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Zhang J, Zhu H, Li L, Gao Y, Yu B, Ma G, Jin X, Sun Y. New mechanism of LncRNA: In addition to act as a ceRNA. Noncoding RNA Res 2024; 9:1050-1060. [PMID: 39022688 PMCID: PMC11254507 DOI: 10.1016/j.ncrna.2024.06.002] [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: 04/07/2024] [Revised: 05/20/2024] [Accepted: 06/03/2024] [Indexed: 07/20/2024] Open
Abstract
Long non-coding RNAs (LncRNAs) are a class of RNA molecules with nucleic acid lengths ranging from 200 bp to 100 kb that cannot code for proteins, which are diverse and widely expressed in both animals and plants. Scholars have found that lncRNAs can regulate human physiological processes at the gene and protein levels, mainly through the regulation of epigenetic, transcriptional and post-transcriptional levels of genes and proteins, as well as in the immune response by regulating the expression of immune cells and inflammatory factors, and thus participate in the occurrence and development of a variety of diseases. From the downstream targets of lncRNAs, we summarize the new research progress of lncRNA mechanisms other than miRNA sponges in recent years, aiming to provide new ideas and directions for the study of lncRNA mechanisms.
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Affiliation(s)
- Jiahao Zhang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Huike Zhu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Linjing Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Gao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- College of Life Sciences, Northwest Normal University, Gansu Province, Lanzhou, 730070, China
| | - Boyi Yu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guorong Ma
- The First Clinical Medical College of Gansu University of Chinese Medicine Gansu Provincial Hospital, Lanzhou, 730000, China
| | - Xiaodong Jin
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou, 730000, China
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2
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Morandell J, Monziani A, Lazioli M, Donzel D, Döring J, Oss Pegorar C, D'Anzi A, Pellegrini M, Mattiello A, Bortolotti D, Bergonzoni G, Tripathi T, Mattis VB, Kovalenko M, Rosati J, Dieterich C, Dassi E, Wheeler VC, Ellederová Z, Wilusz JE, Viero G, Biagioli M. CircHTT(2,3,4,5,6) - co-evolving with the HTT CAG-repeat tract - modulates Huntington's disease phenotypes. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102234. [PMID: 38974999 PMCID: PMC11225910 DOI: 10.1016/j.omtn.2024.102234] [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] [Received: 11/26/2023] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
Circular RNA (circRNA) molecules have critical functions during brain development and in brain-related disorders. Here, we identified and validated a circRNA, circHTT(2,3,4,5,6), stemming from the Huntington's disease (HD) gene locus that is most abundant in the central nervous system (CNS). We uncovered its evolutionary conservation in diverse mammalian species, and a correlation between circHTT(2,3,4,5,6) levels and the length of the CAG-repeat tract in exon-1 of HTT in human and mouse HD model systems. The mouse orthologue, circHtt(2,3,4,5,6), is expressed during embryogenesis, increases during nervous system development, and is aberrantly upregulated in the presence of the expanded CAG tract. While an IRES-like motif was predicted in circH TT (2,3,4,5,6), the circRNA does not appear to be translated in adult mouse brain tissue. Nonetheless, a modest, but consistent fraction of circHtt(2,3,4,5,6) associates with the 40S ribosomal subunit, suggesting a possible role in the regulation of protein translation. Finally, circHtt(2,3,4,5,6) overexpression experiments in HD-relevant STHdh striatal cells revealed its ability to modulate CAG expansion-driven cellular defects in cell-to-substrate adhesion, thus uncovering an unconventional modifier of HD pathology.
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Affiliation(s)
- Jasmin Morandell
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Alan Monziani
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Martina Lazioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Deborah Donzel
- Institute of Biophysics Unit at Trento, National Research Council - CNR, 38123 Trento, Italy
| | - Jessica Döring
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Claudio Oss Pegorar
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Angela D'Anzi
- Cellular Reprogramming Unit Fondazione IRCCS, Casa Sollievo Della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Miguel Pellegrini
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Andrea Mattiello
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Dalia Bortolotti
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Guendalina Bergonzoni
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Takshashila Tripathi
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Virginia B Mattis
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jessica Rosati
- Cellular Reprogramming Unit Fondazione IRCCS, Casa Sollievo Della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zdenka Ellederová
- Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, 277 21 Libechov, Czech Republic
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriella Viero
- Institute of Biophysics Unit at Trento, National Research Council - CNR, 38123 Trento, Italy
| | - Marta Biagioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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3
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Shen R, Yao Q, Tan X, Ren W, Zhong D, Zhang X, Li X, Dong C, Cao X, Tian Y, Zhu JK, Lu Y. In-locus gene silencing in plants using genome editing. THE NEW PHYTOLOGIST 2024; 243:2501-2511. [PMID: 38798233 DOI: 10.1111/nph.19856] [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: 10/24/2023] [Accepted: 05/03/2024] [Indexed: 05/29/2024]
Abstract
Gene silencing is crucial in crop breeding for desired trait development. RNA interference (RNAi) has been used widely but is limited by ectopic expression of transgenes and genetic instability. Introducing an upstream start codon (uATG) into the 5'untranslated region (5'UTR) of a target gene may 'silence' the target gene by inhibiting protein translation from the primary start codon (pATG). Here, we report an efficient gene silencing method by introducing a tailor-designed uATG-containing element (ATGE) into the 5'UTR of genes in plants, occupying the original start site to act as a new pATG. Using base editing to introduce new uATGs failed to silence two of the tested three rice genes, indicating complex regulatory mechanisms. Precisely inserting an ATGE adjacent to pATG achieved significant target protein downregulation. Through extensive optimization, we demonstrated this strategy substantially and consistently downregulated target protein expression. By designing a bidirectional multifunctional ATGE4, we enabled tunable knockdown from 19% to 89% and observed expected phenotypes. Introducing ATGE into Waxy, which regulates starch synthesis, generated grains with lower amylose, revealing the value for crop breeding. Together, we have developed a programmable and robust method to knock down gene expression in plants, with potential for biological mechanism exploration and crop enhancement.
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Affiliation(s)
- Rundong Shen
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qi Yao
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xinhang Tan
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Wendan Ren
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dating Zhong
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Xuening Zhang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinbo Li
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
| | - Chao Dong
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
| | - Xuesong Cao
- Institute of Advanced Biotechnology, and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yifu Tian
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
| | - Jian-Kang Zhu
- Institute of Crop Sciences/National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), and Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Sanya, 572024, China
- Institute of Advanced Biotechnology, and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuming Lu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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4
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Bangash MA, Cubuk C, Iseppon F, Haroun R, Garcia C, Luiz AP, Arcangeletti M, Gossage SJ, Santana-Varela S, Cox JJ, Lewis MJ, Wood JN, Zhao J. Analgesic targets identified in mouse sensory neuron somata and terminal pain translatomes. Cell Rep 2024; 43:114614. [PMID: 39163201 DOI: 10.1016/j.celrep.2024.114614] [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: 11/20/2023] [Revised: 06/07/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024] Open
Abstract
The relationship between transcription and protein expression is complex. We identified polysome-associated RNA transcripts in the somata and central terminals of mouse sensory neurons in control, painful (plus nerve growth factor), and pain-free conditions (Nav1.7-null mice). The majority (98%) of translated transcripts are shared between male and female mice in both the somata and terminals. Some transcripts are highly enriched in the somata or terminals. Changes in the translatome in painful and pain-free conditions include novel and known regulators of pain pathways. Antisense knockdown of selected somatic and terminal polysome-associated transcripts that correlate with pain states diminished pain behavior. Terminal-enriched transcripts included those encoding synaptic proteins (e.g., synaptotagmin), non-coding RNAs, transcription factors (e.g., Znf431), proteins associated with transsynaptic trafficking (HoxC9), GABA-generating enzymes (Gad1 and Gad2), and neuropeptides (Penk). Thus, central terminal translation may well be a significant regulatory locus for peripheral input from sensory neurons.
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Affiliation(s)
- M Ali Bangash
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Cankut Cubuk
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Federico Iseppon
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Rayan Haroun
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Chloe Garcia
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Ana P Luiz
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Manuel Arcangeletti
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Samuel J Gossage
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Sonia Santana-Varela
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - James J Cox
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - John N Wood
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK.
| | - Jing Zhao
- Molecular Nociception Group, Wolfson Institute for Biomedical Research, University College London WC1E 6BT, UK.
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5
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Gong S, Qiao H, Wang JY, Huang SY, He SW, Zhao Y, Tan XR, Ye ML, Li JY, Liang YL, Huang SW, Chen J, Zhu XH, Liu N, Li YQ. Ac4C modification of lncRNA SIMALR promotes nasopharyngeal carcinoma progression through activating eEF1A2 to facilitate ITGB4/ITGA6 translation. Oncogene 2024:10.1038/s41388-024-03133-x. [PMID: 39154122 DOI: 10.1038/s41388-024-03133-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 08/04/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
The dysregulation of long non-coding RNAs (lncRNAs) are involved in regulating tumor progression in multiple manner. However, little is known about whether lncRNA is involved in the translation regulation of proteins. Here, we identified that the suppressor of inflammatory macrophage apoptosis lncRNA (SIMALR) was highly expressed in nasopharyngeal carcinoma (NPC) tissues by analyzing the lncRNA microarray. Clinically, the high expression of SIMALR served as an independent predictor for inferior prognosis in NPC patients. SIMALR functioned as an oncogenic lncRNA that promoted the proliferation and metastasis of NPC cells in vitro and in vivo. Mechanistically, SIMALR served as a critical accelerator of protein synthesis by binding to eEF1A2 (eukaryotic translation elongation factor 1 alpha 2), one of the most crucial regulators in the translation machinery of the eukaryotic cells, and enhancing its endogenous GTPase activity. Furthermore, SIMALR mediated the activation of eEF1A2 phosphorylation to accelerate the translation of ITGB4/ITGA6, ultimately promoting the malignant phenotype of NPC cells. In addition, N-acetyltransferase 10 (NAT10) enhanced the stability of SIMALR and caused its overexpression in NPC through the N4-acetylcytidine (ac4C) modification. In sum, our results illustrate SIMALR functions as an accelerator for protein translation and highlight the oncogenic role of NAT10-SIMALR-eEF1A2-ITGB4/6 axis in NPC.
