1
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Piergentili R, Sechi S. Non-Coding RNAs of Mitochondrial Origin: Roles in Cell Division and Implications in Cancer. Int J Mol Sci 2024; 25:7498. [PMID: 39000605 PMCID: PMC11242419 DOI: 10.3390/ijms25137498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group, in terms of structure and sequence length, consisting of RNA molecules that do not code for proteins. These ncRNAs have a central role in the regulation of gene expression and are virtually involved in every process analyzed, ensuring cellular homeostasis. Although, over the years, much research has focused on the characterization of non-coding transcripts of nuclear origin, improved bioinformatic tools and next-generation sequencing (NGS) platforms have allowed the identification of hundreds of ncRNAs transcribed from the mitochondrial genome (mt-ncRNA), including long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miR). Mt-ncRNAs have been described in diverse cellular processes such as mitochondrial proteome homeostasis and retrograde signaling; however, the function of the majority of mt-ncRNAs remains unknown. This review focuses on a subgroup of human mt-ncRNAs whose dysfunction is associated with both failures in cell cycle regulation, leading to defects in cell growth, cell proliferation, and apoptosis, and the development of tumor hallmarks, such as cell migration and metastasis formation, thus contributing to carcinogenesis and tumor development. Here we provide an overview of the mt-ncRNAs/cancer relationship that could help the future development of new biomedical applications in the field of oncology.
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Affiliation(s)
| | - Stefano Sechi
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Biologia e Biotecnologie, Università Sapienza di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy;
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2
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Piao XM, Kang H, Kim WJ, Yun SJ. Prominence of urinary biomarkers for bladder cancer in the COVID-19 era: From the commercially available to new prospective candidates. Investig Clin Urol 2021; 62:500-519. [PMID: 34488250 PMCID: PMC8421991 DOI: 10.4111/icu.20210194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/24/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022] Open
Abstract
Molecular markers detected in urine may improve our understanding of the evolution of bladder cancer (BCa) and its micro- and macroenvironment. Detection of such markers will identify disease earlier, allow stratification of patients according to risk, and improve prognostication and prediction of outcomes, thereby facilitating targeted therapy. However, current guidelines have yet to embrace such markers for routine management of BCa, and most research studies have focused on urine-based tumor markers. In this review, we summarize known urinary biomarkers for BCa and highlight newly identified molecules. We then discuss the challenges that must be overcome to incorporate these markers into clinical care.
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Affiliation(s)
- Xuan-Mei Piao
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Howon Kang
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea
| | - Wun-Jae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
- Institute of Urotech, Cheongju, Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
- Department of Urology, Chungbuk National University Hospital, Cheongju, Korea.
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3
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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4
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Gossing W, Frohme M, Radke L. Biomarkers for Liquid Biopsies of Pituitary Neuroendocrine Tumors. Biomedicines 2020; 8:biomedicines8060148. [PMID: 32498309 PMCID: PMC7344901 DOI: 10.3390/biomedicines8060148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/27/2020] [Accepted: 05/30/2020] [Indexed: 02/07/2023] Open
Abstract
Pituitary neuroendocrine tumors (PitNET) do not only belong to the most common intracranial neoplasms but seem to be generally more common than has been thought. Minimally invasive liquid biopsies have the potential to improve their early screening efficiency as well as monitor prognosis by facilitating the diagnostic procedures. This review aims to assess the potential of using liquid biopsies of different kinds of biomarker species that have only been obtained from solid pituitary tissues so far. Numerous molecules have been associated with the development of a PitNET, suggesting that it often develops from the cumulative effects of many smaller genetic or epigenetic changes. These minor changes eventually pile up to switch critical molecules into tumor-promoting states, which may be the key regulatory nodes representing the most potent marker substances for a diagnostic test. Drugs targeting these nodes may be superior for the therapeutic outcome and therefore the identification of such pituitary-specific cellular key nodes will help to accelerate their application in medicine. The ongoing genetic degeneration in pituitary adenomas suggests that repeated tumor profiling via liquid biopsies will be necessary for personalized and effective treatment solutions.
