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De Luise M, Iommarini L, Marchio L, Tedesco G, Coadă CA, Repaci A, Turchetti D, Tardio ML, Salfi N, Pagotto U, Kurelac I, Porcelli AM, Gasparre G. Pathogenic Mitochondrial DNA Mutation Load Inversely Correlates with Malignant Features in Familial Oncocytic Parathyroid Tumors Associated with Hyperparathyroidism-Jaw Tumor Syndrome. Cells 2021; 10:2920. [PMID: 34831144 PMCID: PMC8616364 DOI: 10.3390/cells10112920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
While somatic disruptive mitochondrial DNA (mtDNA) mutations that severely affect the respiratory chain are counter-selected in most human neoplasms, they are the genetic hallmark of indolent oncocytomas, where they appear to contribute to reduce tumorigenic potential. A correlation between mtDNA mutation type and load, and the clinical outcome of a tumor, corroborated by functional studies, is currently lacking. Recurrent familial oncocytomas are extremely rare entities, and they offer the chance to investigate the determinants of oncocytic transformation and the role of both germline and somatic mtDNA mutations in cancer. We here report the first family with Hyperparathyroidism-Jaw Tumor (HPT-JT) syndrome showing the inherited predisposition of four individuals to develop parathyroid oncocytic tumors. MtDNA sequencing revealed a rare ribosomal RNA mutation in the germline of all HPT-JT affected individuals whose pathogenicity was functionally evaluated via cybridization technique, and which was counter-selected in the most aggressive infiltrating carcinoma, but positively selected in adenomas. In all tumors different somatic mutations accumulated on this genetic background, with an inverse clear-cut correlation between the load of pathogenic mtDNA mutations and the indolent behavior of neoplasms, highlighting the importance of the former both as modifiers of cancer fate and as prognostic markers.
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Affiliation(s)
- Monica De Luise
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Luisa Iommarini
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Lorena Marchio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Greta Tedesco
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Camelia Alexandra Coadă
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Andrea Repaci
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Division of Medical Genetics, IRCSS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Maria Lucia Tardio
- Unit of Pathology, IRCCS S.Orsola University Hospital, 40138 Bologna, Italy;
| | - Nunzio Salfi
- Pathology Unit, IRCCS Giannina Gaslini Children’s Research Hospital, 16147 Genova, Italy;
| | - Uberto Pagotto
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Anna Maria Porcelli
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center of Industrial Research (CIRI) Life Science and Health Technologies, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
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Qu J, Xu Y, Cui Y, Wu S, Wang L, Liu X, Xing Z, Guo X, Wang S, Li R, Sun X, Li X, Wang X, Liu T, Wang X. MODB: a comprehensive mitochondrial genome database for Mollusca. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6369039. [PMID: 34510194 PMCID: PMC8435058 DOI: 10.1093/database/baab056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/11/2021] [Accepted: 08/21/2021] [Indexed: 11/14/2022]
Abstract
Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We also integrated a series of analysis and visualization tools, such as BLAST, MUSCLE, GENEWISE and LASTZ. In particular, a phylogenetic tree was implemented in this database to visualize the evolutionary relationships between species. The original version contains 616 species whose mitochondrial genomes have been sequenced. The database provides comprehensive information and analysis platform for researchers interested in understanding the biological characteristics of mollusks. Database URL: http://modb.ytu.edu.cn/
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Affiliation(s)
- Jiangyong Qu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Yanran Xu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Yutong Cui
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Sen Wu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Lijun Wang
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Xiumei Liu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Zhikai Xing
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Xiaoyu Guo
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Shanshan Wang
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Ruoran Li
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Xiaoyue Sun
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Xiang Li
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Xiyue Wang
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Tao Liu
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
| | - Xumin Wang
- College of Life Sciences, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, Shandong 264005, China
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Abstract
Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.
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Affiliation(s)
- Piotr K Kopinski
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Smart U, Cihlar JC, Budowle B. International Wildlife Trafficking: A perspective on the challenges and potential forensic genetics solutions. Forensic Sci Int Genet 2021; 54:102551. [PMID: 34134047 DOI: 10.1016/j.fsigen.2021.102551] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 12/29/2022]
Abstract
International wildlife trafficking (IWT) is a thriving and pervasive illegal enterprise that adversely affects modern societies. Yet, despite being globally recognized as a threat to biodiversity, national security, economy, and biosecurity, IWT remains largely unabated and is proliferating at an alarming rate. The increase in IWT is generally attributed to a lack of prioritization to curb wildlife crime through legal and scientific infrastructure. This review: (1) lays out the damaging scope and influence of IWT; (2) discusses the potential of DNA marker systems, barcodes, and emerging molecular technologies, such as long-read portable sequencing, to facilitate rapid, in situ identification of species and individuals; and (3) encourages initiatives that promote quality and innovation. Interdisciplinary collaboration promises to be one of the most effective ways forward to surmounting the complex scientific and legal challenges posed by IWT.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA.
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Holt CL, Stephens KM, Walichiewicz P, Fleming KD, Forouzmand E, Wu SF. Human Mitochondrial Control Region and mtGenome: Design and Forensic Validation of NGS Multiplexes, Sequencing and Analytical Software. Genes (Basel) 2021; 12:genes12040599. [PMID: 33921728 PMCID: PMC8073089 DOI: 10.3390/genes12040599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/11/2021] [Accepted: 03/11/2021] [Indexed: 02/07/2023] Open
Abstract
Forensic mitochondrial DNA (mtDNA) analysis conducted using next-generation sequencing (NGS), also known as massively parallel sequencing (MPS), as compared to Sanger-type sequencing brings modern advantages, such as deep coverage per base (herein referred to as read depth per base pair (bp)), simultaneous sequencing of multiple samples (libraries) and increased operational efficiencies. This report describes the design and developmental validation, according to forensic quality assurance standards, of end-to-end workflows for two multiplexes, comprised of ForenSeq mtDNA control region and mtDNA whole-genome kits the MiSeq FGxTM instrument and ForenSeq universal analysis software (UAS) 2.0/2.1. Polymerase chain reaction (PCR) enrichment and a tiled amplicon approach target small, overlapping amplicons (60–150 bp and 60–209 bp for the control region and mtGenome, respectively). The system provides convenient access to data files that can be used outside of the UAS if desired. Studies assessed a range of environmental and situational variables, including but not limited to buccal samples, rootless hairs, dental and skeletal remains, concordance of control region typing between the two multiplexes and as compared to orthogonal data, assorted sensitivity studies, two-person DNA mixtures and PCR-based performance testing. Limitations of the system and implementation considerations are discussed. Data indicated that the two mtDNA multiplexes, MiSeq FGx and ForenSeq software, meet or exceed forensic DNA quality assurance (QA) guidelines with robust, reproducible performance on samples of various quantities and qualities.
