1
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Piergentili R, Sechi S. Non-Coding RNAs of Mitochondrial Origin: Roles in Cell Division and Implications in Cancer. Int J Mol Sci 2024; 25:7498. [PMID: 39000605 PMCID: PMC11242419 DOI: 10.3390/ijms25137498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/01/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group, in terms of structure and sequence length, consisting of RNA molecules that do not code for proteins. These ncRNAs have a central role in the regulation of gene expression and are virtually involved in every process analyzed, ensuring cellular homeostasis. Although, over the years, much research has focused on the characterization of non-coding transcripts of nuclear origin, improved bioinformatic tools and next-generation sequencing (NGS) platforms have allowed the identification of hundreds of ncRNAs transcribed from the mitochondrial genome (mt-ncRNA), including long non-coding RNA (lncRNA), circular RNA (circRNA), and microRNA (miR). Mt-ncRNAs have been described in diverse cellular processes such as mitochondrial proteome homeostasis and retrograde signaling; however, the function of the majority of mt-ncRNAs remains unknown. This review focuses on a subgroup of human mt-ncRNAs whose dysfunction is associated with both failures in cell cycle regulation, leading to defects in cell growth, cell proliferation, and apoptosis, and the development of tumor hallmarks, such as cell migration and metastasis formation, thus contributing to carcinogenesis and tumor development. Here we provide an overview of the mt-ncRNAs/cancer relationship that could help the future development of new biomedical applications in the field of oncology.
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Affiliation(s)
| | - Stefano Sechi
- Istituto di Biologia e Patologia Molecolari del Consiglio Nazionale delle Ricerche, Dipartimento di Biologia e Biotecnologie, Università Sapienza di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy;
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2
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Zhuang X, Ye R, Zhou Y, Cheng MY, Cui H, Wang L, Zhang S, Wang S, Cui Y, Zhang W. Leveraging new methods for comprehensive characterization of mitochondrial DNA in esophageal squamous cell carcinoma. Genome Med 2024; 16:50. [PMID: 38566210 PMCID: PMC10985887 DOI: 10.1186/s13073-024-01319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Mitochondria play essential roles in tumorigenesis; however, little is known about the contribution of mitochondrial DNA (mtDNA) to esophageal squamous cell carcinoma (ESCC). Whole-genome sequencing (WGS) is by far the most efficient technology to fully characterize the molecular features of mtDNA; however, due to the high redundancy and heterogeneity of mtDNA in regular WGS data, methods for mtDNA analysis are far from satisfactory. METHODS Here, we developed a likelihood-based method dMTLV to identify low-heteroplasmic mtDNA variants. In addition, we described fNUMT, which can simultaneously detect non-reference nuclear sequences of mitochondrial origin (non-ref NUMTs) and their derived artifacts. Using these new methods, we explored the contribution of mtDNA to ESCC utilizing the multi-omics data of 663 paired tumor-normal samples. RESULTS dMTLV outperformed the existing methods in sensitivity without sacrificing specificity. The verification using Nanopore long-read sequencing data showed that fNUMT has superior specificity and more accurate breakpoint identification than the current methods. Leveraging the new method, we identified a significant association between the ESCC overall survival and the ratio of mtDNA copy number of paired tumor-normal samples, which could be potentially explained by the differential expression of genes enriched in pathways related to metabolism, DNA damage repair, and cell cycle checkpoint. Additionally, we observed that the expression of CBWD1 was downregulated by the non-ref NUMTs inserted into its intron region, which might provide precursor conditions for the tumor cells to adapt to a hypoxic environment. Moreover, we identified a strong positive relationship between the number of mtDNA truncating mutations and the contribution of signatures linked to tumorigenesis and treatment response. CONCLUSIONS Our new frameworks promote the characterization of mtDNA features, which enables the elucidation of the landscapes and roles of mtDNA in ESCC essential for extending the current understanding of ESCC etiology. dMTLV and fNUMT are freely available from https://github.com/sunnyzxh/dMTLV and https://github.com/sunnyzxh/fNUMT , respectively.
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Affiliation(s)
- Xuehan Zhuang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Rui Ye
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yong Zhou
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Matthew Yibo Cheng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Heyang Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Longlong Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Shuangping Zhang
- The Department of Thoracic Surgery, Shanxi Cancer Hospital; Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shubin Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China
| | - Yongping Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- The Department of Thoracic Surgery, Shanxi Cancer Hospital; Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
| | - Weimin Zhang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center; Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518000, China.
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute; Research Unit of Molecular Cancer Research, Chinese Academy of Medical Sciences, Beijing, 100142, China.
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3
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Biró B, Gál Z, Fekete Z, Klecska E, Hoffmann OI. Mitochondrial genome plasticity of mammalian species. BMC Genomics 2024; 25:278. [PMID: 38486136 PMCID: PMC10941376 DOI: 10.1186/s12864-024-10201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 03/08/2024] [Indexed: 03/17/2024] Open
Abstract
There is an ongoing process in which mitochondrial sequences are being integrated into the nuclear genome. The importance of these sequences has already been revealed in cancer biology, forensic, phylogenetic studies and in the evolution of the eukaryotic genetic information. Human and numerous model organisms' genomes were described from those sequences point of view. Furthermore, recent studies were published on the patterns of these nuclear localised mitochondrial sequences in different taxa.However, the results of the previously released studies are difficult to compare due to the lack of standardised methods and/or using few numbers of genomes. Therefore, in this paper our primary goal is to establish a uniform mining pipeline to explore these nuclear localised mitochondrial sequences.Our results show that the frequency of several repetitive elements is higher in the flanking regions of these sequences than expected. A machine learning model reveals that the flanking regions' repetitive elements and different structural characteristics are highly influential during the integration process.In this paper, we introduce a general mining pipeline for all mammalian genomes. The workflow is publicly available and is believed to serve as a validated baseline for future research in this field. We confirm the widespread opinion, on - as to our current knowledge - the largest dataset, that structural circumstances and events corresponding to repetitive elements are highly significant. An accurate model has also been trained to predict these sequences and their corresponding flanking regions.
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Affiliation(s)
- Bálint Biró
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary.
- Group BM, Data Insights Team, _VOIS, Kerepesi str. 35, 1087, Budapest, Hungary.
| | - Zoltán Gál
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary
| | - Zsófia Fekete
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary
| | - Eszter Klecska
- FamiCord Group, Krio Institute, Kelemen László str, 1026, Budapest, Hungary
| | - Orsolya Ivett Hoffmann
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Department of Animal Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Györgyi Albert str. 4, 2100, Gödöllő, Hungary.
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4
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Harutyunyan T. The known unknowns of mitochondrial carcinogenesis: de novo NUMTs and intercellular mitochondrial transfer. Mutagenesis 2024; 39:1-12. [PMID: 37804235 DOI: 10.1093/mutage/gead031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/05/2023] [Indexed: 10/09/2023] Open
Abstract
The translocation of mitochondrial DNA (mtDNA) sequences into the nuclear genome, resulted in the occurrence of nuclear sequences of mitochondrial origin (NUMTs) which can be detected in nearly all sequenced eukaryotes. However, de novo mtDNA insertions can contribute to the development of pathological conditions including cancer. Recent data indicate that de novo mtDNA translocation into chromosomes can occur due to genotoxic influence of DNA double-strand break-inducing environmental mutagens. This confirms the hypothesis of the involvement of genome instability in the occurrence of mtDNA fragments in chromosomes. Mounting evidence indicates that mitochondria can be transferred from normal cells to cancer cells and recover cellular respiration. These exchanged mitochondria can facilitate cancer progression and metastasis. This review article provides a comprehensive overview of the potential carcinogenicity of mtDNA insertions, and the relevance of mtDNA escape in cancer progression, metastasis, and treatment resistance in humans. Potential molecular targets involved in mtDNA escape and exchange of mitochondria that can be of possible clinical benefits are presented and discussed. Understanding these processes could lead to improved diagnostic approaches, novel therapeutic strategies, and a deeper understanding of the intricate relationship between mitochondria, nuclear DNA, and cancer biology.
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Affiliation(s)
- Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
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5
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Woronzow V, Möhner J, Remane D, Zischler H. Generation of somatic de novo structural variation as a hallmark of cellular senescence in human lung fibroblasts. Front Cell Dev Biol 2023; 11:1274807. [PMID: 38152346 PMCID: PMC10751365 DOI: 10.3389/fcell.2023.1274807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023] Open
Abstract
Cellular senescence is characterized by replication arrest in response to stress stimuli. Senescent cells accumulate in aging tissues and can trigger organ-specific and possibly systemic dysfunction. Although senescent cell populations are heterogeneous, a key feature is that they exhibit epigenetic changes. Epigenetic changes such as loss of repressive constitutive heterochromatin could lead to subsequent LINE-1 derepression, a phenomenon often described in the context of senescence or somatic evolution. LINE-1 elements decode the retroposition machinery and reverse transcription generates cDNA from autonomous and non-autonomous TEs that can potentially reintegrate into genomes and cause structural variants. Another feature of cellular senescence is mitochondrial dysfunction caused by mitochondrial damage. In combination with impaired mitophagy, which is characteristic of senescent cells, this could lead to cytosolic mtDNA accumulation and, as a genomic consequence, integrations of mtDNA into nuclear DNA (nDNA), resulting in mitochondrial pseudogenes called numts. Thus, both phenomena could cause structural variants in aging genomes that go beyond epigenetic changes. We therefore compared proliferating and senescent IMR-90 cells in terms of somatic de novo numts and integrations of a non-autonomous composite retrotransposons - the so-called SVA elements-that hijack the retropositional machinery of LINE-1. We applied a subtractive and kinetic enrichment technique using proliferating cell DNA as a driver and senescent genomes as a tester for the detection of nuclear flanks of de novo SVA integrations. Coupled with deep sequencing we obtained a genomic readout for SVA retrotransposition possibly linked to cellular senescence in the IMR-90 model. Furthermore, we compared the genomes of proliferative and senescent IMR-90 cells by deep sequencing or after enrichment of nuclear DNA using AluScan technology. A total of 1,695 de novo SVA integrations were detected in senescent IMR-90 cells, of which 333 were unique. Moreover, we identified a total of 81 de novo numts with perfect identity to both mtDNA and nuclear hg38 flanks. In summary, we present evidence for possible age-dependent structural genomic changes by paralogization that go beyond epigenetic modifications. We hypothesize, that the structural variants we observe potentially impact processes associated with replicative aging of IMR-90 cells.
