - Angelo Porreca
- Department of Urology, Veneto Institute of Oncology, 31033 Padua, Italy;
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, 80131 Naples, Italy
- Correspondence: or (A.C.); (D.T.); Tel.: +39-81-746-3617 (D.T.)
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (E.L.C.); (A.L.); (M.C.)
- Correspondence: or (A.C.); (D.T.); Tel.: +39-81-746-3617 (D.T.)
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18
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Alkassis M, Kourie HR, Sarkis J, Nemr E. Predictive biomarkers in bladder cancer. Biomark Med 2021; 15:241-246. [PMID: 33625249 DOI: 10.2217/bmm-2020-0575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Marwan Alkassis
- Department of Urology, Hôtel Dieu de France, Université Saint Joseph, Beirut, Lebanon
| | - Hampig R Kourie
- Department of Hematology-Oncology, Hôtel Dieu de France, Université Saint Josephe, Beirut, Lebanon
| | - Julien Sarkis
- Department of Urology, Hôtel Dieu de France, Université Saint Joseph, Beirut, Lebanon
| | - Elie Nemr
- Department of Urology, Hôtel Dieu de France, Université Saint Joseph, Beirut, Lebanon
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19
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Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue. Cancers (Basel) 2021; 13:cancers13040681. [PMID: 33567603 PMCID: PMC7914980 DOI: 10.3390/cancers13040681] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/29/2021] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary DNA regions having high sequence similarity among human, rat and mouse genomes are defined as Ultraconserved Regions. Non-coding RNA transcripts originating by these regions may play relevant roles in the onset and progression of multiple cancer types. We recently found that ultra-conserved-transcript-8+ (uc.8+) levels correlate with the grading and staging of bladder cancer. The aim of this study is to systematically evaluate the expression of ultra-conserved-transcript-8+ (uc.8+) in biopsies and assess its intracellular localization. Furthermore, we aimed to correlate uc.8+ levels with clinical parameters and patient survival. Our analysis indicates that uc.8+ can localize both in the cytoplasm and nucleus of bladder cells at early stages of tumorigenesis, while in tumors at advanced stages, uc.8+ has a prevalent cytoplasmic localization. These data provide relevant information about uc.8+ localization as a hallmark of tumor stage. Finally, using advanced computer-based techniques, we predicted the binding of uc.8+ to RNA-binding proteins. Our study overall suggests that uc.8+ localization can be used as a prognostic biomarker for bladder cancer. Abstract Non-coding RNA transcripts originating from Ultraconserved Regions (UCRs) have tissue-specific expression and play relevant roles in the pathophysiology of multiple cancer types. Among them, we recently identified and characterized the ultra-conserved-transcript-8+ (uc.8+), whose levels correlate with grading and staging of bladder cancer. Here, to validate uc.8+ as a potential biomarker in bladder cancer, we assessed its expression and subcellular localization by using tissue microarray on 73 human bladder cancer specimens. We quantified uc.8+ by in-situ hybridization and correlated its expression levels with clinical characteristics and patient survival. The analysis of subcellular localization indicated the simultaneous presence of uc.8+ in the cytoplasm and nucleus of cells from the Low-Grade group, whereas a prevalent cytoplasmic localization was observed in samples from the High-Grade group, supporting the hypothesis of uc.8+ nuclear-to-cytoplasmic translocation in most malignant tumor forms. Moreover, analysis of uc.8+ expression and subcellular localization in tumor-surrounding stroma revealed a marked down-regulation of uc.8+ levels compared to the paired (adjacent) tumor region. Finally, deep machine-learning approaches identified nucleotide sequences associated with uc.8+ localization in nucleus and/or cytoplasm, allowing to predict possible RNA binding proteins associated with uc.8+, recognizing also sequences involved in mRNA cytoplasm-translocation. Our model suggests uc.8+ subcellular localization as a potential prognostic biomarker for bladder cancer.
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20
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Pascale E, Beclin C, Fiorenzano A, Andolfi G, Erni A, De Falco S, Minchiotti G, Cremer H, Fico A. Long Non-coding RNA T-UCstem1 Controls Progenitor Proliferation and Neurogenesis in the Postnatal Mouse Olfactory Bulb through Interaction with miR-9. Stem Cell Reports 2020; 15:836-844. [PMID: 32976763 PMCID: PMC7562942 DOI: 10.1016/j.stemcr.2020.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 08/22/2020] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Neural stem cell populations generate a wide spectrum of neuronal and glial cell types in a highly ordered fashion. MicroRNAs are essential regulators of this process. T-UCstem1 is a long non-coding RNA containing an ultraconserved element, and in vitro analyses in pluripotent stem cells provided evidence that it regulates the balance between proliferation and differentiation. Here we investigate the in vivo function of T-UCstem1. We show that T-UCstem1 is expressed in the forebrain neurogenic lineage that generates interneurons for the postnatal olfactory bulb. Gain of function in neural stem cells increased progenitor proliferation at the expense of neuron production, whereas knockdown had the opposite effect. This regulatory function is mediated by its interaction with miR-9-3p and miR-9-5p. Based thereon, we propose a mechanistic model for the role of T-UCstem1 in the dynamic regulation of neural progenitor proliferation during neurogenesis.
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Affiliation(s)
- Emilia Pascale
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy
| | | | - Alessandro Fiorenzano
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, and Lund Stem Cell Centre, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden
| | - Gennaro Andolfi
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy
| | - Andrea Erni
- Aix-Marseille Université, CNRS, IBDM, 13288 Marseille, France
| | - Sandro De Falco
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy
| | - Harold Cremer
- Aix-Marseille Université, CNRS, IBDM, 13288 Marseille, France
| | - Annalisa Fico
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy; Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131 Naples, Italy.
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Wang Y, Zhou D, Feng Y, Chen G, Li N. T-UCRs with digestive and respiratory diseases. Bioorg Med Chem Lett 2020; 30:127306. [PMID: 32631526 DOI: 10.1016/j.bmcl.2020.127306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/23/2022]
Abstract
From the perspective of histoembryology, the lung, gaster, and intestines that derived from the endoderm of the gastrula are structurally homologous. The interplay of intestines and lung in many pathologic changes is called the gut-lung axis. RNAs transcribed from ultraconserved regions (T-UCRs) are highly evolutionarily conserved in many mammalian genomes and have been found to be important in the pathogenesis and diagnosis of many diseases. More and more studies in recent years have shown that T-UCRs play important roles both in digestive and respiratory diseases. Taking the gut-lung axis as the entry point, this review summarizes the T-UCRs related to digestive and respiratory diseases in recent years. Meanwhile, these T-UCRs and their targets can lay a foundation for future drug research.
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Affiliation(s)
- Yajun Wang
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Di Zhou
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuan Feng
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Gang Chen
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ning Li
- School of Traditional Chinese Materia Medica, Key Laboratory of Computational Chemistry-Based Natural Antitumor Drug, Shenyang Pharmaceutical University, Shenyang 110016, China.
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22
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Liu X, Zhou X, Deng CJ, Zhao Y, Shen J, Wang Y, Zhang YL. Comprehensive analyses of T-UCR expression profiles and exploration of the efficacy of uc.63- and uc.280+ as biomarkers for lung cancer in Xuanwei, China. Pathol Res Pract 2020; 216:152978. [PMID: 32360249 DOI: 10.1016/j.prp.2020.152978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/23/2020] [Accepted: 04/13/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Lung cancer in Xuanwei (LCXW), China, is known worldwide for occurring frequently with high morbidity and mortality, which necessitates research to determine its pathogenesis. This study attempted to screen potential transcribed ultraconserved region (T-UCR) biomarkers related to LCXW. METHODS We performed T-UCR microarrays on 26 paired lung adenocarcinoma and adjacent tissues to explore the T-UCR expression profile of LCXW. Then, bioinformatics analysis was carried out to identify potential T-UCRs, which were further validated by real-time quantitative PCR (RT-qPCR). Then, clinical relevance analysis and Kaplan-Meier tests were performed on 50 paired tissues. RESULTS T-UCRs and RNA transcripts whose transcription units overlap UCRs (RTOUs) were significantly dysregulated in LCXW tissues compared with the corresponding noncancerous lung (NCL) tissues and presented an increasing trend from stage I to III. The expression between T-UCRs and host genes or flanking genes presented a positive or negative correlation. RT-qPCR analysis showed that uc.63- and uc.280+ were significantly up-regulated in LCXW tissues (P < 0.05). Uc.63- up-regulation was associated with tumor stage and poor prognosis of patients (P < 0.05), and uc.280+ up-regulation was associated with patient age (P < 0.05). Bioinformatics analysis of RTOUs showed that the transcripts of XPO1, uc002sbh and uc002sbg, were potentially regulated targets of uc.63-. Gene Ontology and pathway analyses showed XPO1 was involved in many important biological functions. CONCLUSION This study depicted T-UCR and RTOU expression profiling of LCXW and revealed some potential T-UCR biomarkers that may be involved in the carcinogenesis of LCXW.