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Affiliation(s)
- Sha Gong
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Han Qiao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jing-Yun Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Sheng-Yan Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Shi-Wei He
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yin Zhao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Xi-Rong Tan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ming-Liang Ye
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jun-Yan Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ye-Lin Liang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Sai-Wei Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jun Chen
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Xun-Hua Zhu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Na Liu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Ying-Qing Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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6
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Huang L, Liu X, Chen Q, Yang J, Zhang D, Zhao Y, Xu L, Li Z, Liu X, Shao S, Li D, Song Y, Liu X, Zhan Q. TGF-β-induced lncRNA TBUR1 promotes EMT and metastasis in lung adenocarcinoma via hnRNPC-mediated GRB2 mRNA stabilization. Cancer Lett 2024; 600:217153. [PMID: 39102940 DOI: 10.1016/j.canlet.2024.217153] [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: 11/07/2023] [Revised: 07/20/2024] [Accepted: 08/01/2024] [Indexed: 08/07/2024]
Abstract
The transforming growth factor-β (TGF-β) signaling pathway is pivotal in inducing epithelial-mesenchymal transition (EMT) and promoting cancer metastasis. Long non-coding RNAs (lncRNAs) have emerged as significant players in these processes, yet their precise mechanisms remain elusive. Here, we demonstrate that TGF-β-upregulated lncRNA 1 (TBUR1) is significantly activated by TGF-β via Smad3/4 signaling in lung adenocarcinoma (LUAD) cells. Functionally, TBUR1 triggers EMT, enhances LUAD cell migration and invasion in vitro, and promotes metastasis in nude mice. Mechanistically, TBUR1 interacts with heterogeneous nuclear ribonucleoprotein C (hnRNPC) to stabilize GRB2 mRNA in an m6A-dependent manner. Clinically, TBUR1 is upregulated in LUAD tissues and correlates with poor prognosis, highlighting its potential as a prognostic biomarker and therapeutic target for LUAD. Taken together, our findings underscore the crucial role of TBUR1 in mediating TGF-β-induced EMT and metastasis in LUAD, providing insights for future therapeutic interventions.
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Affiliation(s)
- Lijie Huang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China; Beijing Neurosurgical Institute, Capital Medical University, Beijing 100070, China
| | - Xiaoxu Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Qiuying Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jingyu Yang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Dongdong Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yabing Zhao
- Liaoning Key Laboratory of Proteomics, Dalian Medical University, Dalian 116044, China
| | - Lele Xu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Zhangfu Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xinyuan Liu
- Liaoning Key Laboratory of Proteomics, Dalian Medical University, Dalian 116044, China
| | - Shujuan Shao
- Liaoning Key Laboratory of Proteomics, Dalian Medical University, Dalian 116044, China
| | - Dan Li
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xuefeng Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China.
| | - Qimin Zhan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Soochow University Cancer Institute, Suzhou 215000, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.
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7
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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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8
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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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Ustyantsev IG, Kosushkin SA, Borodulina OR, Vassetzky NS, Kramerov DA. Ere, a Family of Short Interspersed Elements in the Genomes of Odd-Toed Ungulates (Perissodactyla). Animals (Basel) 2024; 14:1982. [PMID: 38998094 PMCID: PMC11240701 DOI: 10.3390/ani14131982] [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: 06/07/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
Short Interspersed Elements (SINEs) are eukaryotic retrotransposons transcribed by RNA polymerase III (pol III). Many mammalian SINEs (T+ SINEs) contain a polyadenylation signal (AATAAA), a pol III transcription terminator, and an A-rich tail in their 3'-end. The RNAs of such SINEs have the capacity for AAUAAA-dependent polyadenylation, which is unique to pol III-generated transcripts. The structure, evolution, and polyadenylation of the Ere SINE of ungulates (horses, rhinos, and tapirs) were investigated in this study. A bioinformatics analysis revealed the presence of up to ~4 × 105 Ere copies in representatives of all three families. These copies can be classified into two large subfamilies, EreA and EreB, the former distinguished by an additional 60 bp sequence. The 3'-end of numerous EreA and all EreB copies exhibit a 50 bp sequence designated as a terminal domain (TD). The Ere family can be further subdivided into subfamilies EreA_0TD, EreA_1TD, EreB_1TD, and EreB_2TD, depending on the presence and number of terminal domains (TDs). Only EreA_0TD copies can be assigned to T+ SINEs as they contain the AATAAA signal and the TCTTT transcription terminator. The analysis of young Ere copies identified by comparison with related perissodactyl genomes revealed that EreA_0TD and, to a much lesser extent, EreB_2TD have retained retrotranspositional activity in the recent evolution of equids and rhinoceroses. The targeted mutagenesis and transfection of HeLa cells were used to identify sequences in equine EreA_0TD that are critical for the polyadenylation of its pol III transcripts. In addition to AATAAA and the transcription terminator, two sites in the 3' half of EreA, termed the β and τ signals, were found to be essential for this process. The evolution of Ere, with a particular focus on the emergence of T+ SINEs, as well as the polyadenylation signals are discussed in comparison with other T+ SINEs.
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Affiliation(s)
- Ilia G. Ustyantsev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A. Kosushkin
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga R. Borodulina
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nikita S. Vassetzky
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitri A. Kramerov
- Laboratory of Eukaryotic Genome Evolution, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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10
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Xiao F, Zhu H, Xiong Y, Guo Y, Zhang Z, Zeng J, Xiao Y, Liao B, Shang X, Zhao S, Hu G, Huang K, Guo H. Positive feedback loop of c-myc/XTP6/NDH2/NF-κB to promote malignant progression in glioblastoma. J Exp Clin Cancer Res 2024; 43:187. [PMID: 38965580 PMCID: PMC11225266 DOI: 10.1186/s13046-024-03109-5] [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: 04/18/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Recent studies have highlighted the significant role of the NF-κB signaling pathway in the initiation and progression of cancer. Furthermore, long noncoding RNAs (lncRNAs) have been identified as pivotal regulators in sustaining the NF-κB signaling pathway's functionality. Despite these findings, the underlying molecular mechanisms through which lncRNAs influence the NF-κB pathway remain largely unexplored. METHODS Bioinformatic analyses were utilized to investigate the differential expression and prognostic significance of XTP6. The functional roles of XTP6 were further elucidated through both in vitro and in vivo experimental approaches. To estimate the interaction between XTP6 and NDH2, RNA pulldown and RNA Immunoprecipitation (RIP) assays were conducted. The connection between XTP6 and the IκBα promoter was examined using Chromatin Isolation by RNA Purification (ChIRP) assays. Additionally, Chromatin Immunoprecipitation (ChIP) assays were implemented to analyze the binding affinity of c-myc to the XTP6 promoter, providing insights into the regulatory mechanisms at play. RESULTS XTP6 was remarkedly upregulated in glioblastoma multiforme (GBM) tissues and was connected with adverse prognosis in GBM patients. Our investigations revealed that XTP6 can facilitate the malignant progression of GBM both in vitro and in vivo. Additionally, XTP6 downregulated IκBα expression by recruiting NDH2 to the IκBα promoter, which resulted in elevated levels of H3K27me3, thereby reducing the transcriptional activity of IκBα. Moreover, the progression of GBM was further driven by the c-myc-mediated upregulation of XTP6, establishing a positive feedback loop with IκBα that perpetuated the activation of the NF-κB signaling pathway. Notably, the application of an inhibitor targeting the NF-κB signaling pathway effectively inhibited the continuous activation induced by XTP6, leading to a significant reduction in tumor formation in vivo. CONCLUSION The results reveal that XTP6 unveils an innovative epigenetic mechanism instrumental in the sustained activation of the NF-κB signaling pathway, suggesting a promising therapeutic target for the treatment of GBM.
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Affiliation(s)
- Feng Xiao
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Hong Zhu
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Yaping Xiong
- Departments of Anesthesiology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Yun Guo
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Zhe Zhang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Jie Zeng
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Yao Xiao
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Bin Liao
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Xuesong Shang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Siyi Zhao
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Guowen Hu
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Kai Huang
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China
| | - Hua Guo
- Department of Neurosurgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Jiangxi Key Laboratory of Neurological Tumors and Cerebrovascular Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China.
- JXHC key Laboratory of Neurological medicine, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Institute of Neuroscience, Nanchang University, Nanchang, Jiangxi, 330006, China.
- Jiangxi Province Key Laboratory of Neurological Diseases, Nanchang University, Nanchang, Jiangxi, 330006, China.
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11
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Khalilollah S, Kalantari Soltanieh S, Obaid Saleh R, Ali Alzahrani A, Ghaleb Maabreh H, Mazin Al-Hamdani M, Dehghani-Ghorbi M, Shafiei Khonachaei M, Akhavan-Sigari R. LncRNAs involvement in pathogenesis of immune-related disease via regulation of T regulatory cells, an updated review. Cytokine 2024; 179:156585. [PMID: 38579428 DOI: 10.1016/j.cyto.2024.156585] [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: 05/24/2023] [Revised: 03/03/2024] [Accepted: 03/20/2024] [Indexed: 04/07/2024]
Abstract
The pathophysiology of several illnesses, including cancer and autoimmune diseasesdepends on human regulatory T cells (Tregs), and abnormalities in these cells may function as triggers for these conditions. Cancer and autoimmune, and gynecological diseases are associated with the differentiation of the proinflammatory T cell subset TH17 and its balance with the production of Treg. Recently, long non-coding RNAs (lncRNAs) have become important regulatory molecules in a wide range of illnesses. During epigenetic regulation, they can control the expression of important genes at several levels by affecting transcription, post-transcriptional actions, translation, and protein modification. They might connect with different molecules, such as proteins, DNA and RNA, and their structural composition is intricate. Because lncRNAs regulatebiological processes, including cell division, death, and growth, they are linked to severaldiseases. A notable instance of this is the lncRNA NEAT1, which has been the subject of several investigations to ascertain its function in immune cell development. In the context of immune cell development, several additional lncRNAs have been connected to Treg cell differentiation. In this work, we summarize current findings about the diverse functions of lncRNAs in Treg cell differentiation and control of the Th17/Treg homeostasis in autoimmune disorders, cancers, as well as several gynecological diseases where Tregs are key players.
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Affiliation(s)
- Shayan Khalilollah
- Department of Neurosurgery, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | | | - Raed Obaid Saleh
- Department of Pathological Analysis, College of Applied Science, University of Fallujah, Al-Anbar, Iraq.
| | | | - Hatem Ghaleb Maabreh
- Department of Dermatovenerology, Foreign Languages, RUDN University (Peoples' Friendship University of Russia named after Patrice Lumumba), Moscow, Russia.
| | | | - Mahmoud Dehghani-Ghorbi
- Hematology-Oncology Department, Imam Hossein Educational Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | | | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center, Tuebingen, Germany; Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Poland.
