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Bury A, Pyle A, Vincent AE, Actis P, Hudson G. Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues. Sci Rep 2024; 14:13789. [PMID: 38877095 PMCID: PMC11178779 DOI: 10.1038/s41598-024-64455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Mitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissues, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
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Affiliation(s)
- Alexander Bury
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK
- Bragg Centre for Materials Research, Leeds, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK.
- Bragg Centre for Materials Research, Leeds, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
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2
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Pereira-Martins DA, Coelho-Silva JL, Weinhäuser I, Franca-Neto PL, Silveira DR, Ortiz C, Moreira-Aguiar A, Lima MM, Koury LC, de Melo RA, Glória AB, Fagundes EM, Lino BK, Pagnano K, Bittencourt R, Nunes E, Traina F, Figueiredo-Pontes L, Keating A, Tallman MS, Ribeiro RC, Dilon R, Ganser A, Sanz MA, Berliner N, Valk P, Löwenberg B, Ottone T, Noguera NI, Voso MT, Paoloni F, Fazi P, Ammatuna E, Huls G, Schuringa JJ, Rego EM, Lucena-Araujo AR. Clinical significance of mitochondrial DNA content in acute promyelocytic leukaemia. Br J Haematol 2023; 200:170-174. [PMID: 36263593 DOI: 10.1111/bjh.18510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 01/14/2023]
Abstract
Although a growing body of evidence demonstrates that altered mtDNA content (mtDNAc) has clinical implications in several types of solid tumours, its prognostic relevance in acute promyelocytic leukaemia (APL) patients remains largely unknown. Here, we show that patients with higher-than-normal mtDNAc had better outcomes regardless of tumour burden. These results were more evident in patients with low-risk of relapse. The multivariate Cox proportional hazard model demonstrated that high mtDNAc was independently associated with a decreased cumulative incidence of relapse. Altogether, our data highlights the possible role of mitochondrial metabolism in APL patients treated with ATRA.
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Affiliation(s)
- Diego A Pereira-Martins
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands.,Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | - Juan L Coelho-Silva
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil.,Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | - Isabel Weinhäuser
- Department of Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands.,Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | | | - Douglas R Silveira
- Myeloid Leukaemia Genomics and Biology Group, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - César Ortiz
- Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | | | - Marinus M Lima
- Department of Genetics, Federal University of Pernambuco, Recife, Brazil
| | - Luisa C Koury
- Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | - Raul A de Melo
- Department of Internal Medicine, University of Pernambuco, Recife, Brazil
| | - Ana B Glória
- Hematology Division, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Evandro M Fagundes
- Hematology Division, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bruno K Lino
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Katia Pagnano
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | | | - Elenaide Nunes
- Hematology Division, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Fabiola Traina
- Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | - Lorena Figueiredo-Pontes
- Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil
| | - Armand Keating
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Martin S Tallman
- Leukemia Service, Memorial Sloan-Kettering Cancer Center/Weill Cornell Medical College, New York City, New York, USA
| | - Raul C Ribeiro
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Richard Dilon
- Department of Medical and Molecular Genetics, King's College London School of Medicine, London, UK
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Miguel A Sanz
- Department of Hematology, Valencia University Medical School, Valencia, Spain.,CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Nancy Berliner
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Peter Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bob Löwenberg
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy
| | - Nelida I Noguera
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy
| | - Maria T Voso
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy
| | - Francesca Paoloni
- Santa Lucia Foundation, I.R.C.C.S., Neuro-Oncohematology, Rome, Italy
| | - Paola Fazi
- Gruppo Italiano Malattie Ematologiche Maligne dell'Adulto (GIMEMA), GIMEMA Foundation, Rome, Italy
| | - Emanuele Ammatuna
- Department of Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Gerwin Huls
- Department of Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Jan Jacob Schuringa
- Department of Hematology, Cancer Research Centre Groningen, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
| | - Eduardo M Rego
- Department of Medical Imaging, Haematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.,Center for Cell Based Therapy, São Paulo Research Foundation, Ribeirão Preto, SP, Brazil.,Hematology Division, LIM31, Faculdade de Medicina, University of São Paulo, São Paulo, Brazil
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3
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Mertens J, Regin M, De Munck N, Couvreu de Deckersberg E, Belva F, Sermon K, Tournaye H, Blockeel C, Van de Velde H, Spits C. Mitochondrial DNA variants segregate during human preimplantation development into genetically different cell lineages that are maintained postnatally. Hum Mol Genet 2022; 31:3629-3642. [PMID: 35285472 PMCID: PMC9616571 DOI: 10.1093/hmg/ddac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 06/30/2024] Open
Abstract
Humans present remarkable diversity in their mitochondrial DNA (mtDNA) in terms of variants across individuals as well as across tissues and even cells within one person. We have investigated the timing of the first appearance of this variant-driven mosaicism. For this, we deep-sequenced the mtDNA of 254 oocytes from 85 donors, 158 single blastomeres of 25 day-3 embryos, 17 inner cell mass and trophectoderm samples of 7 day-5 blastocysts, 142 bulk DNA and 68 single cells of different adult tissues. We found that day-3 embryos present blastomeres that carry variants only detected in that cell, showing that mtDNA mosaicism arises very early in human development. We classified the mtDNA variants based on their recurrence or uniqueness across different samples. Recurring variants had higher heteroplasmic loads and more frequently resulted in synonymous changes or were located in non-coding regions than variants unique to one oocyte or single embryonic cell. These differences were maintained through development, suggesting that the mtDNA mosaicism arising in the embryo is maintained into adulthood. We observed a decline in potentially pathogenic variants between day 3 and day 5 of development, suggesting early selection. We propose a model in which closely clustered mitochondria carrying specific mtDNA variants in the ooplasm are asymmetrically distributed throughout the cell divisions of the preimplantation embryo, resulting in the earliest form of mtDNA mosaicism in human development.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Neelke De Munck
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Florence Belva
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Herman Tournaye
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
- Research Group Biology of the Testis, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
- Department of Obstetrics, Gynaecology, Perinatology and Reproduction, Institute of Professional Education, Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow 119992, Russia
| | - Christophe Blockeel
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
| | - Hilde Van de Velde
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
- Brussels IVF, Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, 1090 Brussels, Belgium
- Research Group Reproduction and Immunology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
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4
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Jaberi E, Tresse E, Grønbæk K, Weischenfeldt J, Issazadeh-Navikas S. Identification of unique and shared mitochondrial DNA mutations in neurodegeneration and cancer by single-cell mitochondrial DNA structural variation sequencing (MitoSV-seq). EBioMedicine 2020; 57:102868. [PMID: 32629384 PMCID: PMC7334819 DOI: 10.1016/j.ebiom.2020.102868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
Background Point mutations and structural variations (SVs) in mitochondrial DNA (mtDNA) contribute to many neurodegenerative diseases. Technical limitations and heteroplasmy, however, have impeded their identification, preventing these changes from being examined in neurons in healthy and disease states. Methods We have developed a high-resolution technique—Mitochondrial DNA Structural Variation Sequencing (MitoSV-seq)—that identifies all types of mtDNA SVs and single-nucleotide variations (SNVs) in single neurons and novel variations that have been undetectable with conventional techniques. Findings Using MitoSV-seq, we discovered SVs/SNVs in dopaminergic neurons in the Ifnar1−/− murine model of Parkinson disease. Further, MitoSV-seq was found to have broad applicability, delivering high-quality, full-length mtDNA sequences in a species-independent manner from human PBMCs, haematological cancers, and tumour cell lines, regardless of heteroplasmy. We characterised several common SVs in haematological cancers (AML and MDS) that were linked to the same mtDNA region, MT-ND5, using only 10 cells, indicating the power of MitoSV-seq in determining single-cancer-cell ontologies. Notably, the MT-ND5 hotspot, shared between all examined cancers and Ifnar1−/− dopaminergic neurons, suggests that its mutations have clinical value as disease biomarkers. Interpretation MitoSV-seq identifies disease-relevant mtDNA mutations in single cells with high resolution, rendering it a potential drug screening platform in neurodegenerative diseases and cancers. Funding The Lundbeck Foundation, Danish Council for Independent Research-Medicine, and European Union Horizon 2020 Research and Innovation Programme.
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Affiliation(s)
- Elham Jaberi
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Emilie Tresse
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kirsten Grønbæk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; Department of Hematology, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, DK-2200 Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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5
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Maeda R, Kami D, Maeda H, Shikuma A, Gojo S. High throughput single cell analysis of mitochondrial heteroplasmy in mitochondrial diseases. Sci Rep 2020; 10:10821. [PMID: 32616755 PMCID: PMC7331593 DOI: 10.1038/s41598-020-67686-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/11/2020] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial heteroplasmy, which fundamentally means intracellular heterogeneity of mitochondrial DNA (mtDNA), has been measured in a group of cells, regardless of intercellular heterogeneity. Ordinal methods for mitochondrial heteroplasmy cannot discriminate between an intercellular homogenic population composed of cells with similar intracellular heterogeneity for mtDNA and an intercellular heterogenic population composed of cells with different rates of mutated mtDNA. A high-throughput method to determine mitochondrial heteroplasmy in a single cell was developed by using droplet digital PCR with TaqMan polymerase in this study. This technique revealed that there are three different cell populations of cultured fibroblasts derived from patients with mitochondrial disease carrying a mutation in the mtDNA; cells with homoplasmy of either mutated or healthy mtDNA; and cells mixed with mutated and healthy mtDNA. The presence of intercellular heterogeneity, even in uniformed cultured fibroblasts, suggests that heterogeneity should exist among different kinds of cells. The diagnosis of intercellular heterogeneity with respect to mitochondrial heteroplasmy by this methodology could provide novel insight into developing a treatment strategy for mitochondrial diseases.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Hideki Maeda
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan.
