1
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Piergentili R, Sechi S. Non-Coding RNAs of Mitochondrial Origin: Roles in Cell Division and Implications in Cancer. Int J Mol Sci 2024; 25:7498. [PMID: 39000605 PMCID: PMC11242419 DOI: 10.3390/ijms25137498] [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: 06/05/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group, in terms of structure and sequence length, consisting of RNA molecules that do not code for proteins. These ncRNAs have a central role in the regulation of gene expression and are virtually involved in every process analyzed, ensuring cellular homeostasis. Although, over the years, much research has focused on the characterization of non-coding transcripts of nuclear origin, improved bioinformatic tools and next-generation sequencing (NGS) platforms have allowed the identification of hundreds of ncRNAs transcribed from the mitochondrial genome (mt-ncRNA), including long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miR). Mt-ncRNAs have been described in diverse cellular processes such as mitochondrial proteome homeostasis and retrograde signaling; however, the function of the majority of mt-ncRNAs remains unknown. This review focuses on a subgroup of human mt-ncRNAs whose dysfunction is associated with both failures in cell cycle regulation, leading to defects in cell growth, cell proliferation, and apoptosis, and the development of tumor hallmarks, such as cell migration and metastasis formation, thus contributing to carcinogenesis and tumor development. Here we provide an overview of the mt-ncRNAs/cancer relationship that could help the future development of new biomedical applications in the field of oncology.
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Affiliation(s)
| | - Stefano Sechi
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Biologia e Biotecnologie, Università Sapienza di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy;
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2
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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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3
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Araya M, Sepúlveda F, Villegas J, Alarcón L, Burzio LO, Burzio VA, Borgna V. Knockdown of Antisense Noncoding Mitochondrial RNA Reduces Tumorigenicity of Patient-Derived Clear Cell Renal Carcinoma Cells in an Orthotopic Xenograft Mouse Model. Cancers (Basel) 2024; 16:830. [PMID: 38398221 PMCID: PMC10886546 DOI: 10.3390/cancers16040830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent form of renal cancer and its treatment is hindered by a resistance to targeted therapies, immunotherapies and combinations of both. We have reported that the knockdown of the antisense noncoding mitochondrial RNAs (ASncmtRNAs) with chemically modified antisense oligonucleotides induces proliferative arrest and apoptotic death in tumor cells from many human and mouse cancer types. These studies have been mostly performed in vitro and in vivo on commercially available cancer cell lines and have shown that in mouse models tumor growth is stunted by the treatment. The present work was performed on cells derived from primary and metastatic ccRCC tumors. We established primary cultures from primary and metastatic ccRCC tumors, which were subjected to knockdown of ASncmtRNAs in vitro and in vivo in an orthotopic xenograft model in NOD/SCID mice. We found that these primary ccRCC cells are affected in the same way as tumor cell lines and in the orthotopic model tumor growth was significantly reduced by the treatment. This study on patient-derived ccRCC tumor cells represents a model closer to actual patient ccRCC tumors and shows that knockdown of ASncmtRNAs poses a potential treatment option for these patients.
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Affiliation(s)
- Mariela Araya
- Centro Cientifico & Tecnologico de Excelencia Ciencia & Vida, Santiago 8580702, Chile;
| | - Francisca Sepúlveda
- Center for Regenerative Medicine, Faculty of Clinical Medicine, Clínica Alemana, Universidad del Desarrollo, Santiago 7610615, Chile;
- Advanced Center for Chronic Diseases (ACCDiS), Santiago 8380492, Chile
| | - Jaime Villegas
- School of Veterinary Medicine, Faculty of Life Sciences, Universidad Andrés Bello, Santiago 8370251, Chile;
| | - Luis Alarcón
- Urology Service, Hospital Barros Luco-Trudeau, Santiago 8900085, Chile;
| | - Luis O. Burzio
- Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, Santiago 8370251, Chile;
| | - Verónica A. Burzio
- Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, Santiago 8370251, Chile;
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andrés Bello, Santiago 8370134, Chile
| | - Vincenzo Borgna
- Centro Cientifico & Tecnologico de Excelencia Ciencia & Vida, Santiago 8580702, Chile;
- Urology Service, Hospital Barros Luco-Trudeau, Santiago 8900085, Chile;
- School of Medicine, Faculty of Medical Sciences, Universidad de Santiago de Chile, Santiago 9170022, Chile
- Faculty of Medicine and Science, Universidad San Sebastián, Santiago 7510602, Chile
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4
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Hazazi A, AlShehah AA, Khan FR, Hakami MA, Almarshadi F, Abalkhail A, Nassar SA, Almasoudi HH, Ali AA, Abu-Alghayth MH, Kukreti N, Binshaya AS. From diagnosis to therapy: The transformative role of lncRNAs in eye cancer management. Pathol Res Pract 2024; 254:155081. [PMID: 38211388 DOI: 10.1016/j.prp.2023.155081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/13/2024]
Abstract
The genomic era has brought about a transformative shift in our comprehension of cancer, unveiling the intricate molecular landscape underlying disease development. Eye cancers (ECs), encompassing diverse malignancies affecting ocular tissues, pose distinctive challenges in diagnosis and management. Long non-coding RNAs (lncRNAs), an emerging category of non-coding RNAs, are pivotal actors in the genomic intricacies of eye cancers. LncRNAs have garnered recognition for their multifaceted roles in gene expression regulation and influence on many cellular processes. Many studies support that the lncRNAs have a role in developing various cancers. Recent investigations have pinpointed specific lncRNAs associated with ECs, including retinoblastoma and uveal melanoma. These lncRNAs exert control over critical pathways governing tumor initiation, progression, and metastasis, endowing them with the ability to function as evaluation, predictive, and therapeutic indicators. The article aims to synthesize the existing information concerning the functions of lncRNAs in ECs, elucidating their regulatory mechanisms and clinical significance. By delving into the lncRNAs' expanding relevance in the modulation of oncogenic and tumor-suppressive networks, we gain a deeper understanding of the molecular complexities intrinsic to these diseases. In our exploration of the genomic intricacies of ECs, lncRNAs introduce a fresh perspective, providing an opportunity to function as clinical and therapeutic indicators, and they also have therapeutic benefits that show promise for advancing the treatment of ECs. This comprehensive review bridges the intricate relationship between lncRNAs and ECs within the context of the genomic era.
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Affiliation(s)
- Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | | | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al-Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Fahad Almarshadi
- Department of Public Health, College of Public Health and Health Informatics, University of Ha'il, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Qassim, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Amer Al Ali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, P.O. Box 255, Bisha 67714, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Abdulkarim S Binshaya
- Department of Medical Laboratory Sciences, College of Applied medical sciences, Prince Sattam bin Abdulaziz University, Alkharj 11942, Saudi Arabia.
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5
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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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6
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Aydemir HB, Korkmaz EM. microRNAs in Syrista parreyssi (Hymenoptera) and Lepisma saccharina (Zygentoma) possibly involved in the mitochondrial function. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22062. [PMID: 37905458 DOI: 10.1002/arch.22062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023]
Abstract
Mitochondria are essential organelles for maintaining vital cellular functions, and microRNAs (miRNAs) regulate gene expression posttranscriptionally. miRNAs exhibit tissue and time-specific patterns in mitochondria and specifically mitochondrial miRNAs (mitomiRs) can regulate the mRNA expression both originating from mitochondrial and nuclear transcription which affect mitochondrial metabolic activity and cell homeostasis. In this study, miRNAs of two insect species, Syrista parreyssi (Hymenoptera) and Lepisma saccharina (Zygentoma), were investigated for the first time. The known and possible novel miRNAs were predicted and characterized and their potential effects on mitochondrial transcription were investigated in these insect species using deep sequencing. The previously reported mitomiRs were also investigated and housekeeping miRNAs were characterized. miRNAs that are involved in mitochondrial processes such as apoptosis and signaling and that affect genes encoding the subunits of OXPHOS complexes have been identified in each species. Here, 81 and 161 novel mature miRNA candidates were bioinformatically predicted and 9 and 24 of those were aligned with reference mitogenomes of S. parreyssi and L. saccharina, respectively. As a result of RNAHybrid analysis, 51 and 69 potential targets of miRNAs were found in the mitogenome of S. parreyssi and L. saccharina, respectively. cox1 gene was the most targeted gene and cytB, rrnS, and rrnL genes were highly targeted in both of the species by novel miRNAs, hypothetically. We speculate that these novel miRNAs, originating from or targeting mitochondria, influence on rRNA genes or positively selected mitochondrial protein-coding genes. These findings may provide a new perspective in evaluating miRNAs for maintaining mitochondrial function and transcription.
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Affiliation(s)
- Habeş Bilal Aydemir
- Department of Molecular Biology and Genetics, Faculty of Science and Letters, Tokat Gaziosmanpaşa University, Tokat, Turkey
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
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7
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Xiong H, Ren S, Chen J, Yang X, Liu Y, Xu Z, Guo J, Jiang T, Yuan M, Liu Y, Zhang G, Li W, Machens HG, Chen Z. Knockdown of long noncoding RNA SAN rejuvenates aged adipose-derived stem cells via miR-143-3p/ADD3 axis. Stem Cell Res Ther 2023; 14:213. [PMID: 37605290 PMCID: PMC10441736 DOI: 10.1186/s13287-023-03441-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/07/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Senescent adipose-derived stem cells (ASCs) exhibit reduced therapeutic efficacy during wound healing. Transcriptional regulation factors including long noncoding RNAs (lncRNAs) reportedly have essential roles in stem cell aging. However, the mechanisms of which lncRNAs influence mesenchymal stem cell aging and how it works need further investigation. METHODS The expression patterns of lncRNA senescence-associated noncoding RNA (SAN) and miR-143-3p in ASCs obtained from old and young volunteer donors were detected by quantitative polymerase chain reaction. ASCs with overexpression or knockdown of SAN and γ-adducin (ADD3) were constructed by lentiviral transduction. Mimic and inhibitor were used to manipulate the cellular level of miR-143-3p in ASCs. The effects of these RNAs on ASCs proliferation, migration and cellular senescence were examined by EdU, transwell and senescence-activated β-galactosidase (SA-β-gal) staining assays. Wound scratch and tube formation assays were conducted to evaluate the capacities of ASCs in promoting fibroblasts migration and endothelial cells angiogenesis. Furthermore, dual-luciferase assays and rescue experiments were performed to identify the RNA interactions. Finally, the therapeutic effects of SAN-depleted aged ASCs were evaluated in a skin injury model. RESULTS The lncRNA SAN (NONHSAT035482.2) was upregulated in aged ASCs; it controlled cellular senescence in ASCs. lncRNA SAN knockdown in ASCs led to ASC functional enhancement and the inhibition of cellular senescence; it also promoted the effects of conditioned medium (CM) on endothelial cell tube formation and fibroblast migration. Mechanistic analysis showed that SAN serves as a sponge for miR-143-3p, thereby regulating the expression of ADD3. The application of SAN-depleted aged ASCs increased re-epithelialization, collagen deposition, neovascularization and led to accelerated skin wound closure, compared with transplantation of aged ASCs. CONCLUSION The lncRNA SAN mediates ASC senescence by regulating the miR-143-3p/ADD3 pathway, providing a potential target for rejuvenation of senescent ASCs and enhancement of wound repair.
