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Yazdani M. Cellular and Molecular Responses to Mitochondrial DNA Deletions in Kearns-Sayre Syndrome: Some Underlying Mechanisms. Mol Neurobiol 2024; 61:5665-5679. [PMID: 38224444 DOI: 10.1007/s12035-024-03938-7] [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: 01/16/2024]
Abstract
Kearns-Sayre syndrome (KSS) is a rare multisystem mitochondrial disorder. It is caused by mitochondrial DNA (mtDNA) rearrangements, mostly large-scale deletions of 1.1-10 kb. These deletions primarily affect energy supply through impaired oxidative phosphorylation and reduced ATP production. This impairment gives rise to dysfunction of several tissues, in particular those with high energy demand like brain and muscles. Over the past decades, changes in respiratory chain complexes and energy metabolism have been emphasized, whereas little attention has been paid to other reports on ROS overproduction, protein synthesis inhibition, myelin vacuolation, demyelination, autophagy, apoptosis, and involvement of lipid raft and oligodendrocytes in KSS. Therefore, this paper draws attention towards these relatively underemphasized findings that might further clarify the pathologic cascades following deletions in the mtDNA.
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Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, 0027, Norway.
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Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D, Eberwine J. Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons. BMC Biol 2024; 22:162. [PMID: 39075589 PMCID: PMC11287894 DOI: 10.1186/s12915-024-01953-7] [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: 03/11/2024] [Accepted: 07/08/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting "normal" mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes, we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes. In this study, we amplified mt-genomes from 1645 single mitochondria isolated from mouse single astrocytes and neurons to (1) determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, (2) assess differences in mtDNA SNVs between neurons and astrocytes, and (3) study co-segregation of variants in the mouse mtDNA. RESULTS (1) The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. (2) Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G > A and 9419:C > T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. (3) Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461. CONCLUSIONS This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.
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Affiliation(s)
- Parnika S Kadam
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zijian Yang
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hua Zhu
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yasemin Atiyas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nishal Shah
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephen Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - David Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Kadam PS, Yang Z, Lu Y, Zhu H, Atiyas Y, Shah N, Fisher S, Nordgren E, Kim J, Issadore D, Eberwine J. Single-Mitochondrion Sequencing Uncovers Distinct Mutational Patterns and Heteroplasmy Landscape in Mouse Astrocytes and Neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598906. [PMID: 38915628 PMCID: PMC11195285 DOI: 10.1101/2024.06.13.598906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting 'normal' mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes In this study we amplified mt-genomes from 1,645 single mitochondria (mts) isolated from mouse single astrocytes and neurons to 1. determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, 2. assess differences in mtDNA SNVs between neurons and astrocytes, and 3. Study cosegregation of variants in the mouse mtDNA. Results 1. The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. 2. Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G>A and 9419:C>T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. 3. Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461. Conclusion This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.
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Affiliation(s)
- Parnika S Kadam
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zijian Yang
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Youtao Lu
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hua Zhu
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yasemin Atiyas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nishal Shah
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen Fisher
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Nordgren
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences; University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Dobner J, Nguyen T, Pavez-Giani MG, Cyganek L, Distelmaier F, Krutmann J, Prigione A, Rossi A. mtDNA analysis using Mitopore. Mol Ther Methods Clin Dev 2024; 32:101231. [PMID: 38572068 PMCID: PMC10988129 DOI: 10.1016/j.omtm.2024.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 04/05/2024]
Abstract
Mitochondrial DNA (mtDNA) analysis is crucial for the diagnosis of mitochondrial disorders, forensic investigations, and basic research. Existing pipelines are complex, expensive, and require specialized personnel. In many cases, including the diagnosis of detrimental single nucleotide variants (SNVs), mtDNA analysis is still carried out using Sanger sequencing. Here, we developed a simple workflow and a publicly available webserver named Mitopore that allows the detection of mtDNA SNVs, indels, and haplogroups. To simplify mtDNA analysis, we tailored our workflow to process noisy long-read sequencing data for mtDNA analysis, focusing on sequence alignment and parameter optimization. We implemented Mitopore with eliBQ (eliminate bad quality reads), an innovative quality enhancement that permits the increase of per-base quality of over 20% for low-quality data. The whole Mitopore workflow and webserver were validated using patient-derived and induced pluripotent stem cells harboring mtDNA mutations. Mitopore streamlines mtDNA analysis as an easy-to-use fast, reliable, and cost-effective analysis method for both long- and short-read sequencing data. This significantly enhances the accessibility of mtDNA analysis and reduces the cost per sample, contributing to the progress of mtDNA-related research and diagnosis.
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Affiliation(s)
- Jochen Dobner
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Thach Nguyen
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
| | - Mario Gustavo Pavez-Giani
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
| | - Lukas Cyganek
- Clinic for Cardiology and Pneumology, University Medical Center Göttingen, 37075 Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jean Krutmann
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
- Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Andrea Rossi
- Institut für Umweltmedizinische Forschung (IUF)-Leibniz Research Institute for Environmental Medicine, 40225 Düsseldorf, Germany
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Wang B, Zhang G, Hu Y, Mohsin A, Chen Z, Hao W, Li Z, Gao WQ, Guo M, Xu H. Uncovering impaired mitochondrial and lysosomal function in adipose-derived stem cells from obese individuals with altered biological activity. Stem Cell Res Ther 2024; 15:12. [PMID: 38185703 PMCID: PMC10773039 DOI: 10.1186/s13287-023-03625-9] [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: 05/24/2023] [Accepted: 12/22/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Adipose-derived stem cells (ADSCs) have been extensively used in preclinical and clinical trials for treating various diseases. However, the differences between ADSCs from lean individuals (L-ADSCs) and those from obese individuals (O-ADSCs) have not been thoroughly investigated, particularly regarding their mitochondrial and lysosomal functions. Therefore, this study aims to evaluate the differences between L-ADSCs and O-ADSCs in terms of cell biological activity, mitochondria, and lysosomes. METHODS We first isolated and cultured L-ADSCs and O-ADSCs. We then compared the differences between the two groups in terms of biological activity, including cell proliferation, differentiation potential, and their effect on the polarization of macrophages. Additionally, we observed the mitochondrial and lysosomal morphology of ADSCs using an electronic microscope, MitoTracker Red, and lysotracker Red dyes. We assessed mitochondrial function by examining mitochondrial membrane potential and membrane fluidity, antioxidative ability, and cell energy metabolism. Lysosomal function was evaluated by measuring autophagy and phagocytosis. Finally, we performed transcriptome analysis of the ADSCs using RNA sequencing. RESULTS The biological activities of O-ADSCs were decreased, including cell immunophenotypic profiles, cell proliferation, and differentiation potential. Furthermore, compared to L-ADSCs, O-ADSCs promoted M1-type macrophage polarization and inhibited M2-type macrophage polarization. Additionally, the mitochondrial morphology of O-ADSCs was altered, with the size of the cells becoming smaller and mitochondrial fragments increasing. O-ADSCs also exhibited decreased mitochondrial membrane potential and membrane fluidity, antioxidative ability, and energy metabolism. With respect to lysosomes, O-ADSCs contained ungraded materials in their lysosomes, enhanced lysosomal permeability, and reduced autophagy and phagocytosis ability. RNA sequence analysis indicated that the signalling pathways related to cell senescence, cancer, and inflammation were upregulated, whereas the signalling pathways associated with stemness, cell differentiation, metabolism, and response to stress and stimuli were downregulated. CONCLUSIONS This study indicates that ADSCs from individuals (BMI > 30 kg/m2) exhibit impaired mitochondrial and lysosomal function with decreased biological activity.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd., P.O. Box 329#, Shanghai, 200237, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, and Renji-MedX Clinical Stem Cell Research Center RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Ge Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd., P.O. Box 329#, Shanghai, 200237, People's Republic of China
- State Key Laboratory of Oncogenes and Related Genes, and Renji-MedX Clinical Stem Cell Research Center RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Yuwen Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd., P.O. Box 329#, Shanghai, 200237, People's Republic of China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd., P.O. Box 329#, Shanghai, 200237, People's Republic of China
| | - Zhimin Chen
- State Key Laboratory of Oncogenes and Related Genes, and Renji-MedX Clinical Stem Cell Research Center RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Weijie Hao
- State Key Laboratory of Oncogenes and Related Genes, and Renji-MedX Clinical Stem Cell Research Center RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China
| | - Zhanxia Li
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 600 Yishan Road, Xuhui District, Shanghai, 200235, People's Republic of China.
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, and Renji-MedX Clinical Stem Cell Research Center RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, People's Republic of China.
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Rd., P.O. Box 329#, Shanghai, 200237, People's Republic of China.
| | - Huiming Xu
- State Key Laboratory of Oncogenes and Related Genes, and Renji-MedX Clinical Stem Cell Research Center RenJi Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, People's Republic of China.