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6
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Ishikawa K, Kobayashi K, Yamada A, Umehara M, Oka T, Nakada K. Concentration of mitochondrial DNA mutations by cytoplasmic transfer from platelets to cultured mouse cells. PLoS One 2019; 14:e0213283. [PMID: 30830936 PMCID: PMC6398856 DOI: 10.1371/journal.pone.0213283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/18/2019] [Indexed: 01/11/2023] Open
Abstract
Accumulation of mutations in mitochondrial DNA (mtDNA) is thought to be responsible for mitochondrial, and other, diseases and biological phenomena, such as diabetes, cancer, neurodegenerative diseases, and aging. Mouse models may elucidate the relationship between mutations in mtDNA and these abnormalities. However, because of the difficulty of mtDNA manipulation, generation of mouse models has not sufficiently progressed to enable such studies. To overcome this difficulty and to establish a source of diverse mtDNA mutations, we here generated cultured mouse cells containing mtDNA derived from an mtDNA mutator mouse that accumulates random mtDNA mutations with age. Mutation analysis of the obtained transmitochondrial cytoplasmic hybrid cells (cybrids) revealed that the cells harbored diverse mtDNA mutations occurring at a higher frequency than in mouse tissues, and exhibited severe respiration defects that would be lethal in tissues or organs. Abnormal respiratory complex formation and high stress on the mitochondrial protein quality control system appeared to be involved in these severe respiration defects. The mutation rates of the majority of highly accumulated mutations converged to either approximately 5%, 10%, or 40%, suggesting that these mutations are linked on the respective mtDNA molecules, and mtDNA in cybrid cells likely consisted of mtDNA molecules clonally expanded from the small population of introduced mtDNAs. Thus, the linked mutations in these cybrid cells cannot be evaluated individually. In addition, mtDNA mutations homologous to confirmed pathogenic mutations in human were rarely observed in our generated cybrids. However, the transmitochondrial cybrids constitute a useful tool for concentrating pathogenic mtDNA mutations and as a source of diverse mtDNA mutations to elucidate the relationship between mtDNA mutations and diseases.
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Affiliation(s)
- Kaori Ishikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- * E-mail: (KI); (KN)
| | - Kohei Kobayashi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Akihito Yamada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Moe Umehara
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
| | - Toshihiko Oka
- Department of Life Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, Japan
- * E-mail: (KI); (KN)
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7
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Tyagi A, Pramanik R, Vishnubhatla S, Bakhshi R, Bakhshi S. Prognostic impact of mitochondrial DNA D-loop variations in pediatric acute myeloid leukemia. Oncotarget 2019; 10:1334-1343. [PMID: 30863493 PMCID: PMC6407682 DOI: 10.18632/oncotarget.26665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/31/2019] [Indexed: 12/21/2022] Open
Abstract
The role of mitochondrial DNA (mt-DNA) changes, especially those in the regulatory D-loop region in Acute Myeloid Leukemia (AML) remains investigational. Consecutive 151 de novo pediatric AML patients, (≤18 yr) were prospectively enrolled from June 2013-August 2016, to assess the prognostic impact of mt-DNA D-loop variations (somatic/germline) on survival. For each patient, D-loop region was sequenced on baseline bone marrow and buccal swab, and mother’s blood sample. In 151 AML subjects, 1490 variations were found at 237 positions; 80.9% were germline and 19.1% somatic. The mean number of variations per position was 6.3. Variations with frequency ≥6 were analyzed for their impact on survival and 4 categories were created, namely “somatic-protective”, “somatic-hazardous”, “germline-protective” and “germline- hazardous”. Although, somatic-protective could not predict event free survival (EFS) or overall survival (OS), somatic-hazardous [(OS) HR = 2.33, p = 0.06] and germline-hazardous [(OS) HR = 2.85, p < 0.01] significantly predicted OS and EFS. Notably, the germline-protective, could significantly predict EFS (HR = 0.31, p = 0.03) and OS (HR = 0.19, p < 0.01), only when variations at ≥2 positions were present. On multivariate analysis, three positions namely 16111, 16126, 16362 and karyotype were found to be predictive of EFS. A prognostic index (PI) was developed using nomogram PI = (0.8*karyotype) + (1.0*c16111) + (0.7*t16362) + (1.2*t16126). Hazard ratio for EFS increased significantly with increasing PI reaching to a maximum of 3.3 (p < 0.01). In conclusion, the impact of mt-DNA D-loop variations on outcomes in pediatric AML depends on their nature (germline/somatic), position and mutational burden, highlighting their potential role as evolving prognostic biomarkers.
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Affiliation(s)
- Anudishi Tyagi
- Department of Medical Oncology, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Raja Pramanik
- Department of Medical Oncology, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | | | - Radhika Bakhshi
- Department of Biomedical Sciences, Shaheed Rajguru College of Applied Sciences, University of Delhi, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr. B. R. A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
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8
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Kim HR, Kang MG, Lee YE, Na BR, Noh MS, Yang SH, Shin JH, Shin MG. Spectrum of mitochondrial genome instability and implication of mitochondrial haplogroups in Korean patients with acute myeloid leukemia. Blood Res 2018; 53:240-249. [PMID: 30310792 PMCID: PMC6170299 DOI: 10.5045/br.2018.53.3.240] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 11/17/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) mutations may regulate the progression and chemosensitivity of leukemia. Few studies regarding mitochondrial aberrations and haplogroups in acute myeloid leukemia (AML) and their clinical impacts have been reported. Therefore, we focused on the mtDNA length heteroplasmies minisatellite instability (MSI), copy number alterations, and distribution of mitochondrial haplogroups in Korean patients with AML. Methods This study investigated 74 adult patients with AML and 70 controls to evaluate mtDNA sequence alterations, MSI, mtDNA copy number, haplogroups, and their clinical implications. The hypervariable (HV) control regions (HV1 and HV2), tRNAleu1gene, and cytochrome b gene of mtDNA were analyzed. Two mtDNA minisatellite markers, 16189 poly-C (16184CCCCCTCCCC16193, 5CT4C) and 303 poly-C (303CCCCCCCTCCCCC315, 7CT5C), were used to examine the mtDNA MSI. Results In AML, most mtDNA sequence variants were single nucleotide substitutions, but there were no significant differences compared to those in controls. The number of mtMSI patterns increased in AML. The mean mtDNA copy number of AML patients increased approximately 9-fold compared to that of controls (P<0.0001). Haplogroup D4 was found in AML with a higher frequency compared to that in controls (31.0% vs. 15.7%, P=0.046). None of the aforementioned factors showed significant impacts on the outcomes. Conclusion AML cells disclosed more heterogeneous patterns with the mtMSI markers and had increased mtDNA copy numbers. These findings implicate mitochondrial genome instability in primary AML cells. Therefore, mtDNA haplogroup D4 might be associated with AML risk among Koreans.
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Affiliation(s)
- Hye Ran Kim
- College of Korean Medicine, Dongshin University, Naju, Korea
| | - Min-Gu Kang
- Department of Laboratory Medicine, Gwangyang Sarang General Hospital, Gwangyang, Korea
| | - Young Eun Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Bo Ram Na
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Min Seo Noh
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Seung Hyun Yang
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Jong-Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Myun-Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea.,Environmental Health Center for Childhood Leukemia and Cancer, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
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9
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Tyagi A, Pramanik R, Vishnubhatla S, Ali S, Bakhshi R, Chopra A, Singh A, Bakhshi S. Pattern of mitochondrial D-loop variations and their relation with mitochondrial encoded genes in pediatric acute myeloid leukemia. Mutat Res 2018; 810:13-18. [PMID: 29883862 DOI: 10.1016/j.mrfmmm.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/08/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Role of mitochondrial DNA variations, particularly in D loop region, remains investigational in acute myeloid leukaemia (AML). Consecutive 151 pediatric AML patients were prospectively enrolled from June 2013 to August 2016, for evaluating pattern of variations in mitochondrial D-loop region and to determine their association, if any, with expression of mitochondrial-encoded genes. For each patient, D-loop region was sequenced on baseline bone marrow, buccal swab and mother's blood sample. Real time PCR was used for relative gene expression of four mitochondrial DNA encoded genes viz. Nicotinamide-adenine-dineucleotide-dehydrogenase subunit 3 (ND3), Cytochrome-B (Cyt-B), Cytochrome c oxidase-I (COX1) and ATP-synthetase F0 subunit-6 (ATP6). Total 1490 variations were found at 237 positions in D-Loop; 1206 (80.9%) were germline and 284 (19.1%) were somatic. Positions 73-263 were identified as a probable hotspot region. G bases appeared to be most stable nucleotide (least number of single base substitutions) whereas T appeared to be most susceptible to variations with germline T-C being the commonest. Gene expression of Cyt-B was found to be significantly higher for any variation (somatic or germline) at positions 16,192 and 16,327 while it was significantly lower for variations at positions 16,051 and 207. Any variation at positions 152, 207 and 513 significantly decreased COX1 expression while those at positions 16,051 and 152 attenuated ATP6 expression. This first study evaluated type and overall pattern of D-loop variations in AML, and also showed that some of these variations in D loop region might have an effect on the mitochondrial-encoded genes which is new and valuable information in AML genomics.
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Affiliation(s)
- Anudishi Tyagi
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India
| | - Raja Pramanik
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India
| | | | - Safdar Ali
- Shaheed Rajguru College of Applied Sciences, India; University of Delhi , New Delhi
| | - Radhika Bakhshi
- Shaheed Rajguru College of Applied Sciences, India; University of Delhi , New Delhi
| | - Anita Chopra
- Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India; Department of Lab oncology
| | - Archna Singh
- All India Institute of Medical Sciences, New Delhi, India; Department of Biochemistry
| | - Sameer Bakhshi
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India.
