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Hu Z, Yang L, Zhang M, Tang H, Huang Y, Su Y, Ding Y, Li C, Wang M, Zhou Y, Zhang Q, Guo L, Wu Y, Wang Q, Liu N, Kang H, Wu Y, Yao D, Li Y, Ruan Z, Wang H, Bao F, Liu G, Wang J, Wang Y, Wang W, Lu G, Qin D, Pei D, Chan WY, Liu X. A novel protein CYTB-187AA encoded by the mitochondrial gene CYTB modulates mammalian early development. Cell Metab 2024; 36:1586-1597.e7. [PMID: 38703762 DOI: 10.1016/j.cmet.2024.04.012] [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: 02/28/2023] [Revised: 05/10/2023] [Accepted: 04/16/2024] [Indexed: 05/06/2024]
Abstract
The mitochondrial genome transcribes 13 mRNAs coding for well-known proteins essential for oxidative phosphorylation. We demonstrate here that cytochrome b (CYTB), the only mitochondrial-DNA-encoded transcript among complex III, also encodes an unrecognized 187-amino-acid-long protein, CYTB-187AA, using the standard genetic code of cytosolic ribosomes rather than the mitochondrial genetic code. After validating the existence of this mtDNA-encoded protein arising from cytosolic translation (mPACT) using mass spectrometry and antibodies, we show that CYTB-187AA is mainly localized in the mitochondrial matrix and promotes the pluripotent state in primed-to-naive transition by interacting with solute carrier family 25 member 3 (SLC25A3) to modulate ATP production. We further generated a transgenic knockin mouse model of CYTB-187AA silencing and found that reduction of CYTB-187AA impairs females' fertility by decreasing the number of ovarian follicles. For the first time, we uncovered the novel mPACT pattern of a mitochondrial mRNA and demonstrated the physiological function of this 14th protein encoded by mtDNA.
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Affiliation(s)
- Zhijuan Hu
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Liang Yang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Maolei Zhang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Haite Tang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yile Huang
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China
| | - Yujie Su
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yingzhe Ding
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China
| | - Chong Li
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Mengfei Wang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yunhao Zhou
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qing Zhang
- Proteomics and Metabolomics Core Facility, Guangzhou National Laboratory, Guangzhou, China
| | - Liman Guo
- Proteomics and Metabolomics Core Facility, Guangzhou National Laboratory, Guangzhou, China
| | - Yue Wu
- Proteomics and Metabolomics Core Facility, Guangzhou National Laboratory, Guangzhou, China
| | - Qianqian Wang
- State Key Laboratory of Medicinal Chemistry Biology, Nankai University, Tianjin, China
| | - Ning Liu
- State Key Laboratory of Medicinal Chemistry Biology, Nankai University, Tianjin, China
| | - Haoran Kang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yi Wu
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Deyang Yao
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yukun Li
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zifeng Ruan
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hao Wang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Feixiang Bao
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Guopan Liu
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China
| | - Junwei Wang
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yaofeng Wang
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China
| | - Wuming Wang
- CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, CUHK-Jinan University Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Gang Lu
- CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, CUHK-Jinan University Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Dajiang Qin
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China; Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Duanqing Pei
- Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China; Laboratory of Cell Fate Control, School of Life Sciences, Westlake University, Hangzhou, China
| | - Wai-Yee Chan
- CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, CUHK-Jinan University Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Xingguo Liu
- Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong, SAR, China; Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
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2
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Sridhara S. Multiple structural flavors of RNase P in precursor tRNA processing. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1835. [PMID: 38479802 DOI: 10.1002/wrna.1835] [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: 08/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 06/06/2024]
Abstract
The precursor transfer RNAs (pre-tRNAs) require extensive processing to generate mature tRNAs possessing proper fold, structural stability, and functionality required to sustain cellular viability. The road to tRNA maturation follows an ordered process: 5'-processing, 3'-processing, modifications at specific sites, if any, and 3'-CCA addition before aminoacylation and recruitment to the cellular protein synthesis machinery. Ribonuclease P (RNase P) is a universally conserved endonuclease in all domains of life, performing the hydrolysis of pre-tRNA sequences at the 5' end by the removal of phosphodiester linkages between nucleotides at position -1 and +1. Except for an archaeal species: Nanoarchaeum equitans where tRNAs are transcribed from leaderless-position +1, RNase P is indispensable for life and displays fundamental variations in terms of enzyme subunit composition, mechanism of substrate recognition and active site architecture, utilizing in all cases a two metal ion-mediated conserved catalytic reaction. While the canonical RNA-based ribonucleoprotein RNase P has been well-known to occur in bacteria, archaea, and eukaryotes, the occurrence of RNA-free protein-only RNase P in eukaryotes and RNA-free homologs of Aquifex RNase P in prokaryotes has been discovered more recently. This review aims to provide a comprehensive overview of structural diversity displayed by various RNA-based and RNA-free RNase P holoenzymes towards harnessing critical RNA-protein and protein-protein interactions in achieving conserved pre-tRNA processing functionality. Furthermore, alternate roles and functional interchangeability of RNase P are discussed in the context of its employability in several clinical and biotechnological applications. This article is categorized under: RNA Processing > tRNA Processing RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Sagar Sridhara
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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3
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Chen Y, Mateski J, Gerace L, Wheeler J, Burl J, Prakash B, Svedin C, Amrick R, Adams BD. Non-coding RNAs and neuroinflammation: implications for neurological disorders. Exp Biol Med (Maywood) 2024; 249:10120. [PMID: 38463392 PMCID: PMC10911137 DOI: 10.3389/ebm.2024.10120] [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: 09/04/2023] [Accepted: 02/15/2024] [Indexed: 03/12/2024] Open
Abstract
Neuroinflammation is considered a balanced inflammatory response important in the intrinsic repair process after injury or infection. Under chronic states of disease, injury, or infection, persistent neuroinflammation results in a heightened presence of cytokines, chemokines, and reactive oxygen species that result in tissue damage. In the CNS, the surrounding microglia normally contain macrophages and other innate immune cells that perform active immune surveillance. The resulting cytokines produced by these macrophages affect the growth, development, and responsiveness of the microglia present in both white and gray matter regions of the CNS. Controlling the levels of these cytokines ultimately improves neurocognitive function and results in the repair of lesions associated with neurologic disease. MicroRNAs (miRNAs) are master regulators of the genome and subsequently control the activity of inflammatory responses crucial in sustaining a robust and acute immunological response towards an acute infection while dampening pathways that result in heightened levels of cytokines and chemokines associated with chronic neuroinflammation. Numerous reports have directly implicated miRNAs in controlling the abundance and activity of interleukins, TGF-B, NF-kB, and toll-like receptor-signaling intrinsically linked with the development of neurological disorders such as Parkinson's, ALS, epilepsy, Alzheimer's, and neuromuscular degeneration. This review is focused on discussing the role miRNAs play in regulating or initiating these chronic neurological states, many of which maintain the level and/or activity of neuron-specific secondary messengers. Dysregulated miRNAs present in the microglia, astrocytes, oligodendrocytes, and epididymal cells, contribute to an overall glial-specific inflammatory niche that impacts the activity of neuronal conductivity, signaling action potentials, neurotransmitter robustness, neuron-neuron specific communication, and neuron-muscular connections. Understanding which miRNAs regulate microglial activation is a crucial step forward in developing non-coding RNA-based therapeutics to treat and potentially correct the behavioral and cognitive deficits typically found in patients suffering from chronic neuroinflammation.
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Affiliation(s)
- Yvonne Chen
- Department of Biology, Brandeis University, Waltham, MA, United States
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
| | - Julia Mateski
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Biological Sciences, Gustavus Adolphus College, St. Peter, MN, United States
| | - Linda Gerace
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Missouri State University, Springfield, MO, United States
| | - Jonathan Wheeler
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Electrical and Computer Engineering Tech, New York Institute of Tech, Old Westbury, NY, United States
| | - Jan Burl
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Southern New Hampshire University, Manchester, NH, United States
| | - Bhavna Prakash
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Medicine, Tufts Medical Center, Medford, MA, United States
| | - Cherie Svedin
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of Biology, Utah Tech University, St. George, UT, United States
| | - Rebecca Amrick
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
- Department of English, Villanova University, Villanova, PA, United States
| | - Brian D Adams
- Department of RNA Sciences, The Brain Institute of America, New Haven, CT, United States
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Luo L, An X, Xiao Y, Sun X, Li S, Wang Y, Sun W, Yu D. Mitochondrial-related microRNAs and their roles in cellular senescence. Front Physiol 2024; 14:1279548. [PMID: 38250662 PMCID: PMC10796628 DOI: 10.3389/fphys.2023.1279548] [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: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/23/2024] Open
Abstract
Aging is a natural aspect of mammalian life. Although cellular mortality is inevitable, various diseases can hasten the aging process, resulting in abnormal or premature senescence. As cells age, they experience distinctive morphological and biochemical shifts, compromising their functions. Research has illuminated that cellular senescence coincides with significant alterations in the microRNA (miRNA) expression profile. Notably, a subset of aging-associated miRNAs, originally encoded by nuclear DNA, relocate to mitochondria, manifesting a mitochondria-specific presence. Additionally, mitochondria themselves house miRNAs encoded by mitochondrial DNA (mtDNA). These mitochondria-residing miRNAs, collectively referred to as mitochondrial miRNAs (mitomiRs), have been shown to influence mtDNA transcription and protein synthesis, thereby impacting mitochondrial functionality and cellular behavior. Recent studies suggest that mitomiRs serve as critical sensors for cellular senescence, exerting control over mitochondrial homeostasis and influencing metabolic reprogramming, redox equilibrium, apoptosis, mitophagy, and calcium homeostasis-all processes intimately connected to senescence. This review synthesizes current findings on mitomiRs, their mitochondrial targets, and functions, while also exploring their involvement in cellular aging. Our goal is to shed light on the potential molecular mechanisms by which mitomiRs contribute to the aging process.