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12
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Gugnoni M, Lorenzini E, Torricelli F, Donati B, Manicardi V, Vitale E, Muccioli S, Piana S, Lococo F, Zamponi R, Gandellini P, Ciarrocchi A. Linc00941 fuels ribogenesis and protein synthesis by supporting robust cMYC translation in malignant pleural mesothelioma. Cancer Lett 2024; 592:216950. [PMID: 38729555 DOI: 10.1016/j.canlet.2024.216950] [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: 12/05/2023] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/12/2024]
Abstract
Malignant pleural mesothelioma is a rare and lethal cancer caused by exposure to asbestos. The highly inflammatory environment caused by fibers accumulation forces cells to undergo profound adaptation to gain survival advantages. Prioritizing the synthesis of essential transcripts is an efficient mechanism coordinated by multiple molecules, including long non-coding RNAs. Enhancing the knowledge about these mechanisms is an essential weapon in combating mesothelioma. Linc00941 correlates to bad prognosis in various cancers, but it is reported to partake in distinct and apparently irreconcilable processes. In this work, we report that linc00941 supports the survival and aggressiveness of mesothelioma cells by influencing protein synthesis and ribosome biogenesis. Linc00941 binds to the translation initiation factor eIF4G, promoting the selective protein synthesis of cMYC, which, in turn, enhances the expression of key genes involved in translation. We analyzed a retrospective cohort of 97 mesothelioma patients' samples from our institution, revealing that linc00941 expression strongly correlates with reduced survival probability. This discovery clarifies linc00941's role in mesothelioma and proposes a unified mechanism of action for this lncRNA involving the selective translation of essential oncogenes, reconciling the discrepancies about its function.
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Affiliation(s)
- Mila Gugnoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy.
| | - Eugenia Lorenzini
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Benedetta Donati
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Emanuele Vitale
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy; Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Italy
| | - Silvia Muccioli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy; Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Italy
| | | | - Filippo Lococo
- Università Cattolica del Sacro Cuore, Rome, Italy; UOC Chirurgia Toracica, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Raffaella Zamponi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy
| | - Paolo Gandellini
- Department of Biosciences, University of Milan, 20133, Milan, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Italy.
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13
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Huang T, Zhong S, Sun J, Shen D, Zhang X, Zhao Q. Whole transcriptome analysis identifies differentially expressed mRNA, miRNA and lncRNA associated with male sterility in the silkworm, Bombyx mori. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2024; 52:101280. [PMID: 38964195 DOI: 10.1016/j.cbd.2024.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024]
Abstract
Insect sterility technology is gradually being applied to the control of lepidoptera pests, and the target gene for male sterility is the core of this technology. JMS is a mutant silkworm that exhibits male sterility, and to elucidate its formation mechanism, this study conducted a full transcriptome analysis of the testes of JMS and its wild-type silkworms 48 h after pupation, identifying 205 DElncRNAs, 913 mRNAs, and 92 DEmiRNAs. The KEGG pathway enrichment analysis of the DEmRNAs revealed that they were involved in the biosynthesis of amino acids and ECM-receptor interactions. Combined with ceRNA regulatory network KEGG analysis suggests that pathways from amino acid biosynthesis to hydrolytic processes of protein synthesis may play a crucial role in the formation of JMS mutant variants. Our study deepens our understanding of the regulatory network of male sterility genes in silkworms; it also provides a new perspective for insect sterility technology.
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Affiliation(s)
- Tianchen Huang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.
| | - Shanshan Zhong
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.
| | - Juan Sun
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Dongxu Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Xuelian Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Qiaoling Zhao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Scientific Research Center, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.
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14
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Wang W, Yang H, Fan Z, Shi R. STL Inhibited Angiogenesis of DPSCs Through Depressing Mitochondrial Respiration by Enhancing RNF217. Adv Biol (Weinh) 2024:e2400042. [PMID: 38880848 DOI: 10.1002/adbi.202400042] [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: 01/22/2024] [Revised: 05/10/2024] [Indexed: 06/18/2024]
Abstract
Angiogenesis is the determining factor during dental pulp regeneration. Six-twelve leukemia (STL) is identified as a key regulatory factor on the biological function of dental pulp stem cells (DPSCs) under hypoxic conditions, but its effect on angiogenesis is unclear. Co-culture of DPSCs and human umbilical vein endothelial cells (HUVECs) is used to detect tubule formation ability in vitro and the angiogenesis ability in vivo. RNA-seq and bioinformatic analyses are performed to screen differentially expressed genes. Seahorse Cell Mito Stress Test is proceeded to exam mitochondrial respiration. STL decreased tubule formation and mitochondrial respiration of DPSCs in vitro and restrained the number of blood vessels and the expression of VEGF in new formed tissue in vivo. Furthermore, pretreating STL-depleted DPSCs with rotenone, a mitochondrial respiration inhibitor, counteracted the promoting effect of STL knockdown on tubule formation. Then, RNA-seq and bioinformatic analyses identified some angiogenesis relevant genes and pathways in STL-depleted DPSCs. And STL enhanced expression of mRNA-ring finger protein 217 (RNF217), which inhibited the tubule formation and mitochondrial respiration of DPSCs. STL inhibited the angiogenesis of DPSCs through depressing mitochondrial respiration by enhancing RNF217, indicating that STL is a potential target for angiogenesis of DPSCs.
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Affiliation(s)
- Wanqing Wang
- Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China
| | - Haoqing Yang
- Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China
| | - Zhipeng Fan
- Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China
- Beijing Laboratory of Oral Health, Capital Medical University, Beijing, 100069, China
- Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ruitang Shi
- Department of Endodontics, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, 100050, China
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15
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Li K, Xie T, Li Y, Huang X. LncRNAs act as modulators of macrophages within the tumor microenvironment. Carcinogenesis 2024; 45:363-377. [PMID: 38459912 DOI: 10.1093/carcin/bgae021] [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: 11/16/2023] [Revised: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been established as pivotal players in various cellular processes, encompassing the regulation of transcription, translation and post-translational modulation of proteins, thereby influencing cellular functions. Notably, lncRNAs exert a regulatory influence on diverse biological processes, particularly in the context of tumor development. Tumor-associated macrophages (TAMs) exhibit the M2 phenotype, exerting significant impact on crucial processes such as tumor initiation, angiogenesis, metastasis and immune evasion. Elevated infiltration of TAMs into the tumor microenvironment (TME) is closely associated with a poor prognosis in various cancers. LncRNAs within TAMs play a direct role in regulating cellular processes. Functioning as integral components of tumor-derived exosomes, lncRNAs prompt the M2-like polarization of macrophages. Concurrently, reports indicate that lncRNAs in tumor cells contribute to the expression and release of molecules that modulate TAMs within the TME. These actions of lncRNAs induce the recruitment, infiltration and M2 polarization of TAMs, thereby providing critical support for tumor development. In this review, we survey recent studies elucidating the impact of lncRNAs on macrophage recruitment, polarization and function across different types of cancers.
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Affiliation(s)
- Kangning Li
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
- HuanKui Academy, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Tao Xie
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Yong Li
- Department of Anesthesiology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xuan Huang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Jiangxi Medical College, Nanchang University, Nanchang, China
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16
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Lv H, Qian D, Xu S, Fan G, Qian Q, Cha D, Qian X, Zhou G, Lu B. Modulation of long noncoding RNAs by polyphenols as a novel potential therapeutic approach in lung cancer: A comprehensive review. Phytother Res 2024; 38:3240-3267. [PMID: 38739454 DOI: 10.1002/ptr.8202] [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: 11/13/2023] [Revised: 03/10/2024] [Accepted: 03/19/2024] [Indexed: 05/16/2024]
Abstract
Lung cancer stands as a formidable global health challenge, necessitating innovative therapeutic strategies. Polyphenols, bioactive compounds synthesized by plants, have garnered attention for their diverse health benefits, particularly in combating various cancers, including lung cancer. The advent of whole-genome and transcriptome sequencing technologies has illuminated the pivotal roles of long noncoding RNAs (lncRNAs), operating at epigenetic, transcriptional, and posttranscriptional levels, in cancer progression. This review comprehensively explores the impact of polyphenols on both oncogenic and tumor-suppressive lncRNAs in lung cancer, elucidating on their intricate regulatory mechanisms. The comprehensive examination extends to the potential synergies when combining polyphenols with conventional treatments like chemotherapy, radiation, and immunotherapy. Recognizing the heterogeneity of lung cancer subtypes, the review emphasizes the need for the integration of nanotechnology for optimized polyphenol delivery and personalized therapeutic approaches. In conclusion, we collect the latest research, offering a holistic overview of the evolving landscape of polyphenol-mediated modulation of lncRNAs in lung cancer therapy. The integration of polyphenols and lncRNAs into multidimensional treatment strategies holds promise for enhancing therapeutic efficacy and navigating the challenges associated with lung cancer treatment.
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Affiliation(s)
- Hong Lv
- Department of Pulmonary and Critical Care Medicine, Taicang TCM Hospital, Taicang, China
| | - Dawei Qian
- Department of Thoracic Surgery, Tongling Yi'an District People's Hospital, Tongling, China
| | - Shuhua Xu
- Department of Cardiothoracic Surgery, Dongtai Hospital of Traditional Chinese Medicine, Dongtai, China
| | - Guiqin Fan
- Department of Pulmonary and Critical Care Medicine, Taicang TCM Hospital, Taicang, China
| | - Qiuhong Qian
- Department of Pulmonary and Critical Care Medicine, Taicang TCM Hospital, Taicang, China
| | - Dongsheng Cha
- Department of Thoracic Surgery, Tongling Yi'an District People's Hospital, Tongling, China
| | - Xingjia Qian
- Department of Pulmonary and Critical Care Medicine, Taicang TCM Hospital, Taicang, China
| | - Guoping Zhou
- Department of Cardiothoracic Surgery, Dongtai Hospital of Traditional Chinese Medicine, Dongtai, China
| | - Bing Lu
- Department of Pulmonary and Critical Care Medicine, Taicang TCM Hospital, Taicang, China
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17
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Xuan L, Zi-Ming J, Xue-Yan T, Wen-Xuan H, Fa-Xuan W. LncRNA MRAK052509 competitively adsorbs miR-204-3p to regulate silica dust-induced EMT process. ENVIRONMENTAL TOXICOLOGY 2024; 39:3628-3640. [PMID: 38491797 DOI: 10.1002/tox.24218] [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: 12/02/2023] [Revised: 02/07/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Silicosis is a systemic disease caused by long-term inhalation of free SiO2 and retention in the lungs. At present, it is still the most important occupational health hazard disease in the world. Existing studies have shown that non-coding RNA can also participate in complex fibrosis regulatory networks. However, its role in regulating silicotic fibrosis is still unclear. In this study, we constructed a NR8383/RLE-6TN co-culture system to simulate the pathogenesis of silicosis in vitro. Design of miR-204-3p mimics and inhibitors to overexpress or downregulate miR-204-3p in RLE-6TN cells. Design of short hairpin RNA (sh-RNA) to downregulate MRAK052509 in RLE-6TN cells. The regulatory mechanism of miR-204-3p and LncRNA MRAK052509 on EMT process was studied by Quantitative real-time PCR, Western blotting, Immunofluorescence and Cell scratch test. The results revealed that miR-204-3p affects the occurrence of silica dust-induced cellular EMT process mainly through regulating TGF-βRΙ, a key molecule of TGF-β signaling pathway. In contrast, Lnc MRAK052509 promotes the EMT process in epithelial cells by competitively adsorbing miR-204-3p and reducing its inhibitory effect on the target gene TGF-βRΙ, which may influence the development of silicosis fibrosis. This study perfects the targeted regulation relationship between LncRNA MRAK052509, miR-204-3p and TGF-βRΙ, and may provide a new strategy for the study of the pathogenesis and treatment of silicosis.
