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Gupta G, Afzal M, Moglad E, Ali H, Singh TG, Kumbhar P, Disouza J, Almujri SS, Kazmi I, Alzarea SI, Hemalatha KP, Goh BH, Singh SK, Dua K. Non-coding RNAs as key regulators of Gasdermin-D mediated pyroptosis in cancer therapy. Pathol Res Pract 2024; 261:155490. [PMID: 39126977 DOI: 10.1016/j.prp.2024.155490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Pyroptosis is an inflammatory programed cell death process that plays a crucial role in cancer therapeutic, while Gasdermin-D is a critical effector protein for pyroptosis execution. This review discusses the intricate interactions between Gasdermin-D and some non-coding RNAs (lncRNA, miRNA, siRNA) and their potential application in the regulation of pyroptosis as an anticancer therapy. Correspondingly, these ncRNAs significantly implicate in Gasdermin-D expression and function regarding the pyroptosis pathway. Functioning as competing endogenous RNAs (ceRNAs), these ncRNAs might regulate Gasdermin-D at the molecular level, underlying fatal cell death caused by cancer and tumor propagation. Therefore, these interactions appeal to therapeutics, offering new avenues for cancer treatment. It address this research gap by discussing the possible roles of ncRNAs as mediators of gasdermin-D regulation. It suggest therapeutic strategies based on the current research findings to ensure the interchange between the ideal pyroptosis and cancer cell death.
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Affiliation(s)
- Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India; Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | | | - Popat Kumbhar
- Tatyasaheb Kore College of Pharmacy, Warananagar, Tal: Panhala Dist, Kolhapur, Maharashtra 416113, India
| | - John Disouza
- Bombay Institute of Research and Pharmacy, Dombivli, Mumbai, Maharashtra 421203, India
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Aseer 61421, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf 72341, Saudi Arabia
| | - K P Hemalatha
- Sree Siddaganga College of Pharmacy, Tumkur, Karnataka, India
| | - Bey Hing Goh
- Sunway Biofunctional Molecules Discovery Centre (SBMDC), School of Medical and Life Sciences, Sunway University, Sunway, Malaysia; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia
| | - Sachin Kumar Singh
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia; School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, NSW 2007, Australia; Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
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2
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Michas A, Michas V, Anagnostou E, Galanopoulos M, Tolia M, Tsoukalas N. The Clinical Significance of MicroRNAs in Colorectal Cancer Signaling Pathways: A Review. Glob Med Genet 2023; 10:315-323. [PMID: 38025193 PMCID: PMC10665125 DOI: 10.1055/s-0043-1777094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Colorectal carcinoma (colon and rectum) is currently considered among the most prevalent malignancies of Western societies. The pathogenesis and etiological mechanisms underlying colorectal cancer (CRC) development remain complex and heterogeneous. The homeostasis and function of normal human intestinal cells is highly regulated by microRNAs. Therefore, it is not surprising that mutations and inactivation of these molecules appear to be linked with progression of colorectal tumors. Recent studies have reported significant alterations of microRNA expression in adenomas and CRCs compared with adjacent normal tissues. This observed deviation has been proposed to correlate with the progression and survival of disease as well as with choice of optimal treatment and drug resistance. MicroRNAs can adopt either oncogenic or tumor-suppressive roles during regulation of pathways that drive carcinogenesis. Typically, oncogenic microRNAs termed oncomirs, target and silence endogenous tumor-suppressor genes. On the other hand, tumor-suppressive microRNAs are critical in downregulating genes associated with cell growth and malignant capabilities. By extensively evaluating robust studies, we have emphasized and distinguished a discrete set of microRNAs that can modulate tumor progression by silencing specific driver genes crucial in signaling pathways including Wnt/b-catenin, epidermal growth factor receptor, P53, mismatch repair DNA repair, and transforming-growth factor beta.
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Affiliation(s)
- Athanasios Michas
- Department of Oncology, 401 General Military Hospital of Athens, Athens, Greece
| | - Vasileios Michas
- Department of Radiology, Achepa General Hospital Thessaloniki, Thessaloniki, Greece
| | - Evangelos Anagnostou
- Department of Neurosurgery, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | | | - Maria Tolia
- Department of Oncology, 401 General Military Hospital of Athens, Athens, Greece
| | - Nikolaos Tsoukalas
- Department of Oncology, 401 General Military Hospital of Athens, Athens, Greece
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Bhattacharya S, Mahato RK, Singh S, Bhatti GK, Mastana SS, Bhatti JS. Advances and challenges in thyroid cancer: The interplay of genetic modulators, targeted therapies, and AI-driven approaches. Life Sci 2023; 332:122110. [PMID: 37734434 DOI: 10.1016/j.lfs.2023.122110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
Thyroid cancer continues to exhibit a rising incidence globally, predominantly affecting women. Despite stable mortality rates, the unique characteristics of thyroid carcinoma warrant a distinct approach. Differentiated thyroid cancer, comprising most cases, is effectively managed through standard treatments such as thyroidectomy and radioiodine therapy. However, rarer variants, including anaplastic thyroid carcinoma, necessitate specialized interventions, often employing targeted therapies. Although these drugs focus on symptom management, they are not curative. This review delves into the fundamental modulators of thyroid cancers, encompassing genetic, epigenetic, and non-coding RNA factors while exploring their intricate interplay and influence. Epigenetic modifications directly affect the expression of causal genes, while long non-coding RNAs impact the function and expression of micro-RNAs, culminating in tumorigenesis. Additionally, this article provides a concise overview of the advantages and disadvantages associated with pharmacological and non-pharmacological therapeutic interventions in thyroid cancer. Furthermore, with technological advancements, integrating modern software and computing into healthcare and medical practices has become increasingly prevalent. Artificial intelligence and machine learning techniques hold the potential to predict treatment outcomes, analyze data, and develop personalized therapeutic approaches catering to patient specificity. In thyroid cancer, cutting-edge machine learning and deep learning technologies analyze factors such as ultrasonography results for tumor textures and biopsy samples from fine needle aspirations, paving the way for a more accurate and effective therapeutic landscape in the near future.
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Affiliation(s)
- Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151401, Punjab, India
| | - Satwinder Singh
- Department of Computer Science and Technology, Central University of Punjab, Bathinda 151401, Punjab, India.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Sarabjit Singh Mastana
- School of Sport, Exercise and Health Sciences, Loughborough University, Epinal Way, Leicestershire, Loughborough LE11 3TU, UK.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda 151401, Punjab, India.