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5
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Li Y, Li G, Guo X, Yao H, Wang G, Li C. Non-coding RNA in bladder cancer. Cancer Lett 2020; 485:38-44. [PMID: 32437725 DOI: 10.1016/j.canlet.2020.04.023] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/26/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022]
Abstract
Bladder cancer is the tenth most common cancer worldwide and has been associated with high mortality and morbidity. Although the treatment of bladder cancer is based on well-defined tumor classifications and gradings, patients still experience different clinical response. The heterogeneity of this disease calls for substantial research with more in-depth molecular characterization, with the hope of identifying new diagnostic and treatment options. In recent years, non-coding RNAs (ncRNAs), particularly, microRNAs (miRNAs), long non-coding RNA (lncRNAs), and circular RNAs (circRNAs) were found to be associated with bladder cancer occurrence and development. This review highlights the recent findings concerning ncRNAs and their relevance to the pathogenesis of bladder cancer. This may provide a foundation for developing highly specific diagnostic tools and more robust therapeutic strategies in the future.
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Affiliation(s)
- Yi Li
- Department of Anesthesiology, Peking University Third Hospital (PUTH), Beijing, China
| | - Gang Li
- Department of Anesthesiology, Peking University Third Hospital (PUTH), Beijing, China
| | - Xiangyang Guo
- Department of Anesthesiology, Peking University Third Hospital (PUTH), Beijing, China
| | - Haochen Yao
- College of Basic Medical Science, Jilin University (JUT), Changchun, Jilin, China
| | - Guoqing Wang
- College of Basic Medical Science, Jilin University (JUT), Changchun, Jilin, China.
| | - Chong Li
- Core Facility for Protein Research, Institute of Biophysics Chinese Academy of Sciences (IBPCAS), Beijing, China; Beijing Jianlan Institute of Medicine, Beijing, China; Beijing Zhongke Jianlan Biotechnology Co., Ltd., Beijing, China.
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6
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The Urinary Transcriptome as a Source of Biomarkers for Prostate Cancer. Cancers (Basel) 2020; 12:cancers12020513. [PMID: 32098402 PMCID: PMC7072374 DOI: 10.3390/cancers12020513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer (PCa) is the second most common cancer of men and is typically slow-growing and asymptomatic. The use of blood PSA as a screening method has greatly improved PCa diagnosis, but high levels of false positives has raised much interest in alternative biomarkers. We used next-generation sequencing (NGS) to elucidate the urinary transcriptome of whole urine collected from high-stage and low-stage PCa patients as well as from patients with the confounding diagnosis of benign hyperplasia (BPH). We identified and validated five differentially expressed protein-coding genes (FTH1 BRPF1, OSBP, PHC3, and UACA) in an independent validation cohort of small-volume (1 mL) centrifuged urine (n = 94) and non-centrifuged urine (n = 84) by droplet digital (dd)PCR. These biomarkers were able to discriminate between BPH and PCa patients and healthy controls using either centrifuged or non-centrifuged whole urine samples, suggesting that the urinary transcriptome is a valuable source of non-invasive biomarkers for PCa that warrants further investigation.