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Crysup B, Woerner AE, King JL, Budowle B. Graph Algorithms for Mixture Interpretation. Genes (Basel) 2021; 12:genes12020185. [PMID: 33514030 PMCID: PMC7911948 DOI: 10.3390/genes12020185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/22/2021] [Accepted: 01/26/2021] [Indexed: 12/19/2022] Open
Abstract
The scale of genetic methods are presently being expanded: forensic genetic assays previously were limited to tens of loci, but now technologies allow for a transition to forensic genomic approaches that assess thousands to millions of loci. However, there are subtle distinctions between genetic assays and their genomic counterparts (especially in the context of forensics). For instance, forensic genetic approaches tend to describe a locus as a haplotype, be it a microhaplotype or a short tandem repeat with its accompanying flanking information. In contrast, genomic assays tend to provide not haplotypes but sequence variants or differences, variants which in turn describe how the alleles apparently differ from the reference sequence. By the given construction, mitochondrial genetic assays can be thought of as genomic as they often describe genetic differences in a similar way. The mitochondrial genetics literature makes clear that sequence differences, unlike the haplotypes they encode, are not comparable to each other. Different alignment algorithms and different variant calling conventions may cause the same haplotype to be encoded in multiple ways. This ambiguity can affect evidence and reference profile comparisons as well as how “match” statistics are computed. In this study, a graph algorithm is described (and implemented in the MMDIT (Mitochondrial Mixture Database and Interpretation Tool) R package) that permits the assessment of forensic match statistics on mitochondrial DNA mixtures in a way that is invariant to both the variant calling conventions followed and the alignment parameters considered. The algorithm described, given a few modest constraints, can be used to compute the “random man not excluded” statistic or the likelihood ratio. The performance of the approach is assessed in in silico mitochondrial DNA mixtures.
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Affiliation(s)
- Benjamin Crysup
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
- Correspondence:
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA; (A.E.W.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Smart U, Cihlar JC, Mandape SN, Muenzler M, King JL, Budowle B, Woerner AE. A Continuous Statistical Phasing Framework for the Analysis of Forensic Mitochondrial DNA Mixtures. Genes (Basel) 2021; 12:128. [PMID: 33498312 PMCID: PMC7909279 DOI: 10.3390/genes12020128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/16/2022] Open
Abstract
Despite the benefits of quantitative data generated by massively parallel sequencing, resolving mitotypes from mixtures occurring in certain ratios remains challenging. In this study, a bioinformatic mixture deconvolution method centered on population-based phasing was developed and validated. The method was first tested on 270 in silico two-person mixtures varying in mixture proportions. An assortment of external reference panels containing information on haplotypic variation (from similar and different haplogroups) was leveraged to assess the effect of panel composition on phasing accuracy. Building on these simulations, mitochondrial genomes from the Human Mitochondrial DataBase were sourced to populate the panels and key parameter values were identified by deconvolving an additional 7290 in silico two-person mixtures. Finally, employing an optimized reference panel and phasing parameters, the approach was validated with in vitro two-person mixtures with differing proportions. Deconvolution was most accurate when the haplotypes in the mixture were similar to haplotypes present in the reference panel and when the mixture ratios were neither highly imbalanced nor subequal (e.g., 4:1). Overall, errors in haplotype estimation were largely bounded by the accuracy of the mixture's genotype results. The proposed framework is the first available approach that automates the reconstruction of complete individual mitotypes from mixtures, even in ratios that have traditionally been considered problematic.
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Affiliation(s)
- Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jennifer Churchill Cihlar
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - Sammed N. Mandape
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Melissa Muenzler
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Jonathan L. King
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
| | - Bruce Budowle
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
| | - August E. Woerner
- Center for Human Identification, University of North Texas Health Science Center, 3500 Camp, Bowie Blvd., Fort Worth, TX 76107, USA; (U.S.); (J.C.C.); (S.N.M.); (M.M.); (J.L.K.); (B.B.)
- Department of Microbiology, Immunology and Genetics, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107, USA
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Tasdogan A, McFadden DG, Mishra P. Mitochondrial DNA Haplotypes as Genetic Modifiers of Cancer. Trends Cancer 2020; 6:1044-1058. [PMID: 32980320 DOI: 10.1016/j.trecan.2020.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/05/2020] [Accepted: 08/18/2020] [Indexed: 02/06/2023]
Abstract
Mitochondria play an essential role in cellular metabolism, generation of reactive oxygen species (ROS), and the initiation of apoptosis. These properties enable mitochondria to be crucial integrators in the pathways of tumorigenesis. An open question is to what extent variation in the mitochondrial genome (mtDNA) contributes to the biological heterogeneity observed in human tumors. In this review, we summarize our current understanding of the role of mtDNA genetics in relation to human cancers.
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Affiliation(s)
- Alpaslan Tasdogan
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David G McFadden
- Department of Internal Medicine, Department of Biochemistry, Simmons Comprehensive Cancer Center, Division of Endocrinology, Program in Molecular Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prashant Mishra
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pediatrics, Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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9
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Woerner AE, Cihlar JC, Smart U, Budowle B. Numt identification and removal with RtN! Bioinformatics 2020; 36:5115-5116. [DOI: 10.1093/bioinformatics/btaa642] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/15/2020] [Accepted: 07/18/2020] [Indexed: 12/30/2022] Open
Abstract
Abstract
Motivation
Assays in mitochondrial genomics rely on accurate read mapping and variant calling. However, there are known and unknown nuclear paralogs that have fundamentally different genetic properties than that of the mitochondrial genome. Such paralogs complicate the interpretation of mitochondrial genome data and confound variant calling.
Results
Remove the Numts! (RtN!) was developed to categorize reads from massively parallel sequencing data not based on the expected properties and sequence identities of paralogous nuclear encoded mitochondrial sequences, but instead using sequence similarity to a large database of publicly available mitochondrial genomes. RtN! removes low-level sequencing noise and mitochondrial paralogs while not impacting variant calling, while competing methods were shown to remove true variants from mitochondrial mixtures.
Availability and implementation
https://github.com/Ahhgust/RtN
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- August E Woerner
- Department of Microbiology, Immunology and Genetics
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
| | - Jennifer Churchill Cihlar
- Department of Microbiology, Immunology and Genetics
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
| | - Utpal Smart
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
| | - Bruce Budowle
- Department of Microbiology, Immunology and Genetics
- Center for Human Identification, University of North Texas Health Science Center (UNTHSC), Fort Worth, TX 76107, USA
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Preste R, Vitale O, Clima R, Gasparre G, Attimonelli M. HmtVar: a new resource for human mitochondrial variations and pathogenicity data. Nucleic Acids Res 2020; 47:D1202-D1210. [PMID: 30371888 PMCID: PMC6323908 DOI: 10.1093/nar/gky1024] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022] Open
Abstract
Interest in human mitochondrial genetic data is constantly increasing among both clinicians and researchers, due to the involvement of mitochondrial DNA (mtDNA) in a number of physiological and pathological processes. Thanks to new sequencing technologies and modern databases, the large amount of information on mtDNA variability may be exploited to gain insights into the relationship between mtDNA variants, phenotypes and diseases. To facilitate this process, we have developed the HmtVar resource, a variant-focused database that allows the exploration of a dataset of over 40 000 human mitochondrial variants. Mitochondrial variation data, initially gathered from the HmtDB platform, are integrated with in-house pathogenicity assessments based on various evaluation criteria and with a set of additional annotations from third-party resources. The result is a comprehensive collection of information of crucial importance for human mitochondrial variation studies and investigation of common and rare diseases in which the mitochondrion may be involved. HmtVar is accessible at https://www.hmtvar.uniba.it and data may be retrieved using either a web interface through the Query page or a state-of-the-art API for programmatic access.
