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Yu C, Qiu M, Xiong X, Peng H, Han S, Song X, Hu C, Zhang Z, Xia B, Chen J, Zhu S, Yang L, Li W, Yin H, Zhao J, Lin Z, Liu Y, Yang C. Integrative analysis of RNA-seq and Ribo-seq reveals that lncRNA-GRN regulates chicken follicular atresia through miR-103-3p/FBXW7 axis and encoding peptide. Int J Biol Macromol 2024; 278:135051. [PMID: 39182874 DOI: 10.1016/j.ijbiomac.2024.135051] [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: 05/21/2024] [Revised: 07/30/2024] [Accepted: 08/22/2024] [Indexed: 08/27/2024]
Abstract
Follicular atresia in chickens seriously reduced the egg production and economic benefits of chickens. LncRNA plays a key role in the process of follicular atresia. In this study, RNA-seq and Ribo-seq were performed on normal and atretic follicles of Dahen broilers to screen out lncRNAs that may regulate follicle atresia, and to study the molecular mechanisms of their regulation. GRN granulin precursor (lncGRN, ID: 101748909) was highly expressed in atretic follicles with translational ability. A molecular regulatory network of lncGRN/miR-103-3p/FBXW7 was constructed through bioinformatics analysis and dual luciferase reporting. LncGRN promoted the expression of FBXW7 by adsorption of miR-103-3p, thereby inhibiting the proliferation of chicken granulosa cells (GCs), promoting apoptosis of chicken GCs and inhibiting steroid hormone synthesis thus induced follicular atresia. Meanwhile, we also found a micropeptide named GRN-122aa derived by lncGRN which can promote follicular atresia. In conclusion, our study found that lncGRN promoted follicular atresia through the lncGRN/miR-103-3p/FBXW7 axis and the translation micropeptide GRN-122aa. This study provided new insight into the post-transcriptional regulation mechanism of lncGRN suggesting that lncGRN may act as a potential to regulate chicken follicle development, and provided a theoretical argument for further improving the egg production of chickens through molecular breeding.
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Affiliation(s)
- Chunlin Yu
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Mohan Qiu
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xia Xiong
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Han Peng
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Shunshun Han
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Xiaoyan Song
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Chenming Hu
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Zengrong Zhang
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Bo Xia
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Jialei Chen
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Shiliang Zhu
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Li Yang
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China
| | - Wen Li
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Huadong Yin
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jing Zhao
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zhongzhen Lin
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yiping Liu
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Chaowu Yang
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu 610066, China.
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Yang Y, Pu J, Yang Y. Glycolysis and chemoresistance in acute myeloid leukemia. Heliyon 2024; 10:e35721. [PMID: 39170140 PMCID: PMC11336864 DOI: 10.1016/j.heliyon.2024.e35721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024] Open
Abstract
While traditional high-dose chemotherapy can effectively prolong the overall survival of acute myeloid leukemia (AML) patients and contribute to better prognostic outcomes, the advent of chemoresistance is a persistent challenge to effective AML management in the clinic. The therapeutic resistance is thought to emerge owing to the heterogeneous and adaptable nature of tumor cells when exposed to exogenous stimuli. Recent studies have focused on exploring metabolic changes that may afford novel opportunities to treat AML, with a particular focus on glycolytic metabolism. The Warburg effect, a hallmark of cancer, refers to metabolism of glucose through glycolysis under normoxic conditions, which contributes to the development of chemoresistance. Despite the key significance of this metabolic process in the context of malignant transformation, the underlying molecular mechanisms linking glycolysis to chemoresistance in AML remain incompletely understood. This review offers an overview of the current status of research focused on the relationship between glycolytic metabolism and AML resistance to chemotherapy, with a particular focus on the contributions of glucose transporters, key glycolytic enzymes, signaling pathways, non-coding RNAs, and the tumor microenvironment to this relationship. Together, this article will provide a foundation for the selection of novel therapeutic targets and the formulation of new approaches to treating AML.
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Affiliation(s)
- Yan Yang
- Department of Neonatology, Zigong Maternity and Child Health Care Hospital, Zigong, Sichuan, 643000, China
| | - Jianlin Pu
- Department of Psychiatry, The Zigong Affiliated Hospital of Southwest Medical University, Zigong mental health Center, Zigong Institute of Brain Science, Zigong, Sichuan, 643000, China
| | - You Yang
- Department of Pediatrics (Children Hematological Oncology), Birth Defects and Childhood Hematological Oncology Laboratory, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, 646000, China
- The Second Hospital, Centre for Reproductive Medicine, Advanced Medical Research Institute, Key Laboratory for Experimental Teratology of the Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250000, China
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3
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Li A, Zhou H, Xiong S, Li J, Mallik S, Fei R, Liu Y, Zhou H, Wang X, Hei X, Wang L. PLEKv2: predicting lncRNAs and mRNAs based on intrinsic sequence features and the coding-net model. BMC Genomics 2024; 25:756. [PMID: 39095710 PMCID: PMC11295476 DOI: 10.1186/s12864-024-10662-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are RNA transcripts of more than 200 nucleotides that do not encode canonical proteins. Their biological structure is similar to messenger RNAs (mRNAs). To distinguish between lncRNA and mRNA transcripts quickly and accurately, we upgraded the PLEK alignment-free tool to its next version, PLEKv2, and constructed models tailored for both animals and plants. RESULTS PLEKv2 can achieve 98.7% prediction accuracy for human datasets. Compared with classical tools and deep learning-based models, this is 8.1%, 3.7%, 16.6%, 1.4%, 4.9%, and 48.9% higher than CPC2, CNCI, Wen et al.'s CNN, LncADeep, PLEK, and NcResNet, respectively. The accuracy of PLEKv2 was > 90% for cross-species prediction. PLEKv2 is more effective and robust than CPC2, CNCI, LncADeep, PLEK, and NcResNet for primate datasets (including chimpanzees, macaques, and gorillas). Moreover, PLEKv2 is not only suitable for non-human primates that are closely related to humans, but can also predict the coding ability of RNA sequences in plants such as Arabidopsis. CONCLUSIONS The experimental results illustrate that the model constructed by PLEKv2 can distinguish lncRNAs and mRNAs better than PLEK. The PLEKv2 software is freely available at https://sourceforge.net/projects/plek2/ .
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Affiliation(s)
- Aimin Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China.
| | - Haotian Zhou
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Siqi Xiong
- Department of Information Engineering, College of Technology, Hubei Engineering University, Xiaogan, Hubei, 432000, China.
| | - Junhuai Li
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Rong Fei
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Yajun Liu
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Hongfang Zhou
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Xiaofan Wang
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Xinhong Hei
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
| | - Lei Wang
- Shaanxi Key Laboratory for Network Computing and Security Technology, School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi, 710048, China
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4
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Ritz NL, Bastiaanssen TFS, Cowan CSM, Smith L, Theune N, Brocka M, Myers EM, Moloney RD, Moloney GM, Shkoporov AN, Draper LA, Hill C, Dinan TG, Slattery DA, Cryan JF. Social fear extinction susceptibility is associated with Microbiota-Gut-Brain axis alterations. Brain Behav Immun 2024; 120:315-326. [PMID: 38852762 DOI: 10.1016/j.bbi.2024.06.009] [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: 11/21/2023] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024] Open
Abstract
Social anxiety disorder is a common psychiatric condition that severely affects quality of life of individuals and is a significant societal burden. Although many risk factors for social anxiety exist, it is currently unknown how social fear sensitivity manifests biologically. Furthermore, since some individuals are resilient and others are susceptible to social fear, it is important to interrogate the mechanisms underpinning individual response to social fear situations. The microbiota-gut-brain axis has been associated with social behaviour, has recently been linked with social anxiety disorder, and may serve as a therapeutic target for modulation. Here, we assess the potential of this axis to be linked with social fear extinction processes in a murine model of social anxiety disorder. To this end, we correlated differential social fear responses with microbiota composition, central gene expression, and immune responses. Our data provide evidence that microbiota variability is strongly correlated with alterations in social fear behaviour. Moreover, we identified altered gene candidates by amygdalar transcriptomics that are linked with social fear sensitivity. These include genes associated with social behaviour (Armcx1, Fam69b, Kcnj9, Maoa, Serinc5, Slc6a17, Spata2, and Syngr1), inflammation and immunity (Cars, Ckmt1, Klf5, Maoa, Map3k12, Pex5, Serinc5, Sidt1, Spata2), and microbe-host interaction (Klf5, Map3k12, Serinc5, Sidt1). Together, these data provide further evidence for a role of the microbiota-gut-brain axis in social fear responses.
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Affiliation(s)
- Nathaniel L Ritz
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Caitlin S M Cowan
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Linda Smith
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; School of Microbiology, University College Cork, Cork, T12K8AF, Ireland
| | - Nigel Theune
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Marta Brocka
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Eibhlís M Myers
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Rachel D Moloney
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Gerard M Moloney
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Andrey N Shkoporov
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; School of Microbiology, University College Cork, Cork, T12K8AF, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; School of Microbiology, University College Cork, Cork, T12K8AF, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; School of Microbiology, University College Cork, Cork, T12K8AF, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Psychiatry and Neurobehavioural Science, University College Cork, Cork T12YT20, Ireland
| | - David A Slattery
- Dept. of Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, Frankfurt 60528, Germany
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork T12YT20, Ireland; Dept. of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland.