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Affiliation(s)
- Hewei Xiong
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Sen Ren
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Xiaofan Yang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Yutian Liu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Zhao Xu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Jiahe Guo
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Tao Jiang
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Meng Yuan
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Yang Liu
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Guolei Zhang
- Department of Hand and Foot Surgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000, China
| | - Wenqing Li
- Department of Hand and Foot Surgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000, China
| | - Hans-Günther Machens
- Department of Plastic and Hand Surgery, Technical University of Munich, 81675, Munich, Germany
| | - Zhenbing Chen
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China.
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8
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Bink DI, Pauli J, Maegdefessel L, Boon RA. Endothelial microRNAs and long noncoding RNAs in cardiovascular ageing. Atherosclerosis 2023; 374:99-106. [PMID: 37059656 DOI: 10.1016/j.atherosclerosis.2023.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023]
Abstract
Atherosclerosis and numerous other cardiovascular diseases develop in an age-dependent manner. The endothelial cells that line the vessel walls play an important role in the development of atherosclerosis. Non-coding RNA like microRNAs and long non-coding RNAs are known to play an important role in endothelial function and are implicated in the disease progression. Here, we summarize several microRNAs and long non-coding RNAs that are known to have an altered expression with endothelial aging and discuss their role in endothelial cell function and senescence. These processes contribute to aging-induced atherosclerosis development and by targeting the non-coding RNAs controlling endothelial cell function and senescence, atherosclerosis can potentially be attenuated.
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Affiliation(s)
- Diewertje I Bink
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany; German Centre for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Munich, Germany; German Centre for Cardiovascular Research (DZHK), Partner site Munich Heart Alliance, Munich, Germany; Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Reinier A Boon
- Department of Physiology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands; Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands; Institute for Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt am Main, Frankfurt am Main, Germany; German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt Am Main, Germany.
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9
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Peñaherrera S, Ruiz C, Castañeda V, Livingston K, Barba D, Burzio VA, Caicedo A, Singh KK. Exploring the role of mitochondria transfer/transplant and their long-non-coding RNAs in regenerative therapies for skin aging. Mitochondrion 2023; 70:41-53. [PMID: 36921832 PMCID: PMC10400337 DOI: 10.1016/j.mito.2023.02.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Advancing age and environmental stressors lead to mitochondrial dysfunction in the skin, inducing premature aging, impaired regeneration, and greater risk of cancer. Cells rely on the communication between the mitochondria and the nucleus by tight regulation of long non-coding RNAs (lncRNAs) to avoid premature aging and maintain healthy skin. LncRNAs act as key regulators of cell proliferation, differentiation, survival, and maintenance of skin structure. However, research on how the lncRNAs are dysregulated during aging and due to stressors is needed to develop therapies to regenerate skin's function and structure. In this article, we discuss how age and environmental stressors may alter lncRNA homeodynamics, compromising cell survival and skin health, and how these factors may become inducers of skin aging. We describe skin cell types and how they depend on mitochondrial function and lncRNAs. We also provide a list of mitochondria localized and nuclear lncRNAs that can serve to better understand skin aging. Using bioinformatic prediction tools, we predict possible functions of lncRNAs based on their subcellular localization. We also search for experimentally determined protein interactions and the biological processes involved. Finally, we provide therapeutic strategies based on gene editing and mitochondria transfer/transplant (AMT/T) to restore lncRNA regulation and skin health. This article offers a unique perspective in understanding and defining the therapeutic potential of mitochondria localized lncRNAs (mt-lncRNAs) and AMT/T to treat skin aging and related diseases.
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Affiliation(s)
- Sebastian Peñaherrera
- Biotecnología, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
- Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina iBioMed, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
| | - Cristina Ruiz
- Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina iBioMed, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador
| | - Verónica Castañeda
- Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina iBioMed, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
- PhD Program in Biomedicine, Faculty of Medicine, Universidad de los Andes, Santiago, Chile
| | - Kathryn Livingston
- Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina iBioMed, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
- Purdue University, Weldon School of Biomedical Engineering, Indiana, United States
| | - Diego Barba
- Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina iBioMed, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador
| | - Verónica A Burzio
- Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia & Vida, Santiago, Chile
| | - Andrés Caicedo
- Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina iBioMed, Quito, Ecuador
- Mito-Act Research Consortium, Quito, Ecuador
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador
- Sistemas Médicos SIME, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Keshav K. Singh
- Departments of Genetics, Dermatology and Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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10
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Bhatti JS, Khullar N, Vijayvergiya R, Navik U, Bhatti GK, Reddy PH. Mitochondrial miRNA as epigenomic signatures: Visualizing aging-associated heart diseases through a new lens. Ageing Res Rev 2023; 86:101882. [PMID: 36780957 DOI: 10.1016/j.arr.2023.101882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/05/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
Aging bears many hard knocks, but heart disorders earn a particular allusion, being the most widespread. Cardiovascular diseases (CVDs) are becoming the biggest concern to mankind due to sundry health conditions directly or indirectly related to heart-linked abnormalities. Scientists know that mitochondria play a critical role in the pathophysiology of cardiac diseases. Both environment and genetics play an essential role in modulating and controlling mitochondrial functions. Even a minor abnormality may prove detrimental to heart function. Advanced age combined with an unhealthy lifestyle can cause most cardiomyocytes to be replaced by fibrotic tissue which upsets the conducting system and leads to arrhythmias. An aging heart encounters far more heart-associated comorbidities than a young heart. Many state-of-the-art technologies and procedures are already being used to prevent and treat heart attacks worldwide. However, it remains a mystery when this heart bomb would explode because it lacks an alarm. This calls for a novel and effective strategy for timely diagnosis and a sure-fire treatment. This review article provides a comprehensive overture of prospective potentials of mitochondrial miRNAs that predict complicated and interconnected pathways concerning heart ailments and signature compilations of relevant miRNAs as biomarkers to plot the role of miRNAs in epigenomics. This article suggests that analysis of DNA methylation patterns in age-associated heart diseases may determine age-impelled biomarkers of heart disease.
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Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India.
| | - Rajesh Vijayvergiya
- Department of Cardiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
| | - Umashanker Navik
- Department of Pharmacology, Central University of Punjab, Bathinda, India.
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India.
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Neuroscience & Pharmacology, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Departments of Neurology, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA.
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11
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Hasnain A, Naqvi SAH, Ayesha SI, Khalid F, Ellahi M, Iqbal S, Hassan MZ, Abbas A, Adamski R, Markowska D, Baazeem A, Mustafa G, Moustafa M, Hasan ME, Abdelhamid MMA. Plants in vitro propagation with its applications in food, pharmaceuticals and cosmetic industries; current scenario and future approaches. FRONTIERS IN PLANT SCIENCE 2022; 13:1009395. [PMID: 36311115 PMCID: PMC9606719 DOI: 10.3389/fpls.2022.1009395] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/16/2022] [Indexed: 05/03/2023]
Abstract
Plant tissue culture technique employed for the identification and isolation of bioactive phytocompounds has numerous industrial applications. It provides potential benefits for different industries which include food, pharmaceutical and cosmetics. Various agronomic crops i.e., cereals, fruits, vegetables, ornamental plants and forest trees are currently being used for in vitro propagation. Plant tissue culture coupled with biotechnological approaches leads towards sustainable agricultural development providing solutions to major food security issues. Plants are the rich source of phytochemicals with medicinal properties rendering them useful for the industrial production of pharmaceuticals and nutraceuticals. Furthermore, there are numerous plant compounds with application in the cosmetics industry. In addition to having moisturizing, anti-ageing, anti-wrinkle effects; plant-derived compounds also possess pharmacological properties such as antiviral, antimicrobial, antifungal, anticancer, antioxidant, anti-inflammatory, and anti-allergy characteristics. The in vitro propagation of industrially significant flora is gaining attention because of its several advantages over conventional plant propagation methods. One of the major advantages of this technique is the quick availability of food throughout the year, irrespective of the growing season, thus opening new opportunities to the producers and farmers. The sterile or endangered flora can also be conserved by plant micro propagation methods. Hence, plant tissue culture is an extremely efficient and cost-effective technique for biosynthetic studies and bio-production, biotransformation, or bioconversion of plant-derived compounds. However, there are certain limitations of in-vitro plant regeneration system including difficulties with continuous operation, product removal, and aseptic conditions. For sustainable industrial applications of in-vitro regenerated plants on a large scale, these constraints need to be addressed in future studies.
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Affiliation(s)
- Ammarah Hasnain
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Syed Atif Hasan Naqvi
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology (FAST), Bahauddin Zakariya University, Multan, Pakistan
| | - Syeda Iqra Ayesha
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Fatima Khalid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Manahil Ellahi
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Shehzad Iqbal
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Zeeshan Hassan
- Department of Plant Pathology, Faculty of Agricultural Sciences and Technology (FAST), Bahauddin Zakariya University, Multan, Pakistan
| | - Aqleem Abbas
- State Key Laboratory of Agricultural Microbiology and Provincial Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan, China
| | - Robert Adamski
- Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Dorota Markowska
- Faculty of Process and Environmental Engineering, Lodz University of Technology, Lodz, Poland
| | - Alaa Baazeem
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Ghulam Mustafa
- Department of Agriculture (Extension and Adoptive Research), Agriculture Extension Department of Government of Punjab, Lahore, Pakistan
| | - Mahmoud Moustafa
- Department of Biology, Faculty of Science, King Khalid University, Abha, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Mohamed M. A. Abdelhamid
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
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12
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Jiang T, Mei L, Yang X, Sun T, Wang Z, Ji Y. Biomarkers of gastric cancer: current advancement. Heliyon 2022; 8:e10899. [PMID: 36247151 PMCID: PMC9561735 DOI: 10.1016/j.heliyon.2022.e10899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/22/2022] [Accepted: 09/28/2022] [Indexed: 11/06/2022] Open
Abstract
Gastric cancer (GC) is one of the most prevalent malignant types worldwide, especially in East Asia. Due to its frequently advanced stage at diagnosis, the mortality from GC is high and the prognosis is still unsatisfactory. Thus, early detection using effective screening approaches is vital to decrease the morbidity and mortality of GC. Interestingly, biomarkers can be used for diagnosis, prediction of sensitivity to treatment, and prognosis in GC. The potential biomarkers detectable in liquid biopsies such as circulating tumor cells (CTCs), long non-coding RNAs (lncRNAs), cell-free DNA (cfDNA), microRNAs, and exosomes reveal numerous information regarding the early prediction and the outcomes for GC patients. Additionally, using the novel serum biomarkers has opened up new opportunities for diagnosing and monitoring patients with GC. This review mainly summarizes the novel progress and approaches in GC biomarkers, which could be potentially used for early diagnosis and therapy monitoring. Meanwhile, we also discussed the advantages, disadvantages, and future perspectives of GC biomarkers.
