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New insights into the interplay between MALAT1 and mirna-155 to unravel potential diagnostic and prognostic biomarkers of Behçet's disease

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CLINICAL RHEUMATOLOGY 2025年第2期44卷 775-787页

作者： Sayed, Noha H. Shaker, Olfat G. Abd-Elmawla, Mai A. Gamal, Ahmed Fathy, Nevine Cairo Univ Fac Pharm Biochem Dept Cairo 11562 Egypt Cairo Univ Fac Med Med Biochem & Mol Biol Dept Cairo 11562 Egypt Cairo Univ Fac Med Androl Sexol & STIs Dept Cairo 11562 Egypt

The current study was deployed to evaluate the role of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and miR-155, along with the inflammatory markers, TNF alpha and IL-6, and the adhesion molecule, cluster of differentiation 106 (CD106), in Beh & ccedil;et's disease (BD) pathogenesis. The study also assessed MALAT1/miR-155 as promising diagnostic and prognostic biomarkers for BD. The current retrospective case-control study included 74 Egyptian BD patients and 50 age and sex-matched controls. Blood samples were collected, and then, serum samples were separated for further biochemical and molecular investigations. The gene expression of MALAT1 and miR-155 was measured using qRT-PCR, whereas the levels of TNF alpha, IL-6, and CD106 were estimated using ELISA technique. MALAT1 was significantly downregulated, whereas miR-155 was upregulated among BD patients, compared with control subjects. Levels of TNF alpha, IL-6, and CD106 were elevated in BD patients. Further downregulation in MALAT1 together with upregulation of miR-155 was observed in active BD patients, relative to the inactive group. Receiver-operating-characteristic analysis revealed that MALAT1 and miR-155 could discriminate BD patients from controls, on the one hand, and active from inactive BD patients, on the other hand. MALAT1 was negatively correlated with TNF alpha, IL-6, and CD106, while miR-155 was positively correlated with them. Logistic regression analyses demonstrated miR-155 as a significant independent predictor of BD susceptibility, and MALAT1 as an independent negative predictor of BD activity. For the first time, the current research enlightens the role of MALAT1 and miR-155 in BD pathogenesis via impacting IL-6/TNF-alpha/CD-106 signaling. As well, MALAT1 and miR-155 could be regarded as novel non-invasive biomarkers that may improve BD diagnosis and prognosis. Key Points center dot MALAT1/miR-155 exerts potential role in Beh & ccedil;et's *** dot MALAT1/miR-155

关键词： Beh & ccedil et's disease CD106 Disease activity IL-6 non-coding rna TNF alpha

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Identification of mirnas, lncrnas, circrnas, and their cerna networks in the establishment of sexual size dimorphism in the olive flounder (Paralichthys olivaceus)

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AQUACULTURE 2025年 605卷

作者： Zhang, Yuqing Zhang, Wenying Li, Ao Jian, Yanmin Zhang, Shujing Liu, Dongwu Tan, Xungang You, Feng Pang, Qiuxiang Jiao, Shuang Shandong Univ Technol Sch Life Sci & Med Zibo 255000 Peoples R China Chinese Acad Sci Qingdao 266071 Peoples R China Chinese Acad Sci Inst Oceanol Ctr Ocean Mega Sci Shandong Prov Key Lab Expt Marine Biol Qingdao 266071 Peoples R China Qingdao Marine Sci & Technol Ctr Lab Marine Biol & Biotechnol Qingdao 266237 Peoples R China

Olive flounder (Paralichthys olivaceus), a valuable mariculture species, exhibits a significant female-biased sexual size dimorphism (SSD). Despite its economic and biological importance, the molecular mechanisms underlying this phenomenon, in particular the contribution of non-coding rnas (ncrnas) and their associated competitive endogenous rna (cerna) regulatory mechanisms, remain unclear. In this study, we conducted whole transcriptome sequencing of the brains/pituitaries and muscles of olive flounder during the critical period for SSD establishment, identifying 23/282/85 and 25/193/82 differentially expressed (DE) mirnas/circrnas/lncrnas, respectively. Based on the regulatory interactions among these DE rnas, we constructed the lncrna-mirnamrna and circrna-mirna-mrna cerna networks. Our analyses revealed crucial SSD-related pathways regulated by these ncrnas/cerna networks, including "ovarian steroidogenesis", "prolactin signaling pathway", "cell adhesion molecules", "GABAergic synapse", and "dopaminergic synapse" pathways in brains/pituitaries, "ECM-receptor interaction", "PI3K-Akt signaling pathway", "focal adhesion", "regulation of actin cytoskeleton", and several metabolism-related pathways in muscles. Moreover, numerous genes regulated by these ncrnas/ cerna networks emerged as potential candidates for SSD establishment, such as frizzled3 (fzd3), cholecystokinin A receptor (cckar), carbonic anhydrase 4 (ca4), and calcium voltage-gated channel subunit alpha1 B (cacna1b) in brains/ pituitaries, and DNA (cytosine-5) methyltransferase 3A (dnmt3a), Kr & uuml;ppel-like factor 11 (klf11), myocyte enhancer factor 2c (mef2c), insulin receptor (insr), serum- and glucocorticoid-inducible kinase 1 (sgk1), nuclear receptor 4A1 (nr4a1), and apelin in muscles. This study provides the first preliminary insights into the ncrnas and their cerna networks implicated in SSD-related growth traits in flounder, providing potential targets for selective breeding programs aimed at e