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Arnold BH, Sanislav O, Fisher PR, Annesley SJ. Plate-Based Assays for the Characterization of Mitochondrial and Cellular Phenotypes. Methods Mol Biol 2024; 2746:1-20. [PMID: 38070076 DOI: 10.1007/978-1-0716-3585-8_1] [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: 12/18/2023]
Abstract
The mitochondria are essential to eukaryotic life, acting as key drivers of energy generation while also being involved in the regulation of many cellular processes including apoptosis, cell proliferation, calcium homeostasis, and metabolism. Mitochondrial diseases which disrupt these processes lead to a diverse range of pathologies and lack consistency in symptom presentation. In disease, mitochondrial activity and energy homeostasis can be adapted to cellular requirements, and studies using Dictyostelium and human lymphoblastoid cell lines have shown that such changes can be facilitated by the key cellular and energy regulators, TORC1 and AMPK. Fluorescence-based assays are increasingly utilized to measure mitochondrial and cell signalling function in mitochondrial disease research. Here, we describe a streamlined method for the simultaneous measurement of mitochondrial mass, membrane potential, and reactive oxygen species production using MitoTracker Green™ FM, MitoTracker Red™ CMXRos, and DCFH-DA probes. This protocol has been adapted for both Dictyostelium and human lymphoblastoid cell lines. We also describe a method for assessing TORC1 and AMPK activity simultaneously in lymphoblastoid cells. These techniques allow for the characterization of mitochondrial defects in a rapid and easy to implement manner.
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Affiliation(s)
- Benjamin Henry Arnold
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC, Australia
| | - Oana Sanislav
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC, Australia
| | - Paul Robert Fisher
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC, Australia
| | - Sarah Jane Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Melbourne, VIC, Australia.
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de Souza FG, da Silva MB, de Araújo GS, Silva CS, Pinheiro AHG, Cáceres-Durán MÁ, Santana-da-Silva MN, Pinto P, Gobbo AR, da Costa PF, Salgado CG, Ribeiro-Dos-Santos Â, Cavalcante GC. Whole mitogenome sequencing uncovers a relation between mitochondrial heteroplasmy and leprosy severity. Hum Genomics 2023; 17:110. [PMID: 38062538 PMCID: PMC10704783 DOI: 10.1186/s40246-023-00555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In recent years, the mitochondria/immune system interaction has been proposed, so that variants of mitochondrial genome and levels of heteroplasmy might deregulate important metabolic processes in fighting infections, such as leprosy. METHODS We sequenced the whole mitochondrial genome to investigate variants and heteroplasmy levels, considering patients with different clinical forms of leprosy and household contacts. After sequencing, a specific pipeline was used for preparation and bioinformatics analysis to select heteroplasmic variants. RESULTS We found 116 variants in at least two of the subtypes of the case group (Borderline Tuberculoid, Borderline Lepromatous, Lepromatous), suggesting a possible clinical significance to these variants. Notably, 15 variants were exclusively found in these three clinical forms, of which five variants stand out for being missense (m.3791T > C in MT-ND1, m.5317C > A in MT-ND2, m.8545G > A in MT-ATP8, m.9044T > C in MT-ATP6 and m.15837T > C in MT-CYB). In addition, we found 26 variants shared only by leprosy poles, of which two are characterized as missense (m.4248T > C in MT-ND1 and m.8027G > A in MT-CO2). CONCLUSION We found a significant number of variants and heteroplasmy levels in the leprosy patients from our cohort, as well as six genes that may influence leprosy susceptibility, suggesting for the first time that the mitogenome might be involved with the leprosy process, distinction of clinical forms and severity. Thus, future studies are needed to help understand the genetic consequences of these variants.
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Affiliation(s)
- Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Gilderlanio S de Araújo
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Caio S Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Andrey Henrique Gama Pinheiro
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Miguel Ángel Cáceres-Durán
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Mayara Natália Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
| | - Giovanna C Cavalcante
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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Rioux AV, Bergeron NA, Riopel J, Marcoux N, Thériault C, Gould PV, Garneau AP, Isenring P. The ever wider clinical spectrum of RMND1-related disorders and limitedness of phenotype-based classifications. J Mol Med (Berl) 2023; 101:1229-1236. [PMID: 37584739 PMCID: PMC10560146 DOI: 10.1007/s00109-023-02356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023]
Abstract
RMND1 has been identified as a mitochondriopathy-associated gene less than 12 years ago. The most common phenotype related to this gene is an early onset, severe form of encephalomyopathy that leads to death in a medium time of three years after birth. However, milder and later onset presentations have been reported in some individuals, including two in whom the mitochondriopathy was identified at ~ 40 years of age, and the early onset presentations have been the object of no reports in those who survived beyond age 10. It is thus unclear how lethal RMND1-related conditions really are. We herein describe the oldest case to have been identified hitherto with this condition, i.e., that of a white female who was 61 at the time of diagnosis but was still active in her everyday life. The gene defect identified was nonetheless associated with many manifestations including ovarian insufficiency and sensorineural hearing loss (two features of what is currently designated as Perrault syndrome) as well as chronic renal failure, asymptomatic myopathy, leukopenia, and a few others. In our opinion, this case is of great translational interest for at least three reasons. First, it hints towards the possibility of near-normal life expectancies in some if not many individuals with RMND1 insufficiency. Second, it underlines the wide clinical spectrum associated with this gene. Third, it brings us to question the use of eponyms and syndromic features to identify the true etiology of multisystemic phenotypes. KEY MESSAGES: RMND1-related conditions typically manifest at an early age with a progressive and lethal form of encephalomyopathy. More benign presentations have been described with some being categorized as Perrault syndrome but none have been diagnosed after the age of 45. The clinical spectrum and presenting age of RMND1-related mitochondriopathies are probably much more varied than implied in the current literature. The case reported in this manuscript illustrates the limitedness of phenotype-based classifications of genetic disorders to identify the defect at cause.
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Affiliation(s)
- Alexis V Rioux
- CHU de Québec, Service of Nephrology, Faculty of Medicine, Université Laval, QC, G1R 2J6, Québec, Canada
| | - Nicolas Ad Bergeron
- CHU de Québec, Service of Nephrology, Faculty of Medicine, Université Laval, QC, G1R 2J6, Québec, Canada
| | - Julie Riopel
- CHU de Québec, Service of Pathology, Faculty of Medicine, Université Laval, Québec, QC, G1R 2J6, Canada
| | - Nicolas Marcoux
- CHU de Québec, Service of Hematology, Faculty of Medicine, Université Laval, Québec, QC, G1R 2J6, Canada
| | - Catherine Thériault
- CHU de Québec, Service of Pathology, Faculty of Medicine, Université Laval, Québec, QC, G1R 2J6, Canada
| | - Peter V Gould
- CHU de Québec, Service of Pathology, Faculty of Medicine, Université Laval, Québec, QC, G1R 2J6, Canada
| | - Alexandre P Garneau
- Service de Néphrologie-Transplantation Rénale Adultes, Hôpital Necker‑Enfants Malades, AP‑HP, Inserm U1151, Université Paris Cité, rue de Sèvres, Paris, France
| | - Paul Isenring
- CHU de Québec, Service of Nephrology, Faculty of Medicine, Université Laval, QC, G1R 2J6, Québec, Canada.
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Win PW, Singh SM, Castellani CA. Mitochondrial DNA Copy Number and Heteroplasmy in Monozygotic Twins Discordant for Schizophrenia. Twin Res Hum Genet 2023:1-10. [PMID: 37655526 DOI: 10.1017/thg.2023.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Schizophrenia (SZ) is a severe, complex, and common mental disorder with high heritability (80%), an adult age of onset, and high discordance (∼50%) in monozygotic twins (MZ). Extensive studies on familial and non-familial cases have implicated a number of segregating mutations and de novo changes in SZ that may include changes to the mitochondrial genome. Yet, no single universally causal variant has been identified, highlighting its extensive genetic heterogeneity. This report specifically focuses on the assessment of changes in the mitochondrial genome in a unique set of monozygotic twins discordant (MZD) for SZ using blood. Genomic DNA from six pairs of MZD twins and two sets of parents (N = 16) was hybridized to the Affymetrix Human SNP Array 6.0 to assess mitochondrial DNA copy number (mtDNA-CN). Whole genome sequencing (WGS) and quantitative polymerase chain reaction (qPCR) was performed for a subset of MZD pairs and their parents and was also used to derive mtDNA-CN estimates. The WGS data were further analyzed to generate heteroplasmy (HP) estimates. Our results show that mtDNA-CN estimates for within-pair and mother-child differences were smaller than comparisons involving unrelated individuals, as expected. MZD twins showed discordance in mtDNA-CN estimates and displayed concordance in directionality of differences for mtDNA-CN across all technologies. Further, qPCR performed better than Affymetrix in estimating mtDNA-CN based on relatedness. No reliable differences in HP were detected between MZD twins. The within-MZD differences in mtDNA-CN observed represent postzygotic somatic changes that may contribute to discordance of MZ twins for diseases, including SZ.
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Affiliation(s)
- Phyo W Win
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Shiva M Singh
- Department of Biology, Western University, London, Canada
| | - Christina A Castellani
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Canada
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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10
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Xie X, Zhu X. Visualization of mtDNA Using FISH. Methods Mol Biol 2023; 2615:89-98. [PMID: 36807786 DOI: 10.1007/978-1-0716-2922-2_7] [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: 02/23/2023]
Abstract
Proper mitochondrial DNA (mtDNA) levels are critical for many cellular biological functions and are associated with aging and many mitochondria disorders. Defects in core subunits of the mtDNA replication machinery lead to decreased mtDNA levels. Other indirect mitochondrial contexts including ATP concentration, lipid composition, and nucleotide composition also contribute to mtDNA maintenance. Furthermore, mtDNA molecules are distributed evenly throughout the mitochondrial network. This uniform distribution pattern is required for oxidative phosphorylation and ATP production and has been linked to many diseases when perturbed. Thus, it is important to visualize mtDNA in the cellular context. Here we provide detailed protocols for cellular visualization of mtDNA using fluorescence in situ hybridization (FISH). The fluorescent signals are targeted to the mtDNA sequence directly, ensuring both sensitivity and specificity. This mtDNA FISH method can be combined with immunostaining and used for visualizing mtDNA-protein interactions and dynamics.