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Affiliation(s)
- Valentina Woronzow
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Jonas Möhner
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Daniel Remane
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
- HOX Life Science GmbH, Frankfurt, Hessen, Germany
| | - Hans Zischler
- Division of Anthropology, Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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6
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Namasivayam S, Sun C, Bah AB, Oberstaller J, Pierre-Louis E, Etheridge RD, Feschotte C, Pritham EJ, Kissinger JC. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. Proc Natl Acad Sci U S A 2023; 120:e2308569120. [PMID: 37917792 PMCID: PMC10636329 DOI: 10.1073/pnas.2308569120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
Toxoplasma gondii is a zoonotic protist pathogen that infects up to one third of the human population. This apicomplexan parasite contains three genome sequences: nuclear (65 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear integrants of mitochondrial DNA) and NUPTs (nuclear integrants of plastid DNA) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome-the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 mya, revealed that the movement and fixation of five NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb), and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together, these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
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Affiliation(s)
| | - Cheng Sun
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Assiatu B. Bah
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | | | - Edwin Pierre-Louis
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
| | - Ronald Drew Etheridge
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
| | - Cedric Feschotte
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Ellen J. Pritham
- Department of Biology, University of Texas at Arlington, Arlington, TX76019
| | - Jessica C. Kissinger
- Department of Genetics, Institute of Bioinformatics, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA30602
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7
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Vardar Acar N, Özgül RK. A big picture of the mitochondria-mediated signals: From mitochondria to organism. Biochem Biophys Res Commun 2023; 678:45-61. [PMID: 37619311 DOI: 10.1016/j.bbrc.2023.08.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 08/26/2023]
Abstract
Mitochondria, well-known for years as the powerhouse and biosynthetic center of the cell, are dynamic signaling organelles beyond their energy production and biosynthesis functions. The metabolic functions of mitochondria, playing an important role in various biological events both in physiological and stress conditions, transform them into important cellular stress sensors. Mitochondria constantly communicate with the rest of the cell and even from other cells to the organism, transmitting stress signals including oxidative and reductive stress or adaptive signals such as mitohormesis. Mitochondrial signal transduction has a vital function in regulating integrity of human genome, organelles, cells, and ultimately organism.
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Affiliation(s)
- Neşe Vardar Acar
- Department of Pediatric Metabolism, Institute of Child Health, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - R Köksal Özgül
- Department of Pediatric Metabolism, Institute of Child Health, Faculty of Medicine, Hacettepe University, Ankara, Turkey.
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8
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Namasivayam S, Sun C, Bah AB, Oberstaller J, Pierre-Louis E, Etheridge RD, Feschotte C, Pritham EJ, Kissinger JC. Massive invasion of organellar DNA drives nuclear genome evolution in Toxoplasma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.539837. [PMID: 37293002 PMCID: PMC10245829 DOI: 10.1101/2023.05.22.539837] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Toxoplasma gondii is a zoonotic protist pathogen that infects up to 1/3 of the human population. This apicomplexan parasite contains three genome sequences: nuclear (63 Mb); plastid organellar, ptDNA (35 kb); and mitochondrial organellar, mtDNA (5.9 kb of non-repetitive sequence). We find that the nuclear genome contains a significant amount of NUMTs (nuclear DNA of mitochondrial origin) and NUPTs (nuclear DNA of plastid origin) that are continuously acquired and represent a significant source of intraspecific genetic variation. NUOT (nuclear DNA of organellar origin) accretion has generated 1.6% of the extant T. gondii ME49 nuclear genome; the highest fraction ever reported in any organism. NUOTs are primarily found in organisms that retain the non-homologous end-joining repair pathway. Significant movement of organellar DNA was experimentally captured via amplicon sequencing of a CRISPR-induced double-strand break in non-homologous end-joining repair competent, but not ku80 mutant, Toxoplasma parasites. Comparisons with Neospora caninum, a species that diverged from Toxoplasma ~28 MY ago, revealed that the movement and fixation of 5 NUMTs predates the split of the two genera. This unexpected level of NUMT conservation suggests evolutionary constraint for cellular function. Most NUMT insertions reside within (60%) or nearby genes (23% within 1.5 kb) and reporter assays indicate that some NUMTs have the ability to function as cis-regulatory elements modulating gene expression. Together these findings portray a role for organellar sequence insertion in dynamically shaping the genomic architecture and likely contributing to adaptation and phenotypic changes in this important human pathogen.
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Affiliation(s)
- Sivaranjani Namasivayam
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Present address: Clinical Microbiome Unit, Laboratory of Host Immunity and Microbiome, NIAID, NIH, Bethesda, MD 20892, USA
| | - Cheng Sun
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019, USA; Present address: College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Assiatu B Bah
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019
| | - Jenna Oberstaller
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; Present address: Department of Global Health, University of South Florida, Tampa, FL 33620, USA
| | - Edwin Pierre-Louis
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Ronald Drew Etheridge
- Department of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
| | - Cedric Feschotte
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019; Present address: Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-2703, USA
| | - Ellen J. Pritham
- Department of Biology, University of Texas at Arlington, Arlington, TX 76019
| | - Jessica C. Kissinger
- Department of Genetics, Institute of Bioinformatics, and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA 30602, USA
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9
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Zhou W, Karan KR, Gu W, Klein HU, Sturm G, De Jager PL, Bennett DA, Hirano M, Picard M, Mills RE. Somatic nuclear mitochondrial DNA insertions are prevalent in the human brain and accumulate over time in fibroblasts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.03.527065. [PMID: 36778249 PMCID: PMC9915708 DOI: 10.1101/2023.02.03.527065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The transfer of mitochondrial DNA into the nuclear genomes of eukaryotes (Numts) has been linked to lifespan in non-human species 1-3 and recently demonstrated to occur in rare instances from one human generation to the next 4. Here we investigated numtogenesis dynamics in humans in two ways. First, we quantified Numts in 1,187 post-mortem brain and blood samples from different individuals. Compared to circulating immune cells (n=389), post-mitotic brain tissue (n=798) contained more Numts, consistent with their potential somatic accumulation. Within brain samples we observed a 5.5-fold enrichment of somatic Numt insertions in the dorsolateral prefrontal cortex compared to cerebellum samples, suggesting that brain Numts arose spontaneously during development or across the lifespan. Moreover, more brain Numts was linked to earlier mortality. The brains of individuals with no cognitive impairment who died at younger ages carried approximately 2 more Numts per decade of life lost than those who lived longer. Second, we tested the dynamic transfer of Numts using a repeated-measures WGS design in a human fibroblast model that recapitulates several molecular hallmarks of aging 5. These longitudinal experiments revealed a gradual accumulation of one Numt every ~13 days. Numtogenesis was independent of large-scale genomic instability and unlikely driven cell clonality. Targeted pharmacological perturbations including chronic glucocorticoid signaling or impairing mitochondrial oxidative phosphorylation (OxPhos) only modestly increased the rate of numtogenesis, whereas patient-derived SURF1-mutant cells exhibiting mtDNA instability accumulated Numts 4.7-fold faster than healthy donors. Combined, our data document spontaneous numtogenesis in human cells and demonstrate an association between brain cortical somatic Numts and human lifespan. These findings open the possibility that mito-nuclear horizontal gene transfer among human post-mitotic tissues produce functionally-relevant human Numts over timescales shorter than previously assumed.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kalpita R. Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Wenjin Gu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hans-Ulrich Klein
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612 USA
| | - Michio Hirano
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032 USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
- Department of Neurology, H. Houston Merritt Center, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, USA
- New York State Psychiatric Institute, New York, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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10
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Xia Y, He C, Hu Z, Wu Z, Hui Y, Liu YY, Mu C, Zha J. The mitochondrial protein YME1 Like 1 is important for non-small cell lung cancer cell growth. Int J Biol Sci 2023; 19:1778-1790. [PMID: 37063426 PMCID: PMC10092760 DOI: 10.7150/ijbs.82217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 03/03/2023] [Indexed: 04/18/2023] Open
Abstract
The expression and biological function of the mitochondrial inner membrane protease YME1L (YME1 Like 1 ATPase) in NSCLC are tested here. Bioinformatical analyses and results from local human tissues show that YME1L expression is elevated in NSCLC tissues. YME1L upregulation was observed in primary and immortalized NSCLC cells. In NSCLC cells, shRNA-mediated silence of YME1L or dCas9/sgRNA-induced knockout (KO) of YME1L robustly suppressed cell growth and migration, and provoking apoptosis. YME1L shRNA/KO resulted in mitochondrial dysfunctions in NSCLC cells, leading to mitochondrial depolarization, ROS accumulation and ATP depletion. Conversely, ectopic YME1L overexpression augmented NSCLC cell proliferation and motility. Akt-S6K1 phosphorylation was reduced after YME1L shRNA/KO in primary NSCLC cells, but augmented after YME1L overexpression. Importantly, YME1L KO-caused anti-NSCLC cell activity was attenuated by a constitutively-activate Akt1 (S473D) construct. In vivo, subcutaneous NSCLC xenograft growth was remarkably slowed following intratumoral YME1L shRNA AAV injection in nude mice. YME1L knockdown, Akt-mTOR inactivation and ATP reduction were detected in YME1L-silenced NSCLC xenografts. Taken together, overexpressed YME1L in NSCLC exerts pro-tumorigenic function.
