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Genome-wide characterization of coding and non-coding rnas in the ovary of honeybee workers and queens

APIDOLOGIE 2020年第5期51卷 777-792页

作者： Chen, Xiao Shi, Wei Chinese Acad Agr Sci Inst Apicultural Res Beijing Peoples R China Xiangshan Beigou 1 Beijing 100093 Peoples R China

Adult honeybee queens and workers drastically differ in ovary state and ovary size. However, this reproductive bias is only partially understood from the view of a single rna type. In this study, we predicted 10,271 mrnas, 7235 lncrnas, 11,794 circrnas, and 164 mirnas in the ovary of honeybee workers through bioinformatics. Combining rna sequencing data of honeybee virgin queens, 4385 mrnas, 2390 lncrnas, 5602 circrnas, and 75 mirnas were differentially expressed in workers compared with virgins. Compared with egg-laying queens, 6536 mrnas, 3130 lncrnas, 5751 circrnas, and 81 mirnas were differentially expressed in workers. Further, functional annotation revealed that neural regulation was closely related to ovary state. Moreover, the potential interactions among circrnas, mirnas, lncrnas, and mrnas revealed that vitellogenin, ecdysone-induced protein 74, ame_circ_0001176, and ame_circ_0001243 might play critical roles in the competing endogenous rna network. These findings suggest that the integrative rna networks have potential effects in ovarian phenotype differences in honeybees.

关键词： Apis mellifera ligustica ovary caste difference coding rna non-coding rna

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Application value of biofluid-based biomarkers for the diagnosis and treatment of spinal cord injury

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Neural Regeneration Research 2022年第5期17卷 963-971页

作者： Hong-Da Wang Zhi-Jian Wei Jun-Jin Li Shi-Qing Feng Department of Orthopedics Tianjin Medical University General HospitalTianjinChina International Science and Technology Cooperation Base of Spinal Cord Injury Tianjin Key Laboratory of Spine and Spinal CordTianjin Medical University General HospitalTianjinChina Department of Orthopedics Qilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong ProvinceChina Shandong University Center for Orthopedics Cheeloo College of MedicineShandong UniversityJinanShandong ProvinceChina

Recent studies in patients with spinal cord injuries(SCIs)have confirmed the diagnostic potential of biofluid-based biomarkers,as a topic of increasing interest in relation to SCI diagnosis and *** paper reviews the research progress and application prospects of recently identified SCI-related *** structural proteins,such as glial fibrillary acidic protein,S100-β,ubiquitin carboxy-terminal hydrolase-L1,neurofilament light,and tau protein were correlated with the diagnosis,American Spinal Injury Association Impairment Scale,and prognosis of SCI to different *** factors,including interleukin-6,interleukin-8,and tumor necrosis factorα,are also good biomarkers for the diagnosis of acute and chronic SCI,while non-coding rnas(micro rnas and long non-coding rnas)also show diagnostic potential for *** elements(Mg,Se,Cu,Zn)have been shown to be related to motor recovery and can predict motor function after SCI,while humoral markers can reflect the pathophysiological changes after *** factors have the advantages of low cost,convenient sampling,and ease of dynamic tracking,but are also associated with disadvantages,including diverse influencing factors and complex level *** various proteins have been verified as potential biomarkers for SCI,more convincing evidence from large clinical and prospective studies is thus required to identify the most valuable diagnostic and prognostic biomarkers for SCI.

关键词： biomarker diagnosis inflammatory cytokine motor recovery non-coding rna prognosis spinal cord injury structural protein trace element

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Genetic screening for anticancer genes highlights FBLN5 as a synthetic lethal partner of MYC

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Cell Communication and Signaling 2023年第1期21卷 1-16页

作者： Masood, Motasim Ding, Qize Cawte, Adam D. Rueda, David S. Grimm, Stefan W. Yagüe, Ernesto El-Bahrawy, Mona Faculty of Medicine Imperial College London Du Cane Rd London United Kingdom Department of Medicine Faculty of Medicine Imperial College London Du Cane Rd London United Kingdom Single Molecule Imaging Group MRC London Institute of Medical Sciences Du Cane Rd London United Kingdom Department of Infectious Disease Faculty of Medicine Imperial College London Du Cane Rd London United Kingdom Department of Surgery and Cancer Faculty of Medicine Imperial College London Du Cane Rd London United Kingdom Department of Metabolism Digestion and Reproduction Faculty of Medicine Imperial College London Du Cane Rd London United Kingdom Department of Pathology Faculty of Medicine University of Alexandria Alexandria Egypt

