1
|
Kumar A, Choudhary A, Munshi A. Epigenetic reprogramming of mtDNA and its etiology in mitochondrial diseases. J Physiol Biochem 2024:10.1007/s13105-024-01032-z. [PMID: 38865050 DOI: 10.1007/s13105-024-01032-z] [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: 04/03/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024]
Abstract
Mitochondrial functionality and its regulation are tightly controlled through a balanced crosstalk between the nuclear and mitochondrial DNA interactions. Epigenetic signatures like methylation, hydroxymethylation and miRNAs have been reported in mitochondria. In addition, epigenetic signatures encoded by nuclear DNA are also imported to mitochondria and regulate the gene expression dynamics of the mitochondrial genome. Alteration in the interplay of these epigenetic modifications results in the pathogenesis of various disorders like neurodegenerative, cardiovascular, metabolic disorders, cancer, aging and senescence. These modifications result in higher ROS production, increased mitochondrial copy number and disruption in the replication process. In addition, various miRNAs are associated with regulating and expressing important mitochondrial gene families like COX, OXPHOS, ND and DNMT. Epigenetic changes are reversible and therefore therapeutic interventions like changing the target modifications can be utilized to repair or prevent mitochondrial insufficiency by reversing the changed gene expression. Identifying these mitochondrial-specific epigenetic signatures has the potential for early diagnosis and treatment responses for many diseases caused by mitochondrial dysfunction. In the present review, different mitoepigenetic modifications have been discussed in association with the development of various diseases by focusing on alteration in gene expression and dysregulation of specific signaling pathways. However, this area is still in its infancy and future research is warranted to draw better conclusions.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Human Genetics and Molecular Medicines, Central University of Punjab, Bathinda, India
| | - Anita Choudhary
- Department of Human Genetics and Molecular Medicines, Central University of Punjab, Bathinda, India
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicines, Central University of Punjab, Bathinda, India.
| |
Collapse
|
2
|
Xu Y, Hong Z, Yu S, Huang R, Li K, Li M, Xie S, Zhu L. Fresh Insights Into SLC25A26: Potential New Therapeutic Target for Cancers: A Review. Oncol Rev 2024; 18:1379323. [PMID: 38745827 PMCID: PMC11091378 DOI: 10.3389/or.2024.1379323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/02/2024] [Indexed: 05/16/2024] Open
Abstract
SLC25A26 is the only known human mitochondrial S-adenosylmethionine carrier encoding gene. Recent studies have shown that SLC25A26 is abnormally expressed in some cancers, such as cervical cancer, low-grade glioma, non-small cell lung cancer, and liver cancer, which suggests SLC25A26 can affect the occurrence and development of some cancers. This article in brief briefly reviewed mitochondrial S-adenosylmethionine carrier in different species and its encoding gene, focused on the association of SLC25A26 aberrant expression and some cancers as well as potential mechanisms, summarized its potential for cancer prognosis, and characteristics of mitochondrial diseases caused by SLC25A26 mutation. Finally, we provide a brief expectation that needs to be further investigated. We speculate that SLC25A26 will be a potential new therapeutic target for some cancers.
Collapse
Affiliation(s)
- Yangheng Xu
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Zhisheng Hong
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Sheng Yu
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Ronghan Huang
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Kunqi Li
- Science and Engineering, National University of Defense Technology, Changsha, China
| | - Ming Li
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Sisi Xie
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Lvyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| |
Collapse
|
3
|
Gao R, Zhou D, Qiu X, Zhang J, Luo D, Yang X, Qian C, Liu Z. Cancer Therapeutic Potential and Prognostic Value of the SLC25 Mitochondrial Carrier Family: A Review. Cancer Control 2024; 31:10732748241287905. [PMID: 39313442 PMCID: PMC11439189 DOI: 10.1177/10732748241287905] [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: 05/23/2024] [Revised: 08/29/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Transporters of the solute carrier family 25 (SLC25) regulate the intracellular distribution and concentration of nucleotides, amino acids, dicarboxylates, and vitamins within the mitochondrial and cytoplasmic matrices. This mechanism involves changes in mitochondrial function, regulation of cellular metabolism, and the ability to provide energy. In this review, important members of the SLC25 family and their pathways affecting tumorigenesis and progression are elucidated, highlighting the diversity and complexity of these pathways. Furthermore, the significant potential of the members of SLC25 as both cancer therapeutic targets and biomarkers will be emphasized.
Collapse
Affiliation(s)
- Renzhuo Gao
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Dan Zhou
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xingpeng Qiu
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Jiayi Zhang
- School of Queen Mary, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Daya Luo
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Xiaohong Yang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Caiyun Qian
- Department of Blood Transfusion, Key Laboratory of Jiangxi Province for Transfusion Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Zhuoqi Liu
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang, China
| |
Collapse
|
4
|
Alam S, Doherty E, Ortega-Prieto P, Arizanova J, Fets L. Membrane transporters in cell physiology, cancer metabolism and drug response. Dis Model Mech 2023; 16:dmm050404. [PMID: 38037877 PMCID: PMC10695176 DOI: 10.1242/dmm.050404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
By controlling the passage of small molecules across lipid bilayers, membrane transporters influence not only the uptake and efflux of nutrients, but also the metabolic state of the cell. With more than 450 members, the Solute Carriers (SLCs) are the largest transporter super-family, clustering into families with different substrate specificities and regulatory properties. Cells of different types are, therefore, able to tailor their transporter expression signatures depending on their metabolic requirements, and the physiological importance of these proteins is illustrated by their mis-regulation in a number of disease states. In cancer, transporter expression is heterogeneous, and the SLC family has been shown to facilitate the accumulation of biomass, influence redox homeostasis, and also mediate metabolic crosstalk with other cell types within the tumour microenvironment. This Review explores the roles of membrane transporters in physiological and malignant settings, and how these roles can affect drug response, through either indirect modulation of sensitivity or the direct transport of small-molecule therapeutic compounds into cells.
Collapse
Affiliation(s)
- Sara Alam
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Emily Doherty
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Paula Ortega-Prieto
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Julia Arizanova
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Louise Fets
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| |
Collapse
|
5
|
Ma Y, Du J, Chen M, Gao N, Wang S, Mi Z, Wei X, Zhao J. Mitochondrial DNA methylation is a predictor of immunotherapy response and prognosis in breast cancer: scRNA-seq and bulk-seq data insights. Front Immunol 2023; 14:1219652. [PMID: 37457713 PMCID: PMC10339346 DOI: 10.3389/fimmu.2023.1219652] [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: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Background Alterations in Mitochondrial DNA methylation (MTDM) exist in many tumors, but their role in breast cancer (BC) development remains unclear. Methods We analyzed BC patient data by combining scRNA-seq and bulk sequencing. Weighted co-expression network analysis (WGCNA) of TCGA data identified mitochondrial DNA methylation (MTDM)-associated genes in BC. COX regression and LASSO regression were used to build prognostic models. The biological function of MTDM was assessed using various methods, such as signaling pathway enrichment analysis, copynumber karyotyping analysis, and quantitative analysis of the cell proliferation rate. We also evaluated MTDM-mediated alterations in the immune microenvironment using immune microenvironment, microsatellite instability, mutation, unsupervised clustering, malignant cell subtype differentiation, immune cell subtype differentiation, and cell-communication signature analyses. Finally, we performed cellular experiments to validate the role of the MTDM-associated prognostic gene NCAPD3 in BC. Results In this study, MTDM-associated prognostic models divided BC patients into high/low MTDM groups in TCGA/GEO datasets. The difference in survival time between the two groups was statistically significant (P<0.001). We found that high MTDM status was positively correlated with tumor cell proliferation. We analyzed the immune microenvironment and found that low-MTDM group had higher immune checkpoint gene expression/immune cell infiltration, which could lead to potential benefits from immunotherapy. In contrast, the high MTDM group had higher proliferation rates and levels of CD8+T cell exhaustion, which may be related to the secretion of GDF15 by malignant breast epithelial cells with a high MTDM status. Cellular experiments validated the role of the MTDM-associated prognostic gene NCAPD3 (the gene most positively correlated with epithelial malignant cell proliferation in the model) in BC. Knockdown of NCAPD3 significantly reduced the activity and proliferation of MDA-MB-231 and BCAP-37 cells, and significantly reduced their migration ability of BCAP-37 cell line. Conclusion This study presented a holistic evaluation of the multifaceted roles of MTDM in BC. The analysis of MTDM levels not only enables the prediction of response to immunotherapy but also serves as an accurate prognostic indicator for patients with BC. These insightful discoveries provide novel perspectives on tumor immunity and have the potentially to revolutionize the diagnosis and treatment of BC.