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Affiliation(s)
- Yingchen Xia
- Department of Thoracic Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chunyan He
- Department of Clinical Laboratory, Kunshan Hospital of Chinese Medicine, Affiliated Hospital of Yangzhou University, Kunshan, China
| | - Zhi Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhichao Wu
- Department of Thoracic Surgery, Changshu Hospital Affiliated to Nanjing University of Chinese Medicine, Changshu, China
| | - Yin Hui
- Department of Thoracic Surgery, The First Affiliated Hospital of Shaoyang University, Shaoyang, China
- Department of Thoracic Surgery, The Central Hospital of Shaoyang, Shaoyang, China
| | - Yuan-yuan Liu
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Chuanyong Mu
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianhua Zha
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
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11
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Torres J, Touati E. Mitochondrial Function in Health and Disease: Responses to Helicobacter pylori Metabolism and Impact in Gastric Cancer Development. Curr Top Microbiol Immunol 2023; 444:53-81. [PMID: 38231215 DOI: 10.1007/978-3-031-47331-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Mitochondria are major cellular organelles that play an essential role in metabolism, stress response, immunity, and cell fate. Mitochondria are organized in a network with other cellular compartments, functioning as a signaling hub to maintain cells' health. Mitochondrial dysfunctions and genome alterations are associated with diseases including cancer. Mitochondria are a preferential target for pathogens, which have developed various mechanisms to hijack cellular functions for their benefit. Helicobacter pylori is recognized as the major risk factor for gastric cancer development. H. pylori induces oxidative stress and chronic gastric inflammation associated with mitochondrial dysfunction. Its pro-apoptotic cytotoxin VacA interacts with the mitochondrial inner membrane, leading to increased permeability and decreased ATP production. Furthermore, H. pylori induces mitochondrial DNA damage and mutation, concomitant with the development of gastric intraepithelial neoplasia as observed in infected mice. In this chapter, we present diverse aspects of the role of mitochondria as energy supplier and signaling hubs and their adaptation to stress conditions. The metabolic activity of mitochondria is directly linked to biosynthetic pathways. While H. pylori virulence factors and derived metabolites are essential for gastric colonization and niche adaptation, they may also impact mitochondrial function and metabolism, and may have consequences in gastric pathogenesis. Importantly, during its long way to reach the gastric epithelium, H. pylori faces various cellular types along the gastric mucosa. We discuss how the mitochondrial response of these different cells is affected by H. pylori and impacts the colonization and bacterium niche adaptation and point to areas that remain to be investigated.
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Affiliation(s)
- Javier Torres
- Unidad de Investigacion en Enfermedades Infecciosas, UMAE Pediatriıa, Instituto Mexicano del Seguro Social, Ciudad de Mexico, Mexico
| | - Eliette Touati
- Equipe DMic01-Infection, Génotoxicité et Cancer, Département de Microbiologie, UMR CNRS 6047, Institut Pasteur, Université Paris Cité, F-75015, Paris, France.
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12
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Liao WT, Chu PY, Su CC, Wu CC, Li CJ. Mitochondrial AAA protease gene associated with immune infiltration is a prognostic biomarker in human ovarian cancer. Pathol Res Pract 2022; 240:154215. [DOI: 10.1016/j.prp.2022.154215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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13
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Abstract
The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA; New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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14
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Biró B, Gál Z, Schiavo G, Ribari A, Joe Utzeri V, Brookman M, Fontanesi L, Hoffmann OI. Nuclear mitochondrial DNA sequences in the rabbit genome. Mitochondrion 2022; 66:1-6. [PMID: 35842180 DOI: 10.1016/j.mito.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/23/2022] [Accepted: 07/10/2022] [Indexed: 10/17/2022]
Abstract
Numtogenesis is observable in the mammalian genomes resulting in the integration of mitochondrial segments into the nuclear genomes (numts). To identify numts in rabbit, we aligned mitochondrial and nuclear genomes. Alignment significance threshold was calculated and individual characteristics of numts were analysed. We found 153 numts in the nuclear genome. The GC content of numts were significantly lower than the GC content of their genomic flanking regions or the genome itself. The frequency of three mammalian-wide interspersed repeats were increased in the proximity of numts. The decreased GC content around numts strengthen the theory which supposes a link between DNA structural instability and numt integration.
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Affiliation(s)
- Bálint Biró
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary
| | - Zoltán Gál
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary
| | - Giuseppina Schiavo
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Anisa Ribari
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Valerio Joe Utzeri
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Michael Brookman
- Hanze University of Applied Sciences, Department for Biology and Medical Laboratory Research, Zernikeplein 7, 9747 AS Groningen, Netherlands
| | - Luca Fontanesi
- University of Bologna, Department of Agricultural and Food Sciences, Division of Animal Sciences, Viale Fanin 46, 40127 Bologna, Italy
| | - Orsolya Ivett Hoffmann
- Hungarian University of Agricultural and Life Sciences, Institute of Genetics and Biotechnology, Szent-Györgyi Albert Str. 4, H-2100, Gödöllö, Hungary.
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15
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Kit O, Frantsiyants E, Neskubina I, Shikhlyarova A, Kaplieva I. Mitochondrial therapy: a vision of the outlooks for treatment of main twenty-first-century diseases. CARDIOMETRY 2022. [DOI: 10.18137/cardiometry.2022.22.1827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are dynamic organelles which constantly change their shape, size, and location within the cells. Mitochondrial dynamics is associated with mesenchymal metabolism or epithelial-mesenchymal transition to regulate the stem cell differentiation, proliferation, migration, and apoptosis. The transfer of mitochondria from one cell to another is necessary to improve and maintain homeostasis in an organism. Mitochondrial transplantation is a therapeutic approach that involves an introduction of healthy mitochondria into damaged organs. Recent evidence data have shown that the physiological properties of healthy mitochondria provide their ability to replace damaged mitochondria, with suggesting that replacing damaged mitochondria with healthy mitochondria may protect cells from further damage. Moreover, mitochondria can also be actively released into the extracellular space and potentially be transferred between the cells in the central nervous system. This increased interest in mitochondrial therapy calls for a deeper understanding of the mechanisms, which build the basis for mitochondrial transfer, uptake, and cellular defense. In this review, questions related to the involvement of mitochondria in the pathogenesis of cancer will be discussed. Particular attention will be paid to mitochondrial transplantation as a therapeutic approach to treat the mitochondrial dysfunction under some pathological conditions.
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16
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Li Y. Inactivation of PDH can Reduce Anaplastic Thyroid Cancer Cells' Sensitivity to Artemisinin. Anticancer Agents Med Chem 2022; 22:1753-1760. [PMID: 34515013 DOI: 10.2174/1871520621666210910100803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Anaplastic Thyroid Cancer (ATC) is a rare subtype of thyroid tumors with a high mortality rate. Targeted therapies against ATC are ineffective and mostly transient. Artemisinin has shown excellent anti-tumor activity in several cancers, but its effects on ATC are still unknown. OBJECTIVE To evaluate the effects of artemisinin on ATC cells and assess the mechanism underlying drug resistance. METHODS The viability and proliferation rates of the artemisinin-treated CAL-62 and BHT-101 cells were analyzed by MTT and EdU incorporation assays. The protein expression levels were determined by Tandem Mass Tag (TMT) labeling quantitative proteomics and western blotting. RESULTS Artemisinin treatment significantly decreased the expression levels of COX2 and COX7A2 and increased that of COX14, YEM1l1, ALAS1, and OAT after 48h. In addition, FTL was upregulated in the CAL-62 cells and downregulated in BHT-101 cells. The CAL-62 cells showed transient and reversible resistance to artemisinin, which was correlated to time-dependent changes in HIF1α, PDK1, and PDHA levels. CONCLUSION Artemisinin targets the mitochondrial respiratory chain proteins in ATC cells. CAL-62 cells show transient resistance to artemisinin via PDH downregulation, indicating that PDH activation may enhance the cytotoxic effects of artemisinin on ATC cells.