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Affiliation(s)
- Liu Xuan
- School of Public Health, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, China
| | - Jiao Zi-Ming
- School of Public Health, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, China
| | - Tian Xue-Yan
- School of Public Health, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, China
| | - Hu Wen-Xuan
- School of Public Health, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, China
| | - Wang Fa-Xuan
- School of Public Health, Ningxia Medical University, Yinchuan, China
- Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan, China
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18
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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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19
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Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [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: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
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Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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20
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Zhang Y, Liu H, Niu M, Wang Y, Xu R, Guo Y, Zhang C. Roles of long noncoding RNAs in human inflammatory diseases. Cell Death Discov 2024; 10:235. [PMID: 38750059 PMCID: PMC11096177 DOI: 10.1038/s41420-024-02002-6] [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: 07/06/2023] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Chemokines, cytokines, and inflammatory cells mediate the onset and progression of many diseases through the induction of an inflammatory response. LncRNAs have emerged as important regulators of gene expression and signaling pathways. Increasing evidence suggests that lncRNAs are key players in the inflammatory response, making it a potential therapeutic target for various diseases. From the perspective of lncRNAs and inflammatory factors, we summarized the expression level and regulatory mechanisms of lncRNAs in human inflammatory diseases, such as cardiovascular disease, osteoarthritis, sepsis, chronic obstructive pulmonary disease, asthma, acute lung injury, diabetic retinopathy, and Parkinson's disease. We also summarized the functions of lncRNAs in the macrophages polarization and discussed the potential applications of lncRNAs in human inflammatory diseases. Although our understanding of lncRNAs is still in its infancy, these data will provide a theoretical basis for the clinical application of lncRNAs.
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Affiliation(s)
- Yuliang Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
| | - Hongliang Liu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Min Niu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Ying Wang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Rong Xu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Yujia Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China
| | - Chunming Zhang
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
- Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, 030001, Shanxi, China.
- Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
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21
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Li H, Huo S, He X, Guo D, Liu Y, Zheng L, Zhou X. LncRNA CARMN facilitates odontogenic differentiation of dental pulp cells by impairing EZH2. Oral Dis 2024; 30:2387-2397. [PMID: 37222221 DOI: 10.1111/odi.14619] [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: 11/13/2022] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
OBJECTIVE This study aimed to reveal the potential role of CARMN in odontogenic differentiation of dental pulp cells (DPCs). METHODS Laser capture microdissection was used to detect Carmn in DPCs and odontoblasts in P0 mice. After manipulating CARMN expression in odontogenic differentiation induced hDPCs, the state of odontogenic differentiation was evaluated by ALP staining, ARS, and related marker expression in qRT-PCR and western blotting. The subcutaneous transplantation of HA/β-TCP loaded with hDPCs was performed to verify CARMN's role in promoting odontogenic differentiation in vivo. RNAplex and RIP were employed to reveal potential mechanism of CARMN in hDPCs. RESULTS CARMN expressed more abundantly in odontoblasts than DPCs in P0 mice. CARMN expression boosted during in vitro odontogenic differentiation of hDPCs. CARMN overexpression enhanced odontogenic differentiation of hDPCs in vitro, while inhibition impaired the process. CARMN overexpression in HA/β-TCP composites promoted more mineralized nodule formation in vivo. CARMN knockdown led to soared EZH2, while CARMN overexpression brought about EZH2 inhibition. CARMN functioned via direct interaction with EZH2. CONCLUSIONS The results uncovered CARMN as a modulator during the odontogenic differentiation of DPCs. CARMN promoted odontogenic differentiation of DPCs by impairing EZH2.
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Affiliation(s)
- Hongyu Li
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- West China School of Stomatology, Sichuan University, Chengdu, China
| | - Sibei Huo
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- West China School of Stomatology, Sichuan University, Chengdu, China
| | - Xinyu He
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- West China School of Stomatology, Sichuan University, Chengdu, China
| | - Daimo Guo
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yingling Liu
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- West China School of Stomatology, Sichuan University, Chengdu, China
| | - Liwei Zheng
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zhou
- State Key laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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22
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Dos Reis RS, Wagner MCE, McKenna S, Ayyavoo V. Neuroinflammation driven by human immunodeficiency virus-1 (HIV-1) directs the expression of long noncoding RNA RP11-677M14.2 resulting in dysregulation of neurogranin in vivo and in vitro. J Neuroinflammation 2024; 21:107. [PMID: 38659061 PMCID: PMC11043047 DOI: 10.1186/s12974-024-03102-x] [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: 12/27/2023] [Accepted: 04/15/2024] [Indexed: 04/26/2024] Open
Abstract
Neuroinflammation and synaptodendritic damage represent the pathological hallmarks of HIV-1 associated cognitive disorders (HAND). The post-synaptic protein neurogranin (Nrgn) is significantly reduced in the frontal cortex of postmortem brains from people with HIV (PWH) and it is associated with inflammatory factors released by infected microglia/macrophages. However, the mechanism involved in synaptic loss have yet to be elucidated. In this study, we characterized a newly identified long non-coding RNA (lncRNA) transcript (RP11-677M14.2), which is antisense to the NRGN locus and is highly expressed in the frontal cortex of HIV-1 individuals. Further analysis indicates an inverse correlation between the expression of RP11-677M14.2 RNA and Nrgn mRNA. Additionally, the Nrgn-lncRNA axis is dysregulated in neurons exposed to HIV-1 infected microglia conditioned medium enriched with IL-1β. Moreover, in vitro overexpression of this lncRNA impacts Nrgn expression at both mRNA and protein levels. Finally, we modeled the Nrgn-lncRNA dysregulation within an HIV-1-induced inflammatory environment using brain organoids, thereby corroborating our in vivo and in vitro findings. Together, our study implicates a plausible role for lncRNA RP11-677M14.2 in modulating Nrgn expression that might serve as the mechanistic link between Nrgn loss and cognitive dysfunction in HAND, thus shedding new light on the mechanisms underlying synaptodendritic damage.
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Affiliation(s)
- Roberta S Dos Reis
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA
| | - Marc C E Wagner
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA
| | - Savannah McKenna
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA
| | - Velpandi Ayyavoo
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, 2117 Pitt Public Health, 130 DeSoto Street, Pittsburgh, PA, 15260, USA.
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23
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Werner A, Kanhere A, Wahlestedt C, Mattick JS. Natural antisense transcripts as versatile regulators of gene expression. Nat Rev Genet 2024:10.1038/s41576-024-00723-z. [PMID: 38632496 DOI: 10.1038/s41576-024-00723-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as a major class of gene products that have central roles in cell and developmental biology. Natural antisense transcripts (NATs) are an important subset of lncRNAs that are expressed from the opposite strand of protein-coding and non-coding genes and are a genome-wide phenomenon in both eukaryotes and prokaryotes. In eukaryotes, a myriad of NATs participate in regulatory pathways that affect expression of their cognate sense genes. Recent developments in the study of NATs and lncRNAs and large-scale sequencing and bioinformatics projects suggest that whether NATs regulate expression, splicing, stability or translation of the sense transcript is influenced by the pattern and degrees of overlap between the sense-antisense pair. Moreover, epigenetic gene regulatory mechanisms prevail in somatic cells whereas mechanisms dependent on the formation of double-stranded RNA intermediates are prevalent in germ cells. The modulating effects of NATs on sense transcript expression make NATs rational targets for therapeutic interventions.
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Affiliation(s)
| | | | | | - John S Mattick
- University of New South Wales, Sydney, New South Wales, Australia
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24
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Espadas I, Wingfield JL, Nakahata Y, Chanda K, Grinman E, Ghosh I, Bauer KE, Raveendra B, Kiebler MA, Yasuda R, Rangaraju V, Puthanveettil S. Synaptically-targeted long non-coding RNA SLAMR promotes structural plasticity by increasing translation and CaMKII activity. Nat Commun 2024; 15:2694. [PMID: 38538603 PMCID: PMC10973417 DOI: 10.1038/s41467-024-46972-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in maintaining cell homeostasis and function. However, it remains largely unknown whether and how neuronal activity impacts the transcriptional regulation of lncRNAs, or if this leads to synapse-related changes and contributes to the formation of long-term memories. Here, we report the identification of a lncRNA, SLAMR, which becomes enriched in CA1-hippocampal neurons upon contextual fear conditioning but not in CA3 neurons. SLAMR is transported along dendrites via the molecular motor KIF5C and is recruited to the synapse upon stimulation. Loss of function of SLAMR reduces dendritic complexity and impairs activity-dependent changes in spine structural plasticity and translation. Gain of function of SLAMR, in contrast, enhances dendritic complexity, spine density, and translation. Analyses of the SLAMR interactome reveal its association with CaMKIIα protein through a 220-nucleotide element also involved in SLAMR transport. A CaMKII reporter reveals a basal reduction in CaMKII activity with SLAMR loss-of-function. Furthermore, the selective loss of SLAMR function in CA1 disrupts the consolidation of fear memory in male mice, without affecting their acquisition, recall, or extinction, or spatial memory. Together, these results provide new molecular and functional insight into activity-dependent changes at the synapse and consolidation of contextual fear.
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Affiliation(s)
- Isabel Espadas
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Jenna L Wingfield
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | | | - Kaushik Chanda
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Eddie Grinman
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Ilika Ghosh
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Karl E Bauer
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Bindu Raveendra
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA
| | - Michael A Kiebler
- Biomedical Center, Department for Cell Biology, Ludwig-Maximilians-University of Munich, Medical Faculty, 82152, Planegg-Martinsried, Germany
| | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | | | - Sathyanarayanan Puthanveettil
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, FL, USA.
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25
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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26
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Shreeya T, Ansari MS, Kumar P, Saifi M, Shati AA, Alfaifi MY, Elbehairi SEI. Senescence: A DNA damage response and its role in aging and Neurodegenerative Diseases. FRONTIERS IN AGING 2024; 4:1292053. [PMID: 38596783 PMCID: PMC11002673 DOI: 10.3389/fragi.2023.1292053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/09/2023] [Indexed: 04/11/2024]
Abstract
Senescence is a complicated, multi-factorial, irreversible cell cycle halt that has a tumor-suppressing effect in addition to being a significant factor in aging and neurological diseases. Damaged DNA, neuroinflammation, oxidative stress and disrupted proteostasis are a few of the factors that cause senescence. Senescence is triggered by DNA damage which initiates DNA damage response. The DNA damage response, which includes the formation of DNA damage foci containing activated H2AX, which is a key factor in cellular senescence, is provoked by a double strand DNA break. Oxidative stress impairs cognition, inhibits neurogenesis, and has an accelerated aging effect. Senescent cells generate pro-inflammatory mediators known as senescence-associated secretory phenotype (SASP). These pro-inflammatory cytokines and chemokines have an impact on neuroinflammation, neuronal death, and cell proliferation. While it is tempting to think of neurodegenerative diseases as manifestations of accelerated aging and senescence, this review will present information on brain ageing and neurodegeneration as a result of senescence and DNA damage response.
