1
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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2
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Almujri SS, Almalki WH. The paradox of autophagy in cancer: NEAT1's role in tumorigenesis and therapeutic resistance. Pathol Res Pract 2024; 262:155523. [PMID: 39173466 DOI: 10.1016/j.prp.2024.155523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/02/2024] [Accepted: 08/09/2024] [Indexed: 08/24/2024]
Abstract
Cancer remains a current active problem of modern medicine, a process during which cell growth and proliferation become uncontrolled. However, the role of autophagy in the oncological processes is counterintuitive and, at the same time, increasingly influential on the formation, development, and response to therapy of oncological diseases. Autophagy is a vital cellular process that removes defective proteins and organelles and supports cellular homeostasis. Autophagy can enhance the ability to form new tumors and suppress this formation in cancer. The dual potential of apoptosis may be the reason for this duality in either promoting or impeding the survival of cancer cells, depending on the situation, including starvation or treatment stress. Furthermore, long non-coding RNA NEAT1, which has been linked to several stages of carcinogenesis and in all forms of the illness, has drawn attention as a major player in cancer biology. NEAT1 is a structural portion of nuclear paraspeckles and has roles in deactivating expression in both transcriptional and post-transcriptional levels. NEAT1 acts in carcinogenesis in numerous ways, comprising interactions with microRNAs, the influence of gene articulation, regulation of epigenetics, and engagement in signalling cascades. In addition, the complexity of NEAT1's role in cancer occurrence is amplified by its place in regulating cancer stem cells and the tumor microenvironment. NEAT1's interaction with autophagy further complicates the already complicated function of this RNA in cancer biology. NEAT1 has been linked to autophagy in several types of cancer, influencing autophagy pathways and altering its stress response and tumor cell viability. Understanding the interrelation between NEAT1, autophagy, and cancer will enable practitioners to identify novel treatment targets and approaches to disrupt oncogenic processes, reduce the occurrence of treatment resistance, and increase patient survival rates. Specialized treatment strategies and regimens are thus achievable. In the present review, the authors analyze sophisticated relationship schemes in cancer: The NEAT1 pathway and the process of autophagy.
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Affiliation(s)
- Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Aseer 61421, Saudi Arabia.
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
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3
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Khoroshkin M, Buyan A, Dodel M, Navickas A, Yu J, Trejo F, Doty A, Baratam R, Zhou S, Lee SB, Joshi T, Garcia K, Choi B, Miglani S, Subramanyam V, Modi H, Carpenter C, Markett D, Corces MR, Mardakheh FK, Kulakovskiy IV, Goodarzi H. Systematic identification of post-transcriptional regulatory modules. Nat Commun 2024; 15:7872. [PMID: 39251607 PMCID: PMC11385195 DOI: 10.1038/s41467-024-52215-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we perform a systematic annotation of RBP combinatorial interactions via multimodal data integration. We build a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we use CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generate an integrated map of functional RBP interactions. We then use this map to match RBPs to their context-specific functions and validate the predicted functions biochemically for four RBPs. This study provides a detailed map of RBP interactions and deconvolves them into distinct regulatory modules with annotated functions and target regulons. This multimodal and integrative framework provides a principled approach for studying post-transcriptional regulatory processes and enriches our understanding of their underlying mechanisms.
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Affiliation(s)
- Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Andrey Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Albertas Navickas
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
- Institut Curie, UMR3348 CNRS, Inserm, Orsay, France
| | - Johnny Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Fathima Trejo
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Anthony Doty
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, USA
| | - Rithvik Baratam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Shaopu Zhou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sean B Lee
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Tanvi Joshi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Benedict Choi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Sohit Miglani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Vishvak Subramanyam
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Carpenter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Markett
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, USA.
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4
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Camilleri-Robles C, Amador R, Tiebe M, Teleman A, Serras F, Guigó R, Corominas M. Long non-coding RNAs involved in Drosophila development and regeneration. NAR Genom Bioinform 2024; 6:lqae091. [PMID: 39157585 PMCID: PMC11327875 DOI: 10.1093/nargab/lqae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024] Open
Abstract
The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, gene expression, splicing, mRNA degradation, and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon cell death induction. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.
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Affiliation(s)
- Carlos Camilleri-Robles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Raziel Amador
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
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5
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Zhao Q, Li B, Zhang X, Zhao H, Xue W, Yuan Z, Xu S, Duan G. M2 macrophage-derived lncRNA NORAD in EVs promotes NSCLC progression via miR-520g-3p/SMIM22/GALE axis. NPJ Precis Oncol 2024; 8:185. [PMID: 39215037 PMCID: PMC11364787 DOI: 10.1038/s41698-024-00675-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) constitutes the majority of lung cancer cases, accounting for over 80%. RNAs in EVs play a pivotal role in various biological and pathological processes mediated by extracellular vesicle (EV). Long non-coding RNAs (lncRNAs) are widely associated with cancer-related functions, including cell proliferation, migration, invasion, and drug resistance. Tumor-associated macrophages are recognized as pivotal contributors to tumorigenesis. Given these insights, this study aims to uncover the impact of lncRNA NORAD in EVs derived from M2 macrophages in NSCLC cell lines and xenograft mouse models of NSCLC. EVs were meticulously isolated and verified based on their morphology and specific biomarkers. The interaction between lncRNA NORAD and SMIM22 was investigated using immunoprecipitation. The influence of SMIM22/GALE or lncRNA NORAD in EVs on glycolysis was assessed in NSCLC cell lines. Additionally, we evaluated the effects of M2 macrophage-derived lncRNA NORAD in EVs on cell proliferation and apoptosis through colony formation and flow cytometry assays. Furthermore, the impact of M2 macrophage-derived lncRNA NORAD in EVs on tumor growth was confirmed using xenograft tumor animal models. The results underscored the potential role of M2 macrophage-derived lncRNA NORAD in EVs in NSCLC. SMIM22/GALE promoted glycolysis and the proliferation of NSCLC cells. Furthermore, lncRNA NORAD in EVs targeted SMIM22 and miR-520g-3p in NSCLC cells. Notably, lncRNA NORAD in EVs promoted the proliferation of NSCLC cells and facilitated NSCLC tumor growth through the miR-520g-3p axis. In conclusion, M2 macrophage-derived lncRNA NORAD in EVs promotes NSCLC progression through the miR-520g-3p/SMIM22/GALE axis.
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Affiliation(s)
- Qingtao Zhao
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei Province, China
| | - Bin Li
- Hebei Bio-High Technology Development Co.Ltd, Shijiazhuang, Hebei Province, China
| | - Xiaopeng Zhang
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei Province, China
| | - Huanfen Zhao
- Department of Pathology, Hebei General Hospital, Shijiazhuang, Hebei Province, China
| | - Wenfei Xue
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei Province, China
| | - Zheng Yuan
- Department of Nursing, Hebei General Hospital, Shijiazhuang, Hebei Province, China
| | - Shun Xu
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Guochen Duan
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei Province, China.
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6
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Yankey A, Oh M, Lee BL, Desai TK, Somarowthu S. A novel partnership between lncTCF7 and SND1 regulates the expression of the TCF7 gene via recruitment of the SWI/SNF complex. Sci Rep 2024; 14:19384. [PMID: 39169000 PMCID: PMC11339422 DOI: 10.1038/s41598-024-69792-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/08/2024] [Indexed: 08/23/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) play key roles in cellular pathways and disease progression, yet their molecular mechanisms remain largely understudied. The lncRNA lncTCF7 has been shown to promote tumor progression by recruiting the SWI/SNF complex to the TCF7 promoter, activating its expression and the WNT signaling pathway. However, how lncTCF7 recruits SWI/SNF remains to be determined, and lncTCF7-specific binding partners are unknown. Using RNA-pulldown and quantitative mass spectrometry, we identified a novel interacting protein partner for lncTCF7, SND1, a multifunctional RNA binding protein that can also function as a transcription co-activator. Knockdown analysis of lncTCF7 and SND1 reveals that they are both required for the expression of TCF7. Chromatin immunoprecipitation assays suggest that both SND1 and lncTCF7 are required for recruiting the SWI/SNF chromatin remodeling complex, and these functions, in tandem, activate the expression of TCF7. Finally, using structural probing and RNA-pulldown of lncTCF7 and its subdomains, we highlight the potential binding region for SND1 in the 3'-end of lncTCF7. Overall, this study highlights the critical roles lncRNAs play in regulating gene expression and provides new insights into the complex network of interactions that underlie this process.
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Affiliation(s)
- Allison Yankey
- Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Mihyun Oh
- Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Bo Lim Lee
- Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Tisha Kalpesh Desai
- Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, PA, USA
| | - Srinivas Somarowthu
- Department of Biochemistry and Molecular Biology, College of Medicine, Drexel University, Philadelphia, PA, USA.
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7
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Lai Y, Lin Y. Biological functions and therapeutic potential of CKS2 in human cancer. Front Oncol 2024; 14:1424569. [PMID: 39188686 PMCID: PMC11345170 DOI: 10.3389/fonc.2024.1424569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The incidence of cancer is increasing worldwide and is the most common cause of death. Identification of novel cancer diagnostic and prognostic biomarkers is important for developing cancer treatment strategies and reducing mortality. Cyclin-dependent kinase subunit 2 (CKS2) is involved in cell cycle and proliferation processes, and based on these processes, CKS2 was identified as a cancer gene. CKS2 is expressed in a variety of tissues in the human body, but its abnormal expression is associated with cancer in a variety of systems. CKS2 is generally elevated in cancer, plays a role in almost all aspects of cancer biology (such as cell proliferation, invasion, metastasis, and drug resistance) through multiple mechanisms regulating certain important genes, and is associated with clinicopathological features of patients. In addition, CKS2 expression patterns are closely related to cancer type, stage and other clinical variables. Therefore, CKS2 is considered as a tool for cancer diagnosis and prognosis and may be a promising tumor biomarker and therapeutic target. This article reviews the biological function, mechanism of action and potential clinical significance of CKS2 in cancer, in order to provide a new theoretical basis for clinical molecular diagnosis, molecular targeted therapy and scientific research of cancer.
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Affiliation(s)
- Yueliang Lai
- Department of Gastroenterology, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
- The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi, China
| | - Ye Lin
- Department of Gastroenterology, Ganzhou People’s Hospital, Ganzhou, Jiangxi, China
- The Affiliated Ganzhou Hospital of Nanchang University, Ganzhou, Jiangxi, China
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8
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Li MM, Shi MJ, Feng CC, Yu ZY, Bai XF, Lu-Lu. LncRNA KCNQ1OT1 promotes NLRP3 inflammasome activation in Parkinson's disease by regulating pri-miR-186/mature miR-186/NLRP3 axis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167454. [PMID: 39122224 DOI: 10.1016/j.bbadis.2024.167454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 06/07/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
Increasing evidence indicated that neuroinflammation was involved in progression of Parkinson's disease (PD). Long noncoding RNAs (lncRNAs) played important roles in regulating inflammatory processes in multiple kinds of human diseases such as cancer diabetes, cardiomyopathy, and neurodegenerative disorders. The mechanisms by which lncRNAs regulated PD related inflammation and dopaminergic neuronal loss have not yet been fully elucidated. In current study, we intended to explore the function and potential mechanism of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in regulating inflammasome activation in PD. Functional assays confirmed that knockdown of KCNQ1OT1 suppress microglial NLR family pyrin domain containing 3 (NLRP3) inflammasome activation and attenuated dopaminergic neuronal loss in PD model mice. As KCNQ1OT1 located in both cytoplasm and nucleus of microglia, we demonstrated that KCNQ1OT1 promoted microglial NLRP3 inflammasome activation by competitive binding with miR-186 in cytoplasm and inhibited pri-miR-186 mediated NLRP3 silencing through recruitment of DiGeorge syndrome critical region gene 8 (DGCR8) in nucleus, respectively. Our study found a novel lncRNA-pri-miRNA/mature miRNA-mRNA regulatory network in microglia mediated NLRP3 inflammasome activation and dopaminergic neuronal loss, provided further insights for the treatment of Parkinson's disease.
