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The perinucleolar compartment and the oncogenic super-enhancers are part of the same phase-separated structure filled with phosphatidylinositol 4,5-bisphosphate and long non-coding rna HANR

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ADVANCES IN BIOLOGICAL REGULATION 2025年 95卷 101069页

作者： Miladinovic, Ana Antiga, Ludovica Venit, Tomas Bayona-Hernandez, Andrea Cervenka, Jakub Labala, Rajendra Kumar Kolar, Michal Castano, Enrique Sztacho, Martin Hozak, Pavel Czech Acad Sci Inst Mol Genet Dept Biol Cell Nucl Prague Czech Republic Ctr Invest Cient Yucatan Unidad Biol Integrat Calle 43130 Chuburna Hidalgo Merida 97205 Yucatan Mexico Charles Univ Prague Inst Biochem & Expt Oncol Fac Med 1 Lab prote Prague Czech Republic Czech Acad Sci Inst Anim Physiol & Genet Res Ctr PIGMOD Lab Appl Proteome Anal Libechov Czech Republic Czech Acad Sci Inst Mol Genet Lab Genom & Bioinformat Prague Czech Republic Charles Univ Prague Inst Biochem & Expt Oncol Fac Med 1 Lab Canc Cell Architecture Prague Czech Republic

The liquid-liquid phase separation in the cell nucleus regulates various processes such as gene regulation and transcription control, chromatin organization, and DNA repair. A plethora of proteins and rnas contribute to the formation of biomolecular condensates and recently, several nuclear phosphoinositides were shown to be a part of these membrane-less complexes within the nucleus as well. Here we lipid-interacting rna sequencing (LIPrnaseq) and confocal microscopy to uncover the rna-binding capacity and localization of phosphatidylinositol 4,5 bisphosphate (PIP2). We discovered the consensus PIP2-binding AU-rich rna motif and identified long non- coding rna HANR (lncHANR) to colocalize with PIP2 in the proximity to the nucleolus in the perinucleolar compartment (PNC). Colocalization studies with different nuclear markers reveal that PIP2-HANR presence in the PNC correlates with oncogenic super-enhancers, and both PNC and oncogenic enhancers are part of the same structure. As lncHANR, PNC, and oncogenic super- enhancers are associated with cancer cell lines and tumors, we suggest that they can serve as interchangeable prognostic markers. Understanding of the interplay between lipid metabolism,

关键词： Phase separation Perinucleolar compartment PNC Oncogenic super-enhancers long non-coding rna Phosphatidylinositol 4 5-bisphosphate PIP2 HANR

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long non-coding rna in the regulation of cell death in hepatocellular carcinoma

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World Journal of Clinical Oncology 2025年第4期16卷 9-20页

作者： Jiang Wang Zi-Xuan Liu Zhi-Hong Huang Jie Wen Zhou-Zhou Rao Children Medical Center Hunan Provincial People's HospitalThe First Affiliated Hospital of Hunan Normal UniversityChangsha 410013Hunan ProvinceChina Department of Pediatric Orthopedics Hunan Provincial People's HospitalThe First Affiliated Hospital of Hunan Normal UniversityChangsha 410013Hunan ProvinceChina Department of Physiology Hunan Normal University School of MedicineChangsha 410003Hunan ProvinceChina

Hepatocellular carcinoma(HCC)is the predominant form of primary liver cancer,accounting for 90%of all ***,early diagnosis of HCC can be achieved through serum alpha-fetoprotein detection,B-ultrasound,and computed tomography scanning;however,their specificity and sensitivity are *** significant advancements in HCC biomarker detection,the prognosis for patients with HCC remains unfavorable due to tumor heterogeneity and limited understanding of its ***,it is crucial to explore more sensitive HCC biomarkers for improved diagnosis,monitoring,and management of the *** non-coding rna(lncrna)serves as an auxiliary carrier of genetic information and also plays diverse intricate regulatory roles that greatly contribute to genome ***,investigating gene expression regulation networks from the perspective of lncrna may provide insights into the diagnosis and prognosis of *** searched the PubMed database for literature,comprehensively classified regulated cell death mechanisms and systematically reviewed research progress on lncrna-mediated cell death pathways in HCC ***,we prospectively summarize its potential implications in diagnosing and treating HCC.