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7
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Dong Z, Pu L, Cui H. Mitoepigenetics and Its Emerging Roles in Cancer. Front Cell Dev Biol 2020; 8:4. [PMID: 32039210 PMCID: PMC6989428 DOI: 10.3389/fcell.2020.00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
In human beings, there is a ∼16,569 bp circular mitochondrial DNA (mtDNA) encoding 22 tRNAs, 12S and 16S rRNAs, 13 polypeptides that constitute the central core of ETC/OxPhos complexes, and some non-coding RNAs. Recently, mtDNA has been shown to have some covalent modifications such as methylation or hydroxylmethylation, which play pivotal epigenetic roles in mtDNA replication and transcription. Post-translational modifications of proteins in mitochondrial nucleoids such as mitochondrial transcription factor A (TFAM) also emerge as essential epigenetic modulations in mtDNA replication and transcription. Post-transcriptional modifications of mitochondrial RNAs (mtRNAs) including mt-rRNAs, mt-tRNAs and mt-mRNAs are important epigenetic modulations. Besides, mtDNA or nuclear DNA (n-DNA)-derived non-coding RNAs also play important roles in the regulation of translation and function of mitochondrial genes. These evidences introduce a novel concept of mitoepigenetics that refers to the study of modulations in the mitochondria that alter heritable phenotype in mitochondria itself without changing the mtDNA sequence. Since mitochondrial dysfunction contributes to carcinogenesis and tumor development, mitoepigenetics is also essential for cancer. Understanding the mode of actions of mitoepigenetics in cancers may shade light on the clinical diagnosis and prevention of these diseases. In this review, we summarize the present study about modifications in mtDNA, mtRNA and nucleoids and modulations of mtDNA/nDNA-derived non-coding RNAs that affect mtDNA translation/function, and overview recent studies of mitoepigenetic alterations in cancer.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Longjun Pu
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
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8
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Borgna V, Lobos-González L, Guevara F, Landerer E, Bendek M, Ávila R, Silva V, Villota C, Araya M, Rivas A, López C, Socias T, Castillo J, Alarcón L, Burzio LO, Burzio VA, Villegas J. Targeting antisense mitochondrial noncoding RNAs induces bladder cancer cell death and inhibition of tumor growth through reduction of survival and invasion factors. J Cancer 2020; 11:1780-1791. [PMID: 32194789 PMCID: PMC7052861 DOI: 10.7150/jca.38880] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/23/2019] [Indexed: 01/06/2023] Open
Abstract
Knockdown of the antisense noncoding mitochondrial RNAs (ASncmtRNAs) induces apoptotic death of several human tumor cell lines, but not normal cells, supporting a selective therapy against different types of cancer. In this work, we evaluated the effects of knockdown of ASncmtRNAs on bladder cancer (BCa). We transfected the BCa cell lines UMUC-3, RT4 and T24 with the specific antisense oligonucleotide Andes-1537S, targeted to the human ASncmtRNAs. Knockdown induced a strong inhibition of cell proliferation and increase in cell death in all three cell lines. As observed in UMUC-3 cells, the treatment triggered apoptosis, evidenced by loss of mitochondrial membrane potential and Annexin V staining, along with activation of procaspase-3 and downregulation of the anti-apoptotic factors survivin and Bcl-xL. Treatment also inhibited cell invasion and spheroid formation together with inhibition of N-cadherin and MMP 11. In vivo treatment of subcutaneous xenograft UMUC-3 tumors in NOD/SCID mice with Andes-1537S induced inhibition of tumor growth as compared to saline control. Similarly, treatment of a high-grade bladder cancer PDX with Andes-1537S resulted in a strong inhibition of tumor growth. Our results suggest that ASncmtRNAs could be potent targets for bladder cancer as adjuvant therapy.