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Affiliation(s)
- Meng-Meng Li
- Department of Neurology and Institute of Neurology, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200040, China.
| | - Mei-Juan Shi
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Chen-Chen Feng
- Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhong-Yu Yu
- Sijing Community Health Service Center of Songjiang District, Shanghai 201600, China
| | - Xiao-Fei Bai
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Eye Institute of Shandong First Medical University, Qingdao 266071, China
| | - Lu-Lu
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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10
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Habib AM, Cox JJ, Okorokov AL. Out of the dark: the emerging roles of lncRNAs in pain. Trends Genet 2024; 40:694-705. [PMID: 38926010 DOI: 10.1016/j.tig.2024.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/28/2024]
Abstract
The dark genome, the nonprotein-coding part of the genome, is replete with long noncoding RNAs (lncRNAs). These functionally versatile transcripts, with specific temporal and spatial expression patterns, are critical gene regulators that play essential roles in health and disease. In recent years, FAAH-OUT was identified as the first lncRNA associated with an inherited human pain insensitivity disorder. Several other lncRNAs have also been studied for their contribution to chronic pain and genome-wide association studies are frequently identifying single nucleotide polymorphisms that map to lncRNAs. For a long time overlooked, lncRNAs are coming out of the dark and into the light as major players in human pain pathways and as potential targets for new RNA-based analgesic medicines.
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Affiliation(s)
- Abdella M Habib
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - James J Cox
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, UK.
| | - Andrei L Okorokov
- Wolfson Institute for Biomedical Research, Division of Medicine, University College London, London, WC1E 6BT, UK.
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11
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Lee JS, Dan T, Zhang H, Cheng Y, Rehfeld F, Brugarolas J, Mendell JT. An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604857. [PMID: 39091767 PMCID: PMC11291168 DOI: 10.1101/2024.07.23.604857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPRi screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNA Colorectal Neoplasia Differentially Expressed containing an ultraconserved element (UCE), referred to as CRNDE UCE, is required for RCC cell proliferation. CRNDE UCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds to CRNDE UCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
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Affiliation(s)
- Jong-Sun Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tu Dan
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yujing Cheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Frederick Rehfeld
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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12
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Chen HF, Wu KJ. LncRNAs and asymmetric cell division: the epigenetic mechanisms. Biomed J 2024:100774. [PMID: 39059582 DOI: 10.1016/j.bj.2024.100774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024] Open
Abstract
Asymmetric cell division (ACD) plays a pivotal role in development, tissue homeostasis, and stem cell maintenance. Emerging evidence suggests that long non-coding RNAs (lncRNAs) are key regulators of ACD, orchestrating the intricate molecular machinery that governs cell fate determination. This review summarizes current literature to elucidate the diverse roles of lncRNAs in modulating ACD across various biological contexts. The regulatory mechanisms of asymmetric cell division mediated by lncRNAs, including their interactions with protein effectors, epigenetic regulation, and subcellular localization are explored. Additionally, we discuss the implications of dysregulated lncRNAs in mediating ACD that lead to tumorigenesis. By integrating findings from diverse experimental models and cell types, this review provides insights into the multifaceted roles of lncRNAs in governing asymmetric cell division, shedding light on fundamental biological processes. Further research in this area may lead to the development of novel therapies targeting dysregulated lncRNAs to restore proper cell division and function. The knowledge of lncRNAs regulating ACD could potentially revolutionize the field of regenerative medicine and cancer therapy by targeting specific lncRNAs involved in ACD. By unraveling the complex interactions between lncRNAs and cellular processes, the potential novel opportunities for precision medicine approaches may be uncovered.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institutes of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; Graduate Institutes of Cell Biology, China Medical University, Taichung 404, Taiwan.
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan Dist., Taoyuan 333, Taiwan.
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13
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Wischnewski S, Thäwel T, Ikenaga C, Kocharyan A, Lerma-Martin C, Zulji A, Rausch HW, Brenner D, Thomas L, Kutza M, Wick B, Trobisch T, Preusse C, Haeussler M, Leipe J, Ludolph A, Rosenbohm A, Hoke A, Platten M, Weishaupt JH, Sommer CJ, Stenzel W, Lloyd TE, Schirmer L. Cell type mapping of inflammatory muscle diseases highlights selective myofiber vulnerability in inclusion body myositis. NATURE AGING 2024; 4:969-983. [PMID: 38834884 PMCID: PMC11257986 DOI: 10.1038/s43587-024-00645-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/03/2024] [Indexed: 06/06/2024]
Abstract
Inclusion body myositis (IBM) is the most prevalent inflammatory muscle disease in older adults with no effective therapy available. In contrast to other inflammatory myopathies such as subacute, immune-mediated necrotizing myopathy (IMNM), IBM follows a chronic disease course with both inflammatory and degenerative features of pathology. Moreover, causal factors and molecular drivers of IBM progression are largely unknown. Therefore, we paired single-nucleus RNA sequencing with spatial transcriptomics from patient muscle biopsies to map cell-type-specific drivers underlying IBM pathogenesis compared with IMNM muscles and noninflammatory skeletal muscle samples. In IBM muscles, we observed a selective loss of type 2 myonuclei paralleled by increased levels of cytotoxic T and conventional type 1 dendritic cells. IBM myofibers were characterized by either upregulation of cell stress markers featuring GADD45A and NORAD or protein degradation markers including RNF7 associated with p62 aggregates. GADD45A upregulation was preferentially seen in type 2A myofibers associated with severe tissue inflammation. We also noted IBM-specific upregulation of ACHE encoding acetylcholinesterase, which can be regulated by NORAD activity and result in functional denervation of myofibers. Our results provide promising insights into possible mechanisms of myofiber degeneration in IBM and suggest a selective type 2 fiber vulnerability linked to genomic stress and denervation pathways.
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Grants
- R01 AR076390 NIAMS NIH HHS
- U41 HG002371 NHGRI NIH HHS
- European Research Council (DecOmPress ERC StG 950584), German Research Foundation grant (SCHI 1330/2-1, SCHI 1330/4-1, SCHI 1330/6-1, GRK 2727, SPP 2395), Hertie Foundation (P1180016), National Multiple Sclerosis Society (RFA-2203-39300, PA-2002-36405)
- The Myositis Association (90097118)
- German Cancer Aid
- National Human Genome Research Institute (5U41HG002371)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (R01-AR076390), Muscular Dystrophy Association (MDA630399), The Peter and Carmen Lucia Buck Foundation, The Peter Frampton Myositis Research Fund
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Affiliation(s)
- Sven Wischnewski
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Thäwel
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Chiseko Ikenaga
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anna Kocharyan
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Celia Lerma-Martin
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Amel Zulji
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Hans-Werner Rausch
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Brenner
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Department of Neurology, University of Ulm, Ulm, Germany
| | - Leonie Thomas
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Michael Kutza
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Brittney Wick
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Tim Trobisch
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Corinna Preusse
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | | | - Jan Leipe
- Division of Rheumatology, Department of Medicine V, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Albert Ludolph
- Department of Neurology, University of Ulm, Ulm, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen, Ulm, Germany
| | | | - Ahmet Hoke
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center, Heidelberg, Germany
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Jochen H Weishaupt
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Clemens J Sommer
- Institute for Neuropathology, University Medical Center, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Thomas E Lloyd
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Mannheim Institute for Innate Immunoscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany.
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14
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Scholda J, Nguyen TTA, Kopp F. Long noncoding RNAs as versatile molecular regulators of cellular stress response and homeostasis. Hum Genet 2024; 143:813-829. [PMID: 37782337 PMCID: PMC11294412 DOI: 10.1007/s00439-023-02604-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/12/2023] [Indexed: 10/03/2023]
Abstract
Normal cell and body functions need to be maintained and protected against endogenous and exogenous stress conditions. Different cellular stress response pathways have evolved that are utilized by mammalian cells to recognize, process and overcome numerous stress stimuli in order to maintain homeostasis and to prevent pathophysiological processes. Although these stress response pathways appear to be quite different on a molecular level, they all have in common that they integrate various stress inputs, translate them into an appropriate stress response and eventually resolve the stress by either restoring homeostasis or inducing cell death. It has become increasingly appreciated that non-protein-coding RNA species, such as long noncoding RNAs (lncRNAs), can play critical roles in the mammalian stress response. However, the precise molecular functions and underlying modes of action for many of the stress-related lncRNAs remain poorly understood. In this review, we aim to provide a framework for the categorization of mammalian lncRNAs in stress response and homeostasis based on their experimentally validated modes of action. We describe the molecular functions and physiological roles of selected lncRNAs and develop a concept of how lncRNAs can contribute as versatile players in mammalian stress response and homeostasis. These concepts may be used as a starting point for the identification of novel lncRNAs and lncRNA functions not only in the context of stress, but also in normal physiology and disease.
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Affiliation(s)
- Julia Scholda
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Thi Thuy Anh Nguyen
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria
| | - Florian Kopp
- Faculty of Life Sciences, Department of Pharmaceutical Sciences, Clinical Pharmacy Group, University of Vienna, Josef-Holaubek-Platz 2, 1090, Vienna, Austria.
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15
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Zhang J, Tian Z, Qin C, Momeni MR. The effects of exercise on epigenetic modifications: focus on DNA methylation, histone modifications and non-coding RNAs. Hum Cell 2024; 37:887-903. [PMID: 38587596 DOI: 10.1007/s13577-024-01057-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/10/2024] [Indexed: 04/09/2024]
Abstract
Physical activity on a regular basis has been shown to bolster the overall wellness of an individual; research is now revealing that these changes are accompanied by epigenetic modifications. Regular exercise has been proven to make intervention plans more successful and prolong adherence to them. When it comes to epigenetic changes, there are four primary components. This includes changes to the DNA, histones, expression of particular non-coding RNAs and DNA methylation. External triggers, such as physical activity, can lead to modifications in the epigenetic components, resulting in changes in the transcription process. This report pays attention to the current knowledge that pertains to the epigenetic alterations that occur after exercise, the genes affected and the resulting characteristics.