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Affiliation(s)
- Xiao Liu
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China; Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China; Yunnan Institute of Laboratory Diagnosis, Kunming, 650032, China; Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, 650032, China
| | - Xin Zhou
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China; Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China; Yunnan Institute of Laboratory Diagnosis, Kunming, 650032, China; Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, 650032, China
| | - Cheng-Jun Deng
- Department of Gastroenterology, Kunming Children's Hospital, Kunming, 650034, China
| | - Ying Zhao
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China; Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China; Yunnan Institute of Laboratory Diagnosis, Kunming, 650032, China; Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, 650032, China
| | - Jie Shen
- Second Department of Internal Medicine, Kunming Third People's Hospital, Kunming, 650041, China
| | - Yan Wang
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China; Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China; Yunnan Institute of Laboratory Diagnosis, Kunming, 650032, China; Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, 650032, China
| | - Yan-Liang Zhang
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China; Yunnan Key Laboratory of Laboratory Medicine, Kunming, 650032, China; Yunnan Institute of Laboratory Diagnosis, Kunming, 650032, China; Innovation Team of Yunnan Provincial Clinical Laboratory and Diagnosis, Kunming, 650032, China.
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Pisapia L, Terreri S, Barba P, Mastroianni M, Donnini M, Mercadante V, Palmieri A, Verze P, Mirone V, Altieri V, Califano G, Liguori GL, Strazzullo M, Cimmino A, Del Pozzo G. Role of PA2G4P4 pseudogene in bladder cancer tumorigenesis. BIOLOGY 2020; 9:E66. [PMID: 32244410 PMCID: PMC7235711 DOI: 10.3390/biology9040066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Many pseudogenes possess biological activities and play important roles in the pathogenesis of various types of cancer including bladder cancer (BlCa), which still lacks suitable molecular biomarkers. Recently, pseudogenes were found to be significantly enriched in a pan-cancer classification based on the Cancer Genome Atlas gene expression data. Among them, the top-ranking pseudogene was the proliferation-associated 2G4 pseudogene 4 (PA2G4P4). METHODS Genomic and transcript features of PA2G4P4 were determined by GeneBank database analysis followed by 5' RACE experiments. Therefore, we conducted a retrospective molecular study on a cohort of 45 patients of BlCa. PA2G4P4 expression was measured by RT-qPCR, whereas PA2G4P4 transcript distribution was analyzed by in situ hybridization on both normal and cancerous histological sections and compared to the immunolocalization of its parental PA2G4/EBP1 protein. Finally, we tested the effects of PA2G4P4 depletion on proliferation, migration, and death of BlCa cells. RESULTS We showed for the first time PA2G4P4 overexpression in BlCa tissues and in cell lines. PA2G4P4 distribution strictly overlaps PA2G4/EBP1 protein localization. Moreover, we showed that PA2G4P4 knockdown affects both proliferation and migration of BlCa cells, highlighting its potential oncogenic role. CONCLUSIONS PA2G4P4 may play a functional role as an oncogene in BlCa development, suggesting it as a good candidate for future investigation and new clinical applications.
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Affiliation(s)
- Laura Pisapia
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Sara Terreri
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
- B Cell Pathophysiology Unit, IRCCS Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Pasquale Barba
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Marianna Mastroianni
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Maria Donnini
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Vincenzo Mercadante
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Alessandro Palmieri
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (V.M.); (G.C.)
| | - Paolo Verze
- Department of Medicine and Surgery “Scuola medica Salernitana” University of Salerno, 84084 Salerno, Italy; (P.V.); (V.A.)
| | - Vincenzo Mirone
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (V.M.); (G.C.)
| | - Vincenzo Altieri
- Department of Medicine and Surgery “Scuola medica Salernitana” University of Salerno, 84084 Salerno, Italy; (P.V.); (V.A.)
| | - Gianluigi Califano
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; (A.P.); (V.M.); (G.C.)
| | - Giovanna Lucia Liguori
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
| | - Giovanna Del Pozzo
- Institute of Genetics and Biophysics, CNR, 80131 Naples, Italy; (L.P.); (S.T.); (P.B.); (M.M.); (M.D.); (V.M.); (A.C.)
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24
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das Chagas PF, de Sousa GR, Kodama MH, de Biagi Junior CAO, Yunes JA, Brandalise SR, Calin GA, Tone LG, Scrideli CA, de Oliveira JC. Ultraconserved long non-coding RNA uc.112 is highly expressed in childhood T versus B-cell acute lymphoblastic leukemia. Hematol Transfus Cell Ther 2020; 43:28-34. [PMID: 32014474 PMCID: PMC7910170 DOI: 10.1016/j.htct.2019.12.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 10/02/2019] [Accepted: 12/05/2019] [Indexed: 12/29/2022] Open
Abstract
Aberrant expression of long non-coding RNAs (lncRNAs) has been detected in several types of cancer, including acute lymphoblastic leukemia (ALL), but lncRNA mapped on transcribed ultraconserved regions (T-UCRs) are little explored. The T-UCRs uc.112, uc.122, uc.160 and uc.262 were evaluated by quantitative real-time PCR in bone marrow samples from children with T-ALL (n = 32) and common-ALL/pre-B ALL (n = 30). In pediatric ALL, higher expression levels of uc.112 were found in patients with T-ALL, compared to patients with B-ALL. T-cells did not differ significantly from B-cells regarding uc.112 expression in non-tumor precursors from public data. Additionally, among B-ALL patients, uc.112 was also found to be increased in patients with hyperdiploidy, compared to other karyotype results. The uc.122, uc.160, and uc.262 were not associated with biological or clinical features. These findings suggest a potential role of uc.112 in pediatric ALL and emphasize the need for further investigation of T-UCR in pediatric ALL.
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Affiliation(s)
- Pablo Ferreira das Chagas
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil; Universidade Federal de Alfenas (UNIFAL), Alfenas, MG, Brazil
| | - Graziella Ribeiro de Sousa
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Márcio Hideki Kodama
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | | | | | | | | | - Luiz Gonzaga Tone
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Carlos Alberto Scrideli
- Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo (FMRP-USP), Ribeirão Preto, SP, Brazil
| | - Jaqueline Carvalho de Oliveira
- Universidade Federal de Alfenas (UNIFAL), Alfenas, MG, Brazil; Universidade Federal do Paraná (UFPR), Curitiba, PR, Brazil.
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25
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Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M, Paramio JM. Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet. Front Genet 2019; 10:1125. [PMID: 31850055 PMCID: PMC6902278 DOI: 10.3389/fgene.2019.01125] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is the most common neoplasia of the urothelial tract. Due to its high incidence, prevalence, recurrence and mortality, it remains an unsolved clinical and social problem. The treatment of BC is challenging and, although immunotherapies have revealed potential benefit in a percentage of patients, it remains mostly an incurable disease at its advanced state. Epigenetic alterations, including aberrant DNA methylation, altered chromatin remodeling and deregulated expression of non-coding RNAs are common events in BC and can be driver events in BC pathogenesis. Accordingly, these epigenetic alterations are now being used as potential biomarkers for these disorders and are being envisioned as potential therapeutic targets for the future management of BC. In this review, we summarize the recent findings in these emerging and exciting new aspects paving the way for future clinical treatment of this disease.