关键词： Sex-dependent growth differences Whole transcriptome non-coding rna Cerna network

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non-coding rnas: Regulators of valvular calcification

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JOUrnaL OF MOLECULAR AND CELLULAR CARDIOLOGY 2020年 142卷 14-23页

作者： Gupta, Shashi Kumar Kumari, Sunaina Singh, Sandhya Barthwal, Manoj Kumar Singh, Sushil Kumar Thum, Thomas CSIR Cent Drug Res Inst Pharmacol Div Lucknow Uttar Pradesh India King George Med Univ Dept Cardiovasc & Thorac Surg Lucknow Uttar Pradesh India Hannover Med Sch Inst Mol & Translat Therapeut Strategies Hannover Germany

There is currently a growing global burden of valvular heart diseases due to aging populations and changing lifestyles. Valvular heart diseases mainly include the malfunctioning of aortic and mitral valves and are characterized by extensive tissue remodeling, which includes calcification, endothelial dysfunction, and endothelial-mesenchymal transition. These valvular remodeling processes are known to be regulated by protein-coding genes as well as non-coding genes. Here, we have summarized studies highlighting the non-coding rna mediated regulation of valvular tissue remodeling and their potential therapeutic benefits. Additionally, studies investigating the diagnostic capability of circulating non-coding rna molecules in valvular diseases are also summarized. Overall, of the various candidates, several studies have highlighted miR-214 and miR-204 as central regulators of valvular calcification.

关键词： Microrna Lncrna Circular rna non-coding rna Valve calcification Valve stenosis

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The long and short: non-coding rnas in the mammalian inner ear

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HEARING RESEARCH 2023年第1期428卷 108666页

作者： Koffler-Brill, Tal Noy, Yael Avraham, Karen B. Tel Aviv Univ Fac Med Dept Human Mol Genet & Biochem IL-6997801 Tel Aviv Israel Tel Aviv Univ Sagol Sch Neurosci IL-6997801 Tel Aviv Israel

non-coding rnas (ncrnas) play a critical role in the entire body, and their mis-regulation is often as-sociated with disease. In parallel with the advances in high-throughput sequencing technologies, there is a great deal of focus on this broad class of rnas. Although these molecules are not translated into proteins, they are now well established as significant regulatory components in many biological path-ways and pathological conditions. ncrnas can be roughly divided into two main sub-groups based on the length of the transcript, with both the small and long non-coding rnas having diverse regulatory functions. The smaller length group includes ribosomal rnas (rrna), transfer rnas (trna), small nuclear rnas (snrna), small nucleolar rnas (snorna), micrornas (mirna), small interfering rnas (sirna), and PIWI-associated rnas (pirna). The longer length group includes linear long non-coding rnas (lncrna) and circular rnas (circrna). This review is designed to present the different classes of small and long ncrna molecules and describe some of their known roles in physiological and pathological conditions, as well as methods used to assess the validity and function of mirnas and lncrnas, with a focus on their role and functions in the inner ear, hearing and deafness.(c) 2022 Published by Elsevier B.V.

关键词： non-coding rna Microrna Long non-coding rna Inner ear Cochlea Hearing Deafness

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The Role of the Dysregulation of circrnas Expression in Glioblastoma Multiforme

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JOUrnaL OF MOLECULAR NEUROSCIENCE 2025年第1期75卷 1-24页

作者： Wang, Yafei Yu, Ying Yu, Jiahua Wang, Cheng Wang, Yunkun Fu, Runxi Zhang, Chenran Shanghai Jiao Tong Univ Xinhua Hosp Dept Pediat Neurosurg Sch Med Shanghai 200092 Peoples R China Shanghai Jiao Tong Univ Sch Med Shanghai 200025 Peoples R China Shanghai Jiao Tong Univ Xinhua Hosp Dept Pediat Surg Sch Med Shanghai 200092 Peoples R China Shanghai Inst Pediat Res Shanghai Peoples R China