Background: When ectopically overexpressed, anticancer genes, such as TRAIL, PAR4 and ORCTL3, specifically destroy tumour cells without harming untransformed cells. Anticancer genes can not only serve as powerful tumour specific therapy tools but studying their mode of action can reveal mechanisms underlying the neoplastic transformation, sustenance and spread. Methods: Anticancer gene discovery is normally accidental. Here we describe a systematic, gain of function, forward genetic screen in mammalian cells to isolate novel anticancer genes of human origin. Continuing with over 30,000 transcripts from our previous study, 377 cell death inducing genes were subjected to screening. FBLN5 was chosen, as a proof of principle, for mechanistic gene expression profiling, comparison pathways analyses and functional studies. Results: Sixteen novel anticancer genes were isolated;these included non-coding rnas, protein-coding genes and novel transcripts, such as ZNF436-AS1, SMLR1, TMEFF2, LINC01529, HYAL2, NEIL2, FBLN5, YPEL4 and PHKA2-processed transcript. FBLN5 selectively caused inhibition of MYC in COS-7 (transformed) cells but not in CV-1 (normal) cells. MYC was identified as synthetic lethality partner of FBLN5 where MYC transformed CV-1 cells experienced cell death upon FBLN5 transfection, whereas FBLN5 lost cell death induction in MCF-7 cells upon MYC knockdown. Conclusions: Sixteen novel anticancer genes are present in human genome including FBLN5. MYC is a synthetic lethality partner of FBLN5. [MediaObject not available: see fulltext.] © 2023, BioMed Central Ltd., part of Springer Nature.

关键词： Apoptosis Causal analysis Cell death assay Comparison pathway analyses Live cell imaging microrna non-coding rna Targeted therapy TRAIL

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Role of exosomal ncrnas in traumatic brain injury

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non-coding rna RESEARCH 2023年第4期8卷 686-692页

作者： Beylerli, Ozal Tamrazov, Rasim Gareev, Ilgiz Ilyasova, Tatiana Shumadalova, Alina Bai, Yunlong Yang, Baofeng Harbin Med Univ State Prov Key Labs Biomed Pharmaceut China Key Lab Cardiovasc Res Dept PharmacolMinist EducColl Pharm Harbin 150081 Peoples R China Harbin Med Univ Heilongjiang Acad Med Sci Translat Med Res & Cooperat Ctr Northern China Harbin 150081 Peoples R China Tyumen State Med Univ Dept Oncol Radiol & Radiotherapy 54 Odesskaya St Tyumen 625023 Russia Bashkir State Med Univ Cent Res Lab 3 Lenin St Ufa 450008 Russia Bashkir State Med Univ Dept Internal Dis Ufa 450008 Russia Bashkir State Med Univ Dept Gen Chem 3 Lenin St Ufa 450008 Russia

Traumatic brain injury (TBI) is a complex neurological disorder that often results in long-term disabilities, cognitive impairments, and emotional disturbances. Despite significant advancements in understanding the pathophysiology of TBI, effective treatments remain limited. In recent years, exosomal non-coding rnas (ncrnas) have emerged as potential players in TBI pathogenesis and as novel diagnostic and therapeutic targets. Exosomal ncrnas are small rna molecules that are secreted by cells and transported to distant sites, where they can modulate gene expression and cell signaling pathways. They have been shown to play important roles in various aspects of TBI, such as neuroinflammation, blood-brain barrier dysfunction, and neuronal apoptosis. The ability of exosomal ncrnas to cross the blood-brain barrier and reach the brain parenchyma makes them attractive candidates for non-invasive biomarkers and drug delivery systems. However, significant challenges still need to be addressed before exosomal ncrnas can be translated into clinical practice, including standardization of isolation and quantification methods, validation of their diagnostic and prognostic value, and optimization of their therapeutic efficacy and safety. This review aims to summarize the current knowledge regarding the role of exosomal ncrnas in TBI, including their biogenesis, function, and potential applications in diagnosis, prognosis, and treatment. We also discuss the challenges and future perspectives of using exosomal ncrnas as clinical tools for TBI management.