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Affiliation(s)
- Tejal Shreeya
- Institute of Biophysics, Biological Research Center, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Mohd Saifullah Ansari
- Institute of Genetics, Biological Research Center, Szeged, Hungary
- Doctoral School of Biology, University of Szeged, Szeged, Hungary
| | - Prabhat Kumar
- Institute of Physiology, Medical School, University of Pécs, Pécs, Hungary
- Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | | | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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27
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Li T, Shu X, Gao M, Huang C, Li T, Cao J, Ying X, Liu D, Liu J. N4-Allylcytidine: a new nucleoside analogue for RNA labelling and chemical sequencing. RSC Chem Biol 2024; 5:225-235. [PMID: 38456037 PMCID: PMC10915972 DOI: 10.1039/d3cb00189j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/15/2023] [Indexed: 03/09/2024] Open
Abstract
RNA labelling has become indispensable in studying RNA biology. Nucleoside analogues with a chemical sequencing power represent desirable RNA labelling molecules because precise labelling information at base resolution can be obtained. Here, we report a new nucleoside analogue, N4-allylcytidine (a4C), which is able to tag RNA through both in vitro and in vivo pathways and further specifically reacts with iodine to form 3, N4-cyclized cytidine (cyc-C) in a catalyst-free, fast and complete manner. Full spectroscopic characterization concluded that cyc-C consisted of paired diastereoisomers with opposite chiral carbon centers in the fused 3, N4-five-membered ring. During RNA reverse transcription into complementary DNA, cyc-C induces base misincorporation due to the disruption of canonical hydrogen bonding by the cyclized structure and thus can be accurately identified by sequencing at single base resolution. With the chemical sequencing rationale of a4C, successful applications have been performed including pinpointing N4-methylcytidine methyltransferases' substrate modification sites, metabolically labelling mammalian cellular RNAs, and mapping active cellular RNA polymerase locations with the chromatin run-on RNA sequencing technique. Collectively, our work demonstrates that a4C is a promising molecule for RNA labelling and chemical sequencing and expands the toolkit for studying sophisticated RNA biology.
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Affiliation(s)
- Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Chenyang Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Ting Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
- Life Sciences Institute, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Xiner Ying
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Donghong Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
- Life Sciences Institute, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
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Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [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: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
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Lee JD, Solomon IH, Slack FJ, Mavrikaki M. Cognition-associated long noncoding RNAs are dysregulated upon severe COVID-19. Front Immunol 2024; 15:1290523. [PMID: 38410515 PMCID: PMC10894962 DOI: 10.3389/fimmu.2024.1290523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/23/2024] [Indexed: 02/28/2024] Open
Abstract
Severe COVID-19 leads to widespread transcriptomic changes in the human brain, mimicking diminished cognitive performance. As long noncoding RNAs (lncRNAs) play crucial roles in the regulation of gene expression, identification of the lncRNAs differentially expressed upon COVID-19 may nominate key regulatory nodes underpinning cognitive changes. Here we identify hundreds of lncRNAs differentially expressed in the brains of COVID-19 patients relative to uninfected age/sex-matched controls, many of which are associated with decreased cognitive performance and inflammatory cytokine response. Our analyses reveal pervasive transcriptomic changes in lncRNA expression upon severe COVID-19, which may serve as key regulators of neurocognitive changes in the brain.
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Affiliation(s)
- Jonathan D. Lee
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Isaac H. Solomon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Frank J. Slack
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, United States
| | - Maria Mavrikaki
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA, United States
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30
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Godet AC, Roussel E, Laugero N, Morfoisse F, Lacazette E, Garmy-Susini B, Prats AC. Translational control by long non-coding RNAs. Biochimie 2024; 217:42-53. [PMID: 37640229 DOI: 10.1016/j.biochi.2023.08.015] [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: 04/25/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Long non-coding (lnc) RNAs, once considered as junk and useless, are now broadly recognized to have major functions in the cell. LncRNAs are defined as non-coding RNAs of more than 200 nucleotides, regulate all steps of gene expression. Their origin is diverse, they can arise from intronic, intergenic or overlapping region, in sense or antisense direction. LncRNAs are mainly described for their action on transcription, while their action at the translational level is more rarely cited. However, the bibliography in the field is more and more abundant. The present synopsis of lncRNAs involved in the control of translation reveals a wide field of regulation of gene expression, with at least nine distinct molecular mechanisms. Furthermore, it appears that all these lncRNAs are involved in various pathologies including cancer, cardiovascular and neurodegenerative diseases.
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Affiliation(s)
- Anne-Claire Godet
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France; Threonin Design, 220 Chemin de Montabon, Le Touvet, France
| | - Emilie Roussel
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
| | - Nathalie Laugero
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
| | - Florent Morfoisse
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
| | - Eric Lacazette
- UMR 1297-I2MC, Inserm, Université de Toulouse, UT3, Toulouse, France
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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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Chen H, Wang YD, Blan AW, Almanza-Fuerte EP, Bonkowski ES, Bajpai R, Pruett-Miller SM, Mefford HC. Patient derived model of UBA5-associated encephalopathy identifies defects in neurodevelopment and highlights potential therapies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577254. [PMID: 38328212 PMCID: PMC10849720 DOI: 10.1101/2024.01.25.577254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
UBA5 encodes for the E1 enzyme of the UFMylation cascade, which plays an essential role in ER homeostasis. The clinical phenotypes of UBA5-associated encephalopathy include developmental delays, epilepsy and intellectual disability. To date, there is no humanized neuronal model to study the cellular and molecular consequences of UBA5 pathogenic variants. We developed and characterized patient-derived cortical organoid cultures and identified defects in GABAergic interneuron development. We demonstrated aberrant neuronal firing and microcephaly phenotypes in patient-derived organoids. Mechanistically, we show that ER homeostasis is perturbed along with exacerbated unfolded protein response pathway in cells and organoids expressing UBA5 pathogenic variants. We also assessed two gene expression modalities that augmented UBA5 expression to rescue aberrant molecular and cellular phenotypes. Our study provides a novel humanized model that allows further investigations of UBA5 variants in the brain and highlights novel systemic approaches to alleviate cellular aberrations for this rare, developmental disorder.
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Affiliation(s)
- Helen Chen
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Aidan W. Blan
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Edith P. Almanza-Fuerte
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Emily S. Bonkowski
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Richa Bajpai
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis TN, USA
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital, Memphis TN, USA
| | - Heather C. Mefford
- Center for Pediatric Neurological Disease Research, St. Jude Children’s Research Hospital, Memphis, TN, USA
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Xi Z, Huang H, Hu J, Yu Y, Ma X, Xu M, Ming J, Li L, Zhang H, Chen H, Huang T. LINC00571 drives tricarboxylic acid cycle metabolism in triple-negative breast cancer through HNRNPK/ILF2/IDH2 axis. J Exp Clin Cancer Res 2024; 43:22. [PMID: 38238853 PMCID: PMC10795234 DOI: 10.1186/s13046-024-02950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Triple-negative breast cancer is a complex breast malignancy subtype characterized by poor prognosis. The pursuit of effective therapeutic approaches for this subtype is considerably challenging. Notably, recent research has illuminated the key role of the tricarboxylic acid cycle in cancer metabolism and the complex landscape of tumor development. Concurrently, an emerging body of evidence underscores the noteworthy role that long non-coding RNAs play in the trajectory of breast cancer development. Despite this growing recognition, the exploration of whether long non-coding RNAs can influence breast cancer progression by modulating the tricarboxylic acid cycle has been limited. Moreover, the underlying mechanisms orchestrating these interactions have not been identified. METHODS The expression levels of LINC00571 and IDH2 were determined through the analysis of the public TCGA dataset, transcriptome sequencing, qRT‒PCR, and Western blotting. The distribution of LINC00571 was assessed using RNA fluorescence in situ hybridization. Alterations in biological effects were evaluated using CCK-8, colony formation, EdU, cell cycle, and apoptosis assays and a tumor xenograft model. To elucidate the interaction between LINC00571, HNRNPK, and ILF2, RNA pull-down, mass spectrometry, coimmunoprecipitation, and RNA immunoprecipitation assays were performed. The impacts of LINC00571 and IDH2 on tricarboxylic acid cycle metabolites were investigated through measurements of the oxygen consumption rate and metabolite levels. RESULTS This study revealed the complex interactions between a novel long non-coding RNA (LINC00571) and tricarboxylic acid cycle metabolism. We validated the tumor-promoting role of LINC00571. Mechanistically, LINC00571 facilitated the interaction between HNRNPK and ILF2, leading to reduced ubiquitination and degradation of ILF2, thereby stabilizing its expression. Furthermore, ILF2 acted as a transcription factor to enhance the expression of its downstream target gene IDH2. CONCLUSIONS Our study revealed that the LINC00571/HNRNPK/ILF2/IDH2 axis promoted the progression of triple-negative breast cancer by regulating tricarboxylic acid cycle metabolites. This discovery provides a novel theoretical foundation and new potential targets for the clinical treatment of triple-negative breast cancer.
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Affiliation(s)
- Zihan Xi
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Haohao Huang
- Department of Neurosurgery, General Hospital of Central Theater Command of Chinese People's Liberation Army, Wuhan, 430070, China
- General Hospital Of Central Theater Command and Hubei Key Laboratory of Central Nervous System Tumor and Intervention, Wuhan, China
| | - Jin Hu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Yuanhang Yu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xianxiong Ma
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ming Xu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jie Ming
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lei Li
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Hui Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Hengyu Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Hainan Medical University, Haikou, 570216, China.