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Affiliation(s)
- Vincenzo Borgna
- Fundación Ciencia & Vida.,Facultad de Medicina, Universidad De Santiago.,Servicio de Urología, Hospital Barros Luco-Trudeau
| | - Lorena Lobos-González
- Centro de Medicina Regenerativa, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo
| | | | | | | | | | | | - Claudio Villota
- Escuela de Nutrición y Dietética, Facultad de Salud, Universidad Bernardo O'Higgins
| | - Mariela Araya
- Fundación Ciencia & Vida.,Facultad de Ciencias de la Vida, Universidad Andrés Bello
| | | | | | | | - Jorge Castillo
- Servicio de Anatomía Patológica, Hospital Barros Luco-Trudeau. Santiago, Chile
| | - Luis Alarcón
- Servicio de Urología, Hospital Barros Luco-Trudeau
| | - Luis O Burzio
- Fundación Ciencia & Vida.,Andes Biotechnologies SpA.,Facultad de Ciencias de la Vida, Universidad Andrés Bello
| | - Verónica A Burzio
- Fundación Ciencia & Vida.,Andes Biotechnologies SpA.,Facultad de Ciencias de la Vida, Universidad Andrés Bello
| | - Jaime Villegas
- Fundación Ciencia & Vida.,Andes Biotechnologies SpA.,Facultad de Ciencias de la Vida, Universidad Andrés Bello
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9
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Zhao Y, Sun L, Wang RR, Hu JF, Cui J. The effects of mitochondria-associated long noncoding RNAs in cancer mitochondria: New players in an old arena. Crit Rev Oncol Hematol 2018; 131:76-82. [DOI: 10.1016/j.critrevonc.2018.08.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/06/2018] [Accepted: 08/22/2018] [Indexed: 12/17/2022] Open
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10
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Hedberg A, Knutsen E, Løvhaugen AS, Jørgensen TE, Perander M, Johansen SD. Cancer-specific SNPs originate from low-level heteroplasmic variants in human mitochondrial genomes of a matched cell line pair. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:82-91. [PMID: 29671673 DOI: 10.1080/24701394.2018.1461852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Low-level mitochondrial heteroplasmy is a common phenomenon in both normal and cancer cells. Here, we investigate the link between low-level heteroplasmy and mitogenome mutations in a human breast cancer matched cell line by high-throughput sequencing. We identified 23 heteroplasmic sites, of which 15 were common between normal cells (Hs578Bst) and cancer cells (Hs578T). Most sites were clustered within the highly conserved Complex IV and ribosomal RNA genes. Two heteroplasmic variants in normal cells were found as fixed mutations in cancer cells. This indicates a positive selection of these variants in cancer cells. RNA-Seq analysis identified upregulated L-strand specific transcripts in cancer cells, which include three mitochondrial long non-coding RNA molecules. We hypothesize that this is due to two cancer cell-specific mutations in the control region.
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Affiliation(s)
- Annica Hedberg
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Erik Knutsen
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Anne Silje Løvhaugen
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Tor Erik Jørgensen
- b Genomics Group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
| | - Maria Perander
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway
| | - Steinar D Johansen
- a Department of Medical Biology, Faculty of Health Sciences , UiT - The Arctic University of Norway , Tromsø , Norway.,b Genomics Group, Faculty of Biosciences and Aquaculture , Nord University , Bodø , Norway
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11
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Zaporozhchenko IA, Ponomaryova AA, Rykova EY, Laktionov PP. The potential of circulating cell-free RNA as a cancer biomarker: challenges and opportunities. Expert Rev Mol Diagn 2018; 18:133-145. [DOI: 10.1080/14737159.2018.1425143] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ivan A. Zaporozhchenko
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Anastasia A. Ponomaryova
- Laboratory of Immunology, Tomsk Cancer Research Institute of SB RAMS, Tomsk, Russia
- Department of Applied Physics, National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Elena Yu Rykova
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Pavel P. Laktionov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
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12
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Terracciano D, Ferro M, Terreri S, Lucarelli G, D'Elia C, Musi G, de Cobelli O, Mirone V, Cimmino A. Urinary long noncoding RNAs in nonmuscle-invasive bladder cancer: new architects in cancer prognostic biomarkers. Transl Res 2017; 184:108-117. [PMID: 28438520 DOI: 10.1016/j.trsl.2017.03.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 03/22/2017] [Accepted: 03/28/2017] [Indexed: 12/14/2022]
Abstract
Several reports over the last 10 years provided evidence that long noncoding RNAs (lncRNAs) are often altered in bladder cancers. lncRNAs are longer than 200 nucleotides and function as important regulators of gene expression, interacting with the major pathways of cell growth, proliferation, differentiation, and survival. A large number of lncRNAs has oncogenic function and is more expressed in tumor compared with normal tissues. Their overexpression may be associated with tumor formation, progression, and metastasis in a variety of tumors including bladder cancer. Although lncRNAs have been shown to have critical regulatory roles in cancer biology, the biological functions and prognostic values in nonmuscle-invasive bladder cancer remain largely unknown. Nevertheless, a growing body of evidence suggests that several lncRNAs expression profiles in bladder malignancies are associated with poor prognosis, and they can be detected in biological fluids, such as urines. Here, we review current progress in the biology and the implication of lncRNAs associated with bladder cancer, and we discuss their potential use as diagnosis and prognosis biomarkers in bladder malignancies with a focus on their role in high-risk nonmuscle-invasive tumors.