关键词： Hepatocellular carcinoma long non-coding rna Necrosis Apoptosis Iron death Autophagy Cell death

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long non-coding rna LRTOR drives osimertinib resistance in non-small cell lung cancer by boosting YAP positive feedback loop

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Drug Resistance Updates 2025年 101245页

作者： Miao, Zhimin Sha, Zhou He, Jianzhong Liang, Yongkai Tan, Lihua Zhao, Yuxin Cui, Xiaobing Zhong, Jinmiao Zhong, Ruting Liang, Huijun Yue, Wendi Qiu, Boyang Gao, Yunzhen Zhang, Lan Teng, Zixin He, Zeen Chen, Li Xiao, Rufei Pei, Xiaofeng He, Chengwei State Key Laboratory of Quality Research in Chinese Medicine Institute of Chinese Medical Sciences University of Macau Macao SAR Taipa 999078 China Department of Pharmaceutical Sciences Faculty of Health Sciences University of Macau Macao SAR Taipa 999078 China Department of Thoracic Oncology The Cancer Center of The Fifth Affiliated Hospital of Sun Yat-sen University Zhuhai 519000 China Department of Pathology The Fifth Affiliated Hospital of Sun Yat-sen University Zhuhai 519000 China

The therapeutic efficacy of osimertinib (OSI) in EGFR-mutant lung cancer is ultimately limited by the onset of acquired resistance, of which the mechanisms remain poorly understood. Here, we identify a novel long non-coding rna, LRTOR, as a key driver of OSI resistance in non-small cell lung cancer (NSCLC). Clinical data indicate that elevated LRTOR expression correlates with poor prognosis in OSI-resistant patients. Functionally, LRTOR promotes tumor growth and confers OSI resistance both in vitro and in vivo. Mechanistically, LRTOR shields YAP from LATS-mediated phosphorylation at Ser127 and Ser381, preventing its proteasomal degradation. Furthermore, LRTOR facilitates the interaction between YAP and KCMF1, promoting K63-linked ubiquitination, nuclear translocation of YAP, and formation of the YAP/TEAD1 transcriptional complex, which in turn triggers the transcription of LRTOR, establishing a positive feedback loop that amplifies oncogenic signaling of YAP and consequently induces OSI resistance. LRTOR depletion by sirna restores OSI sensitivity in resistant tumors, as demonstrated in patient-derived organoid xenograft models. Our findings unveil LRTOR as a central regulator of OSI resistance in NSCLC and propose it as a promising therapeutic and prognostic target for overcoming acquired OSI resistance in EGFR-mutant lung cancer. © 2025 The Authors

关键词： long non-coding rna non-small cell lung cancer Osimertinib resistance Yes-associated protein

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From non-coding to coding: The importance of long non-coding rna translation in de novo gene birth

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BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 2025年第2期1869卷 130747页

作者： Shiraishi, Taichi Matsumoto, Akinobu Nagoya Univ Grad Sch Sci Div Biol Sci Nagoya 4648602 Japan

Recent emerging evidence demonstrates that some long non-coding rnas (lncrnas) can indeed be translated into functional polypeptides. These discoveries are pivotal for understanding de novo gene birth, the process by which new genes evolve from previously non-genic regions. In this review, we first introduce key methods, such as Ribo-seq and translation initiation site detection by translation complex analysis, for identifying coding sequences within lncrnas and highlight examples of functional polypeptides derived from lncrnas across species. These polypeptides play essential roles in maintaining cellular homeostasis and contribute to pathological processes, including cancer. However, because not all lncrna-derived polypeptides appear to be functional, these lncrnas may act as gene reservoirs. We also discuss how lncrnas change their intracellular localization, how lncrna-derived polypeptides evade immune surveillance, and how they gradually evolve into typical coding rnas, providing evidence for the evolutionary model of de novo gene birth.