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Affiliation(s)
- Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.
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11
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Delivery Systems for Mitochondrial Gene Therapy: A Review. Pharmaceutics 2023; 15:pharmaceutics15020572. [PMID: 36839894 PMCID: PMC9964608 DOI: 10.3390/pharmaceutics15020572] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Mitochondria are membrane-bound cellular organelles of high relevance responsible for the chemical energy production used in most of the biochemical reactions of cells. Mitochondria have their own genome, the mitochondrial DNA (mtDNA). Inherited solely from the mother, this genome is quite susceptible to mutations, mainly due to the absence of an effective repair system. Mutations in mtDNA are associated with endocrine, metabolic, neurodegenerative diseases, and even cancer. Currently, therapeutic approaches are based on the administration of a set of drugs to alleviate the symptoms of patients suffering from mitochondrial pathologies. Mitochondrial gene therapy emerges as a promising strategy as it deeply focuses on the cause of mitochondrial disorder. The development of suitable mtDNA-based delivery systems to target and transfect mammalian mitochondria represents an exciting field of research, leading to progress in the challenging task of restoring mitochondria's normal function. This review gathers relevant knowledge on the composition, targeting performance, or release profile of such nanosystems, offering researchers valuable conceptual approaches to follow in their quest for the most suitable vectors to turn mitochondrial gene therapy clinically feasible. Future studies should consider the optimization of mitochondrial genes' encapsulation, targeting ability, and transfection to mitochondria. Expectedly, this effort will bring bright results, contributing to important hallmarks in mitochondrial gene therapy.
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12
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Mitochondrial transfer/transplantation: an emerging therapeutic approach for multiple diseases. Cell Biosci 2022; 12:66. [PMID: 35590379 PMCID: PMC9121600 DOI: 10.1186/s13578-022-00805-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/01/2022] [Indexed: 12/16/2022] Open
Abstract
Mitochondria play a pivotal role in energy generation and cellular physiological processes. These organelles are highly dynamic, constantly changing their morphology, cellular location, and distribution in response to cellular stress. In recent years, the phenomenon of mitochondrial transfer has attracted significant attention and interest from biologists and medical investigators. Intercellular mitochondrial transfer occurs in different ways, including tunnelling nanotubes (TNTs), extracellular vesicles (EVs), and gap junction channels (GJCs). According to research on intercellular mitochondrial transfer in physiological and pathological environments, mitochondrial transfer hold great potential for maintaining body homeostasis and regulating pathological processes. Multiple research groups have developed artificial mitochondrial transfer/transplantation (AMT/T) methods that transfer healthy mitochondria into damaged cells and recover cellular function. This paper reviews intercellular spontaneous mitochondrial transfer modes, mechanisms, and the latest methods of AMT/T. Furthermore, potential application value and mechanism of AMT/T in disease treatment are also discussed.
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13
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Vikramdeo KS, Sudan SK, Singh AP, Singh S, Dasgupta S. Mitochondrial respiratory complexes: Significance in human mitochondrial disorders and cancers. J Cell Physiol 2022; 237:4049-4078. [PMID: 36074903 DOI: 10.1002/jcp.30869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/18/2022] [Accepted: 08/23/2022] [Indexed: 11/07/2022]
Abstract
Mitochondria are pivotal organelles that govern cellular energy production through the oxidative phosphorylation system utilizing five respiratory complexes. In addition, mitochondria also contribute to various critical signaling pathways including apoptosis, damage-associated molecular patterns, calcium homeostasis, lipid, and amino acid biosynthesis. Among these diverse functions, the energy generation program oversee by mitochondria represents an immaculate orchestration and functional coordination between the mitochondria and nuclear encoded molecules. Perturbation in this program through respiratory complexes' alteration results in the manifestation of various mitochondrial disorders and malignancy, which is alarmingly becoming evident in the recent literature. Considering the clinical relevance and importance of this emerging medical problem, this review sheds light on the timing and nature of molecular alterations in various respiratory complexes and their functional consequences observed in various mitochondrial disorders and human cancers. Finally, we discussed how this wealth of information could be exploited and tailored to develop respiratory complex targeted personalized therapeutics and biomarkers for better management of various incurable human mitochondrial disorders and cancers.
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Affiliation(s)
- Kunwar Somesh Vikramdeo
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Sarabjeet Kour Sudan
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Ajay P Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Seema Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Santanu Dasgupta
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
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14
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Ludwig-Słomczyńska AH, Rehm M. Mitochondrial genome variations, mitochondrial-nuclear compatibility, and their association with metabolic diseases. Obesity (Silver Spring) 2022; 30:1156-1169. [PMID: 35491673 DOI: 10.1002/oby.23424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/10/2022]
Abstract
Two genomes regulate the energy metabolism of eukaryotic cells: the nuclear genome, which codes for most cellular proteins, and the mitochondrial genome, which, together with the nuclear genome, coregulates cellular bioenergetics. Therefore, mitochondrial genome variations can affect, directly or indirectly, all energy-dependent cellular processes and shape the metabolic state of the organism. This review provides a current and up-to-date overview on how codependent these two genomes are, how they appear to have coevolved, and how variations within the mitochondrial genome might be associated with the manifestation of metabolic diseases. This review summarizes and structures results obtained from epidemiological studies that identified links between mitochondrial haplogroups and individual risks for developing obesity and diabetes. This is complemented by findings on the compatibility of mitochondrial and nuclear genomes and cellular bioenergetic fitness, which have been acquired from well-controlled studies in conplastic animal models. These elucidate, more mechanistically, how single-nucleotide variants can influence cellular metabolism and physiology. Overall, it seems that certain mitochondrial genome variations negatively affect mitochondrial-nuclear compatibility and are statistically linked with the onset of metabolic diseases, whereas, for others, greater uncertainty exists, and additional research into this exciting field is required.
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Affiliation(s)
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
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15
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Vilne B, Sawant A, Rudaka I. Examining the Association between Mitochondrial Genome Variation and Coronary Artery Disease. Genes (Basel) 2022; 13:genes13030516. [PMID: 35328073 PMCID: PMC8953999 DOI: 10.3390/genes13030516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Large-scale genome-wide association studies have identified hundreds of single-nucleotide variants (SNVs) significantly associated with coronary artery disease (CAD). However, collectively, these explain <20% of the heritability. Hypothesis: Here, we hypothesize that mitochondrial (MT)-SNVs might present one potential source of this “missing heritability”. Methods: We analyzed 265 MT-SNVs in ~500,000 UK Biobank individuals, exploring two different CAD definitions: a more stringent (myocardial infarction and/or revascularization; HARD = 20,405), and a more inclusive (angina and chronic ischemic heart disease; SOFT = 34,782). Results: In HARD cases, the most significant (p < 0.05) associations were for m.295C>T (control region) and m.12612A>G (ND5), found more frequently in cases (OR = 1.05), potentially related to reduced cardiorespiratory fitness in response to exercise, as well as for m.12372G>A (ND5) and m.11467A>G (ND4), present more frequently in controls (OR = 0.97), previously associated with lower ROS production rate. In SOFT cases, four MT-SNVs survived multiple testing corrections (at FDR < 5%), all potentially conferring increased CAD risk. Of those, m.11251A>G (ND4) and m.15452C>A (CYB) have previously shown significant associations with body height. In line with this, we observed that CAD cases were slightly less physically active, and their average body height was ~2.00 cm lower compared to controls; both traits are known to be related to increased CAD risk. Gene-based tests identified CO2 associated with HARD/SOFT CAD, whereas ND3 and CYB associated with SOFT cases (p < 0.05), dysfunction of which has been related to MT oxidative stress, obesity/T2D (CO2), BMI (ND3), and angina/exercise intolerance (CYB). Finally, we observed that macro-haplogroup I was significantly (p < 0.05) more frequent in HARD cases vs. controls (3.35% vs. 3.08%), potentially associated with response to exercise. Conclusions: We found only spurious associations between MT genome variation and HARD/SOFT CAD and conclude that more MT-SNV data in even larger study cohorts may be needed to conclusively determine the role of MT DNA in CAD.
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Affiliation(s)
- Baiba Vilne
- Bioinformatics Lab, Rīga Stradiņš University, LV-1007 Riga, Latvia;
- Correspondence:
| | - Aniket Sawant
- Bioinformatics Lab, Rīga Stradiņš University, LV-1007 Riga, Latvia;
| | - Irina Rudaka
- Scientific Laboratory of Molecular Genetics, Rīga Stradiņš University, LV-1007 Riga, Latvia;
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16
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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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17
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Almeida J, Pérez-Figueroa A, Alves JM, Valecha M, Prado-López S, Alvariño P, Cameselle-Teijeiro JM, Chantada D, Fonseca MM, Posada D. Single-cell mtDNA heteroplasmy in colorectal cancer. Genomics 2022; 114:110315. [PMID: 35181467 DOI: 10.1016/j.ygeno.2022.110315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 11/19/2022]
Abstract
Human mitochondria can be genetically distinct within the same individual, a phenomenon known as heteroplasmy. In cancer, this phenomenon seems exacerbated, and most mitochondrial mutations seem to be heteroplasmic. How this genetic variation is arranged within and among normal and tumor cells is not well understood. To address this question, here we sequenced single-cell mitochondrial genomes from multiple normal and tumoral locations in four colorectal cancer patients. Our results suggest that single cells, both normal and tumoral, can carry various mitochondrial haplotypes. Remarkably, this intra-cell heteroplasmy can arise before tumor development and be maintained afterward in specific tumoral cell subpopulations. At least in the colorectal patients studied here, the somatic mutations in the single-cells do not seem to have a prominent role in tumorigenesis.