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Affiliation(s)
- Daniela Terracciano
- Department of Translational Medical Sciences, University "Federico II", Naples, Italy.
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, Milan, Italy.
| | - Sara Terreri
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy
| | - Giuseppe Lucarelli
- Department of Emergency and Organ Transplantation-Urology, Andrology and Kidney Transplantation Unit, University of Bari, Bari, Italy
| | - Carolina D'Elia
- Urology Department, Central Hospital of Bolzano, Bolzano, Italy
| | - Gennaro Musi
- Division of Urology, European Institute of Oncology, Milan, Italy
| | | | - Vincenzo Mirone
- Urology Department, University of Naples Federico II, Naples, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics "A. Buzzati Traverso", National Research Council (CNR), Naples, Italy.
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13
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It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research. Int J Mol Sci 2017; 18:ijms18040714. [PMID: 28350330 PMCID: PMC5412300 DOI: 10.3390/ijms18040714] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/27/2022] Open
Abstract
There have been tens of thousands of RNAs deposited in different databases that contain sequences of two genes and are coined chimeric RNAs, or chimeras. However, "chimeric RNA" has never been lucidly defined, partly because "gene" itself is still ill-defined and because the means of production for many RNAs is unclear. Since the number of putative chimeras is soaring, it is imperative to establish a pellucid definition for it, in order to differentiate chimeras from regular RNAs. Otherwise, not only will chimeric RNA studies be misled but also characterization of fusion genes and unannotated genes will be hindered. We propose that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas those RNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimeras. Many RNAs containing sequences of two neighboring genes may be transcribed via a readthrough mechanism, and thus are actually RNAs of unannotated genes or RNA variants of known genes, but not chimeras. In today's chimeric RNA research, there are still several key flaws, technical constraints and understudied tasks, which are also described in this perspective essay.
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14
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Chandra Gupta S, Nandan Tripathi Y. Potential of long non-coding RNAs in cancer patients: From biomarkers to therapeutic targets. Int J Cancer 2016; 140:1955-1967. [DOI: 10.1002/ijc.30546] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/11/2016] [Accepted: 11/30/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Subash Chandra Gupta
- Laboratory for Translational Cancer Research; Department of Biochemistry, Institute of Science, Banaras Hindu University; Varanasi 221 005 India
| | - Yashoda Nandan Tripathi
- Laboratory for Translational Cancer Research; Department of Biochemistry, Institute of Science, Banaras Hindu University; Varanasi 221 005 India
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15
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Chen J, Miao Z, Xue B, Shan Y, Weng G, Shen B. Long Non-coding RNAs in Urologic Malignancies: Functional Roles and Clinical Translation. J Cancer 2016; 7:1842-1855. [PMID: 27698924 PMCID: PMC5039368 DOI: 10.7150/jca.15876] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/29/2016] [Indexed: 12/31/2022] Open
Abstract
Early diagnosis and surveillance for metastasis and recurrences are critical issues of urologic cancer. Deregulation of long non-coding RNAs (lncRNAs) has been implicated in urologic malignancies and represents potential markers or therapeutic targets. However, the utility of lncRNA as biomarkers appears to be overstated due to heterogeneous or irreproducible results from different studies. Thus, a critical and cautious review on the biomarker potential of lncRNAs is needed. This review provides an update on new findings of lncRNA-based markers for urologic cancer. The diverse mechanisms and associated examples of lncRNAs involved during the carcinogenesis of prostate cancer, bladder cancer and renal cancer were discussed in a more balanced and critical manner, as were the suitability of lncRNAs as diagnostic or prognostics markers.