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Chen HF, Chang CT, Hsu KW, Peng PH, Lai JCY, Hung MC, Wu KJ. Epigenetic regulation of asymmetric cell division by the LIBR-BRD4 axis. Nucleic Acids Res 2024; 52:154-165. [PMID: 37986225 PMCID: PMC10783485 DOI: 10.1093/nar/gkad1095] [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: 04/12/2023] [Revised: 09/04/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023] Open
Abstract
Asymmetric cell division (ACD) is a mechanism used by stem cells to maintain the number of progeny. However, the epigenetic mechanisms regulating ACD remain elusive. Here we show that BRD4, a BET domain protein that binds to acetylated histone, is segregated in daughter cells together with H3K56Ac and regulates ACD. ITGB1 is regulated by BRD4 to regulate ACD. A long noncoding RNA (lncRNA), LIBR (LncRNA Inhibiting BRD4), decreases the percentage of stem cells going through ACD through interacting with the BRD4 mRNAs. LIBR inhibits the translation of BRD4 through recruiting a translation repressor, RCK, and inhibiting the binding of BRD4 mRNAs to polysomes. These results identify the epigenetic regulatory modules (BRD4, lncRNA LIBR) that regulate ACD. The regulation of ACD by BRD4 suggests the therapeutic limitation of using BRD4 inhibitors to treat cancer due to the ability of these inhibitors to promote symmetric cell division that may lead to tumor progression and treatment resistance.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan
| | - Chia-Ting Chang
- Graduate Institute of Translational Medicine & New Drug Development, China Medical University, Taichung 406, Taiwan
- General Education Center, Feng Chia University, Taichung 407, Taiwan
| | - Kai-Wen Hsu
- Graduate Institute of Translational Medicine & New Drug Development, China Medical University, Taichung 406, Taiwan
| | - Pei-Hua Peng
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
| | - Joseph Chieh-Yu Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan
| | - Mien-Chie Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 406, Taiwan
- Institutes of Biochemistry and Molecular Biology, Research Center for Cancer Biology, Cancer Biology and Precision Therapeutics Center, and Center for Molecular Medicine, China Medical University, Taichung 406, Taiwan
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan 333, Taiwan
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Reis RSD, Wagner MCE, McKenna S, Ayyavoo V. Neuroinflammation driven by Human Immunodeficiency Virus-1 (HIV-1) directs the expression of long noncoding RNA RP11-677M14.2 resulting in dysregulation of Neurogranin in vivo and in vitro. RESEARCH SQUARE 2024:rs.3.rs-3810214. [PMID: 38260270 PMCID: PMC10802713 DOI: 10.21203/rs.3.rs-3810214/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroinflammation and synaptodendritic damage represent the pathological hallmarks of HIV-1 associated cognitive disorders (HAND). The post-synaptic protein neurogranin (Nrgn) is significantly reduced in the frontal cortex of postmortem brains from people with HIV (PWH) and it is associated with inflammatory factors released by infected microglia/macrophages. However, the mechanism involved in synaptic loss have yet to be elucidated. In this study, we characterized a newly identified long non-coding RNA (lncRNA) transcript (RP11-677M14.2), which is antisense to the NRGN locus and is highly expressed in the frontal cortex of HIV-1 individuals. Further analysis indicates an inverse correlation between the expression of RP11-677M14.2 RNA and Nrgn mRNA. Additionally, the Nrgn-lncRNA axis is dysregulated in neurons exposed to HIV-1 infected microglia conditioned medium enriched with IL-1b. Moreover, in vitro overexpression of this lncRNA impact Nrgn expression at both mRNA and protein levels. Finally, we modeled the Nrgn-lncRNA dysregulation within an HIV-1-induced neuroinflammatory environment using brain organoids, thereby corroborating our in vivo and in vitro findings. Together, our study implicates a plausible role for lncRNA RP11-677M14.2 in modulating Nrgn expression that might serve as the mechanistic link between Nrgn loss and cognitive dysfunction in HAND, thus shedding new light on the mechanisms underlying synaptodendritic damage.
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Banerjee S, Sarkar R, Mukherjee A, Mitra S, Gope A, Chawla-Sarkar M. Rotavirus-induced lncRNA SLC7A11-AS1 promotes ferroptosis by targeting cystine/glutamate antiporter xCT (SLC7A11) to facilitate virus infection. Virus Res 2024; 339:199261. [PMID: 37923170 PMCID: PMC10684390 DOI: 10.1016/j.virusres.2023.199261] [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: 08/23/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 11/07/2023]
Abstract
Rotavirus (RV) is the primary etiological agent of virus-associated gastroenteritis in infants, causing 200,000 childhood death annually. Despite the availability of vaccines, rotaviral diarrhea continues to be a severe issue in underdeveloped nations in Asia and Africa. The situation demands continual studies on host-rotavirus interactions to understand disease pathogenesis and develop effective antiviral therapeutics. Long non-coding RNAs (lncRNAs), which are a subset of non-coding RNAs of more than 200 nucleotides in length, are reported to play a regulatory function in numerous viral infections. Virus infection often alters the host transcriptome including lncRNA that are differentially expressed either to play an antiviral role or to be advantageous towards virus propagation. In the current study, qPCR array-based expression profiling of host lncRNAs was performed in rotavirus-infected HT-29 cells that identified the lncRNA SLC7A11-AS1 to be upregulated during RV infection. Knockdown of SLC7A11-AS1 conspicuously reduced RV titers implying its pro-viral significance. RV-induced SLC7A11-AS1 downregulates the gene SLC7A11/xCT that encodes the light chain subunit of the system XC- cystine-glutamate exchange transporter, leading to decrease in intracellular glutathione level and increase in lipid peroxidation, which are signature features of ferroptotic pathway. Ectopic expression of xCT also abrogated RV infection by reversing the virus optimized levels of intracellular GSH and lipid ROS levels. Cumulatively, the study reveals that RV infection triggers ferroptotic cell death via SLC7A11-AS1/xCT axis to facilitate its own propagation.
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Affiliation(s)
- Shreya Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Rakesh Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Arpita Mukherjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Animesh Gope
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010, India.
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37
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Dong G, Yin X, Liang Y, Chen J, Wang J, Jiang F, Wang C, Guo W, Wang Y. A novel AluYb8 insertion-associated non-coding RNA, lncMUTYH, impairs mitochondrial function and dampens the M2-like polarization of macrophages. Free Radic Res 2024; 58:27-42. [PMID: 38145459 DOI: 10.1080/10715762.2023.2299333] [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: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 12/26/2023]
Abstract
An inverted AluYb8 insertion in the MUTYH intron 15 (AluYb8MUTYH variant) has been reported to be associated with reduced MUTYH1 expression and mitochondrial dysfunction with age. However, the underlying mechanism remains unknown. In this study, we identified a novel transcript associated with the AluYb8MUTYH variant, which revealed that this transcript is about 780 nucleotides in length with a poly-A tail, lacks protein-coding potential, referred to as lncMUTYH. The results from the reporter gene system confirmed that the lncMUTYH down-regulates MUTYH1 expression at the translational level. Site-directed mutagenesis on the 5'-terminal exon sequences of α-MUTYH and lncMUTYH constructs revealed that lncMUTYH can act as a trans-regulator that depends on the partial base pairing between its exonized AluYb8 sequence and the 5'UTR of α-MUTYH to impede MUTYH 1 expression. Furthermore, we have demonstrated a correlation between decreased mitochondrion-localized MUTYH1 caused by lncMUTYH and lowered levels of mitochondrial biological function indicators, such as mtDNA content, mitochondrial regulatory gene expression, oxygen consumption rate, ATP product, and mitochondrial respiratory capacity. Notably, we found that lncMUTYH inhibited the M2-like polarization of macrophages, and CD68/CD206-positive cell fractions were significantly lower in lncMUTYH ectopically expressing cells. The results confirmed that the AluYb8MUTYH-associated lncMUTYH, derived from an AluYb8 insertion mutation, acts as a trans-regulatory factor that inhibits the MUTYH1 protein expression, leading to a progressive mitochondrial dysfunction that may disrupt macrophage differentiation. In summary, lncMUTYH can contribute to AluYb8MUTYH-associated mitochondrial dysfunction with age and hamper the macrophage polarization process, potentially increasing the risk of developing age-related diseases.
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Affiliation(s)
- Gaochao Dong
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Xuewen Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
- Department of Pharmacy, Nanjing Stomatological Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yingkuan Liang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Jingwen Chen
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Jie Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing, China
| | - Chaochen Wang
- ZJU-UoE Institute, Zhejiang University School of Medicine, International Campus, Zhejiang University, Zhejiang, China
| | - Wenwen Guo
- Department of Pathology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaping Wang
- Department of Medical Genetics, Medical School, Nanjing University, Nanjing, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
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38
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Patrick MT, Sreeskandarajan S, Shefler A, Wasikowski R, Sarkar MK, Chen J, Qin T, Billi AC, Kahlenberg JM, Prens E, Hovnanian A, Weidinger S, Elder JT, Kuo CC, Gudjonsson JE, Tsoi LC. Large-scale functional inference for skin-expressing lncRNAs using expression and sequence information. JCI Insight 2023; 8:e172956. [PMID: 38131377 PMCID: PMC10807743 DOI: 10.1172/jci.insight.172956] [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: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 12/23/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate the expression of protein-coding genes and have been shown to play important roles in inflammatory skin diseases. However, we still have limited understanding of the functional impact of lncRNAs in skin, partly due to their tissue specificity and lower expression levels compared with protein-coding genes. We compiled a comprehensive list of 18,517 lncRNAs from different sources and studied their expression profiles in 834 RNA-Seq samples from multiple inflammatory skin conditions and cytokine-stimulated keratinocytes. Applying a balanced random forest to predict involvement in biological functions, we achieved a median AUROC of 0.79 in 10-fold cross-validation, identifying significant DNA binding domains (DBDs) for 39 lncRNAs. G18244, a skin-expressing lncRNA predicted for IL-4/IL-13 signaling in keratinocytes, was highly correlated in expression with F13A1, a protein-coding gene involved in macrophage regulation, and we further identified a significant DBD in F13A1 for G18244. Reflecting clinical implications, AC090198.1 (predicted for IL-17 pathway) and AC005332.6 (predicted for IFN-γ pathway) had significant negative correlation with the SCORAD metric for atopic dermatitis. We also utilized single-cell RNA and spatial sequencing data to validate cell type specificity. Our research demonstrates lncRNAs have important immunological roles and can help prioritize their impact on inflammatory skin diseases.