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Ma J, Wang F, Chen C, Ji J, Huang P, Wei D, Zhang Y, Ren L. Identification of prognostic genes signature and construction of ceRNA network in pirarubicin treatment of triple-negative breast cancer. Breast Cancer 2023; 30:379-392. [PMID: 36622564 DOI: 10.1007/s12282-023-01433-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND The altered long non-coding RNA (lncRNA), circular RNA (circRNA) and mRNA expression in triple-negative breast cancer (TNBC) after pirarubicin (THP) treatment can be a critical factor in the development of tumor. Here, we identify a set of lncRNA, circRNA, and mRNA that can reveal the molecular target and molecular mechanism of THP, and can be used to predict the prognostic characteristics of TNBC. METHODS Affymetrix GeneChip sequencing was performed to determine whether lncRNA, circRNA, and mRNA were changed in MDA-MB-231 cells after THP treatment, and qRT-PCR was used to verify the accuracy of GeneChip results. Bioinformatics methods were used to analyze the differentially expressed (DE) lncRNA, circRNA and mRNA, and the co-expression network and ceRNA network were constructed. The STRING database, Kaplan-meier Mapper database, GEPIA database, and Tumor Immunity Estimation Resource were used to screen hub genes with clinical value and important significance. RESULTS THP 5 μM could significantly inhibit proliferation, migration and invasion of MDA-MB-231 cells for 24 h. 1547 DE lncRNAs, 4992 DE circRNAs, and 5777 DE mRNAs were identified. The reliability of the GeneChip was verified by qRT-PCR. An mRNA-lncRNA/circRNA co-expression network was constructed based on the Pearson correlation coefficient. Finally, we established a new ceRNA network, including three circRNAs, five miRNAs, and three mRNAs. The mRNAs are associated with immune infiltration. The mRNAs and miRNAs are significantly associated with survival outcomes in TNBC. CONCLUSION The results reveal the molecular target and mechanism of THP treatment of TNBC. These ceRNA network can be used as molecular targets for the treatment of TNBC patients and as molecular biomarkers to predict patient prognosis.
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Affiliation(s)
- Jiulong Ma
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Fengjun Wang
- Department of Hepatobiliary Surgery, Songyuan Central Hospital, Songyuan, China
| | - Chen Chen
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Jiahua Ji
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Peng Huang
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Dexian Wei
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Yang Zhang
- Department of Vascular Surgery, The First Hospital of Jilin University, Changchun, China.
| | - Liqun Ren
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China.
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Cai X, Gao C, Lymbery AJ, Armstrong NJ, Ma L, Li C. The immune-related circRNA-miRNA-mRNA ceRNA regulatory network in the liver of turbot (Scophthalmus maximus L.) induced by Vibrio anguillarum. FISH & SHELLFISH IMMUNOLOGY 2023; 132:108506. [PMID: 36574792 DOI: 10.1016/j.fsi.2022.108506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Recently, Vibrio anguillarum, a Gram-negative pathogenic bacterium, has been becoming a major constraint on the development of the turbot aquaculture industry because of its characteristics of worldwide distribution, broad host range and potentially devastating impacts. Although the functions of protein-coding mRNAs in the immune response against bacterial infection have been reported, as well as several non-coding RNAs (ncRNAs), such as circular RNAs (circRNAs) and microRNAs (miRNAs), the relationships between mRNAs and ncRNAs in the immune system of turbot liver are still limited during bacterial infection. In present study, the comprehensive analyses of whole-transcriptome sequencing were conducted in turbot liver infected by V. anguillarum. The differential expression was analyzed in the data of circRNAs, miRNAs, and mRNAs. The interactions of miRNA-circRNA pairs and miRNA-mRNA pairs were predicted basing on the negative regulatory relationships between miRNAs and their target circRNAs\mRNAs. The circRNA-related ceRNA regulatory networks were constructed for the analyses of regulated mechanism in turbot immune system. Subsequently, the RT-qPCR was carried out to verify the results of sequencing. Finally, we identified 31 circRNAs, 53 miRNAs and 948 mRNAs with differential expression. Gene set enrichment analyses using Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways showed that innate immunity was principally activated at the early stages of infection, while adaptive immunity was activated after 24 h. Finally, 65 circRNA-miRNA-mRNA pathways were constructed, based on the hypothesis of ceRNA regulatory networks. In conclusion, our findings provide new insights on the underlying immune response to bacterial infection and identify novel target genes for the prevention and control of disease in turbot.
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Affiliation(s)
- Xin Cai
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Chengbin Gao
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China; Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Alan J Lymbery
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Nicola J Armstrong
- Department of Mathematics and Statistics, Curtin University, Kent Street, Bentley, Perth, WA, 6102, Australia
| | - Le Ma
- Centre for Sustainable Aquatic Ecosystems, Harry Butler Institute, School of Veterinary & Life Sciences, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Li Y, Xia G, Tan Y, Shuai J. Expression profile of circular RNAs in continuous light-induced ovarian dysfunction. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 242:113861. [PMID: 35835072 DOI: 10.1016/j.ecoenv.2022.113861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/23/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
PURPOSE This study aims to elucidate the underlying relationship between the expression profiles of circular RNAs (circRNAs) and the ovarian dysfunction induced by continuous light. METHODS High-throughput sequencing was used to profile the transcriptome of differentially expressed circRNAs (DEcircRNAs) in rat ovary under continuous light exposure (12 h:12 h light/light cycle, L/L group) and a control cycle (12 h:12 h light/dark cycle, L/D group). Gene ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNAs-microRNAs-messenger RNAs networks were performed to predict the role of DEcircRNAs in biological processes and pathways. A quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) assay was conducted to verify the high-throughput sequencing results and the expression level of circadian rhythm genes. RESULTS In total, 305 circRNAs were differentially expressed between the L/L and L/D groups. Among these, 211 circRNAs were up regulated, while 94 were down regulated. Eight candidate circRNAs from 305 DEcircRNAs were verified by qRT-PCR. Further bioinformatics analysis revealed that interactions between DEcircRNAs and a set of microRNAs involved in ovarian dysfunction-related pathways, such as regulation of androgen receptors, gonadotrophin releasing hormone signaling pathway, endocrine resistance, etc. Subsequently, we identified rno_circ:chr2:86868285-86964272 and rno_circ:chr1:62330221-62360073 may participate in the pathophysiology of ovarian dysfunction by constructing circRNAs-microRNAs-messenger RNAs networks. Meanwhile, constant light reduced the expression of circadian rhythm genes CLOCK, BAML1, PER1, and PER2 compared with that of controls. Caspase3 and Bax were up regulated in the L/L group compared with the L/D group, while Bcl-2 was down regulated. CONCLUSIONS In summary, the results reveal that the expression profiles and potential functions of DEcircRNAs in rat ovaries may play important roles in continuous light-induced ovarian dysfunction. These findings provide novel clues and molecular targets for studying the mechanisms and clinical therapy of ovarian dysfunction.