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Affiliation(s)
- Jiajia Chen
- Center for Systems Biology, Soochow University, Suzhou 215006, China; School of Chemistry, Biological Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Zhijun Miao
- Center for Systems Biology, Soochow University, Suzhou 215006, China; Suzhou Dushuhu Hospital, Clinic Center, Soochow University, Suzhou 215123, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yuxi Shan
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Guobin Weng
- Ningbo Urologic and Nephrotic Hospital, Ningbo 315000, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou 215006, China
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Xie B, Yang W, Ouyang Y, Chen L, Jiang H, Liao Y, Liao DJ. Two RNAs or DNAs May Artificially Fuse Together at a Short Homologous Sequence (SHS) during Reverse Transcription or Polymerase Chain Reactions, and Thus Reporting an SHS-Containing Chimeric RNA Requires Extra Caution. PLoS One 2016; 11:e0154855. [PMID: 27148738 PMCID: PMC4858267 DOI: 10.1371/journal.pone.0154855] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/20/2016] [Indexed: 11/18/2022] Open
Abstract
Tens of thousands of chimeric RNAs have been reported. Most of them contain a short homologous sequence (SHS) at the joining site of the two partner genes but are not associated with a fusion gene. We hypothesize that many of these chimeras may be technical artifacts derived from SHS-caused mis-priming in reverse transcription (RT) or polymerase chain reactions (PCR). We cloned six chimeric complementary DNAs (cDNAs) formed by human mitochondrial (mt) 16S rRNA sequences at an SHS, which were similar to several expression sequence tags (ESTs).These chimeras, which could not be detected with cDNA protection assay, were likely formed because some regions of the 16S rRNA are reversely complementary to another region to form an SHS, which allows the downstream sequence to loop back and anneal at the SHS to prime the synthesis of its complementary strand, yielding a palindromic sequence that can form a hairpin-like structure.We identified a 16S rRNA that ended at the 4th nucleotide(nt) of the mt-tRNA-leu was dominant and thus should be the wild type. We also cloned a mouse Bcl2-Nek9 chimeric cDNA that contained a 5-nt unmatchable sequence between the two partners, contained two copies of the reverse primer in the same direction but did not contain the forward primer, making it unclear how this Bcl2-Nek9 was formed and amplified. Moreover, a cDNA was amplified because one primer has 4 nts matched to the template, suggesting that there may be many more artificial cDNAs than we have realized, because the nuclear and mt genomes have many more 4-nt than 5-nt or longer homologues. Altogether, the chimeric cDNAs we cloned are good examples suggesting that many cDNAs may be artifacts due to SHS-caused mis-priming and thus greater caution should be taken when new sequence is obtained from a technique involving DNA polymerization.