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Affiliation(s)
- João Almeida
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - Andrés Pérez-Figueroa
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal; CINBIO, Universidade de Vigo, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - João M Alves
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Monica Valecha
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Sonia Prado-López
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Pilar Alvariño
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - José Manuel Cameselle-Teijeiro
- Department of Pathology, Clinical University Hospital, Galician Healthcare Service (SERGAS), Santiago de Compostela, Spain; Medical Faculty, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Débora Chantada
- Department of Pathology, Hospital Álvaro Cunqueiro, Vigo, Spain
| | - Miguel M Fonseca
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Portugal
| | - David Posada
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain; Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain; Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, 36310 Vigo, Spain.
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18
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Mullin NK, Anfinson KR, Riker MJ, Wieland KL, Tatro NJ, Scheetz TE, Mullins RF, Stone EM, Tucker BA. Sensitive quantification of m.3243A>G mutational proportion in non-retinal tissues and its relationship with visual symptoms. Hum Mol Genet 2021; 31:775-782. [PMID: 34590675 DOI: 10.1093/hmg/ddab289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
The m.3243A>G mutation in the mitochondrial genome commonly causes retinal degeneration in patients with maternally inherited diabetes and deafness (MIDD) and mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS). Like other mitochondrial mutations, m.3243A>G is inherited from the mother with a variable proportion of wild type and mutant mitochondrial genomes in different cells. The mechanism by which the m.3243A>G variant in each tissue relates to the manifestation of disease phenotype is not fully understood. Using a digital PCR assay we found that the % m.3243G in skin derived dermal fibroblasts was positively correlated with that of blood from the same individual. The % m.3243G detected in fibroblast cultures remained constant over multiple passages and was negatively correlated with mtDNA copy number. Although the % m.3243G present in blood was not correlated with severity of vision loss, as quantified by Goldmann visual field, a significant negative correlation between % m.3243G and the age of onset of visual symptoms was detected. Together, these results indicate that precise measurement of % m.3243G in clinically accessible tissues such as skin and blood may yield information relevant to the management of retinal m.3243A>G associated disease.
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Affiliation(s)
- Nathaniel K Mullin
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Kristin R Anfinson
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Megan J Riker
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Kelsey L Wieland
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Nicole J Tatro
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Todd E Scheetz
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Robert F Mullins
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Edwin M Stone
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
| | - Budd A Tucker
- University of Iowa Institute for Vision Research, Iowa City, IA, 52242, United States
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19
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Oxidative Stress, Mitochondrial Dysfunction, and Neuroprotection of Polyphenols with Respect to Resveratrol in Parkinson's Disease. Biomedicines 2021; 9:biomedicines9080918. [PMID: 34440122 PMCID: PMC8389563 DOI: 10.3390/biomedicines9080918] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/24/2021] [Accepted: 07/25/2021] [Indexed: 02/06/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disease and is characterized by dopaminergic neuronal loss. The exact pathogenesis of PD is complex and not yet completely understood, but research has established the critical role mitochondrial dysfunction plays in the development of PD. As the main producer of cytosolic reactive oxygen species (ROS), mitochondria are particularly susceptible to oxidative stress once an imbalance between ROS generation and the organelle’s antioxidative system occurs. An overabundance of ROS in the mitochondria can lead to mitochondrial dysfunction and further vicious cycles. Once enough damage accumulates, the cell may undergo mitochondria-dependent apoptosis or necrosis, resulting in the neuronal loss of PD. Polyphenols are a group of natural compounds that have been shown to offer protection against various diseases, including PD. Among these, the plant-derived polyphenol, resveratrol, exhibits neuroprotective effects through its antioxidative capabilities and provides mitochondria protection. Resveratrol also modulates crucial genes involved in antioxidative enzymes regulation, mitochondrial dynamics, and cellular survival. Additionally, resveratrol offers neuroprotective effects by upregulating mitophagy through multiple pathways, including SIRT-1 and AMPK/ERK pathways. This compound may provide potential neuroprotective effects, and more clinical research is needed to establish the efficacy of resveratrol in clinical settings.
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20
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Salekeen R, Diaconeasa AG, Billah MM, Islam KMD. Energy Metabolism Focused Analysis of Sexual Dimorphism in Biological Aging and Hypothesized Sex-specificity in Sirtuin Dependency. Mitochondrion 2021; 60:85-100. [PMID: 34332101 DOI: 10.1016/j.mito.2021.07.007] [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: 02/03/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 01/09/2023]
Abstract
The process of biological aging or senescence refers to the gradual loss of homeostasis and subsequent loss of function - leading to higher chances of mortality. Many mechanisms and driving forces have been suggested to facilitate the evolution of a molecular circuit acting as a trade-off between survival and proliferation, resulting in senescence. A major observation on biological aging and longevity in humans and model organisms is the prevalence of significant sexual divergence in the onset, mechanisms and effects of aging associated processes. In the current account, we describe possible mechanisms by which aging, sex and reproduction are evolutionarily intertwined in order to maintain systemic energy homeostasis. We also interrogate existing literature on the sexual dimorphism of genetic, cellular, metabolic, endocrine and epigenetic processes driving cellular and systemic aging. Subsequently, based on available evidence, we propose a hypothetic model of sex-limited decoupling of female longevity from sirtuins, a major family of regulator proteins of the survival-proliferation trade-off. We also provide necessary considerations to be made in order to test the hypothesis and explore the physiological and therapeutic implications of this decoupling event in male and female longevity after reaching reproductive maturity. HYPOTHESIS STATEMENT: Sirtuins provide survival benefits in a sex-nonspecific manner but the dependency on sirtuins in driving metabolic networks after reaching reproductive maturity is evolutionarily decoupled from female longevity.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
| | - Amalia Gabriela Diaconeasa
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania.
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
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21
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Mitochondrial Heteroplasmy Shifting as a Potential Biomarker of Cancer Progression. Int J Mol Sci 2021; 22:ijms22147369. [PMID: 34298989 PMCID: PMC8304746 DOI: 10.3390/ijms22147369] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer is a serious health problem with a high mortality rate worldwide. Given the relevance of mitochondria in numerous physiological and pathological mechanisms, such as adenosine triphosphate (ATP) synthesis, apoptosis, metabolism, cancer progression and drug resistance, mitochondrial genome (mtDNA) analysis has become of great interest in the study of human diseases, including cancer. To date, a high number of variants and mutations have been identified in different types of tumors, which coexist with normal alleles, a phenomenon named heteroplasmy. This mechanism is considered an intermediate state between the fixation or elimination of the acquired mutations. It is suggested that mutations, which confer adaptive advantages to tumor growth and invasion, are enriched in malignant cells. Notably, many recent studies have reported a heteroplasmy-shifting phenomenon as a potential shaper in tumor progression and treatment response, and we suggest that each cancer type also has a unique mitochondrial heteroplasmy-shifting profile. So far, a plethora of data evidencing correlations among heteroplasmy and cancer-related phenotypes are available, but still, not authentic demonstrations, and whether the heteroplasmy or the variation in mtDNA copy number (mtCNV) in cancer are cause or consequence remained unknown. Further studies are needed to support these findings and decipher their clinical implications and impact in the field of drug discovery aimed at treating human cancer.
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22
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Mitochondrial DNA Heteroplasmy as an Informational Reservoir Dynamically Linked to Metabolic and Immunological Processes Associated with COVID-19 Neurological Disorders. Cell Mol Neurobiol 2021; 42:99-107. [PMID: 34117968 PMCID: PMC8196276 DOI: 10.1007/s10571-021-01117-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022]
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy is the dynamically determined co-expression of wild type (WT) inherited polymorphisms and collective time-dependent somatic mutations within individual mtDNA genomes. The temporal expression and distribution of cell-specific and tissue-specific mtDNA heteroplasmy in healthy individuals may be functionally associated with intracellular mitochondrial signaling pathways and nuclear DNA gene expression. The maintenance of endogenously regulated tissue-specific copy numbers of heteroplasmic mtDNA may represent a sensitive biomarker of homeostasis of mitochondrial dynamics, metabolic integrity, and immune competence. Myeloid cells, monocytes, macrophages, and antigen-presenting dendritic cells undergo programmed changes in mitochondrial metabolism according to innate and adaptive immunological processes. In the central nervous system (CNS), the polarization of activated microglial cells is dependent on strategically programmed changes in mitochondrial function. Therefore, variations in heteroplasmic mtDNA copy numbers may have functional consequences in metabolically competent mitochondria in innate and adaptive immune processes involving the CNS. Recently, altered mitochondrial function has been demonstrated in the progression of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Accordingly, our review is organized to present convergent lines of empirical evidence that potentially link expression of mtDNA heteroplasmy by functionally interactive CNS cell types to the extent and severity of acute and chronic post-COVID-19 neurological disorders.