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5
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Yang H, Xuan L, Wang S, Luo H, Duan X, Guo J, Cui S, Xin J, Hao J, Li X, Chen J, Sun F, Hu X, Li S, Zhang Y, Jiao L, Yang B, Sun L. LncRNA CCRR maintains Ca 2+ homeostasis against myocardial infarction through the FTO-SERCA2a pathway. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1601-1619. [PMID: 38761356 DOI: 10.1007/s11427-023-2527-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/11/2024] [Indexed: 05/20/2024]
Abstract
Cardiac conduction regulatory RNA (CCRR) has been documented as an antiarrhythmic lncRNA in our earlier investigation. This study aimed to evaluate the effects of CCRR on SERCA2a and the associated Ca2+ homeostasis in myocardial infarction (MI). Overexpression of CCRR via AAV9-mediated delivery not only partially reversed ischemia-induced contractile dysfunction but also alleviated abnormal Ca2+ homeostasis and reduced the heightened methylation level of SERCA2a following MI. These effects were also observed in CCRR over-expressing transgenic mice. A conserved sequence domain of CCRR mimicked the protective function observed with the full length. Furthermore, silencing CCRR in healthy mice led to intracellular Ca2+ overloading of cardiomyocytes. CCRR increased SERCA2a protein stability by upregulating FTO expression. The direct interaction between CCRR and FTO protein was characterized by RNA-binding protein immunoprecipitation (RIP) analysis and RNA pulldown experiments. Activation of NFATc3 was identified as an upstream mechanism responsible for CCRR downregulation in MI. This study demonstrates that CCRR is a protective lncRNA that acts by maintaining the function of FTO, thereby reducing the m6A RNA methylation level of SERCA2a, ultimately preserving calcium homeostasis for myocardial contractile function in MI. Therefore, CCRR may be considered a promising therapeutic strategy with a beneficial role in cardiac pathology.
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Affiliation(s)
- Hua Yang
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Lina Xuan
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Shengjie Wang
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Huishan Luo
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaomeng Duan
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Jianjun Guo
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Shijia Cui
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Jieru Xin
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Junwei Hao
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiufang Li
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Jun Chen
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Feihan Sun
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaolin Hu
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Siyun Li
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Ying Zhang
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Lei Jiao
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Baofeng Yang
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
| | - Lihua Sun
- Department of Pharmacology, Harbin Medical University (State Key Laboratory of Frigid Zone Cardiovascular Disease, the State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education, Joint International Research Laboratory of Cardiovascular Medicine Research, Ministry of Education, China), College of Pharmacy, Harbin Medical University, Harbin, 150081, China.
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6
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Kazmi SSUH, Tayyab M, Pastorino P, Barcelò D, Yaseen ZM, Grossart HP, Khan ZH, Li G. Decoding the molecular concerto: Toxicotranscriptomic evaluation of microplastic and nanoplastic impacts on aquatic organisms. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134574. [PMID: 38739959 DOI: 10.1016/j.jhazmat.2024.134574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
The pervasive and steadily increasing presence of microplastics/nanoplastics (MPs/NPs) in aquatic environments has raised significant concerns regarding their potential adverse effects on aquatic organisms and their integration into trophic dynamics. This emerging issue has garnered the attention of (eco)toxicologists, promoting the utilization of toxicotranscriptomics to unravel the responses of aquatic organisms not only to MPs/NPs but also to a wide spectrum of environmental pollutants. This review aims to systematically explore the broad repertoire of predicted molecular responses by aquatic organisms, providing valuable intuitions into complex interactions between plastic pollutants and aquatic biota. By synthesizing the latest literature, present analysis sheds light on transcriptomic signatures like gene expression, interconnected pathways and overall molecular mechanisms influenced by various plasticizers. Harmful effects of these contaminants on key genes/protein transcripts associated with crucial pathways lead to abnormal immune response, metabolic response, neural response, apoptosis and DNA damage, growth, development, reproductive abnormalities, detoxification, and oxidative stress in aquatic organisms. However, unique challenge lies in enhancing the fingerprint of MPs/NPs, presenting complicated enigma that requires decoding their specific impact at molecular levels. The exploration endeavors, not only to consolidate existing knowledge, but also to identify critical gaps in understanding, push forward the frontiers of knowledge about transcriptomic signatures of plastic contaminants. Moreover, this appraisal emphasizes the imperative to monitor and mitigate the contamination of commercially important aquatic species by MPs/NPs, highlighting the pivotal role that regulatory frameworks must play in protecting all aquatic ecosystems. This commitment aligns with the broader goal of ensuring the sustainability of aquatic resources and the resilience of ecosystems facing the growing threat of plastic pollutants.
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Affiliation(s)
- Syed Shabi Ul Hassan Kazmi
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Muhammad Tayyab
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, PR China
| | - Paolo Pastorino
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, 10154 Torino, Italy
| | - Damià Barcelò
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC), 08034 Barcelona, Spain
| | - Zaher Mundher Yaseen
- Civil and Environmental Engineering Department, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia; Interdisciplinary Research Center for Membranes and Water Security, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia
| | - Hans-Peter Grossart
- Plankton and Microbial Ecology, Leibniz Institute for Freshwater Ecology and Inland Fisheries, (IGB), Alte Fischerhuette 2, Neuglobsow, D-16775, Germany; Institute of Biochemistry and Biology, Potsdam University, Maulbeerallee 2, D-14469 Potsdam, Germany
| | - Zulqarnain Haider Khan
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China.
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7
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Hu S, Han X, Liu G, Wang S. LncRNAs as potential prognosis/diagnosis markers and factors driving drug resistance of osteosarcoma, a review. Front Endocrinol (Lausanne) 2024; 15:1415722. [PMID: 39015175 PMCID: PMC11249743 DOI: 10.3389/fendo.2024.1415722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Osteosarcoma is a common malignancy that often occurs in children, teenagers and young adults. Although the treatment strategy has improved, the results are still poor for most patients with metastatic or recurrent osteosarcomas. Therefore, it is necessary to identify new and effective prognostic biomarkers and therapeutic targets for diseases. Human genomes contain lncRNAs, transcripts with limited or insufficient capacity to encode proteins. They have been implicated in tumorigenesis, particularly regarding the onset, advancement, resistance to treatment, recurrence and remote dissemination of malignancies. Aberrant lncRNA expression in osteosarcomas has been reported by numerous researchers; lncRNAs have the potential to exhibit either oncogenic or tumor-suppressing behaviors and thus, to govern the advancement of this skeletal cancer. They are suspected to influence osteosarcoma cell growth, replication, invasion, migration, remote dissemination and programmed cell death. Additionally, they have been recognized as clinical markers, and may participate in the development of multidrug resistance. Therefore, the study of lncRNAs in the growth, metastasis, treatment and prognosis of osteosarcoma is very important for the active prevention and treatment of osteosarcoma. Consequently, this work reviews the functions of lncRNAs.
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Affiliation(s)
- Siwang Hu
- The Orthopedic Center, Wenling First People’s Hospital (The Affiliated Wenling Hospital of Wenzhou Medical University), Wenling, China
| | - Xuebing Han
- Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Gang Liu
- Hunan Provincial Engineering Research Center of Applied Microbial Resources Development for Livestock and Poultry, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, China
| | - Shuangshuang Wang
- Department of Cardiology, Wenling First People’s Hospital (The Affiliated Wenling Hospital of Wenzhou Medical University), Wenling, China
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8
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Das S, Zea Rojas MP, Tran EJ. Novel insights on the positive correlation between sense and antisense pairs on gene expression. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1864. [PMID: 39087253 DOI: 10.1002/wrna.1864] [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: 11/30/2023] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 08/02/2024]
Abstract
A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Subhadeep Das
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | | | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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9
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Naseer QA, Malik A, Zhang F, Chen S. Exploring the enigma: history, present, and future of long non-coding RNAs in cancer. Discov Oncol 2024; 15:214. [PMID: 38847897 PMCID: PMC11161455 DOI: 10.1007/s12672-024-01077-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Long noncoding RNAs (lncRNAs), which are more than 200 nucleotides in length and do not encode proteins, play crucial roles in governing gene expression at both the transcriptional and posttranscriptional levels. These molecules demonstrate specific expression patterns in various tissues and developmental stages, suggesting their involvement in numerous developmental processes and diseases, notably cancer. Despite their widespread acknowledgment and the growing enthusiasm surrounding their potential as diagnostic and prognostic biomarkers, the precise mechanisms through which lncRNAs function remain inadequately understood. A few lncRNAs have been studied in depth, providing valuable insights into their biological activities and suggesting emerging functional themes and mechanistic models. However, the extent to which the mammalian genome is transcribed into functional noncoding transcripts is still a matter of debate. This review synthesizes our current understanding of lncRNA biogenesis, their genomic contexts, and their multifaceted roles in tumorigenesis, highlighting their potential in cancer-targeted therapy. By exploring historical perspectives alongside recent breakthroughs, we aim to illuminate the diverse roles of lncRNA and reflect on the broader implications of their study for understanding genome evolution and function, as well as for advancing clinical applications.