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Affiliation(s)
- Roberto Preste
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70126, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70126, Italy
| | - Rosanna Clima
- Department of Medical and Surgical Sciences - DIMEC, Medical Genetics Unit, University of Bologna, Bologna 40126, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences - DIMEC, Medical Genetics Unit, University of Bologna, Bologna 40126, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70126, Italy
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11
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Cappa R, de Campos C, Maxwell AP, McKnight AJ. "Mitochondrial Toolbox" - A Review of Online Resources to Explore Mitochondrial Genomics. Front Genet 2020; 11:439. [PMID: 32457801 PMCID: PMC7225359 DOI: 10.3389/fgene.2020.00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mitochondria play a significant role in many biological systems. There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics. There is often a large amount of complex data generated (for example via next generation sequencing), which requires optimised bioinformatics tools to efficiently and effectively generate robust outcomes from these large datasets. Twenty-four online resources dedicated to mitochondrial genomics were reviewed. This 'mitochondrial toolbox' summary resource will enable researchers to rapidly identify the resource(s) most suitable for their needs. These resources fulfil a variety of functions, with some being highly specialised. No single tool will provide all users with the resources they require; therefore, the most suitable tool will vary between users depending on the nature of the work they aim to carry out. Genetics resources are well established for phylogeny and DNA sequence changes, but further epigenetic and gene expression resources need to be developed for mitochondrial genomics.
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Affiliation(s)
- Ruaidhri Cappa
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Cassio de Campos
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Amy J McKnight
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
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12
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Starikovskaya E, Shalaurova S, Dryomov S, Nazhmidenova A, Volodko N, Bychkov I, Mazunin I, Sukernik R. Mitochondrial DNA Variation of Leber's Hereditary Optic Neuropathy in Western Siberia. Cells 2019; 8:E1574. [PMID: 31817256 PMCID: PMC6953113 DOI: 10.3390/cells8121574] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 12/24/2022] Open
Abstract
Our data first represent the variety of Leber's hereditary optic neuropathy (LHON) mutations in Western Siberia. LHON is a disorder caused by pathogenic mutations in mitochondrial DNA (mtDNA), inherited maternally and presents mainly in young adults, predominantly males. Clinically, LHON manifests itself as painless central vision loss, resulting in early onset of disability. The epidemiology of LHON has not been fully investigated yet. In this study, we report 44 genetically unrelated families with LHON manifestation. We performed whole mtDNA genome sequencing and provided genealogical and molecular genetic data on mutations and haplogroup background of LHON patients. Known "primary" pathogenic mtDNA mutations (MITOMAP) were found in 32 families: m.11778G>A represents 53.10% (17/32), m.3460G>A-21.90% (7/32), m.14484T>C-18.75% (6/32), and rare m.10663T>C and m.3635G>A represent 6.25% (2/32). We describe potentially pathogenic m.4659G>A in one subject without known pathogenic mutations, and potentially pathogenic m.6261G>A, m.8412T>C, m.8551T>C, m.9444C>T, m.9921G>A, and m.15077G>A in families with known pathogenic mutations confirmed. We suppose these mutations could contribute to the pathogenesis of optic neuropathy development. Our results indicate that haplogroup affiliation and mutational spectrum of the Western Siberian LHON cohort substantially deviate from those of European populations.
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Affiliation(s)
- Elena Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Sofia Shalaurova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Azhar Nazhmidenova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
| | - Natalia Volodko
- Department of Pediatrics, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Igor Bychkov
- Novosibirsk Branch of S.N. Fedorov NMRC “MNTK Eye Microsurgery”, Moscow 127486, Russia
| | - Ilia Mazunin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
| | - Rem Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk 630090, Russia (S.D.); (A.N.); (R.S.)
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13
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Weerts MJA, Timmermans EC, Vossen RHAM, van Strijp D, Van den Hout-van Vroonhoven MCGN, van IJcken WFJ, van der Zaag PJ, Anvar SY, Sleijfer S, Martens JWM. Sensitive detection of mitochondrial DNA variants for analysis of mitochondrial DNA-enriched extracts from frozen tumor tissue. Sci Rep 2018; 8:2261. [PMID: 29396409 PMCID: PMC5797170 DOI: 10.1038/s41598-018-20623-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/22/2018] [Indexed: 11/25/2022] Open
Abstract
Large variation exists in mitochondrial DNA (mtDNA) not only between but also within individuals. Also in human cancer, tumor-specific mtDNA variation exists. In this work, we describe the comparison of four methods to extract mtDNA as pure as possible from frozen tumor tissue. Also, three state-of-the-art methods for sensitive detection of mtDNA variants were evaluated. The main aim was to develop a procedure to detect low-frequent single-nucleotide mtDNA-specific variants in frozen tumor tissue. We show that of the methods evaluated, DNA extracted from cytosol fractions following exonuclease treatment results in highest mtDNA yield and purity from frozen tumor tissue (270-fold mtDNA enrichment). Next, we demonstrate the sensitivity of detection of low-frequent single-nucleotide mtDNA variants (≤1% allele frequency) in breast cancer cell lines MDA-MB-231 and MCF-7 by single-molecule real-time (SMRT) sequencing, UltraSEEK chemistry based mass spectrometry, and digital PCR. We also show de novo detection and allelic phasing of variants by SMRT sequencing. We conclude that our sensitive procedure to detect low-frequent single-nucleotide mtDNA variants from frozen tumor tissue is based on extraction of DNA from cytosol fractions followed by exonuclease treatment to obtain high mtDNA purity, and subsequent SMRT sequencing for (de novo) detection and allelic phasing of variants.
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Affiliation(s)
- M J A Weerts
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
| | - E C Timmermans
- Philips Research Laboratories, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands
| | - R H A M Vossen
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - D van Strijp
- Philips Research Laboratories, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands
| | | | | | - P J van der Zaag
- Philips Research Laboratories, High Tech Campus 11, 5656 AE, Eindhoven, The Netherlands
| | - S Y Anvar
- Leiden Genome Technology Center (LGTC), Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Clinical Pharmacy and Toxicology, Leiden University Medical Center, Leiden, The Netherlands
| | - S Sleijfer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - J W M Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
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14
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Järviaho T, Hurme-Niiranen A, Soini HK, Niinimäki R, Möttönen M, Savolainen ER, Hinttala R, Harila-Saari A, Uusimaa J. Novel non-neutral mitochondrial DNA mutations found in childhood acute lymphoblastic leukemia. Clin Genet 2017; 93:275-285. [PMID: 28708239 DOI: 10.1111/cge.13100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/29/2017] [Accepted: 07/09/2017] [Indexed: 12/18/2022]
Abstract
Mitochondria produce adenosine triphosphate (ATP) for energy requirements via the mitochondrial oxidative phosphorylation (OXPHOS) system. One of the hallmarks of cancer is the energy shift toward glycolysis. Low OXPHOS activity and increased glycolysis are associated with aggressive types of cancer. Mitochondria have their own genome (mitochondrial DNA [mtDNA]) encoding for 13 essential subunits of the OXPHOS enzyme complexes. We studied mtDNA in childhood acute lymphoblastic leukemia (ALL) to detect potential pathogenic mutations in OXPHOS complexes. The whole mtDNA from blood and bone marrow samples at diagnosis and follow-up from 36 ALL patients were analyzed. Novel or previously described pathogenic mtDNA mutations were identified in 8 out of 36 patients. Six out of these 8 patients had died from ALL. Five out of 36 patients had an identified poor prognosis genetic marker, and 4 of these patients had mtDNA mutations. Missense or nonsense mtDNA mutations were detected in the genes encoding subunits of OXPHOS complexes, as follows: MT-ND1, MT-ND2, MT-ND4L and MT-ND6 of complex I; MT-CO3 of complex IV; and MT-ATP6 and MT-ATP8 of complex V. We discovered mtDNA mutations in childhood ALL supporting the hypothesis that non-neutral variants in mtDNA affecting the OXPHOS function may be related to leukemic clones.