关键词： long non-coding rna Translation Ribo-seq Translation initiation site detection by translation complex analysis Polypeptide De novo gene birth

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Effect of long-stranded non-coding rna-BANCR on the progression of thyroid papillary carcinoma and its mechanism

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DISCOVER ONCOLOGY 2025年第1期16卷 1-11页

作者： Yu, Jiayi Hong, Kai Yao, Lingli Shi, Dongbo Zhang, Jiabo Ningbo Univ Med Sch Ningbo 315211 Zhejiang Peoples R China Zhejiang Univ Affiliated Hosp 4 Sch Med Ctr Metab Med Yiwu 322000 Peoples R China Zhejiang Univ Int Inst Med Int Sch Med Yiwu 322000 Peoples R China Ningbo Univ Dept Breast Surg Affiliated Hosp 1 Ningbo 315010 Zhejiang Peoples R China

Objective This study aims to investigate the role of BRAF-activated long non-coding rna (BANCR) in papillary thyroid carcinoma (PTC) progression and its association with clinical and molecular characteristics. Methods Sixteen PTC patients were stratified into four groups (PTC, HT, HT-LNM, and PTC-LNM) based on cervical lymph node metastasis and concurrent Hashimoto's thyroiditis (HT) to explore BANCR expression and its relationship with immune-related factors and tumor microenvironment (TME). Functional assays, including Transwell invasion, colony formation, and CCK8 were performed to evaluate the biological effects of BANCR in PTC cell lines. Bioinformatics analysis further identified BANCR-related pathways and clinical relevance. Results BANCR expression was significantly reduced in PTC tissues compared to normal thyroid tissues and was inversely correlated with tumor grade, lymph node metastasis, and T stage. Overexpression of BANCR in PTC cell lines inhibited proliferation, invasion and migration. Bioinformatics analysis demonstrated significant associations between BANCR and immune cell infiltration, immune-related genes, and stromal scores. Conclusions BANCR acts as a tumor suppressor in PTC, suppressing tumor growth and metastasis. These findings provide insights into BANCR's potential as a prognostic marker and therapeutic target in PTC.

关键词： long non-coding rna BANCR Papillary thyroid carcinoma Hashimoto's thyroiditis

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long non-coding rna HOTAIR Is Targeted and Regulated by miR-141 in Human Cancer Cells

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JOUrnaL OF BIOLOGICAL CHEMISTRY 2014年第18期289卷 12550-12565页

作者： Chiyomaru, Takeshi Fukuhara, Shinichiro Saini, Sharanjot Majid, Shahana Deng, Guoren Shahryari, Varahram Chang, Inik Tanaka, Yuichiro Enokida, Hideki Nakagawa, Masayuki Dahiya, Rajvir Yamamura, Soichiro San Francisco VA Med Ctr Dept Urol San Francisco CA 94121 USA Univ Calif San Francisco San Francisco CA 94121 USA Yonsei Univ Coll Dent Dept Oral Biol Seoul 120752 South Korea Kagoshima Univ Grad Sch Med & Dent Sci Dept Urol Kagoshima 8908520 Japan

Background: Silencing of long non-coding rna (lncrna) by microrna (mirna) has only been recently observed. Results: miR-141 binds to HOTAIR and suppresses its oncogenic function in Ago2 (Argounaute2). Conclusion: miR-141 targets and silences HOTAIR in an Ago2-dependent manner in cancer cells. Significance: Our results suggest that regulation of lncrna expression by mirna plays essential roles in gene expression and cellular functions. HOTAIR is a long non-coding rna that interacts with the polycomb repressive complex and suppresses its target genes. HOTAIR has also been demonstrated to promote malignancy. Microrna-141 (miR-141) has been reported to play a role in the epithelial to mesenchymal transition process, and the expression of miR-141 is inversely correlated with tumorigenicity and invasiveness in several human cancers. We found that HOTAIR expression is inversely correlated to miR-141 expression in renal carcinoma cells. HOTAIR promotes malignancy, including proliferation and invasion, whereas miR-141 suppresses malignancy in human cancer cells. miR-141 binds to HOTAIR in a sequence-specific manner and suppresses HOTAIR expression and functions, including proliferation and invasion. Both HOTAIR and miR-141 were associated with the immunoprecipitated Ago2 (Argonaute2) complex, and the Ago2 complex cleaved HOTAIR in the presence of miR-141. These results demonstrate that HOTAIR is suppressed by miR-141 in an Ago2-dependent manner.

