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Wang J, Luo H, Yang L, Yuan H. ARAP1-AS1: a novel long non-coding RNA with a vital regulatory role in human cancer development. Cancer Cell Int 2024; 24:270. [PMID: 39090630 PMCID: PMC11295494 DOI: 10.1186/s12935-024-03435-w] [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: 10/08/2023] [Accepted: 07/08/2024] [Indexed: 08/04/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have garnered significant attention in biomedical research due to their pivotal roles in gene expression regulation and their association with various human diseases. Among these lncRNAs, ArfGAP With RhoGAP Domain, Ankyrin Repeat, And PH Domain 1 - Antisense RNA 1 (ARAP1-AS1) has recently emerged as an novel oncogenic player. ARAP1-AS1 is prominently overexpressed in numerous solid tumors and wields influence by modulating gene expression and signaling pathways. This regulatory impact is realized through dual mechanisms, involving both competitive interactions with microRNAs and direct protein binding. ARAP1-AS1 assumes an important role in driving tumorigenesis and malignant tumor progression, affecting biological characteristics such as tumor expansion and metastasis. This paper provides a concise review of the regulatory role of ARAP1-AS1 in malignant tumors and discuss its potential clinical applications as a biomarker and therapeutic target. We also address existing knowledge gaps and suggest avenues for future research. ARAP1-AS1 serves as a prototypical example within the burgeoning field of lncRNA studies, offering insights into the broader landscape of non-coding RNA molecules. This investigation enhances our comprehension of the complex mechanisms that govern the progression of cancer.
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Affiliation(s)
- Jialing Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330008, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330008, China
| | - Lu Yang
- Department of Cardiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330008, China
| | - Huazhao Yuan
- Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi Province, 332007, P.R. China.
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Jabeen S, Ahmed N, Rashid F, Lal N, Kong F, Fu Y, Zhang F. Circular RNAs in tuberculosis and lung cancer. Clin Chim Acta 2024; 561:119810. [PMID: 38866175 DOI: 10.1016/j.cca.2024.119810] [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: 01/30/2024] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 06/14/2024]
Abstract
This review signifies the role of circular RNAs (circRNAs) in tuberculosis (TB) and lung cancer (LC), focusing on pathogenesis, diagnosis, and treatment. CircRNAs, a newly discovered type of non-coding RNA, have emerged as key regulators of gene expression and promising biomarkers in various bodily fluids due to their stability. The current review discusses circRNA biogenesis, highlighting their RNase-R resistance due to their loop forming structure, making them effective biomarkers. It details their roles in gene regulation, including splicing, transcription control, and miRNA interactions, and their impact on cellular processes and diseases. For LC, the review identifies circRNA dysregulation affecting cell growth, motility, and survival, and their potential as therapeutic targets and biomarkers. In TB, it addresses circRNAs' influence on host anti-TB immune responses, proposing their use as early diagnostic markers. The paper also explores the interplay between TB and LC, emphasizing circRNAs as dual biosignatures, and the necessity for differential diagnosis. It concludes that no single circRNA biomarker is universally applicable for both TB and LC. Ultimately, the review highlights the pivotal role of circRNAs in TB and LC, encouraging further research in biomarker identification and therapeutic development concomitant for both diseases.
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Affiliation(s)
- Sadia Jabeen
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China
| | - Niaz Ahmed
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China
| | - Faiqa Rashid
- Department of Bioinformatics And Biosciences, Capital University Of Science & Technology, Islamabad Expressway, Kahuta Road, Zone-V, Islamabad, Pakistan
| | - Nand Lal
- Department of Physiology, School of Biomedical Sciences, Harbin Medical University, 157 Baojian Road, Nangang District, Harbin, 150081, China
| | - Fanhui Kong
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China
| | - Yingmei Fu
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China.
| | - Fengmin Zhang
- Department of Microbiology, Wu Lien Teh Institute, Harbin Medical University, Harbin 150081, China; Heilongjiang Key Laboratory of Immunity and Infection, Harbin 150081, China.
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Zhang X, Liu M, Li Z, Zhuo L, Fu X, Zou Q. Fusion of multi-source relationships and topology to infer lncRNA-protein interactions. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102187. [PMID: 38706631 PMCID: PMC11066462 DOI: 10.1016/j.omtn.2024.102187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Long non-coding RNAs (lncRNAs) are important factors involved in biological regulatory networks. Accurately predicting lncRNA-protein interactions (LPIs) is vital for clarifying lncRNA's functions and pathogenic mechanisms. Existing deep learning models have yet to yield satisfactory results in LPI prediction. Recently, graph autoencoders (GAEs) have seen rapid development, excelling in tasks like link prediction and node classification. We employed GAE technology for LPI prediction, devising the FMSRT-LPI model based on path masking and degree regression strategies and thereby achieving satisfactory outcomes. This represents the first known integration of path masking and degree regression strategies into the GAE framework for potential LPI inference. The effectiveness of our FMSRT-LPI model primarily relies on four key aspects. First, within the GAE framework, our model integrates multi-source relationships of lncRNAs and proteins with LPN's topological data. Second, the implemented masking strategy efficiently identifies LPN's key paths, reconstructs the network, and reduces the impact of redundant or incorrect data. Third, the integrated degree decoder balances degree and structural information, enhancing node representation. Fourth, the PolyLoss function we introduced is more appropriate for LPI prediction tasks. The results on multiple public datasets further demonstrate our model's potential in LPI prediction.
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Affiliation(s)
- Xinyu Zhang
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325027, China
| | - Mingzhe Liu
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325027, China
| | - Zhen Li
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou 510000, China
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou 325027, China
| | - Xiangzheng Fu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410012, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 611730, China
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Pan X, Dai W, Wang Z, Li S, Sun T, Miao N. PIWI-Interacting RNAs: A Pivotal Regulator in Neurological Development and Disease. Genes (Basel) 2024; 15:653. [PMID: 38927589 PMCID: PMC11202748 DOI: 10.3390/genes15060653] [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: 04/13/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs), a class of small non-coding RNAs (sncRNAs) with 24-32 nucleotides (nt), were initially identified in the reproductive system. Unlike microRNAs (miRNAs) or small interfering RNAs (siRNAs), piRNAs normally guide P-element-induced wimpy testis protein (PIWI) families to slice extensively complementary transposon transcripts without the seed pairing. Numerous studies have shown that piRNAs are abundantly expressed in the brain, and many of them are aberrantly regulated in central neural system (CNS) disorders. However, the role of piRNAs in the related developmental and pathological processes is unclear. The elucidation of piRNAs/PIWI would greatly improve the understanding of CNS development and ultimately lead to novel strategies to treat neural diseases. In this review, we summarized the relevant structure, properties, and databases of piRNAs and their functional roles in neural development and degenerative disorders. We hope that future studies of these piRNAs will facilitate the development of RNA-based therapeutics for CNS disorders.
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Affiliation(s)
| | | | | | | | | | - Nan Miao
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen 361021, China; (X.P.); (W.D.); (Z.W.); (S.L.); (T.S.)
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Chen PA, Chang PC, Yeh WW, Hu TY, Hong YC, Wang YC, Huang WJ, Lin TP. The lncRNA TPT1-AS1 promotes the survival of neuroendocrine prostate cancer cells by facilitating autophagy. Am J Cancer Res 2024; 14:2103-2123. [PMID: 38859837 PMCID: PMC11162664 DOI: 10.62347/imbv8599] [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: 02/02/2024] [Accepted: 04/21/2024] [Indexed: 06/12/2024] Open
Abstract
The lncRNA tumor protein translationally controlled 1-antisense RNA 1 (TPT1-AS1) is known for its oncogenic role in various cancers, but its impact on the pathological progression of prostate cancer remains unclear. Our previous study demonstrated that the RE1-silencing transcription factor (REST) regulates neuroendocrine differentiation (NED) in prostate cancer (PCA) by derepressing specific long non-coding RNAs (lncRNAs), including TPT1-AS1. In this study, we revealed that TPT1-AS1 is overexpressed in LNCaP and C4-2B cells after IL-6 and enzalutamide treatment. By analyzing The Cancer Genome Atlas (TCGA) prostate adenocarcinoma dataset, we detected upregulated TPT1-AS1 expression in neuroendocrine-associated PCA but not in prostate adenocarcinoma. Single-cell RNA sequencing data further confirmed the increased TPT1-AS1 levels in neuroendocrine prostate cancer (NEPC) cells. Surprisingly, functional experiments indicated that TPT1-AS1 overexpression had no stimulatory effect on NED in LNCaP cells and that TPT1-AS1 knockdown did not inhibit IL-6-induced NED. Transcriptomic analysis revealed the essential role of TPT1-AS1 in synaptogenesis and autophagy activation in neuroendocrine differentiated PCA cells induced by IL-6 and enzalutamide treatment. TPT1-AS1 was found to regulate the expression of autophagy-related genes that maintain neuroendocrine cell survival through autophagy activation. In conclusion, our data expand the current knowledge of REST-repressed lncRNAs in NED in PCA and highlight the contribution of TPT1-AS1 to protect neuroendocrine cells from cell death rather than inducing NED. Our study suggested that TPT1-AS1 plays a cytoprotective role in NEPC cells; thus, targeting TPT1-AS1 is a potential therapeutic strategy.
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Affiliation(s)
- Po-An Chen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Pei-Ching Chang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Wayne W Yeh
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Tze-Yun Hu
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Yung-Chih Hong
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Yu-Chao Wang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - William J Huang
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
- Department of Urology, School of Medicine and Shu-Tien Urological Research Center, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Tzu-Ping Lin
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
- Department of Urology, School of Medicine and Shu-Tien Urological Research Center, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
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Shen C, Mao D, Tang J, Liao Z, Chen S. Prediction of LncRNA-Protein Interactions Based on Kernel Combinations and Graph Convolutional Networks. IEEE J Biomed Health Inform 2024; 28:1937-1948. [PMID: 37327093 DOI: 10.1109/jbhi.2023.3286917] [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: 06/18/2023]
Abstract
The complexes of long non-coding RNAs bound to proteins can be involved in regulating life activities at various stages of organisms. However, in the face of the growing number of lncRNAs and proteins, verifying LncRNA-Protein Interactions (LPI) based on traditional biological experiments is time-consuming and laborious. Therefore, with the improvement of computing power, predicting LPI has met new development opportunity. In virtue of the state-of-the-art works, a framework called LncRNA-Protein Interactions based on Kernel Combinations and Graph Convolutional Networks (LPI-KCGCN) has been proposed in this article. We first construct kernel matrices by taking advantage of extracting both the lncRNAs and protein concerning the sequence features, sequence similarity features, expression features, and gene ontology. Then reconstruct the existent kernel matrices as the input of the next step. Combined with known LPI interactions, the reconstructed similarity matrices, which can be used as features of the topology map of the LPI network, are exploited in extracting potential representations in the lncRNA and protein space using a two-layer Graph Convolutional Network. The predicted matrix can be finally obtained by training the network to produce scoring matrices w.r.t. lncRNAs and proteins. Different LPI-KCGCN variants are ensemble to derive the final prediction results and testify on balanced and unbalanced datasets. The 5-fold cross-validation shows that the optimal feature information combination on a dataset with 15.5% positive samples has an AUC value of 0.9714 and an AUPR value of 0.9216. On another highly unbalanced dataset with only 5% positive samples, LPI-KCGCN also has outperformed the state-of-the-art works, which achieved an AUC value of 0.9907 and an AUPR value of 0.9267.
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Xie M, Xie R, Wang H. LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm. Methods 2023; 220:98-105. [PMID: 37972912 DOI: 10.1016/j.ymeth.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/14/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Many studies have shown that long-chain noncoding RNAs (lncRNAs) are involved in a variety of biological processes such as post-transcriptional gene regulation, splicing, and translation by combining with corresponding proteins. Predicting lncRNA-protein interactions is an effective approach to infer the functions of lncRNAs. The paper proposes a new computational model named LPI-IBWA. At first, LPI-IBWA uses similarity kernel fusion (SKF) to integrate various types of biological information to construct lncRNA and protein similarity networks. Then, a bounded matrix completion model and a weighted k-nearest known neighbors algorithm are utilized to update the initial sparse lncRNA-protein interaction matrix. Based on the updated lncRNA-protein interaction matrix, the lncRNA similarity network and the protein similarity network are integrated into a heterogeneous network. Finally, an improved Bi-Random walk algorithm is used to predict novel latent lncRNA-protein interactions. 5-fold cross-validation experiments on a benchmark dataset showed that the AUC and AUPR of LPI-IBWA reach 0.920 and 0.736, respectively, which are higher than those of other state-of-the-art methods. Furthermore, the experimental results of case studies on a novel dataset also illustrated that LPI-IBWA could efficiently predict potential lncRNA-protein interactions.