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Affiliation(s)
- Yuling Li
- Nanjing University of Chinese Medicine, Nanjing 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Guicheng Xia
- Nanjing University of Chinese Medicine, Nanjing 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Yong Tan
- Nanjing University of Chinese Medicine, Nanjing 210029, China; Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, China.
| | - Jiaqi Shuai
- Bachelor of Medicine, University of Antwerp, Antwerp, Belgium
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Towle-Miller LM, Miecznikowski JC, Zhang F, Tritchler DL. SuMO-Fil: Supervised multi-omic filtering prior to performing network analysis. PLoS One 2021; 16:e0255579. [PMID: 34343218 PMCID: PMC8330944 DOI: 10.1371/journal.pone.0255579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 07/20/2021] [Indexed: 11/18/2022] Open
Abstract
Multi-omic analyses that integrate many high-dimensional datasets often present significant deficiencies in statistical power and require time consuming computations to execute the analytical methods. We present SuMO-Fil to remedy against these issues which is a pre-processing method for Supervised Multi-Omic Filtering that removes variables or features considered to be irrelevant noise. SuMO-Fil is intended to be performed prior to downstream analyses that detect supervised gene networks in sparse settings. We accomplish this by implementing variable filters based on low similarity across the datasets in conjunction with low similarity with the outcome. This approach can improve accuracy, as well as reduce run times for a variety of computationally expensive downstream analyses. This method has applications in a setting where the downstream analysis may include sparse canonical correlation analysis. Filtering methods specifically for cluster and network analysis are introduced and compared by simulating modular networks with known statistical properties. The SuMO-Fil method performs favorably by eliminating non-network features while maintaining important biological signal under a variety of different signal settings as compared to popular filtering techniques based on low means or low variances. We show that the speed and accuracy of methods such as supervised sparse canonical correlation are increased after using SuMO-Fil, thus greatly improving the scalability of these approaches.
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Affiliation(s)
- Lorin M. Towle-Miller
- Department of Biostatistics, University at Buffalo, Buffalo, NY, United States of America
| | | | - Fan Zhang
- Department of Biostatistics, University at Buffalo, Buffalo, NY, United States of America
| | - David L. Tritchler
- Department of Biostatistics, University at Buffalo, Buffalo, NY, United States of America
- Biostatistics Division, University of Toronto, Toronto, Ontario, Canada
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Salimimoghadam S, Taefehshokr S, Loveless R, Teng Y, Bertoli G, Taefehshokr N, Musaviaroo F, Hajiasgharzadeh K, Baradaran B. The role of tumor suppressor short non-coding RNAs on breast cancer. Crit Rev Oncol Hematol 2020; 158:103210. [PMID: 33385514 DOI: 10.1016/j.critrevonc.2020.103210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 12/15/2020] [Accepted: 12/20/2020] [Indexed: 12/11/2022] Open
Abstract
Characterized by remarkable levels of aggression and malignancy, BC remains one of the leading causes of death in females world wide. Accordingly, significant efforts have been made to develop early diagnostic tools, increase treatment efficacy, and improve patient prognosis. Hopefully, many of the molecular mechanisms underlying BC have been detected and show promising targeting potential. In particular, short and long non-coding RNAs (ncRNAs) are a class of endogenous BC controllers and include a number of different species including microRNAs, Piwi-interacting RNAs, small nucleolar RNA, short interfering RNAs, and tRNA-derivatives. In this review, we discuss the tumor suppressing roles of ncRNAs in the context of BC, and the mechanisms by which ncRNAs target tumor hallmarks, including apoptosis, proliferation, invasion, metastasis, epithelial-mesenchymal transition, angiogenesis, and cell cycle progression, in addition to their diagnostic and prognostic significance in cancer treatment.
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Affiliation(s)
| | - Sina Taefehshokr
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Reid Loveless
- Department of Oral Biology and Diagnostic Sciences, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Augusta University, Augusta, GA, USA.
| | - Yong Teng
- Department of Oral Biology and Diagnostic Sciences, Augusta University, Augusta, GA, USA; Georgia Cancer Center, Augusta University, Augusta, GA, USA.
| | - Gloria Bertoli
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), Segrate, Milan, Italy.
| | - Nima Taefehshokr
- Department of Microbiology and Immunology, Center for Human Immunology, The University of Western Ontario, London, Ontario, Canada.
| | | | | | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Chen H, Fan Y, Jing H, Tang S, Huang Z, Liao M, Lin S, Zhong J, Zhou J. LncRNA Gm12840 mediates WISP1 to regulate ischemia-reperfusion-induced renal fibrosis by sponging miR-677-5p. Epigenomics 2020; 12:2205-2218. [PMID: 33351669 DOI: 10.2217/epi-2020-0054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Aim: We aimed to identify that long noncoding RNAs (lncRNAs) are involved in ischemia-reperfusion (IR)-induced late fibrosis of kidney and may constitute novel therapeutic strategies for acute kidney injury-induced chronic kidney disease. Materials & methods: We performed the mouse model of IR later induced renal fibrosis and analyzed lncRNA profiles using second-generation sequencing during the pathogenesis. Results: The expression levels of 43 lncRNAs and 141 lncRNAs were respectively changed significantly 7 days and 2 weeks after IR treatment. Based on the correlation analysis of the differentially expressed genes, the interaction networks of lncRNAs, miRNAs and mRNA were structured. Conclusion: LncRNA (Gm12840) could act as a sponge for miR-677-5p to mediate fibroblast activation induced by TGF-β1 via the WISP1/PKB (Akt) signaling pathway.
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Affiliation(s)
- Hongtao Chen
- Department of Anesthesiology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, 8 Huaying Road, Guangzhou, Guangdong 510060, PR China
| | - Youling Fan
- Department of Anesthesiology, Panyu Central Hospital, 8 Fuyu West Road, Guangzhou, Guangdong 511400, PR China
| | - Huan Jing
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, 183 Zhongshan West Road, Guangzhou, Guangdong 510630, PR China
| | - Simin Tang
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, 183 Zhongshan West Road, Guangzhou, Guangdong 510630, PR China
| | - Zhenxing Huang
- Department of Anesthesiology, The First People's Hospital of Foshan, 81 North Lingnan Avenue, Foshan, Guangdong 528000, PR China
| | - Meijuan Liao
- Department of Anesthesiology, The First People's Hospital of Foshan, 81 North Lingnan Avenue, Foshan, Guangdong 528000, PR China
| | - Sen Lin
- Department of Anesthesiology, The First People's Hospital of Foshan, 81 North Lingnan Avenue, Foshan, Guangdong 528000, PR China
| | - Jiying Zhong
- Department of Anesthesiology, The First People's Hospital of Foshan, 81 North Lingnan Avenue, Foshan, Guangdong 528000, PR China
| | - Jun Zhou
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, 183 Zhongshan West Road, Guangzhou, Guangdong 510630, PR China
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Pippadpally S, Venkatesh T. Deciphering piRNA biogenesis through cytoplasmic granules, mitochondria and exosomes. Arch Biochem Biophys 2020; 695:108597. [PMID: 32976825 DOI: 10.1016/j.abb.2020.108597] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 12/31/2022]
Abstract
RNA systems biology is marked by a myriad of cellular processes mediated by small and long non-coding RNAs. Small non-coding RNAs include siRNAs (small interfering RNAs), miRNAs (microRNAs), tRFs(tRNA derived fragments), and piRNAs (PIWI-interacting RNAs). piRNAs are vital for the maintenance of the germ-line integrity and repress the transposons either transcriptionally or post-transcriptionally. Studies based on model organisms have shown that defects in the piRNA pathway exhibit impaired gametogenesis and loss of fertility. piRNA biogenesis is marked by transcription of precursor molecules and their subsequent processing in the cytoplasm to generate mature piRNAs. Their biogenesis is unique and complex, which involves non-canonical transcription and self-amplification mechanisms such as the ping-pong cycle. piRNA biogenesis is different in somatic and germ cells and involves the role of cytoplasmic granules in addition to mitochondria. In this review, we discuss the biogenesis and maturation of piRNAs in various cytoplasmic granules such as Yb and nuage bodies. Also, we review the role of P bodies, stress granules, and P granules, and membrane-bound compartments such as mitochondria and exosomes in piRNA biogenesis.