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Affiliation(s)
- Tiantian Jiang
- Department of General Surgery, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, Shaanxi Province, China
| | - Lin Mei
- Scientific Research Center and Precision Medical Institute, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, Shaanxi Province, China
| | - Xiao Yang
- Scientific Research Center and Precision Medical Institute, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, Shaanxi Province, China
| | - Tingkai Sun
- Department of General Surgery, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, Shaanxi Province, China
| | - Zhidong Wang
- Department of General Surgery, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, Shaanxi Province, China,Corresponding author.
| | - Yuanyuan Ji
- Scientific Research Center and Precision Medical Institute, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710004, Shaanxi Province, China,Corresponding author.
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13
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Xu L, Ma W, Jin Y, Sun X, Chen N, Zhu X, Luo J, Li C, Zhao K, Zheng Y, Yu D. N, N-dimethylformamide exposure induced liver abnormal mitophagy by targeting miR-92a-1-5p-BNIP3L pathway in vivo and vitro. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156218. [PMID: 35623527 DOI: 10.1016/j.scitotenv.2022.156218] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
N, N-dimethylformamide (DMF) is a widely existing harmful environmental pollutant from industrial emission which can threat human health for both occupational and general populations. Epidemiological and experimental studies have indicated liver as the primary target organ of DMF. However, the molecular mechanism under DMF-induced hepatoxicity remains unclear. In the present study, we identified that DMF could induce abnormal autophagy flux in cells. We also showed that DMF-induced mitochondrial dysfunction and lethal mitophagy which further leads to autophagic cell death. Next, miRNA microarray analysis identified miR-92a-1-5p as the most down-regulated miRNA upon DMF exposure. Mechanistically, miR-92a-1-5p regulated mitochondrial function and mitophagy by targeting mitochondrial protein BNIP3L. Exogenous miR-92a-1-5p significantly attenuated DMF-induced mitochondrial dysfunction and mitophagy in vitro and in vivo. Our study highlights the mechanistic link between miRNAs and mitophagy under environmental stress, which provided a new clue for the mitochondrial epigenetics mechanism on environmental toxicant-induced hepatoxicity.
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Affiliation(s)
- Lin Xu
- School of Public Health, Qingdao University, Qingdao, China
| | - Wanli Ma
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China
| | - Xueying Sun
- School of Public Health, Qingdao University, Qingdao, China
| | - Ningning Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Xiaoxiao Zhu
- School of Public Health, Qingdao University, Qingdao, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao, China
| | - Chuanhai Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Kunming Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuxin Zheng
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China.
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14
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Mitochondrial Ribosome Dysfunction in Human Alveolar Type II Cells in Emphysema. Biomedicines 2022; 10:biomedicines10071497. [PMID: 35884802 PMCID: PMC9313339 DOI: 10.3390/biomedicines10071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Pulmonary emphysema is characterized by airspace enlargement and the destruction of alveoli. Alveolar type II (ATII) cells are very abundant in mitochondria. OXPHOS complexes are composed of proteins encoded by the mitochondrial and nuclear genomes. Mitochondrial 12S and 16S rRNAs are required to assemble the small and large subunits of the mitoribosome, respectively. We aimed to determine the mechanism of mitoribosome dysfunction in ATII cells in emphysema. ATII cells were isolated from control nonsmokers and smokers, and emphysema patients. Mitochondrial transcription and translation were analyzed. We also determined the miRNA expression. Decreases in ND1 and UQCRC2 expression levels were found in ATII cells in emphysema. Moreover, nuclear NDUFS1 and SDHB levels increased, and mitochondrial transcribed ND1 protein expression decreased. These results suggest an impairment of the nuclear and mitochondrial stoichiometry in this disease. We also detected low levels of the mitoribosome structural protein MRPL48 in ATII cells in emphysema. Decreased 16S rRNA expression and increased 12S rRNA levels were observed. Moreover, we analyzed miR4485-3p levels in this disease. Our results suggest a negative feedback loop between miR-4485-3p and 16S rRNA. The obtained results provide molecular mechanisms of mitoribosome dysfunction in ATII cells in emphysema.
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15
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Kremer V, Stanicek L, van Ingen E, Bink DI, Hilderink S, Tijsen AJ, Wittig I, Mägdefessel L, Nossent AY, Boon RA. Long non-coding RNA MEG8 induces endothelial barrier through regulation of microRNA-370 and -494 processing. J Cell Sci 2022; 135:275515. [PMID: 35611612 PMCID: PMC9270956 DOI: 10.1242/jcs.259671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 05/15/2022] [Indexed: 11/20/2022] Open
Abstract
The 14q32 locus is an imprinted region in the human genome which contains multiple non-coding RNAs. We investigated the role of Maternally Expressed Gene 8 (MEG8) in endothelial function and the underlying mechanism. A 5-fold increase in MEG8 was observed with increased passage number in Human Umbilical Vein Endothelial Cells, suggesting MEG8 is induced during aging. MEG8 knockdown resulted in a 1.8-fold increase in senescence, suggesting MEG8 might be protective during aging. Endothelial barrier was impaired after MEG8 silencing. MEG8 knockdown resulted in reduced expression of miRNA-370 and -494 but not -127, -487b and -410. Overexpression of miRNA-370/-494 partially rescued MEG8-silencing-induced barrier loss. Mechanistically, MEG8 regulates expression of miRNA-370 and -494 at the mature miRNA level through interaction with RNA binding proteins Cold Inducible RNA Binding Protein (CIRBP) and Hydroxyacyl-CoA Dehydrogenase Trifunctional Multi-enzyme Complex Subunit Beta (HADHB). Precursor and mature miRNA-370/-494 were shown to interact with HADHB and CIRBP respectively. CIRBP/HADHB silencing resulted in downregulation of miRNA-370 and induction of miRNA-494. These results suggest MEG8 interacts with CIRBP and HADHB and contributes to miRNA processing at the post-transcriptional level.
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Affiliation(s)
- Veerle Kremer
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Medical Chemistry, Meibergdreef 9, Amsterdam, the Netherlands
| | - Laura Stanicek
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,German Center for Cardiovascular research (DZHK), partner site Munich Heart Alliance, Germany
| | - Eva van Ingen
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands
| | - Diewertje I Bink
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Sarah Hilderink
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands
| | - Anke J Tijsen
- Amsterdam Cardiovascular Sciences, Heart Failure & Arrhythmias, Amsterdam, the Netherlands.,Amsterdam UMC location University of Amsterdam, Department of Experimental Cardiology, Meibergdreef 9, Amsterdam, the Netherlands
| | - Ilka Wittig
- Functional Proteomics, SFB 815 Core Unit, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt am Main, Germany
| | - Lars Mägdefessel
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University of Munich, Germany.,Department of Medicine, Molecular Vascular Medicine Unit, Karolinska Institute, Stockholm, Sweden.,German Center for Cardiovascular research (DZHK), partner site Munich Heart Alliance, Germany
| | - Anne Yaël Nossent
- Department of Surgery and Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, the Netherlands.,Departments of Laboratory Medicine and Internal Medicine II, Medical University of Vienna, Austria
| | - Reinier A Boon
- Amsterdam UMC location Vrije Universiteit, Amsterdam, Department of Physiology, De Boelelaan 1117, Amsterdam, the Netherlands.,Amsterdam Cardiovascular Sciences, Microcirculation, Amsterdam, the Netherlands.,Institute of Cardiovascular Regeneration, Goethe University, Frankfurt am Main, Germany.,German Centre for Cardiovascular Research DZHK, Partner site Frankfurt Rhein/Main, Frankfurt am Main, Germany
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16
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Juni RP, ’t Hart KC, Houtkooper RH, Boon R. Long non‐coding RNAs in cardiometabolic disorders. FEBS Lett 2022; 596:1367-1387. [DOI: 10.1002/1873-3468.14370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Rio P. Juni
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
| | - Kelly C. ’t Hart
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
- Laboratory Genetic Metabolic Diseases Amsterdam University Medical Centers; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Science, University of Amsterdam Frankfurt am Main Germany
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases Amsterdam University Medical Centers; Amsterdam Gastroenterology, Endocrinology, and Metabolism, Amsterdam Cardiovascular Science, University of Amsterdam Frankfurt am Main Germany
| | - Reinier Boon
- Department of Physiology Amsterdam University Medical Centers Amsterdam Cardiovascular Science Frankfurt am Main Germany
- Institute for Cardiovascular Regeneration Centre for Molecular Medicine Goethe University Frankfurt am Main Frankfurt am Main Germany
- German Centre for Cardiovascular Research DZHK Partner site Frankfurt Rhein/Main Frankfurt am Main Germany
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17
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Kuthethur R, Shukla V, Mallya S, Adiga D, Kabekkodu SP, Ramachandra L, Saxena Pu P, Satyamoorthy K, Chakrabarty S. Expression analysis and function of mitochondrial genome-encoded microRNAs. J Cell Sci 2022; 135:274749. [PMID: 35297485 DOI: 10.1242/jcs.258937] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 03/11/2022] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs play a significant role in nuclear and mitochondrial anterograde and retrograde signaling. Most of the miRNAs found inside mitochondria are nuclear genome encoded, with few mitochondrial genome encoded non-coding RNAs have been reported. In this study, we have identified 13 mitochondrial genome-encoded microRNAs (mitomiRs), which were differentially expressed in breast cancer cell lines (MCF-7, MDA-MB-468, and MDA-MB-231), non-malignant breast epithelial cell line (MCF-10A), and normal and breast cancer tissue specimens. We found that mitochondrial DNA depletion and inhibition of mitochondrial transcription leads to reduced expression of mitomiRs in breast cancer cells. MitomiRs physically interact with Ago2, an RNA-induced silencing complex (RISC) protein, in the cytoplasm and inside mitochondria. MitomiRs regulate the expression of both nuclear and mitochondrial transcripts in breast cancer cells. We showed that mitomiR-5 targets PPARGC1A and regulates mtDNA copy number in breast cancer cells. MitomiRs identified in the present study may be a promising tool for expression and functional analysis in patients with a defective mitochondrial phenotype, including cancer and metabolic syndromes.