Primary brain tumors that were the most severe and aggressive were called glioblastoma multiforme (GBM). Cancers are caused in part by aberrant expression of circular rna. Often referred to as competitive endogenous rna (cerna), circrna molecules act as "mirna sponges" in cells by decreasing the inhibitory impact of mirna on their target genes and hence raising the expression levels of those genes. circrna molecules are rich in mirna binding sites. The discovery of more structurally diverse and GBM-related circrnas has great promise for the use of GMB prognostic biomarkers and therapeutic targets, as well as for comprehending the molecular regulatory mechanisms of GBM. In this work, we present an overview of the circrna expression patterns associated with GBM and offer a potential integrated electrochemical strategy for detecting circrna with extreme sensitivity in the diagnosis of *** AbstractThe circular rna (circrna) regulates both physiological and pathological processes in glioblastoma multiforme disease. Hence, it could serve as a biomarker as well as a therapeutic target.

关键词： non-coding rna Microrna Glucose metabolism The tumor microenvironment Epithelial-to-mesenchymal transition Angiogenesis Drug resistance

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ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription

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JOUrnaL OF MOLECULAR BIOLOGY 2025年第1期437卷 168707页

作者： Estell, Chris West, Steven Univ Exeter Living Syst Inst Stocker Rd Exeter EX4 4QD Devon England

The regulation of transcription by rna polymerase II (rnaPII) underpins all cellular processes and is perturbed in thousands of diseases. In humans, rnaPII transcribes 20000 protein-coding genes and engages in apparently futile non-coding transcription at thousands of other sites. Despite being so ubiquitous, this transcription is usually attenuated soon after initiation and the resulting products are immediately degraded by the nuclear exosome. We and others have recently described a new complex, "Restrictor", which appears to control such unproductive transcription. Underpinned by the rna binding protein, ZC3H4, Restrictor curtails unproductive/pervasive transcription genome-wide. Here, we discuss these recent discoveries and speculate on some of the many unknowns regarding Restrictor function and mechanism. (c) 2024 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://***/licenses/by/4.0/).

关键词： restrictor rna polymerase II transcription termination non-coding rna PNUTS

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Modifications of rna in cancer: a comprehensive review

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MOLECULAR BIOLOGY REPORTS 2025年第1期52卷 1-19页

作者： Ranga, Shalu Yadav, Ritu Chauhan, Meenakshi Chhabra, Ravindresh Ahuja, Parul Balhara, Nikita Maharshi Dayanand Univ Dept Genet Rohtak 124001 Haryana India Pandit Bhagwat Dayal Sharma Univ Hlth Sci Dept Obstet & Gynaecol Rohtak 124001 Haryana India Cent Univ Panjab Dept Biochem Bathinda 151401 Panjab India

rna modifications play essential roles in post-transcriptional gene regulation and have emerged as significant contributors to cancer biology. Major chemical modifications of rna include N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudouridine (psi), and N7-methylguanosine (m7G). Their dynamic regulation highlights their roles in gene expression modulation, rna stability, and translation. Advanced high-throughput detection methods, ranging from liquid chromatography-mass spectrometry and high-performance liquid chromatography to next-generation sequencing (NGS) and nanopore direct rna sequencing, have enabled detailed studies of rna modifications in cancer cells. Aberrant rna modifications are associated with the dysregulation of tumor suppressor genes and oncogenes, influencing cancer progression, therapy resistance, and immune evasion. Emerging research suggests the therapeutic potential of targeting rna-modifying enzymes and their inhibitors in cancer treatment. This review compiles and analyzes the latest findings on rna modifications, presenting an in-depth discussion of the diverse chemical alterations that occur in rna and their profound implications in cancer biology. It integrates fundamental principles with cutting-edge research, offering a holistic perspective on how rna modifications influence gene expression, tumor progression, and therapeutic resistance. It emphasizes the need for further studies to elucidate the complex roles of rna modifications in cancer, as well as the potential for multimodality therapeutic strategies that exploit the dynamic and reversible nature of these epitranscriptomic marks. It also attempts to highlight the challenges, gaps, and limitations of rna modifications in cancer that should be tackled before their functional implications. Understanding the interplay between rna modifications, cancer pathways, and their inhibitors will be crucial for developing promising rna-based therapeutic approac

关键词： Chemical modifications rna methylation coding rna non-coding rna Tumorigenesis Epitranscriptomic marks rna-modifying enzymes Therapeutic strategies

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The Long-noncoding rnas: effective players in plant development and stress responses

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JOUrnaL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2025年第1期34卷 35-61页

作者： Bhat, Showkat Ahmad Najar, Mushtaq Ahmad Wani, Aijaz Ahmad Qadir, Shaista John, Riffat Univ Kashmir Dept Bot Plant Mol Biol Lab Srinagar 190006 Jammu & Kashmir India Bose Inst Dept Biol Sci EN 80 Sect 5 Kolkata 700091 India Univ Kashmir Dept Bot Cytogenet & Mol Breeding Lab Srinagar 190006 Jammu & Kashmir India Govt Degree Coll Women Dept Bot MA Rd Srinagar 190001 Jammu & Kashmir India