关键词： Exosomes non-coding rna Exosomal non-coding rna Traumatic brain injury Biomarkers

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CRISPR/Cas9 as precision and high-throughput genetic engineering tools in cancer research and

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INTErnaTIONAL JOUrnaL OF BIOLOGICAL MACROMOLECULES 2022年第PT A期223卷 732-754页

作者： Hosseini, Sayedeh Azimeh Jouneghani, Alizamen Salehifard Ghatrehsamani, Mahdi Yaghoobi, Hajar Elahian, Fatemeh Mirzaei, Seyed Abbas Shahrekord Univ Med Sci Sch Adv Technol Dept Med Biotechnol Shahrekord Iran Shahrekord Univ Med Sci Sch Med Dept Pediat Shahrekord Iran Shahrekord Univ Med Sci Basic Hlth Sci Inst Cellular & Mol Res Ctr Shahrekord Iran Shahrekord Univ Med Sci Basic Hlth Sci Inst Clin Biochem Res Ctr Shahrekord Iran

Gastrointestinal cancer (GI) is one of the most serious and health-threatening diseases worldwide. Many countries have encountered an escalating prevalence of shock. Therefore, there is a pressing need to clarify the molecular pathogenesis of these cancers. The use of high-throughput technologies that allow the precise and simultaneous investigation of thousands of genes, proteins, and metabolites is a critical step in disease diagnosis and cure. Recent innovations have provided easy and reliable methods for genome investigation, including TALENs, ZFNs, and the CRISPR/Cas9 (clustered regularly interspaced palindromic repeats system). Among these, CRISPR/Cas9 has been revolutionary tool in genetic research. Recent years were prosperous years for CRISPR by the discovery of novel Cas enzymes, the Nobel Prize, and the development of critical clinical trials. This technology utilizes comprehensive information on genes associated with tumor development, provides highthroughput libraries for tumor therapy by developing screening platforms, and generates rapid tools for cancer therapy. This review discusses the various applications of CRISPR/Cas9 in genome editing, with a particular focus on genome manipulation, including infection-related genes, rnai targets, pooled library screening for identification of unknown driver mutations, and molecular targets for gastrointestinal cancer modeling. Finally, it provides an overview of CRISPR/Cas9 clinical trials, as well as the challenges associated with its use.

关键词： CRISPR Cas9 Gastrointestinal cancers Genetic engineering Infectious diseases non-coding rna Organoid cancer modeling

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Transforming growth factor-beta (TGF-β) in prostate cancer: A dual function mediator?

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INTErnaTIONAL JOUrnaL OF BIOLOGICAL MACROMOLECULES 2022年 206卷 435-452页

作者： Mirzaei, Sepideh Paskeh, Mahshid Deldar Abad Saghari, Yalda Zarrabi, Ali Hamblin, Michael R. Entezari, Maliheh Hashemi, Mehrdad Aref, Amir Reza Hushmandi, Kiavash Kumar, Alan Prem Rabiee, Navid Ashrafizadeh, Milad Samarghandian, Saeed Islamic Azad Univ Fac Sci Dept Biol Sci & Res Branch Tehran Iran Islamic Azad Univ Fac Adv Sci & Technol Dept Genet Tehran Med Sci Tehran Iran Islamic Azad Univ Farhikhtegan Hosp Tehran Med Sci Farhikhtegan Med Convergence Sci Res Ctr Tehran Iran Istinye Univ Fac Engn & Nat Sci Dept Biomed Engn TR-34396 Istanbul Turkey Univ Johannesburg Fac Hlth Sci Laser Res Ctr ZA-2028 Doornfontein South Africa Iran Univ Med Sci Radiat Biol Res Ctr Tehran Iran Harvard Med Sch Dana Farber Canc Inst Belfer Ctr Appl Canc Sci Boston MA 02115 USA Xsphera Biosci Inc Translat Sci 6 Tide St Boston MA 02210 USA Univ Tehran Fac Vet Med Dept Food Hyg & Qual Control Div Epidemiol Tehran Iran Natl Univ Singapore Canc Sci Inst Singapore Yong Loo Lin Sch Med Singapore 117599 Singapore Natl Univ Singapore Yong Loo Lin Sch Med Dept Pharmacol Singapore 117599 Singapore Natl Univ Singapore Yong Loo Lin Sch Med NUS Ctr Canc Res N2CR Singapore 119228 Singapore Macquarie Univ Sch Engn Sydney NSW 2109 Australia Sabanci Univ Fac Engn & Nat Sci Univ Caddesi 27 TR-34956 Istanbul Turkey Neyshabur Univ Med Sci Noncommunicable Dis Res Ctr Neyshabur Iran