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Affiliation(s)
- Victor G. Martinez
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Ester Munera-Maravilla
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandra Bernardini
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carolina Rubio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristian Suarez-Cabrera
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Cristina Segovia
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Iris Lodewijk
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Marta Dueñas
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mónica Martínez-Fernández
- Genomes & Disease Lab, CiMUS (Center for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesus Maria Paramio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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26
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Pereira Zambalde E, Mathias C, Rodrigues AC, Souza Fonseca Ribeiro EM, Fiori Gradia D, Calin GA, Carvalho de Oliveira J. Highlighting transcribed ultraconserved regions in human diseases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1567. [DOI: 10.1002/wrna.1567] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/02/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022]
Affiliation(s)
| | - Carolina Mathias
- Department of Genetics Universidade Federal do Paraná Curitiba Brazil
| | | | | | | | - George A. Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center University of Texas Houston Texas
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The Transcribed-Ultra Conserved Regions: Novel Non-Coding RNA Players in Neuroblastoma Progression. Noncoding RNA 2019; 5:ncrna5020039. [PMID: 31167408 PMCID: PMC6631508 DOI: 10.3390/ncrna5020039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 05/30/2019] [Accepted: 06/03/2019] [Indexed: 12/15/2022] Open
Abstract
The Transcribed-Ultra Conserved Regions (T-UCRs) are a class of novel non-coding RNAs that arise from the dark matter of the genome. T-UCRs are highly conserved between mouse, rat, and human genomes, which might indicate a definitive role for these elements in health and disease. The growing body of evidence suggests that T-UCRs contribute to oncogenic pathways. Neuroblastoma is a type of childhood cancer that is challenging to treat. The role of non-coding RNAs in the pathogenesis of neuroblastoma, in particular for cancer development, progression, and therapy resistance, has been documented. Exosmic non-coding RNAs are also involved in shaping the biology of the tumor microenvironment in neuroblastoma. In recent years, the involvement of T-UCRs in a wide variety of pathways in neuroblastoma has been discovered. Here, we present an overview of the involvement of T-UCRs in various cellular pathways, such as DNA damage response, proliferation, chemotherapy response, MYCN (v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)) amplification, gene copy number, and immune response, as well as correlate it to patient survival in neuroblastoma.
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28
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Fico A, Fiorenzano A, Pascale E, Patriarca EJ, Minchiotti G. Long non-coding RNA in stem cell pluripotency and lineage commitment: functions and evolutionary conservation. Cell Mol Life Sci 2019; 76:1459-1471. [PMID: 30607432 PMCID: PMC6439142 DOI: 10.1007/s00018-018-3000-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/13/2018] [Accepted: 12/17/2018] [Indexed: 02/07/2023]
Abstract
LncRNAs have recently emerged as new and fundamental transcriptional and post-transcriptional regulators acting at multiple levels of gene expression. Indeed, lncRNAs participate in a wide variety of stem cell and developmental processes, acting in cis and/or in trans in the nuclear and/or in the cytoplasmic compartments, and generating an intricate network of interactions with RNAs, enhancers, and chromatin-modifier complexes. Given the versatility of these molecules to operate in different subcellular compartments, via different modes of action and with different target specificity, the interest in this research field is rapidly growing. Here, we review recent progress in defining the functional role of lncRNAs in stem cell biology with a specific focus on the underlying mechanisms. We also discuss recent findings on a new family of evolutionary conserved lncRNAs transcribed from ultraconserved elements, which show perfect conservation between human, mouse, and rat genomes, and that are emerging as new player in this complex scenario.
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Affiliation(s)
- Annalisa Fico
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy.
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy.
| | - Alessandro Fiorenzano
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, and Lund Stem Cell Centre, Department of Experimental Medical Science, Lund University, 22184, Lund, Sweden
| | - Emilia Pascale
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
| | - Eduardo Jorge Patriarca
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
| | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
- Institute of Genetics and Biophysics "A. Buzzati-Traverso", CNR, 80131, Naples, Italy
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29
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Zhang Z, Dai DQ. MicroRNA-596 acts as a tumor suppressor in gastric cancer and is upregulated by promotor demethylation. World J Gastroenterol 2019; 25:1224-1237. [PMID: 30886505 PMCID: PMC6421237 DOI: 10.3748/wjg.v25.i10.1224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/27/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In the present study, we investigated a suppressive role of microRNA-596 (miR-596) in gastric cancer (GC). Moreover, the downregulation of miR-596 in GC cell lines was associated with an increase of miR-596 promoter methylation. We also established that miR-596 controls the expression of peroxiredoxin 1 (PRDX1), which has never been reported before, suggesting that this interaction could play an important role in GC progression.
AIM To study the potential role and possible regulatory mechanism of miR-596 in GC.
METHODS The expression levels of miR-596 and PRDX1 in gastric cancer tissues and cell lines were detected by quantitative real-time PCR (qRT-PCR). Western blot and luciferase reporter assay were used to detect the effect of miR-596 on PRDX1 expression. Then, the proliferation, metastasis, and invasion of GC cell lines transfected with miR-596 mimics were analyzed, respectively, by Cell Counting Kit-8 proliferation assay, wound healing assay, and transwell invasion assay. Meanwhile, the methylation status of the promoter CpG islands of miR-596 in GC cell lines was detected by methylation-specific PCR (MSP).
RESULTS Expression of miR-596 was decreased and PRDX1 was upregulated in GC tissues and cell lines. Overexpression of miR-596 decreased the expression of PRDX1 and luciferase reporter assays detected the direct binding of miR-596 to the 3'-untranslated region (UTR) of PRDX1 transcripts. Furthermore, we found that overexpression of miR-596 remarkably suppressed cell proliferation, migration, and invasion in GC cells. We further analyzed miR-596 promoter methylation by MSP and qRT-PCR, and found the downregulation of miR-596 was associated with promoter methylation status in GC cell lines. Moreover, DNA demethylation and reactivation of miR-596 after treatment with 5-Aza-2’-deoxycytidine inhibited the proliferative ability of GC cells.
CONCLUSION MiR-596 has a tumor suppressive role in GC and is downregulated partly due to promoter hypermethylation. Furthermore, PRDX1 is one of the putative target genes of miR-596.
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Affiliation(s)
- Zhen Zhang
- Department of Gastroenterological Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
| | - Dong-Qiu Dai
- Department of Gastroenterological Surgery, the Fourth Affiliated Hospital of China Medical University, Shenyang 110032, Liaoning Province, China
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Wen L, Zhang X, Bian J, Han L, Huang H, He M, Wei M, Wang P. The long non-coding RNA LINC00460 predicts the prognosis and promotes the proliferation and migration of cells in bladder urothelial carcinoma. Oncol Lett 2019; 17:3874-3880. [PMID: 30881506 PMCID: PMC6403511 DOI: 10.3892/ol.2019.10023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) may serve an important role in cancer development and may also be suitable for use as prognostic biomarkers. At present, the role of lncRNAs in bladder cancer remains unclear. The present study examined the potential involvement of lncRNA LINC00460 in bladder urothelial carcinoma using data from The Caner Genome Atlas (TCGA) and cell line experiments. The results indicated that LINC00460 expression levels were increased in bladder urothelial carcinoma tissues and bladder cancer 5637 and T24 cell lines compared with corresponding normal controls (P<0.05). TCGA data indicated that LINC00460 expression was negatively correlated with a positive prognosis in patients with bladder urothelial carcinoma (P<0.05). Consistently, the downregulation of LINC00460 with short hairpin RNA significantly suppressed 5637 and T24 cell proliferation and migration. Therefore, it was suggested that strategies that target LINC00460 may be developed as novel therapeutic approaches for the treatment of bladder cancer. In addition, the expression level of androgen receptor (AR) was downregulated in bladder urothelial carcinoma tissues and exhibited a negative correlation with the expression level of LINC00460 (r=−0.43; P<0.0001), based on the data from TCGA. We hypothesized that LINC00460 may serve an oncogenic role by regulating the expression of AR.