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Affiliation(s)
- Qais Ahmad Naseer
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Abdul Malik
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Fengyuan Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
| | - Shengxia Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
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10
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Wei P, Tian K, Liu H, Li K, Alam N, Cheng D, Li M, He X, Guo J, Wang R, Wang W, Bai L, Liu E, Xu B, Li Y, Zhao S. Urotensin II receptor deficiency ameliorates ligation-induced carotid intimal hyperplasia partially through the RhoA-YAP1 pathway. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167170. [PMID: 38631407 DOI: 10.1016/j.bbadis.2024.167170] [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: 12/02/2023] [Revised: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Intimal hyperplasia (IH) is a common pathological feature of vascular proliferative diseases, such as atherosclerosis and restenosis after angioplasty. Urotensin II (UII) and its receptor (UTR) are widely expressed in cardiovascular tissues. However, it remains unclear whether the UII/UTR system is involved in IH. Right unilateral common carotid artery ligation was performed and maintained for 21 days to induce IH in UTR knockout (UTR-/-) and wild-type (WT) mice. Histological analysis revealed that compared with WT mice, UTR-deficient mice exhibited a decreased neointimal area, angiostenosis and intima-media ratio. Immunostaining revealed fewer smooth muscle cells (SMCs), endothelial cells and macrophages in the lesions of UTR-/- mice than in those of WT mice. Protein interaction analysis suggested that the UTR may affect cell proliferation by regulating YAP and its downstream target genes. In vitro experiments revealed that UII can promote the proliferation and migration of SMCs, and western blotting also revealed that UII increased the protein expression of RhoA, CTGF, Cyclin D1 and PCNA and downregulated p-YAP protein expression, while these effects could be partly reversed by urantide. To evaluate the translational value of UTRs in IH management, WT mice were also treated with two doses of urantide, a UTR antagonist, to confirm the benefit of UTR blockade in IH progression. A high dose of urantide (600 μg/kg/day), rather than a low dose (60 μg/kg/day), successfully improved ligation-induced IH compared with that in mice receiving vehicle. The results of the present study suggested that the UII/UTR system may regulate IH partly through the RhoA-YAP signaling pathway.
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MESH Headings
- Animals
- Male
- Mice
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Movement
- Cell Proliferation
- Hyperplasia/metabolism
- Hyperplasia/pathology
- Ligation
- Mice, Inbred C57BL
- Mice, Knockout
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Neointima/metabolism
- Neointima/pathology
- Neointima/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, G-Protein-Coupled/genetics
- rhoA GTP-Binding Protein/metabolism
- rhoA GTP-Binding Protein/genetics
- Signal Transduction
- Tunica Intima/pathology
- Tunica Intima/metabolism
- Urotensins/metabolism
- Urotensins/genetics
- Urotensins/pharmacology
- YAP-Signaling Proteins/metabolism
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Affiliation(s)
- Panpan Wei
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Kangli Tian
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Haole Liu
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Kexin Li
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Naqash Alam
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Daxin Cheng
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Meng Li
- Department of Vascular Surgery, the Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Xue He
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jia Guo
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rong Wang
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Weirong Wang
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Liang Bai
- Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Enqi Liu
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Baohui Xu
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yankui Li
- Department of Vascular Surgery, the Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Sihai Zhao
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China; Laboratory Animal Center, Xi'an Jiaotong University, Xi'an 710061, China.
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11
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Duffy EE, Assad EG, Kalish BT, Greenberg ME. Small but mighty: the rise of microprotein biology in neuroscience. Front Mol Neurosci 2024; 17:1386219. [PMID: 38807924 PMCID: PMC11130481 DOI: 10.3389/fnmol.2024.1386219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
The mammalian central nervous system coordinates a network of signaling pathways and cellular interactions, which enable a myriad of complex cognitive and physiological functions. While traditional efforts to understand the molecular basis of brain function have focused on well-characterized proteins, recent advances in high-throughput translatome profiling have revealed a staggering number of proteins translated from non-canonical open reading frames (ncORFs) such as 5' and 3' untranslated regions of annotated proteins, out-of-frame internal ORFs, and previously annotated non-coding RNAs. Of note, microproteins < 100 amino acids (AA) that are translated from such ncORFs have often been neglected due to computational and biochemical challenges. Thousands of putative microproteins have been identified in cell lines and tissues including the brain, with some serving critical biological functions. In this perspective, we highlight the recent discovery of microproteins in the brain and describe several hypotheses that have emerged concerning microprotein function in the developing and mature nervous system.
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Affiliation(s)
- Erin E. Duffy
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Elena G. Assad
- Department of Neurobiology, Harvard Medical School, Boston, MA, United States
| | - Brian T. Kalish
- Program in Neuroscience and Mental Health, SickKids Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Division of Neonatology, Department of Paediatrics, Hospital for Sick Children, Toronto, ON, Canada
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12
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Das D, Podder S. Microscale marvels: unveiling the macroscopic significance of micropeptides in human health. Brief Funct Genomics 2024:elae018. [PMID: 38706311 DOI: 10.1093/bfgp/elae018] [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: 01/04/2024] [Revised: 04/07/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Non-coding RNA encodes micropeptides from small open reading frames located within the RNA. Interestingly, these micropeptides are involved in a variety of functions within the body. They are emerging as the resolving piece of the puzzle for complex biomolecular signaling pathways within the body. Recent studies highlight the pivotal role of small peptides in regulating important biological processes like DNA repair, gene expression, muscle regeneration, immune responses, etc. On the contrary, altered expression of micropeptides also plays a pivotal role in the progression of various diseases like cardiovascular diseases, neurological disorders and several types of cancer, including colorectal cancer, hepatocellular cancer, lung cancer, etc. This review delves into the dual impact of micropeptides on health and pathology, exploring their pivotal role in preserving normal physiological homeostasis and probing their involvement in the triggering and progression of diseases.
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Affiliation(s)
- Deepyaman Das
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
| | - Soumita Podder
- Computational and Systems Biology Laboratory, Department of Microbiology, Raiganj University, Raiganj, Uttar Dinajpur, West Bengal-733134, India
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13
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Singh AK. Rules and impacts of nonsense-mediated mRNA decay in the degradation of long noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1853. [PMID: 38741356 DOI: 10.1002/wrna.1853] [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: 12/30/2023] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a quality-control process that selectively degrades mRNAs having premature termination codon, upstream open reading frame, or unusually long 3'UTR. NMD detects such mRNAs and rapidly degrades them during initial rounds of translation in the eukaryotic cells. Since NMD is a translation-dependent cytoplasmic mRNA surveillance process, the noncoding RNAs were initially believed to be NMD-resistant. The sequence feature-based analysis has revealed that many putative long noncoding RNAs (lncRNAs) have short open reading frames, most of which have translation potential. Subsequent transcriptome-based molecular studies showed an association of a large set of such putative lncRNAs with translating ribosomes, and some of them produce stable and functionally active micropeptides. The translationally active lncRNAs typically have relatively longer and unprotected 3'UTR, which can induce their NMD-dependent degradation. This review defines the mechanism and regulation of NMD-dependent degradation of lncRNAs and its impact on biological processes related to the functions of lncRNAs or their encoded micropeptides. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Anand Kumar Singh
- Department of Biology, Indian Institute of Science Education and Research Tirupati, Tirupati, Andhra Pradesh, India
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14
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Biferali B, Mocciaro E, Runfola V, Gabellini D. Long non-coding RNAs and their role in muscle regeneration. Curr Top Dev Biol 2024; 158:433-465. [PMID: 38670715 DOI: 10.1016/bs.ctdb.2024.02.010] [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] [Indexed: 04/28/2024]
Abstract
In mammals, most of the genome is transcribed to generate a large and heterogeneous variety of non-protein coding RNAs, that are broadly grouped according to their size. Long noncoding RNAs include a very large and versatile group of molecules. Despite only a minority of them has been functionally characterized, there is emerging evidence indicating long noncoding RNAs as important regulators of expression at multiple levels. Several of them have been shown to be modulated during myogenic differentiation, playing important roles in the regulation of skeletal muscle development, differentiation and homeostasis, and contributing to neuromuscular diseases. In this chapter, we have summarized the current knowledge about long noncoding RNAs in skeletal muscle and discussed specific examples of long noncoding RNAs (lncRNAs and circRNAs) regulating muscle stem cell biology. We have also discussed selected long noncoding RNAs involved in the most common neuromuscular diseases.
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Affiliation(s)
- Beatrice Biferali
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Mocciaro
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Runfola
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Gabellini
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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15
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Shin YJ, Kwon KS, Suh Y, Lee KP. The role of non-coding RNAs in muscle aging: regulatory mechanisms and therapeutic potential. Front Mol Biosci 2024; 10:1308274. [PMID: 38264571 PMCID: PMC10803457 DOI: 10.3389/fmolb.2023.1308274] [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: 10/06/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Muscle aging is a complex physiological process that leads to the progressive decline in muscle mass and function, contributing to debilitating conditions in the elderly such as sarcopenia. In recent years, non-coding RNAs (ncRNAs) have been increasingly recognized as major regulators of muscle aging and related cellular processes. Here, we comprehensively review the emerging role of ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), in the regulation of muscle aging. We also discuss how targeting these ncRNAs can be explored for the development of novel interventions to combat age-related muscle decline. The insights provided in this review offer a promising avenue for future research and therapeutic strategies aimed at improving muscle health during aging.
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Affiliation(s)
- Yeo Jin Shin
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Ki-Sun Kwon
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioscience, KRIBB School, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
- Aventi Inc., Daejeon, Republic of Korea
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University, New York, NY, United States
- Department of Genetics and Development, Columbia University, New York, NY, United States
| | - Kwang-Pyo Lee
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioscience, KRIBB School, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
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16
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Sabikunnahar B, Caldwell S, Varnum S, Hogan T, Lahue KG, Rathkolb B, Gerlini R, Dragano NRV, Aguilar‐Pimentel A, Irmler M, Sanz‐Moreno A, da Silva‐Buttkus P, Beckers J, Wolf E, Gailus‐Durner V, Fuchs H, Hrabe de Angelis M, Ather JL, Poynter ME, Krementsov DN. LncRNA U90926 is dispensable for the development of obesity-associated phenotypes in vivo. Physiol Rep 2024; 12:e15901. [PMID: 38171546 PMCID: PMC10764201 DOI: 10.14814/phy2.15901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Obesity is a global health problem characterized by excessive fat accumulation, driven by adipogenesis and lipid accumulation. Long non-coding RNAs (lncRNAs) have recently been implicated in regulating adipogenesis and adipose tissue function. Mouse lncRNA U90926 was previously identified as a repressor of in vitro adipogenesis in 3T3-L1 preadipocytes. Consequently, we hypothesized that, in vivo, U90926 may repress adipogenesis, and hence its deletion would increase weight gain and adiposity. We tested the hypothesis by applying U90926-deficient (U9-KO) mice to a high-throughput phenotyping pipeline. Compared with WT, U9-KO mice showed no major differences across a wide range of behavioral, neurological, and other physiological parameters. In mice fed a standard diet, we have found no differences in obesity-related phenotypes, including weight gain, fat mass, and plasma concentrations of glucose, insulin, triglycerides, and free fatty acids, in U9-KO mice compared to WT. U90926 deficiency lacked a major effect on white adipose tissue morphology and gene expression profile. Furthermore, in mice fed a high-fat diet, we found increased expression of U90926 in adipose tissue stromal vascular cell fraction, yet observed no effect of U90926 deficiency on weight gain, fat mass, adipogenesis marker expression, and immune cell infiltration into the adipose tissue. These data suggest that the U90926 lacks an essential role in obesity-related phenotypes and adipose tissue biology in vivo.