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Affiliation(s)
- Raviprasad Kuthethur
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vaibhav Shukla
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sandeep Mallya
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Adiga
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Lingadakai Ramachandra
- Department of Surgery, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Prakash Saxena Pu
- Department of Radiation Oncology, Kasturba Medical College, Manipal Academy of Higher Education, Mangalore, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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18
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Pan Y, Wang T, Zhao Z, Wei W, Yang X, Wang X, Xin W. Novel Insights into the Emerging Role of Neat1 and Its Effects Downstream in the Regulation of Inflammation. J Inflamm Res 2022; 15:557-571. [PMID: 35115805 PMCID: PMC8802408 DOI: 10.2147/jir.s338162] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/16/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yongli Pan
- Department of Neurology, Weifang Medical University, Weifang, Shandong, People’s Republic of China
- Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
| | - Ting Wang
- Department of Radiology, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014030, People’s Republic of China
| | - Zhiqiang Zhao
- Department of Neurosurgery, Heji Hospital affiliated Changzhi Medical College, Shanxi, People’s Republic of China
| | - Wei Wei
- Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
- Department of Neurology, Mianyang Central Hospital, Mianyang, Sichuan, People’s Republic of China
| | - Xinyu Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
| | - Xianbin Wang
- Department of Emergency Medicine, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014030, People’s Republic of China
- Xianbin Wang, Department of Emergency Medicine, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014030, People’s Republic of China, Email
| | - Wenqiang Xin
- Georg-August-University of Göttingen, Göttingen, Lower Saxony, Germany
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, People’s Republic of China
- Correspondence: Wenqiang Xin, Department of Neurosurgery, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, People’s Republic of China, Tel +86–18526201182, Fax +86–2260362062, Email
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19
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Farfán N, Sanhueza N, Briones M, Burzio LO, Burzio VA. Antisense noncoding mitochondrial RNA-2 gives rise to miR-4485-3p by Dicer processing in vitro. Biol Res 2021; 54:33. [PMID: 34666824 PMCID: PMC8527801 DOI: 10.1186/s40659-021-00356-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/05/2021] [Indexed: 11/21/2022] Open
Abstract
Background The antisense noncoding mitochondrial RNAs (ASncmtRNAs) derive from the mitochondrial 16S gene. Knockdown of these transcripts with chemically-modified antisense oligonucleotides induces proliferative arrest, apoptosis and invasiveness reduction in tumor but not normal cells. One of these transcripts, ASncmtRNA-2, contains the complete and identical sequence of hsa-miR-4485-3p and, upon knockdown of this transcript, there is a strong increase in levels of this miRNA, suggesting ASncmtRNA-2 as a source for miR-4485-3p, which is supported by several evidences from our group and others, in the ex vivo setting. Results Here we show that incubation of in vitro-transcribed ASncmtRNA-2 with recombinant Dicer produces RNA fragments corresponding to hsa-miR-4485-3p, showing that Dicer binds to and processes ASncmtRNA-2, strongly supporting the hypothesis that ASncmtRNA-2 acts as a precursor for miR-4485-3p. Conclusion The in vitro results presented here strengthen the hypothesis that miR-4485-3p is derived from ASncmtRNA-2 by Dicer processing. Since miR-4485-3p is classified as a tumor suppressor miRNA, this evidence strengthens the application of ASncmtRNA knockdown for cancer therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s40659-021-00356-0.
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Affiliation(s)
- Nicole Farfán
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, Santiago, Chile.,Center for Regenerative Medicine, Faculty of Medicine, Universidad del Desarrollo/Clínica Alemana de Santiago, Santiago, Chile
| | - Nicole Sanhueza
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, Santiago, Chile.,Center for Integrative Biology, Faculty of Science, Universidad Mayor de Chile, Santiago, Chile
| | - Macarena Briones
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, Santiago, Chile
| | - Luis O Burzio
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, Santiago, Chile.,Faculty of Life Sciences, Universidad Andrés Bello, Santiago, Chile
| | - Verónica A Burzio
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, Santiago, Chile. .,Faculty of Life Sciences, Universidad Andrés Bello, Santiago, Chile.
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20
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Zheng H, Liu J, Yu J, McAlinden A. Expression profiling of mitochondria-associated microRNAs during osteogenic differentiation of human MSCs. Bone 2021; 151:116058. [PMID: 34144232 PMCID: PMC8944210 DOI: 10.1016/j.bone.2021.116058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 12/31/2022]
Abstract
Small non-coding microRNAs (miRNAs) have the ability to target and bind to many mRNAs within the cytosol resulting in reduced protein expression and modulation of a number of cellular pathways and networks. In addition to the cytosol, miRNAs have been identified in other cellular compartments and organelles, including the mitochondria. While a few mitochondria-associated miRNAs (mitomiRs) are predicted to be derived from the mitochondrial genome, the majority appear to be transcribed from nuclear DNA and somehow transported into the mitochondria. These findings raise interesting questions about why miRNAs are located in the mitochondria and if they play a role in regulating processes within these organelles. Previously published work from our laboratory showed that miR-181a/b can regulate osteogenesis, in part, by enhancing mitochondrial metabolism. In other published studies, miR-181 paralogs and many other miRNAs have been identified in mitochondrial extracts derived from common cell lines and specific primary cells and tissues. Taken together, we were motivated to identify mitomiR expression profiles during in vitro osteogenesis. Specifically, we obtained RNA from purified mitochondrial extracts of human bone marrow-derived mesenchymal stem/stromal cells (MSCs) and from whole cell extracts of MSCs at day 0 or following osteogenic induction for 3, 7 and 14 days. Utilizing Affymetrix GeneChip™ miRNA 4.0 arrays, mitomiR expression signatures were determined at each time point. Based on the Affymetrix detection above background algorithm, the total number of miRNAs detected in MSC mitochondria extracts was 527 (non-induced MSCs), 627 (day 3 induced), 372 (day 7 induced) and 498 (day 14 induced). In addition, we identified significantly differentially-expressed mitomiRs at day 7 and day 14 of osteogenic induction when compared to day 0 (fold change ≥1.5; adjusted p value <0.05). In general, the most pronounced and highly significant changes in mitomiR expression during osteogenesis were observed at the day 7 time point. Interestingly, most miRNAs found to be differentially-expressed in mitochondria extracts did not show significantly altered expression in whole cell extracts at the same time points during osteoblast differentiation. This array study provides novel information on miRNAs associated with the mitochondria in MSCs during differentiation toward the osteoblast phenotype. These findings will guide future research to identify new miRNA candidates that may function in regulating mitochondrial function and/or bone formation, homeostasis or repair.
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Affiliation(s)
- Hongjun Zheng
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America.
| | - Jin Liu
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America.
| | - Jinsheng Yu
- Genome Technology Access Center, Washington University School of Medicine, St Louis, MO, United States of America.
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America; Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, United States of America; Shriners Hospital for Children - St Louis, St Louis, MO, United States of America.
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21
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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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22
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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23
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Li Q, Xiao Z, Wang Y, Liu X, Liu H, Luo Z, Zheng S. Alterations of long non-coding RNA and mRNA profiles associated with extracellular matrix homeostasis and vascular aging in rats. Bioengineered 2021; 12:832-843. [PMID: 33645431 PMCID: PMC8806258 DOI: 10.1080/21655979.2021.1889129] [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] [Indexed: 12/15/2022] Open
Abstract
Vascular aging has been closely associated with various cardiovascular disorders; however, its molecular mechanism remains poorly understood. In our study, RNA sequencing was utilized to explore the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in the thoracic aortas of young (3 weeks) and old (16 weeks) rats. Functional categorization of differentially expressed mRNAs was evaluated using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, and lncRNA–microRNA–mRNA networks was constructed using Cytoscape software. In addition, three upregulated and three downregulated lncRNAs were further confirmed by quantitative reverse transcriptase-polymerase chain reaction. A total of 36 lncRNAs and 922 mRNAs were differential expression in the thoracic aortas of young and older rats. In addition, we found differentially expressed mRNAs that were enriched in multiple biological processes and signaling pathways associated with angiogenesis, such as extracellular matrix–receptor interaction and adenosine 3ʹ,5ʹ-monophosphate-activated protein kinase (AMPK) signaling. Moreover, AABR07013558.1, AABR07014823.1, and AABR07031489.1 were upregulated and ABR07053849.3, AABR07067310.2, and AC111292.1 were downregulated in the thoracic aortas of older rats compared with the young ones. Therefore, our findings provide several potential lncRNAs and mRNAs and signaling pathways related to vascular aging, which provide new clue for underlying the improvement of vascular aging.
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Affiliation(s)
- Qianqin Li
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
| | - Zezhou Xiao
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
| | - Yongsheng Wang
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
| | - Ximao Liu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
| | - Hao Liu
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
| | - Zhiwen Luo
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
| | - Shaoyi Zheng
- Department of Cardiovascular Surgery, Nanfang Hospital, Southern Medical University, Guangzhou Guangdong, China
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24
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Dong J, Liu J, Wen Y, Tobin SW, Zhang C, Zheng H, Huang Z, Feng Y, Zhang D, Liu S, Zhang Z, Li J. Down-Regulation of Lnc-CYP7A1-1 Rejuvenates Aged Human Mesenchymal Stem Cells to Improve Their Efficacy for Heart Repair Through SYNE1. Front Cell Dev Biol 2020; 8:600304. [PMID: 33330489 PMCID: PMC7710953 DOI: 10.3389/fcell.2020.600304] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/21/2020] [Indexed: 01/08/2023] Open
Abstract
Background Several long non-coding RNAs (lncRNAs) have been associated with cell senescence, termed senescence-associated lncRNAs (SAL-RNAs). However, the mechanisms involved for SAL-RNAs in aging are not fully elucidated. In the present study, we investigated the effects of SAL-RNAs on aged human bone marrow-derived mesenchymal stem cells (hBM-MSCs), and the possible means to counteract such effects to improve the regenerative capacity of aged hBM-MSCs. Methods By comparing the lncRNAs expression of hBM-MSCs derived from young and old individuals, lnc-CYP7A1-1 was identified as being significantly increased with age. Using predictive software, the expression of Spectrin Repeat Containing Nuclear Envelope Protein 1 (SYNE1), was found to be decreased with age. Next, through lentiviral constructs, we downregulated the expression of lnc-CYP7A1-1 or SYNE1 in hBM-MSCs separately. Additionally, hBM-MSCs proliferation, survival, migration, and senescence were investigated in vitro. In vivo, lnc-CYP7A1-1 downregulated aged hBM-MSCs were implanted into infarcted mouse hearts after myocardial infarction (MI), and cardiac function was measured. Through lentivirus-mediated downregulation of lnc-CYP7A1-1 in aged hBM-MSCs, we revealed that cell senescence was decreased, whereas cell proliferation, migration, and survival were increased. On the other hand, downregulation of SYNE1, the target gene of lnc-CYP7A1-1, in young hBM-MSCs increased cell senescence, yet decreased cell proliferation, migration, and survival. Downregulation of lnc-CYP7A1-1 in aged hBM-MSCs induced cell rejuvenation, yet this effect was attenuated by repression of SYNE1. In vivo, transplantation of lnc-CYP7A1-1 downregulated old hBM-MSCs improved cardiac function after MI. Conclusion Down-regulation of lnc-CYP7A1-1 rejuvenated aged hBM-MSCs and improved cardiac function when implanted into the infarcted mouse hearts, possibly through its target gene SYNE1.
