1
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Tapanainen R, Aasumets K, Fekete Z, Goffart S, Dufour E, L O Pohjoismäki J. Species-specific variation in mitochondrial genome tandem repeat polymorphisms in hares (Lepus spp., Lagomorpha, Leporidae) provides insight into their evolution. Gene 2024; 926:148644. [PMID: 38851366 DOI: 10.1016/j.gene.2024.148644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/23/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
The non-coding regions of the mitochondrial DNAs (mtDNAs) of hares, rabbits, and pikas (Lagomorpha) contain short (∼20 bp) and long (130-160 bp) tandem repeats, absent in related mammalian orders. In the presented study, we provide in-depth analysis for mountain hare (Lepus timidus) and brown hare (L. europaeus) mtDNA non-coding regions, together with a species- and population-level analysis of tandem repeat variation. Mountain hare short tandem repeats (SRs) as well as other analyzed hare species consist of two conserved 10 bp motifs, with only brown hares exhibiting a single, more variable motif. Long tandem repeats (LRs) also differ in sequence and copy number between species. Mountain hares have four to seven LRs, median value five, while brown hares exhibit five to nine LRs, median value six. Interestingly, introgressed mountain hare mtDNA in brown hares obtained an intermediate LR length distribution, with median copy number being the same as with conspecific brown hare mtDNA. In contrast, transfer of brown hare mtDNA into cultured mtDNA-less mountain hare cells maintained the original LR number, whereas the reciprocal transfer caused copy number instability, suggesting that cellular environment rather than the nuclear genomic background plays a role in the LR maintenance. Due to their dynamic nature and separation from other known conserved sequence elements on the non-coding region of hare mitochondrial genomes, the tandem repeat elements likely to represent signatures of ancient genetic rearrangements. clarifying the nature and dynamics of these rearrangements may shed light on the possible role of NCR repeated elements in mitochondria and in species evolution.
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Affiliation(s)
- Riikka Tapanainen
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Koit Aasumets
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Zsófia Fekete
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland; Hungarian University of Agriculture and Life Sciences, Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Steffi Goffart
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland
| | - Jaakko L O Pohjoismäki
- University of Eastern Finland, Department of Environmental and Biological Sciences, Joensuu, Finland.
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2
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Wang H, Liu Y, Lu XS, Wu Y, Gu W, Yin G. Targeting POLRMT by IMT1 inhibits colorectal cancer cell growth. Cell Death Dis 2024; 15:643. [PMID: 39227564 PMCID: PMC11372113 DOI: 10.1038/s41419-024-07023-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
This study investigates the potential anti-colorectal cancer (CRC) activity of IMT1, a novel specific inhibitor of mitochondrial RNA polymerase (POLRMT). Single-cell RNA sequencing data reveal that POLRMT is overexpressed in CRC cells. Additionally, elevated POLRMT expression was observed in local CRC tissues and cells, while its expression remained relatively low in colon epithelial tissues and cells. IMT1 significantly inhibited colony formation, cell viability, proliferation, cell cycle progression, and migration in both primary and immortalized CRC cells. Furthermore, IMT1 induced apoptosis and cell death in CRC cells. The inhibition of POLRMT by IMT1 disrupted mitochondrial functions in CRC cells, leading to mitochondrial depolarization, oxidative damage, and decreased ATP levels. Using targeted shRNA to silence POLRMT closely mirrored the effects of IMT1, showing robust anti-CRC cell activity. Crucially, the efficacy of IMT1 was diminished in CRC cells with silenced POLRMT. Contrarily, boosting POLRMT expression externally by a lentiviral construct promoted the proliferation and migration of CRC cells. Importantly, treatment with IMT1 or silencing POLRMT in primary colon cancer cells decreased the phosphorylation of Akt1-S6K1, whereas overexpression of POLRMT had the opposite effect. In nude mice, orally administering IMT1 potently restrained primary colon cancer xenograft growth. IMT1 suppressed POLRMT activity, disrupted mitochondrial function, hindered Akt-mTOR activation, and prompted apoptosis within the xenograft tissues. In addition, IMT1 administration suppressed lung metastasis of primary colon cancer cells in nude mice. These combined results highlight the robust anti-CRC activity of IMT1 by specifically targeting POLRMT.
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Affiliation(s)
- Hao Wang
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
- Department of General Surgery, Yancheng No.1 People's Hospital, Yancheng, China
| | - Yuxin Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xing-Sheng Lu
- Departments of General Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, China.
| | - Yongyou Wu
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China.
| | - Wen Gu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Guojian Yin
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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3
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Kozhukhar N, Alexeyev MF. Efficient Elimination of mtDNA from Mammalian Cells with 2',3'-Dideoxycytidine. DNA 2024; 4:201-211. [PMID: 39035221 PMCID: PMC11259038 DOI: 10.3390/dna4030013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Mammalian cell lines devoid of mitochondrial DNA (mtDNA) are indispensable in studies aimed at elucidating the contribution of mtDNA to various cellular processes or interactions between nuclear and mitochondrial genomes. However, the repertoire of tools for generating such cells (also known as rho-0 or ρ0 cells) remains limited, and approaches remain time- and labor-intensive, ultimately limiting their availability. Ethidium bromide (EtBr), which is most commonly used to induce mtDNA loss in mammalian cells, is cytostatic and mutagenic as it affects both nuclear and mitochondrial genomes. Therefore, there is growing interest in new tools for generating ρ0 cell lines. Here, we examined the utility of 2',3'-dideoxycytidine (ddC, zalcitabine) alone or in combination with EtBr for generating ρ0 cell lines of mouse and human origin as well as inducing the ρ0 state in mouse/human somatic cell hybrids. We report that ddC is superior to EtBr in both immortalized mouse fibroblasts and human 143B cells. Also, unlike EtBr, ddC exhibits no cytostatic effects at the highest concentration tested (200 μM), making it more suitable for general use. We conclude that ddC is a promising new tool for generating mammalian ρ0 cell lines.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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4
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Rai AK, Sanghvi S, Muthukumaran NS, Chandrasekera D, Kadam A, Kishore J, Kyriazis ID, Tomar D, Ponnalagu D, Shettigar V, Khan M, Singh H, Goukassian D, Katare R, Garikipati VNS. Role of mitochondrial ribosomal protein L7/L12 (MRPL12) in diabetic ischemic heart disease. Free Radic Biol Med 2024; 222:531-538. [PMID: 38977138 DOI: 10.1016/j.freeradbiomed.2024.07.003] [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: 05/07/2024] [Revised: 06/19/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024]
Abstract
BACKGROUND Myocardial infarction (MI) is a significant cause of death in diabetic patients. Growing evidence suggests that mitochondrial dysfunction contributes to heart failure in diabetes. However, the molecular mechanisms of mitochondrial dysfunction mediating heart failure in diabetes are still poorly understood. METHODS We examined MRPL12 levels in right atrial appendage tissues from diabetic patients undergoing coronary artery bypass graft (CABG) surgery. Using AC-16 cells overexpressing MRPL12 under normal and hyperglycemic conditions we performed mitochondrial functional assays OXPHOS, bioenergetics, mitochondrial membrane potential, ATP production and cell death. RESULTS We observed elevated MRPL12 levels in heart tissue samples from diabetic patients with ischemic heart disease compared to non-diabetic patients. Overexpression of MRPL12 under hyperglycemic conditions did not affect oxidative phosphorylation (OXPHOS) levels, cellular ATP levels, or cardiomyocyte cell death. However, notable impairment in mitochondrial membrane potential (MMP) was observed under hyperglycemic conditions, along with alterations in both basal respiration oxygen consumption rate (OCR) and maximal respiratory capacity OCR. CONCLUSIONS Overall, our results suggest that MRPL12 may have a compensatory role in the diabetic myocardium with ischemic heart disease, suggesting that MRPL12 may implicate in the pathophysiology of MI in diabetes.
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MESH Headings
- Aged
- Animals
- Female
- Humans
- Male
- Middle Aged
- Adenosine Triphosphate/metabolism
- Atrial Appendage/metabolism
- Atrial Appendage/pathology
- Coronary Artery Bypass
- Diabetes Mellitus, Type 2/metabolism
- Diabetes Mellitus, Type 2/pathology
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/complications
- Membrane Potential, Mitochondrial
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Mitochondria, Heart/genetics
- Mitochondrial Proteins/metabolism
- Mitochondrial Proteins/genetics
- Myocardial Ischemia/metabolism
- Myocardial Ischemia/pathology
- Myocardial Ischemia/genetics
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Oxidative Phosphorylation
- Ribosomal Proteins/metabolism
- Ribosomal Proteins/genetics
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
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Affiliation(s)
- Amit Kumar Rai
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, USA
| | - Shridhar Sanghvi
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Molecular Cellular and Developmental Biology, The Ohio State University, Columbus, OH, USA
| | | | - Dhananjie Chandrasekera
- Department of Physiology, HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ashlesha Kadam
- Section of Cardiovascular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Jahnavi Kishore
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, USA
| | - Ioannis D Kyriazis
- Department of Biology, Faculty of Medicine, University of Thessaly, Larissa, Greece
| | - Dhanendra Tomar
- Section of Cardiovascular Medicine, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Devasena Ponnalagu
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Pharmacology, University of Washington, Seattle, WA, USA
| | - Vikram Shettigar
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, USA
| | - Mahmood Khan
- Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Harpreet Singh
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - David Goukassian
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Rajesh Katare
- Department of Physiology, HeartOtago, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Venkata Naga Srikanth Garikipati
- Aging + Cardiovascular Discovery Center, Department of Cardiovascular Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, USA; Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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5
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Rubalcava-Gracia D, Bubb K, Levander F, Burr SP, August AV, Chinnery PF, Koolmeister C, Larsson NG. LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation. Nucleic Acids Res 2024:gkae662. [PMID: 39087558 DOI: 10.1093/nar/gkae662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
In mammals, the leucine-rich pentatricopeptide repeat protein (LRPPRC) and the stem-loop interacting RNA-binding protein (SLIRP) form a complex in the mitochondrial matrix that is required throughout the life cycle of most mitochondrial mRNAs. Although pathogenic mutations in the LRPPRC and SLIRP genes cause devastating human mitochondrial diseases, the in vivo function of the corresponding proteins is incompletely understood. We show here that loss of SLIRP in mice causes a decrease of complex I levels whereas other OXPHOS complexes are unaffected. We generated knock-in mice to study the in vivo interdependency of SLIRP and LRPPRC by mutating specific amino acids necessary for protein complex formation. When protein complex formation is disrupted, LRPPRC is partially degraded and SLIRP disappears. Livers from Lrpprc knock-in mice had impaired mitochondrial translation except for a marked increase in the synthesis of ATP8. Furthermore, the introduction of a heteroplasmic pathogenic mtDNA mutation (m.C5024T of the tRNAAla gene) into Slirp knockout mice causes an additive effect on mitochondrial translation leading to embryonic lethality and reduced growth of mouse embryonic fibroblasts. To summarize, we report that the LRPPRC/SLIRP protein complex is critical for maintaining normal complex I levels and that it also coordinates mitochondrial translation in a tissue-specific manner.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Bubb
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Levander
- Department en Immunotechnology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Amelie V August
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit,University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Camilla Koolmeister
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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6
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Zhou S, Ze X, Feng D, Liu L, Shi Y, Yu M, Huang L, Wang Y, Men H, Wu J, Yuan Z, Zhou M, Xu J, Li X, Yao H. Identification of 6-Fluorine-Substituted Coumarin Analogues as POLRMT Inhibitors with High Potency and Safety for Treatment of Pancreatic Cancer. J Med Chem 2024. [PMID: 39049433 DOI: 10.1021/acs.jmedchem.4c01178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Increasing evidence has demonstrated that oxidative phosphorylation (OXPHOS) is closely associated with the progression of pancreatic cancer (PC). Given its central role in mitochondrial transcription, the human mitochondrial RNA polymerase (POLRMT) is a promising target for developing PC treatments. Herein, structure-activity relationship exploration led to the identification of compound S7, which was the first reported POLRMT inhibitor possessing single-digit nanomolar potency of inhibiting PC cells proliferation. Mechanistic studies showed that compound S7 exerted antiproliferative effects without affecting the cell cycle, apoptosis, mitochondrial membrane potential (MMP), or intracellular reactive oxygen species (ROS) levels specifically in MIA PaCa-2 cells. Notably, compound S7 inhibited tumor growth in MIA PaCa-2 xenograft tumor model with a tumor growth inhibition (TGI) rate of 64.52% demonstrating significant improvement compared to the positive control (44.80%). In conclusion, this work enriched SARs of POLRMT inhibitors, and compound S7 deserved further investigations of drug-likeness as a candidate for PC treatment.
