1
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Li R, Ji Y, Ye R, Tang G, Wang W, Chen C, Yang Q. Potential therapies for non-coding RNAs in breast cancer. Front Oncol 2024; 14:1452666. [PMID: 39372872 PMCID: PMC11449682 DOI: 10.3389/fonc.2024.1452666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/29/2024] [Indexed: 10/08/2024] Open
Abstract
Breast cancer (BC) is one of the frequent tumors that seriously endanger the physical and mental well-being in women with strong heterogeneity, and its pathogenesis involves multiple risk factors. Depending on the type of BC, hormonal therapy, targeted therapy, and immunotherapy are the current systemic treatment options along with conventional chemotherapy. Despite significant progress in understanding BC pathogenesis and therapeutic options, there is still a need to identify new therapeutic targets and develop more effective treatments. According to recent sequencing and profiling studies, non-coding (nc) RNAs genes are deregulated in human cancers via deletion, amplification, abnormal epigenetic, or transcriptional regulation, and similarly, the expression of many ncRNAs is altered in breast cancer cell lines and tissues. The ability of single ncRNAs to regulate the expression of multiple downstream gene targets and related pathways provides a theoretical basis for studying them for cancer therapeutic drug development and targeted delivery. Therefore, it is far-reaching to explore the role of ncRNAs in tumor development and their potential as therapeutic targets. Here, our review outlines the potential of two major ncRNAs, long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) as diagnostic and prognostic biomarkers as well as targets for new therapeutic strategies in breast cancer.
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Affiliation(s)
- Ruonan Li
- Anhui Provincial Key Laboratory of Tumor Evolution and Intelligent Diagnosis and Treatment, Bengbu Medical University, Bengbu, Anhui, China
- School of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui, China
| | - Yuxin Ji
- Anhui Provincial Key Laboratory of Tumor Evolution and Intelligent Diagnosis and Treatment, Bengbu Medical University, Bengbu, Anhui, China
- School of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui, China
| | - Ruyin Ye
- Anhui Provincial Key Laboratory of Tumor Evolution and Intelligent Diagnosis and Treatment, Bengbu Medical University, Bengbu, Anhui, China
- Department of Life Sciences, Bengbu Medical University, Bengbu, Anhui, China
| | - Guohui Tang
- Anhui Provincial Key Laboratory of Tumor Evolution and Intelligent Diagnosis and Treatment, Bengbu Medical University, Bengbu, Anhui, China
- Department of Life Sciences, Bengbu Medical University, Bengbu, Anhui, China
| | - Wenrui Wang
- Department of Life Sciences, Bengbu Medical University, Bengbu, Anhui, China
| | - Changjie Chen
- School of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui, China
| | - Qingling Yang
- School of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China
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2
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Liu J, Chang X, Manji L, Xu Z, Xiao W. Roles of small peptides encoded by non-coding RNAs in tumor invasion and migration. Front Pharmacol 2024; 15:1442196. [PMID: 39351098 PMCID: PMC11439703 DOI: 10.3389/fphar.2024.1442196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 08/30/2024] [Indexed: 10/04/2024] Open
Abstract
Non-coding RNAs (ncRNAs), which are usually considered not to encode proteins, are widely involved in important activities including signal transduction and cell proliferation. However, recent studies have shown that small peptides encoded by ncRNAs (SPENs) have important roles in the development of malignant tumors. Some SPENs participate in the regulation of skeleton reorganization, intercellular adhesion, signaling and other processes of tumor cells, with effects on the invasive and migratory abilities of the cells. Therefore, SPENs have potential applications as therapeutic targets and biomarkers of malignant tumors. Invasion and migration of malignant tumor cells are the main reasons for poor prognosis of cancer patients and represent the most challenging aspects of treatment of malignant tumors. Currently, the main treatments for tumors include surgery, radiotherapy, targeted drug therapy. Surgery, however, is reserved for early stages of cancer and carries risks and costs. Radiotherapy and targeted therapy have serious side effects. This review describes the mechanisms of SPENs and their roles in tumor invasion and migration, with the aim of providing new targets for tumor diagnosis and treatment.
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Affiliation(s)
- Jie Liu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Xiyue Chang
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang, Liaoning, China
| | - Laeeqa Manji
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhijie Xu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wan’an Xiao
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
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3
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Liu S, Jiang R, Wang X, Zhang Q, Li S, Sun X, Feng Y, Du F, Zheng P, Tian Y, Li Z, Liu S. Comprehensive identification of a disulfidptosis-associated long non-coding RNA signature to predict the prognosis and treatment options in ovarian cancer. Front Endocrinol (Lausanne) 2024; 15:1434705. [PMID: 39345881 PMCID: PMC11427372 DOI: 10.3389/fendo.2024.1434705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Accepted: 07/29/2024] [Indexed: 10/01/2024] Open
Abstract
Purpose Distinguished from cuproptosis and ferroptosis, disulfidptosis has been described as a newly discovered form of non-programmed cell death tightly associated with glucose metabolism. However, the prognostic profile of disulfidptosis-related lncRNAs (DRLRs) in ovarian cancer (OC) and their biological mechanisms need to be further elucidated. Materials and methods First, we downloaded the profiles of RNA transcriptome, clinical information for OC patients from the TCGA database. Generated from Cox regression analysis, prognostic lncRNAs were utilized to identify the risk signature by least absolute shrinkage and selection operator analysis. Then, we explored the intimate correlations between disulfidptosis and lncRNAs. What's more, we performed a series of systemic analyses to assess the robustness of the model and unravel its relationship with the immune microenvironment comprehensively. Results We identified two DRLR clusters, in which OC patients with low-risk scores exhibited a favorable prognosis, up-regulated immune cell infiltrations and enhanced sensitivity to immunotherapy. Furthermore, validation of the signature by clinical features and Cox analysis demonstrated remarkable consistency, suggesting the universal applicability of our model. It's worth noting that high-risk patients showed more positive responses to immune checkpoint inhibitors and potential chemotherapeutic drugs. Conclusion Our findings provided valuable insights into DRLRs in OC for the first time, which indicated an excellent clinical value in the selection of management strategies, spreading brilliant horizons into individualized therapy.
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Affiliation(s)
- Shouze Liu
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Rulan Jiang
- Department of Pain, Cangzhou Hospital of Integrated Traditional Chinese Medicine and Western Medicine (TCM-WM) Hebei, Cangzhou, Hebei, China
| | - Xinxin Wang
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Qianqian Zhang
- Department of Gynecology and Obstetrics, Beijing Tsinghua Changgung Hospital, Beijing, China
| | - Shumei Li
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Xiaoxue Sun
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Yajun Feng
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei, China
| | - Feida Du
- Department of Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Pengtao Zheng
- Department of Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yanpeng Tian
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhongkang Li
- Department of Gynecology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shikai Liu
- Department of Gynecology III, Cangzhou Central Hospital, Cangzhou, Hebei, China
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4
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Poliseno L, Lanza M, Pandolfi PP. Coding, or non-coding, that is the question. Cell Res 2024; 34:609-629. [PMID: 39054345 PMCID: PMC11369213 DOI: 10.1038/s41422-024-00975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/30/2024] [Indexed: 07/27/2024] Open
Abstract
The advent of high-throughput sequencing uncovered that our genome is pervasively transcribed into RNAs that are seemingly not translated into proteins. It was also found that non-coding RNA transcripts outnumber canonical protein-coding genes. This mindboggling discovery prompted a surge in non-coding RNA research that started unraveling the functional relevance of these new genetic units, shaking the classic definition of "gene". While the non-coding RNA revolution was still taking place, polysome/ribosome profiling and mass spectrometry analyses revealed that peptides can be translated from non-canonical open reading frames. Therefore, it is becoming evident that the coding vs non-coding dichotomy is way blurrier than anticipated. In this review, we focus on several examples in which the binary classification of coding vs non-coding genes is outdated, since the same bifunctional gene expresses both coding and non-coding products. We discuss the implications of this intricate usage of transcripts in terms of molecular mechanisms of gene expression and biological outputs, which are often concordant, but can also surprisingly be discordant. Finally, we discuss the methodological caveats that are associated with the study of bifunctional genes, and we highlight the opportunities and challenges of therapeutic exploitation of this intricacy towards the development of anticancer therapies.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy.
- Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Martina Lanza
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
- University of Siena, Siena, Italy
| | - Pier Paolo Pandolfi
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Torino, Italy.
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA.