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Affiliation(s)
- Bristy Sabikunnahar
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Sydney Caldwell
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Stella Varnum
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Tyler Hogan
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Karolyn G. Lahue
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Birgit Rathkolb
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Institute of Molecular Animal Breeding and Biotechnology, Gene CenterLudwig‐Maximilians‐University MünchenMunichGermany
| | - Raffaele Gerlini
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Nathalia R. V. Dragano
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Antonio Aguilar‐Pimentel
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Irmler
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Adrián Sanz‐Moreno
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Patricia da Silva‐Buttkus
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Johannes Beckers
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- TUM School of Life SciencesTechnische Universität MünchenFreisingGermany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene CenterLudwig‐Maximilians‐University MünchenMunichGermany
| | - Valerie Gailus‐Durner
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- TUM School of Life SciencesTechnische Universität MünchenFreisingGermany
| | | | | | - Dimitry N. Krementsov
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
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17
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Fontana F, Esser AK, Egbulefu C, Karmakar P, Su X, Allen JS, Xu Y, Davis JL, Gabay A, Xiang J, Kwakwa KA, Manion B, Bakewell S, Li S, Park H, Lanza GM, Achilefu S, Weilbaecher KN. Transferrin receptor in primary and metastatic breast cancer: Evaluation of expression and experimental modulation to improve molecular targeting. PLoS One 2023; 18:e0293700. [PMID: 38117806 PMCID: PMC10732420 DOI: 10.1371/journal.pone.0293700] [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: 08/09/2023] [Accepted: 10/17/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND Conjugation of transferrin (Tf) to imaging or nanotherapeutic agents is a promising strategy to target breast cancer. Since the efficacy of these biomaterials often depends on the overexpression of the targeted receptor, we set out to survey expression of transferrin receptor (TfR) in primary and metastatic breast cancer samples, including metastases and relapse, and investigate its modulation in experimental models. METHODS Gene expression was investigated by datamining in twelve publicly-available datasets. Dedicated Tissue microarrays (TMAs) were generated to evaluate matched primary and bone metastases as well as and pre and post chemotherapy tumors from the same patient. TMA were stained with the FDA-approved MRQ-48 antibody against TfR and graded by staining intensity (H-score). Patient-derived xenografts (PDX) and isogenic metastatic mouse models were used to study in vivo TfR expression and uptake of transferrin. RESULTS TFRC gene and protein expression were high in breast cancer of all subtypes and stages, and in 60-85% of bone metastases. TfR was detectable after neoadjuvant chemotherapy, albeit with some variability. Fluorophore-conjugated transferrin iron chelator deferoxamine (DFO) enhanced TfR uptake in human breast cancer cells in vitro and proved transferrin localization at metastatic sites and correlation of tumor burden relative to untreated tumor mice. CONCLUSIONS TfR is expressed in breast cancer, primary, metastatic, and after neoadjuvant chemotherapy. Variability in expression of TfR suggests that evaluation of the expression of TfR in individual patients could identify the best candidates for targeting. Further, systemic iron chelation with DFO may upregulate receptor expression and improve uptake of therapeutics or tracers that use transferrin as a homing ligand.
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Affiliation(s)
- Francesca Fontana
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Alison K. Esser
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Christopher Egbulefu
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Partha Karmakar
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Xinming Su
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - John S. Allen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Yalin Xu
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jennifer L. Davis
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Ariel Gabay
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Jingyu Xiang
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Kristin A. Kwakwa
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Brad Manion
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Suzanne Bakewell
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Shunqiang Li
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Haeseong Park
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Gregory M. Lanza
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Samuel Achilefu
- Department of Radiology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Katherine N. Weilbaecher
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States of America
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18
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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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19
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Özdemir S, Aydın Ş, Laçin BB, Arslan H. Identification and characterization of long non-coding RNA (lncRNA) in cypermethrin and chlorpyrifos exposed zebrafish (Danio rerio) brain. CHEMOSPHERE 2023; 344:140324. [PMID: 37778644 DOI: 10.1016/j.chemosphere.2023.140324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023]
Abstract
Pesticides, such as cypermethrin (CYP) and chlorpyrifos (CPF), are widely used around the world and are known to cause toxicological effects in the brains of fish and other non-target organisms. Long non-coding RNAs (LncRNAs) are a new class of non-coding RNAs that are highly expressed in the brain and play crucial roles in brain function by regulating gene expression. Many studies have investigated the toxic effects of CYP and CPF on the brain. However, no study has been conducted on the relationship between LncRNAs and the toxicity caused by these chemicals. Therefore, this study aimed to determine changes in the lncRNA expression profile in the brains of fish exposed to CYP and CPF. Out of a total of 482 lncRNAs that were differentially expressed between control and CPF groups, 53 were found to be up-regulated, and 429 were down-regulated. Similarly, among the 200 lncRNAs differentially expressed between the control and CYP groups, 71 were up-regulated, and 129 were down-regulated. Additionally, 268 differentially expressed lncRNAs were identified between CYP and CPF groups, with 240 being up-regulated and the rest being down-regulated. In addition, LncRNAs expressed from fish brains exposed to CYP and CPF were found to regulate multiple signaling pathways, including MAPK, FoxO, PPAR, TGF-β, and Wnt signaling pathways.
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Affiliation(s)
- Selçuk Özdemir
- Department of Genetics, Faculty of Veterinary Medicine, Atatürk University, Erzurum, Turkey; German Center for Neurodegenerative Diseases, DZNE, Bonn, Germany.
| | - Şeyma Aydın
- Department of Genetics, Faculty of Veterinary Medicine, Atatürk University, Erzurum, Turkey
| | - Burak Batuhan Laçin
- Department of Physiology, Faculty of Veterinary Medicine, Atatürk University, Erzurum, Turkey
| | - Harun Arslan
- Atatürk University, Faculty of Fisheries, Department of Basic Science, Erzurum, Turkey
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20
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Mohsen JJ, Martel AA, Slavoff SA. Microproteins-Discovery, structure, and function. Proteomics 2023; 23:e2100211. [PMID: 37603371 PMCID: PMC10841188 DOI: 10.1002/pmic.202100211] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Advances in proteogenomic technologies have revealed hundreds to thousands of translated small open reading frames (sORFs) that encode microproteins in genomes across evolutionary space. While many microproteins have now been shown to play critical roles in biology and human disease, a majority of recently identified microproteins have little or no experimental evidence regarding their functionality. Computational tools have some limitations for analysis of short, poorly conserved microprotein sequences, so additional approaches are needed to determine the role of each member of this recently discovered polypeptide class. A currently underexplored avenue in the study of microproteins is structure prediction and determination, which delivers a depth of functional information. In this review, we provide a brief overview of microprotein discovery methods, then examine examples of microprotein structures (and, conversely, intrinsic disorder) that have been experimentally determined using crystallography, cryo-electron microscopy, and NMR, which provide insight into their molecular functions and mechanisms. Additionally, we discuss examples of predicted microprotein structures that have provided insight or context regarding their function. Analysis of microprotein structure at the angstrom level, and confirmation of predicted structures, therefore, has potential to identify translated microproteins that are of biological importance and to provide molecular mechanism for their in vivo roles.