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10
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Guo J, Cao B, Xu X, Wu F, Zhu B. Novel CTCF mutations in Chinese patients with ovarian endometriosis. Mol Med Rep 2018; 18:1031-1036. [PMID: 29845264 DOI: 10.3892/mmr.2018.9049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/01/2018] [Indexed: 11/06/2022] Open
Abstract
Endometriosis is a common gynecological disease characterized by the outgrowth of the endometrium, however, the detailed molecular etiology remains largely uncharacterized. Recent studies have implicated that endometriosis is potentially a precancerous lesion, and that CCCTC‑binding factor (CTCF) mutations may be involved in the pathogenesis of this disorder. However, the detailed CTCF mutation spectrum in Chinese patients with ovarian endometriosis remains largely unknown. In the present study, a cohort of 92 patients with ovarian endometriosis were analyzed for the presence of CTCF mutations by sequencing the entire coding regions. In addition, 67 healthy eutopic endometrial tissues and 46 healthy ovarian tissues from control samples (without endometriosis) were also analyzed. In total, two CTCF missense mutations, p.K206E (c.616A>G) and p.H373L (c.1118A>T), were identified in 2/92 (2.2%) endometriotic lesions. The patient with the p.K206E mutation was 26 years old and diagnosed with primary infertility, whereas the patient with the p.H373L mutation was 37 years old and concurrently diagnosed with uterine leiomyoma. The p.H373L mutation was previously identified in endometrial cancer samples with low frequency, while the p.K206E mutation was novel. In addition, no CTCF mutations were detected in the 67 healthy eutopic endometrial and 46 healthy ovarian tissue samples. In silico prediction and evolutionary conservation analysis suggested that these CTCF mutations may be pathogenic. In summary, the present study identified 2 potential pathogenic CTCF mutations in endometriotic lesions from 2/92 patients with ovarian endometriosis. These results, together with a prior exome‑sequencing based study, suggest that CTCF mutations may be involved in the development of ovarian endometriosis.
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Affiliation(s)
- Jiubai Guo
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Bianna Cao
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Xiaoyun Xu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Fei Wu
- Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Bin Zhu
- Gongqing College of Nanchang University, Gongqingcheng, Jiangxi 332020, P.R. China
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11
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Järviaho T, Hurme-Niiranen A, Soini HK, Niinimäki R, Möttönen M, Savolainen ER, Hinttala R, Harila-Saari A, Uusimaa J. Novel non-neutral mitochondrial DNA mutations found in childhood acute lymphoblastic leukemia. Clin Genet 2017; 93:275-285. [PMID: 28708239 DOI: 10.1111/cge.13100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/29/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022]
Abstract
Mitochondria produce adenosine triphosphate (ATP) for energy requirements via the mitochondrial oxidative phosphorylation (OXPHOS) system. One of the hallmarks of cancer is the energy shift toward glycolysis. Low OXPHOS activity and increased glycolysis are associated with aggressive types of cancer. Mitochondria have their own genome (mitochondrial DNA [mtDNA]) encoding for 13 essential subunits of the OXPHOS enzyme complexes. We studied mtDNA in childhood acute lymphoblastic leukemia (ALL) to detect potential pathogenic mutations in OXPHOS complexes. The whole mtDNA from blood and bone marrow samples at diagnosis and follow-up from 36 ALL patients were analyzed. Novel or previously described pathogenic mtDNA mutations were identified in 8 out of 36 patients. Six out of these 8 patients had died from ALL. Five out of 36 patients had an identified poor prognosis genetic marker, and 4 of these patients had mtDNA mutations. Missense or nonsense mtDNA mutations were detected in the genes encoding subunits of OXPHOS complexes, as follows: MT-ND1, MT-ND2, MT-ND4L and MT-ND6 of complex I; MT-CO3 of complex IV; and MT-ATP6 and MT-ATP8 of complex V. We discovered mtDNA mutations in childhood ALL supporting the hypothesis that non-neutral variants in mtDNA affecting the OXPHOS function may be related to leukemic clones.
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Affiliation(s)
- T Järviaho
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - A Hurme-Niiranen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - H K Soini
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - R Niinimäki
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - M Möttönen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - E-R Savolainen
- Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,NordLab Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Department of Clinical Chemistry, University of Oulu, Oulu, Finland
| | - R Hinttala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - A Harila-Saari
- Department of Women's and Children's Health, Karolinska University Hospital Solna, Stockholm, Sweden
| | - J Uusimaa
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
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12
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Jin G, Xu C, Zhang X, Long J, Rezaeian AH, Liu C, Furth ME, Kridel S, Pasche B, Bian XW, Lin HK. Atad3a suppresses Pink1-dependent mitophagy to maintain homeostasis of hematopoietic progenitor cells. Nat Immunol 2017; 19:29-40. [PMID: 29242539 DOI: 10.1038/s41590-017-0002-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/04/2017] [Indexed: 01/13/2023]
Abstract
Although deletion of certain autophagy-related genes has been associated with defects in hematopoiesis, it remains unclear whether hyperactivated mitophagy affects the maintenance and differentiation of hematopoietic stem cells (HSCs) and committed progenitor cells. Here we report that targeted deletion of the gene encoding the AAA+-ATPase Atad3a hyperactivated mitophagy in mouse hematopoietic cells. Affected mice showed reduced survival, severely decreased bone-marrow cellularity, erythroid anemia and B cell lymphopenia. Those phenotypes were associated with skewed differentiation of stem and progenitor cells and an enlarged HSC pool. Mechanistically, Atad3a interacted with the mitochondrial channel components Tom40 and Tim23 and served as a bridging factor to facilitate appropriate transportation and processing of the mitophagy protein Pink1. Loss of Atad3a caused accumulation of Pink1 and activated mitophagy. Notably, deletion of Pink1 in Atad3a-deficient mice significantly 'rescued' the mitophagy defect, which resulted in restoration of the progenitor and HSC pools. Our data indicate that Atad3a suppresses Pink1-dependent mitophagy and thereby serves a key role in hematopoietic homeostasis.
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Affiliation(s)
- Guoxiang Jin
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chuan Xu
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Oncology, Chengdu Military General Hospital, Chengdu, Sichuan, China
| | - Xian Zhang
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Long
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pathology School of Basic Medical Science, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Abdol Hossein Rezaeian
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chunfang Liu
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark E Furth
- Wake Forest Innovations, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA
| | - Steven Kridel
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Boris Pasche
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Xiu-Wu Bian
- Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China.
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA. .,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan. .,Department of Biotechnology, Asia University, Taichung, Taiwan.
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13
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Accurate and comprehensive analysis of single nucleotide variants and large deletions of the human mitochondrial genome in DNA and single cells. Eur J Hum Genet 2017; 25:1229-1236. [PMID: 28832570 DOI: 10.1038/ejhg.2017.129] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/30/2017] [Accepted: 07/18/2017] [Indexed: 01/18/2023] Open
Abstract
Massive parallel sequencing (MPS) can accurately quantify mitochondrial DNA (mtDNA) single nucleotide variants (SNVs), but no MPS methods are currently validated to simultaneously and accurately establish the breakpoints and frequency of large deletions at low heteroplasmic loads. Here we present the thorough validation of an MPS protocol to quantify the load of very low frequency, large mtDNA deletions in bulk DNA and single cells, along with SNV calling by standard methods. We used a set of well-characterized DNA samples, DNA mixes and single cells to thoroughly control the study. We developed a custom script for the detection of mtDNA rearrangements that proved to be more accurate in detecting and quantifying deletions than pre-existing tools. We also show that PCR conditions and primersets must be carefully chosen to avoid biases in the retrieved variants and an increase in background noise, and established a lower detection limit of 0.5% heteroplasmic load for large deletions, and 1.5 and 2% for SNVs, for bulk DNA and single cells, respectively. Finally, the analysis of different single cells provided novel insights into mtDNA cellular mosaicism.
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14
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Pagani IS, Kok CH, Saunders VA, Van der Hoek MB, Heatley SL, Schwarer AP, Hahn CN, Hughes TP, White DL, Ross DM. A Method for Next-Generation Sequencing of Paired Diagnostic and Remission Samples to Detect Mitochondrial DNA Mutations Associated with Leukemia. J Mol Diagn 2017; 19:711-721. [PMID: 28732215 DOI: 10.1016/j.jmoldx.2017.05.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 05/17/2017] [Indexed: 10/19/2022] Open
Abstract
Somatic mitochondrial DNA (mtDNA) mutations have been identified in many human cancers, including leukemia. To identify somatic mutations, it is necessary to have a control tissue from the same individual for comparison. When patients with leukemia achieve remission, the remission peripheral blood may be a suitable and easily accessible control tissue, but this approach has not previously been applied to the study of mtDNA mutations. We have developed and validated a next-generation sequencing approach for the identification of leukemia-associated mtDNA mutations in 26 chronic myeloid leukemia patients at diagnosis using either nonhematopoietic or remission blood samples as the control. The entire mt genome was amplified by long-range PCR and sequenced using Illumina technology. Variant caller software was used to detect mtDNA somatic mutations, and an empirically determined threshold of 2% was applied to minimize false-positive results because of sequencing errors. Mutations were called against both nonhematopoietic and remission controls: the overall concordance between the two approaches was 81% (73/90 mutations). Some discordant results were because of the presence of somatic mutations in remission samples, because of either minimal residual disease or nonleukemic hematopoietic clones. This method could be applied to study somatic mtDNA mutations in leukemia patients who achieve minimal residual disease, and in patients with nonhematopoietic cancers who have a matched uninvolved tissue available.