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Affiliation(s)
- Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, China.
| | - Ruijie Xie
- College of Information Science and Engineering, Hunan Normal University, China.
| | - Hao Wang
- College of Information Science and Engineering, Hunan Normal University, China.
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Hossain MM, Roat R, Christopherson J, Free C, Ansarullah, James B, Guo Z. Exploring lncRNAs associated with human pancreatic islet cell death induced by transfer of adoptive lymphocytes in a humanized mouse model. Front Endocrinol (Lausanne) 2023; 14:1244688. [PMID: 38027148 PMCID: PMC10646418 DOI: 10.3389/fendo.2023.1244688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/29/2023] [Indexed: 12/01/2023] Open
Abstract
Background Long noncoding RNA (lncRNA)-mediated posttranscriptional and epigenetic landscapes of gene regulation are associated with numerous human diseases. However, the regulatory mechanisms governing human β-cell function and survival remain unknown. Owing to technical and ethical constraints, studying the direct role of lncRNAs in β-cell function and survival in humans in vivo is difficult. Therefore, we utilized humanized mice with human islets to investigate lncRNA expression using whole transcriptome shotgun sequencing. Our study aimed to characterize lncRNAs that may be crucial for human islet cell function and survival. Methods Human β-cell death was induced in humanized mice engrafted with functional human islets. Using these humanized mice harboring human islets with induced β-cell death, we investigated lncRNA expression through whole transcriptome shotgun sequencing. Additionally, we systematically identified, characterized, and explored the regulatory functions of lncRNAs that are potentially important for human pancreatic islet cell function and survival. Results Human islet cell death was induced in humanized mice engrafted with functional human islets. RNA sequencing analysis of isolated human islets, islet grafts from humanized mice with and without induced cell death, revealed aberrant expression of a distinct set of lncRNAs that are associated with the deregulated mRNAs important for cellular processes and molecular pathways related to β-cell function and survival. A total of 10 lncRNA isoforms (SCYL1-1:22, POLG2-1:1, CTRB1-1:1, SRPK1-1:1, GTF3C5-1:1, PPY-1:1, CTRB1-1:5, CPA5-1:1, BCAR1-2:1, and CTRB1-1:4) were identified as highly enriched and specific to human islets. These lncRNAs were deregulated in human islets from donors with different BMIs and with type 2 diabetes (T2D), as well as in cultured human islets with glucose stimulation and induced cell death induced by cytokines. Aberrant expression of these lncRNAs was detected in the exosomes from the medium used to culture islets with cytokines. Conclusion Islet-enriched and specific human lncRNAs are deregulated in human islet grafts and cultured human islets with induced cell death. These lncRNAs may be crucial for human β-cell function and survival and could have an impact on identifying biomarkers for β-cell loss and discovering novel therapeutic targets to enhance β-cell function and survival.
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Affiliation(s)
- Md Munir Hossain
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
- Department of Animal Breeding and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Regan Roat
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Jenica Christopherson
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Colette Free
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Ansarullah
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Brian James
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
- Discovery Genomics, Inc., Irvine, CA, United States
| | - Zhiguang Guo
- The Sanford Project/Children Health Research Center, Sanford Research, Sioux Falls, SD, United States
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Lv G, Xia Y, Qi Z, Zhao Z, Tang L, Chen C, Yang S, Wang Q, Gu L. LncRNA-protein interaction prediction with reweighted feature selection. BMC Bioinformatics 2023; 24:410. [PMID: 37904080 PMCID: PMC10617115 DOI: 10.1186/s12859-023-05536-1] [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: 07/15/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
LncRNA-protein interactions are ubiquitous in organisms and play a crucial role in a variety of biological processes and complex diseases. Many computational methods have been reported for lncRNA-protein interaction prediction. However, the experimental techniques to detect lncRNA-protein interactions are laborious and time-consuming. Therefore, to address this challenge, this paper proposes a reweighting boosting feature selection (RBFS) method model to select key features. Specially, a reweighted apporach can adjust the contribution of each observational samples to learning model fitting; let higher weights are given more influence samples than those with lower weights. Feature selection with boosting can efficiently rank to iterate over important features to obtain the optimal feature subset. Besides, in the experiments, the RBFS method is applied to the prediction of lncRNA-protein interactions. The experimental results demonstrate that our method achieves higher accuracy and less redundancy with fewer features.
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Affiliation(s)
- Guohao Lv
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yingchun Xia
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhao Qi
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zihao Zhao
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lianggui Tang
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Cheng Chen
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Shuai Yang
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qingyong Wang
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Lichuan Gu
- School of Information and Computer, Anhui Agricultural University, Hefei, 230036, Anhui, China.
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Zhang YH, Zhao L, Zhang MY, Cao RD, Hou GM, Teng HJ, Zhang JX. Fatty acid metabolism decreased while sexual selection increased in brown rats spreading south. iScience 2023; 26:107742. [PMID: 37731619 PMCID: PMC10507208 DOI: 10.1016/j.isci.2023.107742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/27/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023] Open
Abstract
For mammals that originate in the cold north, adapting to warmer environments is crucial for southwards invasion. The brown rat (Rattus norvegicus) originated in Northeast China and has become a global pest. R. n. humiliatus (RNH) spread from the northeast, where R. n. caraco (RNC) lives, to North China and diverged to form a subspecies. Genomic analyses revealed that subspecies differentiation was promoted by temperature but impeded by gene flow and that genes related to fatty acid metabolism were under the strongest selection. Transcriptome analyses revealed downregulated hepatic genes related to fatty acid metabolism and upregulated those related to pheromones in RNH vs. RNC. Similar patterns were observed in relation to cold/warm acclimation. RNH preferred mates with stronger pheromone signals intra-populationally and more genetic divergence inter-populationally. We concluded that RNH experienced reduced fat utilization and increased pheromone-mediated sexual selection during its invasion from the cold north to warm south.
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Affiliation(s)
- Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
| | - Lei Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming-Yu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Dong Cao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guan-Mei Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hua-Jing Teng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Radiation Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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Chang CH, Cheng TY, Yeh WW, Luo YL, Campbell M, Kuo TC, Shen TW, Hong YC, Tsai CH, Peng YC, Pan CC, Yang MH, Shih JC, Kung HJ, Huang WJ, Chang PC, Lin TP. REST-repressed lncRNA LINC01801 induces neuroendocrine differentiation in prostate cancer via transcriptional activation of autophagy. Am J Cancer Res 2023; 13:3983-4002. [PMID: 37818052 PMCID: PMC10560947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/03/2023] [Indexed: 10/12/2023] Open
Abstract
The association between REST reduction and the development of neuroendocrine prostate cancer (NEPC), a novel drug-resistant and lethal variant of castration-resistant prostate cancer (CRPC), is well established. To better understand the mechanisms underlying this process, we aimed to identify REST-repressed long noncoding RNAs (lncRNAs) that promote neuroendocrine differentiation (NED), thus facilitating targeted therapy-induced resistance. In this study, we used data from REST knockdown RNA sequencing combined with siRNA screening to determine that LINC01801 was upregulated and played a crucial role in NED in prostate cancer (PCa). Using The Cancer Genome Atlas (TCGA) prostate adenocarcinoma database and CRPC samples collected in our laboratory, we demonstrated that LINC01801 expression is upregulated in NEPC. Functional experiments revealed that overexpression of LINC01801 had a slight stimulatory effect on the NED of LNCaP cells, while downregulation of LINC01801 significantly inhibited the induction of NED. Mechanistically, LINC01801 is transcriptionally repressed by REST, and transcriptomic analysis revealed that LINC01801 preferentially affects the autophagy pathway. LINC01801 was found to function as a competing endogenous RNA (ceRNA) to regulate the expression of autophagy-related genes by sponging hsa-miR-6889-3p in prostate cancer cells. In conclusion, our data expand the current knowledge of REST-induced NED and highlight the contribution of the REST-LINC01801-hsa-miR-6889-3p axis to autophagic induction, which may provide promising avenues for therapeutic opportunities.
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Affiliation(s)
- Ching-Hsin Chang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Department of Urology, Taipei Medical University HospitalTaipei 11031, Taiwan
| | - Ting-Yu Cheng
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Wayne W Yeh
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Yun-Li Luo
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Mel Campbell
- Comprehensive Cancer Center, University of California at DavisSacramento, CA 95817, USA
| | - Tse-Chun Kuo
- Institute of Molecular and Genomic Medicine, National Health Research InstitutesZhunan, Miaoli 35053, Taiwan
| | - Tsai-Wen Shen
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
| | - Yung-Chih Hong
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Cheng-Han Tsai
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
| | - Yu-Ching Peng
- Department of Pathology and Laboratory Medicine, Taipei Veterans General HospitalTaipei 11217, Taiwan
| | - Chin-Chen Pan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General HospitalTaipei 11217, Taiwan
| | - Muh-Hwa Yang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Jean-Chen Shih
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern CaliforniaLos Angeles, CA 90089, USA
| | - Hsing-Jien Kung
- Comprehensive Cancer Center, University of California at DavisSacramento, CA 95817, USA
- TMU Research Center of Cancer Translational Medicine, Taipei Medical UniversityTaipei 11031, Taiwan
| | - William J Huang
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
| | - Pei-Ching Chang
- Institute of Microbiology and Immunology, National Yang Ming Chiao Tung UniversityHsinchu 30010, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
| | - Tzu-Ping Lin
- Faculty of Medicine, National Yang Ming Chiao Tung UniversityTaipei 11221, Taiwan
- Department of Urology, Taipei Veterans General HospitalTaipei 11217, Taiwan
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12
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Yu T, Hu C, Zhao X, Cai L, Chen B, Lu L, Yang M. Identification of a novel immune-related long noncoding RNA in carp primary macrophages associated with bisphenol A' s immunoregulatory effects. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 262:106656. [PMID: 37595502 DOI: 10.1016/j.aquatox.2023.106656] [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: 04/20/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/20/2023]
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. However, current studies on lncRNAs mostly focus on mammalian species, with little research on the functional roles of lncRNAs in teleost fish. Here, we identified a novel intergenic lncRNA (linc-93.2) in the head kidney primary macrophages of common carp (Cyprinus carpio) after exposure to a typical environmental endocrine disrupting chemical, bisphenol A (BPA). As a result, linc-93.2 was more than 3,619 bp in length and predominantly localized to the nucleus of primary macrophages other than cytoplasm, with the highest expression level in spleen followed by head kidney among different organs. Bioinformatic analysis predicted a cis-target gene, dennd1b, and 20 trans-target genes including hsp70, gna13 and rasgap, were potentially regulated by linc-93.2; NFκB and estrogen receptor (ERα) binding sites were located in the promoter region upstream of its transcription start site, which together suggested the involvement of linc-93.2 in immune and neurological functions in fish. Based on that, the expression level of linc-93.2 was determined in macrophages following acute lipopolysaccharide (LPS) and BPA treatments, both of which significantly induced linc-93.2 and IL-1β expression in cells. Moreover, a NF-κB inhibitor PDTC significantly reduced linc-93.2 expression in macrophages, but co-exposure of macrophages to PDTC with BPA or LPS could significantly rescue linc-93.2 expression, consistent with the observation on that LPS or BPA alone significantly induced both linc-93.2 and its target gene expression. Interestingly, linc-93.2 and its target gene expression was significantly suppressed by an ER antagonist ICI 182,780, however, the co-exposure of macrophages to ICI 182,780 with BPA failed to attenuate their declined expression. Overall, the current study demonstrated that linc-93.2, a novel immune-related lncRNA, may participate in the immune processes of common carp macrophages via the NF-κB and ER pathway. The results presented in this study enhance our understanding of the immunotoxin mechanisms of BPA in teleost fish.