Transforming growth factor-beta (TGF-beta) is a member of a family of secreted cytokines with vital biological functions in cells. The abnormal expression of TGF-beta signaling is a common finding in pathological conditions, particularly cancer. Prostate cancer (PCa) is one of the leading causes of death among men. Several genetic and epigenetic alterations can result in PCa development, and govern its progression. The present review attempts to shed some light on the role of TGF-beta signaling in PCa. TGF-beta signaling can either stimulate or inhibit proliferation and viability of PCa cells, depending on the context. The metastasis of PCa cells is increased by TGF-beta signaling via induction of EMT and MMPs. Furthermore, TGF-beta signaling can induce drug resistance of PCa cells, and can lead to immune evasion via reducing the anti-tumor activity of cytotoxic T cells and stimulating regulatory T cells. Upstream mediators such as micrornas and lncrnas, can regulate TGF-beta signaling in PCa. Furthermore, some pharmacological compounds such as thymoquinone and valproic acid can suppress TGF-beta signaling for PCa therapy. TGF-beta over-expression is associated with poor prognosis in PCa patients. Furthermore, TGF-beta up regulation before prostatectomy is associated with recurrence of PCa. Overall, current review discusses role of TGF-beta signaling in proliferation, metastasis and therapy response of PCa cells and in order to improve knowledge towards its regulation, upstream mediators of TGF-beta such as non-coding rnas are described. Finally, TGF-beta regulation and its clinical application are discussed.

关键词： TGF-beta Prostate cancer Immunotherapy Biomarker Chemotherapy non-coding rna

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Identify ncrna Subcellular Localization via Graph Regularized k-Local Hyperplane Distance Nearest Neighbor Model on Multi-Kernel Learning

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IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022年第6期19卷 3517-3529页

作者： Zhou, Haohao Wang, Hao Tang, Jijun Ding, Yijie Guo, Fei Tianjin Univ Coll Intelligence & Comp Sch Comp Sci & Technol Tianjin 300072 Peoples R China Univ South Carolina Dept Comp Sci & Engn Columbia SC 29208 USA Univ Elect Sci & Technol China Yangtze Delta Region Inst Quzhou Quzhou 324000 Zhejiang Peoples R China Cent South Univ Sch Comp Sci & Engn Changsha 410083 Hunan Peoples R China

non-coding rnas (ncrnas) are a type of rnas which are not used to encode protein sequences. Emerging evidence shows that lots of ncrnas may participate in many biological processes and must be widely involved in many types of cancers. Therefore, understanding their functionality is of great importance. Similar to proteins, various functions of ncrnas relies on their subcellular localizations. Traditional high-throughput methods in wet-lab to identify subcellular localization is time-consuming and costly. In this paper, we propose a novel computational method based on multi-kernel learning to identify multi-label ncrna subcellular localizations, via graph regularized k-local hyperplane distance nearest neighbor algorithm. First, we construct six types of sequencebased feature descriptors and select important feature vectors. Then, we build a multi-kernel learning model with Hilbert-Schmidt independence criterion (HSIC) to obtain optimal weights for vairous features. Furthermore, we propose the graph regularized k-local hyperplane distance nearest neighbor algorithm (GHKNN) as a binary classification model for detecting one kind of non-coding rna subcellular localization. Finally, we apply One-vs-Rest strategy to decompose multi-label problem of non-coding rna subcellular localizations. Our method achieves excellent performance on three ncrna datasets and three human ncrna datasets, and outperforms other outstanding machine learning methods. Comparing to existing method, our model also performs well especially on small datasets. We expect that this model will be useful for the prediction of subcellular localization and the study of important functional mechanisms of ncrnas. Furthermore, we establish user-friendly web server (http://***/) with the implementation of our method, which can be easily used by most experimental scientists.