Collapse
|
6
|
Rosenbaum A, Dahlin AM, Andersson U, Björkblom B, Wu WYY, Hedman H, Wibom C, Melin B. Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines. Sci Rep 2023; 13:6777. [PMID: 37185361 PMCID: PMC10130147 DOI: 10.1038/s41598-023-33923-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 04/20/2023] [Indexed: 05/17/2023] Open
Abstract
Genome-wide association studies (GWAS) have contributed to our understanding of glioma susceptibility. To date, 25 risk loci for development of any of the glioma subtypes are known. However, GWAS studies reveal little about the molecular processes that lead to increased risk, especially for non-coding single nucleotide polymorphisms (SNP). A particular SNP in intron 2 of LRIG1, rs11706832, has been shown to increase the susceptibility for IDH1 mutated low-grade gliomas (LGG). Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is important in cancer development as it negatively regulates the epidermal growth factor receptor (EGFR); however, the mechanism responsible for this particular risk SNP and its potential effect on LRIG1 are not known. Using CRISPR-CAS9, we edited rs11706832 in HEK293T cells. Four HEK293T clones with the risk allele were compared to four clones with the non-risk allele for LRIG1 and SLC25A26 gene expression using RT-qPCR, for global gene expression using RNA-seq, and for metabolites using gas chromatography-mass spectrometry (GC-MS). The experiment did not reveal any significant effect of the SNP on the expression levels or splicing patterns of LRIG1 or SLC25A26. The global gene expression analysis revealed that the risk allele C was associated with upregulation of several mitochondrial genes. Gene enrichment analysis of 74 differentially expressed genes in the genome revealed a significant enrichment of type I interferon response genes, where many genes were downregulated for the risk allele C. Gene expression data of IDH1 mutated LGGs from the cancer genome atlas (TCGA) revealed a similar under expression of type I interferon genes associated with the risk allele. This study found the expression levels and splicing patterns of LRIG1 and SLC25A26 were not affected by the SNP in HEK293T cells. However, the risk allele was associated with a downregulation of genes involved in the innate immune response both in the HEK293T cells and in the LGG data from TCGA.
Collapse
Affiliation(s)
- Adam Rosenbaum
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden.
| | - Anna M Dahlin
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | - Ulrika Andersson
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | | | - Wendy Yi-Ying Wu
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | - Håkan Hedman
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | - Carl Wibom
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology Umeå University, Umeå, Sweden
| |
Collapse
|
7
|
Low HC, Chilian WM, Ratnam W, Karupaiah T, Md Noh MF, Mansor F, Ng ZX, Pung YF. Changes in Mitochondrial Epigenome in Type 2 Diabetes Mellitus. Br J Biomed Sci 2023; 80:10884. [PMID: 36866104 PMCID: PMC9970885 DOI: 10.3389/bjbs.2023.10884] [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: 09/03/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023]
Abstract
Type 2 Diabetes Mellitus is a major chronic metabolic disorder in public health. Due to mitochondria's indispensable role in the body, its dysfunction has been implicated in the development and progression of multiple diseases, including Type 2 Diabetes mellitus. Thus, factors that can regulate mitochondrial function, like mtDNA methylation, are of significant interest in managing T2DM. In this paper, the overview of epigenetics and the mechanism of nuclear and mitochondrial DNA methylation were briefly discussed, followed by other mitochondrial epigenetics. Subsequently, the association between mtDNA methylation with T2DM and the challenges of mtDNA methylation studies were also reviewed. This review will aid in understanding the impact of mtDNA methylation on T2DM and future advancements in T2DM treatment.
Collapse
Affiliation(s)
- Hui Ching Low
- Division of Biomedical Science, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - William M. Chilian
- Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown Township, OH, United States
| | - Wickneswari Ratnam
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Tilakavati Karupaiah
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor’s University Lakeside Campus, Subang Jaya, Selangor, Malaysia
| | - Mohd Fairulnizal Md Noh
- Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam, Malaysia
| | - Fazliana Mansor
- Nutrition, Metabolism and Cardiovascular Research Centre, Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam, Malaysia
| | - Zhi Xiang Ng
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia
| | - Yuh Fen Pung
- Division of Biomedical Science, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Selangor, Malaysia,*Correspondence: Yuh Fen Pung,
| |
Collapse
|
8
|
Shi ZL, Zhou GQ, Guo J, Yang XL, Yu C, Shen CL, Zhu XG. Identification of a Prognostic Colorectal Cancer Model Including LncRNA FOXP4-AS1 and LncRNA BBOX1-AS1 Based on Bioinformatics Analysis. Cancer Biother Radiopharm 2022; 37:893-906. [PMID: 33481661 PMCID: PMC9805880 DOI: 10.1089/cbr.2020.4242] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Background: Knowledge about the prognostic role of long noncoding RNA (lncRNA) in colorectal cancer (CRC) is limited. Therefore, we constructed a lncRNA-related prognostic model based on data from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Materials and Methods: CRC transcriptome and clinical data were downloaded from the GSE20916 dataset and the TCGA database, respectively. R software was used for data processing and analysis. The differential lncRNA expression within the two datasets was first screened, and then intersections were measured. Cox regression and the Kaplan-Meier method were used to evaluate the effects of various factors on prognosis. The area under the curve (AUC) of the receiver operating characteristic curve and a nomogram based on multivariate Cox analysis were used to estimate the prognostic value of the lncRNA-related model. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were applied to elucidate the significantly involved biological functions and pathways. Results: A total of 11 lncRNAs were crossed. The univariate Cox analysis screened out two lncRNAs, which were analyzed in the multivariate Cox analysis. A nomogram based on the two lncRNAs and other clinicopathological risk factors was constructed. The AUC of the nomogram was 0.56 at 3 years and 0.71 at 5 years. The 3-year nomogram model was compared with the ideal model, which showed that some indices of the 3-year model were consistent with the ideal model, suggesting that our model was highly accurate. The GO and KEGG enrichment analyses showed that positive regulation of secretion by cells, positive regulation of secretion, positive regulation of exocytosis, endocytosis, and the calcium signaling pathway were differentially enriched in the two-lncRNA-associated phenotype. Conclusions: A two-lncRNA prognostic model of CRC was constructed by bioinformatics analysis. The model had moderate prediction accuracy. LncRNA BBOX1-AS1 and lncRNA FOXP4-AS1 were identified as prognostic biomarkers.