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Affiliation(s)
- Ting Yu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Chengzhang Hu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China; Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China
| | - Xiaoyu Zhao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Ling Cai
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005, China.
| | - Bei Chen
- Fisheries Research Institute of Fujian, Key Laboratory of Cultivation and High-Value Utilization of Marine Organisms in Fujian Province, Xiamen, 361013, China
| | - Lingcan Lu
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China
| | - Ming Yang
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai, 200444, China.
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13
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Sheng N, Huang L, Lu Y, Wang H, Yang L, Gao L, Xie X, Fu Y, Wang Y. Data resources and computational methods for lncRNA-disease association prediction. Comput Biol Med 2023; 153:106527. [PMID: 36610216 DOI: 10.1016/j.compbiomed.2022.106527] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/08/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Increasing interest has been attracted in deciphering the potential disease pathogenesis through lncRNA-disease association (LDA) prediction, regarding to the diverse functional roles of lncRNAs in genome regulation. Whilst, computational models and algorithms benefit systematic biology research, even facilitate the classical biological experimental procedures. In this review, we introduce representative diseases associated with lncRNAs, such as cancers, cardiovascular diseases, and neurological diseases. Current publicly available resources related to lncRNAs and diseases have also been included. Furthermore, all of the 64 computational methods for LDA prediction have been divided into 5 groups, including machine learning-based methods, network propagation-based methods, matrix factorization- and completion-based methods, deep learning-based methods, and graph neural network-based methods. The common evaluation methods and metrics in LDA prediction have also been discussed. Finally, the challenges and future trends in LDA prediction have been discussed. Recent advances in LDA prediction approaches have been summarized in the GitHub repository at https://github.com/sheng-n/lncRNA-disease-methods.
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Affiliation(s)
- Nan Sheng
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
| | - Yuting Lu
- School of Artificial Intelligence, Jilin University, Changchun, China
| | - Hao Wang
- Department of Hepatopancreatobiliary Surgery, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lili Yang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China; Department of Obstetrics, The First Hospital of Jilin University, Changchun, China
| | - Ling Gao
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Xuping Xie
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yuan Fu
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China; School of Artificial Intelligence, Jilin University, Changchun, China.
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14
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Hao M, Qi Y, Xu R, Zhao K, Li M, Shan Y, Xia T, Yang K, Hasi W, Zhang C, Li D, Wang Y, Wang P, Kuang H. ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations. Database (Oxford) 2023; 2023:6991525. [PMID: 36653322 PMCID: PMC9849115 DOI: 10.1093/database/baac113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 01/20/2023]
Abstract
ENCD (http://www.bio-server.cn/ENCD/) is a manually curated database that provides comprehensive experimentally supported associations among endocrine system diseases (ESDs) and long non-coding ribonucleic acid (lncRNAs). The incidence of ESDs has increased in recent years, often accompanying other chronic diseases, and can lead to disability. A growing body of research suggests that lncRNA plays an important role in the progression and metastasis of ESDs. However, there are no resources focused on collecting and integrating the latest and experimentally supported lncRNA-ESD associations. Hence, we developed an ENCD database that consists of 1379 associations between 35 ESDs and 501 lncRNAs in 12 human tissues curated from literature. By using ENCD, users can explore the genetic data for diseases corresponding to the body parts of interest as well as study the lncRNA regulating mechanism for ESDs. ENCD also provides a flexible tool to visualize a disease- or gene-centric regulatory network. In addition, ENCD offers a submission page for researchers to submit their newly discovered endocrine disorders-genetic data entries online. Collectively, ENCD will provide comprehensive insights for investigating the ESDs associated with lncRNAs. Database URL http://www.bio-server.cn/ENCD.
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Affiliation(s)
| | | | | | | | - Mingqing Li
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Yongyan Shan
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Tian Xia
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Kun Yang
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Wuyang Hasi
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Cong Zhang
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Daowei Li
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Yi Wang
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, 23 Youzheng Road, Harbin 150081, China
| | - Peng Wang
- *Corresponding author: Tel: +8645185555060; Fax: +8645185555060; Correspondence may also be addressed to Peng Wang. Tel: +8645186669617; Fax: +8645186669617;
| | - Hongyu Kuang
- *Corresponding author: Tel: +8645185555060; Fax: +8645185555060; Correspondence may also be addressed to Peng Wang. Tel: +8645186669617; Fax: +8645186669617;
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15
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Kretzschmar GC, Targa ADS, Soares-Lima SC, dos Santos PI, Rodrigues LS, Macedo DA, Ribeiro Pinto LF, Lima MMS, Boldt ABW. Folic Acid and Vitamin B12 Prevent Deleterious Effects of Rotenone on Object Novelty Recognition Memory and Kynu Expression in an Animal Model of Parkinson's Disease. Genes (Basel) 2022; 13:genes13122397. [PMID: 36553663 PMCID: PMC9778036 DOI: 10.3390/genes13122397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/10/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Parkinson's disease (PD) is characterized by a range of motor signs, but cognitive dysfunction is also observed. Supplementation with folic acid and vitamin B12 is expected to prevent cognitive impairment. To test this in PD, we promoted a lesion within the substantia nigra pars compacta of rats using the neurotoxin rotenone. In the sequence, the animals were supplemented with folic acid and vitamin B12 for 14 consecutive days and subjected to the object recognition test. We observed an impairment in object recognition memory after rotenone administration, which was prevented by supplementation (p < 0.01). Supplementation may adjust gene expression through efficient DNA methylation. To verify this, we measured the expression and methylation of the kynureninase gene (Kynu), whose product metabolizes neurotoxic metabolites often accumulated in PD as kynurenine. Supplementation prevented the decrease in Kynu expression induced by rotenone in the substantia nigra (p < 0.05), corroborating the behavioral data. No differences were observed concerning the methylation analysis of two CpG sites in the Kynu promoter. Instead, we suggest that folic acid and vitamin B12 increased global DNA methylation, reduced the expression of Kynu inhibitors, maintained Kynu-dependent pathway homeostasis, and prevented the memory impairment induced by rotenone. Our study raises the possibility of adjuvant therapy for PD with folic acid and vitamin B12.
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Affiliation(s)
- Gabriela Canalli Kretzschmar
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Adriano D. S. Targa
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Sheila Coelho Soares-Lima
- Molecular Carcinogenesis Program, National Cancer Institute, Research Coordination, Rio de Janeiro 20231-050, RJ, Brazil
| | - Priscila Ianzen dos Santos
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Lais S. Rodrigues
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Daniel A. Macedo
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Luis Felipe Ribeiro Pinto
- Molecular Carcinogenesis Program, National Cancer Institute, Research Coordination, Rio de Janeiro 20231-050, RJ, Brazil
| | - Marcelo M. S. Lima
- Laboratory of Neurophysiology, Department of Physiology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, Curitiba 81531-990, PR, Brazil
- Correspondence: ; Tel.: +55-(41)-3361-1553
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16
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Li Z, Liu L, Feng C, Qin Y, Xiao J, Zhang Z, Ma L. LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations. Nucleic Acids Res 2022; 51:D186-D191. [PMID: 36330950 PMCID: PMC9825513 DOI: 10.1093/nar/gkac999] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been used in a wide range of lncRNA studies across various biological contexts. Here, we present LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), with significant updates and enhancements as follows: (i) incorporation of 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs; (ii) characterization of conservation features of human lncRNA genes across 40 vertebrates; (iii) integration of lncRNA-encoded small proteins; (iv) enrichment of expression and DNA methylation profiles with more biological contexts and (v) identification of lncRNA-protein interactions and improved prediction of lncRNA-miRNA interactions. Collectively, LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional significance of lncRNAs in different biological contexts.
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Affiliation(s)
| | | | | | - Yuxin Qin
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- National Genomics Data Center & CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China,China National Center for Bioinformation, Beijing 100101, China,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhang Zhang
- Correspondence may also be addressed to Zhang Zhang. Tel: +86 10 8409 7261; Fax: +86 10 8409 7298;
| | - Lina Ma
- To whom correspondence should be addressed. Tel: +86 10 8409 7845; Fax: +86 10 8409 7298;
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17
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Peng L, Wang C, Tian X, Zhou L, Li K. Finding lncRNA-Protein Interactions Based on Deep Learning With Dual-Net Neural Architecture. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3456-3468. [PMID: 34587091 DOI: 10.1109/tcbb.2021.3116232] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The identification of lncRNA-protein interactions (LPIs) is important to understand the biological functions and molecular mechanisms of lncRNAs. However, most computational models are evaluated on a unique dataset, thereby resulting in prediction bias. Furthermore, previous models have not uncovered potential proteins (or lncRNAs) interacting with a new lncRNA (or protein). Finally, the performance of these models can be improved. In this study, we develop a Deep Learning framework with Dual-net Neural architecture to find potential LPIs (LPI-DLDN). First, five LPI datasets are collected. Second, the features of lncRNAs and proteins are extracted by Pyfeat and BioTriangle, respectively. Third, these features are concatenated as a vector after dimension reduction. Finally, a deep learning model with dual-net neural architecture is designed to classify lncRNA-protein pairs. LPI-DLDN is compared with six state-of-the-art LPI prediction methods (LPI-XGBoost, LPI-HeteSim, LPI-NRLMF, PLIPCOM, LPI-CNNCP, and Capsule-LPI) under four cross validations. The results demonstrate the powerful LPI classification performance of LPI-DLDN. Case study analyses show that there may be interactions between RP11-439E19.10 and Q15717, and between RP11-196G18.22 and Q9NUL5. The novelty of LPI-DLDN remains, integrating various biological features, designing a novel deep learning-based LPI identification framework, and selecting the optimal LPI feature subset based on feature importance ranking.
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18
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A review on CRISPR/Cas-based epigenetic regulation in plants. Int J Biol Macromol 2022; 219:1261-1271. [DOI: 10.1016/j.ijbiomac.2022.08.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 08/29/2022] [Indexed: 01/09/2023]
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19
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Guo S, Zhang E, Zhang B, Liu Q, Meng Z, Li Z, Wang C, Gong Z, Wu Y. Identification of Key Non-coding RNAs and Transcription Factors in Calcific Aortic Valve Disease. Front Cardiovasc Med 2022; 9:826744. [PMID: 35845040 PMCID: PMC9276990 DOI: 10.3389/fcvm.2022.826744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Background Calcific aortic valve disease (CAVD) is one of the most frequently occurring valvular heart diseases among the aging population. Currently, there is no known pharmacological treatment available to delay or reverse CAVD progression. The regulation of gene expression could contribute to the initiation, progression, and treatment of CAVD. Non-coding RNAs (ncRNAs) and transcription factors play essential regulatory roles in gene expression in CAVD; thus, further research is urgently needed. Materials and Methods The gene-expression profiles of GSE51472 and GSE12644 were obtained from the Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified in each dataset. A protein-protein-interaction (PPI) network of DEGs was then constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins database, and functional modules were analyzed with ClusterOne plugin in Cytoscape. Furthermore, Gene Ontology-functional annotation and Kyoto Encyclopedia of Genes and Genomes-pathway analysis were conducted for each functional module. Most crucially, ncRNAs and transcription factors acting on each functional module were separately identified using the RNAInter and TRRUST databases. The expression of predicted transcription factors and key genes was validated using GSE51472 and GSE12644. Furthermore, quantitative real-time PCR (qRT-PCR) experiments were performed to validate the differential expression of most promising candidates in human CAVD and control samples. Results Among 552 DEGs, 383 were upregulated and 169 were downregulated. In the PPI network, 15 functional modules involving 182 genes and proteins were identified. After hypergeometric testing, 45 ncRNAs and 33 transcription factors were obtained. Among the predicted transcription factors, CIITA, HIF1A, JUN, POU2F2, and STAT6 were differentially expressed in both the training and validation sets. In addition, we found that key genes, namely, CD2, CD86, CXCL8, FCGR3B, GZMB, ITGB2, LY86, MMP9, PPBP, and TYROBP were also differentially expressed in both the training and validation sets. Among the most promising candidates, differential expressions of ETS1, JUN, NFKB1, RELA, SP1, STAT1, ANCR, and LOC101927497 were identified via qRT-PCR experiments. Conclusion In this study, we identified functional modules with ncRNAs and transcription factors involved in CAVD pathogenesis. The current results suggest candidate molecules for further research on CAVD.