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Affiliation(s)
- Srikanth Pippadpally
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, 671316, India
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, 671316, India.
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11
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Qu Y, Liu J. lncRNA MAFG-AS1 Contributes to Esophageal Squamous-Cell Carcinoma Progression via Regulating miR143/LASP1. Onco Targets Ther 2020; 13:8359-8370. [PMID: 32903907 PMCID: PMC7445532 DOI: 10.2147/ott.s258157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/23/2020] [Indexed: 12/14/2022] Open
Abstract
Background Increasing investigations indicate that long noncoding RNA (lncRNA) is responsible for diverse biological functions during the progression of cancer. However, its functions and underlying mechanisms remain elusive. Here, we investigated the MAFG-AS1- expression profile in esophageal squamous-cell carcinoma (ESCC) patients and explored its biological function and potential molecular mechanisms. Methods qRT-PCR and the GEPIA data base were used to evaluate expression levels of MAFG-AS1 in ESCC tissue and cells. WST1-proliferation, -migration, and -invasion assays were performed to define the role of MAFG-AS1 in ESCC. Potential molecular mechanisms of MAFG-AS1 were investigated with online bioinformatic analysis, qRT-PCR, and rescue assays. Results MAFG-AS1 was upregulated in 45 ESCC-tissue samples and cell lines compared to that of adjacent nontumor tissue and normal esophageal cells. Higher MAFG-AS1 expressionindicated poor survival. Gain- and loss-of-function experiments suggested that MAFG-AS1 promoted ESCC-cell proliferation, migration, and invasion. Molecular mechanism analysis and rescue assay showed that miR143 inhibitors partly abolished the suppression of MAFG-AS1 knockdown on EC109-cells proliferation. Moreover, we found that LASP1 specifically targeted miR143. Collectively, these data indicated that MAFG-AS1 served as a ceRNA to elevate LASP1 levels by sponging miR143, and played an oncogenic role in ESCC. Conclusion Our research findings demonstrate that MAFG-AS1 is a key regulator through a novel MAFG-AS1–miR143–LASP1 axis in ESCC development and progression, which may offer a potential therapeutic target for ESCC.
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Affiliation(s)
- Yunhui Qu
- Department of Clinical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Jinbo Liu
- Department of Colorectal Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
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Aggarwal V, Tuli HS, Tania M, Srivastava S, Ritzer EE, Pandey A, Aggarwal D, Barwal TS, Jain A, Kaur G, Sak K, Varol M, Bishayee A. Molecular mechanisms of action of epigallocatechin gallate in cancer: Recent trends and advancement. Semin Cancer Biol 2020; 80:256-275. [PMID: 32461153 DOI: 10.1016/j.semcancer.2020.05.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/17/2020] [Indexed: 12/22/2022]
Abstract
Epigallocatechin gallate (EGCG), also known as epigallocatechin-3-gallate, is an ester of epigallocatechin and gallic acid. EGCG, abundantly found in tea, is a polyphenolic flavonoid that has the potential to affect human health and disease. EGCG interacts with various recognized cellular targets and inhibits cancer cell proliferation by inducing apoptosis and cell cycle arrest. In addition, scientific evidence has illustrated the promising role of EGCG in inhibiting tumor cell metastasis and angiogenesis. It has also been found that EGCG may reverse drug resistance of cancer cells and could be a promising candidate for synergism studies. The prospective importance of EGCG in cancer treatment is owed to its natural origin, safety, and low cost which presents it as an attractive target for further development of novel cancer therapeutics. A major challenge with EGCG is its low bioavailability which is being targeted for improvement by encapsulating EGCG in nano-sized vehicles for further delivery. However, there are major limitations of the studies on EGCG, including study design, experimental bias, and inconsistent results and reproducibility among different study cohorts. Additionally, it is important to identify specific EGCG pharmacological targets in the tumor-specific signaling pathways for development of novel combined therapeutic treatments with EGCG. The present review highlights the ongoing development to identify cellular and molecular targets of EGCG in cancer. Furthermore, the role of nanotechnology-mediated EGCG combinations and delivery systems will also be discussed.
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Affiliation(s)
- Vaishali Aggarwal
- Department of Histopathology, Post Graduate Institute of Medical Education and Research, Chandigarh 160 012, Punjab, India
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala 133 207, Haryana, India.
| | - Mousumi Tania
- Division of Molecular Cancer, Red Green Research Center, Dhaka 1205, Bangladesh
| | - Saumya Srivastava
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211 004, Uttar Pradesh, India
| | - Erin E Ritzer
- Lake Erie College of Osteopathic Medicine, Bradenton 34211, FL, USA
| | - Anjana Pandey
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211 004, Uttar Pradesh, India
| | - Diwakar Aggarwal
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala 133 207, Haryana, India
| | - Tushar Singh Barwal
- Department of Zoology, Central University of Punjab, Bathinda 151 001, Punjab, India
| | - Aklank Jain
- Department of Zoology, Central University of Punjab, Bathinda 151 001, Punjab, India
| | - Ginpreet Kaur
- Department of Pharmacology, Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, Mumbai 400 056, Maharastra, India
| | | | - Mehmet Varol
- Department of Molecular Biology and Genetics, Faculty of Science, Mugla Sitki Kocman University, Muğla TR48000, Turkey
| | - Anupam Bishayee
- Lake Erie College of Osteopathic Medicine, Bradenton 34211, FL, USA.