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23
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Yan YH, Chen SX, Cheng LY, Rodriguez AY, Tang R, Cabrera K, Zhang DY. Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing. Sci Rep 2021; 11:11640. [PMID: 34079006 PMCID: PMC8172533 DOI: 10.1038/s41598-021-91142-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
Whole exome sequencing (WES) is used to identify mutations in a patient's tumor DNA that are predictive of tumor behavior, including the likelihood of response or resistance to cancer therapy. WES has a mutation limit of detection (LoD) at variant allele frequencies (VAF) of 5%. Putative mutations called at ≤ 5% VAF are frequently due to sequencing errors, therefore reporting these subclonal mutations incurs risk of significant false positives. Here we performed ~ 1000 × WES on fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissue biopsy samples from a non-small cell lung cancer patient, and identified 226 putative mutations at between 0.5 and 5% VAF. Each variant was then tested using NuProbe NGSure, to confirm the original WES calls. NGSure utilizes Blocker Displacement Amplification to first enrich the allelic fraction of the mutation and then uses Sanger sequencing to determine mutation identity. Results showed that 52% of the 226 (117) putative variants were disconfirmed, among which 2% (5) putative variants were found to be misidentified in WES. In the 66 cancer-related variants, the disconfirmed rate was 82% (54/66). This data demonstrates Blocker Displacement Amplification allelic enrichment coupled with Sanger sequencing can be used to confirm putative mutations ≤ 5% VAF. By implementing this method, next-generation sequencing can reliably report low-level variants at a high sensitivity, without the cost of high sequencing depth.
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Affiliation(s)
| | - Sherry X Chen
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | - Lauren Y Cheng
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA
| | | | - Rui Tang
- NuProbe USA, Inc., Houston, TX, USA
| | | | - David Yu Zhang
- Department of Bioengineering, Rice University, 6500 Main St, Houston, TX, 77030, USA.
- Systems, Synthetic, and Physical Biology, Rice University, 6500 Main St, Houston, TX, 77030, USA.
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24
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Zhunina OA, Yabbarov NG, Grechko AV, Starodubova AV, Ivanova E, Nikiforov NG, Orekhov AN. The Role of Mitochondrial Dysfunction in Vascular Disease, Tumorigenesis, and Diabetes. Front Mol Biosci 2021; 8:671908. [PMID: 34026846 PMCID: PMC8138126 DOI: 10.3389/fmolb.2021.671908] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/14/2021] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial dysfunction is known to be associated with a wide range of human pathologies, such as cancer, metabolic, and cardiovascular diseases. One of the possible ways of mitochondrial involvement in the cellular damage is excessive production of reactive oxygen and nitrogen species (ROS and RNS) that cannot be effectively neutralized by existing antioxidant systems. In mitochondria, ROS and RNS can contribute to protein and mitochondrial DNA (mtDNA) damage causing failure of enzymatic chains and mutations that can impair mitochondrial function. These processes further lead to abnormal cell signaling, premature cell senescence, initiation of inflammation, and apoptosis. Recent studies have identified numerous mtDNA mutations associated with different human pathologies. Some of them result in imbalanced oxidative phosphorylation, while others affect mitochondrial protein synthesis. In this review, we discuss the role of mtDNA mutations in cancer, diabetes, cardiovascular diseases, and atherosclerosis. We provide a list of currently described mtDNA mutations associated with each pathology and discuss the possible future perspective of the research.
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Affiliation(s)
- Olga A. Zhunina
- Chemical Biology Department, Russian Research Center for Molecular Diagnostics and Therapy, Moscow, Russia
| | - Nikita G. Yabbarov
- Chemical Biology Department, Russian Research Center for Molecular Diagnostics and Therapy, Moscow, Russia
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | | | - Ekaterina Ivanova
- Department of Basic Research, Skolkovo Innovative Center, Institute for Atherosclerosis Research, Moscow, Russia
| | - Nikita G. Nikiforov
- National Medical Research Center of Cardiology, Institute of Experimental Cardiology, Moscow, Russia
- Institute of Gene Biology, Moscow, Russia
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Institute of Human Morphology, Moscow, Russia
| | - Alexander N. Orekhov
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Institute of Human Morphology, Moscow, Russia
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Moscow, Russia
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25
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Li Q, Zhao C. A Review of the Current Status of Clinical Management of COVID-19 in the Elderly. Med Sci Monit 2021; 27:e930278. [PMID: 33833211 PMCID: PMC8043417 DOI: 10.12659/msm.930278] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 01/28/2021] [Indexed: 12/15/2022] Open
Abstract
The high infectivity and severity of SARS-CoV-2 infection (COVID-19), and our limited understanding of the biology of the novel coronavirus, as well as the lack of an effective treatment for COVID-19, have created a global pandemic. Those most likely to become seriously ill with COVID-19 are adults, especially the elderly and those who are already weak or sick. At present, a specific drug for treatment of COVID-19 has not been developed. This, combined with the typical coexistence of a variety of chronic diseases in elderly patients, makes treatment challenging at present. In addition, for elderly patients, COVID-19 isolation measures during the epidemic can easily lead to psychological problems. Thus, how to manage elderly patients has become a focus of social attention in the current circumstances. This article reviews the effects of COVID-19 and makes management suggestions for elderly patients during this epidemic period. In addition to the elderly, critically ill people are also highly susceptible to this novel coronavirus. For elderly COVID-19 patients, antiviral therapy, immune regulation, and even auxiliary respiratory therapy can be given after a comprehensive evaluation of the disease. With the approval and use of COVID-19 vaccines, it is reasonable to expect that we can conquer SARS-CoV-2.
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Affiliation(s)
- Qiaoyun Li
- Graduate School, Qinghai University, Xining, Qinghai, P.R. China
| | - Chengyu Zhao
- Department of Geriatrics, Affiliated Hospital of Qinghai University, Xining, Qinghai, P.R. China
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26
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Mitochondrial Inheritance in Phytopathogenic Fungi-Everything Is Known, or Is It? Int J Mol Sci 2020; 21:ijms21113883. [PMID: 32485941 PMCID: PMC7312866 DOI: 10.3390/ijms21113883] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022] Open
Abstract
Mitochondria are important organelles in eukaryotes that provide energy for cellular processes. Their function is highly conserved and depends on the expression of nuclear encoded genes and genes encoded in the organellar genome. Mitochondrial DNA replication is independent of the replication control of nuclear DNA and as such, mitochondria may behave as selfish elements, so they need to be controlled, maintained and reliably inherited to progeny. Phytopathogenic fungi meet with special environmental challenges within the plant host that might depend on and influence mitochondrial functions and services. We find that this topic is basically unexplored in the literature, so this review largely depends on work published in other systems. In trying to answer elemental questions on mitochondrial functioning, we aim to introduce the aspect of mitochondrial functions and services to the study of plant-microbe-interactions and stimulate phytopathologists to consider research on this important organelle in their future projects.
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Diroma MA, Varvara AS, Attimonelli M, Pesole G, Picardi E. Investigating Human Mitochondrial Genomes in Single Cells. Genes (Basel) 2020; 11:genes11050534. [PMID: 32403285 PMCID: PMC7290567 DOI: 10.3390/genes11050534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondria host multiple copies of their own small circular genome that has been extensively studied to trace the evolution of the modern eukaryotic cell and discover important mutations linked to inherited diseases. Whole genome and exome sequencing have enabled the study of mtDNA in a large number of samples and experimental conditions at single nucleotide resolution, allowing the deciphering of the relationship between inherited mutations and phenotypes and the identification of acquired mtDNA mutations in classical mitochondrial diseases as well as in chronic disorders, ageing and cancer. By applying an ad hoc computational pipeline based on our MToolBox software, we reconstructed mtDNA genomes in single cells using whole genome and exome sequencing data obtained by different amplification methodologies (eWGA, DOP-PCR, MALBAC, MDA) as well as data from single cell Assay for Transposase Accessible Chromatin with high-throughput sequencing (scATAC-seq) in which mtDNA sequences are expected as a byproduct of the technology. We show that assembled mtDNAs, with the exception of those reconstructed by MALBAC and DOP-PCR methods, are quite uniform and suitable for genomic investigations, enabling the study of various biological processes related to cellular heterogeneity such as tumor evolution, neural somatic mosaicism and embryonic development.
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Affiliation(s)
- Maria Angela Diroma
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
| | - Angelo Sante Varvara
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
| | - Ernesto Picardi
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council, Via Giovanni Amendola 118, 70126 Bari, Italy; (M.A.D.); (G.P.)
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari “A. Moro”, Via Orabona 4, 70125 Bari, Italy; (A.S.V.); (M.A.)