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20
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Carvelli A, Setti A, Desideri F, Galfrè SG, Biscarini S, Santini T, Colantoni A, Peruzzi G, Marzi MJ, Capauto D, Di Angelantonio S, Ballarino M, Nicassio F, Laneve P, Bozzoni I. A multifunctional locus controls motor neuron differentiation through short and long noncoding RNAs. EMBO J 2022; 41:e108918. [PMID: 35698802 PMCID: PMC9251839 DOI: 10.15252/embj.2021108918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 12/12/2022] Open
Abstract
The transition from dividing progenitors to postmitotic motor neurons (MNs) is orchestrated by a series of events, which are mainly studied at the transcriptional level by analyzing the activity of specific programming transcription factors. Here, we identify a post‐transcriptional role of a MN‐specific transcriptional unit (MN2) harboring a lncRNA (lncMN2‐203) and two miRNAs (miR‐325‐3p and miR‐384‐5p) in this transition. Through the use of in vitro mESC differentiation and single‐cell sequencing of CRISPR/Cas9 mutants, we demonstrate that lncMN2‐203 affects MN differentiation by sponging miR‐466i‐5p and upregulating its targets, including several factors involved in neuronal differentiation and function. In parallel, miR‐325‐3p and miR‐384‐5p, co‐transcribed with lncMN2‐203, act by repressing proliferation‐related factors. These findings indicate the functional relevance of the MN2 locus and exemplify additional layers of specificity regulation in MN differentiation.
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Affiliation(s)
- Andrea Carvelli
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Silvia Giulia Galfrè
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Silvia Biscarini
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Capauto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | | | - Monica Ballarino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Nicassio
- Center for Genomic Science of Istituto of Italiano di Tecnologia (IIT), Milan, Italy
| | - Pietro Laneve
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), Rome, Italy.,Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
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21
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Abrishamdar M, Jalali MS, Rashno M. MALAT1 lncRNA and Parkinson's Disease: The role in the Pathophysiology and Significance for Diagnostic and Therapeutic Approaches. Mol Neurobiol 2022; 59:5253-5262. [PMID: 35665903 DOI: 10.1007/s12035-022-02899-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/24/2022] [Indexed: 12/25/2022]
Abstract
Parkinson's disease (PD) is the second most common age-related neurodegenerative disorder. PD is characterized by progressive loss of dopamine-producing neurons in the substantia nigra (SN) region of brain tissue followed by the α-synuclein-based Lewy bodies' formation. These conditions are manifested by various motor and non-motor symptoms such as resting tremor, limb rigidity, bradykinesia and posture instability, cognitive impairment, sleep disorders, and emotional and memory dysfunctions. Long non-coding RNAs (lncRNAs) are closely related to protein-coding genes and are involved in various biological processes. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) lncRNA is involved in different pathways, including alternative splicing, transcriptional regulation, and post-transcriptional regulation, and also interacts with RNAs as a miRNA sponge. MALAT1 is highly expressed in brain tissues and several lines of evidence suggested it is probably involved in synapse generation and other neurophysiological pathways. This narrative review discussed all aspects of MALAT1-associated mechanisms involved in the PD pathogenesis, i.e., perturbed α-synuclein homeostasis, apoptosis and autophagy, and neuro-inflammation. Lastly, the possible applications of MALAT1 as a diagnostic biomarker and its importance to developing therapeutic strategies were highlighted. The literature search was conducted using neurodegeneration, neurodegenerative disorders, Parkinson's disease, lncRNA, and MALAT1 as search items in Google Scholar, Web of Knowledge, PubMed, and Scopus up to December 2021.
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Affiliation(s)
| | - M S Jalali
- Persian Gulf Physiology Research Center, Department of Physiology, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - M Rashno
- Department of Immunulogy, Cellular and Molecular Research Center, Medicine Faculty, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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22
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Peng L, Tan J, Tian X, Zhou L. EnANNDeep: An Ensemble-based lncRNA-protein Interaction Prediction Framework with Adaptive k-Nearest Neighbor Classifier and Deep Models. Interdiscip Sci 2022; 14:209-232. [PMID: 35006529 DOI: 10.1007/s12539-021-00483-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 01/08/2023]
Abstract
lncRNA-protein interactions (LPIs) prediction can deepen the understanding of many important biological processes. Artificial intelligence methods have reported many possible LPIs. However, most computational techniques were evaluated mainly on one dataset, which may produce prediction bias. More importantly, they were validated only under cross validation on lncRNA-protein pairs, and did not consider the performance under cross validations on lncRNAs and proteins, thus fail to search related proteins/lncRNAs for a new lncRNA/protein. Under an ensemble learning framework (EnANNDeep) composed of adaptive k-nearest neighbor classifier and Deep models, this study focuses on systematically finding underlying linkages between lncRNAs and proteins. First, five LPI-related datasets are arranged. Second, multiple source features are integrated to depict an lncRNA-protein pair. Third, adaptive k-nearest neighbor classifier, deep neural network, and deep forest are designed to score unknown lncRNA-protein pairs, respectively. Finally, interaction probabilities from the three predictors are integrated based on a soft voting technique. In comparing to five classical LPI identification models (SFPEL, PMDKN, CatBoost, PLIPCOM, and LPI-SKF) under fivefold cross validations on lncRNAs, proteins, and LPIs, EnANNDeep computes the best average AUCs of 0.8660, 0.8775, and 0.9166, respectively, and the best average AUPRs of 0.8545, 0.8595, and 0.9054, respectively, indicating its superior LPI prediction ability. Case study analyses indicate that SNHG10 may have dense linkage with Q15717. In the ensemble framework, adaptive k-nearest neighbor classifier can separately pick the most appropriate k for each query lncRNA-protein pair. More importantly, deep models including deep neural network and deep forest can effectively learn the representative features of lncRNAs and proteins.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China. .,College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China.
| | - Jingwei Tan
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Xiongfei Tian
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, China.
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23
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Construction of integrative transcriptome to boost systematic exploration of Bougainvillea. Sci Rep 2022; 12:923. [PMID: 35042937 PMCID: PMC8766500 DOI: 10.1038/s41598-022-04984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 12/20/2021] [Indexed: 11/08/2022] Open
Abstract
Members of the genus Bougainvillea are rich sources of natural dyes, pigments, and traditional medicines. They are also commonly used as ornamentals in roadside landscape construction. However, the horticultural development of Bougainvillea flowers with extended growth periods and coloration is not always feasible. One reason is limited molecular knowledge and no genomic information for Bougainvillea. Here, we compiled an integrative transcriptome of all expressed transcripts for Bougainvillea × buttiana Miss Manila by integrating 20 Illumina-sequencing RNA transcriptomes. The integrative transcriptome consisted of 97,623 distinct transcripts. Of these, 47,006 were protein-coding, 31,109 were non-coding, and 19,508 were unannotated. In addition, we affirmed that the integrative transcriptome could serve as a surrogate reference to the genome in aiding accurate transcriptome assembly. For convenience, we curated the integrative transcriptome database for Bougainvillea, namely InTransBo, which can be freely accessed at http://www.bio-add.org/InTransBo/index.jsp . To the best of our knowledge, the present study is the most comprehensive genomic resource for Bougainvillea up-to-date. The integrative transcriptome helps fill the genomic gap and elucidate the transcriptional nature of Bougainvillea. It may also advance progress in the precise regulation of flowering in horticulture. The same strategy can be readily applied toward the systematic exploration of other plant species lacking complete genomic information.
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24
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Wang L, Zhong C. gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network. BMC Bioinformatics 2022; 23:11. [PMID: 34983363 PMCID: PMC8729153 DOI: 10.1186/s12859-021-04548-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/21/2021] [Indexed: 01/20/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs) are related to human diseases by regulating gene expression. Identifying lncRNA-disease associations (LDAs) will contribute to diagnose, treatment, and prognosis of diseases. However, the identification of LDAs by the biological experiments is time-consuming, costly and inefficient. Therefore, the development of efficient and high-accuracy computational methods for predicting LDAs is of great significance. Results In this paper, we propose a novel computational method (gGATLDA) to predict LDAs based on graph-level graph attention network. Firstly, we extract the enclosing subgraphs of each lncRNA-disease pair. Secondly, we construct the feature vectors by integrating lncRNA similarity and disease similarity as node attributes in subgraphs. Finally, we train a graph neural network (GNN) model by feeding the subgraphs and feature vectors to it, and use the trained GNN model to predict lncRNA-disease potential association scores. The experimental results show that our method can achieve higher area under the receiver operation characteristic curve (AUC), area under the precision recall curve (AUPR), accuracy and F1-Score than the state-of-the-art methods in five fold cross-validation. Case studies show that our method can effectively identify lncRNAs associated with breast cancer, gastric cancer, prostate cancer, and renal cancer. Conclusion The experimental results indicate that our method is a useful approach for predicting potential LDAs.
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Affiliation(s)
- Li Wang
- School of Computer Science and Engineering, South China University of Technology, Guangzhou, China.,School of Computer, Electronics and Information, Guangxi University, Nanning, China
| | - Cheng Zhong
- School of Computer, Electronics and Information, Guangxi University, Nanning, China. .,Key Laboratory of Parallel and Distributed Computing in Guangxi Colleges and Universities, Guangxi University, Nanning, China.
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25
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Khan S, Khan M, Iqbal N, Amiruddin Abd Rahman M, Khalis Abdul Karim M. Deep-piRNA: Bi-Layered Prediction Model for PIWI-Interacting RNA Using Discriminative Features. COMPUTERS, MATERIALS & CONTINUA 2022; 72:2243-2258. [DOI: 10.32604/cmc.2022.022901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/11/2021] [Indexed: 09/02/2023]
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26
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Peng L, Yuan R, Shen L, Gao P, Zhou L. LPI-EnEDT: an ensemble framework with extra tree and decision tree classifiers for imbalanced lncRNA-protein interaction data classification. BioData Min 2021; 14:50. [PMID: 34861891 PMCID: PMC8642957 DOI: 10.1186/s13040-021-00277-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/22/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have dense linkages with various biological processes. Identifying interacting lncRNA-protein pairs contributes to understand the functions and mechanisms of lncRNAs. Wet experiments are costly and time-consuming. Most computational methods failed to observe the imbalanced characterize of lncRNA-protein interaction (LPI) data. More importantly, they were measured based on a unique dataset, which produced the prediction bias. RESULTS In this study, we develop an Ensemble framework (LPI-EnEDT) with Extra tree and Decision Tree classifiers to implement imbalanced LPI data classification. First, five LPI datasets are arranged. Second, lncRNAs and proteins are separately characterized based on Pyfeat and BioTriangle and concatenated as a vector to represent each lncRNA-protein pair. Finally, an ensemble framework with Extra tree and decision tree classifiers is developed to classify unlabeled lncRNA-protein pairs. The comparative experiments demonstrate that LPI-EnEDT outperforms four classical LPI prediction methods (LPI-BLS, LPI-CatBoost, LPI-SKF, and PLIPCOM) under cross validations on lncRNAs, proteins, and LPIs. The average AUC values on the five datasets are 0.8480, 0,7078, and 0.9066 under the three cross validations, respectively. The average AUPRs are 0.8175, 0.7265, and 0.8882, respectively. Case analyses suggest that there are underlying associations between HOTTIP and Q9Y6M1, NRON and Q15717. CONCLUSIONS Fusing diverse biological features of lncRNAs and proteins and exploiting an ensemble learning model with Extra tree and decision tree classifiers, this work focus on imbalanced LPI data classification as well as interaction information inference for a new lncRNA (or protein).
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, No.88, Taishan West Road, Tianyuan District, Zhuzhou, China.,College of Life Sciences and Chemistry, Hunan University of Technology, No.88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Ruya Yuan
- School of Computer Science, Hunan University of Technology, No.88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Ling Shen
- School of Computer Science, Hunan University of Technology, No.88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Pengfei Gao
- College of Life Sciences and Chemistry, Hunan University of Technology, No.88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, No.88, Taishan West Road, Tianyuan District, Zhuzhou, China.