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Affiliation(s)
- Ling Luo
- Public Research Platform, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xingna An
- Public Research Platform, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yinghui Xiao
- Public Research Platform, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiguang Sun
- Department of Hand Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Sijie Li
- Department of Breast Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yingzhao Wang
- Department of Neurology, Qianwei Hospital of Jilin Province, Changchun, Jilin, China
| | - Weixia Sun
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Dehai Yu
- Public Research Platform, The First Hospital of Jilin University, Changchun, Jilin, China
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Zhang JH, Chen JH, Guo B, Fang Y, Xu ZY, Zhan L, Cao YX. Recent Insights into Noncoding RNAs in Primary Ovarian Insufficiency: Focus on Mechanisms and Treatments. J Clin Endocrinol Metab 2023; 108:1898-1908. [PMID: 36735959 DOI: 10.1210/clinem/dgad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/16/2022] [Accepted: 02/02/2023] [Indexed: 02/05/2023]
Abstract
CONTEXT Primary ovarian insufficiency (POI) is a heterogeneous disease with an unknown underlying trigger or root cause. Recently many studies evaluated noncoding RNAs (ncRNAs), especially microRNAs (miRNAs), long noncoding RNA (lncRNAs), circular RNAs (circRNAs), and small interfering RNAs (siRNAs) for their associations with POI. EVIDENCE ACQUISITION In this review, we outline the biogenesis of various ncRNAs relevant to POI and summarize the evidence for their roles in the regulation of disease occurrence and progression. Articles from 2003 to 2022 were selected for relevance, validity, and quality from results obtained in PubMed and Google Scholar using the following search terms: noncoding RNAs; primary ovarian insufficiency; premature ovarian failure; noncoding RNAs and primary ovarian insufficiency/premature ovarian failure; miRNAs and primary ovarian insufficiency/premature ovarian failure; lncRNAs and primary ovarian insufficiency/premature ovarian failure; siRNAs and primary ovarian insufficiency/premature ovarian failure; circRNAs and primary ovarian insufficiency/premature ovarian failure; pathophysiology; and potential treatment. All articles were independently screened for eligibility by the authors. EVIDENCE SYNTHESIS This review summarizes the biological functions and synthesis of miRNAs, lncRNAs, siRNAs, and circRNAs in POI and discusses the findings of clinical and in vitro and in vivo studies. Although there is variability in the findings of individual studies, overall the available literature justifies the conclusion that dysregulated ncRNAs play significant roles in POI. CONCLUSION The potential of ncRNAs in the treatment of POI requires further investigation, as ncRNAs derived from mesenchymal stem cell-secreted exosomes play pivotal roles and have considerable therapeutic potential in a multitude of diseases.
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Affiliation(s)
- Jun-Hui Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei 230032, Anhui, China
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei 230032, Anhui, China
- Anhui Provincial Engineering Research Center of Biopreservation and Artificial Organs, Hefei 230032, Anhui, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, Anhui, China
| | - Jia-Hua Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui, China
| | - Bao Guo
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui, China
| | - Yuan Fang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Zu-Ying Xu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei 230032, Anhui, China
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei 230032, Anhui, China
- Anhui Provincial Engineering Research Center of Biopreservation and Artificial Organs, Hefei 230032, Anhui, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, Anhui, China
| | - Lei Zhan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui, China
| | - Yun-Xia Cao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei 230032, Anhui, China
- Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei 230032, Anhui, China
- Anhui Provincial Engineering Research Center of Biopreservation and Artificial Organs, Hefei 230032, Anhui, China
- Anhui Provincial Institute of Translational Medicine, Hefei 230032, Anhui, China
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Different platforms for mitomiRs in mitochondria: Emerging facets in regulation of mitochondrial functions. Mitochondrion 2022; 66:67-73. [DOI: 10.1016/j.mito.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022]
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Bayazit MB, Jacovetti C, Cosentino C, Sobel J, Wu K, Brozzi F, Rodriguez-Trejo A, Stoll L, Guay C, Regazzi R. Small RNAs derived from tRNA fragmentation regulate the functional maturation of neonatal β cells. Cell Rep 2022; 40:111069. [PMID: 35830789 DOI: 10.1016/j.celrep.2022.111069] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/03/2022] [Accepted: 06/17/2022] [Indexed: 11/03/2022] Open
Abstract
tRNA-derived fragments (tRFs) are an emerging class of small non-coding RNAs with distinct cellular functions. Here, we studied the contribution of tRFs to the regulation of postnatal β cell maturation, a critical process that may lead to diabetes susceptibility in adulthood. We identified three tRFs abundant in neonatal rat islets originating from 5' halves (tiRNA-5s) of histidine and glutamate tRNAs. Their inhibition in these islets reduced β cell proliferation and insulin secretion. Mitochondrial respiration was also perturbed, fitting with the mitochondrial enrichment of nuclear-encoded tiRNA-5HisGTG and tiRNA-5GluCTC. Notably, tiRNA-5 inhibition reduced Mpc1, a mitochondrial pyruvate carrier whose knock down largely phenocopied tiRNA-5 inhibition. tiRNA-5HisGTG interactome revealed binding to Musashi-1, which was essential for the mitochondrial enrichment of tiRNA-5HisGTG. Finally, tiRNA-5s were dysregulated in the islets of diabetic and diabetes-prone animals. Altogether, tiRNA-5s represent a class of regulators of β cell maturation, and their deregulation in neonatal islets may lead to diabetes susceptibility in adulthood.
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Affiliation(s)
- Mustafa Bilal Bayazit
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Cécile Jacovetti
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Cristina Cosentino
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Jonathan Sobel
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Kejing Wu
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Flora Brozzi
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | | | - Lisa Stoll
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Switzerland; Department of Biomedical Sciences, University of Lausanne, 1005 Lausanne, Switzerland.
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8
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Yin T, Luo J, Huang D, Li H. Current Progress of Mitochondrial Genome Editing by CRISPR. Front Physiol 2022; 13:883459. [PMID: 35586709 PMCID: PMC9108280 DOI: 10.3389/fphys.2022.883459] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/18/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tao Yin
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Junjie Luo
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Danqiong Huang
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Hui Li
- Guangdong Engineering Research Center for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Longhua Innovation Institute for Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- *Correspondence: Hui Li,
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9
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Sang L, Yang L, Ge Q, Xie S, Zhou T, Lin A. Subcellular distribution, localization, and function of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1729. [PMID: 35413151 DOI: 10.1002/wrna.1729] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/06/2022]
Abstract
Eukaryotic cells contain subcellular organelles with spatiotemporal regulation to coordinate various biochemical reactions. The various organelles perform their essential biological functions by employing specific biomolecules, including nucleic acids. Recent studies have revealed that noncoding RNAs (ncRNAs) are highly compartmentalized in cells and that their spatial distribution is intimately related to their functions. Dysregulation of subcellular ncRNAs can disrupt cellular homeostasis and cause human diseases. Mitochondria are responsible for energy generation to fuel cell growth and proliferation. Therefore, identifying mitochondria-associated ncRNAs helps to reveal new regulatory mechanisms and physiological functions of mitochondria. In this review, we summarize the latest advances in subcellular ncRNAs derived from either the nuclear or mitochondrial genome. We also discuss available biological approaches for investigating organelle-specific ncRNAs. Exploring the distribution and function of subcellular ncRNAs may facilitate the understanding of endomembrane dynamics and provide potential strategies for clinical transformation. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Lingjie Sang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luojia Yang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiwei Ge
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Xie
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Aifu Lin
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China
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10
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Robson B. Computers and preventative diagnosis. A survey with bioinformatics examples of mitochondrial small open reading frame peptides as portents of a new generation of powerful biomarkers. Comput Biol Med 2022; 140:105116. [PMID: 34896883 DOI: 10.1016/j.compbiomed.2021.105116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 12/02/2021] [Indexed: 12/27/2022]
Abstract
The present brief survey is to alert developers in datamining, machine learning, inference methods, and other approaches in relation to diagnostic, predictive, and risk assessment medicine about a relatively new class of bioactive messaging peptides in which there is escalating interest. They provide patterns of communication and cross-chatter about states of health and disease within and, importantly, between cells (they also appear extracellularly in biological fluids). This chatter needs to be analyzed somewhat in the manner of the decryption of the Enigma code in the Second World War. It could lead not only to improved diagnosis but to predictive diagnosis, prediction of organ failure, and preventative medicine. This involves peptide products of short reading frames that have been previously somewhat neglected as unlikely gene products, with probably many examples in nuclear DNA, but certainly several known in the mitochondrial DNA. There is a great deal of knowledge now becoming available about the latter and itis believed thatthat the mRNA can be translated both by standard cytosolic and mitochondrial genetic codes, resulting in different peptides, adding a further level of complexity to the applications of bioinformatics and computational biology but a higher level of detail and sophistication to preventative diagnosis. The code to crack could be sophisticated and combinatorically complex to analyze by computers. Mitochondria may have combined with proto-eucaryotic cells some 2 billion years ago, only about a 7th of the age of the universe. Cells appeared some 2 billion years before that, also with possible signaling based on similar ideas. This makes life small in space but huge in time, refinement of which centrally involves these signaling processes.
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Affiliation(s)
- Barry Robson
- Ingine Inc. Viginia, USA and the Dirac Foundation OxfordShire UK.
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11
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Mohammad G, Kowluru RA. Nuclear Genome-Encoded Long Noncoding RNAs and Mitochondrial Damage in Diabetic Retinopathy. Cells 2021; 10:cells10123271. [PMID: 34943778 PMCID: PMC8699566 DOI: 10.3390/cells10123271] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/05/2021] [Accepted: 11/17/2021] [Indexed: 12/16/2022] Open
Abstract
Retinal mitochondria are damaged in diabetes-accelerating apoptosis of capillary cells, and ultimately, leading to degenerative capillaries. Diabetes also upregulates many long noncoding RNAs (LncRNAs), including LncMALAT1 and LncNEAT1. These RNAs have more than 200 nucleotides and no open reading frame for translation. LncMALAT1 and LncNEAT1 are encoded by nuclear genome, but nuclear-encoded LncRNAs can also translocate in the mitochondria. Our aim was to investigate the role of LncMALAT1 and LncNEAT1 in mitochondrial homeostasis. Using human retinal endothelial cells, the effect of high glucose on LncMALAT1 and LncNEAT1 mitochondrial localization was examined by RNA fluorescence in situ hybridization. The role of these LncRNAs in mitochondrial membrane potential (by JC-I staining), mtDNA integrity (by extended length PCR) and in protective mtDNA nucleoids (by SYBR green staining) was examined in MALAT1- or NEAT1-siRNA transfected cells. High glucose increased LncMALAT1 and LncNEAT1 mitochondrial expression, and MALAT1-siRNA or NEAT1-siRNA ameliorated glucose-induced damage to mitochondrial membrane potential and mtDNA, and prevented decrease in mtDNA nucleoids. Thus, increased mitochondrial translocation of LncMALAT1 or LncNEAT1 in a hyperglycemic milieu plays a major role in damaging the mitochondrial structural and genomic integrity. Regulation of these LncRNAs can protect mitochondrial homeostasis, and ameliorate formation of degenerative capillaries in diabetic retinopathy.