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Affiliation(s)
- Jun Dong
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Sunnybrook Research Institute, Toronto, ON, Canada
| | - Jianwei Liu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yueqiang Wen
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Stephanie W Tobin
- Division of Cardiovascular Surgery, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Chongyu Zhang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Division of Cardiovascular Surgery, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Huiling Zheng
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zehan Huang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yongtao Feng
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Dongcheng Zhang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Cardiovascular Surgery, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shiming Liu
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhenhui Zhang
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiao Li
- Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, State Key Laboratory of Respiratory Disease, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Division of Cardiovascular Surgery, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
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25
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Huang M, Peng X, Yang L, Yang S, Li X, Tang S, Li B, Jin H, Wu B, Liu J, Li H. Non-coding RNA derived from extracellular vesicles in cancer immune escape: Biological functions and potential clinical applications. Cancer Lett 2020; 501:234-246. [PMID: 33186654 DOI: 10.1016/j.canlet.2020.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
The tumor microenvironment represents a dynamically composed matrix into which cancer cells and many other cell types are embedded to form organ-like structures. The tumor immune microenvironment (TIME), composed of immune cells, is an inseparable part of the tumor microenvironment. Extracellular vesicles (EVs) participate in the occurrence and development of tumors by delivering various biologically active molecules between cells; their role in cancer immune escape in particular has been widely proven. EVs can carry a wide array of cargo, such as non-coding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, which are selectively loaded by EVs, secreted, and transported to participate in the proliferation of immune cells. Hence, strategies to specifically target EV-ncRNAs could be attractive therapeutic options. In this review, we summarize the current research on the role of EV-ncRNAs in cancer immune escape, and discuss the latest research on the function and regulation mechanism of EV-ncRNAs in cancer immune escape, highlighting and elucidating the potential clinical applications of EV-ncRNAs, including in diagnosis and immunotherapy.
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Affiliation(s)
- Mingyao Huang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Shilei Tang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Bowen Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hongyuan Jin
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Bo Wu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Jingang Liu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
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26
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Zhou Y, Sun W, Qin Z, Guo S, Kang Y, Zeng S, Yu L. LncRNA regulation: New frontiers in epigenetic solutions to drug chemoresistance. Biochem Pharmacol 2020; 189:114228. [PMID: 32976832 DOI: 10.1016/j.bcp.2020.114228] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/09/2023]
Abstract
Long-noncoding RNAs (lncRNAs) have been shown to participate in sensitizing or de-sensitizing cancer cells to chemical drugs during cancer therapeutics. Notably, a plethora of lncRNAs have been confirmed to be associated with epigenetic controllers and regulate histone protein modification or DNA methylation states in the process of gene transcription. This correlation between lncRNAs and epigenetic regulators can induce the expression of core genes to trigger drug resistance. In addition, epigenetic signatures are considered to be effective and attractive biomarkers for monitoring drug therapeutic effects because they are inheritable, dynamic, and reversible. Therefore, the regulatory mechanism between lncRNAs and epigenetic machinery can serve as a novel indicator and target to overcome or reverse drug resistance in cancer therapy. In this review, we also presented a curated selection of computational tools (including online databases and network analysis) in the area of epigenetics. A classic workflow for lncRNA expression network analysis is presented, providing guidance for non-bioinformaticians to identify significant correlation between lncRNAs and other biomolecules.
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Affiliation(s)
- Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wen Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Suhang Guo
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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27
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Insight into the roles of long non-coding RNAs in ultraviolet-induced skin diseases. Chin Med J (Engl) 2020; 134:398-400. [PMID: 32932284 PMCID: PMC7909141 DOI: 10.1097/cm9.0000000000001062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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28
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Fasolo F, Di Gregoli K, Maegdefessel L, Johnson JL. Non-coding RNAs in cardiovascular cell biology and atherosclerosis. Cardiovasc Res 2020; 115:1732-1756. [PMID: 31389987 DOI: 10.1093/cvr/cvz203] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023] Open
Abstract
Atherosclerosis underlies the predominant number of cardiovascular diseases and remains a leading cause of morbidity and mortality worldwide. The development, progression and formation of clinically relevant atherosclerotic plaques involves the interaction of distinct and over-lapping mechanisms which dictate the roles and actions of multiple resident and recruited cell types including endothelial cells, vascular smooth muscle cells, and monocyte/macrophages. The discovery of non-coding RNAs (ncRNAs) including microRNAs, long non-coding RNAs, and circular RNAs, and their identification as key mechanistic regulators of mRNA and protein expression has piqued interest in their potential contribution to atherosclerosis. Accruing evidence has revealed ncRNAs regulate pivotal cellular and molecular processes during all stages of atherosclerosis including cell invasion, growth, and survival; cellular uptake and efflux of lipids, expression and release of pro- and anti-inflammatory intermediaries, and proteolytic balance. The expression profile of ncRNAs within atherosclerotic lesions and the circulation have been determined with the aim of identifying individual or clusters of ncRNAs which may be viable therapeutic targets alongside deployment as biomarkers of atherosclerotic plaque progression. Consequently, numerous in vivo studies have been convened to determine the effects of moderating the function or expression of select ncRNAs in well-characterized animal models of atherosclerosis. Together, clinicopathological findings and studies in animal models have elucidated the multifaceted and frequently divergent effects ncRNAs impose both directly and indirectly on the formation and progression of atherosclerosis. From these findings' potential novel therapeutic targets and strategies have been discovered which may pave the way for further translational studies and possibly taken forward for clinical application.
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Affiliation(s)
- Francesca Fasolo
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar-Technical University Munich, Biedersteiner Strasse 29, Munich, Germany
| | - Karina Di Gregoli
- Laboratory of Cardiovascular Pathology, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar-Technical University Munich, Biedersteiner Strasse 29, Munich, Germany.,Molecular Vascular Medicine, Karolinska Institute, Center for Molecular Medicine L8:03, 17176 Stockholm, Sweden.,German Center for Cardiovascular Research (DZHK), Partner Site Munich (Munich Heart Alliance), Munich, Germany
| | - Jason L Johnson
- Laboratory of Cardiovascular Pathology, Bristol Medical School, University of Bristol, Bristol, UK
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29
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Ghafouri-Fard S, Shoorei H, Taheri M. Non-coding RNAs are involved in the response to oxidative stress. Biomed Pharmacother 2020; 127:110228. [DOI: 10.1016/j.biopha.2020.110228] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 04/20/2020] [Accepted: 05/03/2020] [Indexed: 01/17/2023] Open
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30
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Zhang K, Qiu W, Wu B, Fang F. Long non‑coding RNAs are novel players in oral inflammatory disorders, potentially premalignant oral epithelial lesions and oral squamous cell carcinoma (Review). Int J Mol Med 2020; 46:535-545. [PMID: 32626947 PMCID: PMC7307862 DOI: 10.3892/ijmm.2020.4628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
In recent years, a large number of studies have shown that the abnormal expression of long non‑coding (lnc)RNAs can lead to a variety of different diseases, including inflammatory disorders, cardiovascular disease, nervous system diseases, and cancers. Recent research has demonstrated the biological characteristics of lncRNAs and the important functions of lncRNAs in oral inflammation, precancerous lesions and cancers. The present review aims to explore and discuss the potential roles of candidate lncRNAs in oral diseases by summarizing multiple lncRNA profiles in diseased and healthy oral tissues to determine the altered lncRNA signatures. In addition, to highlight the exact regulatory mechanism of lncRNAs in oral inflammatory disorders, potentially premalignant oral epithelial lesions and oral squamous cell carcinoma. The detection of lncRNAs in oral samples has the potential to be used as a diagnostic and an early detection tool for oral diseases. Furthermore, lncRNAs are promising future therapeutic targets in oral diseases, and research in this field may expand in the future.
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Affiliation(s)
- Kaiying Zhang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Wei Qiu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Buling Wu
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Fuchun Fang
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
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31
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Yuan L, Xu ZY, Ruan SM, Mo S, Qin JJ, Cheng XD. Long non-coding RNAs towards precision medicine in gastric cancer: early diagnosis, treatment, and drug resistance. Mol Cancer 2020; 19:96. [PMID: 32460771 PMCID: PMC7251695 DOI: 10.1186/s12943-020-01219-0] [Citation(s) in RCA: 191] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer is a deadly disease and remains the third leading cause of cancer-related death worldwide. The 5-year overall survival rate of patients with early-stage localized gastric cancer is more than 60%, whereas that of patients with distant metastasis is less than 5%. Surgical resection is the best option for early-stage gastric cancer, while chemotherapy is mainly used in the middle and advanced stages of this disease, despite the frequently reported treatment failure due to chemotherapy resistance. Therefore, there is an unmet medical need for identifying new biomarkers for the early diagnosis and proper management of patients, to achieve the best response to treatment. Long non-coding RNAs (lncRNAs) in body fluids have attracted widespread attention as biomarkers for early screening, diagnosis, treatment, prognosis, and responses to drugs due to the high specificity and sensitivity. In the present review, we focus on the clinical potential of lncRNAs as biomarkers in liquid biopsies in the diagnosis and prognosis of gastric cancer. We also comprehensively discuss the roles of lncRNAs and their molecular mechanisms in gastric cancer chemoresistance as well as their potential as therapeutic targets for gastric cancer precision medicine.
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Affiliation(s)
- Li Yuan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006 China
| | - Zhi-Yuan Xu
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Banshan Road 1#, Gongshu District, Hangzhou, 310022 China
| | - Shan-Ming Ruan
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006 China
| | - Shaowei Mo
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, 310006 China
| | - Jiang-Jiang Qin
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Banshan Road 1#, Gongshu District, Hangzhou, 310022 China
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, 548 Binwen Road, Binjiang District, Hangzhou, 310053 China
| | - Xiang-Dong Cheng
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Banshan Road 1#, Gongshu District, Hangzhou, 310022 China
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32
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Noren Hooten N, Evans MK. Age and poverty status alter the coding and noncoding transcriptome. Aging (Albany NY) 2020; 11:1189-1203. [PMID: 30779705 PMCID: PMC6402526 DOI: 10.18632/aging.101823] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/08/2019] [Indexed: 12/20/2022]
Abstract
Emerging evidence indicates that noncoding RNAs play regulatory roles in aging and disease. The functional roles of long noncoding RNAs (lncRNAs) in physiology and disease are not completely understood. Little is known about lncRNAs in the context of human aging and socio-environmental conditions. Microarray profiling of lncRNAs and mRNAs from peripheral blood mononuclear cells from young and old white (n=16) and African American (AA) males (n=16) living above or below poverty from the Healthy Aging in Neighborhoods of Diversity across the Life Span study revealed changes in both lncRNAs and mRNAs with age and poverty status in white males, but not in AA males. We validated lncRNA changes in an expanded cohort (n=40); CTD-3247F14.2, GAS5, H19, TERC and MEG3 changed significantly with age, whereas AK022914,GAS5, KB-1047C11.2, MEG3 and XLOC_003262 changed with poverty. Mitochondrial function and response to DNA damage and stress were pathways enriched in younger individuals. Response to stress, viral infection, and immune signals were pathways enriched in individuals living above poverty. These data show that both human age and a marker of social adversity influence lncRNA expression, which may provide insight about molecular pathways underlying aging and social factors that affect disparities in aging and disease.