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Affiliation(s)
- Junxiong Zhang
- Xiamen Academy of Art and Design, Fuzhou University, Xiamen, 361024, Fujian, China.
| | - Zhongxin Tian
- College of Physical Education, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China.
| | - Chao Qin
- College of Physical Education, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
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16
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Li P, Yu X. The role of rRNA in maintaining genome stability. DNA Repair (Amst) 2024; 139:103692. [PMID: 38759435 DOI: 10.1016/j.dnarep.2024.103692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 05/19/2024]
Abstract
Over the past few decades, unbiased approaches such as genetic screening and protein affinity purification have unveiled numerous proteins involved in DNA double-strand break (DSB) repair and maintaining genome stability. However, despite our knowledge of these protein factors, the underlying molecular mechanisms governing key cellular events during DSB repair remain elusive. Recent evidence has shed light on the role of non-protein factors, such as RNA, in several pivotal steps of DSB repair. In this review, we provide a comprehensive summary of these recent findings, highlighting the significance of ribosomal RNA (rRNA) as a critical mediator of DNA damage response, meiosis, and mitosis. Moreover, we discuss potential mechanisms through which rRNA may influence genome integrity.
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Affiliation(s)
- Peng Li
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiaochun Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
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17
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Chung TH, Zhuravskaya A, Makeyev EV. Regulation potential of transcribed simple repeated sequences in developing neurons. Hum Genet 2024; 143:875-895. [PMID: 38153590 PMCID: PMC11294396 DOI: 10.1007/s00439-023-02626-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Simple repeated sequences (SRSs), defined as tandem iterations of microsatellite- to satellite-sized DNA units, occupy a substantial part of the human genome. Some of these elements are known to be transcribed in the context of repeat expansion disorders. Mounting evidence suggests that the transcription of SRSs may also contribute to normal cellular functions. Here, we used genome-wide bioinformatics approaches to systematically examine SRS transcriptional activity in cells undergoing neuronal differentiation. We identified thousands of long noncoding RNAs containing >200-nucleotide-long SRSs (SRS-lncRNAs), with hundreds of these transcripts significantly upregulated in the neural lineage. We show that SRS-lncRNAs often originate from telomere-proximal regions and that they have a strong potential to form multivalent contacts with a wide range of RNA-binding proteins. Our analyses also uncovered a cluster of neurally upregulated SRS-lncRNAs encoded in a centromere-proximal part of chromosome 9, which underwent an evolutionarily recent segmental duplication. Using a newly established in vitro system for rapid neuronal differentiation of induced pluripotent stem cells, we demonstrate that at least some of the bioinformatically predicted SRS-lncRNAs, including those encoded in the segmentally duplicated part of chromosome 9, indeed increase their expression in developing neurons to readily detectable levels. These and other lines of evidence suggest that many SRSs may be expressed in a cell type and developmental stage-specific manner, providing a valuable resource for further studies focused on the functional consequences of SRS-lncRNAs in the normal development of the human brain, as well as in the context of neurodevelopmental disorders.
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Affiliation(s)
- Tek Hong Chung
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Anna Zhuravskaya
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, New Hunt's House, King's College London, London, SE1 1UL, UK.
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18
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Wang Y, Lv Y, Jiang X, Yu X, Wang D, Liu D, Liu X, Sun Y. Long non-coding RNA NORAD regulates megakaryocyte differentiation and proplatelet formation via the DUSP6/ERK signaling pathway. Biochem Biophys Res Commun 2024; 715:150004. [PMID: 38678784 DOI: 10.1016/j.bbrc.2024.150004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
Megakaryopoiesis and platelet production is a complex process that is underpotential regulation at multiple stages. Many long non-coding RNAs (lncRNAs) are distributed in hematopoietic stem cells and platelets. lncRNAs may play important roles as key epigenetic regulators in megakaryocyte differentiation and proplatelet formation. lncRNA NORAD can affect cell ploidy by sequestering PUMILIO proteins, although its direct effect on megakaryocyte differentiation and thrombopoiesis is still unknown. In this study, we demonstrate NORAD RNA is highly expressed in the cytoplasm during megakaryocyte differentiation. Interestingly, we identified for the first time that NORAD has a strong inhibitory effect on megakaryocyte differentiation and proplatelet formation from cultured megakaryocytes. DUSP6/ERK1/2 pathway is activated in response to NORAD knockdown during megakaryocytopoiesis, which is achieved by sequestering PUM2 proteins. Finally, compared with the wild-type control mice, NORAD knockout mice show a faster platelet recovery after severe thrombocytopenia induced by 6 Gy total body irradiation. These findings demonstrate lncRNA NORAD has a key role in regulating megakaryocyte differentiation and thrombopoiesis, which provides a promising molecular target for the treatment of platelet-related diseases such as severe thrombocytopenia.
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Affiliation(s)
- Yong Wang
- College of Pharmacy, Binzhou Medical University, China
| | - Yan Lv
- College of Life Science, Yantai University, China
| | - Xiaoli Jiang
- College of Pharmacy, Binzhou Medical University, China
| | - Xin Yu
- College of Pharmacy, Binzhou Medical University, China
| | - Delong Wang
- College of Pharmacy, Binzhou Medical University, China
| | - Desheng Liu
- College of Pharmacy, Binzhou Medical University, China
| | - Xiangyong Liu
- College of Pharmacy, Binzhou Medical University, China
| | - Yeying Sun
- College of Pharmacy, Binzhou Medical University, China.
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19
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Chmielewski PP, Data K, Strzelec B, Farzaneh M, Anbiyaiee A, Zaheer U, Uddin S, Sheykhi-Sabzehpoush M, Mozdziak P, Zabel M, Dzięgiel P, Kempisty B. Human Aging and Age-Related Diseases: From Underlying Mechanisms to Pro-Longevity Interventions. Aging Dis 2024:AD.2024.0280. [PMID: 38913049 DOI: 10.14336/ad.2024.0280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 06/02/2024] [Indexed: 06/25/2024] Open
Abstract
As human life expectancy continues to rise, becoming a pressing global concern, it brings into focus the underlying mechanisms of aging. The increasing lifespan has led to a growing elderly population grappling with age-related diseases (ARDs), which strains healthcare systems and economies worldwide. While human senescence was once regarded as an immutable and inexorable phenomenon, impervious to interventions, the emerging field of geroscience now offers innovative approaches to aging, holding the promise of extending the period of healthspan in humans. Understanding the intricate links between aging and pathologies is essential in addressing the challenges presented by aging populations. A substantial body of evidence indicates shared mechanisms and pathways contributing to the development and progression of various ARDs. Consequently, novel interventions targeting the intrinsic mechanisms of aging have the potential to delay the onset of diverse pathological conditions, thereby extending healthspan. In this narrative review, we discuss the most promising methods and interventions aimed at modulating aging, which harbor the potential to mitigate ARDs in the future. We also outline the complexity of senescence and review recent empirical evidence to identify rational strategies for promoting healthy aging.
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Affiliation(s)
- Piotr Pawel Chmielewski
- Division of Anatomy, Department of Human Morphology and Embryology, Faculty of Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Krzysztof Data
- Division of Anatomy, Department of Human Morphology and Embryology, Faculty of Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Bartłomiej Strzelec
- 2nd Department of General Surgery and Surgical Oncology, Medical University Hospital, Wroclaw, Poland
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Amir Anbiyaiee
- Department of Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Uzma Zaheer
- School of Biosciences, Faculty of Health Sciences and Medicine, The University of Surrey, United Kingdom
| | - Shahab Uddin
- Translational Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, India
| | | | - Paul Mozdziak
- Graduate Physiology Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Maciej Zabel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland
- Division of Anatomy and Histology, The University of Zielona Góra, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland
| | - Bartosz Kempisty
- Division of Anatomy, Department of Human Morphology and Embryology, Faculty of Medicine, Wroclaw Medical University, Wroclaw, Poland
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, Poland
- Physiology Graduate Faculty, North Carolina State University, Raleigh, NC 27695, USA
- Center of Assisted Reproduction, Department of Obstetrics and Gynecology, University Hospital and Masaryk University, Brno, Czech Republic
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20
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Lee YH, Hass EP, Campodonico W, Lee YK, Lasda E, Shah J, Rinn J, Hwang T. Massively parallel dissection of RNA in RNA-protein interactions in vivo. Nucleic Acids Res 2024; 52:e48. [PMID: 38726866 PMCID: PMC11162807 DOI: 10.1093/nar/gkae334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 06/11/2024] Open
Abstract
Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to biology. Here, we present massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) for in vivo high-throughput dissection of RNA-protein interactions and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, MPRNA-IP is able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest, including the long noncoding RNA NORAD, bacteriophage MS2 RNA, and human telomerase RNA, and we use it to interrogate the hitherto unknown sequence or structural RNA-binding preferences of the DNA-looping factor CTCF. By integrating systematic mutation analysis with crosslinking immunoprecipitation, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions in vivo.
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Affiliation(s)
- Yu Hsuan Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Evan P Hass
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Will Campodonico
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Yong Kyu Lee
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Erika Lasda
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Jaynish S Shah
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - John L Rinn
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Taeyoung Hwang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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21
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Regunath K, Fomin V, Liu Z, Wang P, Hoque M, Tian B, Rabadan R, Prives C. Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types. Mol Cancer Res 2024; 22:555-571. [PMID: 38393317 DOI: 10.1158/1541-7786.mcr-23-0295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/04/2023] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
The p53 tumor suppressor protein, a sequence-specific DNA binding transcription factor, regulates the expression of a large number of genes, in response to various forms of cellular stress. Although the protein coding target genes of p53 have been well studied, less is known about its role in regulating long noncoding genes and their functional relevance to cancer. Here we report the genome-wide identification of a large set (>1,000) of long noncoding RNAs (lncRNA), which are putative p53 targets in a colon cancer cell line and in human patient datasets from five different common types of cancer. These lncRNAs have not been annotated by other studies of normal unstressed systems. In the colon cancer cell line, a high proportion of these lncRNAs are uniquely induced by different chemotherapeutic agents that activate p53, whereas others are induced by more than one agent tested. Further, subsets of these lncRNAs independently predict overall and disease-free survival of patients across the five different common cancer types. Interestingly, both genetic alterations and patient survival associated with different lncRNAs are unique to each cancer tested, indicating extraordinary tissue-specific variability in the p53 noncoding response. The newly identified noncoding p53 target genes have allowed us to construct a classifier for tumor diagnosis and prognosis. IMPLICATIONS Our results not only identify myriad p53-regulated long noncoding (lncRNA), they also reveal marked drug-induced, as well as tissue- and tumor-specific heterogeneity in these putative p53 targets and our findings have enabled the construction of robust classifiers for diagnosis and prognosis.