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Affiliation(s)
- Ghulam Mohammad
- Department of Ophthalmology, Visual & Anatomical Sciences, Wayne State University, Detroit, MI 48201, USA;
| | - Renu A. Kowluru
- Kresge Eye Institute, 4717 St. Antoine, Detroit, MI 48201, USA
- Correspondence: ; Tel.: +1-313-993-6714
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12
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Mitochondrial DNA and MitomiR Variations in Pancreatic Cancer: Potential Diagnostic and Prognostic Biomarkers. Int J Mol Sci 2021; 22:ijms22189692. [PMID: 34575852 PMCID: PMC8470532 DOI: 10.3390/ijms22189692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 02/07/2023] Open
Abstract
Pancreatic cancer is an aggressive disease with poor prognosis. Only about 15-20% of patients diagnosed with pancreatic cancer can undergo surgical resection, while the remaining 80% are diagnosed with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC). In these cases, chemotherapy and radiotherapy only confer marginal survival benefit. Recent progress has been made in understanding the pathobiology of pancreatic cancer, with a particular effort in discovering new diagnostic and prognostic biomarkers, novel therapeutic targets, and biomarkers that can predict response to chemo- and/or radiotherapy. Mitochondria have become a focus in pancreatic cancer research due to their roles as powerhouses of the cell, important subcellular biosynthetic factories, and crucial determinants of cell survival and response to chemotherapy. Changes in the mitochondrial genome (mtDNA) have been implicated in chemoresistance and metastatic progression in some cancer types. There is also growing evidence that changes in microRNAs that regulate the expression of mtDNA-encoded mitochondrial proteins (mitomiRs) or nuclear-encoded mitochondrial proteins (mitochondria-related miRs) could serve as diagnostic and prognostic cancer biomarkers. This review discusses the current knowledge on the clinical significance of changes of mtDNA, mitomiRs, and mitochondria-related miRs in pancreatic cancer and their potential role as predictors of cancer risk, as diagnostic and prognostic biomarkers, and as molecular targets for personalized cancer therapy.
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13
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Huang J, Wu S, Wang P, Wang G. Non-coding RNA Regulated Cross-Talk Between Mitochondria and Other Cellular Compartments. Front Cell Dev Biol 2021; 9:688523. [PMID: 34414182 PMCID: PMC8369480 DOI: 10.3389/fcell.2021.688523] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mitochondria are the main hubs for cellular energy production. Metabolites produced in mitochondria not only feed many important biosynthesis pathways but also function as signaling molecules. Mitochondrial biosynthesis requires collaboration of both nuclear and mitochondrial gene expression systems. In addition, mitochondria have to quickly respond to changes inside and outside the cells and have their own functional states reported to the nucleus and other cellular compartments. The underlying molecular mechanisms of these complex regulations have not been well understood. Recent evidence indicates that in addition to small molecules, non-coding RNAs may contribute to the communication between mitochondria and other cellular compartments and may even serve as signals. In this review, we summarize the current knowledge about mitochondrial non-coding RNAs (including nucleus-encoded non-coding RNAs that are imported into mitochondria and mitochondrion-encoded non-coding RNAs that are exported), their trafficking and their functions in co-regulation of mitochondrial and other cellular processes.
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Affiliation(s)
- Jinliang Huang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Sipeng Wu
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Pengcheng Wang
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
| | - Geng Wang
- State Key laboratory for Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, China
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14
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Grammatikakis I, Lal A. Significance of lncRNA abundance to function. Mamm Genome 2021; 33:271-280. [PMID: 34406447 DOI: 10.1007/s00335-021-09901-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as regulators of diverse cellular processes. Although the vast majority of lncRNAs are expressed at lower levels compared to messenger RNAs (mRNAs), many lncRNAs play a central role in the regulation of cellular homeostasis and gene expression. With the advancement of next generation sequencing technologies, recent studies illustrate the diversity of lncRNA function. This diversity can be due to differences in their mechanisms of action, spatio-temporal expression, and/or abundance, all of which can vary depending on the particular cell type or tissue. Here, we discuss how the abundance of lncRNAs is an important feature that is often linked to their functions, and why it is crucial to quantitate lncRNA abundance, its local concentration within a cell or a tissue or the dynamic changes in expression levels during cell cycle progression or upon environmental stimuli, to shed light on their physiological roles.
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Affiliation(s)
- Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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15
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Liu X, Shan G. Mitochondria Encoded Non-coding RNAs in Cell Physiology. Front Cell Dev Biol 2021; 9:713729. [PMID: 34395442 PMCID: PMC8362354 DOI: 10.3389/fcell.2021.713729] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/12/2021] [Indexed: 01/05/2023] Open
Abstract
Mitochondria are the powerhouses of mammalian cells, which participate in series of metabolic processes and cellular events. Mitochondria have their own genomes, and it is generally acknowledged that human mitochondrial genome encodes 13 proteins, 2 rRNAs and 22 tRNAs. However, the complexity of mitochondria derived transcripts is just starting to be envisaged. Currently, there are at least 8 lncRNAs, some dsRNAs, various small RNAs, and hundreds of circRNAs known to be generated from mitochondrial genome. These non-coding RNAs either translocate into cytosol/nucleus or reside in mitochondria to play various biological functions. Here we present an overview of regulatory non-coding RNAs encoded by the mammalian mitochondria genome. For overall understandings of non-coding RNAs in mitochondrial function, a brief summarization of nuclear-encoded non-coding RNAs in mitochondria is also included. We discuss about roles of these non-coding RNAs in cellular physiology and the communication between mitochondria and the nucleus.
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Affiliation(s)
- Xu Liu
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Science and Medicine, Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
| | - Ge Shan
- Hefei National Laboratory for Physical Sciences at Microscale, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Science and Medicine, Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
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16
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Tarasenko TA, Klimenko ES, Tarasenko VI, Koulintchenko MV, Dietrich A, Weber-Lotfi F, Konstantinov YM. Plant mitochondria import DNA via alternative membrane complexes involving various VDAC isoforms. Mitochondrion 2021; 60:43-58. [PMID: 34303006 DOI: 10.1016/j.mito.2021.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/17/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022]
Abstract
Mitochondria possess transport mechanisms for import of RNA and DNA. Based on import into isolated Solanum tuberosum mitochondria in the presence of competitors, inhibitors or effectors, we show that DNA fragments of different size classes are taken up into plant organelles through distinct channels. Alternative channels can also be activated according to the amount of DNA substrate of a given size class. Analyses of Arabidopsis thaliana knockout lines pointed out a differential involvement of individual voltage-dependent anion channel (VDAC) isoforms in the formation of alternative channels. We propose several outer and inner membrane proteins as VDAC partners in these pathways.
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Affiliation(s)
- Tatiana A Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Ekaterina S Klimenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Vladislav I Tarasenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia
| | - Milana V Koulintchenko
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia.
| | - André Dietrich
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Frédérique Weber-Lotfi
- Institut de Biologie Moléculaire des Plantes, CNRS and Université de Strasbourg, 12 Rue du Général Zimmer, 67084 Strasbourg, France
| | - Yuri M Konstantinov
- Siberian Institute of Plant Physiology and Biochemistry, SB RAS, 132 Lermontov St, Irkutsk 664033, Russia; Irkutsk State University, 1 Karl Marx St, Irkutsk 664003, Russia
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17
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The Diversity of the Mitochondrial Outer Membrane Protein Import Channels: Emerging Targets for Modulation. Molecules 2021; 26:molecules26134087. [PMID: 34279427 PMCID: PMC8272145 DOI: 10.3390/molecules26134087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 12/21/2022] Open
Abstract
The functioning of mitochondria and their biogenesis are largely based on the proper function of the mitochondrial outer membrane channels, which selectively recognise and import proteins but also transport a wide range of other molecules, including metabolites, inorganic ions and nucleic acids. To date, nine channels have been identified in the mitochondrial outer membrane of which at least half represent the mitochondrial protein import apparatus. When compared to the mitochondrial inner membrane, the presented channels are mostly constitutively open and consequently may participate in transport of different molecules and contribute to relevant changes in the outer membrane permeability based on the channel conductance. In this review, we focus on the channel structure, properties and transported molecules as well as aspects important to their modulation. This information could be used for future studies of the cellular processes mediated by these channels, mitochondrial functioning and therapies for mitochondria-linked diseases.
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18
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Deciphering the Long Non-Coding RNAs and MicroRNAs Coregulation Networks in Ovarian Cancer Development: An Overview. Cells 2021; 10:cells10061407. [PMID: 34204094 PMCID: PMC8227049 DOI: 10.3390/cells10061407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 01/17/2023] Open
Abstract
Non-coding RNAs are emergent elements from the genome, which do not encode for proteins but have relevant cellular functions impacting almost all the physiological processes occurring in eukaryotic cells. In particular, microRNAs and long non-coding RNAs (lncRNAs) are a new class of small RNAs transcribed from the genome, which modulate the expression of specific genes at transcriptional and posttranscriptional levels, thus adding a new regulatory layer in the flux of genetic information. In cancer cells, the miRNAs and lncRNAs interactions with its target genes and functional pathways are deregulated as a consequence of epigenetic and genetic alterations occurring during tumorigenesis. In this review, we summarize the actual knowledge on the interplay of lncRNAs with its cognate miRNAs and mRNAs pairs, which interact in coregulatory networks with a particular emphasis on the mechanisms underlying its oncogenic behavior in ovarian cancer. Specifically, we reviewed here the evidences unraveling the relevant roles of lncRNAs/miRNAs pairs in altered regulation of cell migration, angiogenesis, therapy resistance, and Warburg effect. Finally, we also discussed its potential clinical implications in ovarian cancer and related endocrine disease therapies.
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19
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Meseguer S. MicroRNAs and tRNA-Derived Small Fragments: Key Messengers in Nuclear-Mitochondrial Communication. Front Mol Biosci 2021; 8:643575. [PMID: 34026824 PMCID: PMC8138316 DOI: 10.3389/fmolb.2021.643575] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/08/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondria are not only important as energy suppliers in cells but also participate in other biological processes essential for cell growth and survival. They arose from α-proteobacterial predecessors through endosymbiosis and evolved transferring a large part of their genome to the host cell nucleus. Such a symbiotic relationship has been reinforced over time through increasingly complex signaling mechanisms between the host cell and mitochondria. So far, we do not have a complete view of the mechanisms that allow the mitochondria to communicate their functional status to the nucleus and trigger adaptive and compensatory responses. Recent findings place two classes of small non-coding RNAs (sncRNAs), microRNAs (miRNAs), and tRNA-derived small fragments, in such a scenario, acting as key pieces in the mitochondria-nucleus cross-talk. This review highlights the emerging roles and the interrelation of these sncRNAs in different signaling pathways between mitochondria and the host cell. Moreover, we describe in what way alterations of these complex regulatory mechanisms involving sncRNAs lead to diseases associated with mitochondrial dysfunction. In turn, these discoveries provide novel prognostic biomarker candidates and/or potential therapeutic targets.