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Huang L, Tang X, Shi X, Su L. miR-532-5p promotes breast cancer proliferation and migration by targeting RERG. Exp Ther Med 2019; 19:400-408. [PMID: 31853317 DOI: 10.3892/etm.2019.8186] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 10/04/2019] [Indexed: 02/06/2023] Open
Abstract
Aberrant expression of microRNAs (miRNAs/miRs) mediates the initiation and progression of breast cancer. Therefore, it is important to investigate the molecular mechanisms of miRNAs and their effects on breast cancer progression. In the present study, miR-532-5p was highly expressed in breast cancer tissues compared with normal tissues. In addition, expression of ras-related and estrogen-regulated growth inhibitor (RERG), a tumor suppressor in breast cancer, was negatively correlated with miR-532-5p expression. Inhibition of miR-532-5p significantly elevated RERG at both mRNA and protein levels and inactivated the mitogen-activated protein kinase (MAPK)/ERK signaling pathway. Overexpression of miR-532-5p decreased RERG expression and activated the MAPK/ERK signaling in breast cancer cell line MDA-MB-231. Bioinformatic analysis indicated that RERG 3'-untraslated region contained a putative binding site for miR-532-5p. Dual luciferase assay further validated RERG as a target gene of miR-532-5p. Notably, downregulation of miR-532-5p inhibited MDA-MB-231 cell proliferation and migration, which was partially attenuated upon RERG knockdown. In conclusion, the current study revealed an oncogenic role of miR-532-5p in breast cancer cells via direct targeting of RERG expression.
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Affiliation(s)
- Lei Huang
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Xiaoqiao Tang
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Xianbiao Shi
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
| | - Lei Su
- Department of Breast and Thyroid Surgery, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu 210008, P.R. China
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Expression Profiles of lncRNAs and circRNAs in Keloid. PLASTIC AND RECONSTRUCTIVE SURGERY-GLOBAL OPEN 2019; 7:e2265. [PMID: 31624676 PMCID: PMC6635192 DOI: 10.1097/gox.0000000000002265] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/27/2019] [Indexed: 12/11/2022]
Abstract
Supplemental Digital Content is available in the text. Background: We hypothesized that crosstalk between noncoding RNAs, including microRNA (miRNA), lncRNA, and circRNA, might play a critical role in keloids development and physiology. To reveal the molecular mechanisms involved in the pathogenesis of keloids, we compared their gene expression profiles and differential expressions in keloid and normal skin tissues. Methods: Expression profiles of mRNAs and lncRNAs and circRNAs in 2 pairs (identification set) of keloid and matched normal skin tissues were analyzed through sequencing. Real-time quantitative PCR was performed to validate the sequencing results using 5 pairs (validation set) of keloid and matched normal skin tissues. Presumed targets of differentially expressed lncRNAs and circRNAs were functionally annotated by bioinformatics approaches. Results: The differential expression of mRNAs in keloid and normal skin by high-throughput sequencing was 2,528, of which 1,271 were downregulated, whereas 1,257 were upregulated. In the meantime, sequencing identified 2,227 differentially expressed lncRNAs, including 1,224 upregulated and 1,003 downregulated in keloid tissue compared with normal skin tissue. Additionally, 154 differentially expressed circRNAs were identified, including 81 upregulated and 73 downregulated in keloid tissue compared with normal skin tissue. Functional annotations of differentially expressed circRNA targets revealed their enrichment in several signaling pathways important for scar wound healing. Conclusions: Expression profiles of mRNAs, lncRNAs, and circRNAs were altered in keloid tissue, which may partly contribute to the etiology of keloids by affecting several signaling pathways relevant to scar wound healing. A better understanding of keloids pathogenesis may identify new therapeutic targets for keloids.
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Xu L, Zhu H, Gao F, Tang Y, Zhu Y, Sun Z, Wang J. Upregulation of the long non-coding RNA CBR3-AS1 predicts tumor prognosis and contributes to breast cancer progression. Gene 2019; 2:100014. [PMID: 32550547 PMCID: PMC7285981 DOI: 10.1016/j.gene.2019.100014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 03/13/2019] [Accepted: 03/16/2019] [Indexed: 01/14/2023]
Abstract
Breast cancer is the most common female malignancy and the major cause of cancer-related death in women. Long non-coding RNAs (lncRNAs), as oncogenic or tumor suppressor factor, involved in the development and progression of various cancers. In this study, we sought to investigate the function of lncRNA CBR3-AS1 in breast cancer. We evaluated the expression pattern of CBR3-AS1 in breast cancer tissues and cell lines, explored the correlation between CBR3-AS1 expression and the survival time of breast cancer patients, and probed the effect of CBR3-AS1 on tumor progression of breast cancer through loss-of-function and gain-of-function strategies. Our results showed that CBR3-AS1 was overexpressed in breast cancer tissues and cell lines and predicted the prognosis of breast cancer patients. And CBR3-AS1 exerted biological function as an oncogenic lncRNA, involved in the regulation of cell proliferation, colony formation, apoptosis and tumor growth in breast cancer. Taken together, CBR3-AS1 was up-regulated in breast cancer and promoted the risk of breast cancer. It may be a novel therapeutic target and potential prognostic marker for breast cancer.
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Affiliation(s)
- Lingyun Xu
- Department of Breast Surgery, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Hong Zhu
- Department of Radiation Oncology, Minhang Branch of Cancer Hospital of Fudan University, Shanghai 200240, China
| | - Fei Gao
- Family Planning Department, The Affiliated Changzhou Maternal and Child Health Care Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Yinghua Tang
- Breast Surgery Department, The Affiliated Changzhou Maternal and Child Health Care Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Yajun Zhu
- Department of Radiation Oncology, Changzhou Jintan District People's Hospital of Jiangsu University, Changzhou 213200, China
| | - Zhiqiang Sun
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou 213001, China
| | - Jian Wang
- Department of Radiotherapy, Jiangyin People's Hospital, Affiliated Hospital of Southeast University, Jiangyin, 214400, China
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Analyzing the Interactions of mRNAs and ncRNAs to Predict Competing Endogenous RNA Networks in Osteosarcoma Chemo-Resistance. Mol Ther 2019; 27:518-530. [PMID: 30692017 DOI: 10.1016/j.ymthe.2019.01.001] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/07/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023] Open
Abstract
Chemo-resistance is a huge obstacle encountered in the osteosarcoma (OS) treatment. Protein-coding mRNAs, as well as non-coding RNAs (ncRNAs), including long ncRNA (lncRNA), circular RNA (circRNA), and microRNA (miRNA), have been demonstrated to play an essential role in the regulation of cancer biology. However, the comprehensive expression profile and competing endogenous RNA (ceRNA) regulatory network between mRNAs and ncRNAs in the OS chemo-resistance still remain unclear. In the current study, we developed whole-transcriptome sequencing (RNA sequencing [RNA-seq]) in the three paired multi-drug chemo-resistant and chemo-sensitive OS cell lines to comprehensively identify differentially expressed lncRNAs, circRNAs, miRNAs, and mRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for mRNAs with significantly different expression. Then the ceRNA networks combining lncRNAs, circRNAs, miRNAs, and mRNAs were predicted and constructed on the basis of the authoritative miRanda and TargetScan databases combined with the widely accepted vital drug resistance-related genes and signal transduction pathways. In addition, two constructed ceRNA regulatory pathways, lncRNAMEG3/hsa-miR-200b-3p/AKT2 and hsa_circ_0001258/hsa-miR-744-3p/GSTM2, were randomly selected and validated by real-time qPCR, RNA immunoprecipitation (RIP), RNA pull-down assay, and dual luciferase reporter gene system. Taken together, our findings may provide new evidence for the underlying mechanism of OS chemo-resistance and uncover some novel targets for reversing it.