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Affiliation(s)
- Ilaria S Pagani
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Chung H Kok
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Verity A Saunders
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Mark B Van der Hoek
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Susan L Heatley
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Anthony P Schwarer
- Australasian Leukaemia and Lymphoma Group, Melbourne, Victoria, Australia; Department of Haematology, Box Hill Hospital, Melbourne, Victoria, Australia
| | - Christopher N Hahn
- School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia; Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia
| | - Timothy P Hughes
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australasian Leukaemia and Lymphoma Group, Melbourne, Victoria, Australia; Centre for Cancer Biology, SA Pathology, Adelaide, South Australia, Australia; Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia
| | - Deborah L White
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australasian Leukaemia and Lymphoma Group, Melbourne, Victoria, Australia; School of Biomedical Sciences, Faculty of Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - David M Ross
- Cancer Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia; School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australasian Leukaemia and Lymphoma Group, Melbourne, Victoria, Australia; Department of Haematology, Royal Adelaide Hospital and SA Pathology, Adelaide, South Australia, Australia; Department of Molecular Medicine and Pathology, Flinders University and Medical Centre, Adelaide, South Australia, Australia.
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15
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Zou Y, Liu FY, Wu J, Wan L, Fang SF, Zhang ZY, Luo Y, Chen MH, Huang MZ, He M, Huang OP. Mutational analysis of the RAS/RAF/MEK/ERK signaling pathway in 260 Han Chinese patients with cervical carcinoma. Oncol Lett 2017; 14:2427-2431. [PMID: 28781678 DOI: 10.3892/ol.2017.6435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/17/2017] [Indexed: 01/02/2023] Open
Abstract
Prevalent mutations in the mitogen-activated protein kinase 1 (MAPK1)/extracellular signal-regulated kinase 2 (ERK2) pathway have been identified in cervical squamous cell carcinoma in a large-scale genome sequencing effort. Furthermore, mutations in the rat sarcoma viral oncogene homolog (RAS)/Raf/Mitogen-activated protein kinase kinase (MEK)/extracellular signal-regulated kinase (ERK) signaling pathway have also been revealed to have important roles in the pathogenesis of human cancer. However, whether the potential hotspot mutations in ERK2 and other components of the RAS/RAF/MEK/ERK signaling pathway also exist in Chinese patients with cervical carcinoma remains to be elucidated. In the present study, a total of 260 patients with cervical carcinoma of distinct subtypes were analyzed for the presence of potential hotspot mutations in the RAS/RAF/MEK/ERK signaling pathway. No ERK2 mutations were detected in these samples; however, Kirsten RAS (KRAS) p.G12D (c.35G>A) mutation was identified in 2/26 (7.7%) cervical adenocarcinoma cases, including 1/20 cervical mucinous adenocarcinoma and 1/6 cervical endometrioid carcinoma cases. In addition, no mutations in the ERK1, neuroblastoma RAS, Harvey RAS or B-Raf proto-oncogene serine/threonine kinase genes were detected in the present study. These results indicated that ethnic differences may be a primary reason for the discrepancy in ERK2 mutation frequencies between the current study and previous studies. Furthermore, mutation in the KRAS gene, but not other genes in the RAS/RAF/MEK/ERK signaling pathway, may have an active role in the pathogenesis of cervical carcinoma.
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Affiliation(s)
- Yang Zou
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Fa-Ying Liu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Juan Wu
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Lei Wan
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Shu-Fen Fang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Zi-Yu Zhang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Yong Luo
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Central Laboratory, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Mei-Hong Chen
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Mei-Zhen Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
| | - Ming He
- Department of Pharmacology and Molecular Therapeutics, Nanchang University School of Pharmaceutical Science, Nanchang 330006, P.R. China
| | - Ou-Ping Huang
- Key Laboratory of Women's Reproductive Health of Jiangxi Province, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China.,Department of Gynecology, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China
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16
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Mitochondrial dysfunction in cancer: Potential roles of ATF5 and the mitochondrial UPR. Semin Cancer Biol 2017; 47:43-49. [PMID: 28499833 DOI: 10.1016/j.semcancer.2017.05.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/26/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022]
Abstract
Mitochondria form a cellular network of organelles, or cellular compartments, that efficiently couple nutrients to energy production in the form of ATP. As cancer cells rely heavily on glycolysis, historically mitochondria and the cellular pathways in place to maintain mitochondrial activities were thought to be more relevant to diseases observed in non-dividing cells such as muscles and neurons. However, more recently it has become clear that cancers rely heavily on mitochondrial activities including lipid, nucleotide and amino acid synthesis, suppression of mitochondria-mediated apoptosis as well as oxidative phosphorylation (OXPHOS) for growth and survival. Considering the variety of conditions and stresses that cancer cell mitochondria may incur such as hypoxia, reactive oxygen species and mitochondrial genome mutagenesis, we examine potential roles for a mitochondrial-protective transcriptional response known as the mitochondrial unfolded protein response (UPRmt) in cancer cell biology.
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17
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Komiyama T, Ogura A, Hirokawa T, Zhijing M, Kamiguchi H, Asai S, Miyachi H, Kobayashi H. Analysis to Estimate Genetic Variations in the Idarubicin-Resistant Derivative MOLT-3. Int J Mol Sci 2016; 18:E12. [PMID: 28025493 PMCID: PMC5297647 DOI: 10.3390/ijms18010012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/06/2016] [Accepted: 12/13/2016] [Indexed: 01/28/2023] Open
Abstract
Gene alterations are a well-established mechanism leading to drug resistance in acute leukemia cells. A full understanding of the mechanisms of drug resistance in these cells will facilitate more effective chemotherapy. In this study, we investigated the mechanism(s) of drug resistance in the human acute leukemia cell line MOLT-3 and its idarubicin-resistant derivative MOLT-3/IDR through complete mitochondrial and nuclear DNA analyses. We identified genetic differences between these two cell lines. The ND3 mutation site (p.Thr61Ile) in the mitochondrial DNA sequence was unique to MOLT-3/IDR cells. Moreover, we identified five candidate genes harboring genetic alterations, including GALNT2, via CGH array analysis. Sequencing of the GALNT2 exon revealed a G1716K mutation present within the stop codon in MOLT-3/IDR cells but absent from MOLT-3 cells. This mutation led to an additional 18 amino acids in the protein encoded by GALNT2. Using real-time PCR, we determined an expression value for this gene of 0.35. Protein structure predictions confirmed a structural change in GALNT2 in MOLT-3/IDR cells that corresponded to the site of the mutation. We speculate that this mutation may be related to idarubicin resistance.
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Affiliation(s)
- Tomoyoshi Komiyama
- Department of Clinical Pharmacology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
| | - Atsushi Ogura
- Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan.
| | - Takatsugu Hirokawa
- The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.
| | - Miao Zhijing
- Department of Clinical Pharmacology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
| | - Hiroshi Kamiguchi
- Support Center for Medical Research and Education, Tokai University, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
| | - Satomi Asai
- Department of Laboratory Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
| | - Hayato Miyachi
- Department of Laboratory Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
| | - Hiroyuki Kobayashi
- Department of Clinical Pharmacology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan.
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18
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Barczak W, Rozwadowska N, Romaniuk A, Lipińska N, Lisiak N, Grodecka-Gazdecka S, Książek K, Rubiś B. Telomere length assessment in leukocytes presents potential diagnostic value in patients with breast cancer. Oncol Lett 2016; 11:2305-2309. [PMID: 26998167 DOI: 10.3892/ol.2016.4188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 01/05/2016] [Indexed: 11/05/2022] Open
Abstract
Telomere shortening is associated with cancer development, primarily through the induction of genomic instability. The majority of studies have indicated that individuals with shorter blood telomeres may be at a higher risk of developing various types of cancer. There is increasing evidence that the study of the alterations in telomere length may improve cancer prognosis. The aim of the present study was to verify the use of telomere length parameters in the diagnostics of breast cancer stage. Telomere length was analyzed in the blood leukocytes of 52 patients with breast cancer relative to 47 control subjects using quantitative polymerase chain reaction. The effects of stage, grade, estrogen receptor, progesterone receptor and human epidermal growth factor 2 (HER2) status were assessed. The current study demonstrated that the average telomeric sequence length was significantly shorter in leukocytes from individuals diagnosed with a more severe stage of breast cancer (T2N1M0) than in leukocytes in the early stages of the disease (T1N0M0) (P=0.0207). Furthermore, the data indicated that telomeres in leukocytes derived from patients with HER2+ breast cancer were significantly longer compared with those with the HER2- type (P=0.0347). These results suggest that the assessment of telomeres in blood leukocytes may, at least partially, correspond with breast cancer staging and HER2 receptor status.