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Affiliation(s)
- Salvador Meseguer
- Molecular and Cellular Immunology Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
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20
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Zhao Y, Zhou L, Li H, Sun T, Wen X, Li X, Meng Y, Li Y, Liu M, Liu S, Kim SJ, Xiao J, Li L, Zhang S, Li W, Cohen P, Hoffman AR, Hu JF, Cui J. Nuclear-Encoded lncRNA MALAT1 Epigenetically Controls Metabolic Reprogramming in HCC Cells through the Mitophagy Pathway. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:264-276. [PMID: 33425485 PMCID: PMC7773746 DOI: 10.1016/j.omtn.2020.09.040] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial dysfunction is a metabolic hallmark of cancer cells. In search of molecular factors involved in this dysregulation in hepatocellular carcinoma (HCC), we found that the nuclear-encoded long noncoding RNA (lncRNA) MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) was aberrantly enriched in the mitochondria of hepatoma cells. Using RNA reverse transcription-associated trap sequencing (RAT-seq), we showed that MALAT1 interacted with multiple loci on mitochondrial DNA (mtDNA), including D-loop, COX2, ND3, and CYTB genes. MALAT1 knockdown induced alterations in the CpG methylation of mtDNA and in mitochondrial transcriptomes. This was associated with multiple abnormalities in mitochondrial function, including altered mitochondrial structure, low oxidative phosphorylation (OXPHOS), decreased ATP production, reduced mitophagy, decreased mtDNA copy number, and activation of mitochondrial apoptosis. These alterations in mitochondrial metabolism were associated with changes in tumor phenotype and in pathways involved in cell mitophagy, mitochondrial apoptosis, and epigenetic regulation. We further showed that the RNA-shuttling protein HuR and the mitochondria transmembrane protein MTCH2 mediated the transport of MALAT1 in this nuclear-mitochondrial crosstalk. This study provides the first evidence that the nuclear genome-encoded lncRNA MALAT1 functions as a critical epigenetic player in the regulation of mitochondrial metabolism of hepatoma cells, laying the foundation for further clarifying the roles of lncRNAs in tumor metabolic reprogramming.
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Affiliation(s)
- Yijing Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Tingge Sun
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xueli Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Ying Meng
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Mengmeng Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jialin Xiao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Lingyu Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew R. Hoffman
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
- Department of Medicine, PAVIR, Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin University, Changchun, Jilin 130021, China
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21
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Guo QQ, Gao J, Wang XW, Yin XL, Zhang SC, Li X, Chi LL, Zhou XM, Wang Z, Zhang QY. RNA-Binding Protein MSI2 Binds to miR-301a-3p and Facilitates Its Distribution in Mitochondria of Endothelial Cells. Front Mol Biosci 2021; 7:609828. [PMID: 33553241 PMCID: PMC7859344 DOI: 10.3389/fmolb.2020.609828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/11/2020] [Indexed: 01/17/2023] Open
Abstract
Numerous miRNAs have been detected in mitochondria, which play important roles in many physiological and pathophysiological processes. However, the dynamic changes of miRNA distribution in mitochondria and their mechanisms in reactive oxygen species (ROS)-induced endothelial injury remain unclear. Therefore, miRNA levels in whole cells and mitochondria of H2O2-treated endothelial cells were analyzed by small RNA sequencing in the present study. The results showed that H2O2 significantly reduced the relative mitochondrial distribution of dozens of miRNAs in human umbilical vein endothelial cells (HUVECs). Among the high-abundance miRNAs, miR-301a-3p has the most significant changes in the redistribution between cytosol and mitochondria confirmed by absolute quantitative polymerase chain reaction (qPCR). To unravel the mechanism of miR-301a-3p distribution in mitochondria, RNA pull-down followed by label-free quantitative proteomic analysis was performed, and RNA-binding protein Musashi RNA binding protein 2 (MSI2) was found to specifically bind to miR-301a-3p. Western blotting and immunofluorescence colocalization assay showed that MSI2 was located in mitochondria of various cell types. H2O2 significantly downregulated MSI2 expression in whole endothelial cells, promoted the distribution of MSI2 in cytosol and decreased its distribution in the mitochondria. Moreover, overexpression of MSI2 increased the mitochondrial distribution of miR-301a-3p, whereas inhibition of MSI2 decreased its distribution in mitochondria. Thus, MSI2 might be responsible for the distribution of miR-301a-3p between cytosol and mitochondria in endothelial cells. Our findings revealed for the first time that MSI2 was involved in the regulation of miRNA distribution in mitochondria and provided valuable insight into the mechanism of mitochondrial distribution of miRNAs.
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Affiliation(s)
- Qian Qian Guo
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese National Health Commission, Shandong University, Jinan, China.,Department of Cardiology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jing Gao
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese National Health Commission, Shandong University, Jinan, China.,Department of Cardiology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Jinan, China
| | - Xiao Wei Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese National Health Commission, Shandong University, Jinan, China.,Department of Cardiology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Jinan, China
| | - Xian Lun Yin
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese National Health Commission, Shandong University, Jinan, China.,Department of Cardiology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Jinan, China
| | - Shu Cui Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese National Health Commission, Shandong University, Jinan, China.,Department of Cardiology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Jinan, China
| | - Xue Li
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Lian Li Chi
- National Glycoengineering Research Center, Shandong University, Qingdao, China
| | - Xiao Ming Zhou
- Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan, China.,Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan, China
| | - Zhe Wang
- Division of Endocrinology and Metabolism, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China.,Division of Geriatrics, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Qun Ye Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese National Health Commission, Shandong University, Jinan, China.,Department of Cardiology, Cheeloo College of Medicine, Qilu Hospital, Shandong University, Jinan, China.,The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Jinan, China.,Cardiovascular Disease Research Center of Shandong First Medical University, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
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22
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Wang B, Lv X, Wang Y, Wang Z, Liu Q, Lu B, Liu Y, Gu F. CRISPR/Cas9-mediated mutagenesis at microhomologous regions of human mitochondrial genome. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1463-1472. [PMID: 33420919 DOI: 10.1007/s11427-020-1819-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022]
Abstract
Genetic manipulation of mitochondrial DNA (mtDNA) could be harnessed for deciphering the gene function of mitochondria; it also acts as a promising approach for the therapeutic correction of pathogenic mutation in mtDNA. However, there is still a lack of direct evidence showing the edited mutagenesis within human mtDNA by clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9). Here, using engineered CRISPR/Cas9, we observed numerous insertion/deletion (InDel) events at several mtDNA microhomologous regions, which were triggered specifically by double-strand break (DSB) lesions within mtDNA. InDel mutagenesis was significantly improved by sgRNA multiplexing and a DSB repair inhibitor, iniparib, demonstrating the evidence of rewiring DSB repair status to manipulate mtDNA using CRISPR/Cas9. These findings would provide novel insights into mtDNA mutagenesis and mitochondrial gene therapy for diseases involving pathogenic mtDNA.
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Affiliation(s)
- Bang Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiujuan Lv
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yufei Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhibo Wang
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qi Liu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200092, China
| | - Bin Lu
- Attardi Institute of Mitochondrial Biomedicine, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yong Liu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China
| | - Feng Gu
- School of Ophthalmology and Optometry, Eye Hospital, State Key Laboratory of Ophthalmology, Optometry and Vision Science, Ministry of Health and Zhejiang Provincial Key Laboratory of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325027, China.
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23
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Chopra N, Wang R, Maloney B, Nho K, Beck JS, Pourshafie N, Niculescu A, Saykin AJ, Rinaldi C, Counts SE, Lahiri DK. MicroRNA-298 reduces levels of human amyloid-β precursor protein (APP), β-site APP-converting enzyme 1 (BACE1) and specific tau protein moieties. Mol Psychiatry 2021; 26:5636-5657. [PMID: 31942037 PMCID: PMC8758483 DOI: 10.1038/s41380-019-0610-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/09/2019] [Accepted: 11/13/2019] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is the most common age-related form of dementia, associated with deposition of intracellular neuronal tangles consisting primarily of hyperphosphorylated microtubule-associated protein tau (p-tau) and extracellular plaques primarily comprising amyloid- β (Aβ) peptide. The p-tau tangle unit is a posttranslational modification of normal tau protein. Aβ is a neurotoxic peptide excised from the amyloid-β precursor protein (APP) by β-site APP-cleaving enzyme 1 (BACE1) and the γ-secretase complex. MicroRNAs (miRNAs) are short, single-stranded RNAs that modulate protein expression as part of the RNA-induced silencing complex (RISC). We identified miR-298 as a repressor of APP, BACE1, and the two primary forms of Aβ (Aβ40 and Aβ42) in a primary human cell culture model. Further, we discovered a novel effect of miR-298 on posttranslational levels of two specific tau moieties. Notably, miR-298 significantly reduced levels of ~55 and 50 kDa forms of the tau protein without significant alterations of total tau or other forms. In vivo overexpression of human miR-298 resulted in nonsignificant reduction of APP, BACE1, and tau in mice. Moreover, we identified two miR-298 SNPs associated with higher cerebrospinal fluid (CSF) p-tau and lower CSF Aβ42 levels in a cohort of human AD patients. Finally, levels of miR-298 varied in postmortem human temporal lobe between AD patients and age-matched non-AD controls. Our results suggest that miR-298 may be a suitable target for AD therapy.