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27
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LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification. BMC Bioinformatics 2021; 22:568. [PMID: 34836494 PMCID: PMC8620196 DOI: 10.1186/s12859-021-04485-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/09/2021] [Indexed: 12/03/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have dense linkages with a plethora of important cellular activities. lncRNAs exert functions by linking with corresponding RNA-binding proteins. Since experimental techniques to detect lncRNA-protein interactions (LPIs) are laborious and time-consuming, a few computational methods have been reported for LPI prediction. However, computation-based LPI identification methods have the following limitations: (1) Most methods were evaluated on a single dataset, and researchers may thus fail to measure their generalization ability. (2) The majority of methods were validated under cross validation on lncRNA-protein pairs, did not investigate the performance under other cross validations, especially for cross validation on independent lncRNAs and independent proteins. (3) lncRNAs and proteins have abundant biological information, how to select informative features need to further investigate. Results Under a hybrid framework (LPI-HyADBS) integrating feature selection based on AdaBoost, and classification models including deep neural network (DNN), extreme gradient Boost (XGBoost), and SVM with a penalty Coefficient of misclassification (C-SVM), this work focuses on finding new LPIs. First, five datasets are arranged. Each dataset contains lncRNA sequences, protein sequences, and an LPI network. Second, biological features of lncRNAs and proteins are acquired based on Pyfeat. Third, the obtained features of lncRNAs and proteins are selected based on AdaBoost and concatenated to depict each LPI sample. Fourth, DNN, XGBoost, and C-SVM are used to classify lncRNA-protein pairs based on the concatenated features. Finally, a hybrid framework is developed to integrate the classification results from the above three classifiers. LPI-HyADBS is compared to six classical LPI prediction approaches (LPI-SKF, LPI-NRLMF, Capsule-LPI, LPI-CNNCP, LPLNP, and LPBNI) on five datasets under 5-fold cross validations on lncRNAs, proteins, lncRNA-protein pairs, and independent lncRNAs and independent proteins. The results show LPI-HyADBS has the best LPI prediction performance under four different cross validations. In particular, LPI-HyADBS obtains better classification ability than other six approaches under the constructed independent dataset. Case analyses suggest that there is relevance between ZNF667-AS1 and Q15717. Conclusions Integrating feature selection approach based on AdaBoost, three classification techniques including DNN, XGBoost, and C-SVM, this work develops a hybrid framework to identify new linkages between lncRNAs and proteins. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04485-x.
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Takeiwa T, Mitobe Y, Ikeda K, Hasegawa K, Horie K, Inoue S. Long Intergenic Noncoding RNA OIN1 Promotes Ovarian Cancer Growth by Modulating Apoptosis-Related Gene Expression. Int J Mol Sci 2021; 22:ijms222011242. [PMID: 34681900 PMCID: PMC8541687 DOI: 10.3390/ijms222011242] [Citation(s) in RCA: 3] [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: 09/21/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 12/22/2022] Open
Abstract
Patients with advanced ovarian cancer usually exhibit high mortality rates, thus more efficient therapeutic strategies are expected to be developed. Recent transcriptomic studies revealed that long intergenic noncoding RNAs (lincRNAs) can be a new class of molecular targets for cancer management, because lincRNAs likely exert tissue-specific activities compared with protein-coding genes or other noncoding RNAs. We here show that an unannotated lincRNA originated from chromosome 10q21 and designated as ovarian cancer long intergenic noncoding RNA 1 (OIN1), is often overexpressed in ovarian cancer tissues compared with normal ovaries as analyzed by RNA sequencing. OIN1 silencing by specific siRNAs significantly exerted proliferation inhibition and enhanced apoptosis in ovarian cancer cells. Notably, RNA sequencing showed that OIN1 expression was negatively correlated with the expression of apoptosis-related genes ras association domain family member 5 (RASSF5) and adenosine A1 receptor (ADORA1), which were upregulated by OIN1 knockdown in ovarian cancer cells. OIN1-specifc siRNA injection was effective to suppress in vivo tumor growth of ovarian cancer cells inoculated in immunodeficient mice. Taken together, OIN1 could function as a tumor-promoting lincRNA in ovarian cancer through modulating apoptosis and will be a potential molecular target for ovarian cancer management.
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Affiliation(s)
- Toshihiko Takeiwa
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (T.T.); (Y.M.); (K.I.)
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
| | - Yuichi Mitobe
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (T.T.); (Y.M.); (K.I.)
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (T.T.); (Y.M.); (K.I.)
| | - Kosei Hasegawa
- Department of Gynecologic Oncology, Saitama Medical University International Medical Center, Hidaka, Saitama 350-1298, Japan;
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (T.T.); (Y.M.); (K.I.)
- Correspondence: (K.H.); (S.I.); Tel.: +81-42-984-4606 (K.H.); +81-3-3964-3241 (S.I.)
| | - Satoshi Inoue
- Division of Systems Medicine & Gene Therapy, Saitama Medical University, Hidaka, Saitama 350-1241, Japan; (T.T.); (Y.M.); (K.I.)
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo 173-0015, Japan
- Correspondence: (K.H.); (S.I.); Tel.: +81-42-984-4606 (K.H.); +81-3-3964-3241 (S.I.)
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29
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Zhou L, Wang Z, Tian X, Peng L. LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA-protein interaction identification. BMC Bioinformatics 2021; 22:479. [PMID: 34607567 PMCID: PMC8489074 DOI: 10.1186/s12859-021-04399-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/14/2021] [Indexed: 12/31/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) play important roles in various biological and pathological processes. Discovery of lncRNA–protein interactions (LPIs) contributes to understand the biological functions and mechanisms of lncRNAs. Although wet experiments find a few interactions between lncRNAs and proteins, experimental techniques are costly and time-consuming. Therefore, computational methods are increasingly exploited to uncover the possible associations. However, existing computational methods have several limitations. First, majority of them were measured based on one simple dataset, which may result in the prediction bias. Second, few of them are applied to identify relevant data for new lncRNAs (or proteins). Finally, they failed to utilize diverse biological information of lncRNAs and proteins. Results Under the feed-forward deep architecture based on gradient boosting decision trees (LPI-deepGBDT), this work focuses on classify unobserved LPIs. First, three human LPI datasets and two plant LPI datasets are arranged. Second, the biological features of lncRNAs and proteins are extracted by Pyfeat and BioProt, respectively. Thirdly, the features are dimensionally reduced and concatenated as a vector to represent an lncRNA–protein pair. Finally, a deep architecture composed of forward mappings and inverse mappings is developed to predict underlying linkages between lncRNAs and proteins. LPI-deepGBDT is compared with five classical LPI prediction models (LPI-BLS, LPI-CatBoost, PLIPCOM, LPI-SKF, and LPI-HNM) under three cross validations on lncRNAs, proteins, lncRNA–protein pairs, respectively. It obtains the best average AUC and AUPR values under the majority of situations, significantly outperforming other five LPI identification methods. That is, AUCs computed by LPI-deepGBDT are 0.8321, 0.6815, and 0.9073, respectively and AUPRs are 0.8095, 0.6771, and 0.8849, respectively. The results demonstrate the powerful classification ability of LPI-deepGBDT. Case study analyses show that there may be interactions between GAS5 and Q15717, RAB30-AS1 and O00425, and LINC-01572 and P35637. Conclusions Integrating ensemble learning and hierarchical distributed representations and building a multiple-layered deep architecture, this work improves LPI prediction performance as well as effectively probes interaction data for new lncRNAs/proteins.
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Affiliation(s)
- Liqian Zhou
- School of Computer Science, Hunan University of Technology, No. 88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Zhao Wang
- School of Computer Science, Hunan University of Technology, No. 88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Xiongfei Tian
- School of Computer Science, Hunan University of Technology, No. 88, Taishan West Road, Tianyuan District, Zhuzhou, China
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, No. 88, Taishan West Road, Tianyuan District, Zhuzhou, China. .,College of Life Sciences and Chemistry, Hunan University of Technology, No. 88, Taishan West Road, Tianyuan District, Zhuzhou, China.
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30
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Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, Karimi M, Soorni A. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 2021; 22:704. [PMID: 34587906 PMCID: PMC8482690 DOI: 10.1186/s12864-021-07989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07989-1.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Marzieh Karimi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, Shahrekord, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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31
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Tian X, Shen L, Wang Z, Zhou L, Peng L. A novel lncRNA-protein interaction prediction method based on deep forest with cascade forest structure. Sci Rep 2021; 11:18881. [PMID: 34556758 PMCID: PMC8460650 DOI: 10.1038/s41598-021-98277-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 08/18/2021] [Indexed: 02/08/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate many biological processes by interacting with corresponding RNA-binding proteins. The identification of lncRNA-protein Interactions (LPIs) is significantly important to well characterize the biological functions and mechanisms of lncRNAs. Existing computational methods have been effectively applied to LPI prediction. However, the majority of them were evaluated only on one LPI dataset, thereby resulting in prediction bias. More importantly, part of models did not discover possible LPIs for new lncRNAs (or proteins). In addition, the prediction performance remains limited. To solve with the above problems, in this study, we develop a Deep Forest-based LPI prediction method (LPIDF). First, five LPI datasets are obtained and the corresponding sequence information of lncRNAs and proteins are collected. Second, features of lncRNAs and proteins are constructed based on four-nucleotide composition and BioSeq2vec with encoder-decoder structure, respectively. Finally, a deep forest model with cascade forest structure is developed to find new LPIs. We compare LPIDF with four classical association prediction models based on three fivefold cross validations on lncRNAs, proteins, and LPIs. LPIDF obtains better average AUCs of 0.9012, 0.6937 and 0.9457, and the best average AUPRs of 0.9022, 0.6860, and 0.9382, respectively, for the three CVs, significantly outperforming other methods. The results show that the lncRNA FTX may interact with the protein P35637 and needs further validation.
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Affiliation(s)
- Xiongfei Tian
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China
| | - Ling Shen
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China
| | - Zhenwu Wang
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China
| | - Liqian Zhou
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China.
| | - Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, 412007, China.
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32
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Far from the nuclear crowd: Cytoplasmic lncRNA and their implications in synaptic plasticity and memory. Neurobiol Learn Mem 2021; 185:107522. [PMID: 34547434 DOI: 10.1016/j.nlm.2021.107522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/20/2021] [Accepted: 09/10/2021] [Indexed: 11/20/2022]
Abstract
A striking proportion of long non-coding RNAs are expressed specifically in the mammalian brain. Advances in genome-wide sequencing detected widespread diversity in neuronal lncRNAs based on their expression pattern, localization and function. A growing body of literature proposes that localization of lncRNAs is a critical determinant of their function. A rising number of recent findings documented distinct cytoplasmic functions of lncRNAs that are linked to activity-induced control of synaptic plasticity. However, the comprehensive role of cytoplasmic lncRNAs in neuronal functions is less understood. This review surveys our current understanding of lncRNAs that regulate the cytoplasmic life of mRNAs. We discuss the necessity of subcellular localization of lncRNAs in neuronal dendrites and the impact of their compartmentalized positioning on localized translation at the synapse. We have highlighted how lncRNAs modify a functional compartment to meet the demand for input-specific control of synaptic plasticity and memory.
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Keihani S, Kluever V, Fornasiero EF. Brain Long Noncoding RNAs: Multitask Regulators of Neuronal Differentiation and Function. Molecules 2021; 26:molecules26133951. [PMID: 34203457 PMCID: PMC8272081 DOI: 10.3390/molecules26133951] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
The extraordinary cellular diversity and the complex connections established within different cells types render the nervous system of vertebrates one of the most sophisticated tissues found in living organisms. Such complexity is ensured by numerous regulatory mechanisms that provide tight spatiotemporal control, robustness and reliability. While the unusual abundance of long noncoding RNAs (lncRNAs) in nervous tissues was traditionally puzzling, it is becoming clear that these molecules have genuine regulatory functions in the brain and they are essential for neuronal physiology. The canonical view of RNA as predominantly a 'coding molecule' has been largely surpassed, together with the conception that lncRNAs only represent 'waste material' produced by cells as a side effect of pervasive transcription. Here we review a growing body of evidence showing that lncRNAs play key roles in several regulatory mechanisms of neurons and other brain cells. In particular, neuronal lncRNAs are crucial for orchestrating neurogenesis, for tuning neuronal differentiation and for the exact calibration of neuronal excitability. Moreover, their diversity and the association to neurodegenerative diseases render them particularly interesting as putative biomarkers for brain disease. Overall, we foresee that in the future a more systematic scrutiny of lncRNA functions will be instrumental for an exhaustive understanding of neuronal pathophysiology.