- Correspondence: ; Tel.: +39-0805442179
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28
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Kowluru RA, Mohammad G. Epigenetics and Mitochondrial Stability in the Metabolic Memory Phenomenon Associated with Continued Progression of Diabetic Retinopathy. Sci Rep 2020; 10:6655. [PMID: 32313015 PMCID: PMC7171070 DOI: 10.1038/s41598-020-63527-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Abstract
Retinopathy continues to progress even when diabetic patients try to control their blood sugar, but the molecular mechanism of this 'metabolic memory' phenomenon remains elusive. Retinal mitochondria remain damaged and vicious cycle of free radicals continues to self-propagate. DNA methylation suppresses gene expression, and diabetes activates DNA methylation machinery. Our aim was to investigate the role of DNA methylation in continued compromised mitochondrial dynamics and genomic stability in diabetic retinopathy. Using retinal endothelial cells, incubated in 20 mM glucose for four days, followed by 5 mM glucose for four days, and retinal microvessels from streptozotocin-induced diabetic rats in poor glycemia for four months, followed by normal glycemia for four additional months, DNA methylation of mitochondrial fusion and mismatch repair proteins, Mfn2 and Mlh1 respectively, was determined. Retinopathy was detected in trypsin-digested microvasculature. Re-institution of good glycemia had no beneficial effect on hypermethylation of Mfn2 and Mlh1 and retinal function (electroretinogram), and the retinopathy continued to progress. However, intervention of good glycemia directly with DNA methylation inhibitors (Azacytidine or Dnmt1-siRNA), prevented Mfn2 and Mlh1 hypermethylation, and ameliorated retinal dysfunction and diabetic retinopathy. Thus, direct regulation of DNA methylation can prevent/reverse diabetic retinopathy by maintaining mitochondrial dynamics and DNA stability, and prevent retinal functional damage.
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MESH Headings
- Animals
- Azacitidine/pharmacology
- Cell Line
- DNA (Cytosine-5-)-Methyltransferase 1/antagonists & inhibitors
- DNA (Cytosine-5-)-Methyltransferase 1/genetics
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA Methylation
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Experimental/therapy
- Diabetic Retinopathy/chemically induced
- Diabetic Retinopathy/genetics
- Diabetic Retinopathy/pathology
- Diabetic Retinopathy/therapy
- Disease Progression
- Electroretinography
- Endothelial Cells/drug effects
- Endothelial Cells/metabolism
- Endothelial Cells/pathology
- Epigenesis, Genetic
- GTP Phosphohydrolases/genetics
- GTP Phosphohydrolases/metabolism
- Glucose/adverse effects
- Humans
- Hyperglycemia/chemically induced
- Hyperglycemia/genetics
- Hyperglycemia/pathology
- Hyperglycemia/therapy
- Male
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Mitochondria/pathology
- MutL Protein Homolog 1/genetics
- MutL Protein Homolog 1/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Rats
- Rats, Wistar
- Retina/drug effects
- Retina/metabolism
- Retina/pathology
- Signal Transduction
- Streptozocin/administration & dosage
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Affiliation(s)
- Renu A Kowluru
- Kresge Eye Institute, Wayne State University, Detroit, MI, USA.
| | - Ghulam Mohammad
- Kresge Eye Institute, Wayne State University, Detroit, MI, USA
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29
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Yan C, Duanmu X, Zeng L, Liu B, Song Z. Mitochondrial DNA: Distribution, Mutations, and Elimination. Cells 2019; 8:E379. [PMID: 31027297 PMCID: PMC6523345 DOI: 10.3390/cells8040379] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 12/21/2022] Open
Abstract
Mitochondrion harbors its own DNA (mtDNA), which encodes many critical proteins for the assembly and activity of mitochondrial respiratory complexes. mtDNA is packed by many proteins to form a nucleoid that uniformly distributes within the mitochondrial matrix, which is essential for mitochondrial functions. Defects or mutations of mtDNA result in a range of diseases. Damaged mtDNA could be eliminated by mitophagy, and all paternal mtDNA are degraded by endonuclease G or mitophagy during fertilization. In this review, we describe the role and mechanism of mtDNA distribution and elimination. In particular, we focus on the regulation of paternal mtDNA elimination in the process of fertilization.
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Affiliation(s)
- Chaojun Yan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiaoying Duanmu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Ling Zeng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Bing Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhiyin Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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30
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Li L, Xing R, Cui J, Li W, Lu Y. Investigation of frequent somatic mutations of MTND5 gene in gastric cancer cell lines and tissues. MITOCHONDRIAL DNA PART B-RESOURCES 2018; 3:1002-1008. [PMID: 33474396 PMCID: PMC7800514 DOI: 10.1080/23802359.2018.1501287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present study investigated the single nucleotide variants (SNVs) in mitochondrial DNA (mtDNA) of 13 paired gastric cancer tissue samples and seven gastric cancer cell lines using direct sequencing analysis of the MTND5 region. Results showed that nuclear mitochondrial pseudogenes (NUMTs) and mitochondrial copy number affected the detection of the SNV frequency in gastric cancer tissue and cell line samples using high-throughput sequencing technique. The heteroplasmic point mutation C12474T and G12835A happened in AGS and BGC823 cell lines, respectively. A total of seven SNVs were found in three paired gastric cancer tissue samples, including five heteroplasmic point mutations (A12406G, C12705T, T12882C, G12501A, and A12584G) and two homoplasmic point mutations (G12561A and C13590T). Gastric cancer tissue sample 16 exhibited the highest SNVs frequency with four SNVs (np 12406, np 12705, np 12882, and np 12501), whereas no SNVs or SNPs were detected in the tissue sample 4. SNP 12705 turned out to be an SNV in gastric cancer tissue sample 16. SNV 12338 detected by exome sequencing approach appeared to be an SNP in this study.
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Affiliation(s)
- Lian Li
- Department of Microbiology, Basic Medical College of Inner Mongolia Medical University, Hohhot, Inner Mongolia, China
| | - Rui Xing
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiantao Cui
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenmei Li
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Youyong Lu
- Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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31
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Jiménez-Morales S, Pérez-Amado CJ, Langley E, Hidalgo-Miranda A. Overview of mitochondrial germline variants and mutations in human disease: Focus on breast cancer (Review). Int J Oncol 2018; 53:923-936. [PMID: 30015870 DOI: 10.3892/ijo.2018.4468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
High lactate production in cells during growth under oxygen-rich conditions (aerobic glycolysis) is a hallmark of tumor cells, indicating the role of mitochondrial function in tumorigenesis. In fact, enhanced mitochondrial biogenesis and impaired quality control are frequently observed in cancer cells. Mitochondrial DNA (mtDNA) encodes 13 subunits of oxidative phosphorylation (OXPHOS), is present in thousands of copies per cell, and has a very high mutation rate. Mutations in mtDNA and nuclear DNA (nDNA) genes encoding proteins that are important players in mitochondrial biogenesis and function are involved in oncogenic processes. A wide range of germline mtDNA polymorphisms, as well as tumor mtDNA somatic mutations have been identified in diverse cancer types. Approximately 72% of supposed tumor-specific somatic mtDNA mutations reported, have also been found as polymorphisms in the general population. The ATPase 6 and NADH dehydrogenase subunit genes of mtDNA are the most commonly mutated genes in breast cancer (BC). Furthermore, nuclear genes playing a role in mitochondrial biogenesis and function, such as peroxisome proliferators-activated receptor gamma coactivator-1 (PGC-1), fumarate hydratase (FH) and succinate dehydrogenase (SDH) are frequently mutated in cancer. In this review, we provide an overview of the mitochondrial germline variants and mutations in cancer, with particular focus on those found in BC.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratory of Cancer Genomics, National Institute of Genomic Medicine, 14610 Mexico City, Mexico
| | - Carlos J Pérez-Amado
- Biochemistry Sciences Program, National Autonomous University of Mexico, 04510 Mexico City, Mexico
| | - Elizabeth Langley
- Department of Basic Research, National Cancer Institute, 14080 Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratory of Cancer Genomics, National Institute of Genomic Medicine, 14610 Mexico City, Mexico
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32
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Araujo LF, Terra AT, Sares CTG, Sobreira CFR, Faria EF, Machado RD, Rodrigues AA, Muglia VF, Silva WA, Reis RB. Mitochondrial genome analysis in penile carcinoma. Mol Biol Rep 2018; 45:591-600. [DOI: 10.1007/s11033-018-4197-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/23/2018] [Indexed: 01/01/2023]
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33
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Stefano GB, Pilonis N, Ptacek R, Raboch J, Vnukova M, Kream RM. Gut, Microbiome, and Brain Regulatory Axis: Relevance to Neurodegenerative and Psychiatric Disorders. Cell Mol Neurobiol 2018; 38:1197-1206. [PMID: 29802603 PMCID: PMC6061125 DOI: 10.1007/s10571-018-0589-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/07/2018] [Indexed: 12/23/2022]
Abstract
It has become apparent that the molecular and biochemical integrity of interactive families, genera, and species of human gut microflora is critically linked to maintaining complex metabolic and behavioral processes mediated by peripheral organ systems and central nervous system neuronal groupings. Relatively recent studies have established intrinsic ratios of enterotypes contained within the human microbiome across demographic subpopulations and have empirically linked significant alterations in the expression of bacterial enterotypes with the initiation and persistence of several major metabolic and psychiatric disorders. Accordingly, the goal of our review is to highlight potential thematic/functional linkages of pathophysiological alterations in gut microbiota and bidirectional gut-brain signaling pathways with special emphasis on the potential roles of gut dysbiosis on the pathophysiology of psychiatric illnesses. We provide critical discussion of putative thematic linkages of Parkinson's disease (PD) data sets to similar pathophysiological events as potential causative factors in the development and persistence of diverse psychiatric illnesses. Finally, we include a concise review of preclinical paradigms that involve immunologically-induced GI deficits and dysbiosis of maternal microflora that are functionally linked to impaired neurodevelopmental processes leading to affective behavioral syndromes in the offspring.