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5
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Zhang J, Lu H, Jiang Y, Ma Y, Deng L. ncRNA Coding Potential Prediction Using BiLSTM and Transformer Encoder-Based Model. J Chem Inf Model 2024; 64:6712-6722. [PMID: 39120528 DOI: 10.1021/acs.jcim.4c01097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Many noncoding RNAs (ncRNAs) have been identified, and many of them play vital roles in various biological processes, including gene expression regulation, epigenetic regulation, transcription, and control. Recently, a few observations revealed that ncRNAs are translated into functional peptides. Moreover, many computational methods have been developed to predict the coding potential of these transcripts, which contributes to a deeper investigation of their functions. However, most of these are used to distinguish ncRNAs and mRNAs. It is important to develop a highly accurate computational tool for identifying the coding potential of ncRNAs, thereby contributing to the discovery of novel peptides. In this Article, we propose a novel BiLSTM And Transformer encoder-based model (nBAT) with intrinsic features encoded for ncRNA coding potential prediction. In nBAT, we introduce a learnable position encoding mechanism to better obtain the embeddings of the ncRNA sequence. Moreover, we extract 43 intrinsic features from different perspectives and encode these features into the Transformer encoder by calculating their distances. Our performance comparisons show that nBAT achieves a superior performance than the state-of-the-art methods for coding potential prediction on different datasets. We also apply the method to new ncRNAs for identifying the coding potential, and the results further indicate the competitive performance of nBAT. We expect the method can be exploited as a useful tool for high-throughput coding potential prediction for ncRNAs.
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Affiliation(s)
- Jingpu Zhang
- School of Computer and Data Science, Henan University of Urban Construction, Pingdingshan 467000, China
| | - Hao Lu
- School of Computer and Data Science, Henan University of Urban Construction, Pingdingshan 467000, China
| | - Ying Jiang
- School of Computer Science and Engineering, Central South University, Changsha 410018, China
| | - Yuanyuan Ma
- School of Computer Engineering, Hubei University of Arts and Science, Xiangyang 441053, China
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410018, China
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6
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Zhang Y. LncRNA-encoded peptides in cancer. J Hematol Oncol 2024; 17:66. [PMID: 39135098 PMCID: PMC11320871 DOI: 10.1186/s13045-024-01591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Long non-coding RNAs (lncRNAs), once considered transcriptional noise, have emerged as critical regulators of gene expression and key players in cancer biology. Recent breakthroughs have revealed that certain lncRNAs can encode small open reading frame (sORF)-derived peptides, which are now understood to contribute to the pathogenesis of various cancers. This review synthesizes current knowledge on the detection, functional roles, and clinical implications of lncRNA-encoded peptides in cancer. We discuss technological advancements in the detection and validation of sORFs, including ribosome profiling and mass spectrometry, which have facilitated the discovery of these peptides. The functional roles of lncRNA-encoded peptides in cancer processes such as gene transcription, translation regulation, signal transduction, and metabolic reprogramming are explored in various types of cancer. The clinical potential of these peptides is highlighted, with a focus on their utility as diagnostic biomarkers, prognostic indicators, and therapeutic targets. The challenges and future directions in translating these findings into clinical practice are also discussed, including the need for large-scale validation, development of sensitive detection methods, and optimization of peptide stability and delivery.
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Affiliation(s)
- Yaguang Zhang
- Laboratory of Gastrointestinal Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
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7
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Hussen BM, Abdullah SR, Mohammed AA, Rasul MF, Hussein AM, Eslami S, Glassy MC, Taheri M. Advanced strategies of targeting circular RNAs as therapeutic approaches in colorectal cancer drug resistance. Pathol Res Pract 2024; 260:155402. [PMID: 38885593 DOI: 10.1016/j.prp.2024.155402] [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: 02/21/2024] [Revised: 06/03/2024] [Accepted: 06/09/2024] [Indexed: 06/20/2024]
Abstract
Colorectal cancer (CRC) stands second in terms of mortality and third among the highest prevalent kinds of cancer globally. CRC prevalence is rising in moderately and poorly developed regions and is greater in economically advanced regions. Despite breakthroughs in targeted therapy, resistance to chemotherapeutics remains a significant challenge in the long-term management of CRC. Circular RNAs (circRNAs) have been involved in growing cancer therapy resistance, particularly in CRC, according to an increasing number of studies in recent years. CircRNAs are one of the novel subclasses of non-coding RNAs, previously thought of as viroid. According to studies, circRNAs have been recommended as biological markers for therapeutic targets and diagnostic and prognostic purposes. That is particularly notable given that the expression of circRNAs has been linked to the hallmarks of CRC since they are responsible for drug resistance in CRC patients; thereby, circRNAs are significant for chemotherapy failure. Moreover, knowledge concerning circRNAs remains relatively unclear despite using all these advanced techniques. Here, in this study, we will go over the most recent published work to highlight the critical roles of circRNAs in CRC development and drug resistance and highlight the main strategies to overcome drug resistance to improve clinical outcomes.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Biomedical Sciences, College of Science, Cihan University-Erbil, Kurdistan Region, Iraq; Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Snur Rasool Abdullah
- Department of Medical Laboratory Science, College of Health Sciences, Lebanese French University, Erbil, Kurdistan Region, Iraq
| | | | - Mohammed Fatih Rasul
- Department of Pharmaceutical Basic Science, Faculty of Pharmacy, Tishk International University, Erbil, Kurdistan Region, Iraq
| | - Ali M Hussein
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Solat Eslami
- Department of Medical Biotechnology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran; Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mark C Glassy
- Translational Neuro-Oncology Laboratory, San Diego (UCSD) Moores Cancer Center, University of California, CA, United States
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
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8
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Adjeroh DA, Zhou X, Paschoal AR, Dimitrova N, Derevyanchuk EG, Shkurat TP, Loeb JA, Martinez I, Lipovich L. Challenges in LncRNA Biology: Views and Opinions. Noncoding RNA 2024; 10:43. [PMID: 39195572 DOI: 10.3390/ncrna10040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
This is a mini-review capturing the views and opinions of selected participants at the 2021 IEEE BIBM 3rd Annual LncRNA Workshop, held in Dubai, UAE. The views and opinions are expressed on five broad themes related to problems in lncRNA, namely, challenges in the computational analysis of lncRNAs, lncRNAs and cancer, lncRNAs in sports, lncRNAs and COVID-19, and lncRNAs in human brain activity.
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Affiliation(s)
- Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University (WVU), Morgantown, WV 26506, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group, Federal University of Technology-Paraná-UTFPR, Curitiba 86300-000, Brazil
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | - Tatiana P Shkurat
- Department of Genetics, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Jeffrey A Loeb
- Department of Neurology and Rehabilitation, The Center for Clinical and Translational Science, The University of Illinois NeuroRepository, University of Illinois, Chicago, IL 60607, USA
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, WVU Cancer Institute, West Virginia University (WVU) School of Medicine, Morgantown, WV 26505, USA
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co., Ltd., Shenzhen 518000, China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, China
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9
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Tian H, Tang L, Yang Z, Xiang Y, Min Q, Yin M, You H, Xiao Z, Shen J. Current understanding of functional peptides encoded by lncRNA in cancer. Cancer Cell Int 2024; 24:252. [PMID: 39030557 PMCID: PMC11265036 DOI: 10.1186/s12935-024-03446-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 07/09/2024] [Indexed: 07/21/2024] Open
Abstract
Dysregulated gene expression and imbalance of transcriptional regulation are typical features of cancer. RNA always plays a key role in these processes. Human transcripts contain many RNAs without long open reading frames (ORF, > 100 aa) and that are more than 200 bp in length. They are usually regarded as long non-coding RNA (lncRNA) which play an important role in cancer regulation, including chromatin remodeling, transcriptional regulation, translational regulation and as miRNA sponges. With the advancement of ribosome profiling and sequencing technologies, increasing research evidence revealed that some ORFs in lncRNA can also encode peptides and participate in the regulation of multiple organ tumors, which undoubtedly opens a new chapter in the field of lncRNA and oncology research. In this review, we discuss the biological function of lncRNA in tumors, the current methods to evaluate their coding potential and the role of functional small peptides encoded by lncRNA in cancers. Investigating the small peptides encoded by lncRNA and understanding the regulatory mechanisms of these functional peptides may contribute to a deeper understanding of cancer and the development of new targeted anticancer therapies.
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Affiliation(s)
- Hua Tian
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
- School of Nursing, Chongqing College of Humanities, Science & Technology, Chongqing, China
| | - Lu Tang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zihan Yang
- Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, China, 646000
| | - Yanxi Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Qi Min
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Mengshuang Yin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Huili You
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
- Gulin Traditional Chinese Medicine Hospital, Luzhou, China.
- Department of Pharmacology, School of Pharmacy, Sichuan College of Traditional Chinese Medicine, Mianyang, China.
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, China.
- Cell Therapy and Cell Drugs of Luzhou Key Laboratory, Luzhou, 646000, China.
- South Sichuan Institute of Translational Medicine, Luzhou, 646000, China.