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Affiliation(s)
- Kausik Regunath
- Department of Biological Sciences, Columbia University, New York, New York
| | - Vitalay Fomin
- Department of Biological Sciences, Columbia University, New York, New York
| | - Zhaoqi Liu
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Pingzhang Wang
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey
| | - Raul Rabadan
- Program for Mathematical Genomics, Departments of Systems Biology and Biomedical Informatics, Columbia University College of Physicians & Surgeons, New York, New York
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, New York
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22
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Meng X, Long M, Yue N, Li Q, Chen J, Zhao H, Deng W. LncRNA MEG3 Restrains Hepatic Lipogenesis via the FOXO1 Signaling Pathway in HepG2 Cells. Cell Biochem Biophys 2024; 82:1253-1259. [PMID: 38713402 PMCID: PMC11344712 DOI: 10.1007/s12013-024-01278-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2024] [Indexed: 05/08/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) become a main public health concern, and is characterized by lipid accumulation in the hepatocytes. We found that overexpression of lncRNA MEG3 significantly reduced the expression of FOXO1, ACC1, and FAS, and subsequently decreased the lipid accumulation in HepG2 cells. Moreover, inhibition of lncRNA MEG3 could increase the lipid accumulation and the mRNA and protein levels of FOXO1, ACC1, and FAS. Further study showed that lncRNA MEG3 regulates the lipogenesis process by inhibiting the entry of FOXO1 into the nucleus translocation. Our study demonstrated that lncRNA MEG3 regulates de novo lipogenesis by decreasing the expression and nucleus translocation of FOXO1 in HepG2 cells, suggesting that lncRNA MEG3 could be a promising therapeutic target in lipid metabolic disorders.
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Affiliation(s)
- Xiangyu Meng
- The Central Laboratory, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China
| | - Mei Long
- Department of Cardiology, ZiBo Central Hospital, Zibo, Shandong, 255000, China
| | - Nanxi Yue
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Neural and Vascular Biology, Ministry of Education of China, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China
| | - Quan Li
- Department of Endocrinology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China
| | - Jia Chen
- Department of Endocrinology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China
| | - Hongye Zhao
- Department of Biochemistry and Molecular Biology, The Key Laboratory of Neural and Vascular Biology, Ministry of Education of China, Hebei Medical University, Shijiazhuang, Hebei, 050017, PR China.
| | - Wei Deng
- Department of Endocrinology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 100035, China.
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23
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Han Y, Pu Q, Fan T, Wei T, Xu Y, Zhao L, Liu S. Long non-coding RNAs as promising targets for controlling disease vector mosquitoes. INSECT SCIENCE 2024. [PMID: 38783627 DOI: 10.1111/1744-7917.13383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Hematophagous female mosquitoes are important vectors of numerous devastating human diseases, posing a major public health threat. Effective prevention and control of mosquito-borne diseases rely considerably on progress in understanding the molecular mechanisms of various life activities, and accordingly, the molecules that regulate the various life activities of mosquitoes are potential targets for implementing future vector control strategies. Many long non-coding RNAs (lncRNAs) have been identified in mosquitoes and significant progress has been made in determining their functions. Here, we present a comprehensive overview of the research advances on mosquito lncRNAs, including their molecular identification, function, and interaction with other non-coding RNAs, as well as their synergistic regulatory roles in mosquito life activities. We also highlight the potential roles of competitive endogenous RNAs in mosquito growth and development, as well as in insecticide resistance and virus-host interactions. Insights into the biological functions and mechanisms of lncRNAs in mosquito life activities, viral replication, pathogenesis, and transmission will contribute to the development of novel drugs and safe vaccines.
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Affiliation(s)
- Yujiao Han
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Qian Pu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Ting Fan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Tianqi Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Yankun Xu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Lu Zhao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Shiping Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
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24
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Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. Genes Dev 2024; 38:294-307. [PMID: 38688681 PMCID: PMC11146593 DOI: 10.1101/gad.351557.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/12/2024] [Indexed: 05/02/2024]
Abstract
Synaptic function in neurons is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear long noncoding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 using antisense oligonucleotides (ASOs) stimulates the expression of particular pre- and postsynaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized in puncta of both axons and dendrites that costain with Staufen1 protein, similar to neuronal RNA granules formed by locally translated mRNAs. Ribosome profiling of cultured mouse cortical neurons identified ribosome footprints within a 5' region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP-coding sequence in mouse embryonic stem cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wild-type neurons and showed that M1 expression was enhanced by synaptic stimulation with KCl. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA;
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, California 90095, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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25
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Scuderi C, Di Bella V, Privitera AP, Giustolisi FM, Barresi V, Condorelli DF. Gain-Type Aneuploidies Influence the Burden of Selective Long Non-Coding Transcripts in Colorectal Cancer. Int J Mol Sci 2024; 25:5538. [PMID: 38791575 PMCID: PMC11122260 DOI: 10.3390/ijms25105538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Chromosomal instability is a hallmark of colorectal carcinogenesis and produces an accumulation of different forms of aneuploidies or broad copy number aberrations. Colorectal cancer is characterized by gain-type broad copy number aberrations, specifically in Chr20, Chr8q, Chr13 and Chr7, but their roles and mechanisms in cancer progression are not fully understood. It has been suggested that broad copy number gains might contribute to tumor development through the so-called caricature transcriptomic effect. We intend to investigate the impact of broad copy number gains on long non-coding RNAs' expression in colorectal cancer, given their well-known role in oncogenesis. The influence of such chromosomal aberrations on lncRNAs' transcriptome profile was investigated by SNP and transcriptome arrays in our series of colorectal cancer samples and cell lines. The correlation between aneuploidies and transcriptomic profiles led us to obtain a class of Over-UpT lncRNAs, which are transcripts upregulated in CRC and further overexpressed in colon tumors bearing specific chromosomal aberrations. The identified lncRNAs can contribute to a wide interaction network to establish the cancer driving effect of gain-type aneuploidies.
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Affiliation(s)
| | | | | | | | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.S.); (V.D.B.); (A.P.P.); (F.M.G.); (D.F.C.)
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26
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Muhtadi R, Stewart S, Bunert F, Fatanmi OO, Wise SY, Gärtner C, Motzke S, Ruf C, Ostheim P, Schüle S, Schwanke D, Singh VK, Port M, Abend M. PUM1 and PGK1 are Favorable Housekeeping Genes over Established Biodosimetry-related Housekeeping Genes such as HPRT1, ITFG1, DPM1, MRPS5, 18S rRNA and Others after Radiation Exposure. Radiat Res 2024; 201:487-498. [PMID: 38471523 DOI: 10.1667/rade-23-00160.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/16/2023] [Indexed: 03/14/2024]
Abstract
In gene expression (GE) studies, housekeeping genes (HKGs) are required for normalization purposes. In large-scale inter-laboratory comparison studies, significant differences in dose estimates are reported and divergent HKGs are employed by the teams. Among them, the 18S rRNA HKG is known for its robustness. However, the high abundance of 18S rRNA copy numbers requires dilution, which is time-consuming and a possible source of errors. This study was conducted to identify the most promising HKGs showing the least radiation-induced GE variance after radiation exposure. In the screening stage of this study, 35 HKGs were analyzed. This included selected HKGs (ITFG1, MRPS5, and DPM1) used in large-scale biodosimetry studies which were not covered on an additionally employed pre-designed 96-well platform comprising another 32 HKGs used for different exposures. Altogether 41 samples were examined, including 27 ex vivo X-ray irradiated blood samples (0, 0.5, 4 Gy), six X-irradiated samples (0, 0.5, 5 Gy) from two cell lines (U118, A549), as well as eight non-irradiated tissue samples to encompass multiple biological entities. In the independent validation stage, the most suitable candidate genes were examined from another 257 blood samples, taking advantage of already stored material originating from three studies. These comprise 100 blood samples from ex vivo X-ray irradiated (0-4 Gy) healthy donors, 68 blood samples from 5.8 Gy irradiated (cobalt-60) Rhesus macaques (RM) (LD29/60) collected 0-60 days postirradiation, and 89 blood samples from chemotherapy-(CTx) treated breast tumor patients. CTx and radiation-induced GE changes in previous studies appeared comparable. RNA was isolated, converted into cDNA, and GE was quantified employing TaqMan assays and quantitative RT-PCR. We calculated the standard deviation (SD) and the interquartile range (IQR) as measures of GE variance using raw cycle threshold (Ct) values and ranked the HKGs accordingly. Dose, time, age, and sex-dependent GE changes were examined employing the parametrical t-test and non-parametrical Kruskal Wallis test, as well as linear regression analysis. Generally, similar ranking results evolved using either SD or IQR GE measures of variance, indicating a tight distribution of GE values. PUM1 and PGK1 showed the lowest variance among the first ten most suitable genes in the screening phase. MRPL19 revealed low variance among the first ten most suitable genes in the screening phase only for blood and cells, but certain comparisons indicated a weak association of MRPL19 with dose (P = 0.02-0.09). In the validation phase, these results could be confirmed. Here, IQR Ct values from, e.g., X-irradiated blood samples were 0.6 raw Ct values for PUM1 and PGK1, which is considered to represent GE differences as expected due to methodological variance. Overall, when compared, the GE variance of both genes was either comparable or lower compared to 18S rRNA. Compared with the IQR GE values of PUM1 and PGKI, twofold-fivefold increased values were calculated for the biodosimetry HKG HPRT1, and comparable values were calculated for biodosimetry HKGs ITFG1, MRPS5, and DPM1. Significant dose-dependent associations were found for ITFG1 and MRPS5 (P = 0.001-0.07) and widely absent or weak (P = 0.02-0.07) for HPRT1 and DPM1. In summary, PUM1 and PGK1 appeared most promising for radiation exposure studies among the 35 HKGs examined, considering GE variance and adverse associations of GE with dose.
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Affiliation(s)
- R Muhtadi
- Bundeswehr Institute of Radiobiology, Munich, Germany
- Technical University Munich, Munich, Germany
| | - S Stewart
- Bundeswehr Institute of Radiobiology, Munich, Germany
- Technical University Munich, Munich, Germany
| | - F Bunert
- Bundeswehr Institute of Radiobiology, Munich, Germany
- Technical University Munich, Munich, Germany
| | - O O Fatanmi
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - S Y Wise
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - C Gärtner
- Microfluidic ChipShop GmbH, Jena, Germany
| | - S Motzke
- Microfluidic ChipShop GmbH, Jena, Germany
| | - C Ruf
- Department of Urology, Federal Armed Services Hospital Ulm, Ulm, Germany
| | - P Ostheim
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - S Schüle
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - D Schwanke
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - V K Singh
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - M Port
- Bundeswehr Institute of Radiobiology, Munich, Germany
| | - M Abend
- Bundeswehr Institute of Radiobiology, Munich, Germany
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27
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Yan Y, Wang J, Xu B, Ni J, Dai T, Wang L, Wang H, Hua Z, Li K, Zhou Y. Exosomal SOX21-AS1 Regulates EREG by Sponging miR-451a and Promotes the Malignancy of Pancreatic Ductal Adenocarcinoma. J Cancer 2024; 15:3321-3337. [PMID: 38817864 PMCID: PMC11134441 DOI: 10.7150/jca.95014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 04/04/2024] [Indexed: 06/01/2024] Open
Abstract
The incidence and mortality of pancreatic ductal adenocarcinoma (PDAC) have increased. Exosomes, as a regulatory mode of intercellular communication, contain lncRNAs. SOX21-AS1 has been studied in other cancers, and its expression is elevated in PDAC, but its role in PDAC remains unclear. First, we analyzed the expression of lncRNAs in PDAC tissues and nontumor tissues through the TCGA database. Next, the results of the RT-qPCR experiment confirmed the prediction that the expression of SOX21-AS1 was elevated in PDAC tissues. In vivo and in vitro cell function assays confirmed that the degree of malignancy of PDAC was proportional to the expression of SOX21-AS1. In addition, through exosome isolation and uptake experiments, we first found that PDAC could secrete exosomal SOX21-AS1 and play an angiogenic role in HUVECs. Subsequently, the relationship between SOX21-AS1, miR-451a and epiregulin (EREG) was verified through database prediction and analysis and RIP assays. Finally, functional recovery assays in vivo and in vitro verified that SOX21-AS1 regulates the expression of EREG through combination with miR-451a and thus promotes the malignancy of PDAC. SOX21-AS1 was upregulated in PDAC. The upregulation of SOX21-AS1 can stimulate the proliferation, migration, invasion, stemness and epithelial-mesenchymal transition (EMT) progression of PDAC cells. Furthermore, PDAC cells secrete exosomal SOX21-AS1, which is absorbed by HUVECs and promotes angiogenesis. Our study first identified that SOX21-AS1 promotes the malignancy of PDAC through the SOX21-AS1/miR-451a/EREG axis, and also that exosomal SOX21-AS1 promotes angiogenesis in PDAC.
