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noncoding rnas in Parasite-Vector-Host Interactions

TRENDS IN PARASITOLOGY 2019年第9期35卷 715-724页

作者： Bensaoud, Chaima Hackenberg, Michael Kotsyfakis, Michail Czech Acad Sci Biol Ctr Branisovska 31 Ceske Budejovice 37005 Czech Republic Univ Granada Fac Ciencias Dept Genet Campus Fuentenueva S-N E-18071 Granada Spain Ctr Invest Biomed CIBM Lab Bioinformat PTS Avda Conocimiento S-N Granada 18100 Spain

Systems biology approaches, especially in the big data era, have revolutionized modem parasitology. Of the many different molecules participating in parasite-host interactions, noncoding rnas (ncrnas) are now known to be (i) transmitted by the vector to possibly modulate vertebrate host responses and favor vector survival and (ii) regulated in the host by parasites to favor parasite survival. Here we provide an overview of the involvement of ncrnas in the parasite-vector-host triad and their effect on host homeostasis based on recent advances and accumulating knowledge about the role of endogenous vertebrate noncoding rnas in vertebrate host physiology.

关键词： noncoding rna parasite-vertebrate-host interaction epigenetics pathogenesis arthropod vectors mirna

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noncoding rnas in Polycomb and Trithorax Regulation: A Quantitative Perspective

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ANNUAL REVIEW OF GENETICS, VOL 51 2017年第1期51卷 385-411页

作者： Ringrose, Leonie Humboldt Univ Integrated Res Inst Life Sci D-10115 Berlin Germany

The question of how noncoding rnas are involved in Polycomb group (PcG) and Trithorax group (TrxG) regulation has been on an extraordinary journey over the last three decades. Favored models have risen and fallen, and healthy debates have swept back and forth. The field has recently reached a critical mass of compelling data that throws light on several previously unresolved issues. The time is ripe for a fruitful combination of these findings with two other long-running avenues of research, namely the biochemical properties of the PcG/TrxG system and the application of theoretical mathematical models toward an understanding of the system's regulatory properties. I propose that integrating our current knowledge of noncoding rna into a quantitative biochemical and theoretical framework for PcG and TrxG regulation has the potential to reconcile several apparently conflicting models and identifies fascinating questions for future research.

关键词： noncoding rna Polycomb Trithorax chromatin bistability mathematical model

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noncoding rnas in Cardiovascular Disease: Pathological Relevance and Emerging Role as Biomarkers and Therapeutics

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AMERICAN JOUrnaL OF HYPERTENSION 2018年第2期31卷 150-165页

作者： Gangwar, Roopesh S. Rajagopalan, Sanjay Natarajan, Rama Deiuliis, Jeffrey A. Case Western Reserve Univ Cardiovasc Res Inst CVRI Cleveland OH 44106 USA Case Western Reserve Univ Ctr RNA Sci & Therapeut Dept Med Cleveland OH 44106 USA City Hope Natl Med Ctr Beckman Res Inst Dept Diabet Complicat & Metab Duarte CA USA

noncoding rnas (ncrna) include a diverse range of functional rna species-micrornas (mirnas) and long noncoding rnas (lncrnas) being most studied in pathophysiology. Cardiovascular morbidity is associated with differential expression of myriad mirnas;miR-21, miR-155, miR-126, miR-146a/b, miR-143/145, miR-223, and miR-221 are the top 9 most reported mirnas in hypertension and atherosclerotic disease. A single mirna may have hundreds of messenger rna targets, which makes a full appreciation of the physiologic ramifications of such broad-ranging effects a challenge. miR-21 is the most prominent ncrna associated with hypertension and atherosclerotic disease due to its role as a "mechano-miR", responding to arterial shear stresses. "Immuno-miRs", such as miR-155 and miR-223, affect cardiovascular disease (CVD) via regulation of hematopoietic cell differentiation, chemotaxis, and activation in response to many pro-atherogenic stimuli. "Myo-miRs", such as miR-1 and miR-133, affect cardiac muscle plasticity and remodeling in response to mechanical overload. This in-depth review analyzes observational and experimental reports of ncrnas in CVD, including future applications of ncrna-based strategies in diagnosis, prediction (e.g., survival and response to small molecule therapy), and biologic therapy.

