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Fundamental Neurochemistry Review: At the intersection between the brain and the immune system: non-coding rnas spanning learning, memory and adaptive immunity

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JOUrnaL OF NEUROCHEMISTRY 2024年第6期168卷 961-976页

作者： Musgrove, Mason R. B. Mikhaylova, Marina Bredy, Timothy W. Univ Queensland Queensland Brain Inst Brisbane Qld Australia Humboldt Univ Inst Biol AG Optobiol Berlin Germany

non-coding rnas (ncrnas) are highly plastic rna molecules that can sequester cellular proteins and other rnas, serve as transporters of cellular cargo and provide spatiotemporal feedback to the genome. Mounting evidence indicates that ncrnas are central to biology, and are critical for neuronal development, metabolism and intra- and intercellular communication in the brain. Their plasticity arises from state-dependent dynamic structure states that can be influenced by cell type and subcellular environment, which can subsequently enable the same ncrna with discrete functions in different contexts. Here, we highlight different classes of brain-enriched ncrnas, including microrna, long non-coding rna and other enigmatic ncrnas, that are functionally important for both learning and memory and adaptive immunity, and describe how they may promote cross-talk between these two evolutionarily ancient biological systems.

关键词： adaptive immunity learning memory non-coding rna vault-associated rna Y-rna

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Identification of the long non-coding rna H19 in plasma as a novel biomarker for diagnosis of gastric cancer

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SCIENTIFIC REPORTS 2015年第1期5卷 11516-11516页

作者： Zhou, Xiaoying Yin, Chengqiang Dang, Yini Ye, Feng Zhang, Guoxin Nanjing Med Univ Affiliated Hosp 1 Dept Gastroenterol Nanjing 210029 Jiangsu Peoples R China Nanjing Med Univ Clin Med Coll 1 Nanjing 210029 Jiangsu Peoples R China

Recent studies have demonstrated that long non-coding rnas (lncrnas) are regarded as useful tools for cancer detection, particularly for the early stage;however, little is known about their diagnostic impact on gastric cancer (GC). We hypothesized that GC-related lncrnas might release into the circulation during tumor initiation and could be utilized to detect and monitor GC. 8 lncrnas which previously found to be differently expressed in GC were selected as candidate targets for subsequent circulating lncrna assay. After validating in 20 pairs of tissues and plasma in training set, H19 was selected for further analysis in another 70 patients and 70 controls. Plasma level of H19 was significantly higher in GC patients compared with normal controls (p < 0.0001). By receiver operating characteristic curve (ROC) analysis, the area under the ROC curve (AUC) was 0.838;p < 0.001;sensitivity, 82.9%;specificity, 72.9%). Furthermore, H19 expression enabled the differentiation of early stage GC from controls with AUC of 0.877;sensitivity, 85.5%;specificity, 80.1%. Besides, plasma levels of H19 were significantly lower in postoperative samples than preoperative samples (p = 0.001). In conclusion, plasma H19 could serve as a potential biomarker for diagnosis of GC, in particular for early tumor screening.

关键词： non-coding rna BLOOD plasma BIOCHEMICAL markers EARLY detection of cancer POLYMERASE chain reaction

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From non-coding rnas to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation

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PLANT PHYSIOLOGY AND BIOCHEMISTRY 2024年 215卷 109070页

作者： Chen, Shengbo Han, Jiazhen Wu, Shu Guo, Shangjing Tang, Yufei Zheng, Yujing Hu, Lei Zhang, Xingxing Zhang, Peng Zhang, Haifeng Ren, Guodong Gao, Shuai Zhejiang A&F Univ Coll Hort Sci Key Lab Qual & Safety Control Subtrop Fruit & Vege Minist Agr & Rural Affairs Hangzhou 311300 Peoples R China Fudan Univ State Key Lab Genet Engn Minist EducSch Life Sci Key Lab Biodivers Sci & Ecol EngnInst Plant Biol Shanghai 200438 Peoples R China Zhejiang Acad Agr Sci Hangzhou 310021 Peoples R China Qingdao Agr Univ Qingdao 266109 Peoples R China Zhejiang DILONG New Mat Co Ltd Hangzhou Peoples R China

Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, rna modifications, and non-coding rnas. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/rna modifications, non-coding rnas, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.