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Affiliation(s)
- Shengnan Zhou
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Xiaotong Ze
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Dazhi Feng
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Lihua Liu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Yuning Shi
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Minghui Yu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Lijuan Huang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Yunyue Wang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Hanlu Men
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Jianbing Wu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Zhenwei Yuan
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Mengze Zhou
- Department of Pharmacology, School of Pharmacy, China Pharmaceutical University, Longmian Avenue 639, Nanjing 211198, China
| | - Jinyi Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Xinnan Li
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
| | - Hong Yao
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, P. R. China
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7
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Schubert E, Mun K, Larsson M, Panagiotou S, Idevall-Hagren O, Svensson C, Punga T. Complex regulation of mitochondrial signaling by human adenovirus minor capsid protein VI. J Virol 2024; 98:e0035624. [PMID: 38837380 PMCID: PMC11265209 DOI: 10.1128/jvi.00356-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024] Open
Abstract
The controlled release of mitochondrial content into the cytosol has emerged as one of the key steps in mitochondrial signaling. In particular, the release of mitochondrial DNA (mtDNA) into the cytosol has been shown to activate interferon beta (IFN-β) gene expression to execute the innate immune response. In this report, we show that human adenovirus type 5 (HAdV-C5) infection induces the release of mtDNA into the cytosol. The release of mtDNA is mediated by the viral minor capsid protein VI (pVI), which localizes to mitochondria. The presence of the mitochondrial membrane proteins Bak and Bax are needed for the mtDNA release, whereas the viral E1B-19K protein blocked pVI-mediated mtDNA release. Surprisingly, the pVI-mediated mtDNA release did not increase but inhibited the IFN-β gene expression. Notably, the pVI expression caused mitochondrial leakage of the HSP60 protein. The latter prevented specific phosphorylation of the interferon regulatory factor 3 (IRF3) needed for IFN-β gene expression. Overall, we assign a new mitochondria and IFN-β signaling-modulating function to the HAdV-C5 minor capsid protein VI. IMPORTANCE Human adenoviruses (HAdVs) are common pathogens causing various self-limiting diseases, including conjunctivitis and the common cold. HAdVs need to interfere with multiple cellular signaling pathways during the infection to gain control over the host cell. In this study, we identified human adenovirus type 5 (HAdV-C5) minor capsid protein VI as a factor modulating mitochondrial membrane integrity and mitochondrial signaling. We show that pVI-altered mitochondrial signaling impedes the cell's innate immune response, which may benefit HAdV growth. Overall, our study provides new detailed insights into the HAdV-mitochondria interactions and signaling. This knowledge is helpful when developing new anti-viral treatments against pathogenic HAdV infections and improving HAdV-based therapeutics.
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Affiliation(s)
- Erik Schubert
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Kwangchol Mun
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mårten Larsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Catharina Svensson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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8
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Liu Y, Liu H, Zhang F, Xu H. The initiation of mitochondrial DNA replication. Biochem Soc Trans 2024; 52:1243-1251. [PMID: 38884788 PMCID: PMC11346463 DOI: 10.1042/bst20230952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
Mitochondrial DNA replication is initiated by the transcription of mitochondrial RNA polymerase (mtRNAP), as mitochondria lack a dedicated primase. However, the mechanism determining the switch between continuous transcription and premature termination to generate RNA primers for mitochondrial DNA (mtDNA) replication remains unclear. The pentatricopeptide repeat domain of mtRNAP exhibits exoribonuclease activity, which is required for the initiation of mtDNA replication in Drosophila. In this review, we explain how this exonuclease activity contributes to primer synthesis in strand-coupled mtDNA replication, and discuss how its regulation might co-ordinate mtDNA replication and transcription in both Drosophila and mammals.
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Affiliation(s)
- Yi Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Haibin Liu
- Hubei Jiangxia Laboratory, Wuhan 430200, China
| | - Fan Zhang
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Hong Xu
- National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, U.S.A
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9
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Huan MJ, Fu PP, Chen X, Wang ZX, Ma ZR, Cai SZ, Jiang Q, Wang Q. Identification of the central role of RNA polymerase mitochondrial for angiogenesis. Cell Commun Signal 2024; 22:343. [PMID: 38907279 PMCID: PMC11191269 DOI: 10.1186/s12964-024-01712-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024] Open
Abstract
Mitochondria are central to endothelial cell activation and angiogenesis, with the RNA polymerase mitochondrial (POLRMT) serving as a key protein in regulating mitochondrial transcription and oxidative phosphorylation. In our study, we examined the impact of POLRMT on angiogenesis and found that its silencing or knockout (KO) in human umbilical vein endothelial cells (HUVECs) and other endothelial cells resulted in robust anti-angiogenic effects, impeding cell proliferation, migration, and capillary tube formation. Depletion of POLRMT led to impaired mitochondrial function, characterized by mitochondrial depolarization, oxidative stress, lipid oxidation, DNA damage, and reduced ATP production, along with significant apoptosis activation. Conversely, overexpressing POLRMT promoted angiogenic activity in the endothelial cells. In vivo experiments demonstrated that endothelial knockdown of POLRMT, by intravitreous injection of endothelial specific POLRMT shRNA adeno-associated virus, inhibited retinal angiogenesis. In addition, inhibiting POLRMT with a first-in-class inhibitor IMT1 exerted significant anti-angiogenic impact in vitro and in vivo. Significantly elevated expression of POLRMT was observed in the retinal tissues of streptozotocin-induced diabetic retinopathy (DR) mice. POLRMT endothelial knockdown inhibited pathological retinal angiogenesis and mitigated retinal ganglion cell (RGC) degeneration in DR mice. At last, POLRMT expression exhibited a substantial increase in the retinal proliferative membrane tissues of human DR patients. These findings collectively establish the indispensable role of POLRMT in angiogenesis, both in vitro and in vivo.
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Affiliation(s)
- Meng-Jia Huan
- Department of Ophthalmology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210029, China
| | - Ping-Ping Fu
- Department of Ophthalmology, Shanghai Eye Diseases Prevention & Treatment Center, Shanghai Eye Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xia Chen
- Department of Anesthesiology, Children's hospital of Soochow University, Suzhou, 215025, China
| | - Zhao-Xia Wang
- Department of Endocrinology, Fengcheng Hospital of Fengxian Distric, Shanghai, China
| | - Zhou-Rui Ma
- Department of Burn and Plastic Surgery, Children's Hospital of Soochow University, Suzhou, China
| | - Shi-Zhong Cai
- Department of Child and Adolescent Healthcare, Children's Hospital of Soochow University, Suzhou, China.
- Key Laboratory of Congenital Structural Malformations of Suzhou City, Suzhou, China.
| | - Qin Jiang
- The Affiliated Eye Hospital, Nanjing Medical University, Nanjing, 210029, China.
| | - Qian Wang
- Department of Anesthesiology, Children's hospital of Soochow University, Suzhou, 215025, China.
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10
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Yan W, Xie C, Sun S, Zheng Q, Wang J, Wang Z, Man CH, Wang H, Yang Y, Wang T, Shi L, Zhang S, Huang C, Xu S, Wang YP. SUCLG1 restricts POLRMT succinylation to enhance mitochondrial biogenesis and leukemia progression. EMBO J 2024; 43:2337-2367. [PMID: 38649537 PMCID: PMC11183053 DOI: 10.1038/s44318-024-00101-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Mitochondria are cellular powerhouses that generate energy through the electron transport chain (ETC). The mitochondrial genome (mtDNA) encodes essential ETC proteins in a compartmentalized manner, however, the mechanism underlying metabolic regulation of mtDNA function remains unknown. Here, we report that expression of tricarboxylic acid cycle enzyme succinate-CoA ligase SUCLG1 strongly correlates with ETC genes across various TCGA cancer transcriptomes. Mechanistically, SUCLG1 restricts succinyl-CoA levels to suppress the succinylation of mitochondrial RNA polymerase (POLRMT). Lysine 622 succinylation disrupts the interaction of POLRMT with mtDNA and mitochondrial transcription factors. SUCLG1-mediated POLRMT hyposuccinylation maintains mtDNA transcription, mitochondrial biogenesis, and leukemia cell proliferation. Specifically, leukemia-promoting FMS-like tyrosine kinase 3 (FLT3) mutations modulate nuclear transcription and upregulate SUCLG1 expression to reduce succinyl-CoA and POLRMT succinylation, resulting in enhanced mitobiogenesis. In line, genetic depletion of POLRMT or SUCLG1 significantly delays disease progression in mouse and humanized leukemia models. Importantly, succinyl-CoA level and POLRMT succinylation are downregulated in FLT3-mutated clinical leukemia samples, linking enhanced mitobiogenesis to cancer progression. Together, SUCLG1 connects succinyl-CoA with POLRMT succinylation to modulate mitochondrial function and cancer development.
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Affiliation(s)
- Weiwei Yan
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Chengmei Xie
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Sijun Sun
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Quan Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jingyi Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Zihao Wang
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China
| | - Cheuk-Him Man
- Division of Haematology, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Haiyan Wang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Yunfan Yang
- Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, 250012, Jinan, China
| | - Tianshi Wang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Leilei Shi
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Shengjie Zhang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China.
| | - Chen Huang
- Department of Gastrointestinal Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China.
| | - Shuangnian Xu
- Department of Hematology, Southwest Hospital, Army Medical University, 400038, Chongqing, China.
| | - Yi-Ping Wang
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China.
- Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, 200032, Shanghai, China.
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11
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Jiang S, Yuan T, Rosenberger FA, Mourier A, Dragano NRV, Kremer LS, Rubalcava-Gracia D, Hansen FM, Borg M, Mennuni M, Filograna R, Alsina D, Misic J, Koolmeister C, Papadea P, de Angelis MH, Ren L, Andersson O, Unger A, Bergbrede T, Di Lucrezia R, Wibom R, Zierath JR, Krook A, Giavalisco P, Mann M, Larsson NG. Inhibition of mammalian mtDNA transcription acts paradoxically to reverse diet-induced hepatosteatosis and obesity. Nat Metab 2024; 6:1024-1035. [PMID: 38689023 PMCID: PMC11199148 DOI: 10.1038/s42255-024-01038-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/28/2024] [Indexed: 05/02/2024]
Abstract
The oxidative phosphorylation system1 in mammalian mitochondria plays a key role in transducing energy from ingested nutrients2. Mitochondrial metabolism is dynamic and can be reprogrammed to support both catabolic and anabolic reactions, depending on physiological demands or disease states. Rewiring of mitochondrial metabolism is intricately linked to metabolic diseases and promotes tumour growth3-5. Here, we demonstrate that oral treatment with an inhibitor of mitochondrial transcription (IMT)6 shifts whole-animal metabolism towards fatty acid oxidation, which, in turn, leads to rapid normalization of body weight, reversal of hepatosteatosis and restoration of normal glucose tolerance in male mice on a high-fat diet. Paradoxically, the IMT treatment causes a severe reduction of oxidative phosphorylation capacity concomitant with marked upregulation of fatty acid oxidation in the liver, as determined by proteomics and metabolomics analyses. The IMT treatment leads to a marked reduction of complex I, the main dehydrogenase feeding electrons into the ubiquinone (Q) pool, whereas the levels of electron transfer flavoprotein dehydrogenase and other dehydrogenases connected to the Q pool are increased. This rewiring of metabolism caused by reduced mtDNA expression in the liver provides a principle for drug treatment of obesity and obesity-related pathology.
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Affiliation(s)
- Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Taolin Yuan
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Arnaud Mourier
- University of Bordeaux, CNRS, Institut de Biochimie et Génétique Cellulaires (IGBC) UMR, Bordeaux, France
| | - Nathalia R V Dragano
- Institute of Experimental Genetics - German Mouse Clinic, Helmholtz Zentrum, Munich, Germany
- German Center for Diabetes Research (DZD), Oberschleißheim-Neuherberg, Neuherberg, Germany
| | - Laura S Kremer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Diana Rubalcava-Gracia
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Melissa Borg
- Department of Physiology and Pharmacology, Section for Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Mara Mennuni
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - David Alsina
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Polyxeni Papadea
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics - German Mouse Clinic, Helmholtz Zentrum, Munich, Germany
- German Center for Diabetes Research (DZD), Oberschleißheim-Neuherberg, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
| | - Lipeng Ren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Anke Unger
- Lead Discovery Center, Dortmund, Germany
| | | | | | - Rolf Wibom
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Juleen R Zierath
- Department of Physiology and Pharmacology, Section for Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Section for Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Krook
- Department of Physiology and Pharmacology, Section for Integrative Physiology, Karolinska Institutet, Stockholm, Sweden
| | - Patrick Giavalisco
- Metabolomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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12
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Guerrero L, Ntziachristos P. A succinylation switch to maligancy: SUCLG1, mitochondrial transcription and leukemia. EMBO J 2024; 43:2291-2293. [PMID: 38724759 PMCID: PMC11183207 DOI: 10.1038/s44318-024-00116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 06/19/2024] Open
Abstract
Recent work uncovers a role of mutant FLT3-driven Krebs cycle enzyme SUCLG1 in AML, derepressing mitochondrial gene expression and mass.