Collapse
Affiliation(s)
- Zhi-Liang Shi
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Guo-Qiang Zhou
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Jian Guo
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Xiao-Ling Yang
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Cheng Yu
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Cheng-Long Shen
- Department of Gastrointestinal Surgery, Changshu No. 2 Hospital, Suzhou, China
| | - Xin-Guo Zhu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China.,Address correspondence to: Xin-Guo Zhu; Department of General Surgery, The First Affiliated Hospital of Soochow University; 188 Shizi Street, Gusu District, Suzhou City, Suzhou 215006, Jiangsu Province, China
| |
Collapse
|
9
|
Monné M, Marobbio CMT, Agrimi G, Palmieri L, Palmieri F. Mitochondrial transport and metabolism of the major methyl donor and versatile cofactor S-adenosylmethionine, and related diseases: A review †. IUBMB Life 2022; 74:573-591. [PMID: 35730628 DOI: 10.1002/iub.2658] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/19/2022] [Indexed: 11/08/2022]
Abstract
S-adenosyl-L-methionine (SAM) is a coenzyme and the most commonly used methyl-group donor for the modification of metabolites, DNA, RNA and proteins. SAM biosynthesis and SAM regeneration from the methylation reaction product S-adenosyl-L-homocysteine (SAH) take place in the cytoplasm. Therefore, the intramitochondrial SAM-dependent methyltransferases require the import of SAM and export of SAH for recycling. Orthologous mitochondrial transporters belonging to the mitochondrial carrier family have been identified to catalyze this antiport transport step: Sam5p in yeast, SLC25A26 (SAMC) in humans, and SAMC1-2 in plants. In mitochondria SAM is used by a vast number of enzymes implicated in the following processes: the regulation of replication, transcription, translation, and enzymatic activities; the maturation and assembly of mitochondrial tRNAs, ribosomes and protein complexes; and the biosynthesis of cofactors, such as ubiquinone, lipoate, and molybdopterin. Mutations in SLC25A26 and mitochondrial SAM-dependent enzymes have been found to cause human diseases, which emphasizes the physiological importance of these proteins.
Collapse
Affiliation(s)
- Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,Department of Sciences, University of Basilicata, Potenza, Italy
| | - Carlo M T Marobbio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| |
Collapse
|
10
|
Aberrant Expression of Mitochondrial SAM Transporter SLC25A26 Impairs Oocyte Maturation and Early Development in Mice. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1681623. [PMID: 35464759 PMCID: PMC9020962 DOI: 10.1155/2022/1681623] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/27/2022] [Accepted: 03/09/2022] [Indexed: 12/06/2022]
Abstract
The immature germinal vesicle (GV) oocytes proceed through metaphase I (MI) division, extrude the first polar body, and become mature metaphase II (MII) oocytes for fertilization which is followed by preimplantation and postimplantation development until birth. Slc25a26 is the gene encoding S-adenosylmethionine carrier (SAMC), a member of the mitochondrial carrier family. Its major function is to catalyze the uptake of S-adenosylmethionine (SAM) from cytosol into mitochondria, which is the only known mitochondrial SAM transporter. In the present study, we demonstrated that excessive SLC25A26 accumulation in mouse oocytes mimicked naturally aged oocytes and resulted in lower oocyte quality with decreased maturation rate and increased reactive oxygen species (ROS) by impairing mitochondrial function. Increased level of Slc25a26 gene impacted gene expression in mouse oocytes such as mt-Cytb which regulates mitochondrial respiratory chain. Furthermore, increased level of Slc25a26 gene in fertilized oocytes slightly compromised blastocyst formation, and Slc25a26 knockout mice displayed embryonic lethality around 10.5 dpc. Taken together, our results showed that Slc25a26 gene plays a critical role in oocyte maturation and early mouse development.
Collapse
|
11
|
Mposhi A, Liang L, Mennega KP, Yildiz D, Kampert C, Hof IH, Jellema PG, de Koning TJ, Faber KN, Ruiters MHJ, Niezen-Koning KE, Rots MG. The Mitochondrial Epigenome: An Unexplored Avenue to Explain Unexplained Myopathies? Int J Mol Sci 2022; 23:ijms23042197. [PMID: 35216315 PMCID: PMC8879787 DOI: 10.3390/ijms23042197] [Citation(s) in RCA: 4] [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: 12/31/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Mutations in either mitochondrial DNA (mtDNA) or nuclear genes that encode mitochondrial proteins may lead to dysfunctional mitochondria, giving rise to mitochondrial diseases. Some mitochondrial myopathies, however, present without a known underlying cause. Interestingly, methylation of mtDNA has been associated with various clinical pathologies. The present study set out to assess whether mtDNA methylation could explain impaired mitochondrial function in patients diagnosed with myopathy without known underlying genetic mutations. Enhanced mtDNA methylation was indicated by pyrosequencing for muscle biopsies of 14 myopathy patients compared to four healthy controls, at selected cytosines in the Cytochrome B (CYTB) gene, but not within the displacement loop (D-loop) region. The mtDNA methylation patterns of the four healthy muscle biopsies were highly consistent and showed intriguing tissue-specific differences at particular cytosines with control skin fibroblasts cultured in vitro. Within individual myopathy patients, the overall mtDNA methylation pattern correlated well between muscle and skin fibroblasts. Despite this correlation, a pilot analysis of four myopathy and five healthy fibroblast samples did not reveal a disease-associated difference in mtDNA methylation. We did, however, detect increased expression of solute carrier family 25A26 (SLC25A26), encoding the importer of S-adenosylmethionine, together with enhanced mtDNA copy numbers in myopathy fibroblasts compared to healthy controls. To confirm that pyrosequencing indeed reflected DNA methylation and not bisulfite accessibility, mass spectrometry was employed. Although no myopathy-related differences in total amount of methylated cytosines were detected at this stage, a significant contribution of contaminating nuclear DNA (nDNA) was revealed, and steps to improve enrichment for mtDNA are reported. In conclusion, in this explorative study we show that analyzing the mitochondrial genome beyond its sequence opens novel avenues to identify potential molecular biomarkers assisting in the diagnosis of unexplained myopathies.
Collapse
Affiliation(s)
- Archibold Mposhi
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Lin Liang
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Kevin P. Mennega
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Dilemin Yildiz
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Crista Kampert
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Ingrid H. Hof
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Pytrick G. Jellema
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Tom J. de Koning
- Department of Genetics, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands;
- Department of Clinical Sciences, Lund University, Lasarettgatan 40, 221 85 Lund, Sweden
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Marcel H. J. Ruiters
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
| | - Klary E. Niezen-Koning
- Department of Laboratory Medicine, Laboratory of Metabolic Diseases, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (D.Y.); (C.K.); (I.H.H.); (K.E.N.-K.)
| | - Marianne G. Rots
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (A.M.); (L.L.); (K.P.M.); (P.G.J.); (M.H.J.R.)
- Correspondence:
| |
Collapse
|
12
|
Wang G, Han JJ. Connections between metabolism and epigenetic modifications in cancer. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:199-221. [PMID: 37724300 PMCID: PMC10388788 DOI: 10.1515/mr-2021-0015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/19/2021] [Indexed: 09/20/2023]
Abstract
How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.