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Affiliation(s)
- Yong Yan
- Department of Hepatobiliary Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Jinyi Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Bin Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianming Ni
- Department of Radiology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
| | - Tu Dai
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Liying Wang
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Hao Wang
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Zhiyuan Hua
- Department of Hepatobiliary Surgery, Jiangnan University Medical Center, JUMC, Wuxi, China
| | - Kuan Li
- Department of Hepatobiliary Surgery, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
| | - Yongping Zhou
- Department of Hepatobiliary Surgery, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, Wuxi, China
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28
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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29
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Syed RU, Afsar S, Aboshouk NAM, Salem Alanzi S, Abdalla RAH, Khalifa AAS, Enrera JA, Elafandy NM, Abdalla RAH, Ali OHH, Satheesh Kumar G, Alshammari MD. LncRNAs in necroptosis: Deciphering their role in cancer pathogenesis and therapy. Pathol Res Pract 2024; 256:155252. [PMID: 38479121 DOI: 10.1016/j.prp.2024.155252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 04/14/2024]
Abstract
Necroptosis, a controlled type of cell death that is different from apoptosis, has become a key figure in the aetiology of cancer and offers a possible target for treatment. A growing number of biological activities, including necroptosis, have been linked to long noncoding RNAs (lncRNAs), a varied family of RNA molecules with limited capacity to code for proteins. The complex interactions between LncRNAs and important molecular effectors of necroptosis, including mixed lineage kinase domain-like pseudokinase (MLKL) and receptor-interacting protein kinase 3 (RIPK3), will be investigated. We will explore the many methods that LncRNAs use to affect necroptosis, including protein-protein interactions, transcriptional control, and post-transcriptional modification. Additionally, the deregulation of certain LncRNAs in different forms of cancer will be discussed, highlighting their dual function in influencing necroptotic processes as tumour suppressors and oncogenes. The goal of this study is to thoroughly examine the complex role that LncRNAs play in controlling necroptotic pathways and how that regulation affects the onset and spread of cancer. In the necroptosis for cancer treatment, this review will also provide insight into the possible therapeutic uses of targeting LncRNAs. Techniques utilising LncRNA-based medicines show promise in controlling necroptotic pathways to prevent cancer from spreading and improve the effectiveness of treatment.
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Affiliation(s)
- Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, Hail 81442, Saudi Arabia.
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | | | | | - Amna Abakar Suleiman Khalifa
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Jerlyn Apatan Enrera
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Nancy Mohammad Elafandy
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Randa Abdeen Husien Abdalla
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Omar Hafiz Haj Ali
- Department of Clinical laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - G Satheesh Kumar
- Department of Pharmaceutical Chemistry, College of Pharmacy, Seven Hills College of Pharmacy, Venkataramapuram, Tirupati, India
| | - Maali D Alshammari
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
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30
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Duan BT, Zhao XK, Cui YY, Liu DZ, Wang L, Zhou L, Zhang XY. Construction and validation of somatic mutation-derived long non-coding RNAs signatures of genomic instability to predict prognosis of hepatocellular carcinoma. World J Gastrointest Surg 2024; 16:842-859. [PMID: 38577085 PMCID: PMC10989333 DOI: 10.4240/wjgs.v16.i3.842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/20/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) have been found to be a potential prognostic factor for cancers, including hepatocellular carcinoma (HCC). Some LncRNAs have been confirmed as potential indicators to quantify genomic instability (GI). Nevertheless, GI-LncRNAs remain largely unexplored. This study established a GI-derived LncRNA signature (GILncSig) that can predict the prognosis of HCC patients. AIM To establish a GILncSig that can predict the prognosis of HCC patients. METHODS Identification of GI-LncRNAs was conducted by combining LncRNA expression and somatic mutation profiles. The GI-LncRNAs were then analyzed for functional enrichment. The GILncSig was established in the training set by Cox regression analysis, and its predictive ability was verified in the testing set and TCGA set. In addition, we explored the effects of the GILncSig and TP53 on prognosis. RESULTS A total of 88 GI-LncRNAs were found, and functional enrichment analysis showed that their functions were mainly involved in small molecule metabolism and GI. The GILncSig was constructed by 5 LncRNAs (miR210HG, AC016735.1, AC116351.1, AC010643.1, LUCAT1). In the training set, the prognosis of high-risk patients was significantly worse than that of low-risk patients, and similar results were verified in the testing set and TCGA set. Multivariate Cox regression analysis and stratified analysis confirmed that the GILncSig could be used as an independent prognostic factor. Receiver operating characteristic curve analysis of the GILncSig showed that the area under the curve (0.773) was higher than the two LncRNA signatures published recently. Furthermore, the GILncSig may have a better predictive performance than TP53 mutation status alone. CONCLUSION We established a GILncSig that can predict the prognosis of HCC patients, which will help to guide prognostic evaluation and treatment decisions.
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Affiliation(s)
- Bo-Tao Duan
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Xue-Kai Zhao
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Yang-Yang Cui
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - De-Zheng Liu
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Lin Wang
- Department of Ophthalmology, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Lei Zhou
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
| | - Xing-Yuan Zhang
- Department of Hepatobiliary Surgery, Binzhou Medical University Hospital, Binzhou 256600, Shandong Province, China
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Dong J, Lv Y, Meng D, Shi R, Li F, Guo R, Wang Y, Guo J, Zhang Y. LncRNA WFDC21P interacts with SEC63 to promote gastric cancer malignant behaviors by regulating calcium homeostasis signaling pathway. Cancer Cell Int 2024; 24:111. [PMID: 38528582 DOI: 10.1186/s12935-024-03297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Gastric cancer is currently estimated to be the fifth leading common cancer in the world, and responsible for about one million new cases and an estimated 769,000 cancer-related deaths each year. WFDC21P is long non-coding RNA and has been reported to play critical roles in serval types of cancer. Our research aims to investigate the biological effects and molecular mechanism of WFDC21P in gastric cancer. METHODS Datasets (GSE53137, GSE58828, and GSE109476) in GEO database were used to screen differential expressed lncRNAs in gastric cancer by online GEO2R analysis tool. Quantitative RT-PCR was used to verify the above prediction in ten pairs of gastric cancer and corresponding paracancerous tissues. Pan-cancer analysis was used to analyze the expression of WFDC21P in different types of cancer. Small interfering RNAs were used to WFDC21P knockdown. CCK-8 and colony formation assays were used to measure the proliferation and tumorigenesis abilities. Wound healing and Transwell assay were used to detect the migration and invasion abilities. Proteins that interact with WFDC21P were predicted by catRAPID database. RNA pull down and RNA Immunoprecipitation were used to confirm the interaction. Western blotting was used to detect the key proteins level in calcium homeostasis signaling pathway. Loss-of-function and rescue assays were used to evaluate the biological function of SEC63 at the background of WFDC21P silencing. RESULTS WFDC21P was upregulated in gastric cancer tissues and cell lines. WFDC21P downregulation suppressed proliferation, tumorigenesis, migration, invasion, and promoted apoptosis in gastric cancer. SEC63 protein had the capability to bind with WFDC21P and the expression of SEC63 was regulated by WFDC21P. SEC63 was also upregulated in gastric cancer and exerted effects during tumor growth and metastasis. CONCLUSIONS This study confirmed that lncRNA WFDC21P aggravated gastric cancer malignant behaviors by interacting with SEC63 to regulate the calcium homeostasis signaling pathway.
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Affiliation(s)
- Jinyao Dong
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Yongqiang Lv
- Scientific Research Department, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, 030013, P. R. China
| | - Debin Meng
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Ruyi Shi
- Department of Cell biology and Genetics, Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China
| | - Feng Li
- Central Laboratory, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi, 030013, P. R. China
| | - Rui Guo
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Yi Wang
- Hepatobiliary Pancreatogastric Surgery, Shanxi Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University , Taiyuan, Shanxi, 030013, P. R. China
| | - Jiansheng Guo
- Gastrointestinal Surgery Department, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China.
| | - Yanyan Zhang
- Hepatobiliary Pancreatic Surgery and Liver Transplantation Center, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, P. R. China.
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Kearly A, Nelson ADL, Skirycz A, Chodasiewicz M. Composition and function of stress granules and P-bodies in plants. Semin Cell Dev Biol 2024; 156:167-175. [PMID: 36464613 DOI: 10.1016/j.semcdb.2022.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
Stress Granules (SGs) and Processing-bodies (P-bodies) are biomolecular condensates formed in the cell with the highly conserved purpose of maintaining balance between storage, translation, and degradation of mRNA. This balance is particularly important when cells are exposed to different environmental conditions and adjustments have to be made in order for plants to respond to and tolerate stressful conditions. While P-bodies are constitutively present in the cell, SG formation is a stress-induced event. Typically thought of as protein-RNA aggregates, SGs and P-bodies are formed by a process called liquid-liquid phase separation (LLPS), and both their function and composition are very dynamic. Both foci are known to contain proteins involved in translation, protein folding, and ATPase activity, alluding to their roles in regulating mRNA and protein expression levels. From an RNA perspective, SGs and P-bodies primarily consist of mRNAs, though long non-coding RNAs (lncRNAs) have also been observed, and more focus is now being placed on the specific RNAs associated with these aggregates. Recently, metabolites such as nucleotides and amino acids have been reported in purified plant SGs with implications for the energetic dynamics of these condensates. Thus, even though the field of plant SGs and P-bodies is relatively nascent, significant progress has been made in understanding their composition and biological role in stress responses. In this review, we discuss the most recent discoveries centered around SG and P-body function and composition in plants.
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Affiliation(s)
- Alyssa Kearly
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | | | | | - Monika Chodasiewicz
- Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Pham TG, Wu J. Recent advances in methods for live-cell RNA imaging. NANOSCALE 2024; 16:5537-5545. [PMID: 38414383 DOI: 10.1039/d4nr00129j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
As one of the most fundamental building blocks of life, RNA plays critical roles in diverse biological processes, from X chromosome inactivation, genome stability maintenance, to embryo development. Being able to visualize the localization and dynamics of RNA can provide critical insights into these fundamental processes. In this review, we provide an overview of current methods for live-cell RNA imaging with a focus on methods for visualizing RNA in living mammalian cells with single-molecule resolution.