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Affiliation(s)
- Nipun Chopra
- grid.257413.60000 0001 2287 3919Laboratory of Molecular Neurogenetics, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA
| | - Ruizhi Wang
- grid.257413.60000 0001 2287 3919Laboratory of Molecular Neurogenetics, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA
| | - Bryan Maloney
- grid.257413.60000 0001 2287 3919Laboratory of Molecular Neurogenetics, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Indiana Alzheimers Disease Center, Indiana University School of Medicine, Indianapolis, IN USA
| | - Kwangsik Nho
- grid.257413.60000 0001 2287 3919Indiana Alzheimers Disease Center, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Departments of Radiology & Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA
| | - John S. Beck
- grid.17088.360000 0001 2150 1785Departments of Translational Neuroscience and Family Medicine, Michigan State University, Grand Rapids, MI USA
| | - Naemeh Pourshafie
- grid.94365.3d0000 0001 2297 5165Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD USA
| | - Alexander Niculescu
- grid.257413.60000 0001 2287 3919Laboratory of Molecular Neurogenetics, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA
| | - Andrew J. Saykin
- grid.257413.60000 0001 2287 3919Indiana Alzheimers Disease Center, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Departments of Radiology & Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN USA
| | - Carlo Rinaldi
- grid.4991.50000 0004 1936 8948Department of Paediatrics, University of Oxford, South Parks Road, Oxford, OX1 3QX UK
| | - Scott E. Counts
- grid.17088.360000 0001 2150 1785Departments of Translational Neuroscience and Family Medicine, Michigan State University, Grand Rapids, MI USA
| | - Debomoy K. Lahiri
- grid.257413.60000 0001 2287 3919Laboratory of Molecular Neurogenetics, Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Indiana Alzheimers Disease Center, Indiana University School of Medicine, Indianapolis, IN USA ,grid.257413.60000 0001 2287 3919Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN USA
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24
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Govers LP, Toka HR, Hariri A, Walsh SB, Bockenhauer D. Mitochondrial DNA mutations in renal disease: an overview. Pediatr Nephrol 2021; 36:9-17. [PMID: 31925537 PMCID: PMC7701126 DOI: 10.1007/s00467-019-04404-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/12/2019] [Accepted: 10/16/2019] [Indexed: 12/28/2022]
Abstract
Kidneys have a high energy demand to facilitate the reabsorption of the glomerular filtrate. For this reason, renal cells have a high density of mitochondria. Mitochondrial cytopathies can be the result of a mutation in both mitochondrial and nuclear DNA. Mitochondrial dysfunction can lead to a variety of renal manifestations. Examples of tubular manifestations are renal Fanconi Syndrome, which is often found in patients diagnosed with Kearns-Sayre and Pearson's marrow-pancreas syndrome, and distal tubulopathies, which result in electrolyte disturbances such as hypomagnesemia. Nephrotic syndrome can be a glomerular manifestation of mitochondrial dysfunction and is typically associated with focal segmental glomerular sclerosis on histology. Tubulointerstitial nephritis can also be seen in mitochondrial cytopathies and may lead to end-stage renal disease. The underlying mechanisms of these cytopathies remain incompletely understood; therefore, current therapies focus mainly on symptom relief. A better understanding of the molecular disease mechanisms is critical in order to improve treatments.
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Affiliation(s)
- Larissa P Govers
- Department of Renal Medicine, University College London, London, UK
| | - Hakan R Toka
- Manatee Kidney Diseases Consultants, Bradenton, USA
| | - Ali Hariri
- Clinical Development, Sanofi Rare Disease, Boston, USA
| | - Stephen B Walsh
- Department of Renal Medicine, University College London, London, UK
| | - Detlef Bockenhauer
- Department of Renal Medicine, University College London, London, UK.
- Renal Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London, UK.
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25
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Li N, Zhan X. MASS SPECTROMETRY-BASED MITOCHONDRIAL PROTEOMICS IN HUMAN OVARIAN CANCERS. MASS SPECTROMETRY REVIEWS 2020; 39:471-498. [PMID: 32020673 DOI: 10.1002/mas.21618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
The prominent characteristics of mitochondria are highly dynamic and regulatory, which have crucial roles in cell metabolism, biosynthetic, senescence, apoptosis, and signaling pathways. Mitochondrial dysfunction might lead to multiple serious diseases, including cancer. Therefore, identification of mitochondrial proteins in cancer could provide a global view of tumorigenesis and progression. Mass spectrometry-based quantitative mitochondrial proteomics fulfils this task by enabling systems-wide, accurate, and quantitative analysis of mitochondrial protein abundance, and mitochondrial protein posttranslational modifications (PTMs). Multiple quantitative proteomics techniques, including isotope-coded affinity tag, stable isotope labeling with amino acids in cell culture, isobaric tags for relative and absolute quantification, tandem mass tags, and label-free quantification, in combination with different PTM-peptide enrichment methods such as TiO2 enrichment of tryptic phosphopeptides and antibody enrichment of other PTM-peptides, increase flexibility for researchers to study mitochondrial proteomes. This article reviews isolation and purification of mitochondria, quantitative mitochondrial proteomics, quantitative mitochondrial phosphoproteomics, mitochondrial protein-involved signaling pathway networks, mitochondrial phosphoprotein-involved signaling pathway networks, integration of mitochondrial proteomic and phosphoproteomic data with whole tissue proteomic and transcriptomic data and clinical information in ovarian cancers (OC) to in-depth understand its molecular mechanisms, and discover effective mitochondrial biomarkers and therapeutic targets for predictive, preventive, and personalized treatment of OC. This proof-of-principle model about OC mitochondrial proteomics is easily implementable to other cancer types. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Na Li
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
| | - Xianquan Zhan
- University Creative Research Initiatives Center, Shandong First Medical University, Shandong, 250062, P. R. China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- Department of Oncology, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 88 Xiangya Road, Changsha, Hunan, 410008, P. R. China
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26
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Ortega MA, Fraile-Martínez O, Guijarro LG, Casanova C, Coca S, Álvarez-Mon M, Buján J, García-Honduvilla N, Asúnsolo Á. The Regulatory Role of Mitochondrial MicroRNAs (MitomiRs) in Breast Cancer: Translational Implications Present and Future. Cancers (Basel) 2020; 12:cancers12092443. [PMID: 32872155 PMCID: PMC7564393 DOI: 10.3390/cancers12092443] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Mitochondrial microRNAs (mitomiRs) are an emerging field of study in a wide range of tumours including breast cancer. By targeting mitochondrial, or non-mitochondrial products, mitomiRs are able to regulate the functions of this organelle, thus controlling multiple carcinogenic processes. The knowledge of this system may provide a novel approach for targeted therapies, as potential biomarkers or helping in the diagnosis of such a complex malignancy. Abstract Breast cancer is the most prevalent and incident female neoplasm worldwide. Although survival rates have considerably improved, it is still the leading cause of cancer-related mortality in women. MicroRNAs are small non-coding RNA molecules that regulate the posttranscriptional expression of a wide variety of genes. Although it is usually located in the cytoplasm, several studies have detected a regulatory role of microRNAs in other cell compartments such as the nucleus or mitochondrion, known as “mitomiRs”. MitomiRs are essential modulators of mitochondrion tasks and their abnormal expression has been linked to the aetiology of several human diseases related to mitochondrial dysfunction, including breast cancer. This review aims to examine basic knowledge of the role of mitomiRs in breast cancer and discusses their prospects as biomarkers or therapeutic targets.
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Affiliation(s)
- Miguel A. Ortega
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Cancer Registry and Pathology Department, Hospital Universitario Principe de Asturias, 28806 Alcalá de Henares, Madrid, Spain
- Correspondence: ; Tel.: +34-91-885-4540; Fax: +34-91-885-4885
| | - Oscar Fraile-Martínez
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
| | - Luis G. Guijarro
- Department of System Biology, Unit of Biochemistry and Molecular Biology (CIBEREHD), University of Alcalá, 28801 Alcalá de Henares, Spain;
| | - Carlos Casanova
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
| | - Santiago Coca
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Melchor Álvarez-Mon
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Immune System Diseases-Rheumatology, Oncology Service an Internal Medicine, University Hospital Príncipe de Asturias, (CIBEREHD), 28806 Alcalá de Henares, Madrid, Spain
| | - Julia Buján
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Natalio García-Honduvilla
- Department of Medicine and Medical Specialities, Unit of Histology and Pathology, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcalá de Henares, Spain; (O.F.-M.); (C.C.); (S.C.); (M.Á.-M.); (J.B.); (N.G.-H.)
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
| | - Ángel Asúnsolo
- Ramón y Cajal Institute of Sanitary Research (IRYCIS), 28034 Madrid, Spain;
- Department of Surgery, Medical and Social Sciences, Faculty of Medicine and Health Sciences, University of Alcalá, 28801 Alcala de Henares, Madrid, Spain
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27
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Barozai MYK, Chaudhuri M. Role of the translocase of the mitochondrial inner membrane in the import of tRNAs into mitochondria in Trypanosoma brucei. Gene 2020; 748:144705. [PMID: 32339625 PMCID: PMC7304388 DOI: 10.1016/j.gene.2020.144705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 04/07/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023]
Abstract
Trypanosomatids are unicellular parasitic protozoa. Many of the species of this genera cause severe diseases in human, such as Leishmaniasis, African trypanosomiasis and Chagas disease. These parasites possess a single reticular mitochondrion with a concatenated structure of mitochondrial DNA known as kinetoplast or kDNA. kDNA encodes few essential mitochondrial proteins but no tRNAs. Therefore, trypanosomatid mitochondrion import a full set of nucleus-encoded tRNAs for mitochondrial translation. Recent advances indicated that mitochondrial protein translocases, particularly the subunits of the ATOM complex, are involved in the import of a tRNA in Trypanosoma brucei. However, the global picture and the role of the translocase components of the mitochondrial inner membrane (TbTims) are not well understood. Here we investigated the relative abundance of 16 different tRNAs in the cytosolic and mitochondrial fractions isolated from the six TbTims knockdown cell lines. We found that knockdown of TbTim17, one of the primary components of the TbTIM complex, reduced the abundance of all of these tRNAs into mitochondria and increased their abundance in the cytosol. Depletion of TbTim62, a TbTim17 associated proteins, also reduced the relative abundance of most of these tRNAs into mitochondria except for tRNAleu, tRNAmet, and tRNAglu. Whereas, knockdown of other TbTims, like TbTim50 and two small TbTims, TbTim10 and TbTim8/13, didn't have any effect on tRNA abundance either in the cytosol or mitochondria. Depletion of any of these TbTims showed minimal effect on the levels of total tRNAs in T. brucei. Absolute quantification of tRNA levels revealed that TbTim17 knockdown reduced the levels of different tRNAs in mitochondria from 3-6% to 0.8-1.4%, which is equivalent to ~70% reduction in average. Whereas, TbTim62 depletion showed somewhat selective effect. Overall, our results suggest that TbTim17 and TbTim62 are essential for tRNA import that further makes a connection between the tRNA and protein import into mitochondria in T. brucei.