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Affiliation(s)
- Bingkun Xie
- Guangxi Institute of Animal Sciences, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, Guangxi, 530001, P.R. China
- * E-mail: (BKX); (HSJ); (DJL)
| | - Wei Yang
- Guangxi Veterinary Research Institute, Nanning, Guangxi, P.R. China
| | - Yongchang Ouyang
- Hormel Institute, University of Minnesota, Austin, Minnesota, 55912, United States of America
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, Minnesota, 55912, United States of America
| | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, P.R. China
- * E-mail: (BKX); (HSJ); (DJL)
| | - Yuying Liao
- Guangxi Institute of Animal Sciences, Guangxi Key Laboratory of Livestock Genetic Improvement, Nanning, Guangxi, 530001, P.R. China
| | - D. Joshua Liao
- Department of Pathology, Guizhou Medical University Hospital, Guizhou, Guiyang, 550004, P.R. China
- * E-mail: (BKX); (HSJ); (DJL)
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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18
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Fernandez-Mercado M, Manterola L, Larrea E, Goicoechea I, Arestin M, Armesto M, Otaegui D, Lawrie CH. The circulating transcriptome as a source of non-invasive cancer biomarkers: concepts and controversies of non-coding and coding RNA in body fluids. J Cell Mol Med 2015; 19:2307-23. [PMID: 26119132 PMCID: PMC4594673 DOI: 10.1111/jcmm.12625] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/07/2015] [Indexed: 12/12/2022] Open
Abstract
The gold standard for cancer diagnosis remains the histological examination of affected tissue, obtained either by surgical excision, or radiologically guided biopsy. Such procedures however are expensive, not without risk to the patient, and require consistent evaluation by expert pathologists. Consequently, the search for non-invasive tools for the diagnosis and management of cancer has led to great interest in the field of circulating nucleic acids in plasma and serum. An additional benefit of blood-based testing is the ability to carry out screening and repeat sampling on patients undergoing therapy, or monitoring disease progression allowing for the development of a personalized approach to cancer patient management. Despite having been discovered over 60 years ago, the clear clinical potential of circulating nucleic acids, with the notable exception of prenatal diagnostic testing, has yet to translate into the clinic. The recent discovery of non-coding (nc) RNA (in particular micro(mi)RNAs) in the blood has provided fresh impetuous for the field. In this review, we discuss the potential of the circulating transcriptome (coding and ncRNA), as novel cancer biomarkers, the controversy surrounding their origin and biology, and most importantly the hurdles that remain to be overcome if they are really to become part of future clinical practice.
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Affiliation(s)
| | - Lorea Manterola
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - Erika Larrea
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - Ibai Goicoechea
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - María Arestin
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - María Armesto
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain
| | - David Otaegui
- Multiple Sclerosis Group, Biodonostia Research Institute, San Sebastian, Spain
| | - Charles H Lawrie
- Oncology Area, Biodonostia Research Institute, San Sebastian, Spain.,Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Sanguedolce F, Cormio A, Bufo P, Carrieri G, Cormio L. Molecular markers in bladder cancer: Novel research frontiers. Crit Rev Clin Lab Sci 2015; 52:242-55. [PMID: 26053693 DOI: 10.3109/10408363.2015.1033610] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Bladder cancer (BC) is a heterogeneous disease encompassing distinct biologic features that lead to extremely different clinical behaviors. In the last 20 years, great efforts have been made to predict disease outcome and response to treatment by developing risk assessment calculators based on multiple standard clinical-pathological factors, as well as by testing several molecular markers. Unfortunately, risk assessment calculators alone fail to accurately assess a single patient's prognosis and response to different treatment options. Several molecular markers easily assessable by routine immunohistochemical techniques hold promise for becoming widely available and cost-effective tools for a more reliable risk assessment, but none have yet entered routine clinical practice. Current research is therefore moving towards (i) identifying novel molecular markers; (ii) testing old and new markers in homogeneous patients' populations receiving homogeneous treatments; (iii) generating a multimarker panel that could be easily, and thus routinely, used in clinical practice; (iv) developing novel risk assessment tools, possibly combining standard clinical-pathological factors with molecular markers. This review analyses the emerging body of literature concerning novel biomarkers, ranging from genetic changes to altered expression of a huge variety of molecules, potentially involved in BC outcome and response to treatment. Findings suggest that some of these indicators, such as serum circulating tumor cells and tissue mitochondrial DNA, seem to be easily assessable and provide reliable information. Other markers, such as the phosphoinositide-3-kinase (PI3K)/AKT (serine-threonine kinase)/mTOR (mammalian target of rapamycin) pathway and epigenetic changes in DNA methylation seem to not only have prognostic/predictive value but also, most importantly, represent valuable therapeutic targets. Finally, there is increasing evidence that the development of novel risk assessment tools combining standard clinical-pathological factors with molecular markers represents a major quest in managing this poorly predictable disease.