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Affiliation(s)
- Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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33
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Li K, Cui M, Zhang K, Wang G, Zhai S. LncRNA CRNDE affects the proliferation and apoptosis of vascular smooth muscle cells in abdominal aortic aneurysms by regulating the expression of Smad3 by Bcl-3. Cell Cycle 2020; 19:1036-1047. [PMID: 32240036 PMCID: PMC7217363 DOI: 10.1080/15384101.2020.1743915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/21/2020] [Accepted: 03/05/2020] [Indexed: 10/24/2022] Open
Abstract
Previous studies show that Long non-coding RNAs (LncRNAs) are involved in the regulation of various human diseases. This study aimed to reveal how LncRNA CRNDE regulated vascular smooth muscle cells (VSMCs) proliferation and apoptosis in abdominal aortic aneurysms (AAA). Here, we found CRNDE was down-regulated in AAA tissues and AngII-stimulated VSMCs. The overexpression of CRNDE promoted VSMCs proliferation and inhibited cell apoptosis. The interaction between CRNDE and Bcl-3 or Bcl-3 and Smad3 was verified. The interference with Bcl-3 or CRNDE reduced Smad3 stability or promoted Smad3 ubiquitination. After pcDNA-CRNDE or pcDNA-CRNDE+si-Bcl-3 was transfected into VSMCs and stimulated with AngII, CRNDE affected VSMCs proliferation and apoptosis via regulating Smad3 via Bcl-3. Vivo experiments showed the overexpression of CRNDE repressed AAA growth. Therefore, we concluded that CRNDE was down-regulated in AAA tissues and AngII-stimulated VSMCs. Furthermore, the overexpression of CRNDE promoted VSMCs proliferation and repressed cell apoptosis in AAA by up-regulating Smad3 via Bcl-3.
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MESH Headings
- Animals
- Aortic Aneurysm, Abdominal/genetics
- Aortic Aneurysm, Abdominal/metabolism
- Aortic Aneurysm, Abdominal/pathology
- Apoptosis/genetics
- B-Cell Lymphoma 3 Protein/genetics
- B-Cell Lymphoma 3 Protein/metabolism
- Cell Proliferation/genetics
- Cells, Cultured
- Disease Models, Animal
- Down-Regulation
- Genetic Vectors/administration & dosage
- Humans
- Mice
- Mice, Inbred C57BL
- Mice, Knockout, ApoE
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/metabolism
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Signal Transduction/genetics
- Smad3 Protein/metabolism
- Transfection
- Up-Regulation/genetics
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Affiliation(s)
- Kun Li
- Department of Vascular and Endovascular Surgery, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Mingzhe Cui
- Department of Vascular and Endovascular Surgery, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Kewei Zhang
- Department of Vascular and Endovascular Surgery, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Guoquan Wang
- Department of Vascular and Endovascular Surgery, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
| | - Shuiting Zhai
- Department of Vascular and Endovascular Surgery, Henan Provincial People’s Hospital, Zhengzhou University People’s Hospital, Henan University People’s Hospital, Zhengzhou, China
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34
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Wang L, Jin S, Dai P, Zhang T, Shi Y, Ai G, Shao X, Xie Y, Xu J, Chen Z, Gao Z. p57 Kip2 is a master regulator of human adipose derived stem cell quiescence and senescence. Stem Cell Res 2020; 44:101759. [PMID: 32224418 DOI: 10.1016/j.scr.2020.101759] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 03/01/2020] [Accepted: 03/05/2020] [Indexed: 12/30/2022] Open
Abstract
Although human adipose derived stem cells (hADSCs) hold great promises for regenerative medicine, their key biological properties remain poorly understood. In particular, proliferation defects resulted from deep quiescence (dormancy) and senescence represent a major hurdle in hADSC production and clinical application. We have developed a model system for mechanistic dissection of hADSC quiescence and senescence. p57Kip2, a major CDK inhibitor, was highly expressed in quiescent and senescent hADSCs but its level quickly declined upon stem cell activation. p57Kip2 overexpression induced quiescence in spite of proliferative signals and its knockdown promoted cell cycle reentry even with induction of quiescence presumably through modulating the CDK2-CyclinE1 complex. Given its key role in quiescence and senescence, p57Kip2 may be exploited for innovative strategies to amplify hADSCs of high quality for clinics.
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Affiliation(s)
- Lian Wang
- Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Gynecologic Minimally Invasive Surgery Research Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China
| | - Shengkai Jin
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China; Advanced Institute of Translational Medicine, Tongji University School of Medicine, Shanghai 200092 China
| | - Peibin Dai
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China; Advanced Institute of Translational Medicine, Tongji University School of Medicine, Shanghai 200092 China
| | - Tianran Zhang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China; Advanced Institute of Translational Medicine, Tongji University School of Medicine, Shanghai 200092 China
| | - Yanghua Shi
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China; Advanced Institute of Translational Medicine, Tongji University School of Medicine, Shanghai 200092 China
| | - Guihai Ai
- Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Gynecologic Minimally Invasive Surgery Research Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiaowen Shao
- Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Gynecologic Minimally Invasive Surgery Research Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China
| | - Yutong Xie
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jun Xu
- East Hospital, Tongji University School of Medicine, Shanghai 200120, China.
| | - Zhongping Chen
- Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Gynecologic Minimally Invasive Surgery Research Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
| | - Zhengliang Gao
- Department of Gynecology and Obstetrics, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Gynecologic Minimally Invasive Surgery Research Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China; The Lifeng institute of Regenerative Medicine, Tongji University, Shanghai 200092, China; Advanced Institute of Translational Medicine, Tongji University School of Medicine, Shanghai 200092 China.
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35
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Cavalcante GC, Magalhães L, Ribeiro-dos-Santos Â, Vidal AF. Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity. Int J Mol Sci 2020; 21:E1838. [PMID: 32155913 PMCID: PMC7084767 DOI: 10.3390/ijms21051838] [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: 01/10/2020] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are organelles responsible for several functions involved in cellular balance, including energy generation and apoptosis. For decades now, it has been well-known that mitochondria have their own genetic material (mitochondrial DNA), which is different from nuclear DNA in many ways. More recently, studies indicated that, much like nuclear DNA, mitochondrial DNA is regulated by epigenetic factors, particularly DNA methylation and non-coding RNAs (ncRNAs). This field is now called mitoepigenetics. Additionally, it has also been established that nucleus and mitochondria are constantly communicating to each other to regulate different cellular pathways. However, little is known about the mechanisms underlying mitoepigenetics and nuclei-mitochondria communication, and also about the involvement of the ncRNAs in mitochondrial functions and related diseases. In this context, this review presents the state-of-the-art knowledge, focusing on ncRNAs as new players in mitoepigenetic regulation and discussing future perspectives of these fields.
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Affiliation(s)
- Giovanna C. Cavalcante
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Researches, Federal University of Pará, Rua dos Mundurucus, 4487, 66073-005 Belém, PA, Brazil
| | - Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
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36
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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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37
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Heidary Z, Zaki-Dizaji M, Saliminejad K, Edalatkhah H, Khorram Khorshid HR. MiR-4485-3p expression reduced in spermatozoa of men with idiopathic asthenozoospermia. Andrologia 2020; 52:e13539. [PMID: 32030798 DOI: 10.1111/and.13539] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/31/2019] [Indexed: 02/06/2023] Open
Abstract
Asthenozoospermia (AZS), which characterised by reduced forward sperm motility, is a common cause of male infertility. Recently, mitochondrial dysfunction reported in AZS men came to attention for finding the molecular aetiology of AZS. Mitochondria-related microRNAs (miRNAs) are the most important regulators of mitochondrial function through post-transcriptionally modulation of gene expression. Therefore, this study aims to evaluate the expression of four recently reported mitochondrial-related miRNAs (miR-4485-3p/4484/4461 and 4463) in the sperm sample of asthenozoospermic men. RNA was extracted from spermatozoa of 74 volunteers (39 patients with idiopathic AZS and 35 controls with normal fertility), and relative gene expression analysis was performed by quantitative PCR. We used SNORD48 as a normaliser gene, and quantification was calculated by 2-ΔΔCt method. The expression of miR-4484 and miR-4461 was not detected in the spermatozoa of cases and controls. However, miR-4485-3p (p = .006) was significantly downregulated in the AZS men compared with the controls, but the miR-4463 expression was not significantly different between the two groups (p = .5). Bioinformatic analysis identified three target genes for miR-4485-3p (DNAH1, KIT and PARK7) that are related to male infertility. In conclusion, the downregulation of miR-4485-3p was associated with idiopathic AZS, which could be a molecular link between mitochondrial dysfunction and AZS.
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Affiliation(s)
- Zohreh Heidary
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Kioomars Saliminejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Haleh Edalatkhah
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Hamid Reza Khorram Khorshid
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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38
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Abstract
Cardiovascular disease is an enormous socioeconomic burden worldwide and remains a leading cause of mortality and disability despite significant efforts to improve treatments and personalize healthcare. Heart failure is the main manifestation of cardiovascular disease and has reached epidemic proportions. Heart failure follows a loss of cardiac homeostasis, which relies on a tight regulation of gene expression. This regulation is under the control of multiple types of RNA molecules, some encoding proteins (the so-called messenger RNAs) and others lacking protein-coding potential, named noncoding RNAs. In this review article, we aim to revisit the notion of regulatory RNA, which has been thus far mainly confined to noncoding RNA. Regulatory RNA, which we propose to abbreviate as regRNA, can include both protein-coding RNAs and noncoding RNAs, as long as they contribute, directly or indirectly, to the regulation of gene expression. We will address the regulation and functional role of messenger RNAs, microRNAs, long noncoding RNAs, and circular RNAs (ie, regRNAs) in heart failure. We will debate the utility of regRNAs to diagnose, prognosticate, and treat heart failure, and we will provide directions for future work.
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Affiliation(s)
| | - Blanche Schroen
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, The Netherlands (B.S., E.L.R., S.H.)
| | - Gabriela M. Kuster
- Clinic of Cardiology and Department of Biomedicine, University Hospital Basel and University of Basel, Switzerland (G.M.K.)
| | - Emma L. Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, The Netherlands (B.S., E.L.R., S.H.)
| | - Kerrie Ford
- Imperial College London, United Kingdom (K.F., C.E.)
| | - Iain B. Squire
- Department of Cardiovascular Sciences, University of Leicester, and NIHR Biomedical Research Centre, Glenfield Hospital, United Kingdom (I.B.S.)
| | - Stephane Heymans
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, The Netherlands (B.S., E.L.R., S.H.)
| | | | | | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg (C.P.d.C.G., Y.D.)
| | - On behalf of the EU-CardioRNA COST Action (CA17129)
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg (C.P.d.C.G., Y.D.)
- Department of Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, The Netherlands (B.S., E.L.R., S.H.)
- Clinic of Cardiology and Department of Biomedicine, University Hospital Basel and University of Basel, Switzerland (G.M.K.)
- Imperial College London, United Kingdom (K.F., C.E.)
- Department of Cardiovascular Sciences, University of Leicester, and NIHR Biomedical Research Centre, Glenfield Hospital, United Kingdom (I.B.S.)
- IRCCS Policlinico San Donato, Milan, Italy (F.M.)