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Affiliation(s)
- Laura Guerrero
- Leukemia Therapy Resistance Unit, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Panagiotis Ntziachristos
- Leukemia Therapy Resistance Unit, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University and University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
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13
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Hughes LA, Rackham O, Filipovska A. Illuminating mitochondrial translation through mouse models. Hum Mol Genet 2024; 33:R61-R79. [PMID: 38779771 PMCID: PMC11112386 DOI: 10.1093/hmg/ddae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are hubs of metabolic activity with a major role in ATP conversion by oxidative phosphorylation (OXPHOS). The mammalian mitochondrial genome encodes 11 mRNAs encoding 13 OXPHOS proteins along with 2 rRNAs and 22 tRNAs, that facilitate their translation on mitoribosomes. Maintaining the internal production of core OXPHOS subunits requires modulation of the mitochondrial capacity to match the cellular requirements and correct insertion of particularly hydrophobic proteins into the inner mitochondrial membrane. The mitochondrial translation system is essential for energy production and defects result in severe, phenotypically diverse diseases, including mitochondrial diseases that typically affect postmitotic tissues with high metabolic demands. Understanding the complex mechanisms that underlie the pathologies of diseases involving impaired mitochondrial translation is key to tailoring specific treatments and effectively targeting the affected organs. Disease mutations have provided a fundamental, yet limited, understanding of mitochondrial protein synthesis, since effective modification of the mitochondrial genome has proven challenging. However, advances in next generation sequencing, cryoelectron microscopy, and multi-omic technologies have revealed unexpected and unusual features of the mitochondrial protein synthesis machinery in the last decade. Genome editing tools have generated unique models that have accelerated our mechanistic understanding of mitochondrial translation and its physiological importance. Here we review the most recent mouse models of disease pathogenesis caused by defects in mitochondrial protein synthesis and discuss their value for preclinical research and therapeutic development.
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Affiliation(s)
- Laetitia A Hughes
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
| | - Oliver Rackham
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- Harry Perkins Institute of Medical Research, 6 Verdun Street, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Curtin Medical School, Curtin University, Kent Street, Bentley, WA 6102, Australia
- Curtin Health Innovation Research Institute, Curtin University, Kent Street, Bentley, WA 6102, Australia
| | - Aleksandra Filipovska
- Telethon Kids Institute, Northern Entrance, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands, WA 6009, Australia
- ARC Centre of Excellence in Synthetic Biology, 35 Stirling Highway, Crawley, WA 6009, The University of Western Australia, Crawley, WA 6009, Australia
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, 19 Innovation Walk, Clayton, Clayton, VIC 3168, Australia
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14
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Wang C, Wang X, Sun S, Chang Y, Lian P, Guo H, Zheng S, Ma R, Li G. Irisin inhibits microglial senescence via TFAM-mediated mitochondrial metabolism in a mouse model of tauopathy. Immun Ageing 2024; 21:30. [PMID: 38745313 PMCID: PMC11092051 DOI: 10.1186/s12979-024-00437-0] [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: 03/19/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND The accumulation of senescent microglia has been highlighted as a critical contributor to the progression of tauopathies. Irisin, a muscle-derived hormone produced by the proteolytic cleavage of Fibronectin-domain III containing 5 (FNDC5), mediates the pleiotropic effects of exercise on the physical body. Herein, we investigate the potential role of irisin in microglial senescence in tauopathies. METHODS To model tauopathies both in vivo and in vitro, we utilized P301S tau transgenic mice and tau K18 fibril-treated microglia BV2 cells, respectively. We first examined the expression of the irisin expression and senescence phenotypes of microglia in tauopathies. Subsequently, we investigated the impact of irisin on microglial senescence and its underlying molecular mechanisms. RESULT We observed a reduction in irisin levels and an onset of premature microglial senescence both in vivo and in vitro. Irisin administration was found to counteract microglial senescence and ameliorate cognitive decline in P301S mice. Mechanistically, irisin effectively inhibited microglial senescence by stimulating the expression of mitochondrial transcription factor A (TFAM), a master regulator of mitochondrial respiratory chain biogenesis, thereby enhancing mitochondrial oxidative phosphorylation (OXPHOS). Silencing TFAM eliminated the inhibitory effect of irisin on microglial senescence as well as the restorative effect of irisin on mitochondrial OXPHOS. Furthermore, the SIRT1/PGC1α signaling pathway appeared to be implicated in irisin-mediated upregulation of TFAM. CONCLUSION Taken together, our study revealed that irisin mitigated microglial senescence via TFAM-driven mitochondrial biogenesis, suggesting a promising new avenue for therapeutic strategies targeting tauopathies.
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Affiliation(s)
- Cailin Wang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiufeng Wang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shangqi Sun
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yanmin Chang
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Piaopiao Lian
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hongxiu Guo
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Siyi Zheng
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Rong Ma
- Department of Pharmacology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Gang Li
- Department of Neurology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China.
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15
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Ramos-Acosta C, Huerta-Pantoja L, Salazar-Hidalgo ME, Mayol E, Jiménez-Vega S, García-Peña P, Jordi-Cruz J, Baquero C, Porras A, Íñigo-Rodríguez B, Benavente CM, López-Pastor AR, Gómez-Delgado I, Urcelay E, Candel FJ, Anguita E. Tigecycline Opposes Bortezomib Effect on Myeloma Cells Decreasing Mitochondrial Reactive Oxygen Species Production. Int J Mol Sci 2024; 25:4887. [PMID: 38732105 PMCID: PMC11084384 DOI: 10.3390/ijms25094887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Multiple myeloma is an incurable plasma cell malignancy. Most patients end up relapsing and developing resistance to antineoplastic drugs, like bortezomib. Antibiotic tigecycline has activity against myeloma. This study analyzed tigecycline and bortezomib combination on cell lines and plasma cells from myeloma patients. Apoptosis, autophagic vesicles, mitochondrial mass, mitochondrial superoxide, cell cycle, and hydrogen peroxide were studied by flow cytometry. In addition, mitochondrial antioxidants and electron transport chain complexes were quantified by reverse transcription real-time PCR (RT-qPCR) or western blot. Cell metabolism and mitochondrial activity were characterized by Seahorse and RT-qPCR. We found that the addition of tigecycline to bortezomib reduces apoptosis in proportion to tigecycline concentration. Supporting this, the combination of both drugs counteracts bortezomib in vitro individual effects on the cell cycle, reduces autophagy and mitophagy markers, and reverts bortezomib-induced increase in mitochondrial superoxide. Changes in mitochondrial homeostasis and MYC upregulation may account for some of these findings. These data not only advise to avoid considering tigecycline and bortezomib combination for treating myeloma, but caution on the potential adverse impact of treating infections with this antibiotic in myeloma patients under bortezomib treatment.
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Affiliation(s)
- Carlos Ramos-Acosta
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Laura Huerta-Pantoja
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Milton Eduardo Salazar-Hidalgo
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Elsa Mayol
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Selene Jiménez-Vega
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Pablo García-Peña
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Jenifeer Jordi-Cruz
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Cristina Baquero
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Universidad Complutense de Madrid (UCM), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (C.B.); (A.P.)
| | - Almudena Porras
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Universidad Complutense de Madrid (UCM), Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (C.B.); (A.P.)
| | - Belén Íñigo-Rodríguez
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Celina M. Benavente
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
| | - Andrea R. López-Pastor
- Laboratory of Genetics and Molecular Bases of Complex Diseases, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.R.L.-P.); (I.G.-D.); (E.U.)
- Networks for Cooperative Research in Health Results (RICORS, REI), 28089 Madrid, Spain
| | - Irene Gómez-Delgado
- Laboratory of Genetics and Molecular Bases of Complex Diseases, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.R.L.-P.); (I.G.-D.); (E.U.)
- Networks for Cooperative Research in Health Results (RICORS, REI), 28089 Madrid, Spain
| | - Elena Urcelay
- Laboratory of Genetics and Molecular Bases of Complex Diseases, Instituto de Investigación Sanitaria San Carlos (IdISSC), 28040 Madrid, Spain; (A.R.L.-P.); (I.G.-D.); (E.U.)
- Networks for Cooperative Research in Health Results (RICORS, REI), 28089 Madrid, Spain
| | - Francisco Javier Candel
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Clinical Microbiology & Infectious Diseases, Transplant Coordination, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, 28040 Madrid, Spain
| | - Eduardo Anguita
- Department of Medicine, Medical School, Universidad Complutense de Madrid (UCM), Plaza Ramón y Cajal s/n, 28040 Madrid, Spain (E.M.); (S.J.-V.); (J.J.-C.); (C.M.B.); (F.J.C.)
- Hematology Department, IML, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Profesor Martín Lagos s/n, 28040 Madrid, Spain (B.Í.-R.)
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16
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Cox SN, Lo Giudice C, Lavecchia A, Poeta ML, Chiara M, Picardi E, Pesole G. Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue. Biomolecules 2024; 14:411. [PMID: 38672428 PMCID: PMC11048214 DOI: 10.3390/biom14040411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.
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Affiliation(s)
- Sharon Natasha Cox
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Claudio Lo Giudice
- Institute of Biomedical Technologies, National Research Council, 70126 Bari, Italy;
| | - Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Maria Luana Poeta
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
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17
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Kiy RT, Khoo SH, Chadwick AE. Assessing the mitochondrial safety profile of the molnupiravir active metabolite, β-d-N4-hydroxycytidine (NHC), in the physiologically relevant HepaRG model. Toxicol Res (Camb) 2024; 13:tfae012. [PMID: 38328743 PMCID: PMC10848230 DOI: 10.1093/toxres/tfae012] [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: 07/26/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Background β-d-N4-Hydroxycytidine (NHC) is the active metabolite of molnupiravir, a broad-spectrum antiviral approved by the MHRA for COVID-19 treatment. NHC induces lethal mutagenesis of the SARS-CoV-2 virus, undergoing incorporation into the viral genome and arresting viral replication. It has previously been reported that several nucleoside analogues elicit off-target inhibition of mitochondrial DNA (mtDNA) or RNA replication. Although NHC does not exert these effects in HepG2 cells, HepaRG are proven to be advantageous over HepG2 for modelling nucleoside analogue-induced mitochondrial dysfunction. Therefore, the objective of this work was to assess the mitotoxic potential of NHC in HepaRG cells, a model more closely resembling physiological human liver. Methods Differentiated HepaRG cells were exposed to 1-60 μM NHC for 3-14 days to investigate effects of sub-, supra-, and clinically-relevant exposures (in the UK, molnupiravir for COVID-19 is indicated for 5 days and reported Cmax is 16 μM). Following drug incubation, cell viability, mtDNA copy number, mitochondrial protein expression, and mitochondrial respiration were assessed. Results NHC induced minor decreases in cell viability at clinically relevant exposures, but did not decrease mitochondrial protein expression. The effects on mtDNA were variable, but typically copy number was increased. At supra-clinical concentrations (60 μM), NHC reduced mitochondrial respiration, but did not appear to induce direct electron transport chain dysfunction. Conclusions Overall, NHC does not cause direct mitochondrial toxicity in HepaRG cells at clinically relevant concentrations, but may induce minor cellular perturbations. As HepaRG cells have increased physiological relevance, these findings provide additional assurance of the mitochondrial safety profile of NHC.