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Affiliation(s)
- T Järviaho
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - A Hurme-Niiranen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - H K Soini
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - R Niinimäki
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - M Möttönen
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - E-R Savolainen
- Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,NordLab Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland.,Department of Clinical Chemistry, University of Oulu, Oulu, Finland
| | - R Hinttala
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland
| | - A Harila-Saari
- Department of Women's and Children's Health, Karolinska University Hospital Solna, Stockholm, Sweden
| | - J Uusimaa
- PEDEGO Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
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15
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Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity. Sci Rep 2017; 7:6193. [PMID: 28733587 PMCID: PMC5522469 DOI: 10.1038/s41598-017-05673-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 06/01/2017] [Indexed: 01/08/2023] Open
Abstract
In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000–5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the ‘local’ Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the ‘immigrant’ haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.
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16
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Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P. Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome. Handb Exp Pharmacol 2017; 240:377-401. [PMID: 27995389 DOI: 10.1007/164_2016_93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the complex involvement of mitochondrial biology in disease development often requires the acquisition, analysis, and integration of large-scale molecular and phenotypic data. An increasing number of bioinformatics tools are currently employed to aid in mitochondrial investigations, most notably in predicting or corroborating the spatial and temporal dynamics of mitochondrial molecules, in retrieving structural data of mitochondrial components, and in aggregating as well as transforming mitochondrial centric biomedical knowledge. With the increasing prevalence of complex Big Data from omics experiments and clinical cohorts, informatics tools have become indispensable in our quest to understand mitochondrial physiology and pathology. Here we present an overview of the various informatics resources that are helping researchers explore this vital organelle and gain insights into its form, function, and dynamics.
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Affiliation(s)
- Anders Olav Garlid
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
| | - Jennifer S Polson
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
| | - Keith D Garlid
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA
| | - Henning Hermjakob
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA
- Molecular Systems Cluster, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Peipei Ping
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Departments of Physiology, Medicine, and Bioinformatics, University of California, Los Angeles, CA, 90095, USA
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17
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Clima R, Preste R, Calabrese C, Diroma MA, Santorsola M, Scioscia G, Simone D, Shen L, Gasparre G, Attimonelli M. HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor. Nucleic Acids Res 2016; 45:D698-D706. [PMID: 27899581 PMCID: PMC5210550 DOI: 10.1093/nar/gkw1066] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 11/04/2016] [Indexed: 11/14/2022] Open
Abstract
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.
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Affiliation(s)
- Rosanna Clima
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy.,Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy
| | - Roberto Preste
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Claudia Calabrese
- European Bioinformatics Institute EMBL Outstation - Hinxton, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Mariangela Santorsola
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Gaetano Scioscia
- IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab Bari, Italy
| | - Domenico Simone
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Lishuang Shen
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, CA 90027, USA
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
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18
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Mkaouar-Rebai E, Felhi R, Tabebi M, Alila-Fersi O, Chamkha I, Maalej M, Ammar M, Kammoun F, Keskes L, Hachicha M, Fakhfakh F. Mitochondrial DNA triplication and punctual mutations in patients with mitochondrial neuromuscular disorders. Biochem Biophys Res Commun 2016; 473:578-85. [PMID: 27033601 DOI: 10.1016/j.bbrc.2016.03.126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 03/26/2016] [Indexed: 12/30/2022]
Abstract
Mitochondrial diseases are a heterogeneous group of disorders caused by the impairment of the mitochondrial oxidative phosphorylation system which have been associated with various mutations of the mitochondrial DNA (mtDNA) and nuclear gene mutations. The clinical phenotypes are very diverse and the spectrum is still expanding. As brain and muscle are highly dependent on OXPHOS, consequently, neurological disorders and myopathy are common features of mtDNA mutations. Mutations in mtDNA can be classified into three categories: large-scale rearrangements, point mutations in tRNA or rRNA genes and point mutations in protein coding genes. In the present report, we screened mitochondrial genes of complex I, III, IV and V in 2 patients with mitochondrial neuromuscular disorders. The results showed the presence the pathogenic heteroplasmic m.9157G>A variation (A211T) in the MT-ATP6 gene in the first patient. We also reported the first case of triplication of 9 bp in the mitochondrial NC7 region in Africa and Tunisia, in association with the novel m.14924T>C in the MT-CYB gene in the second patient with mitochondrial neuromuscular disorder.
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Affiliation(s)
- Emna Mkaouar-Rebai
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Tunisia.
| | - Rahma Felhi
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Université de Sfax, Tunisia
| | - Mouna Tabebi
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Université de Sfax, Tunisia
| | - Olfa Alila-Fersi
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Tunisia
| | - Imen Chamkha
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Tunisia
| | - Marwa Maalej
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Université de Sfax, Tunisia
| | - Marwa Ammar
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Université de Sfax, Tunisia
| | - Fatma Kammoun
- Service de pédiatrie, C.H.U. Hedi Chaker de Sfax, Tunisia
| | - Leila Keskes
- Laboratoire de Génétique Moléculaire Humaine, Faculté de Médecine de Sfax, Université de Sfax, Tunisia
| | | | - Faiza Fakhfakh
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Tunisia.
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19
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Kabekkodu SP, Chakrabarty S, Shukla V, Varghese VK, Singh KK, Thangaraj K, Satyamoorthy K. Mitochondrial biology: From molecules to diseases. Mitochondrion 2015. [PMID: 26210788 DOI: 10.1016/j.mito.2015.07.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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Lloyd RE, Keatley K, Littlewood DTJ, Meunier B, Holt WV, An Q, Higgins SC, Polyzoidis S, Stephenson KF, Ashkan K, Fillmore HL, Pilkington GJ, McGeehan JE. Identification and functional prediction of mitochondrial complex III and IV mutations associated with glioblastoma. Neuro Oncol 2015; 17:942-52. [PMID: 25731774 PMCID: PMC4474231 DOI: 10.1093/neuonc/nov020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/23/2015] [Indexed: 12/30/2022] Open
Abstract
Background Glioblastoma (GBM) is the most common primary brain tumor in adults, with a dismal prognosis. Treatment is hampered by GBM's unique biology, including differential cell response to therapy. Although several mitochondrial abnormalities have been identified, how mitochondrial DNA (mtDNA) mutations contribute to GBM biology and therapeutic response remains poorly described. We sought to determine the spectrum of functional complex III and IV mtDNA mutations in GBM. Methods The complete mitochondrial genomes of 10 GBM cell lines were obtained using next-generation sequencing and combined with another set obtained from 32 GBM tissues. Three-dimensional structural mapping and analysis of all the nonsynonymous mutations identified in complex III and IV proteins was then performed to investigate functional importance. Results Over 200 mutations were identified in the mtDNAs, including a significant proportion with very low mutational loads. Twenty-five were nonsynonymous mutations in complex III and IV, 9 of which were predicted to be functional and affect mitochondrial respiratory chain activity. Most of the functional candidates were GBM specific and not found in the general population, and 2 were present in the germ-line. Patient-specific maps reveal that 43% of tumors carry at least one functional candidate. Conclusions We reveal that the spectrum of GBM-associated mtDNA mutations is wider than previously thought, as well as novel structural-functional links between specific mtDNA mutations, abnormal mitochondria, and the biology of GBM. These results could provide tangible new prognostic indicators as well as targets with which to guide the development of patient-specific mitochondrially mediated chemotherapeutic approaches.