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Affiliation(s)
- Wojciech Barczak
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, Poznan 61-866, Poland; Radiobiology Laboratory, Department of Medical Physics, The Greater Poland Cancer Centre, Poznan 61-866, Poland
| | - Natalia Rozwadowska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan 60-479, Poland
| | - Aleksandra Romaniuk
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | - Natalia Lipińska
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | - Natalia Lisiak
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Krzysztof Książek
- Department of Pathophysiology, Laboratory of Gerontology, Poznan University of Medical Sciences, Poznan 60-781, Poland
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Poznan 60-355, Poland
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Yao YG, Kajigaya S, Young NS. Mitochondrial DNA mutations in single human blood cells. Mutat Res 2015; 779:68-77. [PMID: 26149767 DOI: 10.1016/j.mrfmmm.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 01/07/2023]
Abstract
Determination mitochondrial DNA (mtDNA) sequences from extremely small amounts of DNA extracted from tissue of limited amounts and/or degraded samples is frequently employed in medical, forensic, and anthropologic studies. Polymerase chain reaction (PCR) amplification followed by DNA cloning is a routine method, especially to examine heteroplasmy of mtDNA mutations. In this review, we compare the mtDNA mutation patterns detected by three different sequencing strategies. Cloning and sequencing methods that are based on PCR amplification of DNA extracted from either single cells or pooled cells yield a high frequency of mutations, partly due to the artifacts introduced by PCR and/or the DNA cloning process. Direct sequencing of PCR product which has been amplified from DNA in individual cells is able to detect the low levels of mtDNA mutations present within a cell. We further summarize the findings in our recent studies that utilized this single cell method to assay mtDNA mutation patterns in different human blood cells. Our data show that many somatic mutations observed in the end-stage differentiated cells are found in hematopoietic stem cells (HSCs) and progenitors within the CD34(+) cell compartment. Accumulation of mtDNA variations in the individual CD34+ cells is affected by both aging and family genetic background. Granulocytes harbor higher numbers of mutations compared with the other cells, such as CD34(+) cells and lymphocytes. Serial assessment of mtDNA mutations in a population of single CD34(+) cells obtained from the same donor over time suggests stability of some somatic mutations. CD34(+) cell clones from a donor marked by specific mtDNA somatic mutations can be found in the recipient after transplantation. The significance of these findings is discussed in terms of the lineage tracing of HSCs, aging effect on accumulation of mtDNA mutations and the usage of mtDNA sequence in forensic identification.
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Affiliation(s)
- Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China.
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
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20
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Mitochondrial dependency in progression of acute myeloid leukemia. Mitochondrion 2015; 21:41-8. [PMID: 25640960 DOI: 10.1016/j.mito.2015.01.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/23/2014] [Accepted: 01/21/2015] [Indexed: 11/20/2022]
Abstract
Acute myeloid leukemia (AML) is a clonal hematopoietic malignant disorder which arises due to dysregulated differentiation, uncontrolled growth and inhibition of apoptosis leading to the accumulation of immature myeloid progenitor in the bone marrow. The heterogeneity of the disease at the molecular and cytogenetic level has led to the identification of several alteration of biological and clinical significance. One of the alterations which have gained attention in recent times is the altered energy and metabolic dependency of cancer originally proposed by Warburg. Mitochondria are important cell organelles regulating cellular energetic level, metabolism and apoptosis which in turn can affect cell proliferation and differentiation, the major manifestations of diseases like AML. In recent times the importance of mitochondrial generated ATP and mitochondrial localized metabolic pathways has been shown to play important role in the progression of AML. These studies have also demonstrated the clinical significance of mitochondrial targets for its effectiveness in combating relapsed or refractory AML. Here we review the importance of the mitochondrial dependency for the progression of AML and the emergence of the mitochondrial molecular targets which holds therapeutic importance.
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21
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Kim HR, Won SJ, Fabian C, Kang MG, Szardenings M, Shin MG. Mitochondrial DNA aberrations and pathophysiological implications in hematopoietic diseases, chronic inflammatory diseases, and cancers. Ann Lab Med 2014; 35:1-14. [PMID: 25553274 PMCID: PMC4272938 DOI: 10.3343/alm.2015.35.1.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/07/2014] [Accepted: 11/11/2014] [Indexed: 12/25/2022] Open
Abstract
Mitochondria are important intracellular organelles that produce energy for cellular development, differentiation, and growth. Mitochondrial DNA (mtDNA) presents a 10- to 20-fold higher susceptibility to genetic mutations owing to the lack of introns and histone proteins. The mtDNA repair system is relatively inefficient, rendering it vulnerable to reactive oxygen species (ROS) produced during ATP synthesis within the mitochondria, which can then target the mtDNA. Under conditions of chronic inflammation and excess stress, increased ROS production can overwhelm the antioxidant system, resulting in mtDNA damage. This paper reviews recent literature describing the pathophysiological implications of oxidative stress, mitochondrial dysfunction, and mitochondrial genome aberrations in aging hematopoietic stem cells, bone marrow failure syndromes, hematological malignancies, solid organ cancers, chronic inflammatory diseases, and other diseases caused by exposure to environmental hazards.
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Affiliation(s)
- Hye-Ran Kim
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea. ; Brain Korea 21 Project, Center for Biomedical Human Resources, Chonnam National University, Gwangju, Korea
| | - Stephanie Jane Won
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Claire Fabian
- Department of Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Min-Gu Kang
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea. ; Brain Korea 21 Project, Center for Biomedical Human Resources, Chonnam National University, Gwangju, Korea
| | - Michael Szardenings
- Department of Cell Therapy, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Myung-Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea. ; Brain Korea 21 Project, Center for Biomedical Human Resources, Chonnam National University, Gwangju, Korea. ; Environment Health Center for Childhood Leukemia and Cancer, Chonnam National University Hwasun Hospital, Hwasun, Korea
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22
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Hu SP, Du JP, Li DR, Yao YG. Mitochondrial DNA haplogroup confers genetic susceptibility to nasopharyngeal carcinoma in Chaoshanese from Guangdong, China. PLoS One 2014; 9:e87795. [PMID: 24498198 PMCID: PMC3909237 DOI: 10.1371/journal.pone.0087795] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/02/2014] [Indexed: 02/05/2023] Open
Abstract
Recent studies have shown association of mtDNA background with cancer development. We analyzed mitochondrial DNA (mtDNA) control region variation of 201 patients with nasopharyngeal carcinoma (NPC) and of 201 normal controls from Chaoshan Han Chinese to discern mtDNA haplogroup effect on the disease onset. Binary logistic regression analysis with adjustment for gender and age revealed that the haplogroup R9 (P = 0.011, OR = 1.91, 95% CI = 1.16-3.16), particularly its sub-haplogroup F1 (P = 0.015, OR = 2.43, 95% CI = 1.18-5.00), were associated significantly with increased NPC risk. These haplogroups were further confirmed to confer high NPC risk in males and/or individuals ≥ 40 years of age, but not in females or in subjects <40 years old. Our results indicated that mtDNA background confers genetic susceptibility to NPC in Chaoshan Han Chinese, and R9, particularly its sub-haplogroup F1, is a risk factor for NPC.
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Affiliation(s)
- Sheng-Ping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, Guangdong, China
- * E-mail:
| | - Ju-Ping Du
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, Guangdong, China
| | - De-Rui Li
- Tumor Hospital, Shantou University Medical College, Shantou, Guangdon, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China
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23
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Yao YG, Kajigaya S, Samsel L, McCoy JP, Torelli G, Young NS. Apparent mtDNA sequence heterogeneity in single human blood CD34+ cells is markedly affected by storage and transport. Mutat Res 2013; 751-752:36-41. [PMID: 24044942 DOI: 10.1016/j.mrfmmm.2013.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 09/01/2013] [Accepted: 09/05/2013] [Indexed: 11/30/2022]
Abstract
Single CD34(+) cells from adult human peripheral blood show mtDNA sequence heterogeneity. In this study, we compared mtDNA sequence variation in single CD34(+) cells from peripheral blood (PB) mononuclear cells (MNCs) from the same donors but under different conditions of storage and transport: group I, MNCs from heparinized PB that inadvertently required six days to be transported to the testing laboratory; group II, MNCs which were isolated from PB within a day of phlebotomy and frozen prior to transportation and storage. We observed more cell death for MNCs of group I than group II. Concordantly, group I CD34(+) cells had a very low potential for hematopoietic colony formation in vitro compared with group II cells. CD34(+) cells of group II showed an unexpectedly higher level of mtDNA sequence heterogeneity than was present in group I cells. These observations suggest that reduced mtDNA sequence heterogeneity in single CD34(+) cells of group I was likely due to elimination of cells harboring mutations. CD34(+) cells that survive stress ex vivo may be more enriched in quiescent primitive hematopoietic stem cells, with fewer mtDNA mutations than are present in committed progenitors. Technically, attention is required to conditions of preparation of human blood samples for single cell mtDNA analysis.
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Affiliation(s)
- Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China; Hematology Branch and Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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24
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Silkjaer T, Nyvold CG, Juhl-Christensen C, Hokland P, Nørgaard JM. Mitochondrial cytochrome c oxidase subunit II variations predict adverse prognosis in cytogenetically normal acute myeloid leukaemia. Eur J Haematol 2013; 91:295-303. [PMID: 23826975 DOI: 10.1111/ejh.12166] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2013] [Indexed: 12/31/2022]
Abstract
Alterations in the two catalytic genes cytochrome c oxidase subunits I and II (COI and COII) have recently been suggested to have an adverse impact on prognosis in patients with acute myeloid leukaemia (AML). In order to explore this in further detail, we sequenced these two mitochondrial genes in diagnostic bone marrow or blood samples in 235 patients with AML. In 37 (16%) patients, a non-synonymous variation in either COI or COII could be demonstrated. No patients harboured both COI and COII non-synonymous variations. Twenty-four (10%) patients had non-synonymous variations in COI, whereas 13 (6%) patients had non-synonymous variations in COII. The COI and COII are essential subunits of cytochrome c oxidase that is the terminal enzyme in the oxidative phosphorylation complexes. In terms of disease course, we observed that in patients with a normal cytogenetic analysis at disease presentation (CN-AML) treated with curative intent, the presence of a non-synonymous variation in the COII was an adverse prognostic marker for both overall survival and disease-free survival (DFS) in both univariate (DFS; hazard ratio (HR) 4.4, P = 0.006) and multivariate analyses (DFS; HR 7.2, P = 0.001). This is the first demonstration of a mitochondrial aberration playing an adverse prognostic role in adult AML, and we argue that its role as a potentially novel adverse prognostic marker in the subset of CN-AML should be explored further.