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Affiliation(s)
- Tien G Pham
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
| | - Jiahui Wu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA.
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Adu-Gyamfi EA, Cheeran EA, Salamah J, Enabulele DB, Tahir A, Lee BK. Long non-coding RNAs: a summary of their roles in placenta development and pathology†. Biol Reprod 2024; 110:431-449. [PMID: 38134961 DOI: 10.1093/biolre/ioad179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Long non-coding RNAs are cellular transcripts that have ˃200 nucleotides in length and do not code for proteins. Due to their low expression levels, long non-coding RNAs were previously considered as mere transcriptional noise. However, current evidence indicates that they regulate a myriad of biological processes such as cell proliferation, invasion, and apoptosis. Hence, their expression patterns are crucial indicators of the physiological or pathological states of cells, tissues, and organs. The utilization of long non-coding RNAs as biomarkers and therapeutic targets for the clinical management of several diseases have been suggested. Gradually, long non-coding RNAs are gaining a substantial attention in the field of feto-maternal medicine. After embryo implantation, the interactions between the trophoblast cells from the embryo and the uterus of the mother facilitate placenta development and pregnancy progression. These processes are tightly regulated, and their impairments result in pregnancy pathologies such as miscarriage and preeclampsia. Accumulating evidence implicates long non-coding RNAs in these processes. Herein, we have summarized the roles of several long non-coding RNAs in human placenta development, have proposed some mechanisms by which they participate in physiological and pathological placentation, have revealed some knowledge deficits, and have recommended ideal experimental approaches that will facilitate the clarification of the mechanistic actions of each long non-coding RNA at the feto-maternal interface during healthy and pathological pregnancies.
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Affiliation(s)
- Enoch Appiah Adu-Gyamfi
- Department of Biomedical Sciences, Cancer Research Center, University at Albany - State University of New York, Rensselaer, NY 12144, United States
| | - Elisha Ann Cheeran
- Department of Biomedical Sciences, Cancer Research Center, University at Albany - State University of New York, Rensselaer, NY 12144, United States
| | - Joudi Salamah
- Department of Biomedical Sciences, Cancer Research Center, University at Albany - State University of New York, Rensselaer, NY 12144, United States
| | - Divine Blessing Enabulele
- Department of Biomedical Sciences, Cancer Research Center, University at Albany - State University of New York, Rensselaer, NY 12144, United States
| | - Ayesha Tahir
- Department of Biomedical Sciences, Cancer Research Center, University at Albany - State University of New York, Rensselaer, NY 12144, United States
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany - State University of New York, Rensselaer, NY 12144, United States
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35
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Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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36
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Li B, Xiong X, Xu J, Peng D, Nie G, Wen N, Wang Y, Lu J. METTL3-mediated m 6A modification of lncRNA TSPAN12 promotes metastasis of hepatocellular carcinoma through SENP1-depentent deSUMOylation of EIF3I. Oncogene 2024; 43:1050-1062. [PMID: 38374407 DOI: 10.1038/s41388-024-02970-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/21/2024]
Abstract
In a previous study, we discovered that the level of lnc-TSPAN12 was significantly elevated in hepatocellular carcinoma (HCC) and correlated with a low survival rate. However, the function and mechanism of lnc-TSPAN12 in modulating epithelial-mesenchymal transition (EMT) and metastasis in HCC remains poorly understood. This study demonstrates that lnc-TSPAN12 positively influences migration, invasion, and EMT of HCC cells in vitro and promotes hepatic metastasis in vivo. The modification of N6-methyladenosine, driven by METTL3, is essential for the stability of lnc-TSPAN12, which may partially contribute to the upregulation of lnc-TSPAN12. Mechanistically, lnc-TSPAN12 exhibits direct interactions with EIF3I and SENP1, acting as a scaffold to enhance the SENP1-EIF3I interaction. As a result, the SUMOylation of EIF3I is inhibited, preventing its ubiquitin-mediated degradation. Ultimately, this activates the Wnt/β-catenin signaling pathway, stimulating EMT and metastasis in HCC. Our findings shed light on the regulatory mechanism of lnc-TSPAN12 in HCC metastasis and identify the lnc-TSPAN12-EIF3I/SENP1 axis as a novel therapeutic target for HCC.
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Affiliation(s)
- Bei Li
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xianze Xiong
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jianrong Xu
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Dingzhong Peng
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Guilin Nie
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ningyuan Wen
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yaoqun Wang
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jiong Lu
- Division of Biliary Surgery, Department of General Surgery, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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37
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Liu H, Deng S, Yao X, Liu Y, Qian L, Wang Y, Zhang T, Shan G, Chen L, Zhou Y. Ascites exosomal lncRNA PLADE enhances platinum sensitivity by inducing R-loops in ovarian cancer. Oncogene 2024; 43:714-728. [PMID: 38225339 DOI: 10.1038/s41388-024-02940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/17/2024]
Abstract
Cisplatin resistance is a major cause of therapeutic failure in patients with high-grade serous ovarian cancer (HGSOC). Long noncoding RNAs (lncRNAs) have emerged as key regulators of human cancers; however, their modes of action in HGSOC remain largely unknown. Here, we provide evidence to demonstrate that lncRNA Platinum sensitivity-related LncRNA from Ascites-Derived Exosomes (PLADE) transmitted by ascites exosomes enhance platinum sensitivity in HGSOC. PLADE exhibited significantly decreased expression in ascites exosomes and tumor tissues, as well as in the corresponding metastatic tumors from patients with HGSOC cisplatin-resistance. Moreover, HGSOC patients with higher PLADE expression levels exhibited longer progression-free survival. Gain- and loss-of-function studies have revealed that PLADE promotes cisplatin sensitivity by suppressing cell proliferation, migration and invasion, and enhancing apoptosis in vitro and in vivo. Furthermore, the functions of PLADE in increasing cisplatin sensitivity were proven to be transferred by exosomes to the cultured recipient cells and to the adjacent tumor tissues in mouse models. Mechanistically, PLADE binds to and downregulates heterogeneous nuclear ribonucleoprotein D (HNRNPD) by VHL-mediated ubiquitination, thus inducing an increased amount of RNA: DNA hybrids (R-loop) and DNA damage, consequently promoting cisplatin sensitivity in HGSOC. Collectively, these results shed light on the understanding of the vital roles of long noncoding RNAs in cancers.
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Affiliation(s)
- Hanyuan Liu
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Sisi Deng
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xuelin Yao
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Lili Qian
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yingying Wang
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Tianjiao Zhang
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Ge Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Liang Chen
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ying Zhou
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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Alpuche-Lazcano SP, Scarborough RJ, Gatignol A. MicroRNAs and long non-coding RNAs during transcriptional regulation and latency of HIV and HTLV. Retrovirology 2024; 21:5. [PMID: 38424561 PMCID: PMC10905857 DOI: 10.1186/s12977-024-00637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) and human T cell leukemia virus (HTLV) have replicative and latent stages of infection. The status of the viruses is dependent on the cells that harbour them and on different events that change the transcriptional and post-transcriptional events. Non-coding (nc)RNAs are key factors in the regulation of retrovirus replication cycles. Notably, micro (mi)RNAs and long non-coding (lnc)RNAs are important regulators that can induce switches between active transcription-replication and latency of retroviruses and have important impacts on their pathogenesis. Here, we review the functions of miRNAs and lncRNAs in the context of HIV and HTLV. We describe how specific miRNAs and lncRNAs are involved in the regulation of the viruses' transcription, post-transcriptional regulation and latency. We further discuss treatment strategies using ncRNAs for HIV and HTLV long remission, reactivation or possible cure.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Medicine, Division of Infectious Diseases, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
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Amir N, Taube R. Role of long noncoding RNA in regulating HIV infection-a comprehensive review. mBio 2024; 15:e0192523. [PMID: 38179937 PMCID: PMC10865847 DOI: 10.1128/mbio.01925-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
A complete cure against human immunodeficiency virus (HIV) infection remains out of reach, as the virus persists in stable cell reservoirs that are resistant to antiretroviral therapy. The key to eliminating these reservoirs lies in deciphering the processes that govern viral gene expression and latency. However, while we comprehensively understand how host proteins influence HIV gene expression and viral latency, the emerging role of long noncoding RNAs (lncRNAs) in the context of T cell activation, HIV gene expression, and viral latency remain unexplored. This review dives into the evolving significance of lncRNAs and their impact on HIV gene expression and viral latency. We provide an overview of the current knowledge regarding how lncRNAs regulate HIV gene expression, categorizing them as either activators or inhibitors of viral gene expression and infectivity. Furthermore, we offer insights into the potential therapeutic applications of lncRNAs in combatting HIV. A deeper understanding of how lncRNAs modulate HIV gene transcription holds promise for developing novel RNA-based therapies to complement existing treatment strategies to eradicate HIV reservoirs.
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Affiliation(s)
- Noa Amir
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
| | - Ran Taube
- The Shraga Segal Department of Microbiology Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Negev, Israel
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40
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Zhang J. Non-coding RNAs and angiogenesis in cardiovascular diseases: a comprehensive review. Mol Cell Biochem 2024:10.1007/s11010-023-04919-5. [PMID: 38306012 DOI: 10.1007/s11010-023-04919-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/18/2023] [Indexed: 02/03/2024]
Abstract
Non-coding RNAs (ncRNAs) have key roles in the etiology of many illnesses, including heart failure, myocardial infarction, stroke, and in physiological processes like angiogenesis. In transcriptional regulatory circuits that control heart growth, signaling, and stress response, as well as remodeling in cardiac disease, ncRNAs have become important players. Studies on ncRNAs and cardiovascular disease have made great progress recently. Here, we go through the functions of non-coding RNAs (ncRNAs) like circular RNAs (circRNAs), and microRNAs (miRNAs) as well as long non-coding RNAs (lncRNAs) in modulating cardiovascular disorders.
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Affiliation(s)
- Jie Zhang
- Medical School, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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Zhou Y, Wu Q, Long X, He Y, Huang J. lncRNA HOTAIRM1 Activated by HOXA4 Drives HUVEC Proliferation Through Direct Interaction with Protein Partner HSPA5. Inflammation 2024; 47:421-437. [PMID: 37898994 PMCID: PMC10798933 DOI: 10.1007/s10753-023-01919-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023]
Abstract
Despite the substantial progress in deciphering the pathogenesis of atherosclerosis (AS), cardiovascular mortality is still increasing. Therefore, atherosclerotic cardiovascular disease remains a sweeping epidemic that jeopardizes human health. Disentangling the molecular underpinnings of AS is imperative in the molecular cardiology field. Overwhelming evidence has indicated that the recognition of a fascinating class of players, known as long non-coding RNAs (lncRNAs), provides causality for coordinating AS. However, the function and mechanism of HOTAIRM1 are still poorly understood in human umbilical vein endothelial cells (HUVECs) and AS. Herein, we primarily underscored that lncRNA HOTAIRM1 is potentially responsible for AS; as such, it was dramatically up-regulated in HUVECs upon ox-LDL stimulation. Functionally, HOTAIRM1 knockdown attenuated HUVEC proliferation and potentiated apoptosis in the absence and presence of ox-LDL. Furthermore, HOTAIRM1 was preferentially located in the nuclei of HUVECs. Mechanistically, HOXA4 is directly bound to the HOTAIRM1 promoter and activated its transcription. Of note, a positive feedback signaling between HOXA4 and HOTAIRM1 was determined. Intriguingly, the interplay between HOTAIRM1 and HSPA5 occurred in an RNA-binding protein pattern and a transcription-dependent regulatory manner. In addition, HSPA5 overexpression partially antagonized HUVEC proliferation inhibition of HOTAIRM1 depletion. Taken together, our findings delineate a pivotal functional interaction among HOXA4, HOTAIRM1, and HSPA5 as a novel regulatory circuit for modulating HUVEC proliferation. An in-depth investigation of the HOXA4-HOTAIRM1-HSPA5 axis promises to yield significant breakthroughs in identifying the molecular mechanisms governing AS and developing therapeutic avenues for AS.