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Affiliation(s)
- Rhiannon E Lloyd
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Kathleen Keatley
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - D Timothy J Littlewood
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Brigitte Meunier
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - William V Holt
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Qian An
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Samantha C Higgins
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Stavros Polyzoidis
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Katie F Stephenson
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Keyoumars Ashkan
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Helen L Fillmore
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - Geoffrey J Pilkington
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
| | - John E McGeehan
- Brain Tumour Research Centre (R.E.L., K.K., S.C.H., K.F.S., H.L.F., G.J.P.), Molecular Biophysics Laboratories (K.K., J.E.M.), Epigenetics and Developmental Biology Laboratories (Q.A.), Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK; Department of Life Sciences, Natural History Museum, London, UK (D.T.J.L.); Institut de Biologie Intégrative de la Cellule, Paris-Saclay University, CEA, CNRS, Université Paris-Sud, Gif sur Yvette, France (B.M.); Academic Unit of Reproductive and Developmental Medicine, University of Sheffield, Sheffield, UK (W.V.H.); Department of Neurosurgery, Kings College Hospital, London, UK (S.P., K.A.)
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21
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High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq. Forensic Sci Int Genet 2014; 12:128-35. [DOI: 10.1016/j.fsigen.2014.06.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/29/2014] [Accepted: 06/01/2014] [Indexed: 12/21/2022]
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22
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Vianello D, Sevini F, Castellani G, Lomartire L, Capri M, Franceschi C. HAPLOFIND: a new method for high-throughput mtDNA haplogroup assignment. Hum Mutat 2013; 34:1189-94. [PMID: 23696374 DOI: 10.1002/humu.22356] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 05/03/2013] [Indexed: 11/06/2022]
Abstract
Deep sequencing technologies are completely revolutionizing the approach to DNA analysis. Mitochondrial DNA (mtDNA) studies entered in the "postgenomic era": the burst in sequenced samples observed in nuclear genomics is expected also in mitochondria, a trend that can already be detected checking complete mtDNA sequences database submission rate. Tools for the analysis of these data are available, but they fail in throughput or in easiness of use. We present here a new pipeline based on previous algorithms, inherited from the "nuclear genomic toolbox," combined with a newly developed algorithm capable of efficiently and easily classify new mtDNA sequences according to PhyloTree nomenclature. Detected mutations are also annotated using data collected from publicly available databases. Thanks to the analysis of all freely available sequences with known haplogroup obtained from GenBank, we were able to produce a PhyloTree-based weighted tree, taking into account each haplogroup pattern conservation. The combination of a highly efficient aligner, coupled with our algorithm and massive usage of asynchronous parallel processing, allowed us to build a high-throughput pipeline for the analysis of mtDNA sequences that can be quickly updated to follow the ever-changing nomenclature. HaploFind is freely accessible at the following Web address: https://haplofind.unibo.it.
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Affiliation(s)
- Dario Vianello
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna 40126, Italy.
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23
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Tommaseo-Ponzetta M, Mona S, Calabrese F, Konrad G, Vacca E, Attimonelli M. Mountain Pygmies of Western New Guinea: A Morphological and Molecular Approach. Hum Biol 2013; 85:285-308. [DOI: 10.3378/027.085.0314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2013] [Indexed: 11/05/2022]
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24
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Rubino F, Piredda R, Calabrese FM, Simone D, Lang M, Calabrese C, Petruzzella V, Tommaseo-Ponzetta M, Gasparre G, Attimonelli M. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Res 2011; 40:D1150-9. [PMID: 22139932 PMCID: PMC3245114 DOI: 10.1093/nar/gkr1086] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
HmtDB (http://www.hmtdb.uniba.it:8080/hmdb) is a open resource created to support population genetics and mitochondrial disease studies. The database hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar software based on site-specific nucleotide and amino acid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user. Haplogroup definition is based on the Phylotree system. End-users accessing HmtDB are hence allowed to (i) browse the database through the use of a multi-criterion ‘query’ system; (ii) analyze their own human mitochondrial sequences via the ‘classify’ tool (for complete genomes) or by downloading the ‘fragment-classifier’ tool (for partial sequences); (iii) download multi-alignments with reference genomes as well as variability data.
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Affiliation(s)
- Francesco Rubino
- Dipartimento di Biochimica e Biologia Molecolare E Quagliariello, Università degli studi di Bari, Bari 70126, Italy
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25
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D'Onorio de Meo P, D'Antonio M, Griggio F, Lupi R, Borsani M, Pavesi G, Castrignanò T, Pesole G, Gissi C. MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa. Nucleic Acids Res 2011; 40:D1168-72. [PMID: 22123747 PMCID: PMC3245153 DOI: 10.1093/nar/gkr1144] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa.
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Affiliation(s)
- Paolo D'Onorio de Meo
- CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Rome, Italy
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26
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Blanco R, Mayordomo E, Montoya J, Ruiz-Pesini E. Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge. BMC Bioinformatics 2011; 12:174. [PMID: 21595926 PMCID: PMC3123235 DOI: 10.1186/1471-2105-12-174] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 05/19/2011] [Indexed: 11/21/2022] Open
Abstract
Background Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not limited to screening genetic variation to identify potentially deleterious mutations. However, such advances require efficient solutions to very difficult computational problems, a need that is hampered by the very plenty of data that confers strength to the analysis. Results We develop a systematic, automated methodology to overcome these difficulties, building from readily available, public sequence databases to high-quality alignments and phylogenetic trees. Within each stage in an autonomous workflow, outputs are carefully evaluated and outlier detection rules defined to integrate expert knowledge and automated curation, hence avoiding the manual bottleneck found in past approaches to the problem. Using these techniques, we have performed exhaustive updates to the human mitochondrial phylogeny, illustrating the power and computational scalability of our approach, and we have conducted some initial analyses on the resulting phylogenies. Conclusions The problem at hand demands careful definition of inputs and adequate algorithmic treatment for its solutions to be realistic and useful. It is possible to define formal rules to address the former requirement by refining inputs directly and through their combination as outputs, and the latter are also of help to ascertain the performance of chosen algorithms. Rules can exploit known or inferred properties of datasets to simplify inputs through partitioning, therefore cutting computational costs and affording work on rapidly growing, otherwise intractable datasets. Although expert guidance may be necessary to assist the learning process, low-risk results can be fully automated and have proved themselves convenient and valuable.
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Affiliation(s)
- Roberto Blanco
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, Zaragoza, Spain.
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27
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Gómez-Carballa A, Cerezo M, Balboa E, Heredia C, Castro-Feijóo L, Rica I, Barreiro J, Eirís J, Cabanas P, Martínez-Soto I, Fernández-Toral J, Castro-Gago M, Pombo M, Carracedo Á, Barros F, Salas A. Evolutionary analyses of entire genomes do not support the association of mtDNA mutations with Ras/MAPK pathway syndromes. PLoS One 2011; 6:e18348. [PMID: 21526175 PMCID: PMC3079712 DOI: 10.1371/journal.pone.0018348] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 02/25/2011] [Indexed: 01/23/2023] Open
Abstract
Background There are several known autosomal genes responsible for
Ras/MAPK pathway syndromes, including
Noonan syndrome (NS) and related disorders (such as LEOPARD,
neurofibromatosis type 1), although mutations of these genes do not explain
all cases. Due to the important role played by the mitochondrion in the
energetic metabolism of cardiac muscle, it was recently proposed that
variation in the mitochondrial DNA (mtDNA) genome could be a risk factor in
the Noonan phenotype and in hypertrophic cardiomyopathy (HCM), which is a
common clinical feature in Ras/MAPK pathway syndromes. In order to test
these hypotheses, we sequenced entire mtDNA genomes in the largest series of
patients suffering from Ras/MAPK pathway
syndromes analyzed to date (n = 45),
most of them classified as NS patients
(n = 42). Methods/Principal Findings The results indicate that the observed mtDNA lineages were mostly of European
ancestry, reproducing in a nutshell the expected haplogroup (hg) patterns of
a typical Iberian dataset (including hgs H, T, J, and U). Three new branches
of the mtDNA phylogeny (H1j1, U5b1e, and L2a5) are described for the first
time, but none of these are likely to be related to NS or
Ras/MAPK pathway syndromes when
observed under an evolutionary perspective. Patterns of variation in tRNA
and protein genes, as well as redundant, private and heteroplasmic variants,
in the mtDNA genomes of patients were as expected when compared with the
patterns inferred from a worldwide mtDNA phylogeny based on more than 8700
entire genomes. Moreover, most of the mtDNA variants found in patients had
already been reported in healthy individuals and constitute common
polymorphisms in human population groups. Conclusions/Significance As a whole, the observed mtDNA genome variation in the NS patients was
difficult to reconcile with previous findings that indicated a pathogenic
role of mtDNA variants in NS.