Collapse
Affiliation(s)
- Guangchao Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jingdong J. Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| |
Collapse
|
13
|
Feno S, Munari F, Reane DV, Gissi R, Hoang DH, Castegna A, Chazaud B, Viola A, Rizzuto R, Raffaello A. The dominant-negative mitochondrial calcium uniporter subunit MCUb drives macrophage polarization during skeletal muscle regeneration. Sci Signal 2021; 14:eabf3838. [PMID: 34726954 DOI: 10.1126/scisignal.abf3838] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Simona Feno
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy
| | - Fabio Munari
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy
| | | | - Rosanna Gissi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy
| | - Dieu-Huong Hoang
- INSERM U1217, CNRS 5310, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, 8 Avenue Rockefeller, F-69008 Lyon, France
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70125 Bari, Italy.,IBIOM-CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Giovanni Amendola 122/O, 70126 Bari, Italy
| | - Bénédicte Chazaud
- INSERM U1217, CNRS 5310, Institut NeuroMyoGène, Université Claude Bernard Lyon 1, Université de Lyon, 8 Avenue Rockefeller, F-69008 Lyon, France
| | - Antonella Viola
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy
| | - Rosario Rizzuto
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy
| | - Anna Raffaello
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy.,Myology Center, University of Padua, via G. Colombo 3, 35100 Padova, Italy
| |
Collapse
|
14
|
Patra S, Elahi N, Armorer A, Arunachalam S, Omala J, Hamid I, Ashton AW, Joyce D, Jiao X, Pestell RG. Mechanisms Governing Metabolic Heterogeneity in Breast Cancer and Other Tumors. Front Oncol 2021; 11:700629. [PMID: 34631530 PMCID: PMC8495201 DOI: 10.3389/fonc.2021.700629] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022] Open
Abstract
Reprogramming of metabolic priorities promotes tumor progression. Our understanding of the Warburg effect, based on studies of cultured cancer cells, has evolved to a more complex understanding of tumor metabolism within an ecosystem that provides and catabolizes diverse nutrients provided by the local tumor microenvironment. Recent studies have illustrated that heterogeneous metabolic changes occur at the level of tumor type, tumor subtype, within the tumor itself, and within the tumor microenvironment. Thus, altered metabolism occurs in cancer cells and in the tumor microenvironment (fibroblasts, immune cells and fat cells). Herein we describe how these growth advantages are obtained through either “convergent” genetic changes, in which common metabolic properties are induced as a final common pathway induced by diverse oncogene factors, or “divergent” genetic changes, in which distinct factors lead to subtype-selective phenotypes and thereby tumor heterogeneity. Metabolic heterogeneity allows subtyping of cancers and further metabolic heterogeneity occurs within the same tumor mass thought of as “microenvironmental metabolic nesting”. Furthermore, recent findings show that mutations of metabolic genes arise in the majority of tumors providing an opportunity for the development of more robust metabolic models of an individual patient’s tumor. The focus of this review is on the mechanisms governing this metabolic heterogeneity in breast cancer.
Collapse
Affiliation(s)
- Sayani Patra
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Naveed Elahi
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Aaron Armorer
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Swathi Arunachalam
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Joshua Omala
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Iman Hamid
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Anthony W Ashton
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba.,Program in Cardiovascular Medicine, Lankenau Institute for Medical Research, Wynnewood, PA, United States
| | - David Joyce
- Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Xuanmao Jiao
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Richard G Pestell
- Pensylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, United States.,Xavier University School of Medicine at Aruba, Oranjestad, Aruba.,Cancer Center, Wistar Institute, Philadelphia, PA, United States
| |
Collapse
|
15
|
Menga A, Favia M, Spera I, Vegliante MC, Gissi R, De Grassi A, Laera L, Campanella A, Gerbino A, Carrà G, Canton M, Loizzi V, Pierri CL, Cormio G, Mazzone M, Castegna A. N-acetylaspartate release by glutaminolytic ovarian cancer cells sustains protumoral macrophages. EMBO Rep 2021; 22:e51981. [PMID: 34260142 PMCID: PMC8419692 DOI: 10.15252/embr.202051981] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 02/01/2023] Open
Abstract
Glutaminolysis is known to correlate with ovarian cancer aggressiveness and invasion. However, how this affects the tumor microenvironment is elusive. Here, we show that ovarian cancer cells become addicted to extracellular glutamine when silenced for glutamine synthetase (GS), similar to naturally occurring GS-low, glutaminolysis-high ovarian cancer cells. Glutamine addiction elicits a crosstalk mechanism whereby cancer cells release N-acetylaspartate (NAA) which, through the inhibition of the NMDA receptor, and synergistically with IL-10, enforces GS expression in macrophages. In turn, GS-high macrophages acquire M2-like, tumorigenic features. Supporting this in␣vitro model, in silico data and the analysis of ascitic fluid isolated from ovarian cancer patients prove that an M2-like macrophage phenotype, IL-10 release, and NAA levels positively correlate with disease stage. Our study uncovers the unprecedented role of glutamine metabolism in modulating macrophage polarization in highly invasive ovarian cancer and highlights the anti-inflammatory, protumoral function of NAA.
Collapse
Affiliation(s)
- Alessio Menga
- Department of Molecular Biotechnologies and Health SciencesUniversity of TurinTurinItaly
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Molecular Biotechnology CenterTurinItaly
| | - Maria Favia
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
| | - Iolanda Spera
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Maria C Vegliante
- Haematology and Cell Therapy UnitIRCCS‐Istituto Tumori ‘Giovanni Paolo II'BariItaly
| | - Rosanna Gissi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Anna De Grassi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Luna Laera
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Annalisa Campanella
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Andrea Gerbino
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Giovanna Carrà
- Molecular Biotechnology CenterTurinItaly
- Department of Clinical and Biological SciencesUniversity of TurinOrbassanoItaly
| | - Marcella Canton
- Department of Biomedical SciencesUniversity of PadovaPadovaItaly
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza ‐ IRPPadovaItaly
| | - Vera Loizzi
- Policlinico University of Bari “Aldo Moro”BariItaly
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Gennaro Cormio
- Policlinico University of Bari “Aldo Moro”BariItaly
- Gynecologic Oncology UnitIRCCSIstituto Tumori Giovanni Paolo IIBariItaly
| | - Massimiliano Mazzone
- Department of Molecular Biotechnologies and Health SciencesUniversity of TurinTurinItaly
- Molecular Biotechnology CenterTurinItaly
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer BiologyDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Fondazione Istituto di Ricerca Pediatrica Città della Speranza ‐ IRPPadovaItaly
| |
Collapse
|
16
|
Ji Y, Wang S, Cheng Y, Fang L, Zhao J, Gao L, Xu C. Identification and characterization of novel compound variants in SLC25A26 associated with combined oxidative phosphorylation deficiency 28. Gene 2021; 804:145891. [PMID: 34375635 DOI: 10.1016/j.gene.2021.145891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Combined oxidative phosphorylation deficiency 28 (COXPD28) is associated with mitochondrial dysfunction caused by mutations in SLC25A26, the gene which encodes the mitochondrial S-adenosylmethionine carrier (SAMC) that responsible for the transport of S-adenosylmethionine (SAM) into the mitochondria. OBJECTIVE To identify and characterize pathogenic variants of SLC25A26 in a Chinese pedigree, provide a basis for clinical diagnosis and genetic counseling. METHODS We conducted a systematic analysis of the clinical characteristics of a female with COXPD28. Whole-exome and mitochondrial genome sequencing was applied for the genetic analysis, together with bioinformatic analysis of predicted consequences of the identified variant. A homotrimer model was built to visualize the affected region and predict possible outcomes of this mutation. Then a literature review was performed by online searching all cases reported with COXPD28. RESULTS The novel compound heterozygous SLC25A26 variants (c.34G > C, p.A12P; c.197C > A; p.A66E) were identified in a Chinese patient with COXPD28. These two variants are located in the transmembrane region 1 and transmembrane region 2, respectively. As a member of the mitochondrial carrier family, the transmembrane region of SAMC is highly conserved. The variants were predicted to be pathogenic by in silico analysis and lead to a change in the protein structure of SAMC. And the change of the SAMC structure may lead to insufficient methylation and cause disease by affecting the SAM transport. CONCLUSIONS The variants in this region probably resulted in a variable loss of mitochondrial SAMC transport function and cause the COXPD28. This study that further refine genotype-phenotype associations can provide disease prognosis with a basis and families with reproductive planning options.