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17
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Klinge CM. Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers. Endocr Relat Cancer 2018; 25:R259-R282. [PMID: 29440232 DOI: 10.1530/erc-17-0548] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function. lncRNAs fold into structures that interact with DNA, RNA and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial and thyroid.
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18
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Identification of circular RNAs as a promising new class of diagnostic biomarkers for human breast cancer. Oncotarget 2018; 8:44096-44107. [PMID: 28484086 PMCID: PMC5546465 DOI: 10.18632/oncotarget.17307] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
Endogenous noncoding circular RNAs (circRNAs) have gained attention for their involvement in carcinogenesis, but their expression pattern in breast cancer has remained largely unknown. In this two-stage study, we first used an Arraystar Human circRNA Array to construct a genome-wide circRNA profile. We then selected candidate circRNAs for validation using a quantitative real-time polymerase chain reaction system. CircRNA/miRNA interactions were predicted and sequence analyses were performed. Among 1155 differentially expressed circRNAs, 715 were upregulated and 440 were downregulated in breast cancer tissues. The validation study demonstrated that hsa_circ_103110, hsa_circ_104689 and hsa_circ_104821 levels were elevated in breast cancer tissues, whereas hsa_circ_006054, hsa_circ_100219 and hsa_circ_406697 were downregulated. These circRNAs targeted complementary miRNA response elements. The area under the receiver operating characteristic curve for distinguishing breast cancer was 0.82 (95% CI: 0.73-0.90) when hsa_circ_006054, hsa_circ_100219 and hsa_circ_406697 were used in combination. This study provides evidence that circRNAs are differentially expressed in breast cancer and are important in carcinogenesis because they participate in cancer-related pathways and sequester miRNAs.
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Suresh PS, Tsutsumi R, Venkatesh T. YBX1 at the crossroads of non-coding transcriptome, exosomal, and cytoplasmic granular signaling. Eur J Cell Biol 2018; 97:163-167. [PMID: 29478751 DOI: 10.1016/j.ejcb.2018.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/28/2018] [Accepted: 02/14/2018] [Indexed: 01/09/2023] Open
Abstract
YBX1 (Y box binding protein 1) is an RNA-/DNA-binding multifunctional protein harboring the classical cold shock protein (CSD) domain, an A/P domain, and a long C-terminal domain with alternating positively and negatively charged amino acids. It is a well-established oncogenic transcriptional factor, and regulates apoptosis, translation, cell proliferation, mRNA splicing, repair, differentiation, and stress response. The non-coding transcriptome has added yet another layer of complexity to the YBX1-mediated master regulation of cellular functions. Interestingly, YBX1 has been shown to localize to cytoplasmic granules such as P granules and stress granules. These granules regulate the non-coding transcriptome profile as well as mRNA translation and degradation. In this review, we discuss the recent findings on YBX1 signaling as mediated by various classes of non-coding RNAs, and on the functions of YBX1 at P granules, stress granules, exosomes, and mitochondria. YBX1 is a well-established target for cancer therapy and understanding its functions at organelles and ncRNA transcriptomes will shed new insights for devising organelle based anti-cancer therapies.
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Affiliation(s)
- Padmanaban S Suresh
- Department of Biosciences, Mangalore University, Mangalagangothri, 574199, India
| | - Rie Tsutsumi
- Division of Nutrition and Metabolism, Institute of Biomedical Science, Tokushima University, Tokushima, Japan
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, Kerala, India.
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Affiliation(s)
- Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, Campus GHB ON1, Herestraat 49, 6000, Leuven, Belgium.
| | - Tapio Visakorpi
- Prostate Cancer Research Center, Institute for Biomedical Technology, FI-33014 University of Tampere, Biokatu, 6-8 33520, Tampere, Finland
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Bao J, Zhou C, Zhang J, Mo J, Ye Q, He J, Diao J. Upregulation of the long noncoding RNA FOXD2-AS1 predicts poor prognosis in esophageal squamous cell carcinoma. Cancer Biomark 2018; 21:527-533. [PMID: 29286915 DOI: 10.3233/cbm-170260] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jie Bao
- Department of Internal Medicine, Hospital of South China Normal University, Guangzhou 510631, Guangdong, China
| | - Chenjie Zhou
- Department of Hepatic Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Jiaqing Zhang
- Department of Cardiothoracic Surgery, Zhujiang Hospital of Southern Medical University, Guangzhou, Guangdong, China
| | - Jiaqiang Mo
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of TCM), Guangzhou 510120, Guangdong, China
| | - Qing Ye
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of TCM), Guangzhou 510120, Guangdong, China
| | - Junming He
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of TCM), Guangzhou 510120, Guangdong, China
| | - Jingfang Diao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of TCM), Guangzhou 510120, Guangdong, China
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Lu M, Xu X, Xi B, Dai Q, Li C, Su L, Zhou X, Tang M, Yao Y, Yang J. Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma. Genes (Basel) 2018; 9:E44. [PMID: 29351231 PMCID: PMC5793195 DOI: 10.3390/genes9010044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 12/14/2022] Open
Abstract
RNAs may act as competing endogenous RNAs (ceRNAs), a critical mechanism in determining gene expression regulations in many cancers. However, the roles of ceRNAs in thyroid carcinoma remains elusive. In this study, we have developed a novel pipeline called Molecular Network-based Identification of ceRNA (MNIceRNA) to identify ceRNAs in thyroid carcinoma. MNIceRNA first constructs micro RNA (miRNA)-messenger RNA (mRNA)long non-coding RNA (lncRNA) networks from miRcode database and weighted correlation network analysis (WGCNA), based on which to identify key drivers of differentially expressed RNAs between normal and tumor samples. It then infers ceRNAs of the identified key drivers using the long non-coding competing endogenous database (lnCeDB). We applied the pipeline into The Cancer Genome Atlas (TCGA) thyroid carcinoma data. As a result, 598 lncRNAs, 1025 mRNAs, and 90 microRNA (miRNAs) were inferred to be differentially expressed between normal and thyroid cancer samples. We then obtained eight key driver miRNAs, among which hsa-mir-221 and hsa-mir-222 were key driver RNAs identified by both miRNA-mRNA-lncRNA and WGCNA network. In addition, hsa-mir-375 was inferred to be significant for patients' survival with 34 associated ceRNAs, among which RUNX2, DUSP6 and SEMA3D are known oncogenes regulating cellular proliferation and differentiation in thyroid cancer. These ceRNAs are critical in revealing the secrets behind thyroid cancer progression and may serve as future therapeutic biomarkers.