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Affiliation(s)
- Jessica J. Mohsen
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alina A. Martel
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Sarah A. Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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21
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Kumari N, Das K, Sharma S, Dahal S, Desai SS, Roy U, Sharma A, Manjunath M, Gopalakrishnan V, Retheesh ST, Javadekar SM, Choudhary B, Raghavan SC. Evaluation of potential role of R-loop and G-quadruplex DNA in the fragility of c-MYC during chromosomal translocation associated with Burkitt's lymphoma. J Biol Chem 2023; 299:105431. [PMID: 37926284 PMCID: PMC10704377 DOI: 10.1016/j.jbc.2023.105431] [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: 08/15/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
t(8;14) translocation is the hallmark of Burkitt's lymphoma and results in c-MYC deregulation. During the translocation, c-MYC gene on chromosome 8 gets juxtaposed to the Ig switch regions on chromosome 14. Although the promoter of c-MYC has been investigated for its mechanism of fragility, little is known about other c-MYC breakpoint regions. We have analyzed the translocation break points at the exon 1/intron 1 of c-MYC locus from patients with Burkitt's lymphoma. Results showed that the breakpoint region, when present on a plasmid, could fold into an R-loop confirmation in a transcription-dependent manner. Sodium bisulfite modification assay revealed significant single-strandedness on chromosomal DNA of Burkitt's lymphoma cell line, Raji, and normal lymphocytes, revealing distinct R-loops covering up to 100 bp region. Besides, ChIP-DRIP analysis reveals that the R-loop antibody can bind to the breakpoint region. Further, we show the formation of stable parallel intramolecular G-quadruplex on non-template strand of the genome. Finally, incubation of purified AID in vitro or overexpression of AID within the cells led to enhanced mutation frequency at the c-MYC breakpoint region. Interestingly, anti-γH2AX can bind to DSBs generated at the c-MYC breakpoint region within the cells. The formation of R-loop and G-quadruplex was found to be mutually exclusive. Therefore, our results suggest that AID can bind to the single-stranded region of the R-loop and G4 DNA, leading to the deamination of cytosines to uracil and induction of DNA breaks in one of the DNA strands, leading to double-strand break, which could culminate in t(8;14) chromosomal translocation.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Kohal Das
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Urbi Roy
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Anju Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India; Department of Zoology, St Joseph's College, Irinjalakuda, Kerala, India
| | - S T Retheesh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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22
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Li P, Ma X, Gu X. LncRNA MAFG-AS1 is involved in human cancer progression. Eur J Med Res 2023; 28:497. [PMID: 37941063 PMCID: PMC10631199 DOI: 10.1186/s40001-023-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) refer to a type of non-protein-coding transcript of more than 200 nucleotides. LncRNAs play fundamental roles in disease development and progression, and lncRNAs are dysregulated in many pathophysiological processes. Thus, lncRNAs may have potential value in clinical applications. The lncRNA, MAF BZIP Transcription Factor G (MAFG)-AS1, is dysregulated in several cancer, including breast cancer, lung cancer, liver cancer, bladder cancer, colorectal cancer, gastric cancer, esophagus cancer, prostate cancer, pancreatic cancer, ovarian cancer, and glioma. Altered MAFG-AS1 levels are also associated with diverse clinical characteristics and patient outcomes. Mechanistically, MAFG-AS1 mediates a variety of cellular processes via the regulation of target gene expression. Therefore, the diagnostic, prognostic, and therapeutic aspects of MAFG-AS1 have been widely explored. In this review, we discuss the expression, major roles, and molecular mechanisms of MAFG-AS1, the relationship between MAFG-AS1 and clinical features of diseases, and the clinical applications of MAFG-AS1.
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Affiliation(s)
- Penghui Li
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Xiao Ma
- Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China.
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23
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Kratz A, Ranganathan S. Christian Schönbach 1965-2023. BIOINFORMATICS ADVANCES 2023; 3:vbad147. [PMID: 37886713 PMCID: PMC10599964 DOI: 10.1093/bioadv/vbad147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023]
Affiliation(s)
- Anton Kratz
- The Systems Biology Institute, Tokyo 141-0022, Japan
| | - Shoba Ranganathan
- Applied Biosciences, Macquarie University, Sydney, NSW 2109, Australia
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24
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Sun L, Ding M, Chen F, Zhu D, Xie X. Long non‑coding RNA L13Rik promotes high glucose-induced mesangial cell hypertrophy and matrix protein expression by regulating miR-2861/CDKN1B axis. PeerJ 2023; 11:e16170. [PMID: 37868060 PMCID: PMC10586299 DOI: 10.7717/peerj.16170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/03/2023] [Indexed: 10/24/2023] Open
Abstract
Background Diabetic nephropathy (DN) is a frequent microvascular complication of diabetes. Glomerular mesangial cell (MC) hypertrophy occurs at the initial phase of DN and plays a critical role in the pathogenesis of DN. Given the role of long non coding RNA (lncRNA) in regulating MC hypertrophy and extracellular matrix (ECM) accumulation, our aim was to identify functional lncRNAs during MC hypertrophy. Methods Here, an lncRNA, C920021L13Rik (L13Rik for short), was identified to be up-regulated in DN progression. The expression of L13Rik in DN patients and diabetic mice was assessed using quantitative real-time PCR (qRT-PCR), and the function of L13Rik in regulating HG-induced MC hypertrophy and ECM accumulation was assessed through flow cytometry and western blotting analysis. Results The L13Rik levels were significantly increased while the miR-2861 levels were decreased in the peripheral blood of DN patients, the renal tissues of diabetic mice, and HG-treated MCs. Functionally, both L13Rik depletion and miR-2861 overexpression effectively reduced HG-induced cell hypertrophy and ECM accumulation. Mechanistically, L13Rik functioned as a competing endogenous RNA (ceRNA) to sponge miR-2861, resulting in the de-repression of cyclin-dependent kinase inhibitor 1B (CDKN1B), a gene known to regulate cell cycle and MC hypertrophy. Conclusions Collectively, the current results demonstrate that up-regulated L13Rik is correlated with DN and may be a hopeful therapeutic target for DN.
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Affiliation(s)
- Linlin Sun
- Nephrology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Miao Ding
- Nephrology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fuhua Chen
- Nephrology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dingyu Zhu
- Nephrology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinmiao Xie
- Nephrology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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25
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Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Guo W, Wu F, Feng X, Wang Q, Lu Y, Xu J. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. Int J Mol Sci 2023; 24:15039. [PMID: 37894720 PMCID: PMC10606207 DOI: 10.3390/ijms242015039] [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: 07/25/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m6A), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.
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Affiliation(s)
- Xin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qimeng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoju Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiu Zhong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Mao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wubin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianhong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. The status of the human gene catalogue. Nature 2023; 622:41-47. [PMID: 37794265 PMCID: PMC10575709 DOI: 10.1038/s41586-023-06490-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/27/2023] [Indexed: 10/06/2023]
Abstract
Scientists have been trying to identify every gene in the human genome since the initial draft was published in 2001. In the years since, much progress has been made in identifying protein-coding genes, currently estimated to number fewer than 20,000, with an ever-expanding number of distinct protein-coding isoforms. Here we review the status of the human gene catalogue and the efforts to complete it in recent years. Beside the ongoing annotation of protein-coding genes, their isoforms and pseudogenes, the invention of high-throughput RNA sequencing and other technological breakthroughs have led to a rapid growth in the number of reported non-coding RNA genes. For most of these non-coding RNAs, the functional relevance is currently unclear; we look at recent advances that offer paths forward to identifying their functions and towards eventually completing the human gene catalogue. Finally, we examine the need for a universal annotation standard that includes all medically significant genes and maintains their relationships with different reference genomes for the use of the human gene catalogue in clinical settings.
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Affiliation(s)
- Paulo Amaral
- INSPER Institute of Education and Research, Sao Paulo, Brazil
| | | | - Francisco M De La Vega
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Tempus Labs, Chicago, IL, USA
| | | | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas Gingeras
- Department of Functional Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jennifer L Harrow
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, Royston, UK
| | - Artemis G Hatzigeorgiou
- Department of Computer Science and Biomedical Informatics, Universithy of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens, Greece
| | - 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
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mihaela Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Ales Varabyou
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Christine A Wells
- Stem Cell Systems, Department of Anatomy and Physiology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Yandell
- Departent of Human Genetics, Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Human Technopole, Milan, Italy.
| | - Steven L Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA.
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Wei M, Tang W, Lv D, Liu M, Wang G, Liu Q, Qin L, Huang B, Zhang D. Long-chain noncoding RNA sequencing analysis reveals the molecular profiles of chemically induced mammary epithelial cells. Front Genet 2023; 14:1189487. [PMID: 37745843 PMCID: PMC10514351 DOI: 10.3389/fgene.2023.1189487] [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: 03/19/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) were important regulators affecting the cellular reprogramming process. Previous studies from our group have demonstrated that small molecule compounds can induce goat ear fibroblasts to reprogram into mammary epithelial cells with lactation function. In this study, we used lncRNA-Sequencing (lncRNA-seq) to analyze the lncRNA expression profile of cells before and after reprogramming (CK vs. 5i8 d). The results showed that a total of 3,970 candidate differential lncRNAs were detected, 1,170 annotated and 2,800 new lncRNAs. Compared to 0 d cells, 738 lncRNAs were significantly upregulated and 550 were significantly downregulated in 8 d cells. Heat maps of lncrnas and target genes with significant differences showed that the fate of cell lineages changed. Functional enrichment analysis revealed that these differently expressed (DE) lncRNAs target genes were mainly involved in signaling pathways related to reprogramming and mammary gland development, such as the Wnt signaling pathway, PI3K-Akt signaling pathway, arginine and proline metabolism, ECM-receptor interaction, and MAPK signaling pathway. The accuracy of sequencing was verified by real-time fluorescence quantification (RT-qPCR) of lncRNAs and key candidate genes, and it was also demonstrated that the phenotype and genes of the cells were changed. Therefore, this study offers a foundation for explaining the molecular mechanisms of lncRNAs in chemically induced mammary epithelial cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Ben Huang
- Guangxi Key Laboratory of Eye Health, Guangxi Academy of Medical Sciences, People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Dandan Zhang
- Guangxi Key Laboratory of Eye Health, Guangxi Academy of Medical Sciences, People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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28
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Polina I, Mishra J, Cypress MW, Landherr M, Valkov N, Chaput I, Nieto B, Mende U, Zhang P, Jhun BS, O-Uchi J. Mitochondrial Ca 2+ uniporter (MCU) variants form plasma-membrane channels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551242. [PMID: 37577584 PMCID: PMC10418069 DOI: 10.1101/2023.07.31.551242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
MCU is widely recognized as a responsible gene for encoding a pore-forming subunit of highly mitochondrial-specific and Ca 2+ -selective channel, mitochondrial Ca 2+ uniporter complex (mtCUC). Here, we report a novel short variant derived from the MCU gene (termed MCU-S) which lacks mitochondria-targeted sequence and forms a Ca 2+ - permeable channel outside of mitochondria. MCU-S was ubiquitously expressed in all cell-types/tissues, with particularly high expression in human platelets. MCU-S formed Ca 2+ channels at the plasma membrane, which exhibited similar channel properties to those observed in mtCUC. MCU-S channels at the plasma membrane served as an additional Ca 2+ influx pathway for platelet activation. Our finding is completely distinct from the originally reported MCU gene function and provides novel insights into the molecular basis of MCU variant-dependent cellular Ca 2+ handling.