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Affiliation(s)
- G B Stefano
- Department of Psychiatry, First Faculty of Medicine Charles University in Prague and General University Hospital in Prague, Center for Cognitive and Molecular Neuroscience, Ke Karlovu 11, 120 00, Prague 2, Czech Republic.
| | - N Pilonis
- Warsaw Medical University, Public Central Teaching Hospital, Warsaw, Poland
| | - R Ptacek
- Department of Psychiatry, First Faculty of Medicine Charles University in Prague and General University Hospital in Prague, Center for Cognitive and Molecular Neuroscience, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
| | - J Raboch
- Department of Psychiatry, First Faculty of Medicine Charles University in Prague and General University Hospital in Prague, Center for Cognitive and Molecular Neuroscience, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
| | - M Vnukova
- Department of Psychiatry, First Faculty of Medicine Charles University in Prague and General University Hospital in Prague, Center for Cognitive and Molecular Neuroscience, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
| | - R M Kream
- Department of Psychiatry, First Faculty of Medicine Charles University in Prague and General University Hospital in Prague, Center for Cognitive and Molecular Neuroscience, Ke Karlovu 11, 120 00, Prague 2, Czech Republic
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34
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Liu C, Fetterman JL, Liu P, Luo Y, Larson MG, Vasan RS, Zhu J, Levy D. Deep sequencing of the mitochondrial genome reveals common heteroplasmic sites in NADH dehydrogenase genes. Hum Genet 2018; 137:203-213. [PMID: 29423652 DOI: 10.1007/s00439-018-1873-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/30/2018] [Indexed: 12/17/2022]
Abstract
Increasing evidence implicates mitochondrial dysfunction in aging and age-related conditions. But little is known about the molecular basis for this connection. A possible cause may be mutations in the mitochondrial DNA (mtDNA), which are often heteroplasmic-the joint presence of different alleles at a single locus in the same individual. However, the involvement of mtDNA heteroplasmy in aging and age-related conditions has not been investigated thoroughly. We deep-sequenced the complete mtDNA genomes of 356 Framingham Heart Study participants (52% women, mean age 43, mean coverage 4570-fold), identified 2880 unique mutations and comprehensively annotated them by MITOMAP and PolyPhen-2. We discovered 11 heteroplasmic "hot" spots [NADH dehydrogenase (ND) subunit 1, 4, 5 and 6 genes, n = 7; cytochrome c oxidase I (COI), n = 2; 16S rRNA, n = 1; D-loop, n = 1] for which the alternative-to-reference allele ratios significantly increased with advancing age (Bonferroni correction p < 0.001). Four of these heteroplasmic mutations in ND and COI genes were predicted to be deleterious nonsynonymous mutations which may have direct impact on ATP production. We confirmed previous findings that healthy individuals carry many low-frequency heteroplasmy mutations with potentially deleterious effects. We hypothesize that the effect of a single deleterious heteroplasmy may be minimal due to a low mutant-to-wildtype allele ratio, whereas the aggregate effects of many deleterious mutations may cause changes in mitochondrial function and contribute to age-related diseases. The identification of age-related mtDNA mutations is an important step to understand the genetic architecture of age-related diseases and may uncover novel therapeutic targets for such diseases.
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Affiliation(s)
- Chunyu Liu
- Population Sciences Branch, NHLBI/NHI, Bethesda, MD, USA. .,Framingham Heart Study, Framingham, MA, USA. .,Department of Biostatistics, Boston University, Boston, MA, USA.
| | | | - Poching Liu
- DNA Sequencing and Genomics Core, NHLBI/NIH, Bethesda, MD, USA
| | - Yan Luo
- DNA Sequencing and Genomics Core, NHLBI/NIH, Bethesda, MD, USA
| | - Martin G Larson
- Framingham Heart Study, Framingham, MA, USA.,Department of Biostatistics, Boston University, Boston, MA, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA, USA.,School of Medicine, Boston University, Boston, MA, USA
| | - Jun Zhu
- System Biology Center, NHLBI/NHI, Bethesda, MD, USA
| | - Daniel Levy
- Population Sciences Branch, NHLBI/NHI, Bethesda, MD, USA. .,Framingham Heart Study, Framingham, MA, USA.
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35
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Hertweck KL, Dasgupta S. The Landscape of mtDNA Modifications in Cancer: A Tale of Two Cities. Front Oncol 2017; 7:262. [PMID: 29164061 PMCID: PMC5673620 DOI: 10.3389/fonc.2017.00262] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Accepted: 10/18/2017] [Indexed: 12/25/2022] Open
Abstract
Mitochondria from normal and cancerous cells represent a tale of two cities, wherein both execute similar processes but with different cellular and molecular effects. Given the number of reviews currently available which describe the functional implications of mitochondrial mutations in cancer, this article focuses on documenting current knowledge in the abundance and distribution of somatic mitochondrial mutations, followed by elucidation of processes which affect the fate of mutations in cancer cells. The conclusion includes an overview of translational implications for mtDNA mutations, as well as recommendations for future research uniting mitochondrial variants and tumorigenesis.
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Affiliation(s)
- Kate L Hertweck
- Department of Biology, The University of Texas at Tyler, Tyler, TX, United States
| | - Santanu Dasgupta
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
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Stefano GB, Bjenning C, Wang F, Wang N, Kream RM. Mitochondrial Heteroplasmy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 982:577-594. [PMID: 28551808 DOI: 10.1007/978-3-319-55330-6_30] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic polymorphisms, in concert with well-characterized etiology and progression of major pathologies, plays a significant role in aberrant processes afflicting human populations. Mitochondrial heteroplasmy represents a dynamically determined co-expression of inherited polymorphisms and somatic pathology in varying ratios within individual mitochondrial DNA (mtDNA) genomes with repetitive patterns of tissue specificity. The ratios of the MtDNA genomes represent a balance between healthy and pathological cellular outcomes. Mechanistically, cardiomyopathies have profound alterations of normative mitochondrial function. Certain allele imbalances in the nuclear mitochondrial genome are associated with key energy mitochondrial proteins. Mitochondrial heteroplasmy may manifest itself at critical protein expression points, e.g., cytochrome c oxidase (COX). Pathological mtDNA mutations also are associated with the development of congestive heart failure. Interestingly, mitochondrial 'normal vs. abnormal' ratios of various heteroplasmic populations may occur in families. In the translational context of human health and disease, we discuss the need for determining critical foci to probe multiple biological roles of mitochondrial heteroplasmy in cardiomyopathy.
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Affiliation(s)
- George B Stefano
- International Scientific Information, Inc., 150 Broadhollow Rd, Ste 114, Melville, NY, 11747, USA.
| | - Christina Bjenning
- Cardiometabolic Designs LLC, 160 W15th Ave, Suite 303, Sea Cliff, NY, 11579, USA
| | - Fuzhou Wang
- Division of Neuroscience, Bonoi Academy of Science & Education, Chapel Hill, NC, 27510, USA
| | - Nan Wang
- Department of Anesthesiology, Affiliated Hospital of OB/GYN, Nanjing Medical University, Nanjing, 210004, China
| | - Richard M Kream
- International Scientific Information, Inc., 150 Broadhollow Rd, Ste 114, Melville, NY, 11747, USA
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Stefano GB, Ptacek R, Raboch J, Kream RM. Microbiome: A Potential Component in the Origin of Mental Disorders. Med Sci Monit 2017. [PMID: 28636585 PMCID: PMC5489312 DOI: 10.12659/msm.905425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
It is not surprising to find microbiome abnormalities present in psychiatric disorders such as depressive disorders, bipolar disorders, etc. Evolutionary pressure may provide an existential advantage to the host eukaryotic cells in that it survives in an extracellular environment containing non-self cells (e.g., bacteria). This phenomenon is both positive and negative, as with other intercellular processes. In this specific case, the phenomenal amount of information gained from combined bacterial genome could enhance communication between self and non-self cells. This can be coupled to both pathological processes and healthy ones. In this review, we chose to examine potential associated disorders that may be coupled to the microbiome, from the perspective of their bidirectional communication with eukaryotic cells in the gut. Cognition, being the newest neural networking functionality to evolve, consumes a good amount of organismic energy, 30% of which arises from the gut flora. Furthermore, the mammalian gut is highly innervated and has a highly developed immune component, reflecting brain complexity. The brain-gut axis uses similar molecular messengers as the brain, which affects bacterial processes as well. Thus, any modification of normal bacterial processes may manifest itself in altered behavior/cognition, originating from the gut. The origin of some disorders associated with this bidirectional communication may be harnessed to restore normal functioning.