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Affiliation(s)
- Alberto Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | - María Cerezo
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | - Emilia Balboa
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Claudia Heredia
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Lidia Castro-Feijóo
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Itxaso Rica
- Servicio de Endocrinología Infantil, Hospital de Cruces,
Barakaldo, Basque Country, Spain
| | - Jesús Barreiro
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Jesús Eirís
- Unidad de Neurología Pediátrica, Departamento de
Pediatría, Hospital Clínico Universitario y Universidad de
Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Paloma Cabanas
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Isabel Martínez-Soto
- Unidad de Cardiología Infantil, Departamento de Pediatría,
Hospital Clínico Universitario de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
| | | | - Manuel Castro-Gago
- Unidad de Neurología Pediátrica, Departamento de
Pediatría, Hospital Clínico Universitario y Universidad de
Santiago de Compostela, Santiago de Compostela, Galicia, Spain
| | - Manuel Pombo
- Unidad de Endocrinología Pediátrica, Crecimiento y
Adolescencia, Departamento de Pediatría, Hospital Clínico
Universitario y Universidad de Santiago de Compostela, Santiago de Compostela,
Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Francisco Barros
- Unidad de Medicina Molecular, Fundación Pública Galega de
Medicina Xenómica, CIBERER, Santiago de Compostela, Galicia,
Spain
| | - Antonio Salas
- Unidade de Xenética, Departamento de Anatomía
Patolóxica e Ciencias Forenses, and Instituto de Medicina Legal,
Facultade de Medicina, Universidad de Santiago de Compostela, Santiago de
Compostela, Galicia, Spain
- * E-mail:
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28
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Guerra F, Kurelac I, Cormio A, Zuntini R, Amato LB, Ceccarelli C, Santini D, Cormio G, Fracasso F, Selvaggi L, Resta L, Attimonelli M, Gadaleta MN, Gasparre G. Placing mitochondrial DNA mutations within the progression model of type I endometrial carcinoma. Hum Mol Genet 2011; 20:2394-405. [DOI: 10.1093/hmg/ddr146] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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29
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Gianazza E, Eberini I, Sensi C, Barile M, Vergani L, Vanoni MA. Energy matters: mitochondrial proteomics for biomedicine. Proteomics 2011; 11:657-74. [PMID: 21241019 DOI: 10.1002/pmic.201000412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 09/22/2010] [Accepted: 11/03/2010] [Indexed: 12/16/2022]
Abstract
This review compiles results of medical relevance from mitochondrial proteomics, grouped either according to the type of disease - genetic or degenerative - or to the involved mechanism - oxidative stress or apoptosis. The findings are commented in the light of our current understanding of uniformity/variability in cell responses to different stimuli. Specificities in the conceptual and technical approaches to human mitochondrial proteomics are also outlined.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano, Milano, Italy.
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30
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Fregel R, Delgado S. HaploSearch: a tool for haplotype-sequence two-way transformation. Mitochondrion 2010; 11:366-7. [PMID: 21059407 DOI: 10.1016/j.mito.2010.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 10/27/2010] [Accepted: 11/01/2010] [Indexed: 11/28/2022]
Abstract
Comparison of available mitochondrial DNA data is some times hindered by the data presentation format. HaploSearch is a simple tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large datasets. Although designed for mitochondrial DNA, HaploSearch could be used with any kind of DNA type. HaploSearch program, detailed software instructions and example files are freely available on the web http://www.haplosite.com/haplosearch/.
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Affiliation(s)
- Rosa Fregel
- Department of Genetics, Faculty of Biology, University of La Laguna, La Laguna, Tenerife, Spain.
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31
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Fan L, Yao YG. MitoTool: a web server for the analysis and retrieval of human mitochondrial DNA sequence variations. Mitochondrion 2010; 11:351-6. [PMID: 20933105 DOI: 10.1016/j.mito.2010.09.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 09/28/2010] [Indexed: 10/19/2022]
Abstract
MitoTool, a web-based bioinformatics platform, is designed for deciphering human mitochondrial DNA (mtDNA) data in batch mode. The platform has advantages in (i) parsing diverse types of mtDNA data; (ii) automatically classifying haplogroup according to mtDNA sequences or variants; (iii) discovering possibly missing variants of the samples with claimed haplogroups status; (iv) estimating the evolutionary conservation index, protein coding effect and potential pathogenicity of certain substitutions; (v) performing statistical analysis for haplogroup distribution frequency between case and control groups. Furthermore, it offers an integrated database for retrieving five types of mitochondrion-related information. The MitoTool is freely accessed at http://www.mitotool.org.
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Affiliation(s)
- Long Fan
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China.
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32
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Chang HW, Chuang LY, Cheng YH, Gu DL, Huang HW, Yang CH. An introduction to mitochondrial informatics. Methods Mol Biol 2010; 628:259-74. [PMID: 20238086 DOI: 10.1007/978-1-60327-367-1_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this chapter, we review the public resources available for human mitochondrial DNA and protein related bioinformatics, with a special focus on mitochondrial single nucleotide polymorphisms (mtSNPs). We also review our own freeware tool V-MitoSNP, giving an overview of its implementation and program workflow. Apart from these, we review several protocols for the graphic input of genes, keywords, gene searching by sequence, mtSNP searching by sequence, restriction enzyme mining, primer design, and virtual electrophoresis for PCR-RFLP genotyping. Some databases with similar function are integrated and compared.
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Affiliation(s)
- Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, Center of Excellence for Environmental Medicine, Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung, Taiwan
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33
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Porcelli AM, Ghelli A, Ceccarelli C, Lang M, Cenacchi G, Capristo M, Pennisi LF, Morra I, Ciccarelli E, Melcarne A, Bartoletti-Stella A, Salfi N, Tallini G, Martinuzzi A, Carelli V, Attimonelli M, Rugolo M, Romeo G, Gasparre G. The genetic and metabolic signature of oncocytic transformation implicates HIF1alpha destabilization. Hum Mol Genet 2009; 19:1019-32. [PMID: 20028790 DOI: 10.1093/hmg/ddp566] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We previously showed that disruptive complex I mutations in mitochondrial DNA are the main genetic hallmark of oncocytic tumors of the thyroid and kidney. We here report a high frequency of homoplasmic disruptive mutations in a large panel of oncocytic pituitary and head-and-neck tumors. The presence of such mutations implicates disassembly of respiratory complex I in vivo which in turn contributes to the inability of oncocytic tumors to stabilize HIF1alpha and to display pseudo-hypoxia. By utilizing transmitochondrial cytoplasmic hybrids (cybrids), we induced the shift to homoplasmy of a truncating mutation in the mitochondria-coded MTND1 gene. Such shift is associated with a profound metabolic impairment leading to the imbalance of alpha-ketoglutarate and succinate, the Krebs cycle metabolites which are the main responsible for HIF1alpha stabilization. We conclude that the main hallmarks of oncocytic transformation, namely the occurrence of homoplasmic disruptive mutations and complex I disassembly, may explain the benign nature of oncocytic neoplasms through lack of HIF1alpha stabilization.