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Affiliation(s)
- Muhammad Younas Khan Barozai
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, United States
| | - Minu Chaudhuri
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN 37208, United States.
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28
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Manevski M, Muthumalage T, Devadoss D, Sundar IK, Wang Q, Singh KP, Unwalla HJ, Chand HS, Rahman I. Cellular stress responses and dysfunctional Mitochondrial-cellular senescence, and therapeutics in chronic respiratory diseases. Redox Biol 2020; 33:101443. [PMID: 32037306 PMCID: PMC7251248 DOI: 10.1016/j.redox.2020.101443] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 01/14/2020] [Accepted: 01/22/2020] [Indexed: 02/06/2023] Open
Abstract
The abnormal inflammatory responses due to the lung tissue damage and ineffective repair/resolution in response to the inhaled toxicants result in the pathological changes associated with chronic respiratory diseases. Investigation of such pathophysiological mechanisms provides the opportunity to develop the molecular phenotype-specific diagnostic assays and could help in designing the personalized medicine-based therapeutic approaches against these prevalent diseases. As the central hubs of cell metabolism and energetics, mitochondria integrate cellular responses and interorganellar signaling pathways to maintain cellular and extracellular redox status and the cellular senescence that dictate the lung tissue responses. Specifically, as observed in chronic obstructive pulmonary disease (COPD) and pulmonary fibrosis, the mitochondria-endoplasmic reticulum (ER) crosstalk is disrupted by the inhaled toxicants such as the combustible and emerging electronic nicotine-delivery system (ENDS) tobacco products. Thus, the recent research efforts have focused on understanding how the mitochondria-ER dysfunctions and oxidative stress responses can be targeted to improve inflammatory and cellular dysfunctions associated with these pathologic illnesses that are exacerbated by viral infections. The present review assesses the importance of these redox signaling and cellular senescence pathways that describe the role of mitochondria and ER on the development and function of lung epithelial responses, highlighting the cause and effect associations that reflect the disease pathogenesis and possible intervention strategies.
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Affiliation(s)
- Marko Manevski
- Department of Immunology and NanoMedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Thivanka Muthumalage
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Dinesh Devadoss
- Department of Immunology and NanoMedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Isaac K Sundar
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Qixin Wang
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Kameshwar P Singh
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Hoshang J Unwalla
- Department of Immunology and NanoMedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hitendra S Chand
- Department of Immunology and NanoMedicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA.
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29
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Kanwal S, Guo X, Ward C, Volpe G, Qin B, Esteban MA, Bao X. Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:16-25. [PMID: 32445708 PMCID: PMC7393543 DOI: 10.1016/j.gpb.2019.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 05/25/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
Abstract
The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs (lncRNAs), a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function. Deeper understanding of lncRNAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts, such as development, aging, and cancer. In this review, we summarize the current progress made in profiling and analyzing the role of lncRNAs in various phases of somatic cell reprogramming, with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.
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Affiliation(s)
- Shahzina Kanwal
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Xiangpeng Guo
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Carl Ward
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Giacomo Volpe
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China
| | - Baoming Qin
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (5)Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Miguel A Esteban
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (3)Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China; (6)Institute for Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xichen Bao
- (1)Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Guangzhou 511436, China; (2)Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; (4)Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou 510005, China; (7)Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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30
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Park J, Lee Y, Shin J, Lee HJ, Son YB, Park BW, Kim D, Rho GJ, Kang E. Mitochondrial genome mutations in mesenchymal stem cells derived from human dental induced pluripotent stem cells. BMB Rep 2020. [PMID: 31234953 PMCID: PMC6941757 DOI: 10.5483/bmbrep.2019.52.12.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ethical and safety issues have rendered mesenchymal stem cells (MSCs) popular candidates in regenerative medicine, but their therapeutic capacity is lower than that of induced pluripotent stem cells (iPSCs). This study compared original, dental tissue-derived MSCs with re-differentiated MSCs from iPSCs (iPS-MSCs). CD marker expression in iPS-MSCs was similar to original MSCs. iPS-MSCs expressed higher in pluripotent genes, but lower levels in mesodermal genes than MSCs. In addition, iPS-MSCs did not form teratomas. All iPSCs carried mtDNA mutations; some shared with original MSCs and others not previously detected therein. Shared mutations were synonymous, while novel mutations were non-synonymous or located on RNA-encoding genes. iPS-MSCs also harbored mtDNA mutations transmitted from iPSCs. Selected iPS-MSCs displayed lower mitochondrial respiration than original MSCs. In conclusion, screening for mtDNA mutations in iPSC lines for iPS-MSCs can identify mutation-free cell lines for therapeutic applications. [BMB Reports 2019; 52(12): 689-694].
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Affiliation(s)
- Jumi Park
- Department of Convergence Medicine & Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505; Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Yeonmi Lee
- Department of Convergence Medicine & Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Joosung Shin
- Department of Convergence Medicine & Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Hyeon-Jeong Lee
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Young-Bum Son
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Bong-Wook Park
- Department of Dentistry, Gyeongsang National University School of Medicine, Institute of Health Science, Jinju 52828, Korea
| | - Deokhoon Kim
- Department of Pathology, Asan Institute for Life Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Gyu-Jin Rho
- Department of Theriogenology and Biotechnology, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Korea
| | - Eunju Kang
- Department of Convergence Medicine & Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
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31
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Klinge CM. Estrogenic control of mitochondrial function. Redox Biol 2020; 31:101435. [PMID: 32001259 PMCID: PMC7212490 DOI: 10.1016/j.redox.2020.101435] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/15/2022] Open
Abstract
Sex-based differences in human disease are caused in part by the levels of endogenous sex steroid hormones which regulate mitochondrial metabolism. This review updates a previous review on how estrogens regulate metabolism and mitochondrial function that was published in 2017. Estrogens are produced by ovaries and adrenals, and in lesser amounts by adipose, breast stromal, and brain tissues. At the cellular level, the mechanisms by which estrogens regulate diverse cellular functions including reproduction and behavior is by binding to estrogen receptors α, β (ERα and ERβ) and G-protein coupled ER (GPER1). ERα and ERβ are transcription factors that bind genomic and mitochondrial DNA to regulate gene transcription. A small proportion of ERα and ERβ interact with plasma membrane-associated signaling proteins to activate intracellular signaling cascades that ultimately alter transcriptional responses, including mitochondrial morphology and function. Although the mechanisms and targets by which estrogens act directly and indirectly to regulate mitochondrial function are not fully elucidated, it is clear that estradiol regulates mitochondrial metabolism and morphology via nuclear and mitochondrial-mediated events, including stimulation of nuclear respiratory factor-1 (NRF-1) transcription that will be reviewed here. NRF-1 is a transcription factor that interacts with coactivators including peroxisome proliferator-activated receptor gamma, coactivator 1 alpha (PGC-1α) to regulate nuclear-encoded mitochondrial genes. One NRF-1 target is TFAM that binds mtDNA to regulate its transcription. Nuclear-encoded miRNA and lncRNA regulate mtDNA-encoded and nuclear-encoded transcripts that regulate mitochondrial function, thus acting as anterograde signals. Other estrogen-regulated mitochondrial activities including bioenergetics, oxygen consumption rate (OCR), and extracellular acidification (ECAR), are reviewed.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, 40292, KY, USA.
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32
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Jusic A, Devaux Y. Mitochondrial noncoding RNA-regulatory network in cardiovascular disease. Basic Res Cardiol 2020; 115:23. [PMID: 32140778 DOI: 10.1007/s00395-020-0783-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/17/2020] [Indexed: 12/22/2022]
Abstract
Mitochondrial function and integrity are vital for the maintenance of cellular homeostasis, particularly in high-energy demanding cells. Cardiomyocytes have a large number of mitochondria, which provide a continuous and bulk supply of the ATP necessary for cardiac mechanical function. More than 90% of the ATP consumed by the heart is derived from the mitochondrial oxidative metabolism. Decreased energy supply as the main consequence of mitochondrial dysfunction is closely linked to cardiovascular disease (CVD). The discovery of noncoding RNA (ncRNAs) in the mitochondrial compartment has changed the traditional view of molecular pathways involved in the regulatory network of CVD. Mitochondrial ncRNAs participate in controlling cardiovascular pathogenesis by regulating glycolysis, mitochondrial energy status, and the expression of genes involved in mitochondrial metabolism. Understanding the underlying mechanisms of the association between impaired mitochondrial function resulting from fluctuation in expression levels of ncRNAs and specific disease phenotype can aid in preventing and treating CVD. This review presents an overview of the role of mitochondrial ncRNAs in the complex regulatory network of the cardiovascular pathology. We will summarize and discuss (1) mitochondrial microRNAs (mitomiRs) and long noncoding RNAs (lncRNAs) encoded either by nuclear or mitochondrial genome which are involved in the regulation of mitochondrial metabolism; (2) the role of mitomiRs and lncRNAs in the pathogenesis of several CVD such as hypertension, cardiac hypertrophy, acute myocardial infarction and heart failure; (3) the biomarker and therapeutic potential of mitochondrial ncRNAs in CVD; (4) and the challenges inherent to their translation into clinical application.
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Affiliation(s)
- Amela Jusic
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, 1A-B rue Edison, 1445, Strassen, Luxembourg.
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33
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Gusic M, Prokisch H. ncRNAs: New Players in Mitochondrial Health and Disease? Front Genet 2020; 11:95. [PMID: 32180794 PMCID: PMC7059738 DOI: 10.3389/fgene.2020.00095] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/28/2020] [Indexed: 12/19/2022] Open
Abstract
The regulation of mitochondrial proteome is unique in that its components have origins in both mitochondria and nucleus. With the development of OMICS technologies, emerging evidence indicates an interaction between mitochondria and nucleus based not only on the proteins but also on the non-coding RNAs (ncRNAs). It is now accepted that large parts of the non‐coding genome are transcribed into various ncRNA species. Although their characterization has been a hot topic in recent years, the function of the majority remains unknown. Recently, ncRNA species microRNA (miRNA) and long-non coding RNAs (lncRNA) have been gaining attention as direct or indirect modulators of the mitochondrial proteome homeostasis. These ncRNA can impact mitochondria indirectly by affecting transcripts encoding for mitochondrial proteins in the cytoplasm. Furthermore, reports of mitochondria-localized miRNAs, termed mitomiRs, and lncRNAs directly regulating mitochondrial gene expression suggest the import of RNA to mitochondria, but also transcription from the mitochondrial genome. Interestingly, ncRNAs have been also shown to hide small open reading frames (sORFs) encoding for small functional peptides termed micropeptides, with several examples reported with a role in mitochondria. In this review, we provide a literature overview on ncRNAs and micropeptides found to be associated with mitochondrial biology in the context of both health and disease. Although reported, small study overlap and rare replications by other groups make the presence, transport, and role of ncRNA in mitochondria an attractive, but still challenging subject. Finally, we touch the topic of their potential as prognosis markers and therapeutic targets.