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Affiliation(s)
- Lijie Wen
- Department of Urology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Xiling Zhang
- Department of Urology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Jing Bian
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Li Han
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Haibo Huang
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Miao He
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Minjie Wei
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Ping Wang
- Department of Urology, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
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Quan J, Pan X, Zhao L, Li Z, Dai K, Yan F, Liu S, Ma H, Lai Y. LncRNA as a diagnostic and prognostic biomarker in bladder cancer: a systematic review and meta-analysis. Onco Targets Ther 2018; 11:6415-6424. [PMID: 30323619 PMCID: PMC6177400 DOI: 10.2147/ott.s167853] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Bladder cancer is one of the most common urinary malignancies, and has a high recurrence rate and poor outcomes. In order to identify novel diagnostic and prognostic biomarkers for bladder cancer, we conducted a meta-analysis to analyze the association between long non-coding RNA (lncRNA) expression and survival in bladder cancer. Materials and methods We searched literature from databases using our inclusion and exclusion criteria. STATA 14.0 software was used to analyze the data from collected studies and to construct the forest plots. A different effect size was selected for each meta-analysis. Results After selection, 30 articles were found to be eligible. The present meta-analysis contains data from 13 articles about clinicopathological characteristics, six articles about diagnosis, and 16 articles about prognosis. In the present study, we found that many lncRNAs could function as potential diagnostic and prognostic markers in bladder cancer. Among these findings, UCA1 was expected to be a diagnostic biomarker for bladder cancer, while the aberrant expression of HOTAIR and GAS5 was associated with poor disease-free survival/recurrence-free survival/disease-specific survival. Conclusion Overall, the present study is the first meta-analysis to assess the association between expression of lncRNAs and clinical value in patients with bladder cancer. LncRNAs hold promise as novel diagnostic and prognostic markers in bladder cancer.
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Affiliation(s)
- Jing Quan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China, .,Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Xiang Pan
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China, .,Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Liwen Zhao
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China, .,Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Zuwei Li
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China,
| | - Kangfu Dai
- Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Fangli Yan
- Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Suyue Liu
- Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Hongfei Ma
- Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
| | - Yongqing Lai
- Department of Urology, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China, .,Graduate school, Anhui Medical University, Hefei, Anhui 230032, China,
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Sekino Y, Sakamoto N, Goto K, Honma R, Shigematsu Y, Quoc TP, Sentani K, Oue N, Teishima J, Kawakami F, Karam JA, Sircar K, Matsubara A, Yasui W. Uc.416 + A promotes epithelial-to-mesenchymal transition through miR-153 in renal cell carcinoma. BMC Cancer 2018; 18:952. [PMID: 30286729 PMCID: PMC6172711 DOI: 10.1186/s12885-018-4863-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background The transcribed ultraconserved regions (T-UCRs) are a novel class of non-coding RNAs that are absolutely conserved across species and are involved in carcinogenesis in some cancers. However, the expression and biological role of T-UCRs in renal cell carcinoma (RCC) remain poorly understood. This study aimed to examine the expression and functional role of Uc.416 + A and analyze the association between Uc.416 + A and epithelial-to-mesenchymal transition in RCC. Methods Expression of Uc.416 + A in 35 RCC tissues, corresponding normal kidney tissues and 13 types of normal tissue samples was determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). We performed a cell growth and migration assay in RCC cell line 786-O transfected with negative control and siRNA for Uc.416 + A. We evaluated the relation between Uc.416 + A and miR-153, which has a complimentary site of Uc.416 + A. Results qRT-PCR analysis revealed that the expression of Uc.416 + A was higher in RCC tissues than that in corresponding normal kidney tissues. Inhibition of Uc.416 + A reduced cell growth and cell migration activity. There was an inverse correlation between Uc.416 + A and miR-153. Western blot analysis showed Uc.416 + A modulated E-cadherin, vimentin and snail. The expression of Uc.416 + A was positively associated with the expression of SNAI1, VIM and inversely associated with the expression of CDH1. Conclusions The expression of Uc.416 + A was upregulated in RCC and especially in RCC tissues with sarcomatoid change. Uc.416 + A promoted epithelial-to-mesenchymal transition through miR-153. These results suggest that Uc.416 + A may be a promising therapeutic target. Electronic supplementary material The online version of this article (10.1186/s12885-018-4863-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yohei Sekino
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Naoya Sakamoto
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Keisuke Goto
- Cancer Biology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Ririno Honma
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Yoshinori Shigematsu
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.,Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Thang Pham Quoc
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kazuhiro Sentani
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Jun Teishima
- Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Fumi Kawakami
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jose A Karam
- Departments of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanishka Sircar
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Departments of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akio Matsubara
- Department of Urology, Hiroshima University Institute of Biomedical and Health Sciences, Hiroshima, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Sciences, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
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Differences in Pathologic Results of Repeat Transurethral Resection of Bladder Tumor (TURBT) according to Institution Performing the Initial TURBT: Comparative Analyses between Referred and Nonreferred Group. BIOMED RESEARCH INTERNATIONAL 2018; 2018:9432606. [PMID: 30271788 PMCID: PMC6146742 DOI: 10.1155/2018/9432606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 08/06/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022]
Abstract
Objective Although transurethral resection of bladder tumor (TURBT) is a standard treatment and determines staging for nonmuscle invasive bladder cancer, many deficiencies persist. There is a risk of upstaging and residual cancer when repeat TURBT is performed. Authors compared the results of repeat TURBT by institution performing the initial TURBT. Methods We retrospectively reviewed the medical records of 289 patients who underwent repeat TURBT within 2-6 weeks after initial TURBT between 1998 and 2013. The patients were divided into the referred group and the nonreferred group by institution performing the initial TURBT. And we analyzed the intergroup differences in residual tumor and upstaging rate and the factors significantly correlated with residual tumor. Results The mean age was 69.6 ± 11.1 years and the mean follow-up was 49.7 (range: 0–191) months. The referred group included 69 patients, while the nonreferred group included 220 patients. The referred group included 57 (82.6%) patients with residual tumor after repeat TURBT. Overall upstaging occurred in 15 (21.7%), and upstaging to T2 occurred in 11 (15.9%) of the initial Ta and T1 patients. In the nonreferred group, there were 123 (55.9%) patients with residual tumor. Overall upstaging occurred in 10 (4.5%) and upstaging to T2 occurred in 7 (3.2%) patients. Conclusions Gross hematuria, grade, and tumor quantity and size were significantly associated with residual cancer on multivariate analysis. In the referred group, repeat TURBT and restaging are necessary.
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Wang XS, Zhao MQ, Zhang L, Kong DJ, Ding XZ, Hu XC, Yang JQ, Gao SG. Cell-free DNA in blood and urine as a diagnostic tool for bladder cancer: a meta-analysis. Am J Transl Res 2018; 10:1935-1948. [PMID: 30093933 PMCID: PMC6079140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/08/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To assess the diagnostic performance of cell-free DNA assays in the detection of bladder cancer. PATIENTS AND METHODS The quality of the studies included in this meta-analysis was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. Statistical analyses were performed using the software RevMan 5.3 and Stata 14.0. We assessed the pooled sensitivity and specificity, positive/negative likelihood ratios (PLRs/NLRs), diagnostic odds ratios (DORs), and corresponding 95% confidence intervals (95% CIs). Summary receiver operating characteristic curve (ROC curve) and area under the curve (AUC) were used to summarize the overall test performance. Heterogeneity and publication bias were also examined. RESULTS Eleven studies included 802 bladder cancer patients and 668 controls met the eligibility criteria. The overall diagnostic accuracy was measured as follows: sensitivity 0.71 (95% CI = 0.64-0.77), specificity 0.78 (95% CI = 0.70-0.85), PLR 3.3 (95% CI = 2.4-54.5), NLR 0.37 (95% CI = 0.30-0.46), DOR 9 (95% CI = 6-14), and AUC 0.80 (95% CI = 0.77-0.83). Subgroup analysis suggested that ethnicity significantly accounted for the heterogeneity of specificity. The Deeks' funnel plot asymmetry test (P = 0.97) suggested no potential publication bias. CONCLUSIONS Cell-free DNA has a high diagnostic value in bladder cancer.