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29
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Yin Q, Ma H, Bamunuarachchi G, Zheng X, Ma Y. Long Non-Coding RNAs, Cell Cycle, and Human Breast Cancer. Hum Gene Ther 2023; 34:481-494. [PMID: 37243445 PMCID: PMC10398747 DOI: 10.1089/hum.2023.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) constitute an important class of the human transcriptome. The discovery of lncRNAs provided one of many unexpected results of the post-genomic era and uncovered a huge number of previously ignored transcriptional events. In recent years, lncRNAs are known to be linked with human diseases, with particular focus on cancer. Growing evidence has indicated that dysregulation of lncRNAs in breast cancer (BC) is strongly associated with the occurrence, development, and progress. Increasing numbers of lncRNAs have been found to interact with cell cycle progression and tumorigenesis in BC. The lncRNAs can exert their effect as a tumor suppressor or oncogene and regulate tumor development through direct or indirect regulation of cancer-related modulators and signaling pathways. What is more, lncRNAs are excellent candidates for promising therapeutic targets in BC due to the features of high tissue and cell-type specific expression. However, the underlying mechanisms of lncRNAs in BC still remain largely undefined. Here, we concisely summarize and sort out the current understanding of research progress in relationships of the roles for lncRNA in regulating the cell cycle. We also summarize the evidence for aberrant lncRNA expression in BC, and the potential for lncRNA to improve BC therapy is also discussed. Together, lncRNAs can be considered as exciting therapeutic candidates whose expression can be altered to impede BC progression.
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Affiliation(s)
- Qinan Yin
- Precision Medicine Laboratory, College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Haodi Ma
- Precision Medicine Laboratory, College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Gayan Bamunuarachchi
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Xuewei Zheng
- Precision Medicine Laboratory, College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, China
| | - Yan Ma
- Spatial Navigation and Memory Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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30
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 483] [Impact Index Per Article: 483.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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31
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Barangi S, Hayes AW, Karimi G. The role of lncRNAs/miRNAs/Sirt1 axis in myocardial and cerebral injury. Cell Cycle 2023; 22:1062-1073. [PMID: 36703306 PMCID: PMC10081082 DOI: 10.1080/15384101.2023.2172265] [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: 10/05/2022] [Revised: 11/30/2022] [Accepted: 12/07/2022] [Indexed: 01/28/2023] Open
Abstract
In recent years, researchers have begun to realize the importance of the role of non-coding RNAs in the treatment of cancer and cardiovascular and neurological diseases. LncRNAs and miRNAs are important non-coding RNAs, which regulate gene expression and activate mRNA translation through binding to diverse target sites. Their involvement in the regulation of protein function and the modulation of physiological and pathological conditions continues to be investigated. Sirtuins, especially Sirt1, have a critical function in regulating a variety of physiological processes such as oxidative stress, inflammation, apoptosis, and autophagy. The lncRNAs/miRNAs/Sirt1 axis may be a novel regulatory mechanism, which is involved in the progression and/or prevention of numerous diseases. This review focuses on recent findings on the crosstalk between non-coding RNAs and Sirt1 in myocardial and cerebral injuries and may provide some insight into the development of novel approaches in the treatment of these disorders.Abbreviation: BMECs, brain microvascular endothelial cells; C2dat1, calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D)-associated transcript 1; EPCs, endothelial progenitor cells; FOXOs, forkhead transcription factors; GAS5, growth arrest-specific 5; HAECs, human aortic endothelial cells; HAND2-AS1, HAND2 Antisense RNA 1; HIF-1α, hypoxia-inducible factor-1α; ILF3-AS1, interleukin enhancer-binding factor 3-antisense RNA 1; KLF3-AS1, KLF3 antisense RNA 1; LncRNA, long noncoding RNA; LUADT1, Lung Adenocarcinoma Associated Transcript 1; MALAT1, Metastasis-associated lung adenocarcinoma transcript 1; miRNA, microRNA; NEAT1, nuclear enriched abundant transcript 1; NF-κB, nuclear factor kappa B; OIP5-AS1, Opa-interacting protein 5-antisense transcript 1; Sirt1-AS, Sirt1 Antisense RNA; SNHG7, small nucleolar RNA host gene 7; SNHG8, small nucleolar RNA host gene 8; SNHG12, small nucleolar RNA host gene 12; SNHG15, small nucleolar RNA host gene 15; STAT3, signal transducers and activators of transcription 3; TUG1, taurine up-regulated gene 1; VSMCs, vascular smooth muscle cells; XIST, X inactive specific transcript; ZFAS1, ZNFX1 Antisense RNA 1.
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Affiliation(s)
- Samira Barangi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - A. Wallace Hayes
- Michigan State University, East Lansing, MI, USA
- University of South Florida, Tampa, FL, USA
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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32
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Zhang L, Liang R, Raheem A, Liang L, Zhang X, Cui S. Transcriptomics analysis reveals key lncRNAs and genes related to the infection of feline kidney cell line by panleukopenia virus. Res Vet Sci 2023; 158:203-214. [PMID: 37031469 DOI: 10.1016/j.rvsc.2023.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 03/16/2023] [Accepted: 03/31/2023] [Indexed: 04/08/2023]
Abstract
Feline panleukopenia virus (FPV) can cause a viral disease and is responsible for severe leukopenia, gastroenteritis, and nervous signs with significant economic losses. Biochemically long non-coding RNAs (lncRNAs) can regulate the expression of mRNA in different ways, thereby causing the functional changes in host cells in response to viral infection. However, no attention has been paid until now to investigate the link between FPV pathogenesis and lncRNA. Here, through RNA sequencing, we performed a comprehensive analysis of lncRNA and mRNA in F81 cells after FPV-BJ04 strain infection. Consistent with previous studies, our data showed that lncRNAs have distinct features from mRNA. A total of 291 lncRNAs and 873 mRNAs were differentially expressed in F81 cells after FPV-BJ04 infection. GO and KEGG enrichment analysis showed that the differentially upregulated lncRNAs target genes were mainly involved in the positive regulation of transcription by RNA polymerase II and MAPK signaling pathway. The differentially downregulated lncRNAs target genes were mainly involved in the mRNA splicing and endocytosis. In addition, the differentially expressed immune pathway related genes that are targeted by lncRNA were also screened out to construct a lncRNA-miRNA-mRNA axes as a potential novel biomarkers in regulating the immune response of feline against FPV infection. Our results contribute to understand the basic role of lncRNA in F81 cells during FPV infection and lay the foundation for following research.
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Affiliation(s)
- Lingling Zhang
- Institute of Microbe and Host Health, Linyi University, Linyi, Shandong 276000, China.
| | - Ruiying Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China
| | - Abdul Raheem
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China
| | - Lin Liang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China
| | - Xinglin Zhang
- Institute of Microbe and Host Health, Linyi University, Linyi, Shandong 276000, China
| | - Shangjin Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Technology of Beijing, Ministry of Agriculture, Beijing 100193, China.
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33
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Xu D, Tang L, Kapranov P. Complexities of mammalian transcriptome revealed by targeted RNA enrichment techniques. Trends Genet 2023; 39:320-333. [PMID: 36681580 DOI: 10.1016/j.tig.2022.12.004] [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: 08/29/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023]
Abstract
Studies using highly sensitive targeted RNA enrichment methods have shown that a large portion of the human transcriptome remains to be discovered and that most of the genome is transcribed in a complex, interleaved fashion characterized by a complex web of transcripts emanating from protein coding and noncoding loci. These results resonate with those from single-cell transcriptome profiling endeavors that reveal the existence of multiple novel, cell type-specific transcripts and clearly demonstrate that our understanding of the complexities of the human transcriptome is far from being complete. Here, we review the current status of the targeted RNA enrichment techniques, their application to the discovery of novel cell type-specific transcripts, and their impact on our understanding of the human genome and transcriptome.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China.
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34
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Fu W, Liu H, Wei P, Xia C, Yu Q, Tian K, Li Y, Liu E, Xu B, Miyata M, Wang R, Zhao S. Genetic deficiency of protein inhibitor of activated STAT3 suppresses experimental abdominal aortic aneurysms. Front Cardiovasc Med 2023; 10:1092555. [PMID: 37008329 PMCID: PMC10050368 DOI: 10.3389/fcvm.2023.1092555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
AimSignal transducer and activator of transcription (STAT) signaling is critical for the pathogenesis of abdominal aortic aneurysms (AAAs). Though protein inhibitor of activated STAT3 (PIAS3) negatively modulates STAT3 activity, but its role in AAA disease remains undefined.MethodAAAs were induced in PIAS3 deficient (PIAS3−/−) and wild type (PIAS3+/+) male mice via transient intra-aortic elastase infusion. AAAs were assessed by in situ measurements of infrarenal aortic external diameters prior to (day 0) and 14 days after elastase infusion. Characteristic aneurysmal pathologies were evaluated by histopathology.ResultsFourteen days following elastase infusion, aneurysmal aortic diameter was reduced by an approximately 50% in PIAS3−/− as compared to PIAS3+/+ mice. On histological analyses, PIAS3−/− mice showed less medial elastin degradation (media score: 2.5) and smooth muscle cell loss (media score: 3.0) than those in PIAS3+/+ mice (media score: 4 for both elastin and SMC destruction). Aortic wall leukocyte accumulation including macrophages, CD4+ T cells, CD8+ T cells and B cells as well as mural neovessel formation were significantly reduced in PIAS3−/− as compared to PIAS3+/+ mice. Additionally, PIAS3 deficiency also downregulated the expression levels of matrix metalloproteinases 2 and 9 by 61% and 70%, respectively, in aneurysmal lesion.ConclusionPIAS3 deficiency ameliorated experimental AAAs in conjunction with reduced medial elastin degradation and smooth muscle cell depletion, mural leukocyte accumulation and angiogenesis.