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Affiliation(s)
- Robyn T Kiy
- Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Building, Ashton Street, Liverpool, L69 3GE, United Kingdom
| | - Saye H Khoo
- Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Building, Ashton Street, Liverpool, L69 3GE, United Kingdom
- Tropical Infectious Diseases Unit, Royal Liverpool University Hospital, Prescot Street, Liverpool, L7 8XP, United Kingdom
| | - Amy E Chadwick
- Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Building, Ashton Street, Liverpool, L69 3GE, United Kingdom
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18
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Tan BG, Gustafsson CM, Falkenberg M. Mechanisms and regulation of human mitochondrial transcription. Nat Rev Mol Cell Biol 2024; 25:119-132. [PMID: 37783784 DOI: 10.1038/s41580-023-00661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2023] [Indexed: 10/04/2023]
Abstract
The expression of mitochondrial genes is regulated in response to the metabolic needs of different cell types, but the basic mechanisms underlying this process are still poorly understood. In this Review, we describe how different layers of regulation cooperate to fine tune initiation of both mitochondrial DNA (mtDNA) transcription and replication in human cells. We discuss our current understanding of the molecular mechanisms that drive and regulate transcription initiation from mtDNA promoters, and how the packaging of mtDNA into nucleoids can control the number of mtDNA molecules available for both transcription and replication. Indeed, a unique aspect of the mitochondrial transcription machinery is that it is coupled to mtDNA replication, such that mitochondrial RNA polymerase is additionally required for primer synthesis at mtDNA origins of replication. We discuss how the choice between replication-primer formation and genome-length RNA synthesis is controlled at the main origin of replication (OriH) and how the recent discovery of an additional mitochondrial promoter (LSP2) in humans may change this long-standing model.
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Affiliation(s)
- Benedict G Tan
- Institute for Mitochondrial Diseases and Ageing, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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19
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Sriram K, Qi Z, Yuan D, Malhi NK, Liu X, Calandrelli R, Luo Y, Tapia A, Jin S, Shi J, Salas M, Dang R, Armstrong B, Priceman SJ, Wang PH, Liao J, Natarajan R, Zhong S, Bouman Chen Z. Regulation of nuclear transcription by mitochondrial RNA in endothelial cells. eLife 2024; 13:e86204. [PMID: 38251974 PMCID: PMC10803041 DOI: 10.7554/elife.86204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024] Open
Abstract
Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.
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Affiliation(s)
- Kiran Sriram
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Zhijie Qi
- Department of Bioengineering, University of California San DiegoLa JollaUnited States
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Naseeb Kaur Malhi
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California San DiegoLa JollaUnited States
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Alonso Tapia
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Shengyan Jin
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Ji Shi
- Translura, IncNew HavenUnited States
| | - Martha Salas
- Department of Stem Cell Biology and Regenerative Medicine, City of HopeDuarteUnited States
| | - Runrui Dang
- Department of Bioengineering, University of California RiversideRiversideUnited States
| | - Brian Armstrong
- Department of Stem Cell Biology and Regenerative Medicine, City of HopeDuarteUnited States
| | - Saul J Priceman
- Department of Hematology & Hematopoietic Cell Transplantation, Department of Immuno-oncology, City of HopeDuarteUnited States
| | - Ping H Wang
- Department of Diabetes, Endocrinology, and Metabolism, City of HopeDuarteUnited States
| | - Jiayu Liao
- Department of Bioengineering, University of California RiversideRiversideUnited States
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Sheng Zhong
- Department of Bioengineering, University of California San DiegoLa JollaUnited States
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
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20
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Kong Y, Li X, Zhang H, Fu B, Jiang HY, Yang HL, Dai J. Targeting POLRMT by a first-in-class inhibitor IMT1 inhibits osteosarcoma cell growth in vitro and in vivo. Cell Death Dis 2024; 15:57. [PMID: 38228583 PMCID: PMC10791695 DOI: 10.1038/s41419-024-06444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/18/2024]
Abstract
Osteosarcoma (OS) is a highly aggressive form of bone cancer that predominantly affects adolescents and young adults. In this study, we have undertaken an investigation into the potential anti-OS cell activity of IMT1 (inhibitor of mitochondrial transcription 1), a first-in-class inhibitor of RNA polymerase mitochondrial (POLRMT). IMT1 exhibited a profound inhibitory effect on cell survival, proliferation, cell cycle progression, and migration in primary and immortalized OS cells. Furthermore, this POLRMT inhibitor elicited apoptosis in the OS cells, without, however, inducing cytotoxicity in human osteoblasts or osteoblastic cells. IMT1 disrupted mitochondrial functions in OS cells, resulting in mitochondrial depolarization, oxidative injury, lipid peroxidation, and ATP reduction in OS cells. Silencing POLRMT using targeted shRNA closely mimicked the actions of IMT1 and exerted potent anti-OS cell activity. Importantly, IMT1's effectiveness was diminished in POLRMT-silenced OS cells. Subsequent investigations revealed that IMT1 suppressed the activation of the Akt-mammalian target of rapamycin (mTOR) cascade in OS cells. IMT1 treatment or POLRMT silencing in primary OS cells led to a significant reduction in Akt1-S6K-S6 phosphorylation. Conversely, it was enhanced upon POLRMT overexpression. The restoration of Akt-mTOR activation through the introduction of a constitutively active S473D mutant Akt1 (caAkt1) mitigated IMT1-induced cytotoxicity in OS cells. In vivo, oral administration of IMT1 robustly curtailed the growth of OS xenografts in nude mice. Furthermore, IMT1 suppressed POLRMT activity, impaired mitochondrial function, repressed Akt-mTOR activation, and induced apoptosis within xenograft tissues. Collectively, these findings underscore the potent growth-inhibitory effects attributed to IMT1 via targeted POLRMT inhibition. The utilization of this POLRMT inhibitor carries substantial therapeutic promise in the context of OS treatment.
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Affiliation(s)
- Yang Kong
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Orthopedics, The First People's Hospital of ChuZhou, ChuZhou, China
| | - Xiangrong Li
- Department of Pharmacy, Kongjiang Hospital of Yangpu District, Shanghai, China
| | - Huanle Zhang
- Department of Radiotherapy, Suzhou Ninth People's Hospital, Suzhou, China
| | - Bin Fu
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hua-Ye Jiang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hui-Lin Yang
- Department of Orthopedics, the First Affiliated Hospital of Soochow University, Suzhou, China.
- Orthopedic Institute, Medical College, Soochow University, Suzhou, China.
| | - Jin Dai
- Department of Orthopedics, Suzhou Wujiang District Children's Hospital, Suzhou, China.
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21
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Platz KR, Rudisel EJ, Paluch KV, Laurin TR, Dittenhafer-Reed KE. Assessing the Role of Post-Translational Modifications of Mitochondrial RNA Polymerase. Int J Mol Sci 2023; 24:16050. [PMID: 38003238 PMCID: PMC10671485 DOI: 10.3390/ijms242216050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
The mitochondrial proteome is subject to abundant post-translational modifications, including lysine acetylation and phosphorylation of serine, threonine, and tyrosine. The biological function of the majority of these protein modifications is unknown. Proteins required for the transcription and translation of mitochondrial DNA (mtDNA) are subject to modification. This suggests that reversible post-translational modifications may serve as a regulatory mechanism for mitochondrial gene transcription, akin to mechanisms controlling nuclear gene expression. We set out to determine whether acetylation or phosphorylation controls the function of mitochondrial RNA polymerase (POLRMT). Mass spectrometry was used to identify post-translational modifications on POLRMT. We analyzed three POLRMT modification sites (lysine 402, threonine 315, threonine 993) found in distinct structural regions. Amino acid point mutants that mimic the modified and unmodified forms of POLRMT were employed to measure the effect of acetylation or phosphorylation on the promoter binding ability of POLRMT in vitro. We found a slight decrease in binding affinity for the phosphomimic at threonine 315. We did not identify large changes in viability, mtDNA content, or mitochondrial transcript level upon overexpression of POLRMT modification mimics in HeLa cells. Our results suggest minimal biological impact of the POLRMT post-translational modifications studied in our system.
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22
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Tocantins C, Martins JD, Rodrigues ÓM, Grilo LF, Diniz MS, Stevanovic-Silva J, Beleza J, Coxito P, Rizo-Roca D, Santos-Alves E, Rios M, Carvalho L, Moreno AJ, Ascensão A, Magalhães J, Oliveira PJ, Pereira SP. Metabolic mitochondrial alterations prevail in the female rat heart 8 weeks after exercise cessation. Eur J Clin Invest 2023; 53:e14069. [PMID: 37525474 DOI: 10.1111/eci.14069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
BACKGROUND The consumption of high-caloric diets strongly contributes to the development of non-communicable diseases (NCDs), including cardiovascular disease, the leading cause of mortality worldwide. Exercise (along with diet intervention) is one of the primary non-pharmacological approaches to promote a healthier lifestyle and counteract the rampant prevalence of NCDs. The present study evaluated the effects of exercise cessation after a short period training on the cardiac metabolic and mitochondrial function of female rats. METHODS Seven-week-old female Sprague-Dawley rats were fed a control or a high-fat, high-sugar (HFHS) diet and, after 7 weeks, the animals were kept on a sedentary lifestyle or submitted to endurance exercise for 3 weeks (6 days per week, 20-60 min/day). The cardiac samples were analysed 8 weeks after exercise cessation. RESULTS The consumption of the HFHS diet triggered impaired glucose tolerance, whereas the HFHS diet and physical exercise resulted in different responses in plasma adiponectin and leptin levels. Cardiac mitochondrial respiration efficiency was decreased by the HFHS diet consumption, which led to reduced ATP and increased NAD(P)H mitochondrial levels, which remained prevented by exercise 8 weeks after cessation. Exercise training-induced cardiac adaptations in redox balance, namely increased relative expression of Nrf2 and downstream antioxidant enzymes persist after an eight-week exercise cessation period. CONCLUSIONS Endurance exercise modulated cardiac redox balance and mitochondrial efficiency in female rats fed a HFHS diet. These findings suggest that exercise may elicit cardiac adaptations crucial for its role as a non-pharmacological intervention for individuals at risk of developing NCDs.
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Affiliation(s)
- Carolina Tocantins
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - João D Martins
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Óscar M Rodrigues
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Luís F Grilo
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Mariana S Diniz
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- PhD Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Jelena Stevanovic-Silva
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - Jorge Beleza
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - Pedro Coxito
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - David Rizo-Roca
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
- Department of Cell Biology, Physiology & Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Estela Santos-Alves
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - Manoel Rios
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - Lina Carvalho
- Institute of Anatomical and Molecular Pathology, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - António J Moreno
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Department of Life Sciences, School of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - António Ascensão
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - José Magalhães
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
| | - Paulo J Oliveira
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Susana P Pereira
- CNC-Center for Neuroscience and Cell Biology, CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Laboratory of Metabolism and Exercise (LaMetEx), Research Centre in Physical Activity, Health and Leisure (CIAFEL), Laboratory for Integrative and Translational Research in Population Health (ITR), Faculty of Sports, University of Porto, Porto, Portugal
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23
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McShane E, Couvillion M, Ietswaart R, Prakash G, Smalec BM, Soto I, Baxter-Koenigs AR, Choquet K, Churchman LS. A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527880. [PMID: 36824735 PMCID: PMC9948965 DOI: 10.1101/2023.02.09.527880] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Oxidative phosphorylation (OXPHOS) complexes, encoded by both mitochondrial and nuclear DNA, are essential producers of cellular ATP, but how nuclear and mitochondrial gene expression steps are coordinated to achieve balanced OXPHOS biogenesis remains unresolved. Here, we present a parallel quantitative analysis of the human nuclear and mitochondrial messenger RNA (mt-mRNA) life cycles, including transcript production, processing, ribosome association, and degradation. The kinetic rates of nearly every stage of gene expression differed starkly across compartments. Compared to nuclear mRNAs, mt-mRNAs were produced 700-fold higher, degraded 5-fold faster, and accumulated to 170-fold higher levels. Quantitative modeling and depletion of mitochondrial factors, LRPPRC and FASTKD5, identified critical points of mitochondrial regulatory control, revealing that the mitonuclear expression disparities intrinsically arise from the highly polycistronic nature of human mitochondrial pre-mRNA. We propose that resolving these differences requires a 100-fold slower mitochondrial translation rate, illuminating the mitoribosome as a nexus of mitonuclear co-regulation.