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39
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Dong Z, Pu L, Cui H. Mitoepigenetics and Its Emerging Roles in Cancer. Front Cell Dev Biol 2020; 8:4. [PMID: 32039210 PMCID: PMC6989428 DOI: 10.3389/fcell.2020.00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
In human beings, there is a ∼16,569 bp circular mitochondrial DNA (mtDNA) encoding 22 tRNAs, 12S and 16S rRNAs, 13 polypeptides that constitute the central core of ETC/OxPhos complexes, and some non-coding RNAs. Recently, mtDNA has been shown to have some covalent modifications such as methylation or hydroxylmethylation, which play pivotal epigenetic roles in mtDNA replication and transcription. Post-translational modifications of proteins in mitochondrial nucleoids such as mitochondrial transcription factor A (TFAM) also emerge as essential epigenetic modulations in mtDNA replication and transcription. Post-transcriptional modifications of mitochondrial RNAs (mtRNAs) including mt-rRNAs, mt-tRNAs and mt-mRNAs are important epigenetic modulations. Besides, mtDNA or nuclear DNA (n-DNA)-derived non-coding RNAs also play important roles in the regulation of translation and function of mitochondrial genes. These evidences introduce a novel concept of mitoepigenetics that refers to the study of modulations in the mitochondria that alter heritable phenotype in mitochondria itself without changing the mtDNA sequence. Since mitochondrial dysfunction contributes to carcinogenesis and tumor development, mitoepigenetics is also essential for cancer. Understanding the mode of actions of mitoepigenetics in cancers may shade light on the clinical diagnosis and prevention of these diseases. In this review, we summarize the present study about modifications in mtDNA, mtRNA and nucleoids and modulations of mtDNA/nDNA-derived non-coding RNAs that affect mtDNA translation/function, and overview recent studies of mitoepigenetic alterations in cancer.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
| | - Longjun Pu
- Umeå Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing, China.,Cancer Center, Medical Research Institute, Southwest University, Chongqing, China.,Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Chongqing, China.,Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Chongqing, China
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40
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Noncoding RNAs in Vascular Aging. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:7914957. [PMID: 31998442 PMCID: PMC6969641 DOI: 10.1155/2020/7914957] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023]
Abstract
Increases in age are accompanied by vascular aging, which can lead to a variety of chronic diseases, including atherosclerosis and hypertension. Noncoding RNAs (ncRNAs) have become a research hotspot in different fields of life sciences in recent years. For example, these molecules have been found to have regulatory roles in many physiological and pathological processes. Many studies have shown that microRNAs (miRNAs) and long ncRNAs (lncRNAs) also play a regulatory role in vascular aging. Endothelial cells (ECs) and vascular smooth muscle cells (VSMCs) are important components of blood vessels, and the senescence of both cell types promotes the occurrence of vascular aging. This review provides a contemporary update on the molecular mechanisms underlying the senescence of ECs and VSMCs and the regulatory role of miRNAs and lncRNAs in this process.
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41
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Mishra K, Kanduri C. Understanding Long Noncoding RNA and Chromatin Interactions: What We Know So Far. Noncoding RNA 2019; 5:ncrna5040054. [PMID: 31817041 PMCID: PMC6958424 DOI: 10.3390/ncrna5040054] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022] Open
Abstract
With the evolution of technologies that deal with global detection of RNAs to probing of lncRNA-chromatin interactions and lncRNA-chromatin structure regulation, we have been updated with a comprehensive repertoire of chromatin interacting lncRNAs, their genome-wide chromatin binding regions and mode of action. Evidence from these new technologies emphasize that chromatin targeting of lncRNAs is a prominent mechanism and that these chromatin targeted lncRNAs exert their functionality by fine tuning chromatin architecture resulting in an altered transcriptional readout. Currently, there are no unifying principles that define chromatin association of lncRNAs, however, evidence from a few chromatin-associated lncRNAs show presence of a short common sequence for chromatin targeting. In this article, we review how technological advancements contributed in characterizing chromatin associated lncRNAs, and discuss the potential mechanisms by which chromatin associated lncRNAs execute their functions.
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Affiliation(s)
- Kankadeb Mishra
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden;
- Department of Cell Biology, Memorial Sloan Kettering Cancer Centre, Rockefeller Research Laboratory, 430 East 67th Street, RRL 445, New York, NY 10065, USA
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden;
- Correspondence:
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42
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Villota C, Varas-Godoy M, Jeldes E, Campos A, Villegas J, Borgna V, Burzio LO, Burzio VA. HPV-18 E2 protein downregulates antisense noncoding mitochondrial RNA-2, delaying replicative senescence of human keratinocytes. Aging (Albany NY) 2019; 11:33-47. [PMID: 30595560 PMCID: PMC6339806 DOI: 10.18632/aging.101711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022]
Abstract
Human and mouse cells display a differential expression pattern of a family of mitochondrial noncoding RNAs (ncmtRNAs), according to proliferative status. Normal proliferating and cancer cells express a sense ncmtRNA (SncmtRNA), which seems to be required for cell proliferation, and two antisense transcripts referred to as ASncmtRNA-1 and -2. Remarkably however, the ASncmtRNAs are downregulated in human and mouse cancer cells, including HeLa and SiHa cells, transformed with HPV-18 and HPV-16, respectively. HPV E2 protein is considered a tumor suppressor in the context of high-risk HPV-induced transformation and therefore, to explore the mechanisms involved in the downregulation of ASncmtRNAs during tumorigenesis, we studied human foreskin keratinocytes (HFK) transduced with lentiviral-encoded HPV-18 E2. Transduced cells displayed a significantly extended replicative lifespan of up to 23 population doublings, compared to 8 in control cells, together with downregulation of the ASncmtRNAs. At 26 population doublings, cells transduced with E2 were arrested at G2/M, together with downregulation of E2 and SncmtRNA and upregulation of ASncmtRNA-2. Our results suggest a role for high-risk HPV E2 protein in cellular immortalization. Additionally, we propose a new cellular phenotype according to the expression of the SncmtRNA and the ASncmtRNAs.
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Affiliation(s)
- Claudio Villota
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Departamento de Ciencias Químicas y Biológicas, Facultad de Salud, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Manuel Varas-Godoy
- Centro de Investigación Biomédica, Facultad de Medicina, Universidad de los Andes, Santiago, Chile
| | - Emanuel Jeldes
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - América Campos
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Laboratorio de Comunicaciones Celulares (CEMC) Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jaime Villegas
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Vincenzo Borgna
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Faculty of Medical Sciences, Universidad de Santiago de Chile, Santiago, Chile
| | - Luis O Burzio
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Verónica A Burzio
- Fundación Ciencia & Vida, Santiago, Chile.,Andes Biotechnologies SpA, Santiago, Chile.,Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
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43
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Chen X, Li J, Liang D, Zhang L, Wang Q. LncRNA AWPPH participates in the development of non-traumatic osteonecrosis of femoral head by upregulating Runx2. Exp Ther Med 2019; 19:153-159. [PMID: 31853285 PMCID: PMC6909627 DOI: 10.3892/etm.2019.8185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/26/2019] [Indexed: 02/06/2023] Open
Abstract
AWPPH is a newly discovered long noncoding (lnc)RNA that plays an oncogenic role in development of several types of malignancies, whiles its involvement in non-traumatic osteonecrosis of femoral head (ONFH) is unknown. Therefore, the present study aimed to investigate the functionality of AWPPH in non-traumatic ONFH. Blood and mesenchymal stem cells (MSCs) were obtained from both non-traumatic ONFH patients and healthy controls, and expression of AWPPH in those tissues was detected by RT-qPCR. Receiver operating characteristic curve analysis was performed to investigate the diagnostic value of lncRNA AWPPH expression for non-traumatic ONFH. Bone morphogenic protein (BMP-2) was used to treat MSCs to induce osteogenic differentiation and the effects on lncRNA AWPPH expression was detected by RT-qPCR. LncRNA AWPPH overexpression and short hairpin (sh)RNA silencing cell lines were established and the effects on runt-related transcription factor 2 (Runx2) expression were detected by western blotting. It was demonstrated that AWPPH was significantly downregulated in non-traumatic ONFH patients compared with in healthy controls in both MSCs and serum. Expression of AWPPH in MSCs and serum is a sensitive diagnostic marker for non-traumatic ONFH. Expression of AWPPH exhibited no significant correlation with patients' age, gender and living habits, but was significantly correlated with course of disease. BMP-2 treatment significantly increased the expression level of AWPPH in human MSCs from bone marrow (hMSC-BM). AWPPH overexpression promoted, while AWPPH short hairpin RNA silencing inhibited the expression of Runx2 expression in hMSC-BM cells. Therefore, it was concluded that lncRNA AWPPH may participate in the development of ONFH by upregulating Runx2.
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Affiliation(s)
- Xiantao Chen
- Department of Osteonecrosis of The Femoral Head, Luoyang Orthopedic Hospital of Henan Province, Luoyang, Henan 471000, P.R. China
| | - Jing Li
- Department of Osteonecrosis of The Femoral Head, Luoyang Orthopedic Hospital of Henan Province, Luoyang, Henan 471000, P.R. China
| | - Dawei Liang
- Department of Osteonecrosis of The Femoral Head, Luoyang Orthopedic Hospital of Henan Province, Luoyang, Henan 471000, P.R. China
| | - Leilei Zhang
- Department of Osteonecrosis of The Femoral Head, Luoyang Orthopedic Hospital of Henan Province, Luoyang, Henan 471000, P.R. China
| | - Qingfeng Wang
- Department of Osteonecrosis of The Femoral Head, Luoyang Orthopedic Hospital of Henan Province, Luoyang, Henan 471000, P.R. China
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44
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Ma X, Zhao X, Wang K, Tang X, Guo J, Mi M, Qi Y, Chang L, Huang Y, Tong D. Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection. BMC Genomics 2019; 20:806. [PMID: 31684870 PMCID: PMC6829948 DOI: 10.1186/s12864-019-6156-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/09/2019] [Indexed: 12/28/2022] Open
Abstract
Background Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown. Results In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML). Conclusions The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.
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Affiliation(s)
- Xuelian Ma
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaomin Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Kaili Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Xiaoyi Tang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Jianxiong Guo
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Mi Mi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yanping Qi
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Lingling Chang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Yong Huang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China
| | - Dewen Tong
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
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45
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Hou Y, Zhang R, Sun X. Enhancer LncRNAs Influence Chromatin Interactions in Different Ways. Front Genet 2019; 10:936. [PMID: 31681405 PMCID: PMC6807612 DOI: 10.3389/fgene.2019.00936] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
More than 98% of the human genome does not encode proteins, and the vast majority of the noncoding regions have not been well studied. Some of these regions contain enhancers and functional non-coding RNAs. Previous research suggested that enhancer transcripts could be potent independent indicators of enhancer activity, and some enhancer lncRNAs (elncRNAs) have been proven to play critical roles in gene regulation. Here, we identified enhancer–promoter interactions from high-throughput chromosome conformation capture (Hi-C) data. We found that elncRNAs were highly enriched surrounding chromatin loop anchors. Additionally, the interaction frequency of elncRNA-associated enhancer–promoter pairs was significantly higher than the interaction frequency of other enhancer–promoter pairs, suggesting that elncRNAs may reinforce the interactions between enhancers and promoters. We also found that elncRNA expression levels were positively correlated with the interaction frequency of enhancer–promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Interestingly, G-quadruplexes were found to potentially mediate some enhancer–promoter interaction pairs, and the interaction frequency of these pairs was significantly higher than that of other enhancer–promoter pairs. We also found that the G-quadruplexes on enhancers were highly related to the expression of elncRNAs. G-quadruplexes located in the promoters of elncRNAs led to high expression of elncRNAs, whereas G-quadruplexes located in the gene bodies of elncRNAs generally resulted in low expression of elncRNAs.