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10
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Sanejouand YH. Are Most Human-Specific Proteins Encoded by Long Noncoding RNAs? J Mol Evol 2024:10.1007/s00239-024-10174-z. [PMID: 38916610 DOI: 10.1007/s00239-024-10174-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/03/2024] [Indexed: 06/26/2024]
Abstract
By looking for a lack of homologs in a reference database of 27 well-annotated proteomes of primates and 52 well-annotated proteomes of other mammals, 170 putative human-specific proteins were identified. While most of them are deemed uncertain, 2 are known at the protein level and 23 at the transcript level, according to UniProt. Interestingly, 23 of these 25 proteins are found to be encoded or to have close homologs in an open reading frame of a long noncoding human RNA. However, half of them are predicted to be at least 80% globular, with a single structural domain, according to IUPred, and with at least 80% of ordered residues, according to flDPnn. Strikingly, there is a near-complete lack of structural knowledge about these proteins, with no tertiary structure presently available in the Protein Data Bank and a fair prediction for one of them in the AlphaFold Protein Structure Database. Moreover, knowledge about the function of these possibly key proteins remains scarce.
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Affiliation(s)
- Yves-Henri Sanejouand
- US2B, UMR 6286 of CNRS, Nantes University, 2 rue de la Houssinière, Nantes, 44322, Pays de la Loire, France.
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11
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Yazarlou F, Lipovich L, Loeb JA. Emerging roles of long non-coding RNAs in human epilepsy. Epilepsia 2024; 65:1491-1511. [PMID: 38687769 PMCID: PMC11166529 DOI: 10.1111/epi.17937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
Genome-scale biological studies conducted in the post-genomic era have revealed that two-thirds of human genes do not encode proteins. Most functional non-coding RNA transcripts in humans are products of long non-coding RNA (lncRNA) genes, an abundant but still poorly understood class of human genes. As a result of their fundamental and multitasking regulatory roles, lncRNAs are associated with a wide range of human diseases, including neurological disorders. Approximately 40% of lncRNAs are specifically expressed in the brain, and many of them exhibit distinct spatiotemporal patterns of expression. Comparative genomics approaches have determined that 65%-75% of human lncRNA genes are primate-specific and hence can be posited as a contributing potential cause of the higher-order complexity of primates, including human, brains relative to those of other mammals. Although lncRNAs present important mechanistic examples of epileptogenic functions, the human/primate specificity of lncRNAs questions their relevance in rodent models. Here, we present an in-depth review that supports the contention that human lncRNAs are direct contributors to the etiology and pathogenesis of human epilepsy, as a means to accelerate the integration of lncRNAs into clinical practice as potential diagnostic biomarkers and therapeutic targets. Meta-analytically, the major finding of our review is the commonality of lncRNAs in epilepsy and cancer pathogenesis through mitogen-activated protein kinase (MAPK)-related pathways. In addition, neuroinflammation may be a relevant part of the common pathophysiology of cancer and epilepsy. LncRNAs affect neuroinflammation-related signaling pathways such as nuclear factor kappa- light- chain- enhancer of activated B cells (NF-κB), Notch, and phosphatidylinositol 3- kinase/ protein kinase B (Akt) (PI3K/AKT), with the NF-κB pathway being the most common. Besides the controversy over lncRNA research in non-primate models, whether neuroinflammation is triggered by injury and/or central nervous system (CNS) toxicity during epilepsy modeling in animals or is a direct consequence of epilepsy pathophysiology needs to be considered meticulously in future studies.
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Affiliation(s)
- Fatemeh Yazarlou
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, U.S.A
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co. Ltd., 601 Building C1, Guangming Science Park, Fenghuang Street, 518000, Shenzhen, Guangdong, People’s Republic of China
- College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai District, 325060, Wenzhou, Zhejiang, People’s Republic of China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 3222 Scott Hall, 540 E. Canfield St., Detroit, Michigan 48201, U.S.A
| | - Jeffrey A. Loeb
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, Illinois 60612, U.S.A
- University of Illinois NeuroRepository, University of Illinois at Chicago, Chicago, Illinois 60612, U.S.A
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12
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Erokhina TN, Ryazantsev DY, Zavriev SK, Morozov SY. Biological Activity of Artificial Plant Peptides Corresponding to the Translational Products of Small ORFs in Primary miRNAs and Other Long "Non-Coding" RNAs. PLANTS (BASEL, SWITZERLAND) 2024; 13:1137. [PMID: 38674546 PMCID: PMC11055055 DOI: 10.3390/plants13081137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024]
Abstract
Generally, lncPEPs (peptides encoded by long non-coding RNAs) have been identified in many plant species of several families and in some animal species. Importantly, molecular mechanisms of the miPEPs (peptides encoded by primary microRNAs, pri-miRNAs) are often poorly understood in different flowering plants. Requirement for the additional studies in these directions is highlighted by alternative findings concerning positive regulation of pri-miRNA/miRNA expression by synthetic miPEPs in plants. Further extensive studies are also needed to understand the full set of their roles in eukaryotic organisms. This review mainly aims to consider the available data on the regulatory functions of the synthetic miPEPs. Studies of chemically synthesized miPEPs and analyzing the fine molecular mechanisms of their functional activities are reviewed. Brief description of the studies to identify lncORFs (open reading frames of long non-coding RNAs) and the encoded protein products is also provided.
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Affiliation(s)
- T. N. Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - D. Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. K. Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia (S.K.Z.)
| | - S. Y. Morozov
- Biological Faculty, Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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13
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Mohapatra S, Banerjee A, Rausseo P, Dragomir MP, Manyam GC, Broom BM, Calin GA. FuncPEP v2.0: An Updated Database of Functional Short Peptides Translated from Non-Coding RNAs. Noncoding RNA 2024; 10:20. [PMID: 38668378 PMCID: PMC11054400 DOI: 10.3390/ncrna10020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024] Open
Abstract
Over the past decade, there have been reports of short novel functional peptides (less than 100 aa in length) translated from so-called non-coding RNAs (ncRNAs) that have been characterized using mass spectrometry (MS) and large-scale proteomics studies. Therefore, understanding the bivalent functions of some ncRNAs as transcripts that encode both functional RNAs and short peptides, which we named ncPEPs, will deepen our understanding of biology and disease. In 2020, we published the first database of functional peptides translated from non-coding RNAs-FuncPEP. Herein, we have performed an update including the newly published ncPEPs from the last 3 years along with the categorization of host ncRNAs. FuncPEP v2.0 contains 152 functional ncPEPs, out of which 40 are novel entries. A PubMed search from August 2020 to July 2023 incorporating specific keywords was performed and screened for publications reporting validated functional peptides derived from ncRNAs. We did not observe a significant increase in newly discovered functional ncPEPs, but a steady increase. The novel identified ncPEPs included in the database were characterized by a wide array of molecular and physiological parameters (i.e., types of host ncRNA, species distribution, chromosomal density, distribution of ncRNA length, identification methods, molecular weight, and functional distribution across humans and other species). We consider that, despite the fact that MS can now easily identify ncPEPs, there still are important limitations in proving their functionality.
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Affiliation(s)
- Swati Mohapatra
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.M.); (P.R.)
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
| | - Anik Banerjee
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Paola Rausseo
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.M.); (P.R.)
- Scripps College, Claremont, CA 91711, USA
| | - Mihnea P. Dragomir
- Institute of Pathology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany;
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Berlin Institute of Health at Charité, 10117 Berlin, Germany
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.)
| | - Bradley M. Broom
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (G.C.M.)
| | - George A. Calin
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.M.); (P.R.)
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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14
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Yazarlou F, Alizadeh F, Lipovich L, Giordo R, Ghafouri-Fard S. Tracing vitamins on the long non-coding lane of the transcriptome: vitamin regulation of LncRNAs. GENES & NUTRITION 2024; 19:5. [PMID: 38475720 PMCID: PMC10935982 DOI: 10.1186/s12263-024-00739-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
A major revelation of genome-scale biological studies in the post-genomic era has been that two-thirds of human genes do not encode proteins. The majority of non-coding RNA transcripts in humans are long non-coding RNA (lncRNA) molecules, non-protein-coding regulatory transcripts with sizes greater than 500 nucleotides. LncRNAs are involved in nearly every aspect of cellular physiology, playing fundamental regulatory roles both in normal cells and in disease. As result, they are functionally linked to multiple human diseases, from cancer to autoimmune, inflammatory, and neurological disorders. Numerous human conditions and diseases stem from gene-environment interactions; in this regard, a wealth of reports demonstrate that the intake of specific and essential nutrients, including vitamins, shapes our transcriptome, with corresponding impacts on health. Vitamins command a vast array of biological activities, acting as coenzymes, antioxidants, hormones, and regulating cellular proliferation and coagulation. Emerging evidence suggests that vitamins and lncRNAs are interconnected through several regulatory axes. This type of interaction is expected, since lncRNA has been implicated in sensing the environment in eukaryotes, conceptually similar to riboswitches and other RNAs that act as molecular sensors in prokaryotes. In this review, we summarize the peer-reviewed literature to date that has reported specific functional linkages between vitamins and lncRNAs, with an emphasis on mammalian models and humans, while providing a brief overview of the source, metabolism, and function of the vitamins most frequently investigated within the context of lncRNA molecular mechanisms, and discussing the published research findings that document specific connections between vitamins and lncRNAs.