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Affiliation(s)
- Weilai Fu
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
- Department of Vascular Surgery, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Haole Liu
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
| | - Panpan Wei
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi’an, China
| | - Congcong Xia
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi’an, China
| | - Qingqing Yu
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
| | - Kangli Tian
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
| | - Yankui Li
- Department of Vascular Surgery, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Enqi Liu
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
| | - Baohui Xu
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Masaaki Miyata
- School of Health Science, Faculty of Medicine, Kagoshima University, Kagoshima, Japan
| | - Rong Wang
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
- Correspondence: Rong Wang Sihai Zhao
| | - Sihai Zhao
- Institute of Cardiovascular Science, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi’an, China
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi’an, China
- Correspondence: Rong Wang Sihai Zhao
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35
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Tao X, Li S, Chen G, Wang J, Xu S. Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination. Int J Mol Sci 2023; 24:ijms24065562. [PMID: 36982636 PMCID: PMC10054671 DOI: 10.3390/ijms24065562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.
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Affiliation(s)
- Xiaoyuan Tao
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sujuan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shengchun Xu
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence:
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36
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Mattick JS. RNA out of the mist. Trends Genet 2023; 39:187-207. [PMID: 36528415 DOI: 10.1016/j.tig.2022.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/08/2022] [Accepted: 11/27/2022] [Indexed: 12/23/2022]
Abstract
RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW 2052, Australia; UNSW RNA Institute, UNSW, Sydney, NSW 2052, Australia.
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Reynoso MA, Blanco FA, Zanetti ME. Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence. IUBMB Life 2023. [PMID: 36852968 DOI: 10.1002/iub.2712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/21/2023] [Indexed: 03/01/2023]
Abstract
In this study, we aimed to identify long noncoding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome-associated polyA, and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA-seq data were mapped to the version 5 of the M. truncatula A17 genome and analyzed to identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs. lncRNAs were classified according to their genomic location relative to chromatin accessible regions, protein-coding genes and transposable elements (TE), finding differences between annotated lncRNAs and NRT lncRNAs, both in their genomic position as well as in the type of TEs in their vicinity. We investigated their response to submergence and found a set of regulated lncRNAs that were preferentially upregulated in the nucleus, some of which were located nearby genes of the conserved submergence upregulated gene families, and chromatin accessible regions suggesting a potential regulatory role. Finally, the accumulation of lncRNAs under submergence was validated by reverse transcription quantitative polymerase chain reaction on nuclear RNA, providing additional evidence of their localization, which could ultimately be required for their function.
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Affiliation(s)
- Mauricio A Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina.,Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, USA
| | - Flavio Antonio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, Argentina
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Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes. Int J Mol Sci 2023; 24:ijms24044163. [PMID: 36835575 PMCID: PMC9959880 DOI: 10.3390/ijms24044163] [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: 01/23/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The human genome encodes a multitude of different noncoding transcripts that have been traditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple functional transcripts that warrant future studies.
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Full-Length Transcriptome Analysis of the Ichthyotoxic Harmful Alga Heterosigma akashiwo (Raphidophyceae) Using Single-Molecule Real-Time Sequencing. Microorganisms 2023; 11:microorganisms11020389. [PMID: 36838354 PMCID: PMC9959365 DOI: 10.3390/microorganisms11020389] [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: 11/20/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
The raphidophyte Heterosigma akashiwo is a harmful algal species. The bloom of this organism has been associated with the massive mortality of fish in many coastal waters. To investigate the molecular mechanism of H. akashiwo blooms, having a reliable reference transcriptome of this species is essential. Therefore, in this study, a full-length transcriptome of H. akashiwo was obtained by single-molecule real-time sequencing. In total, 45.44 Gb subread bases were generated, and 16,668 unigenes were obtained after the sequencing data processing. A total of 8666 (52.00%) unigenes were successfully annotated using seven public databases. Among them, mostly phosphorus and nitrogen metabolism genes were detected. Moreover, there were 300 putative transcription factors, 4392 putative long non-coding RNAs, and 7851 simple sequence repeats predicted. This study provides a valuable reference transcriptome for understanding how H. akashiwo blooms at a molecular level.
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Xu JL, Xu Q, Wang YL, Xu D, Xu WX, Zhang HD, Wang DD, Tang JH. Glucose metabolism and lncRNAs in breast cancer: Sworn friend. Cancer Med 2023; 12:5137-5149. [PMID: 36426411 PMCID: PMC9972110 DOI: 10.1002/cam4.5265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/11/2022] [Accepted: 08/26/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Glucose metabolism disorder is a common feature in cancer. Cancer cells generate much energy through anaerobic glycolysis, which promote the development of tumors. However, long non-coding RNA may play an important role in this process. Our aim is to explore a prognostic risk model based on the glucose metabolism-related lncRNAs which provides clues that lncRNAs predict a clinical outcome through glucose metabolism in breast cancer. METHODS 1222 RNA-seq were extracted from the TCGA database, and 74 glucose metabolism-related genes were loaded from the GSEA website. Then, 7 glucose metabolism-related lncRNAs risk score model was developed by univariate, Lasso, and multivariate regression analysis. The lncRNA risk model showed that high-risk patients predict a poor clinical outcome with high reliability (P=2.838×10-6). Univariate and multivariate independent prognostic analysis and ROC curve analysis proved that the risk score was an independent prognostic factor in breast cancer with an AUC value of 0.652. Finally, Gene set enrichment analysis showed that cell cycle-related pathways were significantly enriched in a high-risk group. RESULTS Our results showed that glucose metabolism-related lncRNAs can affect breast cancer progression. 7 glucose metabolism-related lncRNAs prognostic signature was established to evaluate the OS of patients with breast cancer. PICSAR, LINC00839, AP001505.1, LINC00393 were risk factors and expressed highly in the high-risk group. A Nomogram was made based on this signature to judge patients' living conditions and prognosis. CONCLUSION 7 glucose metabolism-related lncRNAs risk score model had a high prognostic value in breast cancer. PICSAR, LINC00839, AP001505.1, LINC00393 were risk factors. AP001505.1 expression was increased in most triple-negative breast cancer cells treated with high glucose, which may also take part in breast cancer progression and potential therapeutic targets.
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Affiliation(s)
- Jia-Lin Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China.,The First Clinical School of Nanjing Medical University, Nanjing, P.R. China
| | - Qi Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China.,The First Clinical School of Nanjing Medical University, Nanjing, P.R. China
| | - Ya-Lin Wang
- School of Clinical Medicine, Xuzhou Medical University, Xuzhou, P.R. China
| | - Di Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China.,The First Clinical School of Nanjing Medical University, Nanjing, P.R. China
| | - Wen-Xiu Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - He-Da Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Dan-Dan Wang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
| | - Jin-Hai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, P.R. China
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41
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Zhang X, Yu H, Wang N, Li C. Comprehensive analysis of long noncoding RNAs and lncRNA-mRNA networks in snakehead (Channa argus) response to Nocardia seriolae infection. FISH & SHELLFISH IMMUNOLOGY 2023; 133:108558. [PMID: 36690266 DOI: 10.1016/j.fsi.2023.108558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
Evidence has been demonstrated that lncRNAs are involved in a variety of immune responses in vertebrate. It has been demonstrated that immune-related lncRNAs play vital functions in immune regulation against infections in teleost. Nocardia seriolae, as one of the Gram-positive bacteria, can cause chronic systemic granulomatous disease for snakehead (Channa argus). However, how lncRNAs function in the immune regulation process once snakehead was infected with N. seriolae infection has not been studied so far. Accordingly, transcription landscapes of lncRNAs and mRNAs in snakehead were investigated. A total of 1,991 lncRNA were obtained. Totally, we predicted 57,584 co-expression and 16,047 co-location lncRNA-mRNA pairs. To further analyze the potential function of these lncRNAs, GO enrichment analysis and KEGG signal pathways were performed on the target mRNAs of these differently expressed lncRNAs, suggesting that lncRNAs may play essential roles in modulating mRNA expression levels, and subsequently trigger downstream immune signaling pathways to regulate the immune response in snakehead. In addition, 9 DEmRNA and 3 lncRNAs were randomly selected for qRT-PCR analyzed, which confirmed the accuracy of transcriptome data. These results can provide novel knowledge about lncRNAs in immune responses process in snakehead, and can serve as important resources for further investigating the roles of lncRNAs during pathogen infections in teleost.
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Affiliation(s)
- Xiaoyan Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Haohui Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Ningning Wang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, China.
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Recent Advances and Future Potential of Long Non-Coding RNAs in Insects. Int J Mol Sci 2023; 24:ijms24032605. [PMID: 36768922 PMCID: PMC9917219 DOI: 10.3390/ijms24032605] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.