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Affiliation(s)
- Matthew T. Patrick
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Sutharzan Sreeskandarajan
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Alanna Shefler
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Rachael Wasikowski
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Mrinal K. Sarkar
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jiahan Chen
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- College of Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Tingting Qin
- Department of Computational Medicine & Bioinformatics and
| | - Allison C. Billi
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Michelle Kahlenberg
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Errol Prens
- Department of Dermatology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Alain Hovnanian
- Laboratory of Genetic Skin Diseases, Imagine Institute, Paris, France
| | - Stephan Weidinger
- Department of Dermatology and Allergy, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - James T. Elder
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, USA
| | - Chao-Chung Kuo
- Institute for Computational Genomics, Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
| | - Johann E. Gudjonsson
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Lam C. Tsoi
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics and
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan, USA
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39
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Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, DeBarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 inhibits miR-15/16 to enhance cytotoxic T cell activation and memory cell formation. eLife 2023; 12:RP87900. [PMID: 38127070 PMCID: PMC10735224 DOI: 10.7554/elife.87900] [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: 12/23/2023] Open
Abstract
Proper activation of cytotoxic T cells via the T cell receptor and the costimulatory receptor CD28 is essential for adaptive immunity against viruses, intracellular bacteria, and cancers. Through biochemical analysis of RNA:protein interactions, we uncovered a non-coding RNA circuit regulating activation and differentiation of cytotoxic T cells composed of the long non-coding RNA Malat1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) and the microRNA family miR-15/16. miR-15/16 is a widely and highly expressed tumor suppressor miRNA family important for cell proliferation and survival. miR-15/16 play important roles in T cell responses to viral infection, including the regulation of antigen-specific T cell expansion and memory. Comparative Argonaute-2 high-throughput sequencing of crosslinking immunoprecipitation (AHC) combined with gene expression profiling in normal and miR-15/16-deficient mouse T cells revealed a large network of hundreds of direct miR-15/16 target mRNAs, many with functional relevance for T cell activation, survival and memory formation. Among these targets, Malat1 contained the largest absolute magnitude miR-15/16-dependent AHC peak. This binding site was among the strongest lncRNA:miRNA interactions detected in the T cell transcriptome. We used CRISPR targeting with homology directed repair to generate mice with a 5-nucleotide mutation in the miR-15/16-binding site in Malat1. This mutation interrupted Malat1:miR-15/16 interaction, and enhanced the repression of other miR-15/16 target genes, including CD28. Interrupting Malat1 interaction with miR-15/16 decreased cytotoxic T cell activation, including the expression of interleukin 2 (IL-2) and a broader CD28-responsive gene program. Accordingly, Malat1 mutation diminished memory cell persistence in mice following LCMV Armstrong and Listeria monocytogenes infection. This study marks a significant advance in the study of long non-coding RNAs in the immune system by ascribing cell-intrinsic, sequence-specific in vivo function to Malat1. These findings have implications for T cell-mediated autoimmune diseases, antiviral and anti-tumor immunity, as well as lung adenocarcinoma and other malignancies where Malat1 is overexpressed.
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Affiliation(s)
- Benjamin D Wheeler
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - John D Gagnon
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Wandi S Zhu
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Priscila Muñoz-Sandoval
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
| | - Simon K Wong
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Dimitre S Simeonov
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
| | - Zhongmei Li
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
| | - Rachel DeBarge
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
| | - Matthew H Spitzer
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Otolaryngology-Head and Neck Surgery, University of California San FranciscoSan FranciscoUnited States
- Parker Institute for Cancer Immunotherapy, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Alexander Marson
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Gladstone-UCSF Institute of Genomic ImmunologySan FranciscoUnited States
- Department of Medicine, University of California San FranciscoLexingtonUnited States
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San FranciscoSan FranciscoUnited States
- Sandler Asthma Basic Research Program, University of California, San FranciscoSan FranciscoUnited States
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40
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Zhu Y, Huang C, Zhang C, Zhou Y, Zhao E, Zhang Y, Pan X, Huang H, Liao W, Wang X. LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation. Nat Commun 2023; 14:8141. [PMID: 38065939 PMCID: PMC10709323 DOI: 10.1038/s41467-023-43974-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Gastric cancer (GC) is a heterogeneous disease, threatening millions of lives worldwide, yet the functional roles of long non-coding RNAs (lncRNAs) in different GC subtypes remain poorly characterized. Microsatellite stable (MSS)/epithelial-mesenchymal transition (EMT) GC is the most aggressive subtype associated with a poor prognosis. Here, we apply integrated network analysis to uncover lncRNA heterogeneity between GC subtypes, and identify MIR200CHG as a master regulator mediating EMT specifically in MSS/EMT GC. The expression of MIR200CHG is silenced in MSS/EMT GC by promoter hypermethylation, associated with poor prognosis. MIR200CHG reverses the mesenchymal identity of GC cells in vitro and inhibits metastasis in vivo. Mechanistically, MIR200CHG not only facilitates the biogenesis of its intronic miRNAs miR-200c and miR-141, but also protects miR-200c from target-directed miRNA degradation (TDMD) through direct binding to miR-200c. Our studies reveal a landscape of a subtype-specific lncRNA regulatory network, providing clinically relevant biological insights towards MSS/EMT GC.
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Grants
- 2020N368 Shenzhen Science and Technology Innovation Commission
- C4024-22GF Research Grants Council, University Grants Committee (RGC, UGC)
- 14104223 Research Grants Council, University Grants Committee (RGC, UGC)
- 11103619 Research Grants Council, University Grants Committee (RGC, UGC)
- 14111522 Research Grants Council, University Grants Committee (RGC, UGC)
- R4017-18 Research Grants Council, University Grants Committee (RGC, UGC)
- 82173289 National Natural Science Foundation of China (National Science Foundation of China)
- 81872401 National Natural Science Foundation of China (National Science Foundation of China)
- Guangdong Basic and Applied Basic Research Foundation (Project No.2019B030302012), a startup grant (Project No. 4937084), direct grant (2021.077), Faculty Postdoctoral Fellowship Scheme 2021/22 (Project No. FPFS/2122/32), Shenzhen Bay Scholars Program.
- Guangdong Basic and Applied Basic Research Foundation (2021A1515010425)
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Affiliation(s)
- Yixiao Zhu
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chengmei Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Chao Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yi Zhou
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Enen Zhao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yaxin Zhang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xingyan Pan
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Wenting Liao
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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41
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Ma M, Chen M, Wu X, Sooranna SR, Liu Q, Shi D, Wang J, Li H. A newly identified lncRNA lnc000100 regulates proliferation and differentiation of cattle skeletal muscle cells. Epigenetics 2023; 18:2270864. [PMID: 37910666 PMCID: PMC10768731 DOI: 10.1080/15592294.2023.2270864] [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: 12/05/2022] [Accepted: 09/01/2023] [Indexed: 11/03/2023] Open
Abstract
Cattle skeletal muscle development is a complex and highly coordinated biological process mediated by a series of myogenic regulators, which plays a critical role in beef yield and quality. Long non-coding RNAs (lncRNAs) have been shown to regulate skeletal muscle development. However, the molecular mechanism by which lncRNAs regulate skeletal muscle development is largely unknown. We performed transcriptome analysis of muscle tissues of adult and embryo Angus cattle to investigate the mechanism by which lncRNA regulates skeletal muscle development between adult and embryo cattle. A total of 37,115 candidate lncRNAs were detected, and a total of 1,998 lncRNAs were differentially expressed between the muscle tissue libraries of adult and embryo cattle, including 1,229 up-regulated lncRNAs and 769 down-regulated lncRNAs (adult cattle were the control group). We verified the expression of 7 differentially expressed lncRNAs by quantitative real-time PCR (RT-qPCR), and analysed the tissue expression profile of lnc000100, which is down-regulated in the longest dorsal muscle during foetal life and which is highly specifically expressed in muscle tissue. We found that the interference of lnc000100 significantly inhibited cell proliferation and promoted cell differentiation. Lnc000100 was located in the nucleus by RNA-FISH. Our research provides certain resources for the analysis of lncRNA regulating cattle skeletal muscle development, and may also provide new insights for improving beef production and breed selection.
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Affiliation(s)
- Mengke Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Suren R. Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Jian Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
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42
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Beylerli O, Ju J, Beilerli A, Gareev I, Shumadalova A, Ilyasova T, Bai Y, Yang B. The roles of long noncoding RNAs in atrial fibrillation. Noncoding RNA Res 2023; 8:542-549. [PMID: 37602317 PMCID: PMC10432912 DOI: 10.1016/j.ncrna.2023.08.004] [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: 07/21/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Atrial fibrillation (AF) is a common cardiac arrhythmia that often occurs in patients with structural heart disease and is a significant cause of morbidity and mortality in clinical settings. AF is typically associated with significant changes of both the structure of the atria and the cardiac conduction system. AF can result in reduced heart function, heart failure, and various other complications. Current drug therapy for AF patients is often ineffective and may have adverse effects. Radiofrequency ablation is more effective than traditional drug therapy, but this invasive procedure carries potential risks and may lead to postoperative recurrence, limiting the clinical benefits to some extent. Therefore, in-depth research into the molecular mechanisms of AF and exploration of new treatment strategies based on research findings are prerequisites for improving the treatment of AF and the associated cardiac conditions. Long noncoding RNAs (lncRNAs) are a new class of noncoding RNA (ncRNAs) with a length exceeding 200 nt, which regulate gene expression at multiple levels. Increasing evidence suggests that lncRNAs participate in many pathological processes of AF initiation, development, and maintenance, such as structural remodeling, electrical remodeling, renin-angiotensin system anomalies, and intracellular calcium deregulation s. LncRNAs that play key roles in structural and electrical remodeling may become molecular markers and targets for AF diagnosis and treatment, respectively, while lncRNAs critical to autonomic nervous system remodeling may bring new insights into the prognosis and recurrence of AF. This review article provides a synopsis on the up-to-date research findings relevant to the roles of lncRNAs in AF.
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Affiliation(s)
- Ozal Beylerli
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Jiaming Ju
- Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin Medical University, Harbin, 150081, China
| | - Aferin Beilerli
- Department of Obstetrics and Gynecology, Tyumen State Medical University, 54 Odesskaya Street, 625023, Tyumen, Russia
| | - Ilgiz Gareev
- Central Research Laboratory, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 3 Lenin Street, 450008, Russia
| | - Alina Shumadalova
- Department of General Chemistry, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 3 Lenin Street, 450008, Russia
| | - Tatiana Ilyasova
- Department of Internal Diseases, Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Yunlong Bai
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Baofeng Yang
- Department of Pharmacology (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
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43
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Rizavi HS, Gavin HE, Krishnan HR, Gavin DP, Sharma RP. Ethanol- and PARP-Mediated Regulation of Ribosome-Associated Long Non-Coding RNA (lncRNA) in Pyramidal Neurons. Noncoding RNA 2023; 9:72. [PMID: 37987368 PMCID: PMC10661276 DOI: 10.3390/ncrna9060072] [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: 07/14/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Although, by definition, long noncoding RNAs (lncRNAs) are not translated, they are sometimes associated with ribosomes. In fact, some estimates suggest the existence of more than 50 K lncRNA molecules that could encode for small peptides. We examined the effects of an ethanol and Poly-ADP Ribose Polymerase (PARP) inhibitor (ABT-888) on ribosome-bound lncRNAs. Mice were administered via intraperitoneal injection (i.p.) either normal saline (CTL) or ethanol (EtOH) twice a day for four consecutive days. On the fourth day, a sub-group of mice administered with ethanol also received ABT-888 (EtOH+ABT). Ribosome-bound lncRNAs in CaMKIIα-expressing pyramidal neurons were measured using the Translating Ribosome Affinity Purification (TRAP) technique. Our findings show that EtOH altered the attachment of 107 lncRNA transcripts, while EtOH+ABT altered 60 lncRNAs. Among these 60 lncRNAs, 49 were altered by both conditions, while EtOH+ABT uniquely altered the attachment of 11 lncRNA transcripts that EtOH alone did not affect. To validate these results, we selected eight lncRNAs (Mir124-2hg, 5430416N02Rik, Snhg17, Snhg12, Snhg1, Mir9-3hg, Gas5, and 1110038B12Rik) for qRT-PCR analysis. The current study demonstrates that ethanol-induced changes in lncRNA attachment to ribosomes can be mitigated by the addition of the PARP inhibitor ABT-888.