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Affiliation(s)
- Anna Maria Porcelli
- Dipartimento di Biologia Evoluzionistica Sperimentale, Università di Bologna, Bologna 40126, Italy
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Kim T, Kim E, Park SJ, Joo H. PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison. Comput Biol Med 2009; 39:689-96. [DOI: 10.1016/j.compbiomed.2009.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
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Kumar S, Ravuri RR, Koneru P, Urade BP, Sarkar BN, Chandrasekar A, Rao VR. Reconstructing Indian-Australian phylogenetic link. BMC Evol Biol 2009; 9:173. [PMID: 19624810 PMCID: PMC2720955 DOI: 10.1186/1471-2148-9-173] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 07/22/2009] [Indexed: 11/10/2022] Open
Abstract
Background An early dispersal of biologically and behaviorally modern humans from their African origins to Australia, by at least 45 thousand years via southern Asia has been suggested by studies based on morphology, archaeology and genetics. However, mtDNA lineages sampled so far from south Asia, eastern Asia and Australasia show non-overlapping distributions of haplogroups within pan Eurasian M and N macrohaplogroups. Likewise, support from the archaeology is still ambiguous. Results In our completely sequenced 966-mitochondrial genomes from 26 relic tribes of India, we have identified seven genomes, which share two synonymous polymorphisms with the M42 haplogroup, which is specific to Australian Aborigines. Conclusion Our results showing a shared mtDNA lineage between Indians and Australian Aborigines provides direct genetic evidence of an early colonization of Australia through south Asia, following the "southern route".
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Affiliation(s)
- Satish Kumar
- Anthropological Survey of India, 27 Jawaharlal Nehru Road, Kolkata, India.
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Rubino F, Attimonelli M. RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences. BMC Bioinformatics 2009; 10 Suppl 6:S5. [PMID: 19534754 PMCID: PMC2697652 DOI: 10.1186/1471-2105-10-s6-s5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One of the most frequent uses of bioinformatics tools concerns functional characterization of a newly produced nucleotide sequence (a query sequence) by applying Blast or FASTA against a set of sequences (the subject sequences). However, in some specific contexts, it is useful to compare the query sequence against a cluster such as a MultiAlignment (MA). We present here the RegExpBlasting (REB) algorithm, which compares an unclassified sequence with a dataset of patterns defined by application of Regular Expression rules to a given-as-input MA datasets. The REB algorithm workflow consists in i. the definition of a dataset of multialignments ii. the association of each MA to a pattern, defined by application of regular expression rules; iii. automatic characterization of a submitted biosequence according to the function of the sequences described by the pattern best matching the query sequence. RESULTS An application of this algorithm is used in the "characterize your sequence" tool available in the PPNEMA resource. PPNEMA is a resource of Ribosomal Cistron sequences from various species, grouped according to nematode genera. It allows the retrieval of plant nematode multialigned sequences or the classification of new nematode rDNA sequences by applying REB. The same algorithm also supports automatic updating of the PPNEMA database. The present paper gives examples of the use of REB within PPNEMA. CONCLUSION The use of REB in PPNEMA updating, the PPNEMA "characterize your sequence" option clearly demonstrates the power of the method. Using REB can also rapidly solve any other bioinformatics problem, where the addition of a new sequence to a pre-existing cluster is required. The statistical tests carried out here show the powerful flexibility of the method.
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Affiliation(s)
- Francesco Rubino
- Department of Biochemistry and Molecular Biology E, Quagliariello - Bari, 70126, Italy.
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Lee HY, Song I, Ha E, Cho SB, Yang WI, Shin KJ. mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences. BMC Bioinformatics 2008; 9:483. [PMID: 19014619 PMCID: PMC2621369 DOI: 10.1186/1471-2105-9-483] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 11/17/2008] [Indexed: 12/05/2022] Open
Abstract
Background For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data. Results We developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode. Conclusion The mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at .
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Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea.
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O'Brien EA, Zhang Y, Wang E, Marie V, Badejoko W, Lang BF, Burger G. GOBASE: an organelle genome database. Nucleic Acids Res 2008; 37:D946-50. [PMID: 18953030 PMCID: PMC2686550 DOI: 10.1093/nar/gkn819] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene products and taxonomy is available, as well as selected genome maps and RNA secondary structures. Recent major enhancements to database functionality include: (i) addition of an interface for RNA editing data, with substitutions, insertions and deletions displayed using multiple alignments; (ii) addition of medically relevant information, such as haplotypes, SNPs and associated disease states, to human mitochondrial sequence data; (iii) addition of fully reannotated genome sequences for Escherichia coli and Nostoc sp., for reference and comparison; and (iv) a number of interface enhancements, such as the availability of both genomic and gene-coding sequence downloads, and a more sophisticated literature reference search functionality with links to PubMed where available. Future projects include the transfer of GOBASE features to NCBI/GenBank, allowing long-term preservation of accumulated expert information. The GOBASE database can be found at http://gobase.bcm.umontreal.ca/. Queries about custom and large-scale data retrievals should be addressed to gobase@bch.umontreal.ca.
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Affiliation(s)
- Emmet A O'Brien
- Robert-Cedergren Center for Bioinformatics and Genomics, Département de Biochimie, Pavillon Roger-Gaudry, Université de Montréal, 2900 Edouard-Montpetit, Montreal QC, Canada H3T 1J4.
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Rosa A, Fonseca BV, Krug T, Manso H, Gouveia L, Albergaria I, Gaspar G, Correia M, Viana-Baptista M, Simões RM, Pinto AN, Taipa R, Ferreira C, Fontes JR, Silva MR, Gabriel JP, Matos I, Lopes G, Ferro JM, Vicente AM, Oliveira SA. Mitochondrial haplogroup H1 is protective for ischemic stroke in Portuguese patients. BMC MEDICAL GENETICS 2008; 9:57. [PMID: 18593462 PMCID: PMC2492853 DOI: 10.1186/1471-2350-9-57] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 07/01/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND The genetic contribution to stroke is well established but it has proven difficult to identify the genes and the disease-associated alleles mediating this effect, possibly because only nuclear genes have been intensely investigated so far. Mitochondrial DNA (mtDNA) has been implicated in several disorders having stroke as one of its clinical manifestations. The aim of this case-control study was to assess the contribution of mtDNA polymorphisms and haplogroups to ischemic stroke risk. METHODS We genotyped 19 mtDNA single nucleotide polymorphisms (SNPs) defining the major European haplogroups in 534 ischemic stroke patients and 499 controls collected in Portugal, and tested their allelic and haplogroup association with ischemic stroke risk. RESULTS Haplogroup H1 was found to be significantly less frequent in stroke patients than in controls (OR = 0.61, 95% CI = 0.45-0.83, p = 0.001), when comparing each clade against all other haplogroups pooled together. Conversely, the pre-HV/HV and U mtDNA lineages emerge as potential genetic factors conferring risk for stroke (OR = 3.14, 95% CI = 1.41-7.01, p = 0.003, and OR = 2.87, 95% CI = 1.13-7.28, p = 0.021, respectively). SNPs m.3010G>A, m.7028C>T and m.11719G>A strongly influence ischemic stroke risk, their allelic state in haplogroup H1 corroborating its protective effect. CONCLUSION Our data suggests that mitochondrial haplogroup H1 has an impact on ischemic stroke risk in a Portuguese sample.