关键词： atherosclerosis biomarker blood pressure hypertension microrna mirna myocardial infarction ncrna noncoding rna

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noncoding rnas in liver cancer stem cells: The big impact of little things

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CANCER LETTERS 2018年 418卷 51-63页

作者： Lv, Hongwei Lv, Guishuai Han, Qin Yang, Wen Wang, Hongyang Second Mil Med Univ Eastern Hepatobiliary Surg Inst Int Cooperat Lab Signal Transduct Shanghai 200438 Peoples R China Natl Ctr Liver Canc Res Shanghai 201805 Peoples R China Shanghai Jiao Tong Univ Renji Hosp Shanghai Canc Inst State Key Lab Oncogenes & Related Genes Shanghai 200032 Peoples R China

The high rate of recurrence and heterogeneity make hepatocellular carcinoma (HCC) as one of the most prevalent malignancy worldwide. Cancer stem cells (CSCs), also known as tumor-initiating cells, are responsible for cancer initiation, metastasis, drug resistance and relapse, accounting for the heterogeneous and hierarchical organizations of HCC. Therefore, CSCs are novel targets for more efficient liver cancer therapies. New data continues to mount on the functions of noncoding rnas in multiple processes of liver CSCs, including malignant proliferation, self-renewal, tumorigenicity, and survival. Thus, it is highly critical to develop improved understanding of the mechanisms by which noncoding rnas control CSCs functions for developing better diagnostic and therapeutic strategies. Herein, we will shed light on the regulatory roles of noncoding rnas, especially micrornas (mirnas) and long noncoding rnas (Incrnas), in liver CSCs acquisition and maintenance after presenting an overview about the characteristics of liver CSCs and their origins. (C) 2018 Elsevier B.V. All rights reserved.

关键词： noncoding rna Microrna (mirna) Long noncoding rna (Incrna) Cancer stem cells (CSCs) Hepatocellular carcinoma (HCC)

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noncoding rnas in disease

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FEBS LETTERS 2018年第17期592卷 2884-2900页

作者： Lekka, Evangelia Hall, Jonathan Swiss Fed Inst Technol Inst Pharmaceut Sci Dept Chem & Appl Biosci CH-8093 Zurich Switzerland

noncoding rnas are emerging as potent and multifunctional regulators in all biological processes. In parallel, a rapidly growing number of studies has unravelled associations between aberrant noncoding rna expression and human diseases. These associations have been extensively reviewed, often with the focus on a particular microrna (mirna) (family) or a selected disease/pathology. In this Mini-Review, we highlight a selection of studies in order to demonstrate the wide-scale involvement of mirnas and long noncoding rnas in the pathophysiology of three types of diseases: cancer, cardiovascular and neurological disorders. This research is opening new avenues to novel therapeutic approaches.

关键词： long noncoding rna microrna noncoding rna

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LPItabformer: Enhancing generalization in predicting lncrna-protein interactions via a tabular Transformer

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Computational and Structural Biotechnology Journal 2025年 27卷 2323-2335页

作者： Qin Lin Jie Sheng Chang Zhou Tao Xiao Yilei Meng Mingxin Lu Junfang Zhang Xueyun Yan Luying Peng Huaming Cao Li Li State Key Laboratory of Cardiovascular Diseases and Medical Innovation Center Shanghai East Hospital School of Medicine Tongji University Shanghai 200120 China Shanghai Arrhythmias Research Center Shanghai East Hospital Tongji University School of Medicine Shanghai 200120 China Stem Cell Research Center Medical School Tongji University Shanghai 200120 China Teaching Laboratory Center Tongji University School of Medicine Shanghai 200331 China Department of Cardiology Shibei Hospital Shanghai 200435 China