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Affiliation(s)
- Erik McShane
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Robert Ietswaart
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gyan Prakash
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M. Smalec
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iliana Soto
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Karine Choquet
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Current affiliation: Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - L. Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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24
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Yuan Y, Tian Y, Jiang H, Cai LY, Song J, Peng R, Zhang XM. Mechanism of PGC-1α-mediated mitochondrial biogenesis in cerebral ischemia-reperfusion injury. Front Mol Neurosci 2023; 16:1224964. [PMID: 37492523 PMCID: PMC10363604 DOI: 10.3389/fnmol.2023.1224964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023] Open
Abstract
Cerebral ischemia-reperfusion injury (CIRI) is a series of cascade reactions that occur after blood flow recanalization in the ischemic zone in patients with cerebral infarction, causing an imbalance in intracellular homeostasis through multiple pathologies such as increased oxygen free radicals, inflammatory response, calcium overload, and impaired energy metabolism, leading to mitochondrial dysfunction and ultimately apoptosis. Rescue of reversibly damaged neurons in the ischemic hemispheric zone is the key to saving brain infarction and reducing neurological deficits. Complex and active neurological functions are highly dependent on an adequate energy supply from mitochondria. Mitochondrial biogenesis (MB), a process that generates new functional mitochondria and restores normal mitochondrial function by replacing damaged mitochondria, is a major mechanism for maintaining intra-mitochondrial homeostasis and is involved in mitochondrial quality control to ameliorate mitochondrial dysfunction and thus protects against CIRI. The main regulator of MB is peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), which improves mitochondrial function to protect against CIRI by activating its downstream nuclear respiratory factor 1 (NRF1) and mitochondrial transcription factor A (TFAM) to promote mitochondrial genome replication and transcription. This paper provides a theoretical reference for the treatment of neurological impairment caused by CIRI by discussing the mechanisms of mitochondrial biogenesis during cerebral ischemia-reperfusion injury.
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Affiliation(s)
- Ying Yuan
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuan Tian
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Hui Jiang
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Luo-yang Cai
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Jie Song
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
| | - Rui Peng
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
- Sub-Health Institute Hubei University of Chinese Medicine, Wuhan, China
| | - Xiao-ming Zhang
- School of Acupuncture-Moxibustion and Orthopedics, Hubei University of Chinese Medicine, Wuhan, China
- Sub-Health Institute Hubei University of Chinese Medicine, Wuhan, China
- Hubei Provincial Collaborative Innovation Center for Preventive Treatment of Disease by Acupuncture, Wuhan, China
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25
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Kozhukhar N, Alexeyev MF. 35 Years of TFAM Research: Old Protein, New Puzzles. BIOLOGY 2023; 12:823. [PMID: 37372108 DOI: 10.3390/biology12060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023]
Abstract
Transcription Factor A Mitochondrial (TFAM), through its contributions to mtDNA maintenance and expression, is essential for cellular bioenergetics and, therefore, for the very survival of cells. Thirty-five years of research on TFAM structure and function generated a considerable body of experimental evidence, some of which remains to be fully reconciled. Recent advancements allowed an unprecedented glimpse into the structure of TFAM complexed with promoter DNA and TFAM within the open promoter complexes. These novel insights, however, raise new questions about the function of this remarkable protein. In our review, we compile the available literature on TFAM structure and function and provide some critical analysis of the available data.
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Affiliation(s)
- Natalya Kozhukhar
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail F Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
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26
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Daglish SCD, Fennell EMJ, Graves LM. Targeting Mitochondrial DNA Transcription by POLRMT Inhibition or Depletion as a Potential Strategy for Cancer Treatment. Biomedicines 2023; 11:1598. [PMID: 37371693 PMCID: PMC10295849 DOI: 10.3390/biomedicines11061598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription of the mitochondrial genome is essential for the maintenance of oxidative phosphorylation (OXPHOS) and other functions directly related to this unique genome. Considerable evidence suggests that mitochondrial transcription is dysregulated in cancer and cancer metastasis and contributes significantly to cancer cell metabolism. Recently, inhibitors of the mitochondrial DNA-dependent RNA polymerase (POLRMT) were identified as potentially attractive new anti-cancer compounds. These molecules (IMT1, IMT1B) inactivate cancer cell metabolism through reduced transcription of mitochondrially-encoded OXPHOS subunits such as ND1-5 (Complex I) and COI-IV (Complex IV). Studies from our lab have discovered small molecule regulators of the mitochondrial matrix caseinolytic protease (ClpP) as probable inhibitors of mitochondrial transcription. These compounds activate ClpP proteolysis and lead to the rapid depletion of POLRMT and other matrix proteins, resulting in inhibition of mitochondrial transcription and growth arrest. Herein we present a comparison of POLRMT inhibition and ClpP activation, both conceptually and experimentally, and evaluate the results of these treatments on mitochondrial transcription, inhibition of OXPHOS, and ultimately cancer cell growth. We discuss the potential for targeting mitochondrial transcription as a cancer cell vulnerability.
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Affiliation(s)
| | | | - Lee M. Graves
- Department of Pharmacology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.C.D.D.); (E.M.J.F.)
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Lin CC, Wang YP, Sun YK, Chiu CH, Lin MW, Tzeng IS. Mitochondrial replication, transcription, and function in obstructive sleep apnea. Respir Physiol Neurobiol 2023:104066. [PMID: 37080370 DOI: 10.1016/j.resp.2023.104066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 03/31/2023] [Accepted: 04/17/2023] [Indexed: 04/22/2023]
Abstract
We assessed mitochondrial replication, transcription, and function in the upper airways of obstructive sleep apnea (OSA) patients and the effects of uvulopalatopharyngoplasty. Twenty subjects with mild and 40 with moderate to severe OSA requiring uvulopalatopharyngoplasty were included. Mitochondrial transcription factor A (TFAM) and peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) in uvula specimens were assessed by immunohistochemical staining, and their mRNA and protein expression was examined using reverse-transcription polymerase chain reaction and western blotting, respectively. The mitochondrial to nuclear DNA (Mt/N) ratio in the blood, exhaled breath condensate (EBC), and uvula was measured using quantitative reverse-transcription polymerase chain reaction. TFAM and PGC-1α protein concentrations in the plasma and EBC were determined using enzyme-linked immunosorbent assay. All tested parameters were higher in the OSA group than in the control. Three months later, 21 uvulopalatopharyngoplasty-responsive patients with OSA showed decreased TFAM and PGC-1α concentrations and EBC Mt/N ratio while these remained high in 19 uvulopalatopharyngoplasty-unresponsive patients. The OSA group showed severe inflammation, increased mitochondrial replication and transcription-related signaling, and mitochondrial dysfunction in the uvula. Successful OSA treatment using uvulopalatopharyngoplasty restored the TFAM and PGC-1α levels and EBC Mt/N ratio.
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Affiliation(s)
- Ching-Chi Lin
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan.
| | - Ying-Piao Wang
- Department of Otolaryngology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Yi-Kun Sun
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Chung-Hsin Chiu
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Mei-Wei Lin
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - I-Shiang Tzeng
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
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Rubalcava-Gracia D, García-Villegas R, Larsson NG. No role for nuclear transcription regulators in mammalian mitochondria? Mol Cell 2023; 83:832-842. [PMID: 36182692 DOI: 10.1016/j.molcel.2022.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/17/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
Although the mammalian mtDNA transcription machinery is simple and resembles bacteriophage systems, there are many reports that nuclear transcription regulators, as exemplified by MEF2D, MOF, PGC-1α, and hormone receptors, are imported into mammalian mitochondria and directly interact with the mtDNA transcription machinery. However, the supporting experimental evidence for this concept is open to alternate interpretations, and a main issue is the difficulty in distinguishing indirect regulation of mtDNA transcription, caused by altered nuclear gene expression, from direct intramitochondrial effects. We provide a critical discussion and experimental guidelines to stringently assess roles of intramitochondrial factors implicated in direct regulation of mammalian mtDNA transcription.
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Affiliation(s)
- Diana Rubalcava-Gracia
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rodolfo García-Villegas
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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29
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Khozhukhar N, Spadafora D, Rodriguez Rodriguez YA, Fayzulin R, Alexeyev M. Generation of Mammalian Cells Devoid of Mitochondrial DNA (ρ 0 cells). Curr Protoc 2023; 3:e679. [PMID: 36809687 PMCID: PMC10151036 DOI: 10.1002/cpz1.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
To cope with DNA damage, mitochondria have developed a pathway whereby severely damaged or unrepairable mitochondrial DNA (mtDNA) molecules can be discarded and degraded, after which new molecules are synthesized using intact templates. In this unit, we describe a method that harnesses this pathway to eliminate mtDNA from mammalian cells by transiently overexpressing the Y147A mutant of human uracil-N-glycosylase (mUNG1) in mitochondria. We also provide alternate protocols for mtDNA elimination using either combined treatment with ethidium bromide (EtBr) and dideoxycytidine (ddC) or clustered regulatory interspersed short palindromic repeat (CRISPR)-Cas9-mediated knockout of TFAM or other genes essential for mtDNA replication. Support protocols detail approaches for several processes: (1) genotyping ρ0 cells of human, mouse, and rat origin by polymerase chain reaction (PCR); (2) quantification of mtDNA by quantitative PCR (qPCR); (3) preparation of calibrator plasmids for mtDNA quantification; and (4) quantification of mtDNA by direct droplet digital PCR (dddPCR). © 2023 Wiley Periodicals LLC. Basic Protocol: Inducing mtDNA loss with mUNG1 Alternate Protocol 1: Generation of ρ0 cells by mtDNA depletion with EtBr and ddC Alternate Protocol 2: Generation of ρ0 cells by knocking out genes critical for mtDNA replication Support Protocol 1: Genotyping ρ0 cells by DirectPCR Support Protocol 2: Determination of mtDNA copy number by qPCR Support Protocol 3: Preparation of calibrator plasmid for qPCR Support Protocol 4: Determination of mtCN by direct droplet digital PCR (dddPCR).
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Affiliation(s)
| | | | | | - Rafik Fayzulin
- University of South Alabama, Department of Physiology and Cell Biology
| | - Mikhail Alexeyev
- University of South Alabama, Department of Physiology and Cell Biology
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The N-terminal domain of human mitochondrial helicase Twinkle has DNA-binding activity crucial for supporting processive DNA synthesis by polymerase γ. J Biol Chem 2022; 299:102797. [PMID: 36528058 PMCID: PMC9860392 DOI: 10.1016/j.jbc.2022.102797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
Twinkle is the ring-shaped replicative helicase within the human mitochondria with high homology to bacteriophage T7 gp4 helicase-primase. Unlike many orthologs of Twinkle, the N-terminal domain (NTD) of human Twinkle has lost its primase activity through evolutionarily acquired mutations. The NTD has no demonstrated activity thus far; its role has remained unclear. Here, we biochemically characterize the isolated NTD and C-terminal domain (CTD) with linker to decipher their contributions to full-length Twinkle activities. This novel CTD construct hydrolyzes ATP, has weak DNA unwinding activity, and assists DNA polymerase γ (Polγ)-catalyzed strand-displacement synthesis on short replication forks. However, CTD fails to promote multikilobase length product formation by Polγ in rolling-circle DNA synthesis. Thus, CTD retains all the motor functions but struggles to implement them for processive translocation. We show that NTD has DNA-binding activity, and its presence stabilizes Twinkle oligomerization. CTD oligomerizes on its own, but the loss of NTD results in heterogeneously sized oligomeric species. The CTD also exhibits weaker and salt-sensitive DNA binding compared with full-length Twinkle. Based on these results, we propose that NTD directly contributes to DNA binding and holds the DNA in place behind the central channel of the CTD like a "doorstop," preventing helicase slippages and sustaining processive unwinding. Consistent with this model, mitochondrial single-stranded DNA-binding protein (mtSSB) compensate for the NTD loss and partially restore kilobase length DNA synthesis by CTD and Polγ. The implications of our studies are foundational for understanding the mechanisms of disease-causing Twinkle mutants that lie in the NTD.
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Marmolejo-Garza A, Medeiros-Furquim T, Rao R, Eggen BJL, Boddeke E, Dolga AM. Transcriptomic and epigenomic landscapes of Alzheimer's disease evidence mitochondrial-related pathways. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119326. [PMID: 35839870 DOI: 10.1016/j.bbamcr.2022.119326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/06/2023]
Abstract
Alzheimers disease (AD) is the main cause of dementia and it is defined by cognitive decline coupled to extracellular deposit of amyloid-beta protein and intracellular hyperphosphorylation of tau protein. Historically, efforts to target such hallmarks have failed in numerous clinical trials. In addition to these hallmark-targeted approaches, several clinical trials focus on other AD pathological processes, such as inflammation, mitochondrial dysfunction, and oxidative stress. Mitochondria and mitochondrial-related mechanisms have become an attractive target for disease-modifying strategies, as mitochondrial dysfunction prior to clinical onset has been widely described in AD patients and AD animal models. Mitochondrial function relies on both the nuclear and mitochondrial genome. Findings from omics technologies have shed light on AD pathophysiology at different levels (e.g., epigenome, transcriptome and proteome). Most of these studies have focused on the nuclear-encoded components. The first part of this review provides an updated overview of the mechanisms that regulate mitochondrial gene expression and function. The second part of this review focuses on evidence of mitochondrial dysfunction in AD. We have focused on published findings and datasets that study AD. We analyzed published data and provide examples for mitochondrial-related pathways. These pathways are strikingly dysregulated in AD neurons and glia in sex-, cell- and disease stage-specific manners. Analysis of mitochondrial omics data highlights the involvement of mitochondria in AD, providing a rationale for further disease modeling and drug targeting.