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Affiliation(s)
- Trine Silkjaer
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
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25
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Kamiński MM, Röth D, Krammer PH, Gülow K. Mitochondria as oxidative signaling organelles in T-cell activation: physiological role and pathological implications. Arch Immunol Ther Exp (Warsz) 2013; 61:367-84. [PMID: 23749029 DOI: 10.1007/s00005-013-0235-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/13/2013] [Indexed: 12/22/2022]
Abstract
Early scientific reports limited the cell biological role of reactive oxygen species (ROS) to the cause of pathological damage. However, extensive research performed over the last decade led to a wide recognition of intracellular oxidative/redox signaling as a crucial mechanism of homeostatic regulation. Amongst different cellular processes known to be influenced by redox signaling, T-cell activation is one of the most established. Numerous studies reported an indispensible role for ROS as modulators of T-cell receptor-induced transcription. Nevertheless, mechanistic details regarding signaling pathways triggered by ROS are far from being delineated. The nature and interplay between enzymatic sources involved in the generation of "oxidative signals" are also a matter of ongoing research. In particular, active participation of the mitochondrial respiratory chain as ROS producer constitutes an intriguing issue with various implications for bioenergetics of activated T cells as well as for T-cell-mediated pathologies. The aim of the current review is to address these interesting concepts.
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Affiliation(s)
- Marcin M Kamiński
- Tumour Immunology Program, Division of Immunogenetics (D030), German Cancer Research Center (DKFZ), Heidelberg, Germany,
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26
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Won EJ, Kim HR, Kim HY, Kook H, Kim HJ, Shin JH, Suh SP, Ryang DW, Shin MG. Diagnostic and Prognostic Value of Mitochondrial DNA Minisatellites after Stem Cell Transplantation. Biol Blood Marrow Transplant 2013; 19:918-24. [DOI: 10.1016/j.bbmt.2013.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 03/05/2013] [Indexed: 11/16/2022]
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27
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Silkjaer T, Nørgaard JM, Aggerholm A, Ebbesen LH, Kjeldsen E, Hokland P, Nyvold CG. Characterization and prognostic significance of mitochondrial DNA variations in acute myeloid leukemia. Eur J Haematol 2013; 90:385-96. [DOI: 10.1111/ejh.12090] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2013] [Indexed: 02/06/2023]
Affiliation(s)
- Trine Silkjaer
- Department of Haematology; Aarhus University Hospital; Aarhus; Denmark
| | | | - Anni Aggerholm
- Department of Haematology; Aarhus University Hospital; Aarhus; Denmark
| | | | - Eigil Kjeldsen
- Department of Haematology; Aarhus University Hospital; Aarhus; Denmark
| | - Peter Hokland
- Department of Haematology; Aarhus University Hospital; Aarhus; Denmark
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28
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Yao YG, Kajigaya S, Feng X, Samsel L, McCoy JP, Torelli G, Young NS. Accumulation of mtDNA variations in human single CD34+ cells from maternally related individuals: effects of aging and family genetic background. Stem Cell Res 2013; 10:361-70. [PMID: 23455392 DOI: 10.1016/j.scr.2013.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 01/17/2013] [Accepted: 01/20/2013] [Indexed: 10/27/2022] Open
Abstract
Marked sequence variation in the mtDNA control region has been observed in human single CD34(+) cells, which persist in vivo and are present also in differentiated hematopoietic cells. In this study, we analyzed 5071 single CD34(+) cells from 49 individuals (including 31 maternally related members from four families and 18 unrelated donors) in order to determine the mutation spectrum within the mtDNA control region in single cells, as related to aging and family genetic background. Many highly mutated sites among family members were hypervariable sites in the mtDNA control region. Further, CD34(+) cells from members of the same family also shared several unique mtDNA variants, suggesting pedigree-specific occurrence of these variants. Overall age-related accumulation of mtDNA mutations in CD34(+) cells varied in different families, suggesting a specific accumulation pattern, which might be modulated by family genetic background. Our current findings have implications for the occurrence of mtDNA mutations in hematopoietic stem cells and progenitors.
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Affiliation(s)
- Yong-Gang Yao
- Hematology Branch and Flow Cytometry Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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29
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de Saint Pierre M, Bravi CM, Motti JMB, Fuku N, Tanaka M, Llop E, Bonatto SL, Moraga M. An alternative model for the early peopling of southern South America revealed by analyses of three mitochondrial DNA haplogroups. PLoS One 2012; 7:e43486. [PMID: 22970129 PMCID: PMC3438176 DOI: 10.1371/journal.pone.0043486] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/20/2012] [Indexed: 11/19/2022] Open
Abstract
After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ~15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.
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Affiliation(s)
- Michelle de Saint Pierre
- Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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The awakening of an advanced malignant cancer: an insult to the mitochondrial genome. Biochim Biophys Acta Gen Subj 2011; 1820:652-62. [PMID: 21920409 DOI: 10.1016/j.bbagen.2011.08.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Revised: 08/26/2011] [Accepted: 08/29/2011] [Indexed: 02/08/2023]
Abstract
BACKGROUND In only months-to-years a primary cancer can progress to an advanced phenotype that is metastatic and resistant to clinical treatments. As early as the 1900s, it was discovered that the progression of a cancer to the advanced phenotype is often associated with a shift in the metabolic profile of the disease from a state of respiration to anaerobic fermentation - a phenomenon denoted as the Warburg Effect. SCOPE OF REVIEW Reports in the literature strongly suggest that the Warburg Effect is generated as a response to a loss in the integrity of the sequence and/or copy number of the mitochondrial genome content within a cancer. MAJOR CONCLUSIONS Multiple studies regarding the progression of cancer indicate that mutation, and/or, a flux in the copy number, of the mitochondrial genome content can support the early development of a cancer, until; the mutational load and/or the reduction-to-depletion of the copy number of the mitochondrial genome content induces the progression of the disease to an advanced phenotype. GENERAL SIGNIFICANCE Collectively, evidence has revealed that the human cell has incorporated the mitochondrial genome content into a cellular mechanism that, when pathologically actuated, can de(un)differentiate a cancer from the parental tissue of origin into an autonomous disease that disrupts the hierarchical structure-and-function of the human body. This article is part of a Special Issue entitled: Biochemistry of Mitochondria.
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Prognostic implications and molecular associations of NADH dehydrogenase subunit 4 (ND4) mutations in acute myeloid leukemia. Leukemia 2011; 26:289-95. [PMID: 21826063 DOI: 10.1038/leu.2011.200] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To study the prevalence and prognostic importance of mutations in NADH dehydrogenase subunit 4 (ND4), a mitochondrial encoded transmembrane component of the electron transport chain respiratory Complex I, 452 AML patients were examined for ND4 mutations by direct sequencing. The prognostic impact of ND4 mutations was evaluated in the context of other clinical prognostic markers and genetic risk factors. In all, 29 of 452 patients (6.4%) had either somatic (n=12) or germline (n=17) ND4 mutations predicted to affect translation. Somatic mutations were more likely to be heteroplasmic (P<0.001), to occur in predicted transmembrane domains (P<0.001) and were predicted to have damaging effects upon translation (P<0.001). Patients with somatically acquired ND4 mutations had significantly longer relapse-free survival (P=0.017) and overall survival (OS) (P=0.021) than ND4(wildtype) patients. Multivariate analysis also demonstrated a tendency for increased survival in patients with somatic ND4 mutations (RFS: hazard ratio (HR) 0.25, confidence interval (CI) 0.06-1.01, P=0.052; OS: HR 0.29, CI 0.74-1.20, P=0.089). Somatic ND4(mutated) patients had a higher prevalence of concomitant DNMT3A mutations (P=0.023) and a higher percentage of the NPM1/FLT3-ITD low-risk genotype (P=0.021). Germline affected cases showed higher BAALC (P=0.036) and MLL5 (P=0.051) expression levels. Further studies are warranted to validate the favorable prognostic influence of acquired ND4 mutations in AML.
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32
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Mitochondrial D-loop polymorphisms and mitochondrial DNA content in childhood acute lymphoblastic leukemia. J Pediatr Hematol Oncol 2011; 33:e239-44. [PMID: 21646920 DOI: 10.1097/mph.0b013e31820a5ece] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The mitochondrial displacement loop (D-loop) controls mitochondrial expression, with mutations and mitochondrial DNA (mtDNA) content linked to oncogenesis. We investigated D-loop polymorphisms and mtDNA content in childhood acute lymphoblastic leukemia (ALL). The D-loop was sequenced in 251 children: precursor B ALL (n=114), with 76 paired remission/relapse samples; T-ALL (n=24); cord blood controls (n=113). The mtDNA copy number was analyzed using real-time quantitative polymerase chain reaction for 92 controls and 54 ALL patients at diagnosis and remission. Polymorphisms around H-strand replication origin (nucleotides 150 to 199) and conserved sequence block II (nucleotides 299 to 317) were associated with leukemia biology and treatment response. T-ALL patients were more likely to have longer nt303 poly-C tract. T199C polymorphism was associated with increased risk of ALL in Malays; T152C was more frequent in good responders. There was no difference in mtDNA content between diagnostic ALL samples and controls; however, there was significant decrease in mtDNA content after treatment, especially in samples with OH polymorphisms. Somatic mutations were found in 13% (9 of 76) of patients, suggesting a link to leukemogenesis. Our results suggest that polymorphisms impacting transcriptional control could affect mtDNA replication. Decrease in mtDNA content after treatment may confer susceptibility to chemotherapy and be a clue to the good prognosis of childhood ALL.