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Affiliation(s)
- Xin-Shuai Wang
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - Meng-Qi Zhao
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - Li Zhang
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - De-Jiu Kong
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - Xue-Zhen Ding
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - Xiao-Chen Hu
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - Jun-Qiang Yang
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
| | - She-Gan Gao
- Henan Key Laboratory of Cancer Epigenetics; Cancer Hospital, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology Luoyang 471003, China
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Regulation of Intestinal Epithelial Barrier Function by Long Noncoding RNA uc.173 through Interaction with MicroRNA 29b. Mol Cell Biol 2018; 38:MCB.00010-18. [PMID: 29632078 DOI: 10.1128/mcb.00010-18] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/02/2018] [Indexed: 12/24/2022] Open
Abstract
The mammalian intestinal epithelium establishes a selectively permeable barrier that supports nutrient absorption and prevents intrusion by noxious luminal substances and microbiota. The effectiveness and integrity of the barrier function are tightly regulated via well-controlled mechanisms. Long noncoding RNAs transcribed from ultraconserved regions (T-UCRs) control diverse cellular processes, but their roles in the regulation of gut permeability remain largely unknown. Here we report that the T-UCR uc.173 enhances intestinal epithelial barrier function by antagonizing microRNA 29b (miR-29b). Decreasing the levels of uc.173 by gene silencing led to dysfunction of the intestinal epithelial barrier in cultured cells and increased the vulnerability of the gut barrier to septic stress in mice. uc.173 specifically stimulated translation of the tight junction (TJ) claudin-1 (CLDN1) by associating with miR-29b rather than by binding directly to CLDN1 mRNA. uc.173 acted as a natural decoy RNA for miR-29b, which interacts with CLDN1 mRNA via the 3' untranslated region and represses its translation. Ectopically expressed uc.173 abolished the association of miR-29b with CLDN1 mRNA and restored claudin-1 expression to normal levels in cells overexpressing miR-29b, thus rescuing the barrier function. These results highlight a novel function of uc.173 in controlling gut permeability and define a mechanism by which uc.173 stimulates claudin-1 translation, by decreasing the availability of miR-29b to CLDN1 mRNA.
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Satake Y, Kuwano Y, Nishikawa T, Fujita K, Saijo S, Itai M, Tanaka H, Nishida K, Rokutan K. Nucleolin facilitates nuclear retention of an ultraconserved region containing TRA2β4 and accelerates colon cancer cell growth. Oncotarget 2018; 9:26817-26833. [PMID: 29928487 PMCID: PMC6003563 DOI: 10.18632/oncotarget.25510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/12/2018] [Indexed: 01/06/2023] Open
Abstract
Transcribed-ultraconserved regions (T-UCRs), which contain conserved sequences with 100% identity across human, rat and mouse species, are a novel category of functional RNAs. The human transformer 2β gene (TRA2B) encodes a UCR that spans exon 2 (276 bp) and its neighboring introns. Among five spliced RNA variants (TRA2β1-5) transcribed from the TRA2B gene, only TRA2β4 contains the conserved exon 2. TRA2β4 is overexpressed in colon cancer cells and accelerates cell growth by blocking the transcription of CDKN1A. However, the mechanisms underlying the overexpression of TRA2β4 in colon cancer cells are unknown. Using biotinylated RNA pull-down assays followed by liquid chromatography-mass spectrometric analysis, we identified nucleolin as a TRA2β4-binding protein. Knockdown of nucleolin reduced the nuclear retention of TRA2β4 and accelerated its degradation in the cytoplasm, whereas nucleolin overexpression increased TRA2β4 levels and its mitogenic activity. Nucleolin directly bound to TRA2β4 exon 2 via the glycine/arginine-rich (GAR) domain. Overexpression of GAR-deficient nucleolin failed to increase TRA2β4 expression and growth of colon cancer cells. RNA fluorescence in situ hybridization showed that TRA2β4 co-localized with nucleolin in nuclei but not with the mutant lacking GAR. Our results suggest that specific interactions between nucleolin and UCR-containing TRA2β4 may be associated with abnormal growth of colon cancer cells.
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Affiliation(s)
- Yuzuru Satake
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Yuki Kuwano
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Tatsuya Nishikawa
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kinuyo Fujita
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Saki Saijo
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Miki Itai
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Hiroki Tanaka
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kensei Nishida
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
| | - Kazuhito Rokutan
- Department of Pathophysiology, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8503, Japan
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Zhou J, Wang C, Gong W, Wu Y, Xue H, Jiang Z, Shi M. uc.454 Inhibited Growth by Targeting Heat Shock Protein Family A Member 12B in Non-Small-Cell Lung Cancer. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 12:174-183. [PMID: 30195756 PMCID: PMC6023848 DOI: 10.1016/j.omtn.2018.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/30/2018] [Accepted: 05/07/2018] [Indexed: 01/18/2023]
Abstract
Transcribed ultraconserved regions (T-UCRs) classified as long non-coding RNAs (Lnc-RNAs) are transcripts longer than 200-nt RNA with no protein-coding capacity. Previous studies showed that T-UCRs serve as novel oncogenes, or tumor suppressors are involved in tumorigenesis and cancer progressive. Nevertheless, the clinicopathologic significance and regulatory mechanism of T-UCRs in lung cancer (LC) remain largely unknown. We found that uc.454 was downregulated in both non-small-cell LC (NSCLC) tissues and LC cell lines, and the downregulated uc.454 is associated with tumor size and tumors with more advanced stages. Transfection with uc.454 markedly induced apoptosis and inhibited cell proliferation in SPC-A-1 and NCI-H2170 LC cell lines. Above results suggested that uc.454 played a suppressive role in LC. Heat shock protein family A member 12B (HSPA12B) protein was negatively regulated by uc.454 at the posttranscriptional level by dual-luciferase reporter assay and affected the expressions of Bcl-2 family members, which finally induced LC apoptosis. The uc.454/HSPA12B axis furthers our understanding of the molecular mechanisms involved in tumor apoptosis, which may potentially serve as a therapeutic target for lung carcinoma.
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Affiliation(s)
- Jun Zhou
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, China; Department of Respiratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Weijuan Gong
- Department of Molecular Immunology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Yandan Wu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Huimin Xue
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Zewei Jiang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, 368 Hanjiang Middle Road, Yangzhou 225009, China
| | - Minhua Shi
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu 215004, China.
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Zhan Y, Li Y, Guan B, Chen X, Chen Z, He A, He S, Gong Y, Peng D, Liu Y, Cai Z, Li X, Zhou L. Increased expression of long non-coding RNA CCEPR is associated with poor prognosis and promotes tumorigenesis in urothelial bladder carcinoma. Oncotarget 2018; 8:44326-44334. [PMID: 28574830 PMCID: PMC5546483 DOI: 10.18632/oncotarget.17872] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 04/22/2017] [Indexed: 11/25/2022] Open
Abstract
Recent emerging evidences have showed that long non-coding RNAs play important regulatory roles in diverse biological processes of tumor development and progression. CCEPR (cervical carcinoma expressed PCNA regulatory lncRNA) is a novel identified lncRNA that acts as a potential biomarker and involves in development and progression of cervical carcinoma. Nevertheless, we know nothing about the clinical significance and molecular mechanism of CCEPR in bladder cancer. In this study, we found that CCEPR was significantly up-regulated in bladder cancer. Furthermore, up-regulated CCEPR expression was positively correlated with advanced TNM stage and higher histological grade. Moreover, further experiments demonstrated that CCEPR promotes cell proliferation and suppresses cell apoptosis in bladder cancer. Mechanistically, we found CCEPR upregulates the expression of PCNA in mRNA and protein level to promote cancer growth. In conclusions, these findings demonstrated that CCEPR plays an important regulatory role in bladder cancer and may serve as a potential diagnostic biomarker and therapeutic target.