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Affiliation(s)
- Alejandro Marmolejo-Garza
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tiago Medeiros-Furquim
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ramya Rao
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands.
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The mitochondrial RNA polymerase POLRMT promotes skin squamous cell carcinoma cell growth. Cell Death Dis 2022; 8:347. [PMID: 35922422 PMCID: PMC9349297 DOI: 10.1038/s41420-022-01148-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/08/2022]
Abstract
RNA polymerase mitochondrial (POLRMT) expression and the potential biological functions in skin squamous cell carcinoma (SCC) were explored. We showed that POLRMT is significantly elevated in skin SCC. Genetic depletion of POLRMT, using shRNA-induced knockdown or CRISPR/Cas9-mediated knockout (KO), resulted in profound anti-skin SCC cell activity. In patient-derived primary skin SCC cells or immortalized lines (A431 and SCC-9), POLRMT shRNA or KO potently suppressed mitochondrial DNA (mtDNA) transcription and suppressed cell viability, proliferation and migration. POLRMT shRNA or KO impaired mitochondrial functions in different skin SCC cells, leading to production of ROS (reactive oxygen species), depolarization of mitochondria and depletion of ATP. Moreover, mitochondrial apoptosis cascade was induced in POLRMT-depleted skin SCC cells. IMT1, a POLRMT inhibitor, largely inhibited proliferation and migration, while inducing depolarization of mitochondria and apoptosis in primary skin SCC cells. Contrarily, ectopic overexpression of POLRMT increased mtDNA transcription and augmented skin SCC cell growth. Importantly, POLRMT shRNA adeno-associated virus injection robustly hindered growth of the subcutaneous A431 xenografts in mice. In the POLRMT shRNA virus-treated A431 xenograft tissues, POLRMT depletion, mtDNA transcription inhibition, cell apoptosis, lipid peroxidation and ATP depletion were detected. Together, overexpressed POLRMT increases mtDNA transcription and promotes skin SCC growth.
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Carbajosa G, Ali AT, Hodgkinson A. Identification of human mitochondrial RNA cleavage sites and candidate RNA processing factors. BMC Biol 2022; 20:168. [PMID: 35869520 PMCID: PMC9308231 DOI: 10.1186/s12915-022-01373-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The human mitochondrial genome is transcribed as long strands of RNA containing multiple genes, which require post-transcriptional cleavage and processing to release functional gene products that play vital roles in cellular energy production. Despite knowledge implicating mitochondrial post-transcriptional processes in pathologies such as cancer, cardiovascular disease and diabetes, very little is known about the way their function varies on a human population level and what drives changes in these processes to ultimately influence disease risk. Here, we develop a method to detect and quantify mitochondrial RNA cleavage events from standard RNA sequencing data and apply this approach to human whole blood data from > 1000 samples across independent cohorts. RESULTS We detect 54 putative mitochondrial RNA cleavage sites that not only map to known gene boundaries, short RNA ends and RNA modification sites, but also occur at internal gene positions, suggesting novel mitochondrial RNA cleavage junctions. Inferred RNA cleavage rates correlate with mitochondrial-encoded gene expression across individuals, suggesting an impact on downstream processes. Furthermore, by comparing inferred cleavage rates to nuclear genetic variation and gene expression, we implicate multiple genes in modulating mitochondrial RNA cleavage (e.g. MRPP3, TBRG4 and FASTKD5), including a potentially novel role for RPS19 in influencing cleavage rates at a site near to the MTATP6-COX3 junction that we validate using shRNA knock down data. CONCLUSIONS We identify novel cleavage junctions associated with mitochondrial RNA processing, as well as genes newly implicated in these processes, and detect the potential impact of variation in cleavage rates on downstream phenotypes and disease processes. These results highlight the complexity of the mitochondrial transcriptome and point to novel mechanisms through which nuclear-encoded genes can potentially influence key mitochondrial processes.
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Affiliation(s)
- Guillermo Carbajosa
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Aminah T Ali
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Alan Hodgkinson
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK.
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Kozhukhar N, Spadafora D, Rodriguez YAR, Alexeyev MF. A Method for In Situ Reverse Genetic Analysis of Proteins Involved mtDNA Replication. Cells 2022; 11:2168. [PMID: 35883613 PMCID: PMC9316749 DOI: 10.3390/cells11142168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/29/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
The unavailability of tractable reverse genetic analysis approaches represents an obstacle to a better understanding of mitochondrial DNA replication. Here, we used CRISPR-Cas9 mediated gene editing to establish the conditional viability of knockouts in the key proteins involved in mtDNA replication. This observation prompted us to develop a set of tools for reverse genetic analysis in situ, which we called the GeneSwap approach. The technique was validated by identifying 730 amino acid (aa) substitutions in the mature human TFAM that are conditionally permissive for mtDNA replication. We established that HMG domains of TFAM are functionally independent, which opens opportunities for engineering chimeric TFAMs with customized properties for studies on mtDNA replication, mitochondrial transcription, and respiratory chain function. Finally, we present evidence that the HMG2 domain plays the leading role in TFAM species-specificity, thus indicating a potential pathway for TFAM-mtDNA evolutionary co-adaptations.
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Affiliation(s)
| | | | | | - Mikhail F. Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA; (N.K.); (D.S.); (Y.A.R.R.)
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Downregulation of PTCD1 in Bladder Urothelial Carcinoma Predicts Poor Prognosis and Levels of Immune Infiltration. JOURNAL OF ONCOLOGY 2022; 2022:1146186. [PMID: 35799606 PMCID: PMC9256401 DOI: 10.1155/2022/1146186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Pentatricopeptide repeat domain 1 (PTCD1) was reported to regulate mitochondrial metabolism and oxidative phosphorylation. However, the effect and mechanism of PTCD1 in the development of bladder urothelial carcinoma (BLCA) remain unclear. The databases from The Cancer Genome Atlas (TCGA) and Human Protein Atlas (HPA) were used to analyze the expression changes, clinical features, and prognostic values of PTCD1. A nomogram was built to predict the prognostic outcomes of BLCA cases. The potential genes interacting with PTCD1 were explored by Weighted Gene Coexpression Network Analysis (WGCNA). The estimation of associations between PTCD1 and tumor mutations, tumor immunities, and m6A methylations was performed. The study found that the gradual decrease of PTCD1 expression was observed with the increase of stage and grade. Low PTCD1 expression was greatly correlated with higher pathological stage, N stage, and poor prognosis in TCGA cohorts; interestingly, low-grade BLCA cases all exhibited high expression of PTCD1. HPA database analysis implied that the expression of PTCD1 protein in BLCA was lower than that in normal bladder tissue, and the protein expression of PTCD1 in high-grade BLCA was lower than that in low-grade BLCA. Multivariate Cox regression analysis indicated that PTCD1 may serve as an independent factor influencing prognosis of BLCA. Mechanistically, PTCD1 played a regulatory role in BLCA progression through multiple tumor-related pathways containing PI3K-Akt signaling, ECM-receptor interaction, oxidative phosphorylation, and extracellular matrix organization. WGCNA reported that PTCD1 had a strong positive correlation with POLR2J, ZNHT1, ATP5MF, PDAP1, BUD31, and COPS6. Besides, the mRNA expression of PTCD1 was negatively associated with immune cells' infiltrations, immune functions, and checkpoints, especially with some m6A methylation regulators in BLCA. In sum, downregulation of PTCD1 expression may be involved in the development of BLCA and remarkably correlated with poor prognosis. Meantime, it showed an influence in immune cell infiltration and may serve as an agreeable prognostic indicator in BLCA.
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Abstract
In the course of its short history, mitochondrial DNA (mtDNA) has made a long journey from obscurity to the forefront of research on major biological processes. mtDNA alterations have been found in all major disease groups, and their significance remains the subject of intense research. Despite remarkable progress, our understanding of the major aspects of mtDNA biology, such as its replication, damage, repair, transcription, maintenance, etc., is frustratingly limited. The path to better understanding mtDNA and its role in cells, however, remains torturous and not without errors, which sometimes leave a long trail of controversy behind them. This review aims to provide a brief summary of our current knowledge of mtDNA and highlight some of the controversies that require attention from the mitochondrial research community.
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Affiliation(s)
- Inna Shokolenko
- Department of Biomedical Sciences, Pat Capps Covey College of Allied Health Professions, University of South Alabama, Mobile, AL 36688, USA
| | - Mikhail Alexeyev
- Department of Physiology and Cell Biology, University of South Alabama, Mobile, AL 36688, USA
- Correspondence:
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37
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Schreier HK, Wiehe RS, Ricchetti M, Wiesmüller L. Polymerase ζ is Involved in Mitochondrial DNA Maintenance Processes in Concert with APE1 Activity. Genes (Basel) 2022; 13:genes13050879. [PMID: 35627264 PMCID: PMC9141751 DOI: 10.3390/genes13050879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial DNA (mtDNA) damaged by reactive oxygen species (ROS) triggers so far poorly understood processes of mtDNA maintenance that are coordinated by a complex interplay among DNA repair, DNA degradation, and DNA replication. This study was designed to identify the proteins involved in mtDNA maintenance by applying a special long-range PCR, reflecting mtDNA integrity in the minor arc. A siRNA screening of literature-based candidates was performed under conditions of enforced oxidative phosphorylation revealing the functional group of polymerases and therein polymerase ζ (POLZ) as top hits. Thus, POLZ knockdown caused mtDNA accumulation, which required the activity of the base excision repair (BER) nuclease APE1, and was followed by compensatory mtDNA replication determined by the single-cell mitochondrial in situ hybridization protocol (mTRIP). Quenching reactive oxygen species (ROS) in mitochondria unveiled an additional, ROS-independent involvement of POLZ in the formation of a typical deletion in the minor arc region. Together with data demonstrating the localization of POLZ in mitochondria, we suggest that POLZ plays a significant role in mtDNA turnover, particularly under conditions of oxidative stress.
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Affiliation(s)
- Heike Katrin Schreier
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Rahel Stefanie Wiehe
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, CEDEX 15, 75724 Paris, France;
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
- Correspondence:
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38
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Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 2022; 23:606-623. [PMID: 35459860 DOI: 10.1038/s41576-022-00480-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
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Liu Y, Chen Z, Wang ZH, Delaney KM, Tang J, Pirooznia M, Lee DY, Tunc I, Li Y, Xu H. The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster. Nat Cell Biol 2022; 24:757-765. [PMID: 35449456 DOI: 10.1038/s41556-022-00887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 03/08/2022] [Indexed: 11/09/2022]
Abstract
Mitochondrial DNA (mtDNA) replication and transcription are of paramount importance to cellular energy metabolism. Mitochondrial RNA polymerase is thought to be the primase for mtDNA replication. However, it is unclear how this enzyme, which normally transcribes long polycistronic RNAs, can produce short RNA oligonucleotides to initiate mtDNA replication. We show that the PPR domain of Drosophila mitochondrial RNA polymerase (PolrMT) has 3'-to-5' exoribonuclease activity, which is indispensable for PolrMT to synthesize short RNA oligonucleotides and prime DNA replication in vitro. An exoribonuclease-deficient mutant, PolrMTE423P, partially restores mitochondrial transcription but fails to support mtDNA replication when expressed in PolrMT-mutant flies, indicating that the exoribonuclease activity is necessary for mtDNA replication. In addition, overexpression of PolrMTE423P in adult flies leads to severe neuromuscular defects and a marked increase in mtDNA transcript errors, suggesting that exoribonuclease activity may contribute to the proofreading of mtDNA transcription.