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Abstract
Mitochondria control essential cellular activities including generation of ATP via oxidative phosphorylation. Mitochondrial DNA (mtDNA) mutations in the regulatory D-loop region and somatic mtDNA mutations are common in primary human cancers. The biological impact of a given mutation may vary, depending on the nature of the mutation and the proportion of mutant mtDNAs carried by the cell. Identification of mtDNA mutations in precancerous lesions supports their early contribution to cell transformation and cancer progression. Introduction of mtDNA mutations in transformed cells has been associated with increased ROS production and tumor growth. Studies reveal that increased and altered mtDNA plays a role in the development of cancer but further work is required to establish the functional significance of specific mitochondrial mutations in cancer and disease progression. This review offers some insight into the extent of mtDNA mutations, their functional consequences in tumorigenesis, mitochondrial therapeutics, and future clinical application.
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Affiliation(s)
- Aditi Chatterjee
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA
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Bi R, Li WL, Chen MQ, Zhu Z, Yao YG. Rapid identification of mtDNA somatic mutations in gastric cancer tissues based on the mtDNA phylogeny. Mutat Res 2011; 709-710:15-20. [PMID: 21419139 DOI: 10.1016/j.mrfmmm.2011.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 12/13/2022]
Abstract
Mitochondrial DNA (mtDNA) somatic mutations have been identified in nearly all kinds of cancer during the past decade. Normally one need to determine the complete mtDNA sequences from both cancerous and normal tissues of the same patient to score the somatic mutation in cancer. In this study, we intended to explore a strategy to quickly identify somatic mutations in the entire mtDNA genome based on its phylogeny. The principal assumption for this strategy is that somatic mutations, as recently accumulated in cancerous tissue, have younger age and will be located in the terminal branches of mtDNA phylogenetic tree. In contrast, the haplogroup-specific variants, which appear as germline variants and have ancient age, will be located in the basal or intermediate-node branches of the tree, depending on their relative age. When the complete mtDNA sequence of the cancerous tissue is determined and is classified relative to the available mtDNA phylogeny, we only need to screen the variants that are located in the terminal branch in the paracancerous tissue or other normal tissue from the same patient to identify somatic mutations in cancer. We validated this strategy by using paired gastric cancer tissue and paracancerous tissue or blood from 10 Chinese patients (including one with gastric stromal tumor). A total of seven somatic mutations were identified in the cancerous tissues from four patients. Our result suggests that employing mtDNA phylogenetic knowledge facilitates rapid identification of mitochondrial genome somatic mutations in cancer.
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Affiliation(s)
- Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
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Yu D, Jia X, Zhang AM, Li S, Zou Y, Zhang Q, Yao YG. Mitochondrial DNA sequence variation and haplogroup distribution in Chinese patients with LHON and m.14484T>C. PLoS One 2010; 5:e13426. [PMID: 20976138 PMCID: PMC2956641 DOI: 10.1371/journal.pone.0013426] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Accepted: 09/22/2010] [Indexed: 12/28/2022] Open
Abstract
Background Leber hereditary optic neuropathy (LHON, MIM 535000) is one of the most common mitochondrial genetic disorders caused by three primary mtDNA mutations (m.3460G>A, m.11778G>A and m. 14484T>C). The clinical expression of LHON is affected by many additional factors, e.g. mtDNA background, nuclear genes, and environmental factors. Hitherto, there is no comprehensive study of Chinese LHON patients with m.14484T>C. Methodology/Principal Findings In this study, we analyzed the mtDNA sequence variations and haplogroup distribution pattern of the largest number of Chinese LHON patients with m.14484T>C to date. We first determined the complete mtDNA sequences in eleven LHON probands with m.14484T>C, to discern the potentially pathogenic mutations that co-segregate with m.14484T>C. We then dissected the matrilineal structure of 52 patients with m.14484T>C (including 14 from unrelated families and 38 sporadic cases) and compared it with the reported Han Chinese from general populations. Complete mtDNA sequencing showed that the eleven matrilines belonged to nine haplogroups including Y2, C4a, M8a, M10a1a, G1a1, G2a1, G2b2, D5a2a1, and D5c. We did not identify putatively pathogenic mutation that was co-segregated with m.14484T>C in these lineages based on the evolutionary analysis. Compared with the reported Han Chinese from general populations, the LHON patients with m.14484T>C had significantly higher frequency of haplogroups C, G, M10, and Y, but a lower frequency of haplogroup F. Intriguingly, we also observed a lower prevalence of F lineages in LHON subjects with m.11778G>A in our previous study, suggesting that this haplogroup may enact similar role during the onset of LHON in the presence of m.14484T>C or m.11778G>A. Conclusions/Significance Our current study provided a comprehensive profile regarding the mtDNA variation and background of Chinese patients with LHON and m.14484T>C. Matrilineal background might affect the expression of LHON in Chinese patients with m.14484T>C.
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Affiliation(s)
- Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - A-Mei Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yang Zou
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
- * E-mail: (Y-GY); (QZ)
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail: (Y-GY); (QZ)
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Abstract
Three general approaches have been used to model myelodysplastic syndrome (MDS) in mice, including treatment with mutagens or carcinogens, xenotransplantation of human MDS cells, and genetic engineering of mouse hematopoietic cells. This article discusses the phenotypes observed in available mouse models for MDS with a concentration on a model that leads to aberrant expression of conserved homeobox genes that are important regulators of normal hematopoiesis. Using these models of MDS should allow a more complete understanding of the disease process and provide a platform for preclinical testing of therapeutic approaches.
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Affiliation(s)
- Sarah H Beachy
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 8901 Wisconsin Avenue, Bethesda, MD 20889-5105, USA
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Sharawat SK, Bakhshi R, Vishnubhatla S, Bakhshi S. Mitochondrial D-loop variations in paediatric acute myeloid leukaemia: a potential prognostic marker. Br J Haematol 2010; 149:391-8. [DOI: 10.1111/j.1365-2141.2010.08084.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cerezo M, Bandelt HJ, Martín-Guerrero I, Ardanaz M, Vega A, Carracedo Á, García-Orad Á, Salas A. High mitochondrial DNA stability in B-cell chronic lymphocytic leukemia. PLoS One 2009; 4:e7902. [PMID: 19924307 PMCID: PMC2775629 DOI: 10.1371/journal.pone.0007902] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 10/20/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Chronic Lymphocytic Leukemia (CLL) leads to progressive accumulation of lymphocytes in the blood, bone marrow, and lymphatic tissues. Previous findings have suggested that the mtDNA could play an important role in CLL. METHODOLOGY/PRINCIPAL FINDINGS The mitochondrial DNA (mtDNA) control-region was analyzed in lymphocyte cell DNA extracts and compared with their granulocyte counterpart extract of 146 patients suffering from B-Cell CLL; B-CLL (all recruited from the Basque country). Major efforts were undertaken to rule out methodological artefacts that would render a high false positive rate for mtDNA instabilities and thus lead to erroneous interpretation of sequence instabilities. Only twenty instabilities were finally confirmed, most of them affecting the homopolymeric stretch located in the second hypervariable segment (HVS-II) around position 310, which is well known to constitute an extreme mutational hotspot of length polymorphism, as these mutations are frequently observed in the general human population. A critical revision of the findings in previous studies indicates a lack of proper methodological standards, which eventually led to an overinterpretation of the role of the mtDNA in CLL tumorigenesis. CONCLUSIONS/SIGNIFICANCE Our results suggest that mtDNA instability is not the primary causal factor in B-CLL. A secondary role of mtDNA mutations cannot be fully ruled out under the hypothesis that the progressive accumulation of mtDNA instabilities could finally contribute to the tumoral process. Recommendations are given that would help to minimize erroneous interpretation of sequencing results in mtDNA studies in tumorigenesis.
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MESH Headings
- Base Sequence
- DNA Primers/genetics
- DNA, Mitochondrial/genetics
- Databases, Genetic
- Granulocytes/cytology
- Haplotypes
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytes/cytology
- Models, Statistical
- Molecular Sequence Data
- Mutation
- Phylogeny
- Sequence Analysis, DNA
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Affiliation(s)
- María Cerezo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | | | - Idoia Martín-Guerrero
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Maite Ardanaz
- Servicio de Hematología, Hospital Txagorritxu, Vitoria, Spain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - África García-Orad
- Laboratorio Interdepartamental de Medicina Molecular, Departamento de Genética Antropología Física y Fisiología Animal, Facultad de Medicina, Universidad del País Vasco- Euskal Herriko Unibertsitatea, Leioa, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, and Departamento de Anatomía Patolóxica y Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain
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Sotiriou E, Coku J, Tanji K, Huang HB, Hirano M, DiMauro S. The m.3244G>A mutation in mtDNA is another cause of progressive external ophthalmoplegia. Neuromuscul Disord 2009; 19:297-9. [PMID: 19285865 DOI: 10.1016/j.nmd.2009.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 01/30/2009] [Indexed: 11/29/2022]
Abstract
We sequenced all mitochondrial tRNA genes in a 61-year-old man with chronic progressive external ophthalmoplegia and mitochondrial myopathy but without mtDNA rearrangements, and identified a heteroplasmic m.3244G>A mutation in the tRNA(Leu(UUR)) gene. This mutation had been previously associated with the MELAS phenotype, but not described in any detail. The mutation load in muscle was 84% and COX-negative fibers harbored greater levels of mutant genomes than COX-positive fibers. The m.3244G>A mutation affects a highly conserved nucleotide in the dihydrouridine loop and has been associated with a wobble modification deficiency of the mutant tRNA.