关键词： Epigenetic regulation Tomato fruit ripening Fruit quality non-coding rna DNA methylation

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Predicted roles of long non-coding rnas in abiotic stress tolerance responses of plants

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Molecular Horticulture 2024年第1期4卷 349-364页

作者： IUH Imaduwage Madhavi Hewadikaram Department of Biomedical Sciences Faculty of ScienceNSBM Green UniversityPitipanaHomagamaSri Lanka

The plant genome exhibits a significant amount of transcriptional activity,with most of the resulting transcripts lacking protein-coding ***-coding rnas play a pivotal role in the development and regulatory processes in *** non-coding rnas(lncrnas),which exceed 200 nucleotides,may play a significant role in enhancing plant resilience to various abiotic stresses,such as excessive heat,drought,cold,and *** addition,the exogenous application of chemicals,such as abscisic acid and salicylic acid,can augment plant defense responses against abiotic *** how lncrnas play a role in abiotic stress tolerance is relatively well-studied in model plants,this review provides a comprehensive overview of the current understanding of this function in horticultural crop *** also delves into the potential role of lncrnas in chemical priming of plants in order to acquire abiotic stress tolerance,although many limitations exist in proving lncrna functionality under such conditions.

关键词： Abiotic stress Chemical treatment Defense response Long non-coding rna non-coding rna Plant stress

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non-coding rna derived from a conservative subtelomeric tandem repeat in chicken and Japanese quail somatic cells

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MOLECULAR CYTOGENETICS 2014年第1期7卷 1-13页

作者： Trofimova, Irina Popova, Darya Vasilevskaya, Elena Krasikova, Alla St Petersburg State Univ Dept Cytol & Histol St Petersburg 198504 Russia

Background: Subtelomeres are located close to the ends of chromosomes and organized by tandemly repetitive sequences, duplicated copies of genes, pseudogenes and retrotransposons. Transcriptional activity of tandemly organized DNA at terminal chromosomal regions and the distribution of subtelomere-derived non-coding rnas are poorly investigated. Here we aimed to analyze transcriptional activity of subtelomeric tandem repeat in somatic tissues and cultured cells of birds. We focused on tissue-specific differences of subtelomeric repeats transcription, structure of the resulting transcripts and the behavior of subtelomere-derived rna during mitosis. Results: Transcriptional activity of short subtelomeric PO41 ("pattern of 41 bp") tandem repeat in the somatic and cultured cells of chicken (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica) was examined using rna fluorescence in situ hybridization approach. We discovered transcripts from both strands of the PO41 repeat in chicken MDCC-MSB1 cells as well as in chicken and Japanese quail somatic tissues, such as tissues of cerebellum, telencephalon, muscles, oviduct, small and large intestine. Normal somatic and transformed cells demonstrate similar distribution of PO41 repeat transcripts in interphase nuclei. We revealed one or two major foci of PO41 repeat transcripts associated with rna polymerase II, representing nascent rna, and dispersed PO41 repeat transcripts localized in euchromatin or interchromatin space, representing released rna. During mitosis PO41 non-coding rna distribute between condensed chromosomes till anaphase, when they concentrate at the cleavage plane. At telophase, clusters of PO41 rna surround terminal regions of chromosomes. Treatments with rnases of different substrate specificity indicate that PO41 repeat transcripts are single-stranded rnas with short double-stranded regions due to appearance of inverted repeats. Conclusion: Transcription of a subtelomeric tandem repeat

关键词： Cell cycle Cell nucleus Chicken Mitosis non-coding rna Subtelomere Tandem repeats Transcription

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non-coding rna enhances cardiac development

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JOUrnaL OF MOLECULAR AND CELLULAR CARDIOLOGY 2014年 76卷 205-207页

作者： Hofmann, Patrick Boon, Reinier A. Goethe Univ Frankfurt Ctr Mol Med Inst Cardiovasc Regenerat D-60054 Frankfurt Germany

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E. coli OxyS non-coding rna does not trigger rnai in C. elegans

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SCIENTIFIC REPORTS 2015年第1期5卷 9597-9597页