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Affiliation(s)
- Minjia Lu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Xingyu Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Baohang Xi
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Qi Dai
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Chenli Li
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
| | - Li Su
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
| | - Xiaonan Zhou
- Institute of Basic Medical Sciences, Wannan Medical College, Hefei 241000, China.
| | - Min Tang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
| | - Yuhua Yao
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
| | - Jialiang Yang
- School of Mathematics and Statistics, Hainan Normal University, Haikou 570100, China.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
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Yuan Y, Jiaoming L, Xiang W, Yanhui L, Shu J, Maling G, Qing M. Analyzing the interactions of mRNAs, miRNAs, lncRNAs and circRNAs to predict competing endogenous RNA networks in glioblastoma. J Neurooncol 2018; 137:493-502. [PMID: 29335913 DOI: 10.1007/s11060-018-2757-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/05/2018] [Indexed: 02/05/2023]
Abstract
Cross-talk between competitive endogenous RNAs (ceRNAs) may play a critical role in revealing potential mechanisms of tumor development and physiology. Glioblastoma is the most common type of malignant primary brain tumor, and the mechanisms of tumor genesis and development in glioblastoma are unclear. Here, to investigate the role of non-coding RNAs and the ceRNA network in glioblastoma, we performed paired-end RNA sequencing and microarray analyses to obtain the expression profiles of mRNAs, lncRNAs, circRNAs and miRNAs. We identified that the expression of 501 lncRNAs, 1999 mRNAs, 2038 circRNAs and 143 miRNAs were often altered between glioblastoma and matched normal brain tissue. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed on these differentially expressed mRNAs and miRNA-mediated target genes of lncRNAs and circRNAs. Furthermore, we used a multi-step computational framework and several bioinformatics methods to construct a ceRNA network combining mRNAs, miRNAs, lncRNAs and circRNA, based on co-expression analysis between the differentially expressed RNAs. We identified that plenty of lncRNAs, CircRNAs and their downstream target genes in the ceRNA network are related to glutamatergic synapse, suggesting that glutamate metabolism is involved in glioma biological functions. Our results will accelerate the understanding of tumorigenesis, cancer progression and even therapeutic targeting in glioblastoma.
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Affiliation(s)
- Yang Yuan
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Li Jiaoming
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Wang Xiang
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Liu Yanhui
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan, China
| | - Jiang Shu
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan, China.
| | - Gou Maling
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China
| | - Mao Qing
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guo Xue Xiang, Chengdu, Sichuan, China.
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Long non-coding RNA00544 serves as a potential novel predictive and prognostic marker for HR+ HER2- subtype breast cancer. Sci Rep 2017; 7:12382. [PMID: 28959047 PMCID: PMC5620366 DOI: 10.1038/s41598-017-11066-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/28/2017] [Indexed: 12/31/2022] Open
Abstract
Luminal breast cancers (BC) account for majority of breast cancer. Due to its heterogeneity and the development of treatment resistance, luminal BC patients can vary substantially. Long noncoding RNAs (lncRNAs), as we known, is involved in breast cancer progression. Here, we aim to identify the lncRNAs which are involved in the particular type luminal BC progression. By Gene Chips analysis, we found a novel lncRNA00544, which was highly expressed in the metastatic axillary nodes compared with corresponding luminal BC tissues (fold change = 2.26, P = 0.043). This result was confirmed in luminal BC cell lines (p = 0.0113) and 49 paired breast cancer samples compared with in corresponding controls (p = 0.011). Furthermore, Kaplan-Meier survival curves of 373 breast cancer patients indicated that disease-free survival was significantly poor in breast cancer patients with high lncRNA00544 expression (p < 0.001). Univariate and multivariate Cox regression analyses showed that lncRNA00544 was a significant independent prognostic biomarker in luminal BC patients. Further analysis showed that the prognosis of high lncRNA00544 expression in breast cancer patients was actually related to HR + HER2- subtype. Together, our studies indicate that lncRNA00544 may represent a novel predictive and prognostic indicator in luminal BC patients.
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Cao T, Rajasingh S, Samanta S, Dawn B, Bittel DC, Rajasingh J. Biology and clinical relevance of noncoding sno/scaRNAs. Trends Cardiovasc Med 2017; 28:81-90. [PMID: 28869095 DOI: 10.1016/j.tcm.2017.08.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/18/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022]
Abstract
Small nucleolar RNAs (snoRNAs) are a group of noncoding RNAs that perform various biological functions, including biochemical modifications of other RNAs, precursors of miRNA, splicing, and telomerase activity. The small Cajal body-associated RNAs (scaRNAs) are a subset of the snoRNA family and collect in the Cajal body where they perform their canonical function to biochemically modify spliceosomal RNAs prior to maturation. Failure of sno/scaRNAs have been implicated in pathology such as congenital heart anomalies, neuromuscular disorders, and various malignancies. Thus, understanding of sno/scaRNAs demonstrates the clinical value.
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Affiliation(s)
- Thuy Cao
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Sheeja Rajasingh
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Saheli Samanta
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | - Buddhadeb Dawn
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS
| | | | - Johnson Rajasingh
- Division of Cardiovascular Diseases, Department of Internal Medicine, Cardiovascular Research Institute, Kansas City, KS; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS.
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Yang Y, Du Y, Liu X, Cho WC. Involvement of Non-coding RNAs in the Signaling Pathways of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 937:19-51. [PMID: 27573893 DOI: 10.1007/978-3-319-42059-2_2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most common diagnosed cancers worldwide. The metastasis and development of resistance to anti-cancer treatment are major challenges in the treatment of CRC. Understanding mechanisms underpinning the pathogenesis is therefore critical in developing novel agents for CRC treatments. A large number of evidence has demonstrated that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs have functional roles in both the physiological and pathological processes by regulating the expression of their target genes. These molecules are engaged in the pathobiology of neoplastic diseases and are targets for the diagnosis, prognosis and therapy of a variety of cancers, including CRC. In this regard, ncRNAs have emerged as one of the hallmarks of CRC pathogenesis and they also play key roles in metastasis, drug resistance and the stemness of CRC stem cell by regulating various signaling networks. Therefore, a better understanding the ncRNAs involved in the signaling pathways of CRC may lead to the development of novel strategy for diagnosis, prognosis and treatment of CRC. In this chapter, we summarize the latest findings on ncRNAs, with a focus on miRNAs and lncRNAs involving in signaling networks and in the regulation of pathogenic signaling pathways in CRC.
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Affiliation(s)
- Yinxue Yang
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yong Du
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Xiaoming Liu
- The General Hospital, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China.