Long-noncoding rnas (Lncrnas) play important roles in physiological and pathological processes. Accurately predicting lncrna-protein interactions (LPIs) is vital strategy for clarify functions and pathogenic mechanisms of lncrnas. Current computational methods for evaluating LPIs with their utility and generalization have significant room for improvement. In this study, data splitting by incorporating protein clusters as group information reveals that lots of LPI prediction methods suffer from generalization flaws due to data leakage caused by ignoring LPI biological properties. To address the issue, we present LPItabformer, a tabular Transformer framework for predicting LPIs, that incorporates a domain shifts with uncertainty (DSU) module for generalization enhancement. The LPItabformer demonstrates a capacity to alleviate the generalization challenges associated with biases in LPI data and preferences in protein binding patterns. In addition, LPItabformer shows greater robustness and generalization on human and mouse LPI datasets compared to state-of-the-art methods. Ultimately, we have verified that the LPItabformer is capable of predicting novel LPIs. Code is available at https://***/Ci-TJ/LPItabformer.

关键词： Ncrna noncoding rna Lncrna Long noncoding rna RBP rna-binding protein LPI Lncrna-protein interaction RPI rna-protein interaction SVM Support Vector Machine RF Random Forest LGBM Light Gradient Boosting Machine CTF Conjoint triad feature CNN Convolutional Neural Network SAE Stacked Autoencoder CLIP-seq Crosslinking Immunoprecipitation Sequencing 5FCV 5-fold cross validation G5FCV Group 5-fold cross validation DSU Domain Shifts with Uncertainty LR Logistic Regression SGD Stochastic Gradient Descent TEDM Transformer Encoder with DSU Module ACC Accuracy AUC Area under the curve PRE Precision SEN Sensitivity SPE Specificity Long non-coding rna Lncrna-protein interactions Tabular Transformer Generalization Deep learning

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noncoding rnas regulating ferroptosis in cardiovascular diseases: novel roles and therapeutic strategies

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MOLECULAR AND CELLULAR BIOCHEMISTRY 2024年第11期479卷 2827-2841页

作者： Wu, Changyong Bao, Suli Sun, Huang Chen, Xiaocui Yang, Lu Li, Ruijie Peng, Yunzhu Kunming Med Univ Affiliated Hosp 1 Dept Cardiol Kunming Peoples R China Panzhihua Univ Affiliated Hosp Dept Gastroenterol Panzhihua Peoples R China

The morbidity and mortality rates of cardiovascular diseases (CVDs) are increasing;thus, they impose substantial health and economic burdens worldwide, and effective interventions are needed for immediate resolution of this issue. Recent studies have suggested that noncoding rnas (ncrnas) play critical roles in the occurrence and development of CVDs and are potential therapeutic targets and novel biomarkers for these diseases. Newly discovered modes of cell death, including necroptosis, pyroptosis, apoptosis, autophagy-dependent cell death and ferroptosis, also play key roles in CVD progression. However, ferroptosis, which differs from the other aforementioned forms of regulated cell death in terms of cell morphology, biochemistry and inhereditability, is a unique iron-dependent mode of nonapoptotic cell death induced by abnormal iron metabolism and excessive accumulation of iron-dependent lipid peroxides and reactive oxygen species (ROS). Increasing evidence has confirmed that ncrna-mediated ferroptosis is involved in regulating tissue homeostasis and CVD-related pathophysiological conditions, such as cardiac ischemia/reperfusion (I/R) injury, myocardial infarction (MI), atrial fibrillation (AF), cardiomyopathy and heart failure (HF). In this review, we summarize the underlying mechanism of ferroptosis, discuss the pathophysiological effects of ncrna-mediated ferroptosis in CVDs and provide ideas for effective therapeutic strategies.