作者： Akay, Alper Sarkies, Peter Miska, Eric A. Univ Cambridge Wellcome Trust Canc Res UK Gurdon Inst Cambridge CB2 1QN England Univ Cambridge Dept Biochem Cambridge CB2 1QN England Univ Cambridge Dept Genet Cambridge CB2 1QN England

The discovery of rna interference (rnai) in C. elegans has had a major impact on scientific research, led to the rapid development of rnai tools and has inspired rna-based therapeutics. Astonishingly, nematodes, planaria and many insects take up double-stranded rna (dsrna) from their environment to elicit rnai;the biological function of this mechanism is unclear. Recently, the E. coli OxyS non-coding rna was shown to regulate gene expression in C. elegans when E. coli is offered as food. This was surprising given that C. elegans is unlikely to encounter E. coli in nature. To directly test the hypothesis that the E. coli OxyS non-coding rna triggers the C. elegans rnai pathway, we sequenced small rnas from C. elegans after feeding with bacteria. We clearly demonstrate that the OxyS non-coding rna does not trigger an rnai response in C. elegans. We conclude that the biology of environmental rnai remains to be discovered.

关键词： CAENORHABDITIS elegans rna interference GENE expression ESCHERICHIA coli genetics rna polymerases non-coding rna

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A potential prognostic long non-coding rna signature to predict metastasis-free survival of breast cancer patients

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SCIENTIFIC REPORTS 2015年第1期5卷 16553-16553页

作者： Sun, Jie Chen, Xihai Wang, Zhenzhen Guo, Maoni Shi, Hongbo Wang, Xiaojun Cheng, Liang Zhou, Meng Harbin Med Univ Coll Bioinformat Sci & Technol Harbin 150081 Peoples R China Harbin Med Univ Affiliated Hosp 4 Dept Gen Surg Harbin 150081 Peoples R China

Long non-coding rnas (lncrnas) have been implicated in a variety of biological processes, and dysregulated lncrnas have demonstrated potential roles as biomarkers and therapeutic targets for cancer prognosis and treatment. In this study, by repurposing microarray probes, we analyzed lncrna expression profiles of 916 breast cancer patients from the Gene Expression Omnibus (GEO). Nine lncrnas were identified to be significantly associated with metastasis-free survival (MFS) in the training dataset of 254 patients using the Cox proportional hazards regression model. These nine lncrnas were then combined to form a single prognostic signature for predicting metastatic risk in breast cancer patients that was able to classify patients in the training dataset into high- and low-risk subgroups with significantly different MFSs (median 2.4 years versus 3.0 years, log-rank test p < 0.001). This nine-lncrna signature was similarly effective for prognosis in a testing dataset and two independent datasets. Further analysis showed that the predictive ability of the signature was independent of clinical variables, including age, ER status, ESR1 status and ERBB2 status. Our results indicated that lncrna signature could be a useful prognostic marker to predict metastatic risk in breast cancer patients and may improve upon our understanding of the molecular mechanisms underlying breast cancer metastasis.

关键词： non-coding rna METASTASIS PROGNOSIS BREAST cancer patients BIOCHEMICAL markers GENE expression

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non-coding rnas in ferroptotic cancer cell death pathway: meet the new masters

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HUMAN CELL 2022年第4期35卷 972-994页

作者： Valashedi, Mehdi Rabiee Bamshad, Chia Najafi-Ghalehlou, Nima Nikoo, Amirsadegh Tomita, Kazuo Kuwahara, Yoshikazu Sato, Tomoaki Roushandeh, Amaneh Mohammadi Roudkenar, Mehryar Habibi Guilan Univ Med Sci Fac Paramed Dept Med Biotechnol Rasht Iran Tabriz Univ Med Sci Fac Paramed Dept Med Lab Sci Tabriz Iran Kagoshima Univ Grad Sch Med & Dent Sci Dept Appl Pharmacol Kagoshima Japan Tohoku Med & Pharmaceut Univ Fac Med Div Radiat Biol & Med Sendai Miyagi Japan Guilan Univ Med Sci Heshmat Hosp Cardiovasc Dis Res Ctr Sch MedDept Cardiol Rasht Iran Guilan Univ Med Sci Velayat Hosp Burn & Regenerat Med Res Ctr Sch Med Rasht Iran