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Affiliation(s)
- George B Stefano
- Department of Psychiatry, Charles University First Faculty of Medicine and General Teaching Hospital, Center for Cognitive Molecular Neuroscience, Prague, Czech Republic
| | - Radek Ptacek
- Department of Psychiatry, Charles University First Faculty of Medicine and General Teaching Hospital, Center for Cognitive Molecular Neuroscience, Prague, Czech Republic
| | - Jiri Raboch
- Department of Psychiatry, Charles University First Faculty of Medicine and General Teaching Hospital, Center for Cognitive Molecular Neuroscience, Prague, Czech Republic
| | - Richard M Kream
- Department of Psychiatry, Charles University First Faculty of Medicine and General Teaching Hospital, Center for Cognitive Molecular Neuroscience, Prague, Czech Republic
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Stefano GB, Kream RM. Aging Reversal and Healthy Longevity is in Reach: Dependence on Mitochondrial DNA Heteroplasmy as a Key Molecular Target. Med Sci Monit 2017; 23:2732-2735. [PMID: 28579605 PMCID: PMC5470867 DOI: 10.12659/msm.902515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Recent trends in biomedical research have highlighted the potential for effecting significant extensions in longevity with enhanced quality of life in aging human populations. Within this context, any proposed method to achieve enhanced life extension must include therapeutic approaches that draw upon essential biochemical and molecular regulatory processes found in relatively simple single cell organisms that are evolutionarily conserved within complex organ systems of higher animals. Current critical thinking has established the primacy of mitochondrial function in maintaining good health throughout plant and animal phyla. The mitochondrion represents an existentially defined endosymbiotic model of complex organelle development driven by evolutionary modification of a permanently enslaved primordial bacterium. Cellular mitochondria are biochemically and morphologically tailored to provide exponentially enhanced ATP-dependent energy production accordingly to tissue- and organ-specific physiological demands. Thus, individual variations in longevity may then be effectively sorted according to age-dependent losses of single-cell metabolic integrity functionally linked to impaired mitochondrial bioenergetics within an aggregate presentation of compromised complex organ systems. Recent empirical studies have focused on the functional role of mitochondrial heteroplasmy in the regulation of normative cellular processes and the initiation and persistence of pathophysiological states. Accordingly, elucidation of the multifaceted functional roles of mitochondrial heteroplasmy in normal aging and enhanced longevity will provide both a compelling genetic basis and potential targets for therapeutic intervention to effect meaningful life extension in human populations.
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Snyder HM, Ahles T, Calderwood S, Carrillo MC, Chen H, Chang CCH, Craft S, De Jager P, Driver JA, Fillit H, Knopman D, Lotze M, Tierney MC, Petanceska S, Saykin A, Seshadri S, Shineman D, Ganguli M. Exploring the nexus of Alzheimer's disease and related dementias with cancer and cancer therapies: A convening of the Alzheimer's Association & Alzheimer's Drug Discovery Foundation. Alzheimers Dement 2017; 13:267-273. [PMID: 27998721 PMCID: PMC5548424 DOI: 10.1016/j.jalz.2016.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 11/16/2016] [Indexed: 12/29/2022]
Abstract
Recent population studies suggest an intriguing inverse relationship between several types of cancer and neurodegenerative diseases, including Alzheimer's disease. Understanding the intersection of the underlying biology for these two distinct families of diseases with one another may offer novel approaches to identify new therapeutic approaches and possible opportunities to repurpose existing drug candidates. The Alzheimer's Association and the Alzheimer's Drug Discovery Foundation convened a one-day workshop to delve into this discussion. Workshop participants outlined research focus areas, potential collaborations, and partnerships for future action.
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Affiliation(s)
- Heather M Snyder
- Division of Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, USA.
| | - Tim Ahles
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stuart Calderwood
- Radiation Oncology, Harvard University Medical School, Boston, MA, USA
| | - Maria C Carrillo
- Division of Medical and Scientific Relations, Alzheimer's Association, Chicago, IL, USA
| | - Honglei Chen
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Chung-Chou H Chang
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Biostatistics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA; Department of Biostatistics, University of Pittsburgh Medical School, Pittsburgh, PA, USA; Clinical and Translational Science, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Suzanne Craft
- Division of Gerontology and Geriatric Medicine, Department of Internal Medicine, Wake Forest University of Medicine, Winston-Salem, NC, USA
| | - Philip De Jager
- Geriatric Research Education and Clinical Center, VA Boston HealthCare System, Boston, MA, USA
| | - Jane A Driver
- Division of Aging, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard University Medical School, Boston, MA, USA
| | - Howard Fillit
- Scientific Affairs, Alzheimer's Drug Discovery Foundation, New York, NY, USA
| | - David Knopman
- Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Michael Lotze
- Departments of Surgery, Immunology and Bioengineering, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Mary C Tierney
- Department of Family and Community Medicine, Sunnybrook Health Science Center, Toronto, Ontario, Canada
| | - Suzana Petanceska
- Division of Neurosciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Saykin
- Department of Radiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sudha Seshadri
- Division of Neurology, Boston University Medical School, Boston, MA, USA
| | - Diana Shineman
- Scientific Affairs, Alzheimer's Drug Discovery Foundation, New York, NY, USA
| | - Mary Ganguli
- Professor of Psychiatry, Neurology, and Epidemiology, University of Pittsburgh School of Medicine and Graduate School of Public Health, Pittsburgh, PA, USA
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Stefano GB, Samuel J, Kream RM. Antibiotics May Trigger Mitochondrial Dysfunction Inducing Psychiatric Disorders. Med Sci Monit 2017; 23:101-106. [PMID: 28063266 PMCID: PMC5240889 DOI: 10.12659/msm.899478] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Clinical usage of several classes of antibiotics is associated with moderate to severe side effects due to the promotion of mitochondrial dysfunction. We contend that this may be due to perturbation of unique evolutionary relationships that link selective biochemical and molecular aspects of mitochondrial biology to conserved enzymatic processes derived from bacterial progenitors. Operationally, stereo-selective conformational matching between mitochondrial respiratory complexes, cytosolic and nuclear signaling complexes appears to support the conservation of a critically important set of chemical messengers required for existential regulation of homeostatic cellular processes. Accordingly, perturbation of normative mitochondrial function by select classes of antibiotics is certainly reflective of the high degree of evolutionary pressure designed to maintain ongoing bidirectional signaling processes between cellular compartments. These issues are of critical importance in evaluating potentially severe side effects of antibiotics on complex behavioral functions mediated by CNS neuronal groups. The CNS is extremely dependent on delivery of molecular oxygen for maintaining a required level of metabolic activity, as reflected by the high concentration of neuronal mitochondria. Thus, it is not surprising to find several distinct behavioral abnormalities conforming to established psychiatric criteria that are associated with antibiotic usage in humans. The manifestation of acute and/or chronic psychiatric conditions following antibiotic usage may provide unique insights into key etiological factors of major psychiatric syndromes that involve rundown of cellular bioenergetics via mitochondrial dysfunction. Thus, a potential window of opportunity exists for development of novel therapeutic agents targeting diminished mitochondrial function as a factor in severe behavioral disorders.
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Affiliation(s)
- George B Stefano
- Department of Research, MitoGenetics Research Institute, Farmingdale, NY, USA
| | - Joshua Samuel
- Department of Research, MitoGenetics Research Institute, Farmingdale, NY, USA
| | - Richard M Kream
- Department of Research, MitoGenetics Research Institute, Farmingdale, NY, USA
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Amer SAM, Al-Harthi HS, Refaat AM, Bakdash A, Kassab AC. Identification of Human Bone Remains by Autosomal STRs and Mitochondrial DNA SNPs. J HARD TISSUE BIOL 2017. [DOI: 10.2485/jhtb.26.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sayed AM Amer
- Biology Department, Faculty of Science, Taif University
| | - Hussam S Al-Harthi
- College of Forensic Sciences, Naif Arab University for Security Sciences
| | - Ahmed M Refaat
- College of Forensic Sciences, Naif Arab University for Security Sciences
| | | | - Ahmed Ch Kassab
- College of Forensic Sciences, Naif Arab University for Security Sciences
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Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations. Comput Struct Biotechnol J 2016; 14:391-403. [PMID: 27830053 PMCID: PMC5094600 DOI: 10.1016/j.csbj.2016.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 01/14/2023] Open
Abstract
Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.
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Stefano GB, Kream RM. Glycolytic Coupling to Mitochondrial Energy Production Ensures Survival in an Oxygen Rich Environment. Med Sci Monit 2016; 22:2571-5. [PMID: 27439008 PMCID: PMC4957629 DOI: 10.12659/msm.899610] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The mitochondrion exhibits biochemical and functional variations that emerged by random chance as an evolutionary survival strategy, which include enhanced energy production driven by anaerobic respiratory mechanisms. In invertebrates, this mitochondrial anaerobic respiration permits survival at a lower energy state suited for this type of environment while yielding more ATP than by glycolysis alone. This ability provides a protective existential advantage in naturally occurring hypoxic environments via diminished free radical generation. In the blue mussel Mytilus edulis and other marine organisms, a functionally active mitochondrial anaerobic respiratory mechanism tailored to hypoxic conditions reflects an evolutionary adaptation/reworking of ancient metabolic pathways. Components of these pathways were also discovered and characterized as metabolic intermediates in plant parasites, specifically crown gall tumors. Mechanistic similarities between anaerobically functioning mitochondria in M. edulis and crown gall tissues and metabolic processes in human tumors are known to occur, demonstrating commonalities in diverse life energy processes. Furthermore, cytoplasmic glycolytic processes are now shown also to exhibit a dynamic capacity for enhanced energy generation by increasing its efficiency in hypoxic environments, making it equally dynamic in meeting its cellular survival goal.
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Affiliation(s)
- George B Stefano
- Department of Research, MitoGenetics Research Institute, Farmingdale, NY, USA
| | - Richard M Kream
- Department of Research, MitoGenetics Research Institute, Farmingdale, NY, USA
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Chimeric mitochondrial peptides from contiguous regular and swinger RNA. Comput Struct Biotechnol J 2016; 14:283-97. [PMID: 27453772 PMCID: PMC4942731 DOI: 10.1016/j.csbj.2016.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist. Chimeric peptides are translated from contiguous regular and swinger RNA They are 200x rarer than mitochondrial swinger peptides Chimeric peptides integrated in regular mitochondrial proteins are downregulated Contiguous regular parts are matched positive controls for swinger parts The last point validates results beyond other statistical tests for robustness
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