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Kim D, Lee WK, Jeong S, Seol MY, Kim H, Kim KS, Lee EJ, Lee J, Jo YS. Upregulation of long noncoding RNA LOC100507661 promotes tumor aggressiveness in thyroid cancer. Mol Cell Endocrinol 2016; 431:36-45. [PMID: 27151833 DOI: 10.1016/j.mce.2016.05.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 04/21/2016] [Accepted: 05/02/2016] [Indexed: 11/30/2022]
Abstract
Recent advances in next-generation sequencing have revealed a variety of long noncoding RNAs (lncRNAs). However, studies of lncRNAs are at a very early stage, our knowledge of the biological functions and clinical implications remains limited. To investigate the roles of lncRNAs in thyroid cancers, we verified 56 lncRNAs identified as potential cancer-promoting genes in a previous study that analyzed 2394 tumor SNP arrays from 12 types of cancer. Based on verified sequence information in NCBI and Ensembl, we ultimately selected three candidate lncRNAs for detailed analysis. One of the candidates, LOC100507661, was strongly upregulated in thyroid cancer tissues relative to paired contralateral normal tissue. LOC100507661 was easily detectable in papillary and anaplastic thyroid cancer cell lines such as TPC1, BCPAP, C643, and 8505C, but not in the follicular thyroid cancer cell line FTC133. Stable overexpression of LOC100507661 promoted cell proliferation, migration, and invasion of thyroid cancer cells. Lymph node metastasis and BRAF V600E mutations were more frequent in papillary thyroid cancers with high LOC100507661 expression. Our data demonstrate that LOC100507661 expression is elevated in human thyroid cancer and may play a critical role in thyroid carcinogenesis.
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Affiliation(s)
- Daham Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Republic of Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Republic of Korea
| | - Woo Kyung Lee
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Republic of Korea; Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seonhyang Jeong
- Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Mi-Youn Seol
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyunji Kim
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyung-Sup Kim
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, Republic of Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Republic of Korea
| | - Eun Jig Lee
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, Republic of Korea; Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jandee Lee
- Department of Surgery, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea.
| | - Young Suk Jo
- Department of Internal Medicine, Open NBI Convergence Technology Research Laboratory, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Abstract
Non-coding (nc)RNAs are divided into small ncRNAs and long ncRNAs (lncRNAs). MicroRNAs (miRNAs) are small ncRNAS which are around 22 nucleotides in length that mediate post-transcriptional gene silencing. LncRNAs are greater than 200 bp in length. Each ncRNA can have multiple targets and can be regulated by multiple genetic factors. Because ncRNAs are not translated into proteins, they can only be detected at the nucleic acid level by in situ hybridization, by RT-PCR, or by sequencing which makes their detection more challenging in the routine pathology laboratory. A great deal of new information has accumulated about miRNAs in thyroid tissues during the past decade. Some of these studies have shown that deregulation of miRNAs may be useful in diagnostic pathology. Information about the role of lncRNA in the development of thyroid tumors is in the early stages of development, but new information is accumulating rapidly. In this review, we will discuss the recent progress in our understanding of the relationship between ncRNAs and the development of thyroid cancers and the potential uses of ncRNAs in the diagnosis and prognosis of thyroid tumors.
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Affiliation(s)
- Ranran Zhang
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53792, USA
| | - Heather Hardin
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53792, USA
| | - Jidong Chen
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53792, USA
| | - Zhenying Guo
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53792, USA
| | - Ricardo V Lloyd
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, 53792, USA.
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Wang Q, Zhang J, Liu Y, Zhang W, Zhou J, Duan R, Pu P, Kang C, Han L. A novel cell cycle-associated lncRNA, HOXA11-AS, is transcribed from the 5-prime end of the HOXA transcript and is a biomarker of progression in glioma. Cancer Lett 2016; 373:251-9. [PMID: 26828136 DOI: 10.1016/j.canlet.2016.01.039] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/08/2016] [Accepted: 01/24/2016] [Indexed: 01/17/2023]
Abstract
The comprehensive lncRNA expression signature in glioma has not yet been fully elucidated. We performed a high-throughput microarray to detect the ncRNA expression profiles of 220 human glioma tissues. Here, we found that a novel lncRNA, HOXA11-AS, was the antisense transcript of the HOX11 gene. It was shown that HOXA11-AS was closely associated with glioma grade and poor prognosis. Multivariate Cox regression analysis revealed that HOXA11-AS was an independent prognostic factor in glioblastoma multiforme patients, and its expression was correlated with the glioma molecular subtypes of the Cancer Genome Atlas. Gene set enrichment analysis indicated that the gene sets most correlated with HOXA11-AS expression were involved in cell cycle progression. Over-expression of the HOXA11-AS transcript promoted cell proliferation in vitro, while knockdown of HOXA11-AS expression repressed cell proliferation via regulation of cell cycle progression. The growth-promoting and growth-inhibiting effects of HOXA11-AS were also demonstrated in a xenograft mouse model. Our data confirms, for the first time, that HOXA11-AS is an important long non-coding RNA that primarily serves as a prognostic factor for glioma patient survival. HOXA11-AS could serve as a biomarker for identifying glioma molecular subtypes and as therapeutic target for glioma patients.
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Affiliation(s)
- Qixue Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Junxia Zhang
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Yanwei Liu
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Glioma Center, Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Wei Zhang
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Glioma Center, Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Junhu Zhou
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Ran Duan
- Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China; Glioma Center, Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Peiyu Pu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Chunsheng Kang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China
| | - Lei Han
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, China; Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin 300052, China; Key Laboratory of Post-trauma Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education, Tianjin 300052, China; Tianjin Key Laboratory of Injuries, Variations and Regeneration of Nervous System, Tianjin 300052, China; Chinese Glioma Cooperative Group (CGCG), 6 Tiantanxi Li, Beijing 100050, China.
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30
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Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A. Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci 2016; 17:ijms17010132. [PMID: 26805815 PMCID: PMC4730372 DOI: 10.3390/ijms17010132] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 12/31/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.
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Affiliation(s)
- Kun Yan
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yasir Arfat
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Dijie Li
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Fan Zhao
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Zhihao Chen
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Chong Yin
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yulong Sun
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Lifang Hu
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Tuanmin Yang
- Department of Bone Disease Oncology, Hong-Hui Hospital, Xi'an Jiaotong University College of Medicine, South Door slightly Friendship Road 555, Xi'an 710054, China.
| | - Airong Qian
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
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31
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Abstract
tRFs and tiRNAs are two new classes of regulatory non-coding small RNAs that are derived from the cleavage of pre-existing tRNAs. tRFs are 18-22 nt long and are classified into the tRF-5, tRF-3, and tRF-1 series. Here, we discuss in detail the regulatory roles of tRFs in translation, viral infections, and carcinogenesis. Moreover, we have reviewed the association of tRFs with Argonaute proteins, including their potential to function as miRNAs. Interestingly, few miRNAs are generated from pre-existing tRNAs. Hence, tRNAs generate similar-sized tRFs and miRNAs, leading to misannotations due to cross mapping of tRFs and tRNA-derived miRNAs during deep sequencing data analysis. Therefore, it is important to catalogue the overlapping sequences between tRNA-derived miRNAs and tRFs. We have catalogued the miRNAs that overlap with tRFs sequences in humans using miRBase. We identified 20 tRNA-derived miRNAs that share sequences with tRFs. Of the 20 miRNAs, 5 miRNAs (miR-3182, miR-4521, miR-1260a, miR-1260b, and miR-7977) showed significant prediction scores. Furthermore, we have identified a lysine degradation pathway as a common regulatory pathway for miR-1260a, miR-1260b, and miR-3182 by using DIANA-mirPath.
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