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Affiliation(s)
- Yonghao Zhan
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China.,Department of Urology, State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Yifan Li
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
| | - Bao Guan
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
| | - Xiaoying Chen
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China.,Department of Urology, State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Zhicong Chen
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China.,Department of Urology, State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Anbang He
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China.,Department of Urology, State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Shiming He
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
| | - Ding Peng
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
| | - Yuchen Liu
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China.,Department of Urology, State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Zhiming Cai
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China.,Department of Urology, State Engineering Laboratory of Medical Key Technologies Application of Synthetic Biology, Key Laboratory of Medical Reprogramming Technology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518035, China
| | - Xuesong Li
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, The Institute of Urology, Peking University, National Urological Cancer Centre, Beijing, 100034, China
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Pu X, Zhu L, Fu Y, Fan Z, Zheng J, Zhang B, Yang J, Guan W, Wu H, Ye Q, Huang Q. Companied P16 genetic and protein status together providing useful information on the clinical outcome of urinary bladder cancer. Medicine (Baltimore) 2018; 97:e0353. [PMID: 29642177 PMCID: PMC5908565 DOI: 10.1097/md.0000000000010353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
SPEC P16/CEN3/7/17 Probe fluorescence-in-situ-hybridization (FISH) has become the most sensitive method in indentifying the urothelial tumors and loss of P16 has often been identified in low-grade urothelial lesions; however, little is known about the significations of other P16 genetic status (normal and amplification) in bladder cancer.We detected P16 gene status by FISH in 259 urine samples and divided these samples into 3 groups: 1, normal P16; 2, loss of P16; and 3, amplified P16. Meanwhile, p16 protein expression was measured by immunocytochemistry and we characterized the clinicopathologic features of cases with P16 gene status.Loss of P16 occurred in 26.2%, P16 amplification occurred in 41.3% and P16 gene normal occurred in 32.4% of all cases. P16 genetic status was significantly associated with tumor grade and primary tumor status (P = .008 and .017), but not with pathological tumor stage, overall survival, and p16 protein expression. However, P16 gene amplification accompanied protein high-expression has shorter overall survival compared with the overall patients (P = .023), and P16 gene loss accompanied loss of protein also had the tendency to predict bad prognosis (P = .067).Studies show that the genetic status of P16 has a close relation with the stages of bladder cancer. Loss of P16 is associated with low-grade urothelial malignancy while amplified P16 donotes high-grade. Neither P16 gene status nor p16 protein expression alone is an independent predictor of urothelial bladder carcinoma, but combine gene and protein status together providing useful information on the clinical outcome of these patients.
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Affiliation(s)
- Xiaohong Pu
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Liya Zhu
- Department of Blood Purification Center, Huan’an First People's Hospital, Nanjing Medical University, Jiangsu, China
| | - Yao Fu
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Zhiwen Fan
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Jinyu Zheng
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Biao Zhang
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Jun Yang
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Wenyan Guan
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Hongyan Wu
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Qing Ye
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
| | - Qing Huang
- Department of Pathology, Nanjing University Medical School affiliated Drum Tower Hospital, Nanjing
- Department of Pathology and Laboratory Medicine, Veterans Affairs Boston Healthcare System and Harvard Medical School, West Roxbury, MA
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40
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Cui X, Jing X, Long C, Yi Q, Tian J, Zhu J. Accuracy of the urine UCA1 for diagnosis of bladder cancer: a meta-analysis. Oncotarget 2018; 8:35222-35233. [PMID: 28415640 PMCID: PMC5471048 DOI: 10.18632/oncotarget.16473] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/11/2017] [Indexed: 01/01/2023] Open
Abstract
Urine UCA1 has been reported as a potential novel diagnostic biomarker for bladder cancer in several studies, but their results are inconsistent. As a result of this, a diagnostic meta-analysis to assess the diagnostic performance of urine UCA1 in detecting bladder cancer was conducted. A systematic electronic and manual search was performed for relevant literatures through PubMed, Cochrane library, Chinese Wan Fang and the China National Knowledge Infrastructure (CNKI) databases up to December 30, 2016. The quality of the studies included in this meta-analysis was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. All analyses were conducted using stata12.0 software. Six studies collectively included 578 bladder cancer patients and 562 controls met the eligible criteria. The overall diagnostic accuracy was measured by the following: sensitivity 0.81 (95% CI = 0.75-0.86), specificity 0.86 (95% CI = 0.73-0.93), positive likelihood ratio 5.85 (95% CI = 2.72-12.57), negative likelihood 0.22 (95% CI = 0.15-0.32), diagnostic odds ratio 27.01 (95% CI = 8.69-83.97), and area under the curve 0.88 (95% CI = 0.85-0.91). Meta-regression analysis suggested that ethnicity significantly accounted for the heterogeneity of sensitivity. Deeks' funnel plot asymmetry test (P = 0.33) suggested no potential publication bias. According to our results, urine UCA1 has greater diagnostic value in diagnosing bladder cancer, however further research studies with more well-designed and large sample sizes are required to confirm our findings.
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Affiliation(s)
- Xiangrong Cui
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Reproductive Medicine Center, Children's Hospital of Shanxi and Women's Health Center of Shanxi, Affiliate of Shanxi Medical University, Taiyuan, Shanxi, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China
| | - Xuan Jing
- Clinical Laboratory, Shanxi Province People's Hospital, Affiliate of Shanxi Medical University, Taiyuan, China
| | - Chunlan Long
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Qin Yi
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Jie Tian
- Cardiovascular Department (Internal Medicine), Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Zhu
- Pediatric Research Institute, Children's Hospital of Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing, China.,Chongqing Key Laboratory of Pediatrics, Chongqing, China
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41
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IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity. Oncotarget 2018; 7:47864-47874. [PMID: 27323856 PMCID: PMC5216984 DOI: 10.18632/oncotarget.10012] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/23/2016] [Indexed: 01/02/2023] Open
Abstract
Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim.
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42
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Zhou J, Wang C, Huang C, Ding Z, Shi M. TUCR.454 inhabits metastasis in lung cancer cells. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:1289-1296. [PMID: 31938224 PMCID: PMC6958125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 02/06/2018] [Indexed: 06/10/2023]
Abstract
Transcribed ultraconserved regions (TUCRs) belong to long non-coding RNAs (lncRNAs) are transcripts longer than 200 base pair RNA with no protein-coding capacity. Previous studies showed that TUCRs serve as oncogenes or tumor suppressor genes are involved in tumorigenesis and cancer progressive. However, little is known about the expression level and biological role of TUCR.454 in lung carcinoma. Our data showed TUCR.454 is significantly down-regulated in NSCLC tissue and lung cancer cell lines, and the down-regulated TUCR.454 is associated with lymph node metastasis. Transfection with TUCR.454 markedly inhibited cell migration and invasion in A549 and H460 lung cancer cell lines. K-Ras was demonstrated to be negatively regulated by TUCR.454 at the posttranscriptional level by dual-luciferase reporter assay. Down-expression of K-Ras via siRNA inhibited NSCLC cell migration and down-regulates P63 and MMP9 in protein level, resembling that of overexpression of TUCR.454. In conclusion, these findings suggested that TUCR.454 acts as a novel tumor suppressor by targeting the K-Ras gene thus inhabiting lung cancer cell migration and invasion.