关键词： rna Location awareness Feature extraction Proteins Kernel Databases Biological information theory non-coding rna subcellular localization multi-label classification multi-kernel learning k-local hyperplane distance nearest neighbor

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noncorna: a database of experimentally supported non-coding rnas and drug targets in cancer

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JOUrnaL OF HEMATOLOGY & ONCOLOGY 2020年第1期13卷 1-4页

作者： Li, Lulu Wu, Pengfei Wang, Zhenyu Meng, Xiangqi Zha, Caijun Li, Ziwei Qi, Tengfei Zhang, Yangong Han, Bo Li, Shupeng Jiang, Chuanlu Zhao, Zheng Cai, Jinquan Harbin Med Univ Heilongjiang Acad Med Sci Affiliated Hosp 2 Neurosci InstDept Neurosurg Harbin 150086 Peoples R China Harbin Med Univ Affiliated Hosp 2 Dept Lab Diag Harbin 150086 Peoples R China Beijing Neurosurg Inst Beijing 100070 Peoples R China

noncorna () is a manually curated database of experimentally supported non-coding rnas (ncrnas) and drug target associations that aim to potentially provide a high-quality data resource for exploring drug sensitivity/resistance-related ncrnas in various human cancers. ncrna are rna molecular that do not encode proteins, but are involved in gene regulation and cellular functions in variety of human diseases, including neurodegenerative diseases and cancers. Here, we developed noncorna which contained 8233 entries between 5568 ncrnas and 154 drugs in 134 cancers. Each entry in the noncorna contains detailed information on the ncrnas, drugs, and cancers, the ncrna expression pattern and experimental detection techniques, drug response and other targets, literature references, and other information. noncorna offers a user-friendly, open access web interface to easily browse, search, and download data. noncorna also provides a submission page for researchers to submit newly validated ncrna-drug-cancer associations. noncorna might serve as an immeasurable resource for understanding the roles of ncrnas in cancer therapy.

关键词： Database non-coding rna Drug resistance Human cancer

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Interactome battling of lncrna CCDC144NL-AS1: Its role in the emergence and ferocity of cancer and beyond

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INTErnaTIONAL JOUrnaL OF BIOLOGICAL MACROMOLECULES 2022年第PT B期222卷 1676-1687页

作者： Abd El Fattah, Yasmine K. Abulsoud, Ahmed I. AbdelHamid, Sherihan G. Hamdy, Nadia M. Heliopolis Univ Fac Pharm Dept Biochem Cairo Egypt Al Azhar Univ Fac Pharm Dept Biochem Boys Branch Nasr City Cairo Egypt Ain Shams Univ Fac Pharm Biochem Dept Cairo Egypt Ain Shams Univ Fac Pharm Abbasiya 11566 Cairo Egypt

Long non-coding rnas (lncrnas) were, once, viewed as "noise" for transcription. Recently, many lncrnas are functionally linked to several human disorders, including cancer. Coiled-Coil Domain Containing 144 N -Ter-minal-Like antisense1 (CCDC144NL-AS1) is a newly discovered cytosolic lncrna. Aberrant CCDC144NL-AS1 expression was discovered in hepatocellular carcinoma (HCC), ovarian cancer (OC), gastric cancer (GC), non -small cell lung cancer (NSCLC), and osteosarcoma. CCDC144NL-AS1 could be a promising prognostic biolog-ical marker and therapeutic target for cancer. In this review, we will collect and highlight the available infor-mation about CCDC144NL-AS1 role in various cancers. Moreover, we will discuss the diagnostic and prognostic utility of CCDC144NL-AS1 as a new molecular biomarker for several human malignancies, besides its potential therapeutic importance.

关键词： Epigenetics non-coding rna CCDC144NL-AS1 cancer hallmarks microrna

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Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on non-coding rnas

Bioinformatics Approaches for Determining the Functional Imp...

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作者： Chao Zeng Atsushi Takeda Kotaro Sekine Naoki Osato Tsukasa Fukunaga Michiaki Hamada

With a large number of annotated non-coding rnas (ncrnas), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncrnas that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncrnas. This chapter summarizes recent findings that reveal the role of repetitive elements in ncrnas. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncrnas. less

关键词： Bioinformatics Transposable element ncrna non-coding rna Repetitive element Functional element

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