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Affiliation(s)
- Yitian Li
- Research Department of Jining Medical University, Jining, Shandong, China
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17
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Thyroid Cancer-Associated Mitochondrial DNA Mutation G3842A Promotes Tumorigenicity via ROS-Mediated ERK1/2 Activation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9982449. [PMID: 35464760 PMCID: PMC9020963 DOI: 10.1155/2022/9982449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/09/2021] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations have been identified in various human cancers, including thyroid cancer. However, the relationship between mtDNA and thyroid cancer remains unclear. Previous studies by others and us strongly suggested that mtDNA mutations in complex I may participate in thyroid cancer processes according to sequencing results of thyroid cancer tissue, although the associated pathogenic processes remain unknown. Here, to investigate whether mtDNA mutations contribute to thyroid cancer, we reanalyzed our sequencing results and characterized thyroid cancer-associated mutations in the mitochondrial complex. The results identified the highest mutation frequencies in nicotinamide adenine dinucleotide hydride (NADH) dehydrogenase subunit 4 gene (ND4) and cytochrome c oxidase subunit 1 gene (COI), which also harbored the highest rates of
substitutions, with most of the mutations resulting in changes in the polarity of amino acids. We then established cybrids containing the G3842A mutation identified in papillary thyroid carcinoma, which revealed it as a mutation in NADH dehydrogenase subunit 1 gene (ND1) and is previously reported in follicular thyroid carcinoma, thereby suggesting a possibly pathogenic role in thyroid carcinoma. Additionally, we found that the G3842A mutation accelerates tumorigenicity and decreases the abundance and activity of mitochondrial complex I, the oxygen consumption rate, and adenosine triphosphate levels. By contrast, the levels of reactive oxygen species (ROS) were increased to activate extracellular signal-regulated kinase (ERK1/2) signaling, which contributed to tumorigenicity. These findings suggest for the first time that mtDNA mutations help drive tumor development and that G3842A may represent a new risk factor for thyroid cancer. Furthermore, our findings indicate that drugs targeting ROS and ERK1/2 may serve as a viable therapeutic strategy for thyroid cancer.
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18
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Singh LN, Kao SH, Wallace DC. Unlocking the Complexity of Mitochondrial DNA: A Key to Understanding Neurodegenerative Disease Caused by Injury. Cells 2021; 10:cells10123460. [PMID: 34943968 PMCID: PMC8715673 DOI: 10.3390/cells10123460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders that are triggered by injury typically have variable and unpredictable outcomes due to the complex and multifactorial cascade of events following the injury and during recovery. Hence, several factors beyond the initial injury likely contribute to the disease progression and pathology, and among these are genetic factors. Genetics is a recognized factor in determining the outcome of common neurodegenerative diseases. The role of mitochondrial genetics and function in traditional neurodegenerative diseases, such as Alzheimer’s and Parkinson’s diseases, is well-established. Much less is known about mitochondrial genetics, however, regarding neurodegenerative diseases that result from injuries such as traumatic brain injury and ischaemic stroke. We discuss the potential role of mitochondrial DNA genetics in the progression and outcome of injury-related neurodegenerative diseases. We present a guide for understanding mitochondrial genetic variation, along with the nuances of quantifying mitochondrial DNA variation. Evidence supporting a role for mitochondrial DNA as a risk factor for neurodegenerative disease is also reviewed and examined. Further research into the impact of mitochondrial DNA on neurodegenerative disease resulting from injury will likely offer key insights into the genetic factors that determine the outcome of these diseases together with potential targets for treatment.
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Affiliation(s)
- Larry N. Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- Correspondence:
| | - Shih-Han Kao
- Resuscitation Science Center, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
- Department of Pediatrics, Division of Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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19
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Microtubule-Based Mitochondrial Dynamics as a Valuable Therapeutic Target in Cancer. Cancers (Basel) 2021; 13:cancers13225812. [PMID: 34830966 PMCID: PMC8616325 DOI: 10.3390/cancers13225812] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/14/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria constitute an ever-reorganizing dynamic network that plays a key role in several fundamental cellular functions, including the regulation of metabolism, energy production, calcium homeostasis, production of reactive oxygen species, and programmed cell death. Each of these activities can be found to be impaired in cancer cells. It has been reported that mitochondrial dynamics are actively involved in both tumorigenesis and metabolic plasticity, allowing cancer cells to adapt to unfavorable environmental conditions and, thus, contributing to tumor progression. The mitochondrial dynamics include fusion, fragmentation, intracellular trafficking responsible for redistributing the organelle within the cell, biogenesis, and mitophagy. Although the mitochondrial dynamics are driven by the cytoskeleton-particularly by the microtubules and the microtubule-associated motor proteins dynein and kinesin-the molecular mechanisms regulating these complex processes are not yet fully understood. More recently, an exchange of mitochondria between stromal and cancer cells has also been described. The advantage of mitochondrial transfer in tumor cells results in benefits to cell survival, proliferation, and spreading. Therefore, understanding the molecular mechanisms that regulate mitochondrial trafficking can potentially be important for identifying new molecular targets in cancer therapy to interfere specifically with tumor dissemination processes.
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20
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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21
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Alikhani M, Touati E, Karimipoor M, Vosough M, Mohammadi M. Mitochondrial DNA Copy Number Variations in Gastrointestinal Tract Cancers: Potential Players. J Gastrointest Cancer 2021; 53:770-781. [PMID: 34486088 DOI: 10.1007/s12029-021-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Alterations of mitochondria have been linked to several cancers. Also, the mitochondrial DNA copy number (mtDNA-CN) is altered in various cancers, including gastrointestinal tract (GIT) cancers, and several research groups have investigated its potential as a cancer biomarker. However, the exact causes of mtDNA-CN variations are not yet revealed. This review discussed the conceivable players in this scheme, including reactive oxygen species (ROS), mtDNA genetic variations, DNA methylation, telomere length, autophagy, immune system activation, aging, and infections, and discussed their possible impact in the initiation and progression of cancer. By further exploring such mechanisms, mtDNA-CN variations may be effectively utilized as cancer biomarkers and provide grounds for developing novel cancer therapeutic agents.
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Affiliation(s)
- Mehdi Alikhani
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS UMR2001, Institut Pasteur, 25-28 Rue du Dr Roux cedex 15, 75724, Paris, France
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marjan Mohammadi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
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22
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Abstract
Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.
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Affiliation(s)
- Piotr K Kopinski
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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23
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Mazzocca A, Fais S. New hypotheses for cancer generation and progression. Med Hypotheses 2021; 152:110614. [PMID: 34087614 DOI: 10.1016/j.mehy.2021.110614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/29/2021] [Accepted: 05/24/2021] [Indexed: 01/14/2023]
Abstract
Since Nixon famously declared war on cancer in 1971, trillions of dollars have been spent on cancer research but the life expectancy for most forms of cancer is still poor. There are many reasons for the partial success of cancer translational research. One of these can be the predominance of certain paradigms that potentially narrowed the vision in interpreting cancer. The main paradigm to explain carcinogenesis is based on DNA mutations, which is well interpreted by the somatic mutation theory (SMT). However, a different theory claims that cancer is instead a tissue disease as proposed by the Tissue Organization Field Theory (TOFT). Here, we propose new hypotheses to explain the origin and pathogenesis of cancer. In this perspective, the systemic-evolutionary theory of cancer (SETOC) is discussed as well as how the microenvironment affects the adaptation of transformed cells and the reversion to a unicellular-like or embryo-like phenotype.
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Affiliation(s)
- Antonio Mazzocca
- Interdisciplinary Department of Medicine, University of Bari School of Medicine, Piazza G. Cesare, 11, 70124 Bari, Italy.
| | - Stefano Fais
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità (National Institute of Health), Viale Regina Elena, 299, 00161 Rome, Italy.
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24
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Sprenger HG, MacVicar T, Bahat A, Fiedler KU, Hermans S, Ehrentraut D, Ried K, Milenkovic D, Bonekamp N, Larsson NG, Nolte H, Giavalisco P, Langer T. Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity. Nat Metab 2021; 3:636-650. [PMID: 33903774 PMCID: PMC8144018 DOI: 10.1038/s42255-021-00385-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Cytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP-AMP synthase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS-STING-TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflammation in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS-STING-TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.
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Affiliation(s)
- Hans-Georg Sprenger
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thomas MacVicar
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Amir Bahat
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Kai Uwe Fiedler
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Steffen Hermans
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Katharina Ried
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Nina Bonekamp
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nils-Göran Larsson
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hendrik Nolte
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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25
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Brandeis M. Were eukaryotes made by sex?: Sex might have been vital for merging endosymbiont and host genomes giving rise to eukaryotes. Bioessays 2021; 43:e2000256. [PMID: 33860546 DOI: 10.1002/bies.202000256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 11/10/2022]
Abstract
I hypothesize that the appearance of sex facilitated the merging of the endosymbiont and host genomes during early eukaryote evolution. Eukaryotes were formed by symbiosis between a bacterium that entered an archaeon, eventually giving rise to mitochondria. This entry was followed by the gradual transfer of most bacterial endosymbiont genes into the archaeal host genome. I argue that the merging of the mitochondrial genes into the host genome was vital for the evolution of genuine eukaryotes. At the time this process commenced it was unprecedented and required a novel mechanism. I suggest that this mechanism was meiotic sex, and that its appearance might have been THE crucial step that enabled the evolution of proper eukaryotes from early endosymbiont containing proto-eukaryotes. Sex might continue to be essential today for keeping genome insertions in check. Also see the video abstract here: https://youtu.be/aVMvWMpomac.