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Affiliation(s)
- Yi Liu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhe Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zong-Heng Wang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine M Delaney
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Juanjie Tang
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Pirooznia
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Duck-Yeon Lee
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ilker Tunc
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuesheng Li
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hong Xu
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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40
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Miranda M, Bonekamp NA, Kühl I. Starting the engine of the powerhouse: mitochondrial transcription and beyond. Biol Chem 2022; 403:779-805. [PMID: 35355496 DOI: 10.1515/hsz-2021-0416] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 03/09/2022] [Indexed: 12/25/2022]
Abstract
Mitochondria are central hubs for cellular metabolism, coordinating a variety of metabolic reactions crucial for human health. Mitochondria provide most of the cellular energy via their oxidative phosphorylation (OXPHOS) system, which requires the coordinated expression of genes encoded by both the nuclear (nDNA) and mitochondrial genomes (mtDNA). Transcription of mtDNA is not only essential for the biogenesis of the OXPHOS system, but also generates RNA primers necessary to initiate mtDNA replication. Like the prokaryotic system, mitochondria have no membrane-based compartmentalization to separate the different steps of mtDNA maintenance and expression and depend entirely on nDNA-encoded factors imported into the organelle. Our understanding of mitochondrial transcription in mammalian cells has largely progressed, but the mechanisms regulating mtDNA gene expression are still poorly understood despite their profound importance for human disease. Here, we review mechanisms of mitochondrial gene expression with a focus on the recent findings in the field of mammalian mtDNA transcription and disease phenotypes caused by defects in proteins involved in this process.
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Affiliation(s)
- Maria Miranda
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, D-50931, Germany
| | - Nina A Bonekamp
- Department of Neuroanatomy, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, Heidelberg University, Mannheim, D-68167, Germany
| | - Inge Kühl
- Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC), UMR9198, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, F-91190, France
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Yu HJ, Xiao GL, Zhao YY, Wang XX, Lan R. Targeting Mitochondrial Metabolism and RNA Polymerase POLRMT to Overcome Multidrug Resistance in Cancer. Front Chem 2022; 9:775226. [PMID: 34976949 PMCID: PMC8716502 DOI: 10.3389/fchem.2021.775226] [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: 09/22/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Clinically, the prognosis of tumor therapy is fundamentally affected by multidrug resistance (MDR), which is primarily a result of enhanced drug efflux mediated by channels in the membrane that reduce drug accumulation in tumor cells. How to restore the sensitivity of tumor cells to chemotherapy is an ongoing and pressing clinical issue. There is a prevailing view that tumor cells turn to glycolysis for energy supply due to hypoxia. However, studies have shown that mitochondria also play crucial roles, such as providing intermediates for biosynthesis through the tricarboxylic acid (TCA) cycle and a plenty of ATP to fuel cells through the complete breakdown of organic matter by oxidative phosphorylation (OXPHOS). High OXPHOS have been found in some tumors, particularly in cancer stem cells (CSCs), which possess increased mitochondria mass and may be depends on OXPHOS for energy supply. Therefore, they are sensitive to inhibitors of mitochondrial metabolism. In view of this, we should consider mitochondrial metabolism when developing drugs to overcome MDR, where mitochondrial RNA polymerase (POLRMT) would be the focus, as it is responsible for mitochondrial gene expression. Inhibition of POLRMT could disrupt mitochondrial metabolism at its source, causing an energy crisis and ultimately eradicating tumor cells. In addition, it may restore the energy supply of MDR cells to glycolysis and re-sensitize them to conventional chemotherapy. Furthermore, we discuss the rationale and strategies for designing new therapeutic molecules for MDR cancers by targeting POLRMT.
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Affiliation(s)
- Hui-Jing Yu
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Guan-Li Xiao
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Yu-Ying Zhao
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Xin-Xin Wang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
| | - Rongfeng Lan
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Shenzhen University Health Science Center, Shenzhen, China
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Horibe S, Ishikawa K, Nakada K, Wake M, Takeda N, Tanaka T, Kawauchi S, Sasaki N, Rikitake Y. Mitochondrial DNA mutations are involved in the acquisition of cisplatin resistance in human lung cancer A549 cells. Oncol Rep 2021; 47:32. [PMID: 34935060 PMCID: PMC8717125 DOI: 10.3892/or.2021.8243] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
The efficacy of cisplatin (CDDP) has been demonstrated in the treatment of various cancers as monotherapy and combination therapy with immunotherapy. However, acquired CDDP resistance is a major obstacle to successful treatment. In the present study, the mechanisms underlying acquired CDDP resistance were examined using ACR20 cells, which are CDDP-resistant cells derived from A549 lung cancer cells. CDDP induces cytotoxicity by binding nuclear DNA and generating reactive oxygen species (ROS). Contrary to our expectation, ROS levels were elevated in ACR20 cells not treated with CDDP. Pretreatment with an ROS inhibitor enhanced the sensitivity of ACR20 cells to CDDP and prevented the activation of nuclear factor (NF)-кB signaling and upregulation of inhibitor of apoptosis proteins (IAPs). Notably, evaluation of the mitochondrial oxygen consumption rate and mitochondrial superoxide levels revealed a deterioration of mitochondrial function in ACR20 cells. Mitochondrial DNA PCR-RFLP analysis revealed four mutations with varying percentage levels in ACR20 cells. In addition, in cytoplasmic hybrids with mitochondria from ACR20 cells, intrinsic ROS levels were elevated, expression of IAPs was increased, and complex I activity and sensitivity to CDDP were decreased. Analysis of three-dimensional structure data indicated that a mutation (ND2 F40L) may impact the proton translocation pathway, thereby affecting mitochondrial complex I activity. Together, these findings suggest that intrinsic ROS levels were elevated by mitochondrial DNA mutations, which decreased the sensitivity to CDDP via activation of NF-κB signaling and induction of IAP expression in ACR20 cells. These findings indicate that newly identified mutations in mitochondrial DNA may lead to acquired cisplatin resistance in cancer.
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Affiliation(s)
- Sayo Horibe
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, Higashinada‑ku, Kobe, Hyogo 658‑8558, Japan
| | - Kaori Ishikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305‑8572, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305‑8572, Japan
| | - Masaki Wake
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, Yakushiji, Shimotsuke‑shi, Tochigi 329‑0498, Japan
| | - Norihiko Takeda
- Division of Cardiology and Metabolism, Center for Molecular Medicine, Jichi Medical University, Yakushiji, Shimotsuke‑shi, Tochigi 329‑0498, Japan
| | - Toru Tanaka
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, Higashinada‑ku, Kobe, Hyogo 658‑8558, Japan
| | - Shoji Kawauchi
- Comprehensive Education and Research Center, Kobe Pharmaceutical University, Higashinada‑ku, Kobe, Hyogo 658‑8558, Japan
| | - Naoto Sasaki
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, Higashinada‑ku, Kobe, Hyogo 658‑8558, Japan
| | - Yoshiyuki Rikitake
- Laboratory of Medical Pharmaceutics, Kobe Pharmaceutical University, Higashinada‑ku, Kobe, Hyogo 658‑8558, Japan
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Wei WS, Wang N, Deng MH, Dong P, Liu JY, Xiang Z, Li XD, Li ZY, Liu ZH, Peng YL, Li Z, Jiang LJ, Yao K, Ye YL, Lu WH, Zhang ZL, Zhou FJ, Liu ZW, Xie D, Yu CP. LRPPRC regulates redox homeostasis via the circANKHD1/FOXM1 axis to enhance bladder urothelial carcinoma tumorigenesis. Redox Biol 2021; 48:102201. [PMID: 34864630 PMCID: PMC8645923 DOI: 10.1016/j.redox.2021.102201] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/03/2023] Open
Abstract
Reactive oxygen species (ROS) which are continuously generated mainly by mitochondria, have been proved to play an important role in the stress signaling of cancer cells. Moreover, pentatricopeptide repeat (PPR) proteins have been suggested to take part in mitochondrial metabolism. However, the mechanisms integrating the actions of these distinct networks in urothelial carcinoma of the bladder (UCB) pathogenesis are elusive. In this study, we found that leucine rich pentatricopeptide repeat containing (LRPPRC) was frequently upregulated in UCB and that it was an independent prognostic factor in UCB. We further revealed that LRPPRC promoted UCB tumorigenesis by regulating the intracellular ROS homeostasis. Mechanistically, LRPPRC modulates ROS balance and protects UCB cells from oxidative stress via mt-mRNA metabolism and the circANKHD1/FOXM1 axis. In addition, the SRA stem-loop interacting RNA binding protein (SLIRP) directly interacted with LRPPRC to protect it from ubiquitination and proteasomal degradation. Notably, we showed that LRPPRC modulated the tumorigenesis of UCB cells in a circANKHD1-FOXM1-dependent manner. In conclusion, LRPPRC exerts critical roles in regulating UCB redox homeostasis and tumorigenesis, and is a prognostic factor for UCB; suggesting that LRPPRC may serve as an exploitable therapeutic target in UCB.
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Affiliation(s)
- Wen-Su Wei
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Ning Wang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Min-Hua Deng
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Pei Dong
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Jian-Ye Liu
- Department of Urology, Xiangya Third Hospital, No. 106, 2nd Zhongshan Road, Changsha, PR China
| | - Zhen Xiang
- Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Xiang-Dong Li
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Zhi-Yong Li
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Zhen-Hua Liu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Yu-Lu Peng
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Zhen Li
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Li-Juan Jiang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Kai Yao
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Yun-Lin Ye
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Wen-Hua Lu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Zhi-Ling Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Fang-Jian Zhou
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China
| | - Zhuo-Wei Liu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China.
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Chun-Ping Yu
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, No. 651, Dongfeng Road East, Guangzhou, PR China; Department of Urology, Sun Yat-Sen University Cancer Center, No. 651, Dongfeng Road East, Guangzhou, PR China.
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Velasco-Ruiz A, Nuñez-Torres R, Pita G, Wildiers H, Lambrechts D, Hatse S, Delombaerde D, Van Brussel T, Alonso MR, Alvarez N, Herraez B, Vulsteke C, Zamora P, Lopez-Fernandez T, Gonzalez-Neira A. POLRMT as a Novel Susceptibility Gene for Cardiotoxicity in Epirubicin Treatment of Breast Cancer Patients. Pharmaceutics 2021; 13:1942. [PMID: 34834357 PMCID: PMC8622627 DOI: 10.3390/pharmaceutics13111942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/06/2021] [Accepted: 11/12/2021] [Indexed: 11/27/2022] Open
Abstract
Anthracyclines are among the most used chemotherapeutic agents in breast cancer (BC). However their use is hampered by anthracycline-induced cardiotoxicity (AIC). The currently known clinical and genetic risk factors do not fully explain the observed inter-individual variability and only have a limited ability to predict which patients are more likely to develop this severe toxicity. To identify novel predictive genes, we conducted a two-stage genome-wide association study in epirubicin-treated BC patients. In the discovery phase, we genotyped over 700,000 single nucleotide variants in a cohort of 227 patients. The most interesting finding was rs62134260, located 4kb upstream of POLRMT (OR = 5.76, P = 2.23 × 10-5). We replicated this association in a validation cohort of 123 patients (P = 0.021). This variant regulates the expression of POLRMT, a gene that encodes a mitochondrial DNA-directed RNA polymerase, responsible for mitochondrial gene expression. Individuals harbouring the risk allele had a decreased expression of POLRMT in heart tissue that may cause an impaired capacity to maintain a healthy mitochondrial population in cardiomyocytes under stressful conditions, as is treatment with epirubicin. This finding suggests a novel molecular mechanism involved in the development of AIC and may improve our ability to predict patients who are at risk.
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Affiliation(s)
- Alejandro Velasco-Ruiz
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
| | - Rocio Nuñez-Torres
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
| | - Guillermo Pita
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
| | - Hans Wildiers
- Department of General Medical Oncology, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Multidisciplinary Breast Centre, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Laboratory of Experimental Oncology (LEO), Department of Oncology, Katholieke Universiteit (KU) Leuven, Oude Markt 13, 3000 Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Centre for Cancer Biology (CCB), Flanders Institute for Biotechnology (VIB), Rijvisschestraat 120, 9052 Leuven, Belgium; (D.L.); (T.V.B.)
| | - Sigrid Hatse
- Multidisciplinary Breast Centre, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium;
- Laboratory of Experimental Oncology (LEO), Department of Oncology, Katholieke Universiteit (KU) Leuven, Oude Markt 13, 3000 Leuven, Belgium
| | - Danielle Delombaerde
- Integrated Cancer Center Ghent, Department of Medical Oncology, AZ Maria Middelares, 9000 Ghent, Belgium; (D.D.); (C.V.)
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Thomas Van Brussel
- Laboratory of Translational Genetics, Centre for Cancer Biology (CCB), Flanders Institute for Biotechnology (VIB), Rijvisschestraat 120, 9052 Leuven, Belgium; (D.L.); (T.V.B.)
| | - M. Rosario Alonso
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
| | - Nuria Alvarez
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
| | - Belen Herraez
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
| | - Christof Vulsteke
- Integrated Cancer Center Ghent, Department of Medical Oncology, AZ Maria Middelares, 9000 Ghent, Belgium; (D.D.); (C.V.)