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Affiliation(s)
- Jun Zhou
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Soochow University1055 Sanxiang Road, Suzhou 215004, Jiangsu, China
- Department of Respiratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Caihong Huang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Zhiyan Ding
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou UniversityYangzhou, China
| | - Minhua Shi
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Soochow University1055 Sanxiang Road, Suzhou 215004, Jiangsu, China
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43
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An Ultraconserved Element Containing lncRNA Preserves Transcriptional Dynamics and Maintains ESC Self-Renewal. Stem Cell Reports 2018; 10:1102-1114. [PMID: 29456181 PMCID: PMC5918197 DOI: 10.1016/j.stemcr.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/16/2022] Open
Abstract
Ultraconserved elements (UCEs) show the peculiar feature to retain extended perfect sequence identity among human, mouse, and rat genomes. Most of them are transcribed and represent a new family of long non-coding RNAs (lncRNAs), the transcribed UCEs (T-UCEs). Despite their involvement in human cancer, the physiological role of T-UCEs is still unknown. Here, we identify a lncRNA containing the uc.170+, named T-UCstem1, and provide in vitro and in vivo evidence that it plays essential roles in embryonic stem cells (ESCs) by modulating cytoplasmic miRNA levels and preserving transcriptional dynamics. Specifically, while T-UCstem1::miR-9 cytoplasmic interplay regulates ESC proliferation by reducing miR-9 levels, nuclear T-UCstem1 maintains ESC self-renewal and transcriptional identity by stabilizing polycomb repressive complex 2 on bivalent domains. Altogether, our findings provide unprecedented evidence that T-UCEs regulate physiological cellular functions and point to an essential role of T-UCstem1 in preserving ESC identity. The transcribed ultraconserved element T-UCstem1 exerts a dual function in ESCs T-UCstem1 controls ESC proliferation by regulating the miR-9/Lin28b molecular axis T-UCstem1 maintains ESC self-renewal T-UCstem1 preserves ESC transcriptional identity by stabilizing PRC2
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44
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LncRNA Uc.173 is a key molecule for the regulation of lead-induced renal tubular epithelial cell apoptosis. Biomed Pharmacother 2018; 100:101-107. [PMID: 29425744 DOI: 10.1016/j.biopha.2018.01.112] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/21/2018] [Accepted: 01/24/2018] [Indexed: 01/28/2023] Open
Abstract
Transcribed ultra-conserved region (T-UCR) transcripts are a novel class of long non-coding RNAs (lncRNAs) transcribed from ultra-conserved region which is highly conserved in human, rat, and mouse genome. LncRNA UC.173 has been found significantly down-regulated in lead-exposed population and lead-exposed animal mode, and had an inhibitory effect on lead-induced nerve cell apoptosis. We supposed that lncRNA UC.173 had an inhibitory effect on lead-induced renal tubular epithelial cell apoptosis. Thus, the aim of our study was to explore the function of lncRNA UC.173 in lead-exposed renal tubular epithelial cells. In our results, lead exposure inhibited renal tubular epithelial cells viability and promoted cell apoptosis and apoptosis-associated genes expression, but no effect on cell-cycle distribution. Lead exposure inhibited the expression of lncRNA UC.173 in renal tubular epithelial cells, and the inhibition effect was time-dependent and concentration-dependent. Up-regulation of lncRNA UC.173 had no effect on renal tubular epithelial cell viability, cell cycle and apoptosis, but significantly rescued lead-induced inhibition of renal tubular epithelial cell viability and suppressed lead-induced cell apoptosis. In summary, our experiments suggest that lncRNA UC.173 is certainly involved in the regulation of lead-induced renal tubular epithelial cell apoptosis, which may supply a new strategy to minimize lead-induced nephrotoxicity.
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45
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Polychronopoulos D, King JWD, Nash AJ, Tan G, Lenhard B. Conserved non-coding elements: developmental gene regulation meets genome organization. Nucleic Acids Res 2018; 45:12611-12624. [PMID: 29121339 PMCID: PMC5728398 DOI: 10.1093/nar/gkx1074] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs), are non-randomly distributed across chromosomes and tend to cluster in the vicinity of genes with regulatory roles in multicellular development and differentiation. CNEs are organized into functional ensembles called genomic regulatory blocks–dense clusters of elements that collectively coordinate the expression of shared target genes, and whose span in many cases coincides with topologically associated domains. CNEs display sequence properties that set them apart from other sequences under constraint, and have recently been proposed as useful markers for the reconstruction of the evolutionary history of organisms. Disruption of several of these elements is known to contribute to diseases linked with development, and cancer. The emergence, evolutionary dynamics and functions of CNEs still remain poorly understood, and new approaches are required to enable comprehensive CNE identification and characterization. Here, we review current knowledge and identify challenges that need to be tackled to resolve the impasse in understanding extreme non-coding conservation.
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Affiliation(s)
- Dimitris Polychronopoulos
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - James W D King
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Alexander J Nash
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Ge Tan
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
| | - Boris Lenhard
- Computational Regulatory Genomics Group, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5008 Bergen, Norway
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46
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Wang L, Wang XC, Li X, Gu Y, Zhou J, Jiang S, Liu J, Wu C, Ding Z, Wan Y, Wang C. Expression of uc.189 and its clinicopathologic significance in gynecological cancers. Oncotarget 2017; 9:7453-7463. [PMID: 29484123 PMCID: PMC5800915 DOI: 10.18632/oncotarget.23761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 12/23/2017] [Indexed: 01/01/2023] Open
Abstract
In recent decades, emerging evidence demonstrates that ultraconserved elements (UCEs) encoding noncoding RNAs serve as regulators of gene expression. Until now, the role of uc.189 in human cancers remains undefined and the clinical significance of uc.189 in gynecological cancers remains unknown. This study was to identify the prognostic value of uc.189 expression in gynecological cancers. Tissue microarrays were constructed with 243 samples including 116 cervical squamous cell carcinomas (CSCCs), 98 endometrial adenocarcinomas (EACs), 29 ovarian cystoadenocarcinomas(OCAs), and corresponding normal tissues. In CSCC, uc.189 expression was increased in 78.5% of cases (91/116), decreased in 4.3% (5/116), and unchanged in 17.2% (20/116). In EAC its expression was increased in 74.5% (73/98), decreased in 3.1% (3/98), and unchanged in 22.4% (22/98). Expression of uc.189 was increased in 23, and unchanged/decreased in 6, of 29 cases of ovarian cystoadenocarcinomas. Univariate and multivariate Cox regression analysis demonstrated that over-expression of uc.189 predicted poor prognosis in CSCC and EAC. Thus, these findings suggested uc.189 might be an evaluating prognosis marker of gynecological tumors.
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Affiliation(s)
- Lei Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Xing Cheng Wang
- Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Xinyu Li
- Department of Basic Medical, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Yan Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China
| | - Jun Zhou
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Shuwan Jiang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Jiajia Liu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Chong Wu
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhiyan Ding
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yafeng Wan
- Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
| | - Chenghai Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu 225009, China.,Department of Pharmacy, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, Jiangsu 225001, China.,Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou, Jiangsu 225001, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu 225009, China
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47
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Vannini I, Wise PM, Challagundla KB, Plousiou M, Raffini M, Bandini E, Fanini F, Paliaga G, Crawford M, Ferracin M, Ivan C, Fabris L, Davuluri RV, Guo Z, Cortez MA, Zhang X, Chen L, Zhang S, Fernandez-Cymering C, Han L, Carloni S, Salvi S, Ling H, Murtadha M, Neviani P, Gitlitz BJ, Laird-Offringa IA, Nana-Sinkam P, Negrini M, Liang H, Amadori D, Cimmino A, Calin GA, Fabbri M. Transcribed ultraconserved region 339 promotes carcinogenesis by modulating tumor suppressor microRNAs. Nat Commun 2017; 8:1801. [PMID: 29180617 PMCID: PMC5703849 DOI: 10.1038/s41467-017-01562-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/27/2017] [Indexed: 01/05/2023] Open
Abstract
The transcribed ultraconserved regions (T-UCRs) encode long non-coding RNAs implicated in human carcinogenesis. Their mechanisms of action and the factors regulating their expression in cancers are poorly understood. Here we show that high expression of uc.339 correlates with lower survival in 210 non-small cell lung cancer (NSCLC) patients. We provide evidence from cell lines and primary samples that TP53 directly regulates uc.339. We find that transcribed uc.339 is upregulated in archival NSCLC samples, functioning as a decoy RNA for miR-339-3p, -663b-3p, and -95-5p. As a result, Cyclin E2, a direct target of all these microRNAs is upregulated, promoting cancer growth and migration. Finally, we find that modulation of uc.339 affects microRNA expression. However, overexpression or downregulation of these microRNAs causes no significant variations in uc.339 levels, suggesting a type of interaction for uc.339 that we call "entrapping". Our results support a key role for uc.339 in lung cancer.