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Affiliation(s)
- Yu Zhou
- Medical College, Guizhou University, Guiyang, 550025, Guizhou, China
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Qiang Wu
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China.
| | - Xiangshu Long
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Youfu He
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
| | - Jing Huang
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, 550002, Guizhou, China
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Capela AM, Tavares-Marcos C, Estima-Arede HF, Nóbrega-Pereira S, Bernardes de Jesus B. NORAD-Regulated Signaling Pathways in Breast Cancer Progression. Cancers (Basel) 2024; 16:636. [PMID: 38339387 PMCID: PMC10854850 DOI: 10.3390/cancers16030636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Long non-coding RNA activated by DNA damage (NORAD) has recently been associated with pathologic mechanisms underlying cancer progression. Due to NORAD's extended range of interacting partners, there has been contradictory data on its oncogenic or tumor suppressor roles in BC. This review will summarize the function of NORAD in different BC subtypes and how NORAD impacts crucial signaling pathways in this pathology. Through the preferential binding to pumilio (PUM) proteins PUM1 and PUM2, NORAD has been shown to be involved in the control of cell cycle, angiogenesis, mitosis, DNA replication and transcription and protein translation. More recently, NORAD has been associated with PUM-independent roles, accomplished by interacting with other ncRNAs, mRNAs and proteins. The intricate network of NORAD-mediated signaling pathways may provide insights into the potential design of novel unexplored strategies to overcome chemotherapy resistance in BC treatment.
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Affiliation(s)
| | | | | | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.C.); (C.T.-M.); (H.F.E.-A.)
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences, Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal; (A.M.C.); (C.T.-M.); (H.F.E.-A.)
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Xiao W, Halabi R, Lin CH, Nazim M, Yeom KH, Black DL. The lncRNA Malat1 is trafficked to the cytoplasm as a localized mRNA encoding a small peptide in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578240. [PMID: 38352368 PMCID: PMC10862813 DOI: 10.1101/2024.02.01.578240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Synaptic function is modulated by local translation of mRNAs that are transported to distal portions of axons and dendrites. The Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is broadly expressed across cell types, almost exclusively as a nuclear non-coding RNA. We found that in differentiating neurons, a portion of Malat1 RNA redistributes to the cytoplasm. Depletion of Malat1 from neurons stimulated expression of particular pre- and post- synaptic proteins, implicating Malat1 in their regulation. Neuronal Malat1 is localized to both axons and dendrites in puncta that co-stain with Staufen1 protein, similar to neuronal granules formed by locally translated mRNAs. Ribosome profiling of mouse cortical neurons identified ribosome footprints within a region of Malat1 containing short open reading frames. The upstream-most reading frame (M1) of the Malat1 locus was linked to the GFP coding sequence in mouse ES cells. When these gene-edited cells were differentiated into glutamatergic neurons, the M1-GFP fusion protein was expressed. Antibody staining for the M1 peptide confirmed its presence in wildtype neurons, and showed enhancement of M1 expression after synaptic stimulation with KCL. Our results indicate that Malat1 serves as a cytoplasmic coding RNA in the brain that is both modulated by and modulates synaptic function.
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Affiliation(s)
- Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Reem Halabi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Mohammad Nazim
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Kyu-Hyeon Yeom
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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Hazazi A, AlShehah AA, Khan FR, Hakami MA, Almarshadi F, Abalkhail A, Nassar SA, Almasoudi HH, Ali AA, Abu-Alghayth MH, Kukreti N, Binshaya AS. From diagnosis to therapy: The transformative role of lncRNAs in eye cancer management. Pathol Res Pract 2024; 254:155081. [PMID: 38211388 DOI: 10.1016/j.prp.2023.155081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
The genomic era has brought about a transformative shift in our comprehension of cancer, unveiling the intricate molecular landscape underlying disease development. Eye cancers (ECs), encompassing diverse malignancies affecting ocular tissues, pose distinctive challenges in diagnosis and management. Long non-coding RNAs (lncRNAs), an emerging category of non-coding RNAs, are pivotal actors in the genomic intricacies of eye cancers. LncRNAs have garnered recognition for their multifaceted roles in gene expression regulation and influence on many cellular processes. Many studies support that the lncRNAs have a role in developing various cancers. Recent investigations have pinpointed specific lncRNAs associated with ECs, including retinoblastoma and uveal melanoma. These lncRNAs exert control over critical pathways governing tumor initiation, progression, and metastasis, endowing them with the ability to function as evaluation, predictive, and therapeutic indicators. The article aims to synthesize the existing information concerning the functions of lncRNAs in ECs, elucidating their regulatory mechanisms and clinical significance. By delving into the lncRNAs' expanding relevance in the modulation of oncogenic and tumor-suppressive networks, we gain a deeper understanding of the molecular complexities intrinsic to these diseases. In our exploration of the genomic intricacies of ECs, lncRNAs introduce a fresh perspective, providing an opportunity to function as clinical and therapeutic indicators, and they also have therapeutic benefits that show promise for advancing the treatment of ECs. This comprehensive review bridges the intricate relationship between lncRNAs and ECs within the context of the genomic era.
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Affiliation(s)
- Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | | | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Fahad Almarshadi
- Department of Public Health, College of Public Health and Health Informatics, University of Ha'il, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Qassim, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Amer Al Ali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Abdulkarim S Binshaya
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
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Xie T, Huang Q, Huang Q, Huang Y, Liu S, Zeng H, Liu J. Dysregulated lncRNAs regulate human umbilical cord mesenchymal stem cell differentiation into insulin-producing cells by forming a regulatory network with mRNAs. Stem Cell Res Ther 2024; 15:22. [PMID: 38273351 PMCID: PMC10809572 DOI: 10.1186/s13287-023-03572-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/16/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE In recent years, cell therapy has emerged as a new research direction in the treatment of diabetes. However, the underlying molecular mechanisms of mesenchymal stem cell (MSC) differentiation necessary to form such treatment have not been clarified. METHODS In this study, human umbilical cord mesenchymal stem cells (HUC-MSCs) isolated from newborns were progressively induced into insulin-producing cells (IPCs) using small molecules. HUC-MSC (S0) and four induced stage (S1-S4) samples were prepared. We then performed transcriptome sequencing experiments to obtain the dynamic expression profiles of both mRNAs and long noncoding RNAs (lncRNAs). RESULTS We found that the number of differentially expressed lncRNAs and mRNAs trended downwards during differentiation. Gene Ontology (GO) analysis showed that the target genes of differentially expressed lncRNAs were associated with translation, cell adhesion, and cell connection. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the NF-KB signalling pathway, MAPK signalling pathway, HIPPO signalling pathway, PI3K-Akt signalling pathway, and p53 signalling pathway were enriched in these differentially expressed lncRNA-targeting genes. We also found that the coexpression of the lncRNA CTBP1-AS2 with PROX1 and the lncRNAs AC009014.3 and GS1-72M22.1 with JARID2 mRNA was related to the development of pancreatic beta cells. Moreover, the coexpression of the lncRNAs: XLOC_ 050969, LINC00883, XLOC_050981, XLOC_050925, MAP3K14- AS1, RP11-148K1.12, and CTD2020K17.3 with p53, regulated insulin secretion by pancreatic beta cells. CONCLUSION In this study, HUC-MSCs combined with small molecule compounds were successfully induced into IPCs. Differentially expressed lncRNAs may regulate the insulin secretion of pancreatic beta cells by regulating multiple signalling pathways. The lncRNAs AC009014.3, Gs1-72m21.1, and CTBP1-AS2 may be involved in the development of pancreatic beta cells, and the lncRNAs: XLOC_050969, LINC00883, XLOC_050981, XLOC_050925, MAP3K14-AS1, RP11-148K1.12, and CTD2020K17.3 may be involved in regulating the insulin secretion of pancreatic beta cells, thus providing a lncRNA catalogue for future research regarding the mechanism of the transdifferentiation of HUC-MSCs into IPCs. It also provides a new theoretical basis for the transplantation of insulin-producing cells into diabetic patients in the future.
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Affiliation(s)
- Tianqin Xie
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Qiming Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translation Medicine, Nanchang University, Nanchang of Jiangxi, China
| | - Qiulan Huang
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Yanting Huang
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Shuang Liu
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Haixia Zeng
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China
| | - Jianping Liu
- Department of Endocrinology Medicine, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang of Jiangxi, 330006, China.
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陶 若, 张 水, 郭 文, 闫 志. [Research Progress in the Role of Liquid-Liquid Phase Separation in Human Cancer]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:24-30. [PMID: 38322521 PMCID: PMC10839487 DOI: 10.12182/20240160503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Indexed: 02/08/2024]
Abstract
Liquid-liquid phase separation (LLPS) is a reversible process, during which biological macromolecules, including proteins and nucleic acids, condense into liquid membraneless organelles under the influence of weak multivalent interactions. Currently, fluorescence recovery after photobleaching is the primary method used to detect the phase separation of biological macromolecules. Recent studies have revealed the link between abnormal LLPS and the pathogenesis and development of various human cancers. Through phase separation or abnormal phase separation, tumor-related biological macromolecules, such as mRNA, long noncoding RNAs (lncRNAs), and tumor-related proteins, can affect transcriptional translation and DNA damage repair, regulate the autophagy and ferroptosis functions of cells, and thus regulate the development of various tumors. In this review, we summarized the latest research findings on the mechanism of LLPS in the pathogenesis and progression of tumors and elaborated on the promotion or inhibition of autophagy, tumor immunity, DNA damage repair, and cell ferroptosis after abnormal phase separation of biomolecules, including mRNA, lncRNA, and proteins, which subsequently affects the pathogenesis and progression of tumors. According to published findings, many biological macromolecules can regulate transcriptional translation, expression, post-transcriptional modification, cell signal transduction, and other biological processes through phase separation. Therefore, further expansion of the research field of phase separation and in-depth investigation of its molecular mechanisms and regulatory processes hold extensive research potential.