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Affiliation(s)
- Michael Brandeis
- The Department of Genetics, The Hebrew University of Jerusalem, Jerusalem, Israel
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26
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Li X, Xu D, Cheng B, Zhou Y, Chen Z, Wang Y. Mitochondrial DNA insert into CD40 ligand gene-associated X-linked hyper-IgM syndrome. Mol Genet Genomic Med 2021; 9:e1646. [PMID: 33764006 PMCID: PMC8172197 DOI: 10.1002/mgg3.1646] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND X-linked hyper-IgM (X-HIGM), which results from mutations in the CD40LG gene located on chromosome Xq26.3, is the most common form of HIGM. To date, more than 130 variants of the CD40L gene have been reported. We described a patient with novel de novo nuclear mitochondrial DNA sequences (NUMTs) in the CD40LG gene that have resulted in X-HIGM. METHODS Whole-exome sequencing (WES) analysis was used to screen for causal variants in the genome, and the candidate breakpoint was confirmed by Sanger sequencing. RESULTS A new mutation of CD40LG, which deletes A at position 17 followed by a 147-nucleotide from mitochondrial DNA copies insertion in exon 1, was detected in a 20-month-old boy harbouring an X-HIGM combined with immunodeficiency syndrome. CONCLUSION This is one of the few cases of a human genetic disease caused by nuclear mitochondrial DNA sequences (NUMTs). The presented data serve to demonstrate that de novo NUMT transfer of nucleic acid is a novel mechanism of X-HIGM.
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Affiliation(s)
- Xuejing Li
- Department of Pulmonology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Dan Xu
- Department of Pulmonology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Beilei Cheng
- Department of Pulmonology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yunlian Zhou
- Department of Pulmonology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhimin Chen
- Department of Pulmonology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Yingshuo Wang
- Department of Pulmonology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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Picca A, Calvani R, Coelho-Junior HJ, Marzetti E. Cell Death and Inflammation: The Role of Mitochondria in Health and Disease. Cells 2021; 10:cells10030537. [PMID: 33802550 PMCID: PMC7998762 DOI: 10.3390/cells10030537] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria serve as a hub for a multitude of vital cellular processes. To ensure an efficient deployment of mitochondrial tasks, organelle homeostasis needs to be preserved. Mitochondrial quality control (MQC) mechanisms (i.e., mitochondrial dynamics, biogenesis, proteostasis, and autophagy) are in place to safeguard organelle integrity and functionality. Defective MQC has been reported in several conditions characterized by chronic low-grade inflammation. In this context, the displacement of mitochondrial components, including mitochondrial DNA (mtDNA), into the extracellular compartment is a possible factor eliciting an innate immune response. The presence of bacterial-like CpG islands in mtDNA makes this molecule recognized as a damaged-associated molecular pattern by the innate immune system. Following cell death-triggering stressors, mtDNA can be released from the cell and ignite inflammation via several pathways. Crosstalk between autophagy and apoptosis has emerged as a pivotal factor for the regulation of mtDNA release, cell’s fate, and inflammation. The repression of mtDNA-mediated interferon production, a powerful driver of immunological cell death, is also regulated by autophagy–apoptosis crosstalk. Interferon production during mtDNA-mediated inflammation may be exploited for the elimination of dying cells and their conversion into elements driving anti-tumor immunity.
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Affiliation(s)
- Anna Picca
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (E.M.)
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, 17165 Stockholm, Sweden
| | - Riccardo Calvani
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (E.M.)
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, 17165 Stockholm, Sweden
- Correspondence: ; Tel.: +39-(06)-3015-5559; Fax: +39-(06)-3051-911
| | - Hélio José Coelho-Junior
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy;
| | - Emanuele Marzetti
- Fondazione Policlinico Universitario “Agostino Gemelli” IRCCS, 00168 Rome, Italy; (A.P.); (E.M.)
- Università Cattolica del Sacro Cuore, Institute of Internal Medicine and Geriatrics, 00168 Rome, Italy;
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Bahat A, MacVicar T, Langer T. Metabolism and Innate Immunity Meet at the Mitochondria. Front Cell Dev Biol 2021; 9:720490. [PMID: 34386501 PMCID: PMC8353256 DOI: 10.3389/fcell.2021.720490] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 07/05/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are master regulators of metabolism and have emerged as key signalling organelles of the innate immune system. Each mitochondrion harbours potent agonists of inflammation, including mitochondrial DNA (mtDNA), which are normally shielded from the rest of the cell and extracellular environment and therefore do not elicit detrimental inflammatory cascades. Mitochondrial damage and dysfunction can lead to the cytosolic and extracellular exposure of mtDNA, which triggers inflammation in a number of diseases including autoimmune neurodegenerative disorders. However, recent research has revealed that the extra-mitochondrial exposure of mtDNA is not solely a negative consequence of mitochondrial damage and pointed to an active role of mitochondria in innate immunity. Metabolic cues including nucleotide imbalance can stimulate the release of mtDNA from mitochondria in order to drive a type I interferon response. Moreover, important effectors of the innate immune response to pathogen infection, such as the mitochondrial antiviral signalling protein (MAVS), are located at the mitochondrial surface and modulated by the cellular metabolic status and mitochondrial dynamics. In this review, we explore how and why metabolism and innate immunity converge at the mitochondria and describe how mitochondria orchestrate innate immune signalling pathways in different metabolic scenarios. Understanding how cellular metabolism and metabolic programming of mitochondria are translated into innate immune responses bears relevance to a broad range of human diseases including cancer.
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Affiliation(s)
- Amir Bahat
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas MacVicar
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Thomas Langer
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Thomas Langer,
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29
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Fisher KE, Bradbury SP, Coates BS. Prediction of mitochondrial genome-wide variation through sequencing of mitochondrion-enriched extracts. Sci Rep 2020; 10:19123. [PMID: 33154458 PMCID: PMC7645498 DOI: 10.1038/s41598-020-76088-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022] Open
Abstract
Although mitochondrial DNA (mtDNA) haplotype variation is often applied for estimating population dynamics and phylogenetic relationships, economical and generalized methods for entire mtDNA genome enrichment prior to high-throughput sequencing are not readily available. This study demonstrates the utility of differential centrifugation to enrich for mitochondrion within cell extracts prior to DNA extraction, short-read sequencing, and assembly using exemplars from eight maternal lineages of the insect species, Ostrinia nubilalis. Compared to controls, enriched extracts showed a significant mean increase of 48.2- and 86.1-fold in mtDNA based on quantitative PCR, and proportion of subsequent short sequence reads that aligned to the O. nubilalis reference mitochondrial genome, respectively. Compared to the reference genome, our de novo assembled O. nubilalis mitochondrial genomes contained 82 intraspecific substitution and insertion/deletion mutations, and provided evidence for correction of mis-annotated 28 C-terminal residues within the NADH dehydrogenase subunit 4. Comparison to a more recent O. nubilalis mtDNA assembly from unenriched short-read data analogously showed 77 variant sites. Twenty-eight variant positions, and a triplet ATT codon (Ile) insertion within ATP synthase subunit 8, were unique within our assemblies. This study provides a generalizable pipeline for whole mitochondrial genome sequence acquisition adaptable to applications across a range of taxa.
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Affiliation(s)
- Kelsey E Fisher
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA.
| | - Steven P Bradbury
- Department of Entomology, Iowa State University, Ames, IA, 50011, USA
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA, 50011, USA
| | - Brad S Coates
- Department of Agriculture, Agriculture Research Station, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
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30
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Doxorubicin-Induced Translocation of mtDNA into the Nuclear Genome of Human Lymphocytes Detected Using a Molecular-Cytogenetic Approach. Int J Mol Sci 2020; 21:ijms21207690. [PMID: 33080837 PMCID: PMC7589397 DOI: 10.3390/ijms21207690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/27/2020] [Accepted: 10/14/2020] [Indexed: 11/17/2022] Open
Abstract
Translocation of mtDNA in the nuclear genome is an ongoing process that contributes to the development of pathological conditions in humans. However, the causal factors of this biological phenomenon in human cells are poorly studied. Here we analyzed mtDNA insertions in the nuclear genome of human lymphocytes after in vitro treatment with doxorubicin (DOX) using a fluorescence in situ hybridization (FISH) technique. The number of mtDNA insertions positively correlated with the number of DOX-induced micronuclei, suggesting that DOX-induced chromosome breaks contribute to insertion events. Analysis of the odds ratios (OR) revealed that DOX at concentrations of 0.025 and 0.035 µg/mL significantly increases the rate of mtDNA insertions (OR: 3.53 (95% CI: 1.42–8.76, p < 0.05) and 3.02 (95% CI: 1.19–7.62, p < 0.05), respectively). Analysis of the distribution of mtDNA insertions in the genome revealed that DOX-induced mtDNA insertions are more frequent in larger chromosomes, which are more prone to the damaging action of DOX. Overall, our data suggest that DOX-induced chromosome damage can be a causal factor for insertions of mtDNA in the nuclear genome of human lymphocytes. It can be assumed that the impact of a large number of external and internal mutagenic factors contributes significantly to the origin and amount of mtDNA in nuclear genomes.