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34
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Bella F, Campo S. Long non-coding RNAs and their involvement in bipolar disorders. Gene 2021; 796-797:145803. [PMID: 34175394 DOI: 10.1016/j.gene.2021.145803] [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: 03/03/2021] [Accepted: 06/22/2021] [Indexed: 01/22/2023]
Abstract
Non-coding RNAs (nc-RNAs) can be defined as RNA molecules that are not translated into proteins. Although the functional meaning of many nc-RNAs remains still to be verified, several of these molecules have a clear biological importance, which goes from translation of mRNAs to DNA replication. Indeed, regulatory nc-RNAs can be classified into two groups: short non-coding RNAs (sncRNAs) and long-non coding RNAs (lncRNAs). In the last years, lncRNAs have gained increasing importance in the study of gene regulation, helping authors understand the molecular mechanisms underlying cellular physiology and pathology. LncRNAs are greater than 200 bp and accumulate in nucleus, cytoplasm and exosomes with high tissue specificity, acting in cis or in trans in order to exert enhancer or silencer modulation on gene expression. Such regulatory features, which are widespread in human cells and tissues, can be disrupted in several morbid states. Recent evidences may suggest a disruption of lncRNAs in bipolar disorders, a cluster of severe, chronic and disabling psychiatric diseases, which are characterized by major depressive states cyclically alternating with manic episodes. Here, the authors reviewed genes, classification, biogenesis, structures, functions and databases regarding lncRNAs, and also focused on bipolar disorders, in which some lncRNAs, especially those involved in inflammation and neuronal development, has reported to be dysregulated.
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Affiliation(s)
- Fabrizio Bella
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy
| | - Salvatore Campo
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy.
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Zhang Q, Wu E, Tang Y, Cai T, Zhang L, Wang J, Hao Y, Zhang B, Zhou Y, Guo X, Luo J, Chen R, Yang F. Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs. Mol Cell Proteomics 2021; 20:100109. [PMID: 34129944 PMCID: PMC8335655 DOI: 10.1016/j.mcpro.2021.100109] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Many small ORFs embedded in long noncoding RNA (lncRNA) transcripts have been shown to encode biologically functional polypeptides (small ORF-encoded polypeptides [SEPs]) in different organisms. Despite some novel SEPs have been found, the identification is still hampered by their poor predictability, diminutive size, and low relative abundance. Here, we take advantage of NONCODE, a repository containing the most complete collection and annotation of lncRNA transcripts from different species, to build a novel database that attempts to maximize a collection of SEPs from human and mouse lncRNA transcripts. In order to further improve SEP discovery, we implemented two effective and complementary polypeptide enrichment strategies using 30-kDa molecular weight cutoff filter and C8 solid-phase extraction column. These combined strategies enabled us to discover 353 SEPs from eight human cell lines and 409 SEPs from three mouse cell lines and eight mouse tissues. Importantly, 19 of them were then verified through in vitro expression, immunoblotting, parallel reaction monitoring, and synthetic peptides. Subsequent bioinformatics analysis revealed that some of the physical and chemical properties of these novel SEPs, including amino acid composition and codon usage, are different from those commonly found in canonical proteins. Intriguingly, nearly 65% of the identified SEPs were found to be initiated with non-AUG start codons. The 762 novel SEPs probably represent the largest number of SEPs detected by MS reported to date. These novel SEPs might not only provide new clues for the annotation of noncoding elements in the genome but also serve as a valuable resource for functional study.
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Affiliation(s)
- Qing Zhang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Erzhong Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yiheng Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tanxi Cai
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lili Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jifeng Wang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yajing Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Bao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yue Zhou
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Thermofisher Scientific, Shanghai, China
| | - Xiaojing Guo
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianjun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Runsheng Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Guangdong Geneway Decoding Bio-Tech Co Ltd, Foshan, China.
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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36
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Multi-omics annotation of human long non-coding RNAs. Biochem Soc Trans 2021; 48:1545-1556. [PMID: 32756901 DOI: 10.1042/bst20191063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
LncRNAs (long non-coding RNAs) are pervasively transcribed in the human genome and also extensively involved in a variety of essential biological processes and human diseases. The comprehensive annotation of human lncRNAs is of great significance in navigating the functional landscape of the human genome and deepening the understanding of the multi-featured RNA world. However, the unique characteristics of lncRNAs as well as their enormous quantity have complicated and challenged the annotation of lncRNAs. Advances in high-throughput sequencing technologies give rise to a large volume of omics data that are generated at an unprecedented rate and scale, providing possibilities in the identification, characterization and functional annotation of lncRNAs. Here, we review the recent important discoveries of human lncRNAs through analysis of various omics data and summarize specialized lncRNA database resources. Moreover, we highlight the multi-omics integrative analysis as a powerful strategy to efficiently discover and characterize the functional lncRNAs and elucidate their potential molecular mechanisms.
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Zhang J, Li Y, Liu Y, Xu G, Hei Y, Lu X, Liu W. Long non‑coding RNA NEAT1 regulates glioma cell proliferation and apoptosis by competitively binding to microRNA‑324‑5p and upregulating KCTD20 expression. Oncol Rep 2021; 46:125. [PMID: 33982764 PMCID: PMC8129970 DOI: 10.3892/or.2021.8076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Previous studies have demonstrated that long non‑coding RNAs (lncRNAs) serve a key role in the development and progression of several types of cancer, including glioma. The lncRNA nuclear paraspeckle assembly transcript 1 (NEAT1) contributes to cancer growth through its effects on cell proliferation, migration, invasion and drug resistance. However, the exact regulatory mechanisms via which NEAT1 acts in glioma are unclear. In the present study, the expression levels and function of NEAT1 in glioma tissues and cell lines were examined in vitro and in vivo. By reverse transcription‑quantitative PCR and fluorescence in situ hybridization analysis, NEAT1 expression was upregulated in glioma tissues compared with in adjacent normal brain tissues, and elevated NEAT1 levels were associated with poor prognosis. Cell Counting Kit‑8, colony formation, ethynyldeoxyuridine, flow cytometry and western blotting assays were performed to detect the effects of NEAT1 on cell biological behavior. Knockdown of NEAT1 in glioma cell lines was associated with cell cycle arrest at the G0/G1 phase, decreased proliferation and elevated apoptosis in vitro, and resulted in reduced tumor growth and increased survival in a mouse xenograft model of glioma. Using bioinformatics analysis, RNA immunoprecipitation experiments and luciferase reporter assays, it was demonstrated that NEAT1 may competitively bind to microRNA (miR)‑324‑5p, thus blocking its interaction with target mRNAs. Potassium channel tetramerization protein domain containing 20 (KCTD20) was identified as a specific miR‑324‑5p target. Accordingly, the inhibition of NEAT1 resulted in the downregulation of KCTD20 through competitive binding with miR‑324‑5p, decreased cell proliferation and increased apoptosis. Concomitant NEAT1 knockdown and inhibition of miR‑324‑5p partially reversed the effects of NEAT1 knockdown on cell proliferation and apoptosis, and further regulated KCTD20 expression. Collectively, the present findings demonstrated that NEAT1 acted as a competing endogenous RNA for miR‑324‑5p, and identified the NEAT1/miR‑324‑5p/KCTD20 axis as a novel regulatory axis and a potential therapeutic target for human glioma.
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Affiliation(s)
- Jiale Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yangyang Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Yuqi Liu
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Guangzhi Xu
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yue Hei
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Xiaoming Lu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210029, P.R. China
| | - Weiping Liu
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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Chen Q, Lai D, Lan W, Wu X, Chen B, Liu J, Chen YPP, Wang J. ILDMSF: Inferring Associations Between Long Non-Coding RNA and Disease Based on Multi-Similarity Fusion. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1106-1112. [PMID: 31443046 DOI: 10.1109/tcbb.2019.2936476] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The dysregulation and mutation of long non-coding RNAs (lncRNAs) have been proved to result in a variety of human diseases. Identifying potential disease-related lncRNAs may benefit disease diagnosis, treatment and prognosis. A number of methods have been proposed to predict the potential lncRNA-disease relationships. However, most of them may give rise to incorrect results due to relying on single similarity measure. This article proposes a novel framework (ILDMSF) by fusing the lncRNA similarities and disease similarities, which are measured by lncRNA-related gene and known lncRNA-disease interaction and disease semantic interaction, and known lncRNA-disease interaction, respectively. Further, the support vector machine is employed to identify the potential lncRNA-disease associations based on the integrated similarity. The leave-one-out cross validation is performed to compare ILDMSF with other state of the art methods. The experimental results demonstrate our method is prospective in exploring potential correlations between lncRNA and disease.
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Shen K, Li R, Zhang X, Qu G, Li R, Wang Y, Liu B, Lv C, Li M, Song X. Acetyl oxygen benzoate engeletin ester promotes KLF4 degradation leading to the attenuation of pulmonary fibrosis via inhibiting TGFβ1-smad/p38MAPK-lnc865/lnc556-miR-29b-2-5p-STAT3 signal pathway. Aging (Albany NY) 2021; 13:13807-13821. [PMID: 33929970 PMCID: PMC8202900 DOI: 10.18632/aging.202975] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/02/2021] [Indexed: 11/25/2022]
Abstract
Pulmonary fibrosis is a common pulmonary interstitial disease of pathogenesis without effective drugs for treatment. Therefore, discovering new and effective drugs is urgently needed. In the present study, we prepared a novel compound named acetyl oxygen benzoate engeletin ester (AOBEE), investigated its effect on experimental pulmonary fibrosis, and proposed a long non-coding RNA (lncRNA)-mediated mechanism of its action. Bleomycin-induced pulmonary fibrosis in mice exhibited that AOBEE improved forced vital capacity (FVC) and alveolar structure and inhibited α-SMA, vimentin, and collagen expression. TGFβ1-stimulated fibroblast L929 cells showed that AOBEE reduced these fibrotic proteins expression and inhibited the activated-fibroblast proliferation and migration. Whole transcriptome sequencing was performed to screen out lncRNA-lnc865 and lnc556 with high expression under bleomycin treatment, but AOBEE caused a considerable decrease in lnc865 and lnc556. Mechanistic study elucidated that AOBEE alleviated pulmonary fibrosis through lnc865- and lnc556-mediated mechanism, in which both lnc865 and lnc556 sponged miR-29b-2-5p to target signal transducer and activator of transcription 3 (STAT3). Further signal pathway inhibitors and the Cignal Finder 45-pathway reporter array illustrated that the up- and downstream pathways were TGFβ1-smad2/3 and p38MAPK, and Krüppel-like factor 4 (KLF4), respectively. In conclusion, AOBEE promoted KLF4 degradation leading to the attenuation of pulmonary fibrosis by inhibiting TGFβ1-smad/p38MAPK-lnc865/lnc556-miR-29b-2-5p-STAT3 signal pathway. We hope this work will provide valuable information to design new drugs and therapeutic targets of lncRNAs for pulmonary fibrosis treatment.