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Affiliation(s)
- Ivan Vannini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Petra M Wise
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Kishore B Challagundla
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Meropi Plousiou
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Mirco Raffini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Erika Bandini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Francesca Fanini
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Giorgia Paliaga
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Gene Therapy Unit, 47014, Meldola (FC), Italy
| | - Melissa Crawford
- Department of Internal Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine-DIMES, University of Bologna, 40126, Bologna, Italy
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Linda Fabris
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Ramana V Davuluri
- Departments of Preventive Medicine and Neurological Surgery, Northwestern University-Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Zhiyi Guo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Maria Angelica Cortez
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xinna Zhang
- The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA.,Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Lu Chen
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shuxing Zhang
- Integrated Molecular Discovery Laboratory, Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cecilia Fernandez-Cymering
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Ohio State University, Columbus, OH, 43210, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Silvia Carloni
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Biosciences Laboratory Unit, 47014, Meldola (FC), Italy
| | - Samanta Salvi
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, Biosciences Laboratory Unit, 47014, Meldola (FC), Italy
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mariam Murtadha
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Paolo Neviani
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA
| | - Barbara J Gitlitz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Ite A Laird-Offringa
- Departments of Surgery and Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine and Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121, Ferrara, Italy
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dino Amadori
- Department of Oncology Unit, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) S.r.l., IRCCS, 47014, Meldola (FC), Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics, National Research Council, 80131, Naples, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. .,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA.
| | - Muller Fabbri
- Departments of Pediatrics and Molecular Microbiology & Immunology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Children's Center for Cancer and Blood Diseases and The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, 90027, USA.
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48
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Liu SM, Lin CH, Lu J, Lin IY, Tsai MS, Chen MH, Ma N. miR-596 Modulates Melanoma Growth by Regulating Cell Survival and Death. J Invest Dermatol 2017; 138:911-921. [PMID: 29183729 DOI: 10.1016/j.jid.2017.11.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 02/06/2023]
Abstract
Tumors grow because cancer cells lack the ability to balance cell survival and death signaling pathways. miR-596, a microRNA located at the 8p23.3 locus, has been shown by the TCGA-Assembler to be deleted in a significant number of melanoma samples. Here, we also validated the low levels of miR-596 in melanoma compared to tissue nevi, and Kaplan-Meier curve analysis revealed that low miR-596 expression was associated with worse overall survival. Moreover, we showed that miR-596 overexpression effectively inhibited MAPK/ERK signaling, cell proliferation, migration, and invasion and increased the cell apoptosis of melanoma cells. In addition, we found that miR-596 directly targets MEK1 and two apoptotic proteins, MCL1, and BCL2L1, in melanoma cells. Our findings indicated that miR-596 is an important miRNA that both negatively regulates the MAPK/ERK signaling pathway by targeting MEK1 and modulates the apoptosis pathway by targeting MCL1 and BCL2L1, suggesting that miR-596 could be a therapeutic candidate for treating melanoma, and a prognostic factor for melanoma patients.
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Affiliation(s)
- Szu-Mam Liu
- Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Taoyuan, Taiwan
| | - Chen-Huan Lin
- Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Taoyuan, Taiwan
| | - Jean Lu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - In-Yu Lin
- Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Taoyuan, Taiwan
| | - Mu-Shiun Tsai
- Department of Pathology, Landseed Hospital, Taoyuan, Taiwan
| | - Ming-Hong Chen
- Department of Pathology, Saint Paul's Hospital, Taoyuan, Taiwan
| | - Nianhan Ma
- Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, Taoyuan, Taiwan.
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Role of Non-Coding RNAs in the Etiology of Bladder Cancer. Genes (Basel) 2017; 8:genes8110339. [PMID: 29165379 PMCID: PMC5704252 DOI: 10.3390/genes8110339] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 11/03/2017] [Accepted: 11/07/2017] [Indexed: 12/21/2022] Open
Abstract
According to data of the International Agency for Research on Cancer and the World Health Organization (Cancer Incidence in Five Continents, GLOBOCAN, and the World Health Organization Mortality), bladder is among the top ten body locations of cancer globally, with the highest incidence rates reported in Southern and Western Europe, North America, Northern Africa and Western Asia. Males (M) are more vulnerable to this disease than females (F), despite ample frequency variations in different countries, with a M:F ratio of 4.1:1 for incidence and 3.6:1 for mortality, worldwide. For a long time, bladder cancer was genetically classified through mutations of two genes, fibroblast growth factor receptor 3 (FGFR3, for low-grade, non-invasive papillary tumors) and tumor protein P53 (TP53, for high-grade, muscle-invasive tumors). However, more recently scientists have shown that this disease is far more complex, since genes directly involved are more than 150; so far, it has been described that altered gene expression (up- or down-regulation) may be present for up to 500 coding sequences in low-grade and up to 2300 in high-grade tumors. Non-coding RNAs are essential to explain, at least partially, this ample dysregulation. In this review, we summarize the present knowledge about long and short non-coding RNAs that have been linked to bladder cancer etiology.
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50
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Zhou J, Wang R, Zhang J, Zhu L, Liu W, Lu S, Chen P, Li H, Yin B, Yuan J, Qiang B, Shu P, Peng X. Conserved expression of ultra-conserved noncoding RNA in mammalian nervous system. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:1159-1168. [PMID: 29055695 DOI: 10.1016/j.bbagrm.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/08/2017] [Accepted: 10/11/2017] [Indexed: 02/07/2023]
Abstract
T-UCRs, a class of long non-coding RNAs that are transcribed from ultra-conserved regions (UCRs), might play an important role in development and diseases. However, the amount of T-UCRs that are conservatively expressed in the developing nervous systems of mice, monkeys and humans is still unknown. In this study, we screened the RNA sequence signals of 481 identified UCRs in an E14.5 mouse brain from the ENCODE database and found 76 UCRs that may be transcribed into T-UCRs. To verify the expression of these potential T-UCRs, we used an RT-PCR experiment and identified that 60 T-UCRs can be expressed in the E14.5 mouse brain. Furthermore, we detected the expression conservation of 76 potential T-UCRs in two comparisons: postnatal day 0 brains of a mouse and a rhesus monkey and neural stem cells of mouse and human by RT-PCR experimentation. It was found that up to 65% of these T-UCRs were expressed in mouse, rhesus monkey and human nervous systems. Next, by testing the spatiotemporal expression pattern of these T-UCRs expressed in mouse, rhesus monkey and human nervous systems, we found that approximately 30% of the T-UCRs showed a relatively high and dynamical expression during mouse brain development. Finally, through biological process and molecular function gene ontology analysis of the host genes of intronic or exonic-antisense T-UCRs, it was discovered that most of the genes were involved in RNA splicing or RNA binding. These results suggest that T-UCRs are likely to participate in nervous system development through RNA processing.
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Affiliation(s)
- Junjie Zhou
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Ruiyu Wang
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Jing Zhang
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Liyuan Zhu
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Wei Liu
- Department of Anatomy and Histology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Shuaiyao Lu
- Institute of Medical Biology Chinese Academy of Medical Sciences, Chinese Academy of Medical Science and Peking Union Medical College, Kunming 650118, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Pan Chen
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Hanlu Li
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Bin Yin
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Jiangang Yuan
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Boqin Qiang
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China
| | - Pengcheng Shu
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China.
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Medical Primate Research Center, Neuroscience Center, and Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China; Medical Primate Research Center, Chinese Academy of Medical Science, Peking Union Medical College, Beijing 100005, China.
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