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Lascaro D, Castellana S, Gasparre G, Romeo G, Saccone C, Attimonelli M. The RHNumtS compilation: features and bioinformatics approaches to locate and quantify Human NumtS. BMC Genomics 2008; 9:267. [PMID: 18522722 PMCID: PMC2447851 DOI: 10.1186/1471-2164-9-267] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 06/03/2008] [Indexed: 11/21/2022] Open
Abstract
Background To a greater or lesser extent, eukaryotic nuclear genomes contain fragments of their mitochondrial genome counterpart, deriving from the random insertion of damaged mtDNA fragments. NumtS (Nuclear mt Sequences) are not equally abundant in all species, and are redundant and polymorphic in terms of copy number. In population and clinical genetics, it is important to have a complete overview of NumtS quantity and location. Searching PubMed for NumtS or Mitochondrial pseudo-genes yields hundreds of papers reporting Human NumtS compilations produced by in silico or wet-lab approaches. A comparison of published compilations clearly shows significant discrepancies among data, due both to unwise application of Bioinformatics methods and to a not yet correctly assembled nuclear genome. To optimize quantification and location of NumtS, we produced a consensus compilation of Human NumtS by applying various bioinformatics approaches. Results Location and quantification of NumtS may be achieved by applying database similarity searching methods: we have applied various methods such as Blastn, MegaBlast and BLAT, changing both parameters and database; the results were compared, further analysed and checked against the already published compilations, thus producing the Reference Human Numt Sequences (RHNumtS) compilation. The resulting NumtS total 190. Conclusion The RHNumtS compilation represents a highly reliable reference basis, which may allow designing a lab protocol to test the actual existence of each NumtS. Here we report preliminary results based on PCR amplification and sequencing on 41 NumtS selected from RHNumtS among those with lower score. In parallel, we are currently designing the RHNumtS database structure for implementation in the HmtDB resource. In the future, the same database will host NumtS compilations from other organisms, but these will be generated only when the nuclear genome of a specific organism has reached a high-quality level of assembly.
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Affiliation(s)
- Daniela Lascaro
- Dipartimento di Biochimica e Biologia Molecolare E, Quagliariello, Università di Bari, Via E, Orabona 4, 70126 Bari, Italy.
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Gasparre G, Porcelli AM, Bonora E, Pennisi LF, Toller M, Iommarini L, Ghelli A, Moretti M, Betts CM, Martinelli GN, Ceroni AR, Curcio F, Carelli V, Rugolo M, Tallini G, Romeo G. Disruptive mitochondrial DNA mutations in complex I subunits are markers of oncocytic phenotype in thyroid tumors. Proc Natl Acad Sci U S A 2007; 104:9001-6. [PMID: 17517629 PMCID: PMC1885617 DOI: 10.1073/pnas.0703056104] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oncocytic tumors are a distinctive class of proliferative lesions composed of cells with a striking degree of mitochondrial hyperplasia that are particularly frequent in the thyroid gland. To understand whether specific mitochondrial DNA (mtDNA) mutations are associated with the accumulation of mitochondria, we sequenced the entire mtDNA in 50 oncocytic lesions (45 thyroid tumors of epithelial cell derivation and 5 mitochondrion-rich breast tumors) and 52 control cases (21 nononcocytic thyroid tumors, 15 breast carcinomas, and 16 gliomas) by using recently developed technology that allows specific and reliable amplification of the whole mtDNA with quick mutation scanning. Thirteen oncocytic lesions (26%) presented disruptive mutations (nonsense or frameshift), whereas only two samples (3.8%) presented such mutations in the nononcocytic control group. In one case with multiple thyroid nodules analyzed separately, a disruptive mutation was found in the only nodule with oncocytic features. In one of the five mitochondrion-rich breast tumors, a disruptive mutation was identified. All disruptive mutations were found in complex I subunit genes, and the association between these mutations and the oncocytic phenotype was statistically significant (P=0.001). To study the pathogenicity of these mitochondrial mutations, primary cultures from oncocytic tumors and corresponding normal tissues were established. Electron microscopy and biochemical and molecular analyses showed that primary cultures derived from tumors bearing disruptive mutations failed to maintain the mutations and the oncocytic phenotype. We conclude that disruptive mutations in complex I subunits are markers of thyroid oncocytic tumors.
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Affiliation(s)
- Giuseppe Gasparre
- *Unità di Genetica Medica, Policlinico Universitario S. Orsola-Malpighi
| | | | - Elena Bonora
- *Unità di Genetica Medica, Policlinico Universitario S. Orsola-Malpighi
- To whom correspondence should be addressed at:
Dipartimento Medicina Interna, Cardioangiologia ed Epatologia, U.O. Genetica Medica, Padiglione 11, Policlinico S. Orsola-Malpighi, via Massarenti, 9, 40138 Bologna, Italy. E-mail:
| | | | - Matteo Toller
- Dipartimento di Patologia e Medicina Sperimentale e Clinica and Centro Interdipartimentale di Medicina Rigenerativa, University of Udine,33100 Udine, Italy
| | | | - Anna Ghelli
- Dipartimento di Biologia Evoluzionistica Sperimentale
| | - Massimo Moretti
- Dipartimento di Patologia e Medicina Sperimentale e Clinica and Centro Interdipartimentale di Medicina Rigenerativa, University of Udine,33100 Udine, Italy
| | | | | | | | - Francesco Curcio
- Dipartimento di Patologia e Medicina Sperimentale e Clinica and Centro Interdipartimentale di Medicina Rigenerativa, University of Udine,33100 Udine, Italy
| | | | | | - Giovanni Tallini
- Dipartimento di Anatomia Patologica, Ospedale Bellaria, University of Bologna, 40126 Bologna, Italy; and
| | - Giovanni Romeo
- *Unità di Genetica Medica, Policlinico Universitario S. Orsola-Malpighi
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Accetturo M, Santamaria M, Lascaro D, Rubino F, Achilli A, Torroni A, Tommaseo-Ponzetta M, Attimonelli M. Human mtDNA site-specific variability values can act as haplogroup markers. Hum Mutat 2006; 27:965-74. [PMID: 16865696 DOI: 10.1002/humu.20365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Sequencing of entire human mtDNA genomes has become rapid and efficient, leading to the production of a great number of complete mtDNA sequences from a wide range of human populations. We introduce here a new statistical approach for classifying mtDNA nucleotide sites, simply by comparing the mean simple deviation (MSD) of their specific variability values estimated on continent-specific dataset sequences, without the need for any reference sequence. Excellent correspondence was observed between sites with the highest MSD values and those marking known mtDNA haplogroups. This in turn supports the classification of 81 sites (23 in Africa, eight in Asia, eight in Europe, 34 in Oceania, and eight in America) as novel markers of 47 mtDNA haplogroups not yet identified by phylogeographic studies. Not only does this approach allow refinement of mtDNA phylogeny, an essential requirement also for mitochondrial disease studies, but may greatly facilitate the discrimination of candidate disease-causing mutations from haplogroup-specific polymorphisms in mtDNA sequences of patients affected by mitochondrial disorders.
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Affiliation(s)
- Matteo Accetturo
- Dipartimento di Biochimica e Biologia Molecolare, Università degli Studi di Bari, Bari, Italy
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Helmer-Citterich M, Casadio R, Guffanti A, Mauri G, Milanesi L, Pesole G, Valle G, Saccone C. Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. BMC Bioinformatics 2005. [PMCID: PMC1866399 DOI: 10.1186/1471-2105-6-s4-s1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan. This Editorial provides a brief overview of the Conference topics and introduces the peer-reviewed manuscripts accepted for publication in this Supplement.
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