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Affiliation(s)
- Evangelia Sotiriou
- Department of Neurology, Columbia University Medical Center, New York, NY 10032, USA
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Shi H, Pan L, Song T. Impact of Platinum on the Whole Mitochondrial Genome of Ovarian Carcinomas Both In Vivo and In Vitro. Int J Gynecol Cancer 2009; 19:423-30. [DOI: 10.1111/igc.0b013e3181a19ff0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Objectives:To investigate somatic mitochondrial DNA mutation in primary and recurrent ovarian carcinoma tissues as well as that in drug-resistant cell lines to illuminate the impact of chemotherapeutic drugs on mitochondrial DNA (mtDNA).Methods:Complete mtDNA genomes of 20 pairs of ovarian carcinomas and their matched normal tissues together with 2 ovarian carcinoma cell lines and their 4 platinum-resistant cell lines were sequenced. Mitochondrial DNA alterations, consequent amino acid alterations were compared between the 2 groups of patients and the 2 types of cell lines.Results:A large number of mtDNA new polymorphisms (55) and mutations (18) were identified in 20 ovarian carcinoma samples. Platinum-based chemotherapy did not increase the number of new polymorphisms (P = 0.094), mutations (P = 0.688), and consequent amino acid alterations (P = 0.202 and 0.795). Data gained from the cell lines also indicated that platinum had some effect on the mitochondrial genome but not specific to particular positions.Conclusions:What we found suggested that mtDNA damage could be made by chemotherapeutic drugs but not as much as imagined in ovarian carcinomas. Some of the mtDNA defects might be part of the disease processes and cell properties as well as a consequence of treatment.
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MtDNA mutation associated with mitochondrial dysfunction in megakaryoblastic leukaemic cells. Leukemia 2008; 22:1938-41. [DOI: 10.1038/leu.2008.69] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wang CY, Wang HW, Yao YG, Kong QP, Zhang YP. Somatic mutations of mitochondrial genome in early stage breast cancer. Int J Cancer 2007; 121:1253-6. [PMID: 17514652 DOI: 10.1002/ijc.22822] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The complete mitochondrial genomes of the primary cancerous, matched paracancerous normal and distant normal tissues from 10 early-stage breast cancer patients were analyzed in this study, with special attempt (i) to investigate whether the reported high frequency of mitochondrial DNA (mtDNA) somatic mutations in breast cancer could be repeated under a stringent data quality control, and (ii) to characterize the spectrum of mtDNA somatic mutations in Chinese breast cancer patients and evaluate their potential significance in early cancer diagnosis. Two heteroplasmic somatic transitions (T2275C and A8601G) were identified in our samples. The transition A8601G was present in the primary cancerous and paracancerous normal tissues from patient no. 3. Transition T2275C was found in the primary cancerous tissue but not in other normal tissues from patient no. 6; this transition has been reported in the colonic crypts and is located at a highly conserved site in the 16S rRNA gene. Subsequent cloning sequencing confirmed the absence of both mutations in the distant normal tissues from the 2 patients. The overall rate of somatic mutations in our patients was much lower than those of previous studies of breast cancer. Our results gave support to the recent claim that the high frequency of mtDNA somatic mutations in cancer studies is overestimated. Based on the mtDNA mutation pattern in early stage breast cancer observed in this study, we cautioned the enthusiasm and efforts to look for somatic mutations that were of diagnostic value in cancer early detection.
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Affiliation(s)
- Cheng-Ye Wang
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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Lutz-Bonengel S, Sänger T, Parson W, Müller H, Ellwart JW, Follo M, Bonengel B, Niederstätter H, Heinrich M, Schmidt U. Single lymphocytes from two healthy individuals with mitochondrial point heteroplasmy are mainly homoplasmic. Int J Legal Med 2007; 122:189-97. [PMID: 17922134 DOI: 10.1007/s00414-007-0190-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Accepted: 07/26/2007] [Indexed: 11/26/2022]
Abstract
The nature of mitochondrial DNA heteroplasmy is still unclear. It could either be caused by two mitochondrial DNA (mtDNA) haplotypes coexisting within a single cell or by an admixture of homoplasmic cells, each of which contains only one type of mtDNA molecule. To address this question, single lymphocytes were separated by flow cytometry assisted cell sorting and analyzed by cycle sequencing or minisequencing. To attain the required PCR sensitivity, the reactions were carried out on the surface of chemically structured glass slides in a reaction volume of 1-2 microl. In this study, blood samples from two healthy donors showing mitochondrial point heteroplasmy in direct sequencing (195Y and 234R, respectively) were analyzed. Nearly 96% of single lymphocytes tested were found to be in a homoplasmic state, but heteroplasmic cells were also detected. These results suggest that mitochondrial point heteroplasmy in blood may well be mainly due to the mixture of homoplasmic cells.
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Affiliation(s)
- Sabine Lutz-Bonengel
- Institute of Legal Medicine, Albert Ludwig University Freiburg, Albertstrasse 9, 79104 Freiburg, Germany.
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Yao YG, Bandelt HJ, Young NS. External contamination in single cell mtDNA analysis. PLoS One 2007; 2:e681. [PMID: 17668059 PMCID: PMC1930155 DOI: 10.1371/journal.pone.0000681] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Accepted: 06/19/2007] [Indexed: 12/31/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) variation in single hematopoietic cells, muscle fibers, oocytes, and from tiny amount of tumor tissues and degraded clinical specimens has been reported in many medical publications. External DNA contamination, notoriously difficult to avoid, threatens the integrity of such studies. Methodology/Principal Findings Employing a phylogenetic approach, we analyzed the geographic origins of mtDNA sequence anomalies observed during multiple studies of mtDNA sequence variation in a total of 7094 single hematopoietic cells. 40 events with irregular mtDNA patterns were detected: eight instances (from seven different haplotypes) could be traced to laboratory personnel; six cases were caused by sample cross-contamination. The sources of the remaining events could not be identified, and the anomalous sequence variation referred to matrilines from East Asia, Africa, or West Eurasia, respectively. These mtDNA sequence anomalies could be best explained by contamination. Conclusions Using the known world mtDNA phylogeny, we could distinguish the geographic origin of the anomalous mtDNA types, providing some useful information regarding the source of contamination. Our data suggest that routine mtDNA sequence analysis of laboratory personnel is insufficient to identify and eliminate all contaminants. A rate of 0.6% of external contamination in this study, while low, is not negligible: Unrecognized contaminants will be mistaken as evidence of remarkable somatic mutations associated with the development of cancer and other diseases. The effective contamination rate can increase by a factor of more than an order of magnitude in some studies that did not institute high standards. Our results are of particular relevance to mtDNA research in medicine, and such an approach should be adopted to maintain and improve quality control in single-cell analyses.
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Affiliation(s)
- Yong-Gang Yao
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America.
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Yao YG, Childs RW, Kajigaya S, McCoy JP, Young NS. Mitochondrial DNA sequence heterogeneity of single CD34+ cells after nonmyeloablative allogeneic stem cell transplantation. Stem Cells 2007; 25:2670-6. [PMID: 17628021 DOI: 10.1634/stemcells.2007-0269] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We applied a single-cell method to detect mitochondrial DNA (mtDNA) mutations to evaluate the reconstitution of hematopoietic stem cells (HSCs) and committed progenitor cells after nonmyeloablative allogeneic stem cell transplantation in humans. In a total of 1,958 single CD34(+) cells from six human leukocyte antigen-matched sibling donor and recipient pairs, individual CD34(+) clones were recognized based on the observed donor- or recipient-specific mtDNA sequence somatic alteration. There was no overall reduction of mtDNA heterogeneity among CD34(+) cells from the recipient after transplantation. Samples collected from two donors over time showed the persistence of certain CD34(+) clones marked by specific mutations. Our results demonstrate the feasibility of distinguishing donor and recipient individual CD34(+) clones based on mtDNA mutations during engraftment. HSCs were not limited in number, and similar mtDNA heterogeneity levels suggested representation of the total stem cell compartment during rapid hematopoietic reconstitution in the recipient. Disclosure of potential conflicts of interest is found at the end of this article.
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Affiliation(s)
- Yong-Gang Yao
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Building 10 CRC, Room 3E-5140, 10 Center Drive, Bethesda, Maryland 20892-1202, USA.
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Yao YG, Ellison FM, McCoy JP, Chen J, Young NS. Age-dependent accumulation of mtDNA mutations in murine hematopoietic stem cells is modulated by the nuclear genetic background. Hum Mol Genet 2006; 16:286-94. [PMID: 17185390 DOI: 10.1093/hmg/ddl457] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Alterations in mitochondrial DNA (mtDNA) and consequent loss of mitochondrial function underlie the mitochondrial theory of aging. In this study, we systematically analyzed the mtDNA control region somatic mutation pattern in 2864 single hematopoietic stem cells (HSCs) and progenitors, isolated by flow cytometry sorting on Lin(-)Kit(+)CD34(-) parameters from young and old C57BL/6 (B6) and BALB/cBy (BALB) mice, to test the hypothesis that the accumulated mtDNA mutations in HSCs were strain-correlated and associated with HSC functional senescence during aging. An increased level of mtDNA mutations in single HSCs was observed in old B6 when compared with young B6 mice (P=0.003); in contrast, no significant age-dependent accumulation of mutations was observed in BALB mice (old versus young, P=0.202) and the level of mutations in both young and old BALB mice was close to that of old B6 mice (P>0.280). Cellular reactive oxygen species (ROS) in mouse HSCs could not be correlated with the level of mtDNA mutations in these cells, although B6 mice had a higher proportion of ROS(-) cells when compared with the BALB mice. Propagation assays of single HSCs showed B6 cells form larger colonies compared with cells from BALB mice, irrespective of age and mtDNA mutation load. We infer from our data that age-related mtDNA somatic mutation accumulation in mouse HSCs is influenced by the nuclear genetic background and that these mutations may not obviously correlate to either cellular ROS content or HSC senescence.
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Affiliation(s)
- Yong-Gang Yao
- Hematology Branch, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892-1202, USA .
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