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Affiliation(s)
- Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Munich, Germany
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34
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Abstract
The mitochondrial genome encodes 13 proteins that are components of the oxidative phosphorylation system (OXPHOS), suggesting that precise regulation of these genes is crucial for maintaining OXPHOS functions, including ATP production, calcium buffering, cell signaling, ROS production, and apoptosis. Furthermore, heteroplasmy or mis-regulation of gene expression in mitochondria frequently is associated with human mitochondrial diseases. Thus, various approaches have been developed to investigate the roles of genes encoded by the mitochondrial genome. In this review, we will discuss a wide range of techniques available for investigating the mitochondrial genome, mitochondrial transcription, and mitochondrial translation, which provide a useful guide to understanding mitochondrial gene expression.
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Affiliation(s)
- Dongkeun Park
- Department of Biological Sciences, School of Life Sciences, Ulsan 44919, Korea
- National Creative Research Initiative Center for Proteostasis, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Soyeon Lee
- Department of Biological Sciences, School of Life Sciences, Ulsan 44919, Korea
- National Creative Research Initiative Center for Proteostasis, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Kyung-Tai Min
- Department of Biological Sciences, School of Life Sciences, Ulsan 44919, Korea
- National Creative Research Initiative Center for Proteostasis, Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
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35
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Mu W, Provaznik J, Hackert T, Zöller M. Tspan8-Tumor Extracellular Vesicle-Induced Endothelial Cell and Fibroblast Remodeling Relies on the Target Cell-Selective Response. Cells 2020; 9:cells9020319. [PMID: 32013145 PMCID: PMC7072212 DOI: 10.3390/cells9020319] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/26/2020] [Indexed: 12/12/2022] Open
Abstract
Tumor cell-derived extracellular vesicles (TEX) expressing tetraspanin Tspan8-alpha4/beta1 support angiogenesis. Tspan8-alpha6/beta4 facilitates lung premetastatic niche establishment. TEX-promoted target reprogramming is still being disputed, we explored rat endothelial cell (EC) and lung fibroblast (Fb) mRNA and miRNA profile changes after coculture with TEX. TEX were derived from non-metastatic BSp73AS (AS) or metastatic BSp73ASML (ASML) rat tumor lines transfected with Tspan8 (AS-Tspan8) or Tspan8-shRNA (ASML-Tspan8kd). mRNA was analyzed by deep sequencing and miRNA by array analysis of EC and Fb before and after coculture with TEX. EC and Fb responded more vigorously to AS-Tspan8- than AS-TEX. Though EC and Fb responses differed, both cell lines predominantly responded to membrane receptor activation with upregulation and activation of signaling molecules and transcription factors. Minor TEX-initiated changes in the miRNA profile relied, at least partly, on long noncoding RNA (lncRNA) that also affected chromosome organization and mRNA processing. These analyses uncovered three important points. TEX activate target cell autonomous programs. Responses are initiated by TEX targeting units and are target cell-specific. The strong TEX-promoted lncRNA impact reflects lncRNA shuttling and location-dependent distinct activities. These informations urge for an in depth exploration on the mode of TEX-initiated target cell-specific remodeling including, as a major factor, lncRNA.
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Affiliation(s)
- Wei Mu
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (W.M.); (M.Z.); Tel.: +86-021-6384-6590 (W.M.); +49-6221-484-730 (M.Z.)
| | - Jan Provaznik
- EMBL Genomics Core Facility, 69117 Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
| | - Margot Zöller
- Department of General, Visceral and Transplantation Surgery, Pancreas Section, University of Heidelberg, 69120 Heidelberg, Germany
- Correspondence: (W.M.); (M.Z.); Tel.: +86-021-6384-6590 (W.M.); +49-6221-484-730 (M.Z.)
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36
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Wang Y, Luo X, Liu Y, Han G, Sun D. Long noncoding RNA RMRP promotes proliferation and invasion via targeting miR‐1‐3p in non–small‐cell lung cancer. J Cell Biochem 2019; 120:15170-15181. [PMID: 31050363 DOI: 10.1002/jcb.28779] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 12/30/2018] [Accepted: 01/09/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Yi Wang
- Department of Clinical Laboratory The Third Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Xigang Luo
- Department of Clinical Laboratory The Third Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Yang Liu
- Department of Clinical Laboratory The Third Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Guanying Han
- Department of Medical The First Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
| | - Dapeng Sun
- Department of Medical The First Affiliated Hospital of Jinzhou Medical University Jinzhou Liaoning P.R. China
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37
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Zhao Y, Liu S, Zhou L, Li X, Meng Y, Li Y, Li L, Jiao B, Bai L, Yu Y, Zhang S, Li W, Hoffman AR, Hu JF, Cui J. Aberrant shuttling of long noncoding RNAs during the mitochondria-nuclear crosstalk in hepatocellular carcinoma cells. Am J Cancer Res 2019; 9:999-1008. [PMID: 31218107 PMCID: PMC6556595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/04/2019] [Indexed: 06/09/2023] Open
Abstract
There is intense crosstalk between mitochondria and the nucleus that is mediated by proteins and long noncoding RNAs (lncRNAs). Using a modified RNA fluorescent in situ hybridization (RNA-FISH) assay coupled with MitoTracker staining, we tracked the mitochondrial localization of lncRNAs, including lncND6 and lncCytB. The nuclear genome-transcribed lncRNA MALAT1 was enriched in the mitochondria of hepatocellular carcinoma cells. Knockdown of MALAT1 significantly impaired mitochondrial function and alter tumor phenotype in HepG2 cells. The localization of the mitochondria-encoded lncRNA lncCytB was also abnormal in HepG2 cells. In normal hepatic HL7702 cells, lncCytB was located in mitochondria, but in HepG2 cells, it was enriched considerably in the nucleus. These data suggest that aberrant shuttling of lncRNAs, whether nuclear genome-encoded or mitochondrial genome-transcribed, may play a critical role in abnormal mitochondrial metabolism in cancer cells. This data lays the foundation for further clarifying the roles of mitochondria-associated lncRNAs in cancers.
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Affiliation(s)
- Yijing Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Xueli Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Ying Meng
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Yan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Lingyu Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
| | - Benzheng Jiao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Ling Bai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
| | - Yu Yu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
- Stanford University Medical School, VA Palo Alto Health Care SystemPalo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Cancer Center, The First Hospital of Jilin UniversityChangchun 130021, Jilin, China
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38
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Jeandard D, Smirnova A, Tarassov I, Barrey E, Smirnov A, Entelis N. Import of Non-Coding RNAs into Human Mitochondria: A Critical Review and Emerging Approaches. Cells 2019; 8:E286. [PMID: 30917553 PMCID: PMC6468882 DOI: 10.3390/cells8030286] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/19/2019] [Accepted: 03/23/2019] [Indexed: 01/26/2023] Open
Abstract
Mitochondria harbor their own genetic system, yet critically depend on the import of a number of nuclear-encoded macromolecules to ensure their expression. In all eukaryotes, selected non-coding RNAs produced from the nuclear genome are partially redirected into the mitochondria, where they participate in gene expression. Therefore, the mitochondrial RNome represents an intricate mixture of the intrinsic transcriptome and the extrinsic RNA importome. In this review, we summarize and critically analyze data on the nuclear-encoded transcripts detected in human mitochondria and outline the proposed molecular mechanisms of their mitochondrial import. Special attention is given to the various experimental approaches used to study the mitochondrial RNome, including some recently developed genome-wide and in situ techniques.
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Affiliation(s)
- Damien Jeandard
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Anna Smirnova
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Ivan Tarassov
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
| | - Eric Barrey
- GABI-UMR1313, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | | | - Nina Entelis
- UMR 7156 GMGM Strasbourg University/CNRS, 67000 Strasbourg, France.
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Zhao Y, Sun L, Wang RR, Hu JF, Cui J. The effects of mitochondria-associated long noncoding RNAs in cancer mitochondria: New players in an old arena. Crit Rev Oncol Hematol 2018; 131:76-82. [DOI: 10.1016/j.critrevonc.2018.08.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/06/2018] [Accepted: 08/22/2018] [Indexed: 12/17/2022] Open
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Golzarroshan B, Lin CL, Li CL, Yang WZ, Chu LY, Agrawal S, Yuan HS. Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities. Nucleic Acids Res 2018; 46:8630-8640. [PMID: 30020492 PMCID: PMC6144817 DOI: 10.1093/nar/gky642] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/13/2018] [Accepted: 07/16/2018] [Indexed: 11/13/2022] Open
Abstract
Human polynucleotide phosphorylase (PNPase) is an evolutionarily conserved 3'-to-5' exoribonuclease principally located in mitochondria where it is responsible for RNA turnover and import. Mutations in PNPase impair structured RNA transport into mitochondria, resulting in mitochondrial dysfunction and disease. PNPase is a trimeric protein with a doughnut-shaped structure hosting a central channel for single-stranded RNA binding and degradation. Here, we show that the disease-linked human PNPase mutants, Q387R and E475G, form dimers, not trimers, and have significantly lower RNA binding and degradation activities compared to wild-type trimeric PNPase. Moreover, S1 domain-truncated PNPase binds single-stranded RNA but not the stem-loop signature motif of imported structured RNA, suggesting that the S1 domain is responsible for binding structured RNAs. We further determined the crystal structure of dimeric PNPase at a resolution of 2.8 Å and, combined with small-angle X-ray scattering, show that the RNA-binding K homology and S1 domains are relatively inaccessible in the dimeric assembly. Taken together, these results show that mutations at the interface of the trimeric PNPase tend to produce a dimeric protein with destructive RNA-binding surfaces, thus impairing both of its RNA import and degradation activities and leading to mitochondria disorders.