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Affiliation(s)
- Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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46
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Harky A, Fan KS, Fan KH. The genetics and biomechanics of thoracic aortic diseases. VASCULAR BIOLOGY 2019; 1:R13-R25. [PMID: 32923967 PMCID: PMC7439919 DOI: 10.1530/vb-19-0027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022]
Abstract
Thoracic aortic aneurysms and aortic dissections (TAAD) are highly fatal emergencies within cardiothoracic surgery. With increasing age, thoracic aneurysms become more prevalent and pose an even greater threat when they develop into aortic dissections. Both diseases are multifactorial and are influenced by a multitude of physiological and biomechanical processes. Structural stability of aorta can be disrupted by genes, such as those for extracellular matrix and contractile protein, as well as telomere dysfunction, which leads to senescence of smooth muscle and endothelial cells. Biomechanical changes such as increased luminal pressure imposed by hypertension are also very prevalent and lead to structural instability. Furthermore, ageing is associated with a pro-inflammatory state that exacerbates degeneration of vessel wall, facilitating the development of both aortic aneurysms and aortic dissection. This literature review provides an overview of the aetiology and pathophysiology of both thoracic aneurysms and aortic dissections. With an improved understanding, new therapeutic targets may eventually be identified to facilitate treatment and prevention of these diseases.
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Affiliation(s)
- Amer Harky
- Department of Cardiothoracic Surgery, Liverpool Heart and Chest, Liverpool, UK
| | - Ka Siu Fan
- St. George's Medical School, University of London, London, UK
| | - Ka Hay Fan
- Faculty of Medicine, Imperial College London, London, UK
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47
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A Cell's Fate: An Overview of the Molecular Biology and Genetics of Apoptosis. Int J Mol Sci 2019; 20:ijms20174133. [PMID: 31450613 PMCID: PMC6747454 DOI: 10.3390/ijms20174133] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 12/30/2022] Open
Abstract
Apoptosis is one of the main types of regulated cell death, a complex process that can be triggered by external or internal stimuli, which activate the extrinsic or the intrinsic pathway, respectively. Among various factors involved in apoptosis, several genes and their interactive networks are crucial regulators of the outcomes of each apoptotic phase. Furthermore, mitochondria are key players in determining the way by which cells will react to internal stress stimuli, thus being the main contributor of the intrinsic pathway, in addition to providing energy for the whole process. Other factors that have been reported as important players of this intricate molecular network are miRNAs, which regulate the genes involved in the apoptotic process. Imbalance in any of these mechanisms can lead to the development of several illnesses, hence, an overall understanding of these processes is essential for the comprehension of such situations. Although apoptosis has been widely studied, the current literature lacks an updated and more general overview on this subject. Therefore, here, we review and discuss the mechanisms of apoptosis, highlighting the roles of genes, miRNAs, and mitochondria involved in this type of cell death.
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48
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Gao H, Li Y, Lin T, Cheng Y, Ma Y. Downregulation of CIP2A inhibits cancer cell proliferation and vascularization in renal clear cell carcinoma. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2019; 164:196-202. [PMID: 31431792 DOI: 10.5507/bp.2019.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/26/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND CIP2A has been proved to play a role as an oncogene in various types of malignancies while its functionality in renal clear cell carcinoma has not been investigated. Our study aimed to investigate the role of CIP2A in renal clear cell carcinoma and to explore the possible mechanisms. METHODS A total of 80 patients with renal clear cell carcinoma and 32 healthy people were included in the study. Expression of CIP2A was detected by qRT-PCR. CIP2A silencing renal clear cell carcinoma cell line was established. Its effects on cell proliferation and migration were verified by CCK-8 assay and Transwell cell assay, respectively. The effects of CIP2A overexpression on AKT and VEGF were investigated. RESULTS CIP2A expression level was increased in tumor tissues compared to adjacent healthy tissues. Serum levels of CIP2A protein were higher in cancer patients than in healthy controls, and serum levels of CIP2A protein were increased with increased stage of primary tumor. Serum CIP2A protein can be used to accurately predict renal clear cell carcinoma and its prognosis. CIP2A siRNA silencing inhibited tumor cell proliferation, and treatment with Akt activator reduced this inhibitory effect. CIP2A siRNA silencing decreased the expression level of VEGF and phosphorylation levels of AKT in renal clear cell carcinoma cells, while AKT activator treatment showed no significant effects on CIP2A expression. CONCLUSION Downregulation of CIP2A can inhibit cancer cell proliferation and vascularization in renal clear cell carcinoma through inactivation of the Akt pathway and its downstream VEGF.
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Affiliation(s)
- Hui Gao
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Yuqiao Li
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Tao Lin
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Yan Cheng
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
| | - Yunbo Ma
- Department of Urology, Liaocheng People's Hospital, Liaocheng City, Shandong Province, P. R. China, 252000
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49
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Fitzpatrick C, Bendek MF, Briones M, Farfán N, Silva VA, Nardocci G, Montecino M, Boland A, Deleuze JF, Villegas J, Villota C, Silva V, Lobos-Gonzalez L, Borgna V, Barrey E, Burzio LO, Burzio VA. Mitochondrial ncRNA targeting induces cell cycle arrest and tumor growth inhibition of MDA-MB-231 breast cancer cells through reduction of key cell cycle progression factors. Cell Death Dis 2019; 10:423. [PMID: 31142736 PMCID: PMC6541642 DOI: 10.1038/s41419-019-1649-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/05/2019] [Accepted: 04/29/2019] [Indexed: 12/24/2022]
Abstract
The family of long noncoding mitochondrial RNAs (ncmtRNAs), comprising sense (SncmtRNA), and antisense (ASncmtRNA-1 and ASncmtRNA-2) members, are differentially expressed according to cell proliferative status; SncmtRNA is expressed in all proliferating cells, while ASncmtRNAs are expressed in normal proliferating cells, but is downregulated in tumor cells. ASncmtRNA knockdown with an antisense oligonucleotide induces massive apoptosis in tumor cell lines, without affecting healthy cells. Apoptotic death is preceded by proliferation blockage, suggesting that these transcripts are involved in cell cycle regulation. Here, we show that ASncmtRNA knockdown induces cell death preceded by proliferative blockage in three different human breast cancer cell lines. This effect is mediated by downregulation of the key cell cycle progression factors cyclin B1, cyclin D1, CDK1, CDK4, and survivin, the latter also constituting an essential inhibitor of apoptosis, underlying additionally the onset of apoptosis. The treatment also induces an increase in the microRNA hsa-miR-4485-3p, whose sequence maps to ASncmtRNA-2 and transfection of MDA-MB-231 cells with a mimic of this miRNA induces cyclin B1 and D1 downregulation. Other miRNAs that are upregulated include nuclear-encoded hsa-miR-5096 and hsa-miR-3609, whose mimics downregulate CDK1. Our results suggest that ASncmtRNA targeting blocks tumor cell proliferation through reduction of essential cell cycle proteins, mediated by mitochondrial and nuclear miRNAs. This work adds to the elucidation of the molecular mechanisms behind cell cycle arrest preceding tumor cell apoptosis induced by ASncmtRNA knockdown. As proof-of-concept, we show that in vivo knockdown of ASncmtRNAs results in drastic inhibition of tumor growth in a xenograft model of MDA-MB-231 subcutaneous tumors, further supporting this approach for the development of new therapeutic strategies against breast cancer.
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Affiliation(s)
- Christopher Fitzpatrick
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, 8370134, Santiago, Chile
| | - Maximiliano F Bendek
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, 8370134, Santiago, Chile
| | - Macarena Briones
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile
| | - Nicole Farfán
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, 8370134, Santiago, Chile
| | - Valeria A Silva
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Valparaíso Interdisciplinary Neuroscience Center, Faculty of Sciences, Universidad de Valparaíso, Valparaíso, 2360102, Chile
| | - Gino Nardocci
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Life Sciences and Faculty of Medicine, Universidad Andrés Bello, 8370134, Santiago, Chile
| | - Martín Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Faculty of Life Sciences and Faculty of Medicine, Universidad Andrés Bello, 8370134, Santiago, Chile
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Evry, France
| | - Jaime Villegas
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, 8370134, Santiago, Chile.,Andes Biotechnologies Global Inc., Burlingame, CA, USA.,Center for Veterinary Medicine, Faculty of Life Sciences, Universidad Andrés Bello, Santiago, Chile
| | - Claudio Villota
- School of Nutrition and Diet, Faculty of Health, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Verónica Silva
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile
| | - Lorena Lobos-Gonzalez
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Center for Regenerative Medicine, Faculty of Medicine, Clínica Alemana & Universidad del Desarrollo, Santiago, Chile
| | - Vincenzo Borgna
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Faculty of Medical Sciences, Universidad de Santiago de Chile, Santiago, Chile
| | - Eric Barrey
- INRA, Génétique Animale et Biologie Intégrative UMR1313, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Luis O Burzio
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, 8370134, Santiago, Chile.,Andes Biotechnologies Global Inc., Burlingame, CA, USA
| | - Verónica A Burzio
- Fundación Ciencia & Vida/Andes Biotechnologies SpA, 7780272, Santiago, Chile. .,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andrés Bello, 8370134, Santiago, Chile. .,Andes Biotechnologies Global Inc., Burlingame, CA, USA.
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LncRNAs Regulatory Networks in Cellular Senescence. Int J Mol Sci 2019; 20:ijms20112615. [PMID: 31141943 PMCID: PMC6600251 DOI: 10.3390/ijms20112615] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/19/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are a class of transcripts longer than 200 nucleotides with no open reading frame. They play a key role in the regulation of cellular processes such as genome integrity, chromatin organization, gene expression, translation regulation, and signal transduction. Recent studies indicated that lncRNAs are not only dysregulated in different types of diseases but also function as direct effectors or mediators for many pathological symptoms. This review focuses on the current findings of the lncRNAs and their dysregulated signaling pathways in senescence. Different functional mechanisms of lncRNAs and their downstream signaling pathways are integrated to provide a bird’s-eye view of lncRNA networks in senescence. This review not only highlights the role of lncRNAs in cell fate decision but also discusses how several feedback loops are interconnected to execute persistent senescence response. Finally, the significance of lncRNAs in senescence-associated diseases and their therapeutic and diagnostic potentials are highlighted.
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