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Affiliation(s)
- Fatemeh Yazarlou
- Center for Childhood Cancer, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Box 505055, Dubai, United Arab Emirates
| | - Fatemeh Alizadeh
- Department of Genomic Psychiatry and Behavioral Genomics (DGPBG), Roozbeh Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Leonard Lipovich
- Department of Biology, College of Science, Mathematics, and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang Province, China
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co. Ltd., 601 Building C1, Guangming Science Park, Fenghuang Street, 518000, Shenzhen, Guangdong, People's Republic of China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 3222 Scott Hall, 540 E. Canfield St., Detroit, MI, 48201, USA
| | - Roberta Giordo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Box 505055, Dubai, United Arab Emirates.
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro, Sassari, 07100, Italy.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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15
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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Heydarnia E, Dorostgou Z, Hedayati N, Mousavi V, Yahyazadeh S, Alimohammadi M, Gheibi M, Heidari P, Igder S, Mafi A, Vakili O. Circular RNAs and cervical cancer: friends or foes? A landscape on circRNA-mediated regulation of key signaling pathways involved in the onset and progression of HPV-related cervical neoplasms. Cell Commun Signal 2024; 22:107. [PMID: 38341592 PMCID: PMC10859032 DOI: 10.1186/s12964-024-01494-0] [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: 09/30/2023] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Cervical cancer (CC) is a common gynecologic malignancy, accounting for a significant proportion of women death worldwide. Human papillomavirus (HPV) infection is one of the major etiological causes leading to CC onset; however, genetic, and epigenetic factors are also responsible for disease expansion. Circular RNAs (circRNAs), which are known as a particular subset of non-coding RNA (ncRNA) superfamily, with covalently closed loop structures, have been reported to be involved in the progression of diverse diseases, especially neoplasms. In this framework, abnormally expressed circRNAs are in strong correlation with CC pathogenesis through regulating substantial signaling pathways. Also, these RNA molecules can be considered as promising biomarkers and therapeutic targets for CC diagnosis/prognosis and treatment, respectively. Herein, we first review key molecular mechanisms, including Wnt/β-catenin, MAPK, and PI3K/Akt/mTOR signaling pathways, as well as angiogenesis and metastasis, by which circRNAs interfere with CC development. Then, diagnostic, prognostic, and therapeutic potentials of these ncRNA molecules will be highlighted in depth.
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Affiliation(s)
- Emad Heydarnia
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Dorostgou
- Department of Biochemistry, Neyshabur Branch, Islamic Azad University, Neyshabur, Iran
| | - Neda Hedayati
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Vahide Mousavi
- School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Sheida Yahyazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Alimohammadi
- Student Research Committee, Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mobina Gheibi
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Parasta Heidari
- School of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran.
| | - Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Omid Vakili
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran.
- Autophagy Research Center, Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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17
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Gilyazova I, Gimalova G, Nizamova A, Galimova E, Ishbulatova E, Pavlov V, Khusnutdinova E. Non-Coding RNAs as Key Regulators in Lung Cancer. Int J Mol Sci 2023; 25:560. [PMID: 38203731 PMCID: PMC10778604 DOI: 10.3390/ijms25010560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
For several decades, most lung cancer investigations have focused on the search for mutations in candidate genes; however, in the last decade, due to the fact that most of the human genome is occupied by sequences that do not code for proteins, much attention has been paid to non-coding RNAs (ncRNAs) that perform regulatory functions. In this review, we principally focused on recent studies of the function, regulatory mechanisms, and therapeutic potential of ncRNAs including microRNA (miRNA), long ncRNA (lncRNA), and circular RNA (circRNA) in different types of lung cancer.
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Affiliation(s)
- Irina Gilyazova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Galiya Gimalova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Aigul Nizamova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
| | - Elmira Galimova
- Department of Pathological Physiology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Ekaterina Ishbulatova
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Department of Urology, Bashkir State Medical University, 450008 Ufa, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, 450054 Ufa, Russia
- Institute of Urology and Clinical Oncology, Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
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18
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Lu Y, Ran Y, Li H, Wen J, Cui X, Zhang X, Guan X, Cheng M. Micropeptides: origins, identification, and potential role in metabolism-related diseases. J Zhejiang Univ Sci B 2023; 24:1106-1122. [PMID: 38057268 PMCID: PMC10710913 DOI: 10.1631/jzus.b2300128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 06/06/2023] [Indexed: 12/08/2023]
Abstract
With the development of modern sequencing techniques and bioinformatics, genomes that were once thought to be noncoding have been found to encode abundant functional micropeptides (miPs), a kind of small polypeptides. Although miPs are difficult to analyze and identify, a number of studies have begun to focus on them. More and more miPs have been revealed as essential for energy metabolism homeostasis, immune regulation, and tumor growth and development. Many reports have shown that miPs are especially essential for regulating glucose and lipid metabolism and regulating mitochondrial function. MiPs are also involved in the progression of related diseases. This paper reviews the sources and identification of miPs, as well as the functional significance of miPs for metabolism-related diseases, with the aim of revealing their potential clinical applications.
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Affiliation(s)
| | | | | | | | | | | | | | - Min Cheng
- School of Basic Medicine Sciences, Weifang Medical University, Weifang 261053, China.
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19
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Deng J, Xu W, Jie Y, Chong Y. Subcellular localization and relevant mechanisms of human cancer-related micropeptides. FASEB J 2023; 37:e23270. [PMID: 37994683 DOI: 10.1096/fj.202301019rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/17/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023]
Abstract
Rapid advances in high-quality sequencing and bioinformatics have invalidated the argument that noncoding RNAs (ncRNAs) are junk transcripts that do not encode proteins. Increasing evidence suggests that small open reading frames (sORFs) in ncRNAs can encode micropeptides and polypeptides within 100 amino acids in length. Several micropeptides have been characterized and proven to have various functions in human physiology and pathology, particularly in cancer. The present review mainly highlights the latest studies on ncRNA-encoded micropeptides in different cancers and categorizes them based on their subcellular localization, thereby providing a theoretical basis for micropeptide applications in the early diagnosis and prognosis of cancer and as therapeutic targets. However, considering the inherent characteristics of micropeptides and the limitations of the assay technology methods, more detailed information is warranted.
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Affiliation(s)
- Jing Deng
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenli Xu
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yusheng Jie
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yutian Chong
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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20
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Wang J, Wang W, Ma F, Qian H. A hidden translatome in tumors-the coding lncRNAs. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2755-2772. [PMID: 37154857 DOI: 10.1007/s11427-022-2289-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 05/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been extensively identified in eukaryotic genomes and have been shown to play critical roles in the development of multiple cancers. Through the application and development of ribosome analysis and sequencing technologies, advanced studies have discovered the translation of lncRNAs. Although lncRNAs were originally defined as noncoding RNAs, many lncRNAs actually contain small open reading frames that are translated into peptides. This opens a broad area for the functional investigation of lncRNAs. Here, we introduce prospective methods and databases for screening lncRNAs with functional polypeptides. We also summarize the specific lncRNA-encoded proteins and their molecular mechanisms that promote or inhibit cancerous. Importantly, the role of lncRNA-encoded peptides/proteins holds promise in cancer research, but some potential challenges remain unresolved. This review includes reports on lncRNA-encoded peptides or proteins in cancer, aiming to provide theoretical basis and related references to facilitate the discovery of more functional peptides encoded by lncRNA, and to further develop new anti-cancer therapeutic targets as well as clinical biomarkers of diagnosis and prognosis.