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Affiliation(s)
- 若琳 陶
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
| | - 水军 张
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
| | - 文治 郭
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
| | - 志平 闫
- 郑州大学第一附属医院 肝胆胰外科 (郑州 450000)Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- 河南省消化器官移植重点实验室 (郑州 450000)Henan Key Laboratory for Digestive Organ Transplantation, Zhengzhou 450000, China
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Wang Y, Xu C, Liu P, He Q, Zhang S, Liu Z, Ni C, Chen L, Zhi T, Xu L, Cheng L, Lin X, Yao M, Ni H. LncRNA 51325 Alleviates Bone Cancer Induced Hyperalgesia Through Inhibition of Pum2. J Pain Res 2024; 17:265-284. [PMID: 38249568 PMCID: PMC10799577 DOI: 10.2147/jpr.s446635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/07/2024] [Indexed: 01/23/2024] Open
Abstract
Background Bone cancer pain (BCP) represents one of the most challenging comorbidities associated with cancer metastasis. Long non-coding RNAs (lncRNAs) have garnered attention as potential therapeutic agents in managing neuropathic pain. However, their role in the regulation of nociceptive information processing remains poorly understood. In this study, we observed a significant down-regulation of the spinal lncRNA ENSRNOG00000051325 (lncRNA51325) in a rat model of bone cancer pain. Our study sought to elucidate the potential involvement of lncRNA51325 in the development of BCP by modulating the expression of molecules associated with pain modulation. Methods We established the BCP model by injecting Walker 256 cells into the tibial plateau of rats. We conducted tests on the pain behaviors and anxiety-like responses of rats through von-Frey test, Gait analysis, and Open Field Test. Spinal lumbar expansion was harvested for molecular biology experiments to explore the relationship between lncRNA51325 and Pumilio RNA binding family member 2 (Pum2). Results Notably, the overexpression of lncRNA51325 effectively attenuated mechanical allodynia in rats afflicted with BCP, whereas the knockdown of lncRNA51325 induced pain behaviors and anxiety-like responses in naïve rats. Additionally, we observed a time-dependent increase in the expression of Pum2 in BCP-afflicted rats, and intrathecal injection of Pum2-siRNA alleviated hyperalgesia. Furthermore, our investigations revealed that lncRNA51325 exerts a negative modulatory effect on Pum2 expression. The overexpression of lncRNA51325 significantly suppressed Pum2 expression in BCP rats, while the knockdown of lncRNA51325 led to elevated Pum2 protein levels in the spinal cord of naïve rats. Subsequent treatment with Pum2-siRNA mitigated the downregulation of lncRNA51325-induced mechanical allodynia in naïve rats. Conclusion Our findings indicate that lncRNA51325 plays a role in regulating bone cancer pain by inhibiting Pum2 expression, offering a promising avenue for novel treatments targeting nociceptive hypersensitivity induced by bone metastatic cancer.
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Affiliation(s)
- Yahui Wang
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
- Department of Pain Management, the First Affiliated Hospital of Bengbu Medical College, Bengbu City, 233000, People’s Republic of China
| | - Chengfei Xu
- Department of Anesthesiology, Bengbu Third People’s Hospital, Bengbu City, 233000, People’s Republic of China
| | - Peng Liu
- Department of Pain Management, the First Affiliated Hospital of Bengbu Medical College, Bengbu City, 233000, People’s Republic of China
| | - Qiuli He
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Shihua Zhang
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Zhihao Liu
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Chaobo Ni
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Liping Chen
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Tong Zhi
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Longsheng Xu
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Liang Cheng
- Department of Anesthesiology, Bengbu Third People’s Hospital, Bengbu City, 233000, People’s Republic of China
| | - Xuewu Lin
- Department of Pain Management, the First Affiliated Hospital of Bengbu Medical College, Bengbu City, 233000, People’s Republic of China
| | - Ming Yao
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
| | - Huadong Ni
- Department of Anesthesiology and Pain Research Center, the Affiliated Hospital of Jiaxing University, Jiaxing, 314001, People’s Republic of China
- Institute of Neuroscience, Soochow University, Suzhou, 215123, People’s Republic of China
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Zhang T, Huang H, Liang L, Lu H, Liang D. Long non-coding RNA (LncRNA) non-coding RNA activated by DNA damage (NORAD) knockdown alleviates airway remodeling in asthma via regulating miR-410-3p/RCC2 and inhibiting Wnt/β-catenin pathway. Heliyon 2024; 10:e23860. [PMID: 38261955 PMCID: PMC10796956 DOI: 10.1016/j.heliyon.2023.e23860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024] Open
Abstract
Background Asthma is a chronic inflammatory disorder with high prevalence in childhood. Airway remodeling, an important structural change of the airways, is resulted from epithelial-mesenchymal transition. Long non-coding RNA non-coding RNA activated by DNA damage (NORAD) has been found to promote epithelial-mesenchymal transition in multiple cancers. This study aimed to analyze the role of NORAD in asthma, mainly focusing on epithelial-mesenchymal transition-mediated airway remodeling, and further explored the NORAD-miRNA-mRNA network. Methods NORAD expression was analyzed in transforming growth factor-β1-induced BEAS-2B human bronchial epithelial cells and ovalbumin-challenged asthmatic mice. The influences of NORAD on the epithelial-mesenchymal transition characteristics and Wnt/β-catenin pathway activation were analyzed in vitro. The interactions between NORAD and miR-410-3p as well as miR-410-3p and regulator of chromosome condensation 2 were detected by dual-luciferase reporter assay and RNA pull-down assay. Rescue experiments using miR-410-3p antagonist and chromosome condensation 2 overexpression were used to confirm the mechanism of NORAD. Additionally, the role and mechanism of NORAD were further evaluated in asthmatic mice. Results NORAD expression was elevated in both asthmatic models. Knockdown of NORAD impeded spindle-like morphology changes, elevated E-cadherin expression, decreased N-cadherin expression, suppressed cell migration, and inactivated the Wnt/β-catenin pathway in transforming growth factor-β1-stimulated BEAS-2B cells. NORAD acted as a sponge of miR-410-3p to regulate chromosome condensation 2 expression. Rescue assays demonstrated that silencing of NORAD ameliorated transforming growth factor-β1-induced EMT via miR-410-3p/chromosome condensation 2/Wnt/β-catenin axis. In vivo, knockdown of NORAD led to the reduction of inflammatory cell infiltration and collagen deposition, suppression of IL-4, IL-13, transforming growth factor-β1 and immunoglobulin E production, decreasing of N-cadherin, chromosome condensation 2, β-catenin and c-Myc expression, but increasing of E-cadherin and miR-410-3p expression. Conclusions Silencing of NORAD alleviated epithelial-mesenchymal transition-mediated airway remodeling in asthma via mediating miR-410-3p/chromosome condensation 2/Wnt/β-catenin pathway.
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Affiliation(s)
- Ting Zhang
- Department of Respiratory, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450000, China
| | - Han Huang
- Department of Respiratory, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450000, China
| | - Lihong Liang
- Department of Respiratory, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450000, China
| | - Hongxia Lu
- Department of Respiratory, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450000, China
| | - Dongge Liang
- Department of Respiratory, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou 450000, China
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Mahato RK, Bhattacharya S, Khullar N, Sidhu IS, Reddy PH, Bhatti GK, Bhatti JS. Targeting long non-coding RNAs in cancer therapy using CRISPR-Cas9 technology: A novel paradigm for precision oncology. J Biotechnol 2024; 379:98-119. [PMID: 38065367 DOI: 10.1016/j.jbiotec.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Cancer is the second leading cause of death worldwide, despite recent advances in its identification and management. To improve cancer patient diagnosis and care, it is necessary to identify new biomarkers and molecular targets. In recent years, long non-coding RNAs (lncRNAs) have surfaced as important contributors to various cellular activities, with growing proof indicating their substantial role in the genesis, development, and spread of cancer. Their unique expression profiles within specific tissues and their wide-ranging functionalities make lncRNAs excellent candidates for potential therapeutic intervention in cancer management. They are implicated in multiple hallmarks of cancer, such as uncontrolled proliferation, angiogenesis, and immune evasion. This review article explores the innovative application of CRISPR-Cas9 technology in targeting lncRNAs as a cancer therapeutic strategy. The CRISPR-Cas9 system has been widely applied in functional genomics, gene therapy, and cancer research, offering a versatile platform for lncRNA targeting. CRISPR-Cas9-mediated targeting of lncRNAs can be achieved through CRISPR interference, activation or the complete knockout of lncRNA loci. Combining CRISPR-Cas9 technology with high-throughput functional genomics makes it possible to identify lncRNAs critical for the survival of specific cancer subtypes, opening the door for tailored treatments and personalised cancer therapies. CRISPR-Cas9-mediated lncRNA targeting with other cutting-edge cancer therapies, such as immunotherapy and targeted molecular therapeutics can be used to overcome the drug resistance in cancer. The synergy of lncRNA research and CRISPR-Cas9 technology presents immense potential for individualized cancer treatment, offering renewed hope in the battle against this disease.
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Affiliation(s)
- Rahul Kumar Mahato
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Srinjan Bhattacharya
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Inderpal Singh Sidhu
- Department of Zoology, Sri Guru Gobind Singh College, Sector 26, Chandigarh, India
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Pharmacology & Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
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Amin HM, Abukhairan R, Szabo B, Jacksi M, Varady G, Lozsa R, Schad E, Tantos A. KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing. Protein Sci 2024; 33:e4847. [PMID: 38058280 PMCID: PMC10731558 DOI: 10.1002/pro.4847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/30/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Histone lysine methyltransferases (HKMTs) perform vital roles in cellular life by controlling gene expression programs through the posttranslational modification of histone tails. Since many of them are intimately involved in the development of different diseases, including several cancers, understanding the molecular mechanisms that control their target recognition and activity is vital for the treatment and prevention of such conditions. RNA binding has been shown to be an important regulatory factor in the function of several HKMTs, such as the yeast Set1 and the human Ezh2. Moreover, many HKMTs are capable of RNA binding in the absence of a canonical RNA binding domain. Here, we explored the RNA binding capacity of KMT2D, one of the major H3K4 monomethyl transferases in enhancers, using RNA immunoprecipitation followed by sequencing. We identified a broad range of coding and non-coding RNAs associated with KMT2D and confirmed their binding through RNA immunoprecipitation and quantitative PCR. We also showed that a separated RNA binding region within KMT2D is capable of binding a similar RNA pool, but differences in the binding specificity indicate the existence of other regulatory elements in the sequence of KMT2D. Analysis of the bound mRNAs revealed that KMT2D preferentially binds co-transcriptionally to the mRNAs of the genes under its control, while also interacting with super enhancer- and splicing-related non-coding RNAs. These observations, together with the nuclear colocalization of KMT2D with differentially phosphorylated forms of RNA Polymerase II suggest a so far unexplored role of KMT2D in the RNA processing of the nascent transcripts.
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Affiliation(s)
- Harem Muhamad Amin
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
- Doctoral School of Biology and Institute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
- Department of Biology, College of ScienceUniversity of SulaimaniSulaymaniyahIraq
| | - Rawan Abukhairan
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Beata Szabo
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Mevan Jacksi
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
- Doctoral School of Biology and Institute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Gyorgy Varady
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Rita Lozsa
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Eva Schad
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Agnes Tantos
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
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