关键词： noncoding rna Ferroptosis Cardiovascular diseases Iron metabolism Lipid peroxidation Molecular mechanism

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The Emerging Field of noncoding rnas and Their Importance in Pediatric Diseases

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JOUrnaL OF PEDIATRICS 2020年第Sup期221卷 S11-S19页

作者： Zhou, Rui Joshi, Piyush Katsushima, Keisuke Liang, Weihong Liu, Wei Goldenberg, Neil A. Dover, George Perera, Ranjan J. Johns Hopkins Univ Sch Med Dept Oncol Baltimore MD 21205 USA Johns Hopkins Univ Sch Med Dept Biol Chem Baltimore MD 21205 USA Johns Hopkins All Childrens Hosp Inst Fundamental Biomed Res St Petersburg FL USA Johns Hopkins Univ Sch Med Dept Pediat Baltimore MD 21205 USA Johns Hopkins All Childrens Inst Clin & Translat St Petersburg FL USA

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Crosstalk between N6-methyladenosine modification and ncrnas in rheumatic diseases: therapeutic and diagnostic implications

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Inflammation Research 2025年第1期74卷 1-12页

作者： Wen, Jianting Liu, Jian Wan, Lei Sun, Yue Wang, Fanfan Department of Rheumatology and Immunology First Affiliated Hospital of Anhui University of Chinese Medicine Hefei China Institute of Rheumatology Anhui Academy of Chinese Medicine Hefei China Anhui Province Key Laboratory of Modern Chinese Medicine Department of Internal Medicine Application Foundation Research and Development Hefei China

In eukaryotic cells, N6-methyladenosine (m6A) is the most prevalent rna methylation modification and plays a fundamental role in regulating diverse biological processes through the modulation of non-coding rna (ncrna) expression and activity. The role of m6A modification in developing rheumatic diseases is crucial but remains inadequately studied. Characterized by pain and inflammation, rheumatic diseases like rheumatoid arthritis (RA), osteoarthritis (OA), ankylosing spondylitis (AS), and systemic lupus erythematosus (SLE) are autoimmune disorders. Recent findings emphasize the importance of m6A modifications and non-coding rnas in the biological processes underlying rheumatic diseases. This review elucidates the fundamental concept of m6A modification and the associated research methodologies. Subsequently, it systematically consolidates modern knowledge on the influence of m6A regulators and m6A modification-related ncrnas on rheumatic diseases, incorporating perspectives on traditional Chinese medicine interventions. Offering a comprehensive overview of m6A-related ncrnas in the context of rheumatic diseases, this review proposes new therapeutic avenues by targeting m6A modification pathways.

关键词： Crosstalk Molecular mechanisms N6-methyladenosine noncoding rna Rheumatic diseases

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Novel approaches for efficient in vivo fermentation production of noncoding rnas

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APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 2020年第5期104卷 1927-1937页

作者： Yu, Ai-Ming Batra, Neelu Tu, Mei-Juan Sweeney, Colleen Univ Calif Davis Sch Med Dept Biochem & Mol Med Sacramento CA 95817 USA

Genome-derived noncoding rnas (ncrnas), including micrornas (mirnas), small interfering rnas (sirnas), and long noncoding rnas (lncrnas), play an essential role in the control of target gene expression underlying various cellular processes, and dysregulation of ncrnas is involved in the pathogenesis and progression of various diseases in virtually all species including humans. Understanding ncrna biology has opened new avenues to develop novel rna-based therapeutics. Presently, ncrna research and drug development is dominated by the use of ncrna mimics that are synthesized chemically in vitro and supplemented with extensive and various types of artificial modifications and thus may not necessarily recapitulate the properties of natural rnas generated and folded in living cells in vivo. Therefore, there are growing interests in developing novel technologies for in vivo production of rna molecules. The two most recent major breakthroughs in achieving an efficient, large-scale, and cost-effective fermentation production of recombinant or bioengineered rnas (e.g., tens of milligrams from 1 L of bacterial culture) are (1) using stable rna carriers and (2) direct overexpression in rnase III-deficient bacteria, while other approaches offer a low yield (e.g., nano- to microgram scales per liter). In this article, we highlight these novel microbial fermentation-based technologies that have shifted the paradigm to the production of true biological ncrna molecules for research and development.

关键词： noncoding rna Microrna sirna Bioengineering Biotechnology

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