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Affiliation(s)
- Jinsong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wenna Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fei Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Haili Qian
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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21
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Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes Dis 2023; 10:2491-2510. [PMID: 37554208 PMCID: PMC10404890 DOI: 10.1016/j.gendis.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in various biological processes across several species. Though many efforts have been devoted to the expansion of the lncRNAs landscape, much about lncRNAs is still unknown due to their great complexity. The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases. In this review, we introduced genome-wide research of lncRNAs in three parts: (i) novel lncRNA identification by high-throughput sequencing and computational pipelines; (ii) functional characterization of lncRNAs by expression atlas profiling, genome-scale screening, and the research of cancer-related lncRNAs; (iii) mechanism research by large-scale experimental technologies and computational analysis. Besides, primary experimental methods and bioinformatic pipelines related to these three parts are summarized. This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
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Affiliation(s)
- Shuang Tao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yarui Hou
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Liting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yanxia Hu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wanyi Xu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shujuan Xie
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
- Institute of Vaccine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Zhendong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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22
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Zhang M, Zhao J, Wu J, Wang Y, Zhuang M, Zou L, Mao R, Jiang B, Liu J, Song X. In-depth characterization and identification of translatable lncRNAs. Comput Biol Med 2023; 164:107243. [PMID: 37453378 DOI: 10.1016/j.compbiomed.2023.107243] [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: 04/30/2023] [Revised: 06/16/2023] [Accepted: 07/07/2023] [Indexed: 07/18/2023]
Abstract
Long non-coding RNAs (LncRNAs) are non-protein coding transcripts more than 200 nucleotides in length. Deep sequencing technologies have unveiled lncRNAs can harbor translatable short open reading frames (sORFs). Yet the regulatory mechanisms governing lncRNA translation events remain poorly understood. Here, we exhaustively detected the sequence, functional element, and structure features relevant to lncRNA translation in human. Extensive identification and analysis reveal that translatable lncRNAs contain richer protein-coding related sequence features, cap-dependent and cap-independent translation initiation mechanisms, and more stable secondary structures, as compared to untranslatable lncRNAs. These findings strongly support lncRNAs serve as a repository for the production of new small peptides. Based on the feature fusion affecting translation and the extreme gradient boosting (XGBoost) algorithm, we developed the first computational tool that dedicated for predicting translatable lncRNAs, named TransLncPred. Benchmark experimental results show that our method outperforms several state-of-the-art RNA coding potential prediction tools on the same training and testing datasets. The 100-time 10-fold cross-validation tests also demonstrate that regulatory element-derived features, especially N7-methylguanosine (m7G) and internal ribosome entry site (IRES), contribute to the improvement in predictive performance.
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Affiliation(s)
- Meng Zhang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jian Zhao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China.
| | - Jing Wu
- School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, 211166, China
| | - Yulan Wang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Minhui Zhuang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Lingxiao Zou
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Renlong Mao
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Bin Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China.
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23
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Pisignano G, Michael DC, Visal TH, Pirlog R, Ladomery M, Calin GA. Going circular: history, present, and future of circRNAs in cancer. Oncogene 2023; 42:2783-2800. [PMID: 37587333 PMCID: PMC10504067 DOI: 10.1038/s41388-023-02780-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023]
Abstract
To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.
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Affiliation(s)
- Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - David C Michael
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tanvi H Visal
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radu Pirlog
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol, BS16 1QY, UK
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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24
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Gao K, Li X, Ni J, Wu B, Guo J, Zhang R, Wu G. Non-coding RNAs in enzalutamide resistance of castration-resistant prostate cancer. Cancer Lett 2023; 566:216247. [PMID: 37263338 DOI: 10.1016/j.canlet.2023.216247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/03/2023]
Abstract
Enzalutamide (Enz) is a next-generation androgen receptor (AR) antagonist used to treat castration-resistant prostate cancer (CRPC). Unfortunately, the relapsing nature of CRPC results in the development of Enz resistance in many patients. Non-coding RNAs (ncRNAs) are RNA molecules that do not encode proteins, which include microRNAs (miRNA), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and other ncRNAs with known and unknown functions. Recently, dysregulation of ncRNAs in CRPC, particularly their regulatory function in drug resistance, has attracted more and more attention. Herein, we introduce the roles of dysregulation of different ncRNAs subclasses in the development of CRPC progression and Enz resistance. Recently determined mechanisms of Enz resistance are discussed, focusing mainly on the role of AR-splice variant-7 (AR-V7), mutations, circRNAs and lncRNAs that act as miRNA sponges. Also, the contributions of epithelial-mesenchymal transition and glucose metabolism to Enz resistance are discussed. We summarize the different mechanisms of miRNAs, lncRNAs, and circRNAs in the progression of CRPC and Enz resistance, and highlight the prospect of future therapeutic strategies against Enz resistance.
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MESH Headings
- Male
- Humans
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/therapeutic use
- RNA, Circular/genetics
- Drug Resistance, Neoplasm/genetics
- Neoplasm Recurrence, Local
- Nitriles
- Androgen Receptor Antagonists/therapeutic use
- MicroRNAs/genetics
- MicroRNAs/therapeutic use
- Cell Line, Tumor
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Affiliation(s)
- Ke Gao
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China; The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Xiaoshun Li
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Jianxin Ni
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Bin Wu
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
| | - Jiaheng Guo
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China; The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Rui Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi'an, 710032, China; The State Key Laboratory of Cancer Biology, Department of Immunology, The Fourth Military Medical University, Xi'an, 710032, China.
| | - Guojun Wu
- Department of Urology, Xi'an People's Hospital(Xi'an Fourth Hospital), School of Life Sciences and Medicine, Northwest University, Xi'an, 710199, China.
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25
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Jaiswal A, Kaushik N, Choi EH, Kaushik NK. Functional impact of non-coding RNAs in high-grade breast carcinoma: Moving from resistance to clinical applications: A comprehensive review. Biochim Biophys Acta Rev Cancer 2023; 1878:188915. [PMID: 37196783 DOI: 10.1016/j.bbcan.2023.188915] [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: 01/22/2023] [Revised: 04/08/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Despite the recent advances in cancer therapy, triple-negative breast cancers (TNBCs) are the most relapsing cancer sub-type. It is partly due to their propensity to develop resistance against the available therapies. An intricate network of regulatory molecules in cellular mechanisms leads to the development of resistance in tumors. Non-coding RNAs (ncRNAs) have gained widespread attention as critical regulators of cancer hallmarks. Existing research suggests that aberrant expression of ncRNAs modulates the oncogenic or tumor suppressive signaling. This can mitigate the responsiveness of efficacious anti-tumor interventions. This review presents a systematic overview of biogenesis and down streaming molecular mechanism of the subgroups of ncRNAs. Furthermore, it explains ncRNA-based strategies and challenges to target the chemo-, radio-, and immunoresistance in TNBCs from a clinical standpoint.
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Affiliation(s)
- Apurva Jaiswal
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, Suwon 18323, Republic of Korea.
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, Seoul 01897, Republic of Korea.
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26
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Obaidat D, Giordo R, Kleinbrink EL, Banisad E, Grossman LI, Arshad R, Stark A, Maroun MC, Lipovich L, Fernandez-Madrid F. Non-coding regions of nuclear-DNA-encoded mitochondrial genes and intergenic sequences are targeted by autoantibodies in breast cancer. Front Genet 2023; 13:970619. [PMID: 37082114 PMCID: PMC10111166 DOI: 10.3389/fgene.2022.970619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/15/2022] [Indexed: 03/31/2023] Open
Abstract
Autoantibodies against mitochondrial-derived antigens play a key role in chronic tissue inflammation in autoimmune disorders and cancers. Here, we identify autoreactive nuclear genomic DNA (nDNA)-encoded mitochondrial gene products (GAPDH, PKM2, GSTP1, SPATA5, MFF, TSPOAP1, PHB2, COA4, and HAGH) recognized by breast cancer (BC) patients’ sera as nonself, supporting a direct relationship of mitochondrial autoimmunity to breast carcinogenesis. Autoreactivity of multiple nDNA-encoded mitochondrial gene products was mapped to protein-coding regions, 3’ untranslated regions (UTRs), as well as introns. In addition, autoantibodies in BC sera targeted intergenic sequences that may be parts of long non-coding RNA (lncRNA) genes, including LINC02381 and other putative lncRNA neighbors of the protein-coding genes ERCC4, CXCL13, SOX3, PCDH1, EDDM3B, and GRB2. Increasing evidence indicates that lncRNAs play a key role in carcinogenesis. Consistent with this, our findings suggest that lncRNAs, as well as mRNAs of nDNA-encoded mitochondrial genes, mechanistically contribute to BC progression. This work supports a new paradigm of breast carcinogenesis based on a globally dysfunctional genome with altered function of multiple mitochondrial and non-mitochondrial oncogenic pathways caused by the effects of autoreactivity-induced dysregulation of multiple genes and their products. This autoimmunity-based model of carcinogenesis will open novel avenues for BC treatment.
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Affiliation(s)
- Deya Obaidat
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Roberta Giordo
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Erica L. Kleinbrink
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
| | - Emilia Banisad
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lawrence I. Grossman
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Rooshan Arshad
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Azadeh Stark
- Department of Pathology, Henry Ford Health System, Detroit, MI, United States
| | - Marie-Claire Maroun
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Leonard Lipovich
- Department of Basic Medical Sciences, College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Shenzhen Huayuan Biotechnology Co. Ltd, Shenzhen Huayuan Biological Science Research Institute, Shenzhen, Guangdong, China
- *Correspondence: Leonard Lipovich, ; Félix Fernandez-Madrid,
| | - Félix Fernandez-Madrid
- Department of Internal Medicine, Division of Rheumatology, Wayne State University School of Medicine, Detroit, MI, United States
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
- *Correspondence: Leonard Lipovich, ; Félix Fernandez-Madrid,
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27
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Zhao A, Zhou H, Yang J, Li M, Niu T. Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Affiliation(s)
- Ailin Zhao
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Hui Zhou
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Jinrong Yang
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Meng Li
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China
| | - Ting Niu
- Department of Hematology, West China Hospital, Sichuan University, 610041, Chengdu, Sichuan, China.