关键词： Cancer Biology Cell Growth Gene Regulation Invasion Microrna Genistein HOTAIR long non-coding rna miR-141 Renal Carcinoma

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long non-coding rna DUXAP9 promotes hepatocellular carcinoma cell stemness via directly interacting with sox9

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ENVIRONMENTAL TOXICOLOGY 2021年第9期36卷 1793-1801页

作者： Zeng, Ru Wang, Chunyue Wang, Wenyi Wang, Shuangjia Xiamen Univ Dept Med Oncol Affiliated Hosp 1 Xiamen Fujian Peoples R China Xiamen Univ Dept Hepatobiliary Pancreat & Vasc Surg Affiliated Hosp 1 Xiamen Fujian Peoples R China

long non-coding rna (Lncrna) DUXAP9 expression was recently found to be higher in hepatocellular carcinoma (HCC) tissues and cells, and correlated with a shorter overall survival of HCC patients. However, its roles in HCC progression have never been revealed. Here, the roles of DUXAP9 in HCC cell stemness are explored as cancer stem cells (CSCs) contribute to one of the root of cancer progression. We found that DUXAP9 positively regulated HCC cell stemness, as characterized by the change of sphere-formation ability, ALDH activity and stemness marker expression. Further luciferase reporter, mrna stability and rna-rna in vitro interaction assays indicated that DUXAP9 directly bound to the 3 ' untranslated region (UTR) of sox9, enhanced the mrna stability of sox9 and thus increased sox9 expression. Notably, the effects induced by DUXAP9 on HCC cell stemness depended on sox9 expression. Therefore, this work identifies a novel DUXAP9/sox9 axis essential for HCC cell stemness.

关键词： DUXAP9 hepatocellular carcinoma long non-coding rna Sox9 stemness

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long non-coding rna TDRG1 aggravates colorectal cancer stemness by binding with miR-873-5p to upregulate PRKAR2

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ENVIRONMENTAL TOXICOLOGY 2022年第10期37卷 2366-2374页

作者： Hong, Qingqi Mai, Peishan Wu, Bin Wang, Haibin Xiao, Mingzhe You, Jun Xiamen Univ Dept Gastrointestinal Oncol Surg Affiliated Hosp 1 Sch Med Xiamen 361003 Peoples R China Fujian Med Univ Sch Clin Med Xiamen Peoples R China Fujian Med Univ Grad Sch Xiamen Peoples R China Xiamen Univ Affiliated Hosp 1 Sch Med Dept Radiol Xiamen Peoples R China Jiangsu Simcere Diagnost Co Ltd State Key Lab Translat Med & Innovat Drug Dev Nanjing Peoples R China

The effects of long non-coding rna TDRG1 have been established in several tumors;however, its roles in colorectal cancer (CRC) progression are never been found. Here, we found that TDRG1 level was upregulated in CRC cells compared to that in normal colon epithelial cells. Additionally, TDRG1 level was remarkably upregulated in 3D non-adherent spheres derived from the parental CRC cells. Further in vitro and in vivo revealed that TDRG1 knockdown suppressed the stemness of CRC cells. What's more, combined with bioinformatics analysis, luciferase reporter and rna pull down experiments showed that TDRG1 could bind to miR-873-5p, downregulated its level and thus increase the expression of PRKAR2. Finally, it was shown that TDRG1 functioned through the miR-873-5p/PRKAR2 axis. This study demonstrated a novel TDRG1/miR-873-5p/PRKAR2 signaling in CRC progression.