Collapse
Affiliation(s)
- Yiming Ji
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan 250021, Shandong, China; Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan 250021, Shandong, China
| | - Shuping Wang
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Department of Endocrinology and Metabolism, Dongying People's Hospital, Dongying, Shandong 257000, China
| | - Yiping Cheng
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan 250021, Shandong, China; Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan 250021, Shandong, China
| | - Li Fang
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan 250021, Shandong, China; Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan 250021, Shandong, China
| | - Jiajun Zhao
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan 250021, Shandong, China; Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan 250021, Shandong, China
| | - Ling Gao
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan 250021, Shandong, China; Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan 250021, Shandong, China
| | - Chao Xu
- Department of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250021, China; Institute of Endocrinology, Shandong Academy of Clinical Medicine, Jinan 250021, Shandong, China; Shandong Clinical Medical Center of Endocrinology and Metabolism, Jinan 250021, Shandong, China.
| |
Collapse
|
17
|
Manjunath M, Yan J, Youn Y, Drucker KL, Kollmeyer TM, McKinney AM, Zazubovich V, Zhang Y, Costello JF, Eckel-Passow J, Selvin PR, Jenkins RB, Song JS. Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. Neuro Oncol 2021; 23:638-649. [PMID: 33130899 DOI: 10.1093/neuonc/noaa248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Large-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals' risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (LGGs), but their molecular functions remain largely unknown. METHODS We hypothesized that GWAS loci contain causal single nucleotide polymorphisms (SNPs) that reside in accessible open chromatin regions and modulate the expression of target genes by perturbing the binding affinity of transcription factors (TFs). We performed an integrative analysis of genomic and epigenomic data from The Cancer Genome Atlas and other public repositories to identify candidate causal SNPs within linkage disequilibrium blocks of LGG GWAS loci. We assessed their potential regulatory role via in silico TF binding sequence perturbations, convolutional neural network trained on TF binding data, and simulated annealing-based interpretation methods. RESULTS We built an interactive website (http://education.knoweng.org/alg3/) summarizing the functional footprinting of 280 variants in 25 LGG GWAS regions, providing rich information for further computational and experimental scrutiny. We identified as case studies PHLDB1 and SLC25A26 as candidate target genes of rs12803321 and rs11706832, respectively, and predicted the GWAS variant rs648044 to be the causal SNP modulating ZBTB16, a known tumor suppressor in multiple cancers. We showed that rs648044 likely perturbed the binding affinity of the TF MAFF, as supported by RNA interference and in vitro MAFF binding experiments. CONCLUSIONS The identified candidate (causal SNP, target gene, TF) triplets and the accompanying resource will help accelerate our understanding of the molecular mechanisms underlying genetic risk factors for gliomas.
Collapse
Affiliation(s)
- Mohith Manjunath
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jialu Yan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kristen L Drucker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew M McKinney
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal, Québec, Canada
| | - Yi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | | | - Paul R Selvin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| |
Collapse
|
18
|
Li KC, Girardi E, Kartnig F, Grosche S, Pemovska T, Bigenzahn JW, Goldmann U, Sedlyarov V, Bensimon A, Schick S, Lin JMG, Gürtl B, Reil D, Klavins K, Kubicek S, Sdelci S, Superti-Furga G. Cell-surface SLC nucleoside transporters and purine levels modulate BRD4-dependent chromatin states. Nat Metab 2021; 3:651-664. [PMID: 33972798 PMCID: PMC7612075 DOI: 10.1038/s42255-021-00386-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/24/2021] [Indexed: 02/03/2023]
Abstract
Metabolism negotiates cell-endogenous requirements of energy, nutrients and building blocks with the immediate environment to enable various processes, including growth and differentiation. While there is an increasing number of examples of crosstalk between metabolism and chromatin, few involve uptake of exogenous metabolites. Solute carriers (SLCs) represent the largest group of transporters in the human genome and are responsible for the transport of a wide variety of substrates, including nutrients and metabolites. We aimed to investigate the possible involvement of SLC-mediated solutes uptake and cellular metabolism in regulating cellular epigenetic states. Here, we perform a CRISPR-Cas9 transporter-focused genetic screen and a metabolic compound library screen for the regulation of BRD4-dependent chromatin states in human myeloid leukaemia cells. Intersection of the two orthogonal approaches reveal that loss of transporters involved with purine transport or inhibition of de novo purine synthesis lead to dysfunction of BRD4-dependent transcriptional regulation. Through mechanistic characterization of the metabolic circuitry, we elucidate the convergence of SLC-mediated purine uptake and de novo purine synthesis on BRD4-chromatin occupancy. Moreover, adenine-related metabolite supplementation effectively restores BRD4 functionality on purine impairment. Our study highlights the specific role of purine/adenine metabolism in modulating BRD4-dependent epigenetic states.
Collapse
Affiliation(s)
- Kai-Chun Li
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Enrico Girardi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Felix Kartnig
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sarah Grosche
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tea Pemovska
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Ulrich Goldmann
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sandra Schick
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jung-Ming G Lin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Gürtl
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Daniela Reil
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristaps Klavins
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sara Sdelci
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
19
|
Carrà G, Ermondi G, Riganti C, Righi L, Caron G, Menga A, Capelletto E, Maffeo B, Lingua MF, Fusella F, Volante M, Taulli R, Guerrasio A, Novello S, Brancaccio M, Piazza R, Morotti A. IκBα targeting promotes oxidative stress-dependent cell death. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:136. [PMID: 33863364 PMCID: PMC8050912 DOI: 10.1186/s13046-021-01921-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/21/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Oxidative stress is a hallmark of many cancers. The increment in reactive oxygen species (ROS), resulting from an increased mitochondrial respiration, is the major cause of oxidative stress. Cell fate is known to be intricately linked to the amount of ROS produced. The direct generation of ROS is also one of the mechanisms exploited by common anticancer therapies, such as chemotherapy. METHODS We assessed the role of NFKBIA with various approaches, including in silico analyses, RNA-silencing and xenotransplantation. Western blot analyses, immunohistochemistry and RT-qPCR were used to detect the expression of specific proteins and genes. Immunoprecipitation and pull-down experiments were used to evaluate protein-protein interactions. RESULTS Here, by using an in silico approach, following the identification of NFKBIA (the gene encoding IκBα) amplification in various cancers, we described an inverse correlation between IκBα, oxidative metabolism, and ROS production in lung cancer. Furthermore, we showed that novel IκBα targeting compounds combined with cisplatin treatment promote an increase in ROS beyond the tolerated threshold, thus causing death by oxytosis. CONCLUSIONS NFKBIA amplification and IκBα overexpression identify a unique cancer subtype associated with specific expression profile and metabolic signatures. Through p65-NFKB regulation, IκBα overexpression favors metabolic rewiring of cancer cells and distinct susceptibility to cisplatin. Lastly, we have developed a novel approach to disrupt IκBα/p65 interaction, restoring p65-mediated apoptotic responses to cisplatin due to mitochondria deregulation and ROS-production.
Collapse
Affiliation(s)
- Giovanna Carrà
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Turin, Italy
| | - Chiara Riganti
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Luisella Righi
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Turin, Italy
| | - Alessio Menga
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Turin, Italy
| | - Enrica Capelletto
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Beatrice Maffeo
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | | | - Federica Fusella
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Turin, Italy
| | - Marco Volante
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Riccardo Taulli
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Angelo Guerrasio
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Silvia Novello
- Department of Oncology, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Via Nizza 52, 10126, Turin, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca and San Gerardo Hospital, 20900, Monza, Italy
| | - Alessandro Morotti
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043, Orbassano, Italy.
| |
Collapse
|
20
|
Kahya U, Köseer AS, Dubrovska A. Amino Acid Transporters on the Guard of Cell Genome and Epigenome. Cancers (Basel) 2021; 13:E125. [PMID: 33401748 PMCID: PMC7796306 DOI: 10.3390/cancers13010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/26/2020] [Accepted: 12/27/2020] [Indexed: 02/06/2023] Open
Abstract
Tumorigenesis is driven by metabolic reprogramming. Oncogenic mutations and epigenetic alterations that cause metabolic rewiring may also upregulate the reactive oxygen species (ROS). Precise regulation of the intracellular ROS levels is critical for tumor cell growth and survival. High ROS production leads to the damage of vital macromolecules, such as DNA, proteins, and lipids, causing genomic instability and further tumor evolution. One of the hallmarks of cancer metabolism is deregulated amino acid uptake. In fast-growing tumors, amino acids are not only the source of energy and building intermediates but also critical regulators of redox homeostasis. Amino acid uptake regulates the intracellular glutathione (GSH) levels, endoplasmic reticulum stress, unfolded protein response signaling, mTOR-mediated antioxidant defense, and epigenetic adaptations of tumor cells to oxidative stress. This review summarizes the role of amino acid transporters as the defender of tumor antioxidant system and genome integrity and discusses them as promising therapeutic targets and tumor imaging tools.