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28
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Yu J, Jiang W, Zhu SB, Liao Z, Dou X, Liu J, Guo FB, Dong C. Prediction of protein-coding small ORFs in multi-species using integrated sequence-derived features and the random forest model. Methods 2023; 210:10-19. [PMID: 36621557 DOI: 10.1016/j.ymeth.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023] Open
Abstract
Proteins encoded by small open reading frames (sORFs) can serve as functional elements playing important roles in vivo. Such sORFs also constitute the potential pool for facilitating the de novo gene birth, driving evolutionary innovation and species diversity. Therefore, their theoretical and experimental identification has become a critical issue. Herein, we proposed a protein-coding sORFs prediction method merely based on integrative sequence-derived features. Our prediction performance is better or comparable compared with other nine prevalent methods, which shows that our method can provide a relatively reliable research tool for the prediction of protein-coding sORFs. Our method allows users to estimate the potential expression of a queried sORF, which has been demonstrated by the correlation analysis between our possibility estimation and codon adaption index (CAI). Based on the features that we used, we demonstrated that the sequence features of the protein-coding sORFs in the two domains have significant differences implying that it might be a relatively hard task in terms of cross-domain prediction, hence domain-specific models were developed, which allowed users to predict protein-coding sORFs both in eukaryotes and prokaryotes. Finally, a web-server was developed and provided to boost and facilitate the study of the related field, which is freely available at http://guolab.whu.edu.cn/codingCapacity/index.html.
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Affiliation(s)
- Jiafeng Yu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Wenwen Jiang
- Department of Bioinformatics, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Sen-Bin Zhu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Zhen Liao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xianghua Dou
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Feng-Biao Guo
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
| | - Chuan Dong
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.
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29
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Zheng X, Guo Y, Zhang R, Chen H, Liu S, Qiu S, Xiang M. The mitochondrial micropeptide Stmp1 promotes retinal cell differentiation. Biochem Biophys Res Commun 2022; 636:79-86. [DOI: 10.1016/j.bbrc.2022.10.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
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30
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Zheng X, Xiang M. Mitochondrion-located peptides and their pleiotropic physiological functions. FEBS J 2022; 289:6919-6935. [PMID: 35599630 DOI: 10.1111/febs.16532] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 01/13/2023]
Abstract
With the development of advanced technologies, many small open reading frames (sORFs) have been found to be translated into micropeptides. Interestingly, a considerable proportion of micropeptides are located in mitochondria, which are designated here as mitochondrion-located peptides (MLPs). These MLPs often contain a transmembrane domain and show a high degree of conservation across species. They usually act as co-factors of large proteins and play regulatory roles in mitochondria such as electron transport in the respiratory chain, reactive oxygen species (ROS) production, metabolic homeostasis, and so on. Deficiency of MLPs disturbs diverse physiological processes including immunity, differentiation, and metabolism both in vivo and in vitro. These findings reveal crucial functions for MLPs and provide fresh insights into diverse mitochondrion-associated biological processes and diseases.
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Affiliation(s)
- Xintong Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China
| | - Mengqing Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
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31
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Sruthi KB, Menon A, P A, Vasudevan Soniya E. Pervasive translation of small open reading frames in plant long non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2022; 13:975938. [PMID: 36352887 PMCID: PMC9638090 DOI: 10.3389/fpls.2022.975938] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) are primarily recognized as non-coding transcripts longer than 200 nucleotides with low coding potential and are present in both eukaryotes and prokaryotes. Recent findings reveal that lncRNAs can code for micropeptides in various species. Micropeptides are generated from small open reading frames (smORFs) and have been discovered frequently in short mRNAs and non-coding RNAs, such as lncRNAs, circular RNAs, and pri-miRNAs. The most accepted definition of a smORF is an ORF containing fewer than 100 codons, and ribosome profiling and mass spectrometry are the most prevalent experimental techniques used to identify them. Although the majority of micropeptides perform critical roles throughout plant developmental processes and stress conditions, only a handful of their functions have been verified to date. Even though more research is being directed toward identifying micropeptides, there is still a dearth of information regarding these peptides in plants. This review outlines the lncRNA-encoded peptides, the evolutionary roles of such peptides in plants, and the techniques used to identify them. It also describes the functions of the pri-miRNA and circRNA-encoded peptides that have been identified in plants.
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32
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Choo SW, Zhong Y, Sendler E, Goustin AS, Cai J, Ju D, Kosir MA, Giordo R, Lipovich L. Estrogen distinctly regulates transcription and translation of lncRNAs and pseudogenes in breast cancer cells. Genomics 2022; 114:110421. [PMID: 35779786 DOI: 10.1016/j.ygeno.2022.110421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 05/25/2022] [Accepted: 06/25/2022] [Indexed: 11/04/2022]
Abstract
Estrogen drives key transcriptional changes in breast cancer and stimulates breast cancer cells' growth with multiple mechanisms to coordinate transcription and translation. In addition to protein-coding transcripts, estrogen can regulate long non-coding RNA (lncRNA) transcripts, plus diverse non-coding RNAs including antisense, enhancer, and intergenic. LncRNA genes comprise the majority of human genes. The accidental, or regulated, translation of their short open reading frames by ribosomes remains a controversial topic. Here we report for the first time an integrated analysis of RNA abundance and ribosome occupancy level, using Ribo-seq combined with RNA-Seq, in the estrogen-responsive, estrogen receptor α positive, human breast cancer cell model MCF7, before and after hormone treatment. Translational profiling can determine, in an unbiased manner, which fraction of the genome is actually translated into proteins, as well as resolving whether transcription and translation respond concurrently, or differentially, to estrogen treatment. Our data showed specific transcripts more robustly detected in RNA-Seq than in the ribosome-profiling data, and vice versa, suggesting distinct gene-specific estrogen responses at the transcriptional and the translational level, respectively. Here, we showed that estrogen stimulation affects the expression levels of numerous lncRNAs, but not their association with ribosomes, and that most lncRNAs are not ribosome-bound. For the first time, we also demonstrated the transcriptional and translational response of expressed pseudogenes to estrogen, pointing to new perspectives for drug-target development in breast cancer in the future.
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Affiliation(s)
- Siew-Woh Choo
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou, Zhejiang Province, China; Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou, Zhejiang Province, China.
| | - Yu Zhong
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Edward Sendler
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, USA
| | - Anton-Scott Goustin
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, USA
| | - Juan Cai
- Department of Biochemistry, Microbiology and Immunology School of Medicine, Wayne State University, Detroit, USA
| | - Donghong Ju
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, USA; Department of Surgery and Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, USA
| | - Mary Ann Kosir
- Department of Surgery and Karmanos Cancer Institute, School of Medicine, Wayne State University, Detroit, USA
| | - Roberta Giordo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
| | - Leonard Lipovich
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.
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33
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Cancer-related micropeptides encoded by ncRNAs: Promising drug targets and prognostic biomarkers. Cancer Lett 2022; 547:215723. [DOI: 10.1016/j.canlet.2022.215723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 02/07/2023]
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34
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Targeting non-coding RNAs to overcome cancer therapy resistance. Signal Transduct Target Ther 2022; 7:121. [PMID: 35418578 PMCID: PMC9008121 DOI: 10.1038/s41392-022-00975-3] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
It is now well known that non-coding RNAs (ncRNAs), rather than protein-coding transcripts, are the preponderant RNA transcripts. NcRNAs, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Despite recent discoveries in cancer therapy, resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy continue to be a major setback. Recent studies have shown that ncRNAs also play a major role in resistance to different cancer therapies by rewiring essential signaling pathways. In this review, we present the intricate mechanisms through which dysregulated ncRNAs control resistance to the four major types of cancer therapies. We will focus on the current clinical implications of ncRNAs as biomarkers to predict treatment response (intrinsic resistance) and to detect resistance to therapy after the start of treatment (acquired resistance). Furthermore, we will present the potential of targeting ncRNA to overcome cancer treatment resistance, and we will discuss the challenges of ncRNA-targeted therapy—especially the development of delivery systems.