Despite the recent advances in cancer therapy, cancer chemoresistance looms large along with radioresistance, a major challenge in dire need of thorough and minute investigation. Not long ago, cancer cells were reported to have proven refractory to the ferroptotic cell death, a newly discovered form of regulated cell death (RCD), conspicuous enough to draw attention from scholars in terms of targeting ferroptosis as a prospective therapeutic strategy. However, our knowledge concerning the underlying molecular mechanisms through which cancer cells gain immunity against ferroptosis is still in its infancy. Of late, the implication of non-coding rnas (ncrnas), including circular rnas (circrnas), micrornas (mirnas), and long non-coding rnas (lncrnas) in ferroptosis has been disclosed. Nevertheless, precisely explaining the molecular mechanisms behind the contribution of ncrnas to cancer radio/chemotherapy resistance remains a challenge, requiring further clarification. In this review, we have presented the latest available information on the ways and means of regulating ferroptosis by ncrnas. Moreover, we have provided important insights about targeting ncrnas implicated in ferroptosis with the hope of opening up new horizons for overcoming cancer treatment modalities. Though a long path awaits until we make this ambitious dream come true, recent progress in gene therapy, including gene-editing technology will aid us to be optimistic that ncrnas-based ferroptosis targeting would soon be on stream as a novel therapeutic strategy for treating cancer.

关键词： Ferroptosis non-coding rna Cancer therapy Cell death Oxidative stress

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non-coding rnas and glioblastoma: Insight into their roles in metastasis

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MOLECULAR THERAPY ONCOLYTICS 2022年 24卷 262-287页

作者： Mousavi, Seyed Mojtaba Derakhshan, Maryam Baharloii, Fatereh Dashti, Fatemeh Mirazimi, Seyed Mohammad Ali Mahjoubin-Tehran, Maryam Hosseindoost, Saereh Goleij, Pouya Rahimian, Neda Hamblin, Michael R. Mirzaei, Hamed Univ Tehran Med Sci Sch Adv Technol Med Dept Neurosci & Addict Studies Tehran Iran Isfahan Univ Med Sci Dept Pathol Esfahan Iran Isfahan Univ Med Sci Chamran Cardiovasc Res Educ Hosp Dept Cardiol Esfahan Iran Kashan Univ Med Sci Sch Med Kashan Iran Kashan Univ Med Sci Student Res Comm Kashan Iran Mashhad Univ Med Sci Fac Med Dept Med Biotechnol & Nanotechnol Mashhad Iran Univ Tehran Med Sci Imam Khomeini Hosp Brain & Spinal Cord Res Ctr Tehran Iran Sana Inst Higher Educ Fac Biol Dept Genet Sari Iran Iran Univ Med Sci IUMS Endocrine Res Ctr Inst Endocrinol & Metab Tehran Iran Univ Johannesburg Fac Hlth Sci Laser Res Ctr ZA-2028 Doornfontein South Africa Iran Univ Med Sci Radiat Biol Res Ctr Tehran Iran Kashan Univ Med Sci Res Ctr Biochem & Nutr Metab Dis Inst Basic Sci Kashan Iran Iran Univ Med Sci Firoozgar Hosp Sch Med Dept Internal Med Tehran Iran

Glioma, also known as glioblastoma multiforme (GBM), is the most prevalent and most lethal primary brain tumor in adults. Gliomas are highly invasive tumors with the highest death rate among all primary brain malignancies. Metastasis occurs as the tumor cells spread from the site of origin to another site in the brain. Metastasis is a multifactorial process, which depends on alterations in metabolism, genetic mutations, and the cancer microenvironment. During recent years, the scientific study of non-coding rnas (ncrnas) has led to new insight into the molecular mechanisms involved in glioma. Many studies have reported that ncrnas play major roles in many biological procedures connected with the development and progression of glioma. Long ncrnas (lncrnas), micrornas (mirnas), and circular rnas (circrnas) are all types of ncrnas, which are commonly dysregulated in GBM. Dysregulation of ncrnas can facilitate the invasion and metastasis of glioma. The present review highlights some ncrnas that have been associated with metastasis in GBM. mirnas, circrnas, and lncrnas are discussed in detail with respect to their relevant signaling pathways involved in metastasis.

关键词： glioblastoma non-coding rna metastasis microrna long non-coding rna circular rna

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