Collapse
Affiliation(s)
- Uğur Kahya
- OncoRay–National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, 01309 Dresden, Germany; (U.K.); (A.S.K.)
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, 01328 Dresden, Germany
| | - Ayşe Sedef Köseer
- OncoRay–National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, 01309 Dresden, Germany; (U.K.); (A.S.K.)
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, 01328 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Anna Dubrovska
- OncoRay–National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Helmholtz-Zentrum Dresden-Rossendorf, 01309 Dresden, Germany; (U.K.); (A.S.K.)
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiooncology-OncoRay, 01328 Dresden, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| |
Collapse
|
21
|
Kaplan P, Tatarkova Z, Sivonova MK, Racay P, Lehotsky J. Homocysteine and Mitochondria in Cardiovascular and Cerebrovascular Systems. Int J Mol Sci 2020; 21:ijms21207698. [PMID: 33080955 PMCID: PMC7589705 DOI: 10.3390/ijms21207698] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/20/2022] Open
Abstract
Elevated concentration of homocysteine (Hcy) in the blood plasma, hyperhomocysteinemia (HHcy), has been implicated in various disorders, including cardiovascular and neurodegenerative diseases. Accumulating evidence indicates that pathophysiology of these diseases is linked with mitochondrial dysfunction. In this review, we discuss the current knowledge concerning the effects of HHcy on mitochondrial homeostasis, including energy metabolism, mitochondrial apoptotic pathway, and mitochondrial dynamics. The recent studies suggest that the interaction between Hcy and mitochondria is complex, and reactive oxygen species (ROS) are possible mediators of Hcy effects. We focus on mechanisms contributing to HHcy-associated oxidative stress, such as sources of ROS generation and alterations in antioxidant defense resulting from altered gene expression and post-translational modifications of proteins. Moreover, we discuss some recent findings suggesting that HHcy may have beneficial effects on mitochondrial ROS homeostasis and antioxidant defense. A better understanding of complex mechanisms through which Hcy affects mitochondrial functions could contribute to the development of more specific therapeutic strategies targeted at HHcy-associated disorders.
Collapse
|
22
|
Novel copper complex CTB regulates methionine cycle induced TERT hypomethylation to promote HCC cells senescence via mitochondrial SLC25A26. Cell Death Dis 2020; 11:844. [PMID: 33041323 PMCID: PMC7548283 DOI: 10.1038/s41419-020-03048-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/19/2022]
Abstract
Related research has recognized the vital role of methionine cycle metabolism in cancers. However, the role and mechanism of methionine cycle metabolism in hepatocellular carcinoma are still unknown. In this study, we found that [Cu(ttpy-tpp)Br2]Br (Referred to as CTB) could induce hepatocellular carcinoma cells senescence, which is a new copper complex synthesized by our research group. Interestingly, CTB induces senescence by inhibiting the methionine cycle metabolism of HCC cells. Furthermore, the inhibitory effect of CTB on the methionine cycle depends on mitochondrial carrier protein SLC25A26, which was also required for CTB-induced HCC cells senescence. Importantly, we found that CTB-induced upregulation of SLC25A26 could cause abnormal methylation of TERT and inhibited TERT expression, which is considered to be an essential cause of cell senescence. The same results were also obtained in vivo, CTB inhibits the growth of subcutaneously implanted tumors in nude mice and promoted the expression of senescence markers in tumor tissues, and interference with SLC25A26 partially offset the antitumor effect of CTB.
Collapse
|
23
|
Menga A, Serra M, Todisco S, Riera‐Domingo C, Ammarah U, Ehling M, Palmieri EM, Di Noia MA, Gissi R, Favia M, Pierri CL, Porporato PE, Castegna A, Mazzone M. Glufosinate constrains synchronous and metachronous metastasis by promoting anti-tumor macrophages. EMBO Mol Med 2020; 12:e11210. [PMID: 32885605 PMCID: PMC7539200 DOI: 10.15252/emmm.201911210] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 01/19/2023] Open
Abstract
Glutamine synthetase (GS) generates glutamine from glutamate and controls the release of inflammatory mediators. In macrophages, GS activity, driven by IL10, associates to the acquisition of M2-like functions. Conditional deletion of GS in macrophages inhibits metastasis by boosting the formation of anti-tumor, M1-like, tumor-associated macrophages (TAMs). From this basis, we evaluated the pharmacological potential of GS inhibitors in targeting metastasis, identifying glufosinate as a specific human GS inhibitor. Glufosinate was tested in both cultured macrophages and on mice bearing metastatic lung, skin and breast cancer. We found that glufosinate rewires macrophages toward an M1-like phenotype both at the primary tumor and metastatic site, countering immunosuppression and promoting vessel sprouting. This was also accompanied to a reduction in cancer cell intravasation and extravasation, leading to synchronous and metachronous metastasis growth inhibition, but no effects on primary tumor growth. Glufosinate treatment was well-tolerated, without liver and brain toxicity, nor hematopoietic defects. These results identify GS as a druggable enzyme to rewire macrophage functions and highlight the potential of targeting metabolic checkpoints in macrophages to treat cancer metastasis.
Collapse
Affiliation(s)
- Alessio Menga
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Marina Serra
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Simona Todisco
- Department of SciencesUniversity of BasilicataPotenzaItaly
| | - Carla Riera‐Domingo
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Ummi Ammarah
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| | - Manuel Ehling
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
| | - Erika M Palmieri
- Cancer & Inflammation ProgramNational Cancer InstituteFrederickMDUSA
| | | | - Rosanna Gissi
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Maria Favia
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Ciro L Pierri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
| | - Paolo E Porporato
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| | - Alessandra Castegna
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- IBIOM‐CNRInstitute of Biomembranes, Bioenergetics and Molecular BiotechnologiesNational Research CouncilBariItaly
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and AngiogenesisCenter for Cancer Biology (CCB)VIBLeuvenBelgium
- Laboratory of Tumor Inflammation and AngiogenesisDepartment of OncologyKU LeuvenLeuvenBelgium
- Department of Molecular Biotechnology and Health ScienceMolecular Biotechnology CentreUniversity of TorinoTorinoItaly
| |
Collapse
|
24
|
Jia L, Zeng Y, Hu Y, Liu J, Yin C, Niu Y, Wang C, Li J, Jia Y, Hong J, Zhao R. Homocysteine impairs porcine oocyte quality via deregulation of one-carbon metabolism and hypermethylation of mitochondrial DNA†. Biol Reprod 2020; 100:907-916. [PMID: 30395161 DOI: 10.1093/biolre/ioy238] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/22/2018] [Accepted: 11/02/2018] [Indexed: 01/08/2023] Open
Abstract
Homocysteine (Hcy) is an intermediate in the one-carbon metabolism that donates methyl groups for methylation processes involved in epigenetic gene regulation. Although poor oocyte quality in polycystic ovarian syndrome (PCOS) patients is associated with elevated Hcy concentration in serum and follicular fluid, whether Hcy directly affects oocyte quality and its mechanisms are poorly understood. Here we show that Hcy treatment impaired oocyte quality and developmental competence, indicated by significantly reduced survival rate, polar body extrusion rate, and cleavage rate. Hcy treatment resulted in mitochondrial dysfunction, with increased production of mitochondrial ROS, reduced mtDNA copy number, and the expression of 7 out of 13 mtDNA-encoded genes and 2 ribosome RNA genes, 12S rRNA and 16S rRNA. Upon Hcy treatment, the expression of one-carbon metabolic enzymes and DNMT1 was enhanced. Interestingly, DNA methyltransferase inhibitor 5'AZA rescued Hcy-induced mitochondrial dysfunction, impaired oocyte quality and developmental competence. Concurrently, expression of one-carbon metabolic enzymes and methylation status of mtDNA coding sequences were also normalized, at least partially, by 5'AZA treatment. Our findings not only extend the understanding about how Hcy induces poor oocyte quality, but also contribute to a novel angle of identifying targets for enhancing the quality of oocyte from PCOS patients.