- Center for Oncological Research (CORE), Integrated Personalized and Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Pilar Zamora
- Department of Medical Oncology, University Hospital La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain;
| | - Teresa Lopez-Fernandez
- Department of Cardiology, University Hospital La Paz, Paseo de la Castellana 261, 28046 Madrid, Spain;
| | - Anna Gonzalez-Neira
- Human Genotyping Unit, CeGen (Spanish National Genotyping Centre), Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Alamagro, 3, 28029 Madrid, Spain; (A.V.-R.); (R.N.-T.); (G.P.); (M.R.A.); (N.A.); (B.H.)
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Inatomi T, Matsuda S, Ishiuchi T, Do Y, Nakayama M, Abe S, Kasho K, Wanrooij S, Nakada K, Ichiyanagi K, Sasaki H, Yasukawa T, Kang D. TFB2M and POLRMT are essential for mammalian mitochondrial DNA replication. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119167. [PMID: 34744028 DOI: 10.1016/j.bbamcr.2021.119167] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022]
Abstract
Two classes of replication intermediates have been observed from mitochondrial DNA (mtDNA) in many mammalian tissue and cells with two-dimensional agarose gel electrophoresis. One is assigned to leading-strand synthesis in the absence of synchronous lagging-strand synthesis (strand-asynchronous replication), and the other has properties of coupled leading- and lagging-strand synthesis (strand-coupled replication). While strand-asynchronous replication is primed by long noncoding RNA synthesized from a defined transcription initiation site, little is known about the commencement of strand-coupled replication. To investigate it, we attempted to abolish strand-asynchronous replication in cultured human cybrid cells by knocking out the components of the transcription initiation complexes, mitochondrial transcription factor B2 (TFB2M/mtTFB2) and mitochondrial RNA polymerase (POLRMT/mtRNAP). Unexpectedly, removal of either protein resulted in complete mtDNA loss, demonstrating for the first time that TFB2M and POLRMT are indispensable for the maintenance of human mtDNA. Moreover, a lack of TFB2M could not be compensated for by mitochondrial transcription factor B1 (TFB1M/mtTFB1). These findings indicate that TFB2M and POLRMT are crucial for the priming of not only strand-asynchronous but also strand-coupled replication, providing deeper insights into the molecular basis of mtDNA replication initiation.
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Affiliation(s)
- Teppei Inatomi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shigeru Matsuda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai-shi, Miyagi 980-8575, Japan
| | - Takashi Ishiuchi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Yura Do
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Masunari Nakayama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Kazutoshi Kasho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba-shi, Ibaraki 305-8572, Japan
| | - Kenji Ichiyanagi
- Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya-shi, Aichi 464-8601, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan; Department of Pathology and Oncology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka 812-8582, Japan
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Allkanjari K, Baldock RA. Beyond base excision repair: an evolving picture of mitochondrial DNA repair. Biosci Rep 2021; 41:BSR20211320. [PMID: 34608928 PMCID: PMC8527207 DOI: 10.1042/bsr20211320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are highly specialised organelles required for key cellular processes including ATP production through cellular respiration and controlling cell death via apoptosis. Unlike other organelles, mitochondria contain their own DNA genome which encodes both protein and RNA required for cellular respiration. Each cell may contain hundreds to thousands of copies of the mitochondrial genome, which is essential for normal cellular function - deviation of mitochondrial DNA (mtDNA) copy number is associated with cellular ageing and disease. Furthermore, mtDNA lesions can arise from both endogenous or exogenous sources and must either be tolerated or corrected to preserve mitochondrial function. Importantly, replication of damaged mtDNA can lead to stalling and introduction of mutations or genetic loss, mitochondria have adapted mechanisms to repair damaged DNA. These mechanisms rely on nuclear-encoded DNA repair proteins that are translocated into the mitochondria. Despite the presence of many known nuclear DNA repair proteins being found in the mitochondrial proteome, it remains to be established which DNA repair mechanisms are functional in mammalian mitochondria. Here, we summarise the existing and emerging research, alongside examining proteomic evidence, demonstrating that mtDNA damage can be repaired using Base Excision Repair (BER), Homologous Recombination (HR) and Microhomology-mediated End Joining (MMEJ). Critically, these repair mechanisms do not operate in isolation and evidence for interplay between pathways and repair associated with replication is discussed. Importantly, characterising non-canonical functions of key proteins and understanding the bespoke pathways used to tolerate, repair or bypass DNA damage will be fundamental in fully understanding the causes of mitochondrial genome mutations and mitochondrial dysfunction.
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Affiliation(s)
- Kathrin Allkanjari
- Formerly: Solent University Southampton, East Park Terrace, Southampton, SO14 0YN, UK
| | - Robert A. Baldock
- School of Natural and Social Sciences, University of Gloucestershire, Francis Close Hall, Swindon Road, Cheltenham GL50 4AZ, UK
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Lu Y, Gu X, Wan Q, Feng H, Liu Y. Co-immunofluorescence of MRPL12 and Nrf2 in HK2 Cells. Bio Protoc 2021; 11:e4191. [PMID: 34761064 DOI: 10.21769/bioprotoc.4191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/12/2021] [Accepted: 07/26/2021] [Indexed: 11/02/2022] Open
Abstract
Immunofluorescence is a technique to visualize the localization of specific molecule targets within cells using the specificity of antibodies. Here, we describe a protocol to detect two different protein components in a cell simultaneously. Antibody concentrations to be used vary from cell to cell and should be optimized for different cell types. In this protocol, we perform co-immunofluorescence of mitochondrial ribosomal protein L7/L12 (MRPL12) and nuclear factor erythroid 2-related factor 2 (Nrf2), a potential transcription factor of MRPL12, in HK-2 cells, as an example. Taking advantage of the diverse set of antibodies raised in different species, we are able to analyze the colocalization and expression of these proteins.
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Affiliation(s)
- Yao Lu
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Xia Gu
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qiang Wan
- Translational Research Center, Jinan Central Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Hong Feng
- Cancer Center, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yi Liu
- Department of Respiratory Medicine, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
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Aasumets K, Basikhina Y, Pohjoismäki JL, Goffart S, Gerhold J. TFAM knockdown-triggered mtDNA-nucleoid aggregation and a decrease in mtDNA copy number induce the reorganization of nucleoid populations and mitochondria-associated ER-membrane contacts. Biochem Biophys Rep 2021; 28:101142. [PMID: 34622037 PMCID: PMC8479621 DOI: 10.1016/j.bbrep.2021.101142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/20/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022] Open
Abstract
The correct organization of mitochondrial DNA (mtDNA) in nucleoids and the contacts of mitochondria with the ER play an important role in maintaining the mitochondrial genome distribution within the cell. Mitochondria-associated ER membranes (MAMs) consist of interacting proteins and lipids located in the outer mitochondrial membrane and ER membrane, forming a platform for the mitochondrial inner membrane-associated genome replication factory as well as connecting the nucleoids with the mitochondrial division machinery. We show here that knockdown of a core component of mitochondrial nucleoids, TFAM, causes changes in the mitochondrial nucleoid populations, which subsequently impact ER-mitochondria membrane contacts. Knockdown of TFAM causes a significant decrease in the copy number of mtDNA as well as aggregation of mtDNA nucleoids. At the same time, it causes significant upregulation of the replicative TWNK helicase in the membrane-associated nucleoid fraction. This is accompanied by a transient elevation of MAM proteins, indicating a rearrangement of the linkage between ER and mitochondria triggered by changes in mitochondrial nucleoids. Reciprocal knockdown of the mitochondrial replicative helicase TWNK causes a decrease in mtDNA copy number and modifies mtDNA membrane association, however, it does not cause nucleoid aggregation and considerable alterations of MAM proteins in the membrane-associated fraction. Our explanation is that the aggregation of mitochondrial nucleoids resulting from TFAM knockdown triggers a compensatory mechanism involving the reorganization of both mitochondrial nucleoids and MAM. These results could provide an important insight into pathological conditions associated with impaired nucleoid organization or defects of mtDNA distribution.
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Affiliation(s)
- Koit Aasumets
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
| | - Yuliya Basikhina
- Faculty of Medicine and Health Technology, Tampere University, FI-33014, Finland
| | - Jaakko L Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI 80101, Joensuu, Finland
| | - Joachim Gerhold
- Institute of Technology, University of Tartu, Nooruse 1, 50411, Tartu, Estonia
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Azzarà A, Rendeli C, Crivello AM, Brugnoletti F, Rumore R, Ausili E, Sangiorgi E, Gurrieri F. Identification of new candidate genes for spina bifida through exome sequencing. Childs Nerv Syst 2021; 37:2589-2596. [PMID: 33855610 DOI: 10.1007/s00381-021-05153-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022]
Abstract
PURPOSE Neural tube defects are a group of birth defects caused by failure of neural tube closure during development. The etiology of NTD, requiring a complex interaction between environmental and genetic factors, is not well understood. METHODS We performed whole-exome sequencing (WES) in six trios, with a single affected proband with spina bifida, to identify rare/novel variants as potential causes of the NTD. RESULTS Our analysis identified four de novo and ten X-linked recessive variants in four of the six probands, all of them in genes previously never implicated in NTD. Among the 14 variants, we ruled out six of them, based on different criteria and pursued the evaluation of eight potential candidates in the following genes: RXRγ, DTX1, COL15A1, ARHGAP36, TKTL1, AMOT, GPR50, and NKRF. The de novo variants where located in the RXRγ, DTX1, and COL15A1 genes while ARHGAP36, TKTL1, AMOT, GPR50, and NKRF carry X-linked recessive variants. This analysis also revealed that four patients presented multiple variants, while we were unable to identify any significant variant in two patients. CONCLUSIONS Our preliminary conclusion support a major role for the de novo variants with respect to the X-linked recessive variants where the X-linked could represent a contribution to the phenotype in an oligogenic model.
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Affiliation(s)
- Alessia Azzarà
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia. .,Unità di Genetica Medica, Università Campus Bio-Medico, Roma, Italia.
| | - Claudia Rendeli
- Spina Bifida Center, Dipartimento di Scienze della Vita e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Anna Maria Crivello
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Fulvia Brugnoletti
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Roberto Rumore
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia
| | - Emanuele Ausili
- Spina Bifida Center, Dipartimento di Scienze della Vita e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Eugenio Sangiorgi
- Dipartimento di Scienze della Vita e di Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, Roma, Italia.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italia
| | - Fiorella Gurrieri
- Unità di Genetica Medica, Università Campus Bio-Medico, Roma, Italia
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Zhou T, Sang YH, Cai S, Xu C, Shi MH. The requirement of mitochondrial RNA polymerase for non-small cell lung cancer cell growth. Cell Death Dis 2021; 12:751. [PMID: 34326320 PMCID: PMC8322058 DOI: 10.1038/s41419-021-04039-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022]
Abstract
POLRMT (RNA polymerase mitochondrial) is responsible for the transcription of mitochondrial genome encoding key components of oxidative phosphorylation. This process is important for cancer cell growth. The current study tested expression and potential functions of POLRMT in non-small cell lung cancer (NSCLC). TCGA cohorts and the results from the local lung cancer tissues showed that POLRMT is overexpressed in human lung cancer tissues. In both primary human NSCLC cells and A549 cells, POLRMT silencing (by targeted lentiviral shRNAs) or knockout (through CRSIPR/Cas9 gene editing method) potently inhibited cell viability, proliferation, migration, and invasion, and induced apoptosis activation. On the contrast, ectopic overexpression of POLRMT using a lentiviral construct accelerated cell proliferation and migration in NSCLC cells. The mtDNA contents, mRNA levels of mitochondrial transcripts, and subunits of respiratory chain complexes, as well as S6 phosphorylation, were decreased in POLRMT-silenced or -knockout NSCLC cells, but increased after ectopic POLRMT overexpression. In vivo, intratumoral injection of POLRMT shRNA adeno-associated virus (AAV) potently inhibited NSCLC xenograft growth in severe combined immune deficiency mice. The mtDNA contents, mRNA levels of mitochondria respiratory chain complex subunits, and S6 phosphorylation were decreased in POLRMT shRNA AAV-injected NSCLC xenograft tissues. These results show that POLRMT is a novel and important oncogene required for NSCLC cell growth in vitro and in vivo.
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Affiliation(s)
- Tong Zhou
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yong-Hua Sang
- Department of Thoracic Surgery, The Second affiliated Hospital of Soochow University, Suzhou, China
| | - Shang Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chun Xu
- Department of Cardio-Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Min-Hua Shi
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China.
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