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35
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Ilina A, Khavinson V, Linkova N, Petukhov M. Neuroepigenetic Mechanisms of Action of Ultrashort Peptides in Alzheimer's Disease. Int J Mol Sci 2022; 23:ijms23084259. [PMID: 35457077 PMCID: PMC9032300 DOI: 10.3390/ijms23084259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 12/23/2022] Open
Abstract
Epigenetic regulation of gene expression is necessary for maintaining higher-order cognitive functions (learning and memory). The current understanding of the role of epigenetics in the mechanism of Alzheimer’s disease (AD) is focused on DNA methylation, chromatin remodeling, histone modifications, and regulation of non-coding RNAs. The pathogenetic links of this disease are the misfolding and aggregation of tau protein and amyloid peptides, mitochondrial dysfunction, oxidative stress, impaired energy metabolism, destruction of the blood–brain barrier, and neuroinflammation, all of which lead to impaired synaptic plasticity and memory loss. Ultrashort peptides are promising neuroprotective compounds with a broad spectrum of activity and without reported side effects. The main aim of this review is to analyze the possible epigenetic mechanisms of the neuroprotective action of ultrashort peptides in AD. The review highlights the role of short peptides in the AD pathophysiology. We formulate the hypothesis that peptide regulation of gene expression can be mediated by the interaction of short peptides with histone proteins, cis- and transregulatory DNA elements and effector molecules (DNA/RNA-binding proteins and non-coding RNA). The development of therapeutic agents based on ultrashort peptides may offer a promising addition to the multifunctional treatment of AD.
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Affiliation(s)
- Anastasiia Ilina
- Department of Biogerontology, Saint Petersburg Institute of Bioregulation and Gerontology, 19711 Saint Petersburg, Russia; (V.K.); (N.L.)
- Department of General Pathology and Pathological Physiology, Institute of Experimental Medicine, 197376 Saint Petersburg, Russia
- Correspondence: ; Tel.: +7-(953)145-89-58
| | - Vladimir Khavinson
- Department of Biogerontology, Saint Petersburg Institute of Bioregulation and Gerontology, 19711 Saint Petersburg, Russia; (V.K.); (N.L.)
- Group of Peptide Regulation of Aging, Pavlov Institute of Physiology, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
| | - Natalia Linkova
- Department of Biogerontology, Saint Petersburg Institute of Bioregulation and Gerontology, 19711 Saint Petersburg, Russia; (V.K.); (N.L.)
| | - Mikhael Petukhov
- Department of Molecular Radiation Biophysics, Petersburg Nuclear Physics Institute Named after B.P. Konstantinov, NRC “Kurchatov Institute”, 188300 Gatchina, Russia;
- Group of Biophysics, Higher Engineering and Technical School, Peter the Great St. Petersburg Polytechnic University, 195251 Saint Petersburg, Russia
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36
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Liu T, Wu J, Wu Y, Hu W, Fang Z, Wang Z, Jiang C, Li S. LncPep: A Resource of Translational Evidences for lncRNAs. Front Cell Dev Biol 2022; 10:795084. [PMID: 35141219 PMCID: PMC8819059 DOI: 10.3389/fcell.2022.795084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are a type of transcript that is >200 nucleotides long with no protein-coding capacity. Accumulating studies have suggested that lncRNAs contain open reading frames (ORFs) that encode peptides. Although several noncoding RNA-encoded peptide-related databases have been developed, most of them display only a small number of experimentally validated peptides, and resources focused on lncRNA-encoded peptides are still lacking. We used six types of evidence, coding potential assessment tool (CPAT), coding potential calculator v2.0 (CPC2), N6-methyladenosine modification of RNA sites (m6A), Pfam, ribosome profiling (Ribo-seq), and translation initiation sites (TISs), to evaluate the coding potential of 883,804 lncRNAs across 39 species. We constructed a comprehensive database of lncRNA-encoded peptides, LncPep (http://www.shenglilabs.com/LncPep/). LncPep provides three major functional modules: 1) user-friendly searching/browsing interface, 2) prediction and BLAST modules for exploring novel lncRNAs and peptides, and 3) annotations for lncRNAs, peptides and supporting evidence. Taken together, LncPep is a user-friendly and convenient platform for discovering and investigating peptides encoded by lncRNAs.
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Affiliation(s)
- Teng Liu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingni Wu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yangjun Wu
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Hu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhixiao Fang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zishan Wang
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Chunjie Jiang
- Institute for Diabetes Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Shengli Li,
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37
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Luo X, Huang Y, Li H, Luo Y, Zuo Z, Ren J, Xie Y. SPENCER: a comprehensive database for small peptides encoded by noncoding RNAs in cancer patients. Nucleic Acids Res 2022; 50:D1373-D1381. [PMID: 34570216 PMCID: PMC8728293 DOI: 10.1093/nar/gkab822] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 01/07/2023] Open
Abstract
As an increasing number of noncoding RNAs (ncRNAs) have been suggested to encode short bioactive peptides in cancer, the exploration of ncRNA-encoded small peptides (ncPEPs) is emerging as a fascinating field in cancer research. To assist in studies on the regulatory mechanisms of ncPEPs, we describe here a database called SPENCER (http://spencer.renlab.org). Currently, SPENCER has collected a total of 2806 mass spectrometry (MS) data points from 55 studies, covering 1007 tumor samples and 719 normal samples. Using an MS-based proteomics analysis pipeline, SPENCER identified 29 526 ncPEPs across 15 different cancer types. Specifically, 22 060 of these ncPEPs were experimentally validated in other studies. By comparing tumor and normal samples, the identified ncPEPs were divided into four expression groups: tumor-specific, upregulated in cancer, downregulated in cancer, and others. Additionally, since ncPEPs are potential targets for neoantigen-based cancer immunotherapy, SPENCER also predicted the immunogenicity of all the identified ncPEPs by assessing their MHC-I binding affinity, stability, and TCR recognition probability. As a result, 4497 ncPEPs curated in SPENCER were predicted to be immunogenic. Overall, SPENCER will be a useful resource for investigating cancer-associated ncPEPs and may boost further research in cancer.
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Affiliation(s)
- Xiaotong Luo
- School of Life Sciences, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Yuantai Huang
- School of Life Sciences, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Huiqin Li
- School of Life Sciences, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Yihai Luo
- School of Life Sciences, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Ren
- School of Life Sciences, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Yubin Xie
- School of Life Sciences, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
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38
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Ping J, Li L, Dong Y, Wu X, Huang X, Sun B, Zeng B, Xu F, Liang W. The Role of Long Non-Coding RNAs and Circular RNAs in Bone Regeneration: Modulating MiRNAs Function. J Tissue Eng Regen Med 2021; 16:227-243. [PMID: 34958714 DOI: 10.1002/term.3277] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 12/04/2021] [Accepted: 12/10/2021] [Indexed: 11/06/2022]
Abstract
Although bone is a self-healing organ and is able to repair and restore most fractures, large bone fractures, about 10%, are not repairable. Bone grafting, as a gold standard, and bone tissue engineering using biomaterials, growth factors, and stem cells have been developed to restore large bone defects. Since bone regeneration is a complex and multiple-step process and the majority of the human genome, about 98%, is composed of the non-protein-coding regions, non-coding RNAs (ncRNAs) play essential roles in bone regeneration. Recent studies demonstrated that long ncRNAs (lncRNAs) and circular RNAs (circRNAs), as members of ncRNAs, are widely involved in bone regeneration by interaction with microRNAs (miRNAs) and constructing a lncRNA or circRNA/miRNA/mRNA regulatory network. The constructed network regulates the differentiation of stem cells into osteoblasts and their commitment to osteogenesis. This review will present the structure and biogenesis of lncRNAs and circRNAs, the mechanism of bone repair, and the bone tissue engineering in bone defects. Finally, we will discuss the role of lncRNAs and circRNAs in osteogenesis and bone fracture healing through constructing various lncRNA or circRNA/miRNA/mRNA networks and the involved pathways. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jianfeng Ping
- Department of Orthopaedics, Shaoxing People's Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, 312000, Zhejiang Province, China
| | - Laifeng Li
- Department of Traumatic Orthopaedics, Affiliated Jinan Third Hospital of Jining Medical University, Jinan, 250132, Shandong Province, China
| | - Yongqiang Dong
- Department of Orthopaedics, Xinchang People's Hospital, Shaoxing, 312500, Zhejiang Province, China
| | - Xudong Wu
- Department of Orthopaedics, Zhoushan Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Zhoushan, 316000, Zhejiang Province, China
| | - Xiaogang Huang
- Department of Orthopaedics, Zhoushan Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Zhoushan, 316000, Zhejiang Province, China
| | - Bin Sun
- Department of Orthopaedics, Zhoushan Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Zhoushan, 316000, Zhejiang Province, China
| | - Bin Zeng
- Department of Orthopaedics, Zhoushan Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Zhoushan, 316000, Zhejiang Province, China
| | - Fangming Xu
- Department of Orthopaedics, Zhoushan Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Zhoushan, 316000, Zhejiang Province, China
| | - Wenqing Liang
- Department of Orthopaedics, Zhoushan Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Zhoushan, 316000, Zhejiang Province, China
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39
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Fesenko I, Shabalina SA, Mamaeva A, Knyazev A, Glushkevich A, Lyapina I, Ziganshin R, Kovalchuk S, Kharlampieva D, Lazarev V, Taliansky M, Koonin EV. A vast pool of lineage-specific microproteins encoded by long non-coding RNAs in plants. Nucleic Acids Res 2021; 49:10328-10346. [PMID: 34570232 DOI: 10.1093/nar/gkab816] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/17/2021] [Accepted: 09/17/2021] [Indexed: 12/17/2022] Open
Abstract
Pervasive transcription of eukaryotic genomes results in expression of long non-coding RNAs (lncRNAs) most of which are poorly conserved in evolution and appear to be non-functional. However, some lncRNAs have been shown to perform specific functions, in particular, transcription regulation. Thousands of small open reading frames (smORFs, <100 codons) located on lncRNAs potentially might be translated into peptides or microproteins. We report a comprehensive analysis of the conservation and evolutionary trajectories of lncRNAs-smORFs from the moss Physcomitrium patens across transcriptomes of 479 plant species. Although thousands of smORFs are subject to substantial purifying selection, the majority of the smORFs appear to be evolutionary young and could represent a major pool for functional innovation. Using nanopore RNA sequencing, we show that, on average, the transcriptional level of conserved smORFs is higher than that of non-conserved smORFs. Proteomic analysis confirmed translation of 82 novel species-specific smORFs. Numerous conserved smORFs containing low complexity regions (LCRs) or transmembrane domains were identified, the biological functions of a selected LCR-smORF were demonstrated experimentally. Thus, microproteins encoded by smORFs are a major, functionally diverse component of the plant proteome.