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Noncoding RNA Expression During Viral Infection: The Long and the Short of It. MICRORNAS AND OTHER NON-CODING RNAS IN INFLAMMATION 2015. [PMCID: PMC7123390 DOI: 10.1007/978-3-319-13689-9_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Nanoparticle-based detection of cancer-associated RNA. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:384-97. [DOI: 10.1002/wnan.1266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/06/2014] [Accepted: 02/08/2014] [Indexed: 12/12/2022]
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Rockenbach L, Braganhol E, Dietrich F, Figueiró F, Pugliese M, Edelweiss MIA, Morrone FB, Sévigny J, Battastini AMO. NTPDase3 and ecto-5'-nucleotidase/CD73 are differentially expressed during mouse bladder cancer progression. Purinergic Signal 2014; 10:421-30. [PMID: 24464643 DOI: 10.1007/s11302-014-9405-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/06/2014] [Indexed: 12/20/2022] Open
Abstract
According to the World Health Organization, bladder cancer is the seventh most common cancer among men in the world. The current treatments for this malignancy are not efficient to prevent the recurrence and progression of tumors. Then, researches continue looking for better therapeutic targets which can end up in new and more efficient treatments. One of the recent findings was the identification that the purinergic system was involved in bladder tumorigenesis. The ectonucleotidases, mainly ecto-5'-nucleotidase/CD73 have been revealed as new players in cancer progression and malignity. In this work, we investigated the NTPDase3 and ecto-5'-nucleotidase/CD73 expression in cancer progression in vivo. Bladder tumor was induced in mice by the addition of 0.05 % of N-butyl-N-(hydroxybutyl)-nitrosamine (BBN) in the drinking water for 4, 8, 12, 18, and 24 weeks. After this period, mice bladders were removed for histopathology analysis and immunofluorescence assays. The bladder of animals which has received BBN had alterations, mainly inflammation, in initial times of tumor induction. After 18 weeks, mice's bladder has developed histological alterations similar to human transitional cell carcinoma. The cancerous urothelium, from mice that received BBN for 18 and 24 weeks, presented a weak immunostaining to NTPDase3, in contrast to an increased expression of ecto-5'-nucleotidase/CD73. The altered expression of NTPDase3 and ecto-5'-nucleotidase/CD73 presented herein adds further evidence to support the idea that alterations in ectonucleotidases are involved in bladder tumorigenesis and reinforce the ecto-5'-nucleotidase/CD73 as a future biomarker and/or a target for pharmacological therapy of bladder cancer.
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Affiliation(s)
- Liliana Rockenbach
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil,
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Zhang Q, Su M, Lu G, Wang J. The complexity of bladder cancer: long noncoding RNAs are on the stage. Mol Cancer 2013; 12:101. [PMID: 24006935 PMCID: PMC3846905 DOI: 10.1186/1476-4598-12-101] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/15/2013] [Indexed: 12/26/2022] Open
Abstract
The mammalian genome encodes thousands of long noncoding RNAs (lncRNAs) and it is increasingly clear that lncRNAs are key regulators of cellular function and development. Gain and/or loss of function studies in cell culture indicate that lncRNAs can regulate gene transcription indirectly through the targeting and recruitment of chromatin-modifying complexes as well as directly at the transcriptional or posttranscriptional levels. LncRNA biology is attracting great attention in cancer research because dysregulated lncRNAs occur in a variety of cancers, placing lncRNAs on the stage of cancer genome research. We briefly describe the latest lncRNA biology and discuss the oncogenic lncRNAs involved in core pathways in bladder cancer and the application of lncRNAs to its diagnosis and targeted treatment. LncRNAs are becoming essential components of the gene regulatory circuitry in the complexity of bladder cancer.
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Affiliation(s)
- Quanan Zhang
- Department of Pathology, Laboratory of Molecular Pathology and Molecular Imaging, Jinling Hospital, School of Medicine Nanjing University, 305 Zhong Shan Dong Lu, 210002 Nanjing, China.
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