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Affiliation(s)
- Hooriyah S. Rizavi
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| | - Hannah E. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Harish R. Krishnan
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - David P. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Rajiv P. Sharma
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
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44
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Dutriaux A, Diazzi S, Bresesti C, Hardouin S, Deshayes F, Collignon J, Flagiello D. LADON, a Natural Antisense Transcript of NODAL, Promotes Tumour Progression and Metastasis in Melanoma. Noncoding RNA 2023; 9:71. [PMID: 37987367 PMCID: PMC10661258 DOI: 10.3390/ncrna9060071] [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: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
The TGFβ family member NODAL, repeatedly required during embryonic development, has also been associated with tumour progression. Our aim was to clarify the controversy surrounding its involvement in melanoma tumour progression. We found that the deletion of the NODAL exon 2 in a metastatic melanoma cell line impairs its ability to form tumours and colonize distant tissues. However, we show that this phenotype does not result from the absence of NODAL, but from a defect in the expression of a natural antisense transcript of NODAL, here called LADON. We show that LADON expression is specifically activated in metastatic melanoma cell lines, that its transcript is packaged in exosomes secreted by melanoma cells, and that, via its differential impact on the expression of oncogenes and tumour suppressors, it promotes the mesenchymal to amoeboid transition that is critical for melanoma cell invasiveness. LADON is, therefore, a new player in the regulatory network governing tumour progression in melanoma and possibly in other types of cancer.
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Affiliation(s)
| | | | | | | | | | - Jérôme Collignon
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France; (A.D.); (S.D.)
| | - Domenico Flagiello
- Institut Jacques Monod, Université Paris Cité, CNRS, F-75013 Paris, France; (A.D.); (S.D.)
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45
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Morgenstern E, Kretz M. The human long non-coding RNA LINC00941 and its modes of action in health and disease. Biol Chem 2023; 404:1025-1036. [PMID: 37418674 DOI: 10.1515/hsz-2023-0183] [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: 04/13/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
Long non-coding RNAs have gained attention in recent years as they were shown to play crucial roles in the regulation of cellular processes, but the understanding of the exact mechanisms is still incomplete in most cases. This is also true for long non-coding RNA LINC00941, which was recently found to be highly upregulated in various types of cancer influencing cell proliferation and metastasis. Initial studies could not elucidate the mode of action to understand the role and real impact of LINC00941 in tissue homeostasis and cancer development. However, recent analyses have demonstrated multiple potential modes of action of LINC00941 influencing the functionality of various cancer cell types. Correspondingly, LINC00941 was proposed to be involved in regulation of mRNA transcription and modulation of protein stability, respectively. In addition, several experimental approaches suggest a function of LINC00941 as competitive endogenous RNA, thus acting in a post-transcriptional regulatory fashion. This review summarizes our recent knowledge about the mechanisms of action of LINC00941 elucidated so far and discusses its putative role in miRNA sequestering processes. In addition, the functional role of LINC00941 in regulating human keratinocytes is discussed to also highlight its role in normal tissue homeostasis tissue aside from its involvement in cancer.
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Affiliation(s)
- Eva Morgenstern
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
| | - Markus Kretz
- Regensburg Center for Biochemistry (RCB), University of Regensburg, 93053 Regensburg, Germany
- Institute for Molecular Medicine, MSH Medical School Hamburg, 20457 Hamburg, Germany
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46
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Ballarino M, Pepe G, Helmer-Citterich M, Palma A. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs. Comput Struct Biotechnol J 2023; 21:4706-4716. [PMID: 37841333 PMCID: PMC10568309 DOI: 10.1016/j.csbj.2023.09.041] [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: 08/12/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
In recent years, research on long non-coding RNAs (lncRNAs) has gained considerable attention due to the increasing number of newly identified transcripts. Several characteristics make their functional evaluation challenging, which called for the urgent need to combine molecular biology with other disciplines, including bioinformatics. Indeed, the recent development of computational pipelines and resources has greatly facilitated both the discovery and the mechanisms of action of lncRNAs. In this review, we present a curated collection of the most recent computational resources, which have been categorized into distinct groups: databases and annotation, identification and classification, interaction prediction, and structure prediction. As the repertoire of lncRNAs and their analysis tools continues to expand over the years, standardizing the computational pipelines and improving the existing annotation of lncRNAs will be crucial to facilitate functional genomics studies.
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Affiliation(s)
- Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00161 Rome, Italy
| | - Gerardo Pepe
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy
| | - Manuela Helmer-Citterich
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy
| | - Alessandro Palma
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00161 Rome, Italy
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47
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Wang P, Paquet ÉR, Robert C. Comprehensive transcriptomic analysis of long non-coding RNAs in bovine ovarian follicles and early embryos. PLoS One 2023; 18:e0291761. [PMID: 37725621 PMCID: PMC10508637 DOI: 10.1371/journal.pone.0291761] [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: 05/17/2023] [Accepted: 09/05/2023] [Indexed: 09/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been the subject of numerous studies over the past decade. First thought to come from aberrant transcriptional events, lncRNAs are now considered a crucial component of the genome with roles in multiple cellular functions. However, the functional annotation and characterization of bovine lncRNAs during early development remain limited. In this comprehensive analysis, we review lncRNAs expression in bovine ovarian follicles and early embryos, based on a unique database comprising 468 microarray hybridizations from a single platform designed to target 7,724 lncRNA transcripts, of which 5,272 are intergenic (lincRNA), 958 are intronic, and 1,524 are antisense (lncNAT). Compared to translated mRNA, lncRNAs have been shown to be more tissue-specific and expressed in low copy numbers. This analysis revealed that protein-coding genes and lncRNAs are both expressed more in oocytes. Differences between the oocyte and the 2-cell embryo are also more apparent in terms of lncRNAs than mRNAs. Co-expression network analysis using WGCNA generated 25 modules with differing proportions of lncRNAs. The modules exhibiting a higher proportion of lncRNAs were found to be associated with fewer annotated mRNAs and housekeeping functions. Functional annotation of co-expressed mRNAs allowed attribution of lncRNAs to a wide array of key cellular events such as meiosis, translation initiation, immune response, and mitochondrial related functions. We thus provide evidence that lncRNAs play diverse physiological roles that are tissue-specific and associated with key cellular functions alongside mRNAs in bovine ovarian follicles and early embryos. This contributes to add lncRNAs as active molecules in the complex regulatory networks driving folliculogenesis, oogenesis and early embryogenesis all of which are necessary for reproductive success.
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Affiliation(s)
- Pengmin Wang
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Québec City, Québec, Canada
| | - Éric R. Paquet
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Québec City, Québec, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l’agriculture et de l’alimentation, Université Laval, Québec City, Québec, Canada
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48
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Wei C, Xu Y, Shen Q, Li R, Xiao X, Saw PE, Xu X. Role of long non-coding RNAs in cancer: From subcellular localization to nanoparticle-mediated targeted regulation. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:774-793. [PMID: 37655045 PMCID: PMC10466435 DOI: 10.1016/j.omtn.2023.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a class of RNA transcripts more than 200 nucleotides in length that play crucial roles in cancer development and progression. With the rapid development of high-throughput sequencing technology, a considerable number of lncRNAs have been identified as novel biomarkers for predicting the prognosis of cancer patients and/or therapeutic targets for cancer therapy. In recent years, increasing evidence has shown that the biological functions and regulatory mechanisms of lncRNAs are closely associated with their subcellular localization. More importantly, based on the important roles of lncRNAs in regulating cancer progression (e.g., growth, therapeutic resistance, and metastasis) and the specific ability of nucleic acids (e.g., siRNA, mRNA, and DNA) to regulate the expression of any target genes, much effort has been exerted recently to develop nanoparticle (NP)-based nucleic acid delivery systems for in vivo regulation of lncRNA expression and cancer therapy. In this review, we introduce the subcellular localization and regulatory mechanisms of various functional lncRNAs in cancer and systemically summarize the recent development of NP-mediated nucleic acid delivery for targeted regulation of lncRNA expression and effective cancer therapy.
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Affiliation(s)
- Chunfang Wei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, China
| | - Ya Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, China
| | - Qian Shen
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Rong Li
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xiaoyun Xiao
- Department of Ultrasound, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-Sen Memorial Hospital, Foshan 528200, China
- The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
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49
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Bachhav B, de Rossi J, Llanos CD, Segatori L. Cell factory engineering: Challenges and opportunities for synthetic biology applications. Biotechnol Bioeng 2023; 120:2441-2459. [PMID: 36859509 PMCID: PMC10440303 DOI: 10.1002/bit.28365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/14/2023] [Accepted: 02/27/2023] [Indexed: 03/03/2023]
Abstract
The production of high-quality recombinant proteins is critical to maintaining a continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories presents a number of limitations typically associated with the proteotoxic stress induced upon aberrant accumulation of off-pathway protein folding intermediates, which eventually culminate in the induction of apoptosis. In this review, we will discuss advances in cell engineering and their applications at different hierarchical levels of control of the expression of recombinant proteins, from transcription and translational to posttranslational modifications and subcellular trafficking. We also highlight challenges and unique opportunities to apply modern synthetic biology tools to the design of programmable cell factories for improved biomanufacturing of therapeutic proteins.
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Affiliation(s)
- Bhagyashree Bachhav
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
| | - Jacopo de Rossi
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Carlos D. Llanos
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
| | - Laura Segatori
- Department of Chemical and Biochemical Engineering, Rice University, Houston, United States
- Systems, Synthetic, and Physical Biology, Rice University, Houston, United States
- Department of Bioengineering, Rice University, Houston, United States
- Department of Biosciences, Rice University, Houston, United States
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50
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Feng YZ, Zhu QF, Xue J, Chen P, Yu Y. Shining in the dark: the big world of small peptides in plants. ABIOTECH 2023; 4:238-256. [PMID: 37970469 PMCID: PMC10638237 DOI: 10.1007/s42994-023-00100-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/24/2023] [Indexed: 11/17/2023]
Abstract
Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.
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Affiliation(s)
- Yan-Zhao Feng
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Qing-Feng Zhu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jiao Xue
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Pei Chen
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yang Yu
- Guangdong Key Laboratory of Crop Germplasm Resources Preservation and Utilization, Key Laboratory of South China Modern Biological Seed Industry, Ministry of Agriculture and Rural Affairs, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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