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Affiliation(s)
- Igor Fesenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna Mamaeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Andrey Knyazev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Anna Glushkevich
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Irina Lyapina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Rustam Ziganshin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergey Kovalchuk
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Daria Kharlampieva
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation
| | - Vassili Lazarev
- Department of Cell Biology, Federal Research and Clinical Center of Physical -Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russian Federation.,Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow region, 141701, Russian Federation
| | - Michael Taliansky
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russian Federation.,The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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40
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Lv D, Chang Z, Cai Y, Li J, Wang L, Jiang Q, Xu K, Ding N, Li X, Xu J, Li Y. TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome. Nucleic Acids Res 2021; 50:D413-D420. [PMID: 34570220 PMCID: PMC8728190 DOI: 10.1093/nar/gkab847] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 01/10/2023] Open
Abstract
LncRNAs are not only well-known as non-coding elements, but also serve as templates for peptide translation, playing important roles in fundamental cellular processes and diseases. Here, we describe a database, TransLnc (http://bio-bigdata.hrbmu.edu.cn/TransLnc/), which aims to provide comprehensive experimentally supported and predicted lncRNA peptides in multiple species. TransLnc currently documents approximate 583 840 peptides encoded by 33 094 lncRNAs. Six types of direct and indirect evidences supporting the coding potential of lncRNAs were integrated, and 65.28% peptides entries were with at least one type of evidence. Considering the strong tissue-specific expression of lncRNAs, TransLnc allows users to access lncRNA peptides in any of the 34 tissues involved in. In addition, both the unique characteristic and homology relationship were also predicted and provided. Importantly, TransLnc provides computationally predicted tumour neoantigens from peptides encoded by lncRNAs, which would provide novel insights into cancer immunotherapy. There were 220 791 and 237 915 candidate neoantigens binding by major histocompatibility complex (MHC) class I or II molecules, respectively. Several flexible tools were developed to aid retrieve and analyse, particularly lncRNAs tissue expression patterns, clinical relevance across cancer types. TransLnc will serve as a valuable resource for investigating the translation capacity of lncRNAs and greatly extends the cancer immunopeptidome.
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Affiliation(s)
- Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Zhenghong Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Yangyang Cai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Junyi Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Liping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Qiushuang Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Kang Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, China.,Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, College of Biomedical Information and Engineering, Hainan Women and Children's Medical Center, Hainan Medical University, Haikou, 571199, China
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41
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Zheng H, Talukder A, Li X, Hu H. A systematic evaluation of the computational tools for lncRNA identification. Brief Bioinform 2021; 22:6343529. [PMID: 34368833 DOI: 10.1093/bib/bbab285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
The computational identification of long non-coding RNAs (lncRNAs) is important to study lncRNAs and their functions. Despite the existence of many computation tools for lncRNA identification, to our knowledge, there is no systematic evaluation of these tools on common datasets and no consensus regarding their performance and the importance of the features used. To fill this gap, in this study, we assessed the performance of 17 tools on several common datasets. We also investigated the importance of the features used by the tools. We found that the deep learning-based tools have the best performance in terms of identifying lncRNAs, and the peptide features do not contribute much to the tool accuracy. Moreover, when the transcripts in a cell type were considered, the performance of all tools significantly dropped, and the deep learning-based tools were no longer as good as other tools. Our study will serve as an excellent starting point for selecting tools and features for lncRNA identification.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
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42
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Sabo AA, Dudau M, Constantin GL, Pop TC, Geilfus CM, Naccarati A, Dragomir MP. Two Worlds Colliding: The Interplay Between Natural Compounds and Non-Coding Transcripts in Cancer Therapy. Front Pharmacol 2021; 12:652074. [PMID: 34295245 PMCID: PMC8290364 DOI: 10.3389/fphar.2021.652074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/07/2021] [Indexed: 12/25/2022] Open
Abstract
Cancer is a devastating disease and has recently become the leading cause of death in western countries, representing an immense public health burden. When it comes to cancer treatment, chemotherapy is one of the main pillars, especially for advanced stage tumors. Over the years, natural compounds have emerged as one of the most valuable resources for new chemotherapies. It is estimated that more than half of the currently used chemotherapeutic agents are derived from natural compounds. Usually, natural compounds are discovered empirically and an important limitation of introducing new anti-cancer natural products is lack of knowledge with regard to their mechanism of action. Recent data has proven that several natural compounds may function via modulating the expression and function of non-coding RNAs (ncRNAs). NcRNAs are a heterogenous class of RNA molecules which are usually not translated into proteins but have an important role in gene expression regulation and are involved in multiple tumorigenic processes, including response/resistance to pharmacotherapy. In this review, we will discuss how natural compounds function via ncRNAs while summarizing the available data regarding their effects on over 15 types of cancer. Moreover, we will critically analyze the current advances and limitations in understanding the way natural compounds exert these health-promoting effects by acting on ncRNAs. Finally, we will propose several hypotheses that may open new avenues and perspectives regarding the interaction between natural compounds and ncRNAs, which could lead to improved natural compound-based therapeutic strategies in cancer.
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Affiliation(s)
- Alexandru A. Sabo
- Pediatrics 2 (General and Special Pediatrics), Klinikum Stuttgart, Olgahospital, Zentrum für Kinder, Jugend- und Frauenmedizin, Stuttgart, Germany
| | - Maria Dudau
- Biochemistry-Proteomics Department, Victor Babes National Institute of Pathology, Bucharest, Romania
- Department of Cellular and Molecular Biology and Histology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - George L. Constantin
- Division of Soil Science and Site Science, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Tudor C. Pop
- Department of Pediatrics, Marie Curie Emergency Clinical Hospital for Children, Bucharest, Romania
| | - Christoph-M. Geilfus
- Division of Controlled Environment Horticulture, Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alessio Naccarati
- IIGM Italian Institute for Genomic Medicine, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Mihnea P. Dragomir
- Department of Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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43
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Xing J, Liu H, Jiang W, Wang L. LncRNA-Encoded Peptide: Functions and Predicting Methods. Front Oncol 2021; 10:622294. [PMID: 33520729 PMCID: PMC7842084 DOI: 10.3389/fonc.2020.622294] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/30/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) was originally defined as the representative of the non-coding RNAs and unable to encode. However, recent reports suggest that some lncRNAs actually contain open reading frames that encode peptides. These coding products play important roles in the pathogenesis of many diseases. Here, we summarize the regulatory pathways of mammalian lncRNA-encoded peptides in influencing muscle function, mRNA stability, gene expression, and so on. We also address the promoting and inhibiting functions of the peptides in different cancers and other diseases. Then we introduce the computational predicting methods and data resources to predict the coding ability of lncRNA. The intention of this review is to provide references for further coding research and contribute to reveal the potential prospects for targeted tumor therapy.
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Affiliation(s)
- Jiani Xing
- Department of Pathophysiology, Medical College of Southeast University, Nanjing, China
| | - Haizhou Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Wei Jiang
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Lihong Wang
- Department of Pathophysiology, Medical College of Southeast University, Nanjing, China.,Jiangsu Provincial Key Laboratory of Critical Care Medicine, Nanjing, China
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