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Affiliation(s)
- Ke Shen
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Ruiqiong Li
- School of Nursing, Binzhou Medical University, Yantai 264003, China
| | - Xiaoli Zhang
- School of Nursing, Binzhou Medical University, Yantai 264003, China
| | - Guiwu Qu
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Rongrong Li
- Department of Respiratory Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256602, China
| | - Youlei Wang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Bo Liu
- Department of Respiratory Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256602, China
| | - Changjun Lv
- Department of Respiratory Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou 256602, China
| | - Minge Li
- School of Nursing, Binzhou Medical University, Yantai 264003, China
| | - Xiaodong Song
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
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Mishra SK, Wang H. Computational Analysis Predicts Hundreds of Coding lncRNAs in Zebrafish. BIOLOGY 2021; 10:biology10050371. [PMID: 33925925 PMCID: PMC8145020 DOI: 10.3390/biology10050371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Noncoding RNAs (ncRNAs) regulate a variety of fundamental life processes such as development, physiology, metabolism and circadian rhythmicity. RNA-sequencing (RNA-seq) technology has facilitated the sequencing of the whole transcriptome, thereby capturing and quantifying the dynamism of transcriptome-wide RNA expression profiles. However, much remains unrevealed in the huge noncoding RNA datasets that require further bioinformatic analysis. In this study, we applied six bioinformatic tools to investigate coding potentials of approximately 21,000 lncRNAs. A total of 313 lncRNAs are predicted to be coded by all the six tools. Our findings provide insights into the regulatory roles of lncRNAs and set the stage for the functional investigation of these lncRNAs and their encoded micropeptides. Abstract Recent studies have demonstrated that numerous long noncoding RNAs (ncRNAs having more than 200 nucleotide base pairs (lncRNAs)) actually encode functional micropeptides, which likely represents the next regulatory biology frontier. Thus, identification of coding lncRNAs from ever-increasing lncRNA databases would be a bioinformatic challenge. Here we employed the Coding Potential Alignment Tool (CPAT), Coding Potential Calculator 2 (CPC2), LGC web server, Coding-Non-Coding Identifying Tool (CNIT), RNAsamba, and MicroPeptide identification tool (MiPepid) to analyze approximately 21,000 zebrafish lncRNAs and computationally to identify 2730–6676 zebrafish lncRNAs with high coding potentials, including 313 coding lncRNAs predicted by all the six bioinformatic tools. We also compared the sensitivity and specificity of these six bioinformatic tools for identifying lncRNAs with coding potentials and summarized their strengths and weaknesses. These predicted zebrafish coding lncRNAs set the stage for further experimental studies.
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Affiliation(s)
- Shital Kumar Mishra
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China;
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, China;
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, China
- Correspondence: or ; Tel.: +86-512-6588-2115
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Li J, Fan S, Liu S, Yang G, Jin Q, Xiao Z. LncRNA NOP14-AS1 Promotes Tongue Squamous Cell Carcinoma Progression by Targeting MicroRNA-665/HMGB3 Axis. Cancer Manag Res 2021; 13:2821-2834. [PMID: 33814931 PMCID: PMC8009347 DOI: 10.2147/cmar.s293322] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/04/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose The expression profile, clinical effects, and detailed roles of NOP14 antisense RNA 1 (NOP14-AS1) in tongue squamous cell carcinoma (TSCC) remain ambiguous and need to be further explored. Thus, this work was initiated to offer further solid evidence regarding the expression and roles of NOP14-AS1 in TSCC. Furthermore, additional efforts were exerted to reveal the molecular events by which NOP14-AS1 affects the malignant behaviours of TSCC. Methods NOP14-AS1 expression was detected in TSCC tissues and cell lines using quantitative reverse transcription-polymerase chain reaction. Cell Counting Kit-8 assay, flow cytometric analysis, Transwell migration and invasion assays, and xenograft tumor model analysis were performed to assess the malignant biological behaviors of TSCC cells after NOP14-AS1 depletion. Mechanistic studies were performed using bioinformatics analysis, luciferase reporter assay, RNA immunoprecipitation, and rescue experiments. Results NOP14-AS1 upregulation was identified in TSCC tissues and cell lines. Patients with TSCC exhibiting a high NOP14-AS1 expression faced shorter overall survival than those with a low NOP14-AS1 expression. Functionally, NOP14-AS1 depletion facilitated apoptosis and impeded cell proliferation, migration, and invasion in TSCC. In vivo, the growth of TSCC cells was hindered by NOP14-AS1 depletion. Mechanically, NOP14-AS1 functioned as a competing endogenous RNA by sponging microRNA-665 (miR-665), thereby overexpressing the target high mobility group box 3 (HMGB3) of miR-665. Lastly, rescue experiments confirmed that the introduction of HMGB3 overexpression plasmid or miR-665 inhibitor could abrogate the inhibition of aggressive phenotypes triggered by NOP14-AS1 knockdown. Conclusion NOP14-AS1 executed pro-oncogenic activities in TSCC cells by targeting the miR-665/HMGB3 axis. The NOP14-AS1/miR-665/HMGB pathway may be a valuable prognostic indicator and therapeutic target for preventing TSCC.
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Affiliation(s)
- Jiayi Li
- Department of Stomatology, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, Heilongjiang, 161000, People's Republic of China
| | - Shuxia Fan
- Department of Stomatology, Qiqihaer Eye & ENT Hospital, Qiqihar, Heilongjiang, 161000, People's Republic of China
| | - Shuang Liu
- Department of Stomatology, The First Hospital of Qiqihar (The Affiliated Qiqihar Hospital of Southern Medical University), Qiqihar, Heilongjiang, 161000, People's Republic of China
| | - Guang Yang
- Department of Stomatology, The First Hospital of Qiqihar (The Affiliated Qiqihar Hospital of Southern Medical University), Qiqihar, Heilongjiang, 161000, People's Republic of China
| | - Qingsong Jin
- Department of Stomatology, The First Hospital of Qiqihar (The Affiliated Qiqihar Hospital of Southern Medical University), Qiqihar, Heilongjiang, 161000, People's Republic of China
| | - Zhen Xiao
- Department of Stomatology, The First Hospital of Qiqihar (The Affiliated Qiqihar Hospital of Southern Medical University), Qiqihar, Heilongjiang, 161000, People's Republic of China
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Corradi C, Gentiluomo M, Gajdán L, Cavestro GM, Kreivenaite E, Di Franco G, Sperti C, Giaccherini M, Petrone MC, Tavano F, Gioffreda D, Morelli L, Soucek P, Andriulli A, Izbicki JR, Napoli N, Małecka-Panas E, Hegyi P, Neoptolemos JP, Landi S, Vashist Y, Pasquali C, Lu Y, Cervena K, Theodoropoulos GE, Moz S, Capurso G, Strobel O, Carrara S, Hackert T, Hlavac V, Archibugi L, Oliverius M, Vanella G, Vodicka P, Arcidiacono PG, Pezzilli R, Milanetto AC, Lawlor RT, Ivanauskas A, Szentesi A, Kupcinskas J, Testoni SGG, Lovecek M, Nentwich M, Gazouli M, Luchini C, Zuppardo RA, Darvasi E, Brenner H, Gheorghe C, Jamroziak K, Canzian F, Campa D. Genome-wide scan of long noncoding RNA single nucleotide polymorphisms and pancreatic cancer susceptibility. Int J Cancer 2021; 148:2779-2788. [PMID: 33534179 DOI: 10.1002/ijc.33475] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 02/05/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is projected to become the second cancer-related cause of death by 2030. Identifying novel risk factors, including genetic risk loci, could be instrumental in risk stratification and implementation of prevention strategies. Long noncoding RNAs (lncRNAs) are involved in regulation of key biological processes, and the possible role of their genetic variability has been unexplored so far. Combining genome wide association studies and functional data, we investigated the genetic variability in all lncRNAs. We analyzed 9893 PDAC cases and 9969 controls and identified a genome-wide significant association between the rs7046076 SNP and risk of developing PDAC (P = 9.73 × 10-9 ). This SNP is located in the NONHSAG053086.2 (lnc-SMC2-1) gene and the risk allele is predicted to disrupt the binding of the lncRNA with the micro-RNA (miRNA) hsa-mir-1256 that regulates several genes involved in cell cycle, such as CDKN2B. The CDKN2B region is pleiotropic and its genetic variants have been associated with several human diseases, possibly though an imperfect interaction between lncRNA and miRNA. We present a novel PDAC risk locus, supported by a genome-wide statistical significance and a plausible biological mechanism.
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Affiliation(s)
| | | | - László Gajdán
- Szent György University Teaching Hospital of Fejér County, Székesfehérvár, Hungary
| | - Giulia Martina Cavestro
- Division of Experimental Oncology, Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Edita Kreivenaite
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gregorio Di Franco
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Cosimo Sperti
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padova, Italy
| | | | - Maria Chiara Petrone
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Domenica Gioffreda
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Luca Morelli
- General Surgery Unit, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Angelo Andriulli
- Division of Gastroenterology and Research Laboratory, IRCCS Scientific Institute and Regional General Hospital "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Niccolò Napoli
- UO Chirurgia Generale e dei Trapianti, Università di Pisa, Pisa, Italy
| | - Ewa Małecka-Panas
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Péter Hegyi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary.,First Department of Medicine, University of Szeged, Szeged, Hungary
| | - John P Neoptolemos
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudio Pasquali
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padova, Italy
| | - Ye Lu
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klara Cervena
- Institute of Biology and Medical Genetics, First Medical Faculty, Prague, Czech Republic.,Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - George E Theodoropoulos
- Colorectal Unit, First Department of Propaedeutic Surgery, Athens Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Stefania Moz
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padova, Italy
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Sant'Andrea Hospital, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Oliver Strobel
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Silvia Carrara
- Department of Gastroenterology, IRCCS Humanitas Research Hospital - Endoscopic Unit, Milan, Italy
| | - Thilo Hackert
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Viktor Hlavac
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Sant'Andrea Hospital, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Martin Oliverius
- Department of Surgery, Faculty Hospital Kralovske Vinohrady and Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Giuseppe Vanella
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Sant'Andrea Hospital, Faculty of Medicine and Psychology, Sapienza University of Rome, Rome, Italy
| | - Pavel Vodicka
- Institute of Biology and Medical Genetics, First Medical Faculty, Prague, Czech Republic.,Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Anna Caterina Milanetto
- Department of Surgery, Oncology and Gastroenterology-DiSCOG, University of Padova, Padova, Italy
| | - Rita T Lawlor
- ARC-NET: Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Audrius Ivanauskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Andrea Szentesi
- Institute for Translational Medicine, Medical School, University of Pécs, Pécs, Hungary.,First Department of Medicine, University of Szeged, Szeged, Hungary
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sabrina G G Testoni
- Pancreato-Biliary Endoscopy and Endosonography Division, Pancreas Translational and Clinical Research Center, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Martin Lovecek
- Department of Surgery I, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Michael Nentwich
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of pathology, University of Verona, Verona, Italy
| | - Raffaella Alessia Zuppardo
- Division of Experimental Oncology, Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Erika Darvasi
- First Department of Medicine, University of Szeged, Szeged, Hungary
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Cristian Gheorghe
- Center of Gastroenterology, Fundeni Clinical Institute, Bucharest, Romania
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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Li Z, Liu L, Jiang S, Li Q, Feng C, Du Q, Zou D, Xiao J, Zhang Z, Ma L. LncExpDB: an expression database of human long non-coding RNAs. Nucleic Acids Res 2021; 49:D962-D968. [PMID: 33045751 PMCID: PMC7778919 DOI: 10.1093/nar/gkaa850] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/12/2020] [Accepted: 09/22/2020] [Indexed: 12/14/2022] Open
Abstract
Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes' expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.
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Affiliation(s)
- Zhao Li
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Liu
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Shuai Jiang
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qianpeng Li
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Changrui Feng
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Qiang Du
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Zou
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Zhang
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100101, China
| | - Lina Ma
- China National Center for Bioinformation, Beijing 100101, China.,National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
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44
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Zhao L, Wang J, Li Y, Song T, Wu Y, Fang S, Bu D, Li H, Sun L, Pei D, Zheng Y, Huang J, Xu M, Chen R, Zhao Y, He S. NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. Nucleic Acids Res 2021; 49:D165-D171. [PMID: 33196801 PMCID: PMC7779048 DOI: 10.1093/nar/gkaa1046] [Citation(s) in RCA: 150] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
NONCODE (http://www.noncode.org/) is a comprehensive database of collection and annotation of noncoding RNAs, especially long non-coding RNAs (lncRNAs) in animals. NONCODEV6 is dedicated to providing the full scope of lncRNAs across plants and animals. The number of lncRNAs in NONCODEV6 has increased from 548 640 to 644 510 since the last update in 2017. The number of human lncRNAs has increased from 172 216 to 173 112. The number of mouse lncRNAs increased from 131 697 to 131 974. The number of plant lncRNAs is 94 697. The relationship between lncRNAs in human and cancer were updated with transcriptome sequencing profiles. Three important new features were also introduced in NONCODEV6: (i) updated human lncRNA-disease relationships, especially cancer; (ii) lncRNA annotations with tissue expression profiles and predicted function in five common plants; iii) lncRNAs conservation annotation at transcript level for 23 plant species. NONCODEV6 is accessible through http://www.noncode.org/.