Collapse
Affiliation(s)
- Longfei Jia
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, P. R. China.,Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yaqiong Zeng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yun Hu
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, P. R. China.,Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Jie Liu
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, P. R. China.,Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Chao Yin
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, P. R. China.,Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yingjie Niu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Chenfei Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yimin Jia
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, P. R. China.,Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| | - Jian Hong
- College of Life Science and Technology, Yancheng Teachers University, Yancheng, P. R., China
| | - Ruqian Zhao
- MOE Joint International Research Laboratory of Animal Health & Food Safety, Nanjing Agricultural University, Nanjing, P. R. China.,Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, P. R. China
| |
Collapse
|
25
|
Wang D, Liu M, Li X, Wang X, Shen Y. Expression, purification and oligomerization of the S-adenosylmethionine transporter. Protein Expr Purif 2020; 173:105648. [PMID: 32335303 DOI: 10.1016/j.pep.2020.105648] [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: 02/10/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 11/16/2022]
Abstract
The S-adenosylmethionine carrier (SAMC) is a membrane transport protein located on the inner membrane of mitochondria that catalyzes the import of S-adenosylmethionine (SAM) into the mitochondrial matrix. SAMC mutations can cause a series of mitochondrial defects, including those affecting RNA stability, protein modification, mitochondrial translation and biosynthesis. Here, we describe the expression, purification and oligomerization of SAMC. The SAMC genes from three species were cloned into a eukaryotic expression vector with a GFP tag, and confocal microscopy analysis showed that these SAMCs were localized to mitochondria. A BacMam expression system was used for the expression of D. rerio SAMC with a FLAG tag. A size-exclusion chromatography analysis showed that SAMC may form a hexamer. A negative-staining electron microscopy analysis showed that SAMC formed tiny uniform particles and also confirmed the oligomerization of SAMC.
Collapse
Affiliation(s)
- Dandan Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300350, China; College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Meizi Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300350, China; College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Xuemiao Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300350, China; College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Xiaoqiang Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300350, China; College of Pharmacy, Nankai University, Tianjin, 300350, China.
| | - Yuequan Shen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin, 300350, China; College of Life Sciences, Nankai University, Tianjin, 300071, China.
| |
Collapse
|
26
|
Zhu X, Xuan Z, Chen J, Li Z, Zheng S, Song P. How DNA methylation affects the Warburg effect. Int J Biol Sci 2020; 16:2029-2041. [PMID: 32549751 PMCID: PMC7294934 DOI: 10.7150/ijbs.45420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/05/2020] [Indexed: 12/13/2022] Open
Abstract
Significant enhancement of the glycolysis pathway is a major feature of tumor cells, even in the presence of abundant oxygen; this enhancement is known as the Warburg effect, and also called aerobic glycolysis. The Warburg effect was discovered nearly a hundred years ago, but its specific mechanism remains difficult to explain. DNA methylation is considered to be a potential trigger for the Warburg effect, as the two processes have many overlapping links during tumorigenesis. Based on a widely recognized potential mechanism of the Warburg effect, we here summarized the relationship between DNA methylation and the Warburg effect with regard to cellular energy metabolism factors, such as glycolysis related enzymes, mitochondrial function, glycolysis bypass pathways, the tumor oxygen sensing pathway and abnormal methylation conditions. We believe that clarifying the relationship between these different mechanisms may further help us understand how DNA methylation works on tumorigenesis and provide new opportunities for cancer therapy.
Collapse
Affiliation(s)
- Xingxin Zhu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Zefeng Xuan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Jun Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Zequn Li
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| | - Penghong Song
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University.,NHC Key Laboratory of Combined Multi-organ Transplantation.,Key Laboratory of the diagnosis and treatment of organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences (2019RU019).,Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
| |
Collapse
|
27
|
Shi Z, Xu S, Xing S, Yao K, Zhang L, Xue L, Zhou P, Wang M, Yan G, Yang P, Liu J, Hu Z, Lan F. Mettl17, a regulator of mitochondrial ribosomal RNA modifications, is required for the translation of mitochondrial coding genes. FASEB J 2019; 33:13040-13050. [PMID: 31487196 DOI: 10.1096/fj.201901331r] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Embryonic stem cells (ESCs) are pluripotent stem cells with the ability to self-renew and to differentiate into any cell types of the 3 germ layers. Recent studies have demonstrated that there is a strong connection between mitochondrial function and pluripotency. Here, we report that methyltransferase like (Mettl) 17, identified from the clustered regularly interspaced short palindromic repeats knockout screen, is required for proper differentiation of mouse embryonic stem cells (mESCs). Mettl17 is located in mitochondria through its N-terminal targeting sequence and specifically interacts with 12S mitochondrial ribosomal RNA (mt-rRNA) as well as small subunits of mitochondrial ribosome (MSSUs). Loss of Mettl17 affects the stability of both 12S mt-rRNA and its associated proteins of MSSUs. We further showed that Mettl17 is an S-adenosyl methionine (SAM)-binding protein and regulates mitochondrial ribosome function in a SAM-binding-dependent manner. Loss of Mettl17 leads to around 70% reduction of m4C840 and 50% reduction of m5C842 of 12S mt-rRNA, revealing the first regulator of the m4C840 and indicating a crosstalk between the 2 nearby modifications. The defects of mitochondrial ribosome caused by deletion of Mettl17 lead to the impaired translation of mitochondrial protein-coding genes, resulting in significant changes in mitochondrial oxidative phosphorylation and cellular metabolome, which are important for mESC pluripotency.-Shi, Z., Xu, S., Xing, S., Yao, K., Zhang, L., Xue, L., Zhou, P., Wang, M., Yan, G., Yang, P., Liu, J., Hu, Z., Lan, F. Mettl17, a regulator of mitochondrial ribosomal RNA modifications, is required for the translation of mitochondrial coding genes.