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Affiliation(s)
- Bagher Golzarroshan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Chia-Liang Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Chia-Lung Li
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
| | - Lee-Ya Chu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan 30013, Republic of China
| | - Sashank Agrawal
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan 11490, Republic of China
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
- Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan 11529, Republic of China
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Loutre R, Heckel AM, Smirnova A, Entelis N, Tarassov I. Can Mitochondrial DNA be CRISPRized: Pro and Contra. IUBMB Life 2018; 70:1233-1239. [PMID: 30184317 DOI: 10.1002/iub.1919] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 01/08/2023]
Abstract
Mitochondria represent a chimera of macromolecules encoded either in the organellar genome, mtDNA, or in the nuclear one. If the pathway of protein targeting to different sub-compartments of mitochondria was relatively well studied, import of small noncoding RNAs into mammalian mitochondria still awaits mechanistic explanations and its functional issues are often not understood thus raising polemics. At the same time, RNA mitochondrial import pathway has an obvious attractiveness as it appears as a unique natural mechanism permitting to address nucleic acids into the organelles. Deciphering the function(s) of imported RNAs inside the mitochondria is extremely complicated due to their relatively low abundance, which suggests their regulatory role. We previously demonstrated that mitochondrial targeting of small noncoding RNAs able to specifically anneal with the mutant mitochondrial DNA led to a decrease of the mtDNA heteroplasmy level by inhibiting mutant mtDNA replication. We then demonstrated that increasing level of expression of such antireplicative recombinant RNAs increases significantly the antireplicative effect. In this report, we present a new data investigating the possibility to establish a CRISPR-Cas9 system targeting mtDNA exploiting of the pathway of RNA import into mitochondria. Mitochondrially addressed Cas9 versions and a set of mitochondrially targeted guide RNAs were tested in vitro and in vivo and their effect on mtDNA copy number was demonstrated. So far, the system appeared as more complicated for use than previously found for nuclear DNA, because only application of a pair of guide RNAs produced the effect of mtDNA depletion. We discuss, in a critical way, these results and put them in a broader context of polemics concerning the possibilities of manipulation of mtDNA in mammalians. The findings described here prove the potential of the RNA import pathway as a tool for studying mtDNA and for future therapy of mitochondrial disorders. © The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1233-1239, 2018.
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Affiliation(s)
- Romuald Loutre
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Anne-Marie Heckel
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Anna Smirnova
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Nina Entelis
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
| | - Ivan Tarassov
- UMR 7156 GMGM (Molecular Genetics, Genomics, Microbiology), University of Strasbourg - CNRS, Strasbourg, France
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Abstract
MicroRNAs (miRNAs) are known as the master regulators of gene expression, and for the last two decades our knowledge of their functional reach keeps expanding. Recent studies have shown that a miRNA’s role in regulation extends to extracellular and intracellular organelles. Several studies have shown a role for miRNA in regulating the mitochondrial genome in normal and disease conditions. Mitochondrial dysfunction occurs in many human pathologies, such as cardiovascular disease, diabetes, cancer, and neurological diseases. These studies have shed some light on regulation of the mitochondrial genome as well as helped to explain the role of miRNA in altering mitochondrial function and the ensuing effects on cells. Although the field has grown in recent years, many questions still remain. For example, little is known about how nuclear-encoded miRNAs translocate to the mitochondrial matrix. Knowledge of the mechanisms of miRNA transport into the mitochondrial matrix is likely to provide important insights into our understanding of disease pathophysiology and could represent new targets for therapeutic intervention. For this review, our focus will be on the role of a subset of miRNAs, known as MitomiR, in mitochondrial function. We also discuss the potential mechanisms used by these nuclear-encoded miRNAs for import into the mitochondrial compartment. Listen to this article’s corresponding podcast at http://ajpheart.podbean.com/e/microrna-translocation-into-the-mitochondria/ .
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Affiliation(s)
| | - Samarjit Das
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
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Krause HM. New and Prospective Roles for lncRNAs in Organelle Formation and Function. Trends Genet 2018; 34:736-745. [PMID: 30017312 DOI: 10.1016/j.tig.2018.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/14/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023]
Abstract
The observation that long noncoding RNAs (lncRNAs) represent the majority of transcripts in humans has led to a rapid increase in interest and study. Most of this interest has focused on their roles in the nucleus. However, increasing evidence is beginning to reveal even more functions outside the nucleus, and even outside cells. Many of these roles are mediated by newly discovered properties, including the ability of lncRNAs to interact with lipids, membranes, and disordered protein domains, and to form differentially soluble RNA-protein sub-organelles. This review explores the possibilities enabled by these new properties and abilities, such as likely roles in exosome formation and function.
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Affiliation(s)
- Henry M Krause
- Donnelly Centre for Cellular and Biomolecular Research, Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
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Loutre R, Heckel AM, Jeandard D, Tarassov I, Entelis N. Anti-replicative recombinant 5S rRNA molecules can modulate the mtDNA heteroplasmy in a glucose-dependent manner. PLoS One 2018; 13:e0199258. [PMID: 29912984 PMCID: PMC6005506 DOI: 10.1371/journal.pone.0199258] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
Mutations in mitochondrial DNA are an important source of severe and incurable human diseases. The vast majority of these mutations are heteroplasmic, meaning that mutant and wild-type genomes are present simultaneously in the same cell. Only a very high proportion of mutant mitochondrial DNA (heteroplasmy level) leads to pathological consequences. We previously demonstrated that mitochondrial targeting of small RNAs designed to anneal with mutant mtDNA can decrease the heteroplasmy level by specific inhibition of mutant mtDNA replication, thus representing a potential therapy. We have also shown that 5S ribosomal RNA, partially imported into human mitochondria, can be used as a vector to deliver anti-replicative oligoribonucleotides into human mitochondria. So far, the efficiency of cellular expression of recombinant 5S rRNA molecules bearing therapeutic insertions remained very low. In the present study, we designed new versions of anti-replicative recombinant 5S rRNA targeting a large deletion in mitochondrial DNA which causes the KSS syndrome, analyzed their specific annealing to KSS mitochondrial DNA and demonstrated their import into mitochondria of cultured human cells. To obtain an increased level of the recombinant 5S rRNA stable expression, we created transmitochondrial cybrid cell line bearing a site for Flp-recombinase and used this system for the recombinase-mediated integration of genes coding for the anti-replicative recombinant 5S rRNAs into nuclear genome. We demonstrated that stable expression of anti-replicative 5S rRNA versions in human transmitochondrial cybrid cells can induce a shift in heteroplasmy level of KSS mutation in mtDNA. This shift was directly dependent on the level of the recombinant 5S rRNA expression and the sequence of the anti-replicative insertion. Quantification of mtDNA copy number in transfected cells revealed the absence of a non-specific effect on wild type mtDNA replication, indicating that the decreased proportion between mutant and wild type mtDNA molecules is not a consequence of a random repopulation of depleted pool of mtDNA genomes. The heteroplasmy change could be also modulated by cell growth conditions, namely increased by cells culturing in a carbohydrate-free medium, thus forcing them to use oxidative phosphorylation and providing a selective advantage for cells with improved respiration capacities. We discuss the advantages and limitations of this approach and propose further development of the anti-replicative strategy based on the RNA import into human mitochondria.
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Affiliation(s)
- Romuald Loutre
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg, France
| | - Anne-Marie Heckel
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg, France
| | - Damien Jeandard
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg, France
| | - Ivan Tarassov
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg, France
| | - Nina Entelis
- UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg, France
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Verechshagina N, Nikitchina N, Yamada Y, Harashima Н, Tanaka M, Orishchenko K, Mazunin I. Future of human mitochondrial DNA editing technologies. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:214-221. [PMID: 29764251 DOI: 10.1080/24701394.2018.1472773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
ATP and other metabolites, which are necessary for the development, maintenance, and functioning of bodily cells are all synthesized in the mitochondria. Multiple copies of the genome, present within the mitochondria, together with its maternal inheritance, determine the clinical manifestation and spreading of mutations in mitochondrial DNA (mtDNA). The main obstacle in the way of thorough understanding of mitochondrial biology and the development of gene therapy methods for mitochondrial diseases is the absence of systems that allow to directly change mtDNA sequence. Here, we discuss existing methods of manipulating the level of mtDNA heteroplasmy, as well as the latest systems, that could be used in the future as tools for human mitochondrial genome editing.
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Affiliation(s)
- N Verechshagina
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| | - N Nikitchina
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
| | - Y Yamada
- b Faculty of Pharmaceutical Sciences, Laboratory for Molecular Design of Pharmaceutics , Hokkaido University , Sapporo , Japan
| | - Н Harashima
- b Faculty of Pharmaceutical Sciences, Laboratory for Molecular Design of Pharmaceutics , Hokkaido University , Sapporo , Japan
| | - M Tanaka
- c Department for Health and Longevity Research , National Institutes of Biomedical Innovation, Health and Nutrition , Ibaraki City, Osaka , Japan.,d Department of Neurology , Juntendo University Graduate School of Medicine , Tokyo , Japan
| | - K Orishchenko
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia.,e Laboratory of Cell Technologies , Institute of Cytology and Genetics SB RAS , Novosibirsk , Russia
| | - I Mazunin
- a Laboratory of Molecular Genetics Technologies , Immanuel Kant Baltic Federal University , Kaliningrad , Russia
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Klinge CM. Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers. Endocr Relat Cancer 2018; 25:R259-R282. [PMID: 29440232 DOI: 10.1530/erc-17-0548] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
The human genome is 'pervasively transcribed' leading to a complex array of non-coding RNAs (ncRNAs) that far outnumber coding mRNAs. ncRNAs have regulatory roles in transcription and post-transcriptional processes as well numerous cellular functions that remain to be fully described. Best characterized of the 'expanding universe' of ncRNAs are the ~22 nucleotide microRNAs (miRNAs) that base-pair to target mRNA's 3' untranslated region within the RNA-induced silencing complex (RISC) and block translation and may stimulate mRNA transcript degradation. Long non-coding RNAs (lncRNAs) are classified as >200 nucleotides in length, but range up to several kb and are heterogeneous in genomic origin and function. lncRNAs fold into structures that interact with DNA, RNA and proteins to regulate chromatin dynamics, protein complex assembly, transcription, telomere biology and splicing. Some lncRNAs act as sponges for miRNAs and decoys for proteins. Nuclear-encoded lncRNAs can be taken up by mitochondria and lncRNAs are transcribed from mtDNA. Both miRNAs and lncRNAs are dysregulated in endocrine cancers. This review provides an overview on the current understanding of the regulation and function of selected lncRNAs and miRNAs, and their interaction, in endocrine-related cancers: breast, prostate, endometrial and thyroid.
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47
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De Paepe B, Lefever S, Mestdagh P. How long noncoding RNAs enforce their will on mitochondrial activity: regulation of mitochondrial respiration, reactive oxygen species production, apoptosis, and metabolic reprogramming in cancer. Curr Genet 2017; 64:163-172. [DOI: 10.1007/s00294-017-0744-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 12/13/2022]
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