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Liu Q, Bao H, Zhang S, Song T, Li C, Sun G, Sun X, Fu T, Wang Y, Liang P. Identification of a cellular senescence-related-lncRNA (SRlncRNA) signature to predict the overall survival of glioma patients and the tumor immune microenvironment. Front Genet 2023; 14:1096792. [PMID: 36911393 PMCID: PMC9998504 DOI: 10.3389/fgene.2023.1096792] [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: 11/12/2022] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
Background: Gliomas are brain tumors that arise from glial cells, and they are the most common primary intracranial tumors with a poor prognosis. Cellular senescence plays a critical role in cancer, especially in glioma. In this study, we constructed a senescence-related lncRNA (SRlncRNA) signature to assess the prognosis of glioma. Methods: The Cancer Genome Atlas was used to collect SRlncRNA transcriptome profiles and clinical data about glioma. Patients were randomized to training, testing, and whole cohorts. LASSO and Cox regression analyses were employed to construct the SRlncRNA signature, and Kaplan-Meier (K-M) analysis was performed to determine each cohort's survival. Receiver operating characteristic (ROC) curves were applied to verify the accuracy of this signature. Gene set enrichment analysis was used to visualize functional enrichment (GSEA). The CIBERSORT algorithm, ESTIMATE and TIMER databases were utilized to evaluate the differences in the infiltration of 22 types of immune cells and their association with the signature. RT-qPCR and IHC were used to identify the consistency of the signature in tumor tissue. Results: An SRlncRNA signature consisting of six long non-coding RNAs (lncRNAs) was constructed, and patients were divided into high-risk and low-risk groups by the median of their riskscore. The KM analysis showed that the high-risk group had worse overall survival, and the ROC curve confirmed that the riskscore had more accurate predictive power. A multivariate Cox analysis and its scatter plot with clinical characteristics confirmed the riskscore as an independent risk factor for overall survival. GSEA showed that the GO and KEGG pathways were mainly enriched in the immune response to tumor cells, p53 signaling pathway, mTOR signaling pathway, and Wnt signaling pathway. Further validation also yielded significant differences in the risk signature in terms of immune cell infiltration, which may be closely related to prognostic differences, and qRT-PCR and IHC confirmed the consistency of the expression differences in the major lncRNAs with those in the prediction model. Conclusion Our findings indicated that the SRlncRNA signature might be used as a predictive biomarker and that there is a link between it and immune infiltration. This discovery is consistent with the present categorization system and may open new avenues for research and personalized therapy.
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Affiliation(s)
- Qing Liu
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Hongbo Bao
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Sibin Zhang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tianjun Song
- Department of Medicine II, University Hospital LMU Munich, Munich, Germany
| | - Chenlong Li
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Guiyin Sun
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xiaoyang Sun
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Tianjiao Fu
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yujie Wang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Peng Liang
- Department of Neurosurgery, Harbin Medical University Cancer Hospital, Harbin, China
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Wen D, Zhou L, Zheng Z, Surapaneni A, Ballantyne CM, Hoogeveen RC, Shlipak MG, Waikar SS, Vasan RS, Kimmel PL, Dubin RF, Deo R, Feldman HI, Ganz P, Coresh J, Grams ME, Rhee EP. Testican-2 Is Associated with Reduced Risk of Incident ESKD. J Am Soc Nephrol 2023; 34:122-131. [PMID: 36288905 PMCID: PMC10101586 DOI: 10.1681/asn.2022020216] [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: 11/14/2022] [Revised: 08/23/2022] [Accepted: 11/14/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Testican-2 was recently identified as a podocyte-derived protein that is released into circulation by the kidneys and is positively correlated with eGFR and eGFR slope. However, whether higher testican-2 levels are associated with lower risk of ESKD is unknown. METHODS Aptamer-based proteomics assessed blood testican-2 levels among participants in the African American Study of Kidney Disease and Hypertension (AASK, n =703), the Chronic Renal Insufficiency Cohort (CRIC) study ( n =3196), and the Atherosclerosis Risk in Communities (ARIC) study ( n =4378). We compared baseline characteristics by testican-2 tertile and used Cox proportional hazards models to study the association of testican-2 with incident ESKD. RESULTS Higher testican-2 levels were associated with higher measured GFR (mGFR) in AASK, higher eGFR in the CRIC and ARIC studies, and lower albuminuria in all cohorts. Baseline testican-2 levels were significantly associated with incident ESKD in Cox proportional hazards models adjusted for age, sex, and race (model 1) and model 1+mGFR or eGFR+comorbidities (model 2). In model 3 (model 2+proteinuria), the associations between testican-2 (per SD increase) and incident ESKD were AASK (hazard ratio [HR]=0.84 [0.72 to 0.98], P =0.023), CRIC (HR=0.95 [0.89 to 1.02], P =0.14), ARIC (HR=0.54 [0.36 to 0.83], P =0.0044), and meta-analysis (HR=0.92 [0.86 to 0.98], P =0.0073). CONCLUSIONS Across three cohorts spanning >8000 individuals, testican-2 is associated with kidney health and prognosis, with higher levels associated with reduced risk of ESKD.
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Affiliation(s)
- Donghai Wen
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Linda Zhou
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Zihe Zheng
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aditya Surapaneni
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christie M. Ballantyne
- Section of Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ron C. Hoogeveen
- Section of Cardiology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Michael G. Shlipak
- Kidney Health Research Collaborative, Department of Medicine, San Francisco Veterans Affairs Health Care System
- University of California, San Francisco, California
| | - Sushrut S. Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Sections of Preventive Medicine and Epidemiology and Cardiology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - Paul L. Kimmel
- Division of Kidney Urologic and Hematologic Diseases, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ruth F. Dubin
- Division of Nephrology, San Francisco VA Medical Center, University of California, San Francisco, California
| | - Rajat Deo
- Division of Cardiology, Electrophysiology Section, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold I. Feldman
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter Ganz
- Cardiovascular Division, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Morgan E. Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Eugene P. Rhee
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
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Haridevamuthu B, Guru A, Velayutham M, Snega Priya P, Arshad A, Arockiaraj J. Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost. REVIEWS IN AQUACULTURE 2023; 15:163-178. [DOI: 10.1111/raq.12709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 10/16/2023]
Abstract
AbstractThe global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.
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Affiliation(s)
- B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Ajay Guru
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Manikandan Velayutham
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - P. Snega Priya
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
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Suzuki T. Overview of single-cell RNA sequencing analysis and its application to spermatogenesis research. Reprod Med Biol 2023; 22:e12502. [PMID: 36726594 PMCID: PMC9884325 DOI: 10.1002/rmb2.12502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/18/2022] [Accepted: 01/10/2023] [Indexed: 01/30/2023] Open
Abstract
Background Single-cell transcriptomics allows parallel analysis of multiple cell types in tissues. Because testes comprise somatic cells and germ cells at various stages of spermatogenesis, single-cell RNA sequencing is a powerful tool for investigating the complex process of spermatogenesis. However, single-cell RNA sequencing analysis needs extensive knowledge of experimental technologies and bioinformatics, making it difficult for many, particularly experimental biologists and clinicians, to use it. Methods Aiming to make single-cell RNA sequencing analysis familiar, this review article presents an overview of experimental and computational methods for single-cell RNA sequencing analysis with a history of transcriptomics. In addition, combining the PubMed search and manual curation, this review also provides a summary of recent novel insights into human and mouse spermatogenesis obtained using single-cell RNA sequencing analyses. Main Findings Single-cell RNA sequencing identified mesenchymal cells and type II innate lymphoid cells as novel testicular cell types in the adult mouse testes, as well as detailed subtypes of germ cells. This review outlines recent discoveries into germ cell development and subtypes, somatic cell development, and cell-cell interactions. Conclusion The findings on spermatogenesis obtained using single-cell RNA sequencing may contribute to a deeper understanding of spermatogenesis and provide new directions for male fertility therapy.
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Affiliation(s)
- Takahiro Suzuki
- RIKEN Center for Integrated Medical Science (IMS)Yokohama CityKanagawaJapan
- Graduate School of Medical Life ScienceYokohama City UniversityYokohama CityKanagawaJapan
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Yang J, Liu M, Fang X, Zhang H, Ren Q, Zheng Y, Wang Y, Zhou Y. Advances in peptides encoded by non-coding RNAs: A cargo in exosome. Front Oncol 2022; 12:1081997. [PMID: 36620552 PMCID: PMC9822543 DOI: 10.3389/fonc.2022.1081997] [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: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.
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Affiliation(s)
- Jing Yang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengxiao Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xidong Fang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China,Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Qian Ren
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Ya Zheng
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuping Wang
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
| | - Yongning Zhou
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China,Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, China,*Correspondence: Yongning Zhou, ; Yuping Wang,
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Hao Y, Xie B, Fu X, Xu R, Yang Y. New Insights into lncRNAs in Aβ Cascade Hypothesis of Alzheimer's Disease. Biomolecules 2022; 12:biom12121802. [PMID: 36551230 PMCID: PMC9775548 DOI: 10.3390/biom12121802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Alzheimer's disease (AD) is the most common type of dementia, but its pathogenesis is not fully understood, and effective drugs to treat or reverse the progression of the disease are lacking. Long noncoding RNAs (lncRNAs) are abnormally expressed and deregulated in AD and are closely related to the occurrence and development of AD. In addition, the high tissue specificity and spatiotemporal specificity make lncRNAs particularly attractive as diagnostic biomarkers and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in AD is essential for developing new treatment strategies. In this review, we discuss the unique regulatory functions of lncRNAs in AD, ranging from Aβ production to clearance, with a focus on their interaction with critical molecules. Additionally, we highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets in AD and present future perspectives in clinical practice.
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Affiliation(s)
- Yitong Hao
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Bo Xie
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Xiaoshu Fu
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Rong Xu
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun 130021, China
| | - Yu Yang
- Department of Neurology and Neuroscience Center, The First Hospital of Jilin University, Changchun 130021, China
- Correspondence:
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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Guan X, Sun Y, Zhang C. LncRNAs in blood cells: Roles in cell development and potential pathogenesis in hematological malignancies. Crit Rev Oncol Hematol 2022; 180:103849. [DOI: 10.1016/j.critrevonc.2022.103849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 09/11/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
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