关键词： colorectal cancer long non-coding rna MiR-873-5p PRKAR2 Stemness

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long non-coding rna MEG3 regulates autophagy after cerebral ischemia/reperfusion injury

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Neural Regeneration Research 2022年第4期17卷 824-831页

作者： Tian-Hao Li Hong-Wei Sun Lai-Jun Song Bo Yang Peng Zhang Dong-Ming Yan Xian-Zhi Liu Yu-Ru Luo Department of Neurosurgery The First Affiliated Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina

Severe cerebral ischemia/reperfusion injury has been shown to induce high-level autophagy and neuronal ***,it is extremely important to search for a target that inhibits autophagy *** non-coding rna MEG3 participates in ***,it remains unclear whether it can be targeted to regulate cerebral ischemia/reperfusion *** results revealed that in oxygen and glucose deprivation/reoxygenation-treated HT22 cells,MEG3 expression was obviously upregulated,and autophagy was increased,while knockdown of MEG3 expression greatly reduced ***,MEG3 bound mi R-181 c-5 p and inhibited its expression,while mi R-181 c-5 p bound to autophagy-related gene ATG7 and inhibited its *** experiments revealed that mir-181 c-5 p overexpression reversed the effect of MEG3 on autophagy and ATG7 expression in HT22 cells subjected to oxygen and glucose deprivation/*** vivo experiments revealed that MEG3 knockdown suppressed autophagy,infarct volume and behavioral deficits in cerebral ischemia/reperfusion *** findings suggest that MEG3 knockdown inhibited autophagy and alleviated cerebral ischemia/reperfusion injury through the mi R-181 c-5 p/ATG7 signaling ***,MEG3 can be considered as an intervention target for the treatment of cerebral ischemia/reperfusion *** study was approved by the Animal Ethics Committee of the First Affiliated Hospital of Zhengzhou University,China(approval ***20190538)on January 4,2019.

关键词： ATG7 autophagy cerebral infarction cerebral ischemia/reperfusion injury long non-coding rna miR-181c-5p neuron oxygen and glucose deprivation/reoxygenation

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long non-coding rna molecules in tuberculosis

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INTErnaTIONAL JOUrnaL OF BIOLOGICAL MACROMOLECULES 2020年第0期156卷 340-346页

作者： Fathizadeh, Hadis Hayat, Seyed Mohammad Gheibi Dao, Sounkalo Ganbarov, Khudaverdi Tanomand, Asghar Asgharzadeh, Mohammad Kafil, Hossein Samadi Kashan Univ Med Sci Dept Microbiol & Immunol Kashan Iran Shahid Sadoughi Univ Med Sci Sch Med Dept Med Genet Yazd Iran Univ Bamako Fac Med Pharm & Odontostomatol FMPOS Bamako Mali Baku State Univ Dept Microbiol Baku Azerbaijan Maragheh Univ Med Sci Dept Basic Sci Maragheh Iran Tabriz Univ Med Sci Biotechnol Res Ctr Tabriz Iran Tabriz Univ Med Sci Fac Med Drug Appl Res Ctr Tabriz Iran

Tuberculosis (TB), a chronic disease caused by Mycobacterium tuberculosis, is one of the deadliest infectious diseases in the world. Despite significant advances in detection techniques and therapeutic approaches for tuberculosis, there is still no suitable solution for early screening and reducing the number of individuals affected and their effective treatment. Various cellular events can disrupt the development of TB. The basis of these events is dysregulating of genes expression patterns related with specific molecules. long non-coding rnas (lncrnas) are molecules discovered to regulate the expression of protein-coding genes and participate in gene silencing, cell cycle regulation and cellular differentiation processes. Dysregulation of lncrnas has been found to be associated with many diseases, including cancers and infectious diseases. Thus, the recognition of lncrnas as novel molecular biomarkers and therapeutic targets for tuberculosis is promising. In the present review, we try to summarize the current findings of lncrna expression patterns and its role in tuberculosis infection process. (C) 2020 Elsevier B.V. All rights reserved.

关键词： long non-coding rna Mycobacterium tuberculosis Tuberculosis infection

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