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31
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Tracking the Distribution and Burst of Nuclear Mitochondrial DNA Sequences (NUMTs) in Fig Wasp Genomes. INSECTS 2020; 11:insects11100680. [PMID: 33036463 PMCID: PMC7600805 DOI: 10.3390/insects11100680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/29/2020] [Accepted: 10/06/2020] [Indexed: 11/17/2022]
Abstract
Simple Summary Nuclear mitochondrial DNA sequences (NUMTs), which result from the insertion of exogenous mtDNA into the nuclear genome, are widely distributed in eukaryotes. However, how NUMTs are inserted into the nuclear genome and their post-insertion fates remain a mystery. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, which will be helpful to study the biological issues of NUMTs. We here select 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results show that the distributions of NUMTs are species- or lineage-specific. Furthermore, genomic environmental factors such as genome size, the damage-prone regions, and the mode of TE dynamics can determine the insertion and post-insertion fate of NUMTs. Especially because of TEs, the fragmentation and duplication of NUMTs, and thus their burst, are common. This is a relatively comprehensive investigation of the specific distribution of NUMTs and its influencing factors. Our study will help people to understand the evolution of exogenous fragments in the nuclear genome. Abstract Mitochondrial DNA sequences can be transferred into the nuclear genome, giving rise to nuclear mitochondrial DNA sequences (NUMTs). NUMTs have been described in numerous eukaryotes. However, the studies on the distribution of NUMTs and its influencing factors are still inadequate and even controversial. Previous studies have suggested that Hymenoptera may be a group rich in NUMTs, in which we selected 11 species of fig wasps (Chalcidoidea, Hymenoptera) to analyze the distribution and evolution of NUMTs at the genomic level. The results showed that the contents of NUMTs varied greatly in these species, and bursts of NUMTs existed in some species or lineages. Further detailed analyses showed that the large number of NUMTs might be related to the large genomes; NUMTs tended to be inserted into unstable regions of the genomes; and the inserted NUMTs might also be affected by transposable elements (TEs) in the neighbors, leading to fragmentations and duplications, followed by bursts of NUMTs. In summary, our results suggest that a variety of genomic environmental factors can determine the insertion and post-insertion fate of NUMTs, resulting in their species- or lineage-specific distribution patterns, and that studying the evolution of NUMTs can provide good evidence and theoretical basis for exploring the dynamics of exogenous DNA entering into the nuclear genome.
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Puertas MJ, González-Sánchez M. Insertions of mitochondrial DNA into the nucleus—effects and role in cell evolution. Genome 2020; 63:365-374. [DOI: 10.1139/gen-2019-0151] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We review the insertion of mitochondrial DNA (mtDNA) fragments into nuclear DNA (NUMTS) as a general and ongoing process that has occurred many times during genome evolution. Fragments of mtDNA are generated during the lifetime of organisms in both somatic and germinal cells, by the production of reactive oxygen species in the mitochondria. The fragments are inserted into the nucleus during the double-strand breaks repair via the non-homologous end-joining machinery, followed by genomic instability, giving rise to the high variability observed in NUMT patterns among species, populations, or genotypes. Some de novo produced mtDNA insertions show harmful effects, being involved in human diseases, carcinogenesis, and ageing. NUMT generation is a non-stop process overpassing the Mendelian transmission. This parasitic property ensures their survival even against their harmful effects. The accumulation of mtDNA fragments mainly at pericentromeric and subtelomeric regions is important to understand the transmission and integration of NUMTs into the genomes. The possible effect of female meiotic drive for mtDNA insertions at centromeres remains to be studied. In spite of the harmful feature of NUMTs, they are important in cell evolution, representing a major source of genomic variation.
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Affiliation(s)
- María J. Puertas
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
| | - Mónica González-Sánchez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
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33
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Yang K, Forman MR, Graham BH, Monahan PO, Giovannucci EL, De Vivo I, Chan AT, Nan H. Association between pre-diagnostic leukocyte mitochondrial DNA copy number and survival among colorectal cancer patients. Cancer Epidemiol 2020; 68:101778. [PMID: 32674053 DOI: 10.1016/j.canep.2020.101778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/29/2020] [Accepted: 07/04/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mitochondrial DNA copy number (mtDNAcn) is considered a biomarker for mitochondrial function and oxidative stress. Although previous studies have suggested a potential relationship between mtDNAcn at the time of colorectal cancer (CRC) diagnosis and CRC prognosis, findings have been inconsistent, and no study has specifically investigated the association of pre-diagnostic mtDNAcn with CRC survival. METHODS We examined the association of pre-diagnostic leukocyte mtDNAcn (measured by qPCR) with overall and CRC-specific survival among 587 patients in Nurses' Health Study and Health Professionals Follow-Up Study. Cox models were constructed to estimate hazard ratios (HRs) and 95 % confidence intervals (95 % CIs). RESULTS During a mean follow-up of 10.5 years, 395 deaths were identified; 180 were due to CRC. Overall, we did not observe significant associations between mtDNAcn and either overall or CRC-specific survival among all cases or by cancer location, grade, or stage. In an exploratory stratified analysis, a suggestive inverse association of mtDNAcn and overall death risk appeared among current smokers [HR (95 % CI) for 1 SD decrease in mtDNAcn = 1.50 (0.98, 2.32), P-trend = 0.06]. Reduced mtDNAcn and lower CRC-specific death risk was observed among patients aged ≤ 70.5 at diagnosis [HR (95 % CI) for 1 SD decrease of mtDNAcn = 0.71 (0.52, 0.97), P-trend = 0.03], ≤ 5 years from blood collection to diagnosis [HR (95 % CI) for 1 SD decrease in mtDNAcn = 0.65 (0.44, 0.96), P-trend = 0.03] and those consuming a low-inflammatory diet [HR (95 % CI) for 1 SD decrease in mtDNAcn = 0.61 (0.42, 0.88), P-trend = 0.009]. CONCLUSION no significant associations between pre-diagnostic leukocyte mtDNAcn and either overall or CRC-specific survival appeared but exploratory analysis identified potential sub-group associations.
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Affiliation(s)
- Keming Yang
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Michele R Forman
- Department of Nutrition Science, College of Health and Human Science, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Patrick O Monahan
- Department of Biostatistics, School of Medicine and Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA
| | - Edward L Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Immaculata De Vivo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrew T Chan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Hongmei Nan
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA; Department of Global Health, Richard M. Fairbanks School of Public Health, Indiana University, Indianapolis, IN, USA; IU Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA.
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34
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Regulation of mitochondrial plasticity by the i-AAA protease YME1L. Biol Chem 2020; 401:877-890. [DOI: 10.1515/hsz-2020-0120] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 02/19/2020] [Indexed: 12/22/2022]
Abstract
AbstractMitochondria are multifaceted metabolic organelles and adapt dynamically to various developmental transitions and environmental challenges. The metabolic flexibility of mitochondria is provided by alterations in the mitochondrial proteome and is tightly coupled to changes in the shape of mitochondria. Mitochondrial proteases are emerging as important posttranslational regulators of mitochondrial plasticity. The i-AAA protease YME1L, an ATP-dependent proteolytic complex in the mitochondrial inner membrane, coordinates mitochondrial biogenesis and dynamics with the metabolic output of mitochondria. mTORC1-dependent lipid signaling drives proteolytic rewiring of mitochondria by YME1L. While the tissue-specific loss of YME1L in mice is associated with heart failure, disturbed eye development, and axonal degeneration in the spinal cord, YME1L activity supports growth of pancreatic ductal adenocarcinoma cells. YME1L thus represents a key regulatory protease determining mitochondrial plasticity and metabolic reprogramming and is emerging as a promising therapeutic target.
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35
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Reynolds JC, Bwiza CP, Lee C. Mitonuclear genomics and aging. Hum Genet 2020; 139:381-399. [PMID: 31997134 PMCID: PMC7147958 DOI: 10.1007/s00439-020-02119-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/17/2020] [Indexed: 12/25/2022]
Abstract
Our cells operate based on two distinct genomes that are enclosed in the nucleus and mitochondria. The mitochondrial genome presumably originates from endosymbiotic bacteria. With time, a large portion of the original genes in the bacterial genome is considered to have been lost or transferred to the nuclear genome, leaving a reduced 16.5 Kb circular mitochondrial DNA (mtDNA). Traditionally only 37 genes, including 13 proteins, were thought to be encoded within mtDNA, its genetic repertoire is expanding with the identification of mitochondrial-derived peptides (MDPs). The biology of aging has been largely unveiled to be regulated by genes that are encoded in the nuclear genome, whereas the mitochondrial genome remained more cryptic. However, recent studies position mitochondria and mtDNA as an important counterpart to the nuclear genome, whereby the two organelles constantly regulate each other. Thus, the genomic network that regulates lifespan and/or healthspan is likely constituted by two unique, yet co-evolved, genomes. Here, we will discuss aspects of mitochondrial biology, especially mitochondrial communication that may add substantial momentum to aging research by accounting for both mitonuclear genomes to more comprehensively and inclusively map the genetic and molecular networks that govern aging and age-related diseases.
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Affiliation(s)
- Joseph C Reynolds
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Conscience P Bwiza
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA.
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea.
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36
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Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet 2020; 52:342-352. [PMID: 32024997 PMCID: PMC7058535 DOI: 10.1038/s41588-019-0557-x] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/21/2019] [Indexed: 02/06/2023]
Abstract
Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome Consortium/The Cancer Genome Atlas Pan-Cancer Analysis of Whole Genomes Consortium, which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we performed a multidimensional, integrated characterization of mitochondrial genomes and related RNA sequencing data. Our analysis presents the most definitive mutational landscape of mitochondrial genomes and identifies several hypermutated cases. Truncating mutations are markedly enriched in kidney, colorectal and thyroid cancers, suggesting oncogenic effects with the activation of signaling pathways. We find frequent somatic nuclear transfers of mitochondrial DNA, some of which disrupt therapeutic target genes. Mitochondrial copy number varies greatly within and across cancers and correlates with clinical variables. Co-expression analysis highlights the function of mitochondrial genes in oxidative phosphorylation, DNA repair and the cell cycle, and shows their connections with clinically actionable genes. Our study lays a foundation for translating mitochondrial biology into clinical applications.