Plants adjust to the changing environment through intricate and highly regulated mechanisms of gene regulation. The genome of eukaryotes, both plants and animals, codes for protein-coding rna and non-protein-coding rna. Recent reports shed light on the key role of long non-coding rnas (lncrnas) in regulating not only gene expression networks but also growth and development in plants at epigenetic, transcriptional, and post-transcriptional levels. Here, we review the newly emerging updates and the role of lncrnas in modulating plant development ranging from the regulation of root development, lateral root development, symbiotic nodule formation, photomorphogenesis, and flowering. Furthermore, we have discussed the growing role of lncrnas in the regulation of plant cell response to environmental stress. Moreover, we have highlighted the biogenesis of lncrnas and their types, their role in rna-directed DNA methylation (RdDM), and how lncrnas act as scaffolds/sponges/decoys for protein modules for their proper functioning.

关键词： non-coding rna Lncrnas Gene regulation Plant-pathogen interactions Next-generation sequencing Abiotic stress

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Intercellular Epigenomic Signalling via Extracellular Vesicles During B Cell Maturation

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JOUrnaL OF EXTRACELLULAR VESICLES 2025年第1期14卷 e70040页

作者： Yim, Kevin Ho Wai Al Hrout, Ala'a Chahwan, Richard Univ Zurich Inst Expt Immunol Zurich Switzerland EVIIVE AG Zurich Switzerland

B cell maturation is crucial for effective adaptive immunity. It requires a complex signalling network to mediate antibody diversification through mutagenesis. B cells also rely on queues from other cells within the germinal centre. Recently, a novel class of intercellular signals mediated by extracellular vesicles (EVs) has emerged. Studies have shown that B cell EV-mediated signalling is involved in immune response regulation and tumorigenesis. However, the mechanistic role of B cell EVs is not yet established. We herein study the biological properties and physiological function of B cell EVs during B cell maturation. We use emerging technologies to profile B cell EV surface marker signatures at the single particle level, molecular cargo and physiological roles in B cell maturation. EV ncrna cargo, characterised by rna-seq, identified an EV-mediated novel non-coding rna (ncrna) regulatory network for B cell maturation. We show that a previously uncharacterised micro-rna (miR-5099) in combination with a set of long ncrna are carried within B cell EVs and could contribute to antibody diversification. The physiological role of EVs in B cell maturation is investigated using EV blockade assays and complementation studies using diverse EV sources further confirmed the physiological role and mode of action of EVs in B cell maturation.

关键词： antibody maturation extracellular vesicles intercellular epigenomic signalling non-coding rna single particle analysis

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Broadening horizons: molecular mechanisms and disease implications of endothelial-to-mesenchymal transition

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CELL COMMUNICATION AND SIGNALING 2025年第1期23卷 1-21页

作者： Qian, Cheng Dong, Guanglu Yang, Chunmei Zheng, Weiwei Zhong, Chongjin Shen, Qiuhong Lu, Yin Zhao, Yang Nanjing Univ Chinese Med Sch Med Nanjing 210023 Peoples R China Nanjing Univ Chinese Med Jiangsu Key Lab Pharmacol & Safety Evaluat Chinese Jiangsu Joint Int Res Lab Chinese Med & Regenerat Nanjing 210023 Peoples R China

Endothelial-mesenchymal transition (EndMT) is defined as an important process of cellular differentiation by which endothelial cells (ECs) are prone to lose their characteristics and transform into mesenchymal cells. During EndMT, reduced expression of endothelial adhesion molecules disrupts intercellular adhesion, triggering cytoskeletal reorganization and mesenchymal transition. Numerous studies have proved that EndMT is a multifaceted biological event driven primarily by cytokines such as TGF-beta, TNF-alpha, and IL-1 beta, alongside signaling pathways like WNT, Smad, MEK-ERK, and Notch. Nevertheless, the exact roles of EndMT in complicated diseases have not been comprehensively reviewed. In this review, we summarize the predominant molecular regulatory mechanisms and signaling pathways that contribute to the development of EndMT, as well as highlight the contributions of a series of imperative non-coding rnas in curbing the initiation of EndMT. Furthermore, we discuss the significant impact of EndMT on worsening vasculature-related diseases, including cancer, cardiovascular diseases, atherosclerosis, pulmonary vascular diseases, diabetes-associated fibrotic conditions, and cerebral cavernous malformation, providing the implications that targeting EndMT holds promise as a therapeutic strategy to mitigate disease progression.

关键词： Endothelial-mesenchymal transition Endothelial cells Mesenchymal phenotype non-coding rna TGF-beta signaling pathway

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