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Affiliation(s)
- Lianhe Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Wang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingrui Song
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Wu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuangsang Fang
- Beijing University of Chinese Medicine, Chaoyang District, Beijing 100029, China
| | - Dechao Bu
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Li
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Liang Sun
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yu Zheng
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqin Huang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Lin'an, Hangzhou 311300, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 518102, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,Guangdong Geneway Decoding Bio-Tech Co. Ltd, Foshan 528316, China.,National Genomics Data Center, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,National Genomics Data Center, Chinese Academy of Sciences, Beijing 100101, China
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45
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Zhou B, Ji B, Liu K, Hu G, Wang F, Chen Q, Yu R, Huang P, Ren J, Guo C, Zhao H, Zhang H, Zhao D, Li Z, Zeng Q, Yu J, Bian Y, Cao Z, Xu S, Yang Y, Zhou Y, Wang J. EVLncRNAs 2.0: an updated database of manually curated functional long non-coding RNAs validated by low-throughput experiments. Nucleic Acids Res 2021; 49:D86-D91. [PMID: 33221906 PMCID: PMC7778902 DOI: 10.1093/nar/gkaa1076] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important functional roles in many diverse biological processes. However, not all expressed lncRNAs are functional. Thus, it is necessary to manually collect all experimentally validated functional lncRNAs (EVlncRNA) with their sequences, structures, and functions annotated in a central database. The first release of such a database (EVLncRNAs) was made using the literature prior to 1 May 2016. Since then (till 15 May 2020), 19 245 articles related to lncRNAs have been published. In EVLncRNAs 2.0, these articles were manually examined for a major expansion of the data collected. Specifically, the number of annotated EVlncRNAs, associated diseases, lncRNA-disease associations, and interaction records were increased by 260%, 320%, 484% and 537%, respectively. Moreover, the database has added several new categories: 8 lncRNA structures, 33 exosomal lncRNAs, 188 circular RNAs, and 1079 drug-resistant, chemoresistant, and stress-resistant lncRNAs. All records have checked against known retraction and fake articles. This release also comes with a highly interactive visual interaction network that facilitates users to track the underlying relations among lncRNAs, miRNAs, proteins, genes and other functional elements. Furthermore, it provides links to four new bioinformatics tools with improved data browsing and searching functionality. EVLncRNAs 2.0 is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs2/.
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Affiliation(s)
- Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Baohua Ji
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Fei Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Pingping Huang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jing Ren
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Chengang Guo
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Huiying Zhao
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Hongmei Zhang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Dongbo Zhao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Zhiwei Li
- Department of General Surgery, Dezhou Municipal Hospital, Dezhou 253012, China
| | - Qiangcheng Zeng
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Shicai Xu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou 510275, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD 4222, Australia
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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Abstract
Long noncoding RNAs (lncRNAs) are involved in many regulatory mechanisms in practically every step of the RNA cycle, from transcription to RNA stability and translation. They are a highly heterogeneous class of molecules in terms of site of production, interaction networks, and functions. More and more databases are available on the web with the aim to make public information about lncRNA accessible to the scientific community. Here we review the most interesting resources with the purpose to organize a compendium of useful tools to interrogate before studying a lncRNA of interest.
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47
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Luo B, He Z, Huang S, Wang J, Han D, Xue H, Liu P, Zeng X, Lu D. Long Non-Coding RNA 554 Promotes Cardiac Fibrosis via TGF-β1 Pathway in Mice Following Myocardial Infarction. Front Pharmacol 2020; 11:585680. [PMID: 33390954 PMCID: PMC7772239 DOI: 10.3389/fphar.2020.585680] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Rationale: Cardiac fibrosis is observed in nearly every form of myocardial disease. Long non-coding RNAs (lncRNAs) have been shown to play an important role in cardiac fibrosis, but the detailed molecular mechanism remains unknown. Object: We aimed at characterizing lncRNA 554 expression in murine cardiac fibroblasts (CFs) after myocardial infarction (MI) to identify CF-enriched lncRNA and investigate its function and contribution to cardiac fibrosis and function. Methods and Results: In this study, we identified lncRNA NONMMUT022554 (lncRNA 554) as a regulator of MI-induced cardiac fibrosis. We found that lncRNA 554 was significantly up-regulated in the mouse hearts following MI. Further study showed that lncRNA 554 was predominantly expressed in cardiac fibroblasts, indicating a potential role of lncRNA 554 in cardiac fibrosis. In vitro knockdown of lncRNA 554 by siRNA suppressed fibroblasts migration and expression of extracellular matrix (ECM); while overexpression of lncRNA 554 promoted expression of ECM genes. Consistently, lentivirus mediated in vivo knockdown of lncRNA 554 could inhibit cardiac fibrosis and improve cardiac function in mouse model of MI. More importantly, TGF-β1 inhibitor (TEW-7197) could reverse the pro-fibrotic function of lncRNA 554 in CFs. This suggests that the effects of lncRNA 554 on cardiac fibrosis is TGF-β1 dependent. Conclusion: Collectively, our study illustrated the role of lncRNA 554 in cardiac fibrosis, suggested that lncRNA 554 might be a novel target for cardiac fibrosis.
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Affiliation(s)
- Bihui Luo
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Zhiyu He
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Shijun Huang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China.,Department of Cardiovascular Medicine, Yue Bei People's Hospital, Guangdong, China
| | - Jinping Wang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Dunzheng Han
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Hao Xue
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Peiying Liu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Xiaojun Zeng
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
| | - Dongfeng Lu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangdong, China
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48
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Association of Long Non-Coding RNA Polymorphisms with Gastric Cancer and Atrophic Gastritis. Genes (Basel) 2020; 11:genes11121505. [PMID: 33333725 PMCID: PMC7765138 DOI: 10.3390/genes11121505] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNA) play an important role in the carcinogenesis of various tumours, including gastric cancer. This study aimed to assess the associations of lncRNA ANRIL, H19, MALAT1, MEG3, HOTAIR single-nucleotide polymorphisms (SNPs) with gastric cancer and atrophic gastritis. SNPs were analyzed in 613 gastric cancer patients, 118 patients with atrophic gastritis and 476 controls from three tertiary centers in Germany, Lithuania and Latvia. Genomic DNA was extracted from peripheral blood leukocytes. SNPs were genotyped by the real-time polymerase chain reaction. Results showed that carriers of MALAT1 rs3200401 CT genotype had the significantly higher odds of atrophic gastritis than those with CC genotype (OR-1.81; 95% CI 1.17–2.80, p = 0.0066). Higher odds of AG were found in a recessive model (CC vs. TT + CT) for ANRIL rs1333045 (OR-1.88; 95% CI 1.19–2.95, p = 0.0066). Carriers of ANRIL (rs17694493) GG genotype had higher odds of gastric cancer (OR-4.93; 95% CI 1.28–19.00) and atrophic gastritis (OR-5.11; 95% CI 1.10–23.80) compared with the CC genotype, and carriers of HOTAIR rs17840857 TG genotype had higher odds of atrophic gastritis (OR-1.61 95% CI 1.04–2.50) compared with the TT genotype; however, the ORs did not reach the adjusted significance threshold (p < 0.007). In summary, our data provide novel evidence for a possible link between lncRNA SNPs and premalignant condition of gastric cancer, suggesting the involvement of lncRNAs in gastric cancer development.
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49
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Yang J, Xu QC, Wang ZY, Lu X, Pan LK, Wu J, Wang C. Integrated Analysis of an lncRNA-Associated ceRNA Network Reveals Potential Biomarkers for Hepatocellular Carcinoma. J Comput Biol 2020; 28:330-344. [PMID: 33185458 DOI: 10.1089/cmb.2019.0250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumor worldwide. In this study, we aimed to explore the potential biomarkers and key regulatory pathways related to HCC using integrated bioinformatic analysis and validation. The microarray data of GSE12717 and GSE54238 were downloaded from the Gene Expression Omnibus database. A competing endogenous RNA (ceRNA) network was constructed based on potential long-noncoding RNA (lncRNA)-microRNA (miRNA)-mRNA interactions. A total of 191 mRNAs, 8 miRNAs, and 5 lncRNAs were selected to construct the ceRNA network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to predict their biological functions. The PI3K-Akt signaling pathway was significantly enriched. Kaplan-Meier survival analysis based on the Gene Expression Profiling Interactive Analysis (GEPIA) database was conducted for the weighted mRNAs and lncRNAs. The results showed that SRC, GMPS, CDK2, FEN1, EZH2, ZWINT, MTHFD1L, GINS2, and MAPKAPK5-AS1 were significantly upregulated in tumor tissues. The relative expression levels of these genes were significantly upregulated in HCC patients based on the StarBase database. For further validation, the expression levels of these genes were detected by real-time quantitative reverse transcription-polymerase chain reaction in 20 HCC tumor tissues and paired paracancerous tissues. Receiver operating characteristic analysis revealed that CDK2, MTHFD1L, SRC, ZWINT, and MAPKAPK5-AS1 had significant diagnostic value in HCC, but further studies are needed to explore their mechanisms in HCC.
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Affiliation(s)
- Jie Yang
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
| | - Qing-Chun Xu
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
| | - Zhen-Yu Wang
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
| | - Xun Lu
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
| | - Liu-Kui Pan
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
| | - Jun Wu
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
| | - Chen Wang
- Department of Emergency Surgery, The Second People's Hospital of Wuhu, Wuhu, China
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50
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Jin Y, Zhang M, Duan R, Yang J, Yang Y, Wang J, Jiang C, Yao B, Li L, Yuan H, Zha X, Ma C. Long noncoding RNA FGF14-AS2 inhibits breast cancer metastasis by regulating the miR-370-3p/FGF14 axis. Cell Death Discov 2020; 6:103. [PMID: 33083023 PMCID: PMC7548970 DOI: 10.1038/s41420-020-00334-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/20/2020] [Accepted: 09/03/2020] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have emerged as important regulators in cancers, including breast cancer. However, the overall biological roles and clinical significance of most lncRNAs are not fully understood. This study aimed to elucidate the potential role of a novel lncRNA FGF14-AS2 and the mechanisms underlying metastasis in breast cancer. The lncRNA FGF14-AS2 was significantly downregulated in breast cancer tissues; patients with lower FGF14-AS2 expression had advanced clinical stage. In vitro and in vivo assays of FGF14-AS2 alterations revealed a complex integrated phenotype affecting breast cancer cell migration, invasion, and tumor metastasis. Mechanistically, FGF14-AS2 functioned as a competing endogenous RNA of miR-370-3p, thereby leading to the activation of its coding counterpart, FGF14. Clinically, we observed increased miR-370-3p expression in breast cancer tissues, whereas FGF14 expression was decreased in breast cancer tissues compared to the adjacent normal breast tissues. FGF14-AS2 expression was significantly negatively correlated with miR-370-3p expression, and correlated positively to FGF14 expression. Collectively, our findings support a model in which the FGF14-AS2/miR-370-3p/FGF14 axis is a critical regulator in breast cancer metastasis, suggesting a new therapeutic direction in breast cancer.
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Affiliation(s)
- Yucui Jin
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China.,Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Ming Zhang
- Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Rui Duan
- Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Jiashu Yang
- Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Ying Yang
- Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Jue Wang
- Division of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Chaojun Jiang
- Division of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Bing Yao
- Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Lingyun Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China.,Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
| | - Hongyan Yuan
- Department of Oncology and Lombardi Comprehensive Cancer Center, Lombardi Comprehensive Cancer Center, Washington, DC USA
| | - Xiaoming Zha
- Division of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
| | - Changyan Ma
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China.,Department of Medical Genetics, Nanjing Medical University, Longmian Road 101, Nanjing, People's Republic of China
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