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Affiliation(s)
- Yuan Yuan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Young Seok Ju
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Youngwook Kim
- Department of Health Science and Technology, Samsung Advanced Institute for Health Science and Technology, Sungkyunkwan University School of Medicine, Seoul, Korea
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Jun Li
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yumeng Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Christopher J Yoon
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Yang Yang
- Division of Biostatistics, The University of Texas Health Science Center at Houston School of Public Health, Houston, TX, USA
| | | | - Chad J Creighton
- Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, USA
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yanxun Xu
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Korea
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Keunchil Park
- Division of Hematology/Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
- Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University School of Medicine, Seoul, South Korea.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Quantitative and Computational Biosciences Graduate Program, Baylor College of Medicine, Houston, TX, USA.
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Seligmann H. Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry? DNA Cell Biol 2019; 38:1257-1268. [DOI: 10.1089/dna.2019.4858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem, Israel
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38
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Mazzocca A. The Systemic-Evolutionary Theory of the Origin of Cancer (SETOC): A New Interpretative Model of Cancer as a Complex Biological System. Int J Mol Sci 2019; 20:ijms20194885. [PMID: 31581628 PMCID: PMC6801598 DOI: 10.3390/ijms20194885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/29/2019] [Accepted: 09/30/2019] [Indexed: 12/16/2022] Open
Abstract
The Systemic–Evolutionary Theory of Cancer (SETOC) is a recently proposed theory based on two important concepts: (i) Evolution, understood as a process of cooperation and symbiosis (Margulian-like), and (ii) The system, in terms of the integration of the various cellular components, so that the whole is greater than the sum of the parts, as in any complex system. The SETOC posits that cancer is generated by the de-emergence of the “eukaryotic cell system” and by the re-emergence of cellular subsystems such as archaea-like (genetic information) and/or prokaryotic-like (mitochondria) subsystems, featuring uncoordinated behaviors. One of the consequences is a sort of “cellular regression” towards ancestral or atavistic biological functions or behaviors similar to those of protists or unicellular organisms in general. This de-emergence is caused by the progressive breakdown of the endosymbiotic cellular subsystem integration (mainly, information = nucleus and energy = mitochondria) as a consequence of long-term injuries. Known cancer-promoting factors, including inflammation, chronic fibrosis, and chronic degenerative processes, cause prolonged damage that leads to the breakdown or failure of this form of integration/endosymbiosis. In normal cells, the cellular “subsystems” must be fully integrated in order to maintain the differentiated state, and this integration is ensured by a constant energy intake. In contrast, when organ or tissue damage occurs, the constant energy intake declines, leading, over time, to energy shortage, failure of endosymbiosis, and the de-differentiated state observed in dysplasia and cancer.
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Affiliation(s)
- Antonio Mazzocca
- Interdisciplinary Department of Medicine, University of Bari School of Medicine, Piazza G. Cesare, 11, 70124 Bari, Italy.
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39
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Barja G. Towards a unified mechanistic theory of aging. Exp Gerontol 2019; 124:110627. [DOI: 10.1016/j.exger.2019.05.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/08/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
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Kaufman BA, Picard M, Sondheimer N. Mitochondrial DNA, nuclear context, and the risk for carcinogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:455-462. [PMID: 29332303 PMCID: PMC6045969 DOI: 10.1002/em.22169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/25/2017] [Accepted: 12/20/2017] [Indexed: 05/05/2023]
Abstract
The inheritance of mitochondrial DNA (mtDNA) from mother to child is complicated by differences in the stability of the mitochondrial genome. Although the germ line mtDNA is protected through the minimization of replication between generations, sequence variation can occur either through mutation or due to changes in the ratio between distinct genomes that are present in the mother (known as heteroplasmy). Thus, the unpredictability in transgenerational inheritance of mtDNA may cause the emergence of pathogenic mitochondrial and cellular phenotypes in offspring. Studies of the role of mitochondrial metabolism in cancer have a long and rich history, but recent evidence strongly suggests that changes in mitochondrial genotype and phenotype play a significant role in the initiation, progression and treatment of cancer. At the intersection of these two fields lies the potential for emerging mtDNA mutations to drive carcinogenesis in the offspring. In this review, we suggest that this facet of transgenerational carcinogenesis remains underexplored and is a potentially important contributor to cancer. Environ. Mol. Mutagen. 60:455-462, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Brett A. Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Vascular Medicine Institute, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA (USA)
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY 10032 USA
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY 10032 USA
- Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY 10032 USA
| | - Neal Sondheimer
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada M5G1X8
- Department of Paediatrics, The University of Toronto School of Medicine, Toronto, ON, Canada M5G1X8
- Correspondence to: Neal Sondheimer, 555 University Avenue, Toronto ON M5G 1X8, p – 416-813-7654 x 301480, f – 416-813-5345,
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Li W, Freudenberg J, Freudenberg J. Alignment-free approaches for predicting novel Nuclear Mitochondrial Segments (NUMTs) in the human genome. Gene 2019; 691:141-152. [PMID: 30630097 DOI: 10.1016/j.gene.2018.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/14/2018] [Indexed: 10/27/2022]
Abstract
The nuclear human genome harbors sequences of mitochondrial origin, indicating an ancestral transfer of DNA from the mitogenome. Several Nuclear Mitochondrial Segments (NUMTs) have been detected by alignment-based sequence similarity search, as implemented in the Basic Local Alignment Search Tool (BLAST). Identifying NUMTs is important for the comprehensive annotation and understanding of the human genome. Here we explore the possibility of detecting NUMTs in the human genome by alignment-free sequence similarity search, such as k-mers (k-tuples, k-grams, oligos of length k) distributions. We find that when k=6 or larger, the k-mer approach and BLAST search produce almost identical results, e.g., detect the same set of NUMTs longer than 3 kb. However, when k=5 or k=4, certain signals are only detected by the alignment-free approach, and these may indicate yet unrecognized, and potentially more ancestral NUMTs. We introduce a "Manhattan plot" style representation of NUMT predictions across the genome, which are calculated based on the reciprocal of the Jensen-Shannon divergence between the nuclear and mitochondrial k-mer frequencies. The further inspection of the k-mer-based NUMT predictions however shows that most of them contain long-terminal-repeat (LTR) annotations, whereas BLAST-based NUMT predictions do not. Thus, similarity of the mitogenome to LTR sequences is recognized, which we validate by finding the mitochondrial k-mer distribution closer to those for transposable sequences and specifically, close to some types of LTR.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Jerome Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Jan Freudenberg
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
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42
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Giant viruses as protein-coated amoeban mitochondria? Virus Res 2018; 253:77-86. [DOI: 10.1016/j.virusres.2018.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/13/2018] [Accepted: 06/14/2018] [Indexed: 01/18/2023]
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Liang B, Wang N, Li N, Kimball RT, Braun EL. Comparative Genomics Reveals a Burst of Homoplasy-Free Numt Insertions. Mol Biol Evol 2018; 35:2060-2064. [DOI: 10.1093/molbev/msy112] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Bin Liang
- Department of Biology, University of Florida, Gainesville, FL
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
- Forestry Research Institute of Hainan Province, Haikou, Hainan, P. R. China
| | - Ning Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Nan Li
- Department of Chemistry and Biochemistry, UC San Diego, La Jolla, CA
| | | | - Edward L Braun
- Department of Biology, University of Florida, Gainesville, FL
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Hopkins JF, Denroche RE, Aguiar JA, Notta F, Connor AA, Wilson JM, Stein LD, Gallinger S, Boutros PC. Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress. Gastroenterology 2018; 154:1620-1624.e5. [PMID: 29378198 DOI: 10.1053/j.gastro.2018.01.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 11/27/2017] [Accepted: 01/07/2018] [Indexed: 01/17/2023]
Abstract
Somatic mutations have been found in the mitochondria in different types of cancer cells, but it is not clear whether these affect tumorigenesis or tumor progression. We analyzed mitochondrial genomes of 268 early-stage, resected pancreatic ductal adenocarcinoma tissues and paired non-tumor tissues. We defined a mitochondrial somatic mutation (mtSNV) as a position where the difference in heteroplasmy fraction between tumor and normal sample was ≥0.2. Our analysis identified 304 mtSNVs, with at least 1 mtSNV in 61% (164 of 268) of tumor samples. The noncoding control region had the greatest proportion of mtSNVs (60 of 304 mutations); this region contains sites that regulate mitochondrial DNA transcription and replication. Frequently mutated genes included ND5, RNR2, and CO1, plus 29 mutations in transfer RNA genes. mtSNVs in 2 separate mitochondrial genes (ND4 and ND6) were associated with shorter overall survival time. This association appeared to depend on the level of mtSNV heteroplasmy. Non-random co-occurrence between mtSNVs and mutations in nuclear genes indicates interactions between nuclear and mitochondrial DNA. In an analysis of primary tumors and metastases from 6 patients, we found tumors to accumulate mitochondrial mutational mutations as they progress.
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Affiliation(s)
- Julia F Hopkins
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Robert E Denroche
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jennifer A Aguiar
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ashton A Connor
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Julie M Wilson
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lincoln D Stein
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada; Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada.