Collapse
Affiliation(s)
- Zhennan Shi
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Siyuan Xu
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shenghui Xing
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, China
| | - Luxi Xue
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peng Zhou
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ming Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guoquan Yan
- Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, China
| | - Pengyuan Yang
- Institutes of Biomedical Sciences and Department of Systems Biology for Medicine, Basic Medical College, Fudan University, Shanghai, China
| | - Jing Liu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Fei Lan
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
28
|
Transcriptional Regulation Factors of the Human Mitochondrial Aspartate/Glutamate Carrier Gene, Isoform 2 ( SLC25A13): USF1 as Basal Factor and FOXA2 as Activator in Liver Cells. Int J Mol Sci 2019; 20:ijms20081888. [PMID: 30995827 PMCID: PMC6515469 DOI: 10.3390/ijms20081888] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/12/2019] [Accepted: 04/14/2019] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial carriers catalyse the translocation of numerous metabolites across the inner mitochondrial membrane, playing a key role in different cell functions. For this reason, mitochondrial carrier gene expression needs tight regulation. The human SLC25A13 gene, encoding for the mitochondrial aspartate/glutamate carrier isoform 2 (AGC2), catalyses the electrogenic exchange of aspartate for glutamate plus a proton, thus taking part in many metabolic processes including the malate-aspartate shuttle. By the luciferase (LUC) activity of promoter deletion constructs we identified the putative promoter region, comprising the proximal promoter (-442 bp/-19 bp), as well as an enhancer region (-968 bp/-768 bp). Furthermore, with different approaches, such as in silico promoter analysis, gene silencing and chromatin immunoprecipitation, we identified two transcription factors responsible for SLC25A13 transcriptional regulation: FOXA2 and USF1. USF1 acts as a positive transcription factor which binds to the basal promoter thus ensuring SLC25A13 gene expression in a wide range of tissues. The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC).
Collapse
|
29
|
Cianciulli A, Menga A, Ferdinando P, Iacobazzi V. FOXD3 acts as a repressor of the mitochondrial S-adenosylmethionine carrier (SLC25A26) gene expression in cancer cells. Biochimie 2018; 154:25-34. [DOI: 10.1016/j.biochi.2018.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/30/2018] [Indexed: 01/24/2023]
|
30
|
Mechta M, Ingerslev LR, Barrès R. Methodology for Accurate Detection of Mitochondrial DNA Methylation. J Vis Exp 2018:57772. [PMID: 29863674 PMCID: PMC6101301 DOI: 10.3791/57772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Quantification of DNA methylation can be achieved using bisulfite sequencing, which takes advantage of the property of sodium bisulfite to convert unmethylated cytosine into uracil, in a single-stranded DNA context. Bisulfite sequencing can be targeted (using PCR) or performed on the whole genome and provides absolute quantification of cytosine methylation at the single base-resolution. Given the distinct nature of nuclear- and mitochondrial DNA, notably in the secondary structure, adaptions of bisulfite sequencing methods for investigating cytosine methylation in mtDNA should be made. Secondary and tertiary structure of mtDNA can indeed lead to bisulfite sequencing artifacts leading to false-positives due to incomplete denaturation poor access of bisulfite to single-stranded DNA. Here, we describe a protocol using an enzymatic digestion of DNA with BamHI coupled with bioinformatic analysis pipeline to allow accurate quantification of cytosine methylation levels in mtDNA. In addition, we provide guidelines for designing the bisulfite sequencing primers specific to mtDNA, in order to avoid targeting undesirable NUclear MiTochondrial segments (NUMTs) inserted into the nuclear genome.
Collapse
Affiliation(s)
- Mie Mechta
- The Novo Nordisk Foundation for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
| | - Lars Roed Ingerslev
- The Novo Nordisk Foundation for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen
| | - Romain Barrès
- The Novo Nordisk Foundation for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen;
| |
Collapse
|
31
|
Ghosh S, Ranawat AS, Tolani P, Scaria V. Mitoepigenome KB a comprehensive resource for human mitochondrial epigenetic data. Mitochondrion 2017; 42:54-58. [PMID: 29129553 DOI: 10.1016/j.mito.2017.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 09/21/2017] [Accepted: 11/02/2017] [Indexed: 01/31/2023]
Abstract
Epigenetic modifications in the mitochondrial genome has been an emerging area of interest in the recent years in the field of mitochondrial biology. The renewed interest in the area has been largely fueled by a number of reports in the recent years suggesting the presence of epigenetic modifications in human mitochondrial genome and their associations with exposure to environmental factors and human diseases and or traits. Nevertheless there has been no systematic effort to curate, organize this information to enable cross-comparison between studies and datasets. We compiled 62 datasets from 9 studies on the epigenetic modifications in human mitochondrial genome to create a comprehensive catalog. This catalog is available as a user friendly interface - mitoepigenomeKB, where the data could be searched, browsed or visualized. The resource is available at URL: http://clingen.igib.res.in/mitoepigenome/. We hope mitoepigenomeKB would emerge as a central resource for datasets on epigenetic modifications in human mitochondria and would serve as the starting point to understanding the biology of human mitochondrial epigenome.
Collapse
Affiliation(s)
- Sourav Ghosh
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110 025, India
| | - Anop Singh Ranawat
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - Priya Tolani
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110 025, India; Academy of Scientific and Innovative Research, CSIR-IGIB South Campus, Mathura Road, Delhi 110 025, India.
| |
Collapse
|
32
|
Mechta M, Ingerslev LR, Fabre O, Picard M, Barrès R. Evidence Suggesting Absence of Mitochondrial DNA Methylation. Front Genet 2017; 8:166. [PMID: 29163634 PMCID: PMC5671948 DOI: 10.3389/fgene.2017.00166] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 10/16/2017] [Indexed: 11/28/2022] Open
Abstract
Methylation of nuclear genes encoding mitochondrial proteins participates in the regulation of mitochondria function. The existence of cytosine methylation in the mitochondrial genome is debated. To investigate whether mitochondrial DNA (mtDNA) is methylated, we used both targeted- and whole mitochondrial genome bisulfite sequencing in cell lines and muscle tissue from mouse and human origin. While unconverted cytosines were detected in some portion of the mitochondrial genome, their abundance was inversely associated to the sequencing depth, indicating that sequencing analysis can bias the estimation of mtDNA methylation levels. In intact mtDNA, few cytosines remained 100% unconverted. However, removal of supercoiled structures of mtDNA with the restriction enzyme BamHI prior to bisulfite sequencing decreased cytosine unconversion rate to <1.5% at all the investigated regions: D-loop, tRNA-F+12S, 16S, ND5 and CYTB, suggesting that mtDNA supercoiled structure blocks the access to bisulfite conversion. Here, we identified an artifact of mtDNA bisulfite sequencing that can lead to an overestimation of mtDNA methylation levels. Our study supports that cytosine methylation is virtually absent in mtDNA.
Collapse
Affiliation(s)
- Mie Mechta
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars R Ingerslev
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Odile Fabre
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Picard
- Department of Psychiatry and Neurology, Division of Behavioral Medicine, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY, United States
| | - Romain Barrès
- Section of Integrative Physiology, Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
33
|
Saini SK, Mangalhara KC, Prakasam G, Bamezai RNK. DNA Methyltransferase1 (DNMT1) Isoform3 methylates mitochondrial genome and modulates its biology. Sci Rep 2017; 7:1525. [PMID: 28484249 PMCID: PMC5431478 DOI: 10.1038/s41598-017-01743-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/12/2017] [Indexed: 12/21/2022] Open
Abstract
Here we demonstrate localization of the isoform3 of DNA Methyltransferase1 (DNMT1) enzyme to mitochondria, instead of isoform1 as reported earlier. The fused DNMT1-isoform1, reported earlier to localize in mitochondria, surprisingly showed its exclusive presence inside the nucleus after its ectopic expression; and failed to localize in mitochondria. On the other hand, ectopically expressed DNMT1-isoform3 targeted itself to mitochondria and subsequently methylated CpG regions in the mitochondrial genome. In addition, overexpression of DNMT1-isoform3 affected mitochondrial biology and regulated its function. Under different conditions of oxidative and nutritional stress, this isoform was down-regulated, resulting in hypomethylation of mitochondrial genome. Our study reveals how DNMT1-isoform3, instead of isoform1, is responsible for mtDNA methylation, influencing its biology.
Collapse
Affiliation(s)
- Sunil Kumar Saini
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Kailash Chandra Mangalhara
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Gopinath Prakasam
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - R N K Bamezai
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|