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45
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Models, methods, and approaches to study mitochondrial functioning in vitro, in situ, and in vivo: Editorial for the special issue on Mitochondrial Biochemistry and Bioenergetics. Anal Biochem 2018; 552:1-3. [PMID: 29678762 DOI: 10.1016/j.ab.2018.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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46
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Johnson J, Bessette DC, Saunus JM, Smart CE, Song S, Johnston RL, Cocciardi S, Rozali EN, Johnstone CN, Vargas AC, Kazakoff SH, BioBank VC, Khanna KK, Lakhani SR, Chenevix-Trench G, Simpson PT, Nones K, Waddell N, Al-Ejeh F. Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient. Breast Cancer Res Treat 2018; 170:179-188. [DOI: 10.1007/s10549-018-4719-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/15/2018] [Indexed: 02/03/2023]
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Penrose HM, Heller S, Cable C, Nakhoul H, Ungerleider N, Baddoo M, Pursell ZF, Flemington EK, Crawford SE, Savkovic SD. In colonic ρ 0 (rho0) cells reduced mitochondrial function mediates transcriptomic alterations associated with cancer. Oncoscience 2017; 4:189-198. [PMID: 29344557 PMCID: PMC5769983 DOI: 10.18632/oncoscience.386] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/11/2017] [Indexed: 12/19/2022] Open
Abstract
Background Mitochondrial reprogramming has emerged as a hallmark of cancer pathobiology. Although it is believed this reprogramming is essential for cancer cells to thrive, how it supports cancer pathobiology is unclear. We previously generated colonic ρ0 (rho0) cells with reduced mitochondrial energy function and acquired their transcriptional signature. Here, we utilized a bioinformatics approach to identify their changes linked to cancer pathobiology. Methods Human colon cancer HCT116 cells, control and ρ0, were used for qPCR. Bioinformatics analysis: GeneCards, Kaplan-Meier Survival, GENT, cBioPortal. Results The colonic ρ0 transcriptome was linked with proliferation, DNA replication, survival, tumor morphology, and cancer. Among differentially expressed transcripts, 281 were regulators or biomarkers of human colon cancer especially those with inflammatory microsatellite instability (MSI). We identified and validated novel transcripts in ρ0 cells with altered expression in human colon cancer. Among them DGK1, HTR7, FLRT3, and ZBTB18 co-occurred with established regulators of human colon cancer pathobiology. Also, increased levels of DGKI, FLRT3, ZBTB18, and YPEL1 as well as decreased levels of HTR7, and CALML6 were linked to substantially poorer patient survival. Conclusion We identified established and novel regulators in colon cancer pathobiology that are dependent on mitochondrial energy reprogramming and linked to poorer patient survival.
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Affiliation(s)
- Harrison M Penrose
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Sandra Heller
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Chloe Cable
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Hani Nakhoul
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Nate Ungerleider
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Erik K Flemington
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Susan E Crawford
- Department of Surgery, NorthShore Research Institute, Affiliate of University of Chicago Pritzker School of Medicine, Evanston, IL 60201, USA
| | - Suzana D Savkovic
- Department of Pathology and Laboratory Medicine, Tulane University, New Orleans, LA 70112, USA
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Choudhury AR, Singh KK. Mitochondrial determinants of cancer health disparities. Semin Cancer Biol 2017; 47:125-146. [PMID: 28487205 PMCID: PMC5673596 DOI: 10.1016/j.semcancer.2017.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 01/10/2023]
Abstract
Mitochondria, which are multi-functional, have been implicated in cancer initiation, progression, and metastasis due to metabolic alterations in transformed cells. Mitochondria are involved in the generation of energy, cell growth and differentiation, cellular signaling, cell cycle control, and cell death. To date, the mitochondrial basis of cancer disparities is unknown. The goal of this review is to provide an understanding and a framework of mitochondrial determinants that may contribute to cancer disparities in racially different populations. Due to maternal inheritance and ethnic-based diversity, the mitochondrial genome (mtDNA) contributes to inherited racial disparities. In people of African ancestry, several germline, population-specific haplotype variants in mtDNA as well as depletion of mtDNA have been linked to cancer predisposition and cancer disparities. Indeed, depletion of mtDNA and mutations in mtDNA or nuclear genome (nDNA)-encoded mitochondrial proteins lead to mitochondrial dysfunction and promote resistance to apoptosis, the epithelial-to-mesenchymal transition, and metastatic disease, all of which can contribute to cancer disparity and tumor aggressiveness related to racial disparities. Ethnic differences at the level of expression or genetic variations in nDNA encoding the mitochondrial proteome, including mitochondria-localized mtDNA replication and repair proteins, miRNA, transcription factors, kinases and phosphatases, and tumor suppressors and oncogenes may underlie susceptibility to high-risk and aggressive cancers found in African population and other ethnicities. The mitochondrial retrograde signaling that alters the expression profile of nuclear genes in response to dysfunctional mitochondria is a mechanism for tumorigenesis. In ethnic populations, differences in mitochondrial function may alter the cross talk between mitochondria and the nucleus at epigenetic and genetic levels, which can also contribute to cancer health disparities. Targeting mitochondrial determinants and mitochondrial retrograde signaling could provide a promising strategy for the development of selective anticancer therapy for dealing with cancer disparities. Further, agents that restore mitochondrial function to optimal levels should permit sensitivity to anticancer agents for the treatment of aggressive tumors that occur in racially diverse populations and hence help in reducing racial disparities.
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Affiliation(s)
| | - Keshav K Singh
- Departments of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Departments of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Departments of Environmental Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Center for Aging, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, 35294, USA; Birmingham Veterans Affairs Medical Center, Birmingham, AL, 35294, USA.
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49
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Singh B, Modica-Napolitano JS, Singh KK. Defining the momiome: Promiscuous information transfer by mobile mitochondria and the mitochondrial genome. Semin Cancer Biol 2017; 47:1-17. [PMID: 28502611 PMCID: PMC5681893 DOI: 10.1016/j.semcancer.2017.05.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/20/2017] [Accepted: 05/07/2017] [Indexed: 12/30/2022]
Abstract
Mitochondria are complex intracellular organelles that have long been identified as the powerhouses of eukaryotic cells because of the central role they play in oxidative metabolism. A resurgence of interest in the study of mitochondria during the past decade has revealed that mitochondria also play key roles in cell signaling, proliferation, cell metabolism and cell death, and that genetic and/or metabolic alterations in mitochondria contribute to a number of diseases, including cancer. Mitochondria have been identified as signaling organelles, capable of mediating bidirectional intracellular information transfer: anterograde (from nucleus to mitochondria) and retrograde (from mitochondria to nucleus). More recently, evidence is now building that the role of mitochondria extends to intercellular communication as well, and that the mitochondrial genome (mtDNA) and even whole mitochondria are indeed mobile and can mediate information transfer between cells. We define this promiscuous information transfer function of mitochondria and mtDNA as "momiome" to include all mobile functions of mitochondria and the mitochondrial genome. Herein, we review the "momiome" and explore its role in cancer development, progression, and treatment.
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Affiliation(s)
- Bhupendra Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Keshav K Singh
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Environmental Health, Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA; Center for Aging, University of Alabama at Birmingham, Birmingham, AL, USA; UAB Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA; Birmingham Veterans Affairs Medical Center, Birmingham, AL, USA.
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50
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Zhu PT, Mao M, Liu ZG, Tao L, Yan BC. Scutellarin suppresses human colorectal cancer metastasis and angiogenesis by targeting ephrinb2. Am J Transl Res 2017; 9:5094-5104. [PMID: 29218107 PMCID: PMC5714793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 10/31/2017] [Indexed: 06/07/2023]
Abstract
Tumor induced angiogenesis is an attractive target for anti-cancer drug treatment. Scutellarin, which is a native compound derived from scutellaria altissima leaves, has already been proved to possess anti-tumor activities. Nevertheless, their effects in colorectal cancer metastasis and angiogenesis have not been evaluated. In order to reveal the anti-angiogenic and anti-metastasis capacity of scutellarin, wound healing and Transwell chamber inserts invasion were done in colorectal cancer cells, and cell proliferation as wells colony formation were conducted to identify the proliferation inhibition of colorectal cancer in vitro. The growth inhibition of scutellarin was further definite by a mouse colorectal xenograft model in vivo. Herein, we demonstrated scutellarin suppressed colorectal cancer cell viability and colony formation in vitro, and remarkably reduced tumor growth in vivo mouse xenografts. Additionally, scutellarin restrained colorectal cancer cells-induced angiogenesis, inhibited human umbilical vascular endothelial cells (HUVECs) migration, tube formation of HUVECs, and micro-vessel formation in chick embnyo chorioallantoic menbreme (CAM) assay. Altogether, our results exhibited the evidence that scutellarin inhibit colorectal cancer angiogenesis and metastasis via targeting ephrinb2 signaling, with the potential of an anti-tumor agent for cancer treatment.
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Affiliation(s)
- Ping Ting Zhu
- School of Nursing, Yangzhou University88 South University Ave., Yangzhou 225009, Jiangsu Province, China
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese MedicineNanjing 210023, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou 225009, China
| | - Ming Mao
- School of Nursing, Yangzhou University88 South University Ave., Yangzhou 225009, Jiangsu Province, China
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou 225009, China
| | - Zhao Guo Liu
- School of Pharmacy, Nantong University19 Qixiu Road, Nantong 226001, Jiangsu Province, China
| | - Li Tao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese MedicineNanjing 210023, Jiangsu, China
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou 225009, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile DiseasesYangzhou 225001, China
| | - Bing Chun Yan
- Jiangsu Key Laboratory of Zoonosis, Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou 225009, China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile DiseasesYangzhou 225001, China
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