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Aneli S, Ceccatelli Berti C, Gilea AI, Birolo G, Mutti G, Pavesi A, Baruffini E, Goffrini P, Capelli C. Functional characterization of archaic-specific variants in mitonuclear genes: insights from comparative analysis in S. cerevisiae. Hum Mol Genet 2024; 33:1152-1163. [PMID: 38558123 DOI: 10.1093/hmg/ddae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/29/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024] Open
Abstract
Neanderthal and Denisovan hybridisation with modern humans has generated a non-random genomic distribution of introgressed regions, the result of drift and selection dynamics. Cross-species genomic incompatibility and more efficient removal of slightly deleterious archaic variants have been proposed as selection-based processes involved in the post-hybridisation purge of archaic introgressed regions. Both scenarios require the presence of functionally different alleles across Homo species onto which selection operated differently according to which populations hosted them, but only a few of these variants have been pinpointed so far. In order to identify functionally divergent archaic variants removed in humans, we focused on mitonuclear genes, which are underrepresented in the genomic landscape of archaic humans. We searched for non-synonymous, fixed, archaic-derived variants present in mitonuclear genes, rare or absent in human populations. We then compared the functional impact of archaic and human variants in the model organism Saccharomyces cerevisiae. Notably, a variant within the mitochondrial tyrosyl-tRNA synthetase 2 (YARS2) gene exhibited a significant decrease in respiratory activity and a substantial reduction of Cox2 levels, a proxy for mitochondrial protein biosynthesis, coupled with the accumulation of the YARS2 protein precursor and a lower amount of mature enzyme. Our work suggests that this variant is associated with mitochondrial functionality impairment, thus contributing to the purging of archaic introgression in YARS2. While different molecular mechanisms may have impacted other mitonuclear genes, our approach can be extended to the functional screening of mitonuclear genetic variants present across species and populations.
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Affiliation(s)
- Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, C.so Galileo Galilei 22, Turin 10126, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, Via Santena 5, Turin 10126, Italy
| | - Giacomo Mutti
- Barcelona Supercomputing Centre (BSC-CNS), Department of Life Sciences, Plaça Eusebi Güell, 1-3, Barcelona 08034, Spain
- Institute for Research in Biomedicine (IRB Barcelona), Department of Mechanisms of Disease, The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Angelo Pavesi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
| | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/a, Parma 43124, Italy
- Department of Biology, University of Oxford, 11a Mansfield Rd, Oxford OX1 3SZ, United Kingdom
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Duarte Hospital C, Tête A, Debizet K, Imler J, Tomkiewicz-Raulet C, Blanc EB, Barouki R, Coumoul X, Bortoli S. SDHi fungicides: An example of mitotoxic pesticides targeting the succinate dehydrogenase complex. ENVIRONMENT INTERNATIONAL 2023; 180:108219. [PMID: 37778286 DOI: 10.1016/j.envint.2023.108219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/15/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Succinate dehydrogenase inhibitors (SDHi) are fungicides used to control the proliferation of pathogenic fungi in crops. Their mode of action is based on blocking the activity of succinate dehydrogenase (SDH), a universal enzyme expressed by all species harboring mitochondria. The SDH is involved in two interconnected metabolic processes for energy production: the transfer of electrons in the mitochondrial respiratory chain and the oxidation of succinate to fumarate in the Krebs cycle. In humans, inherited SDH deficiencies may cause major pathologies including encephalopathies and cancers. The cellular and molecular mechanisms related to such genetic inactivation have been well described in neuroendocrine tumors, in which it induces an oxidative stress, a pseudohypoxic phenotype, a metabolic, epigenetic and transcriptomic remodeling, and alterations in the migration and invasion capacities of cancer cells, in connection with the accumulation of succinate, an oncometabolite, substrate of the SDH. We will discuss recent studies reporting toxic effects of SDHi in non-target organisms and their implications for risk assessment of pesticides. Recent data show that the SDH structure is highly conserved during evolution and that SDHi can inhibit SDH activity in mitochondria of non-target species, including humans. These observations suggest that SDHi are not specific inhibitors of fungal SDH. We hypothesize that SDHi could have toxic effects in other species, including humans. Moreover, the analysis of regulatory assessment reports shows that most SDHi induce tumors in animals without evidence of genotoxicity. Thus, these substances could have a non-genotoxic mechanism of carcinogenicity that still needs to be fully characterized and that could be related to SDH inhibition. The use of pesticides targeting mitochondrial enzymes encoded by tumor suppressor genes raises questions on the risk assessment framework of mitotoxic pesticides. The issue of SDHi fungicides is therefore a textbook case that highlights the urgent need for changes in regulatory assessment.
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Affiliation(s)
| | - Arnaud Tête
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Kloé Debizet
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Jules Imler
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | | | - Etienne B Blanc
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Robert Barouki
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris
| | - Xavier Coumoul
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris.
| | - Sylvie Bortoli
- Université Paris Cité, INSERM UMR-S 1124, T3S, 45 rue des Saints-Pères, 75006 Paris.
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Zheng J, Liu S, Wang D, Li L, Sarsaiya S, Zhou H, Cai H. Unraveling the functional consequences of a novel germline missense mutation (R38C) in the yeast model of succinate dehydrogenase subunit B: insights into neurodegenerative disorders. Front Mol Neurosci 2023; 16:1246842. [PMID: 37840772 PMCID: PMC10568460 DOI: 10.3389/fnmol.2023.1246842] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
This study explores the implications of a novel germline missense mutation (R38C) in the succinate dehydrogenase (SDH) subunit B, which has been linked to neurodegenerative diseases. The mutation was identified from the SDH mutation database and corresponds to the SDH2R32C allele, mirroring the human SDHBR38C mutation. By subjecting the mutant yeast model to hydrogen peroxide (H2O2) stress, simulating oxidative stress, we observed heightened sensitivity to oxidative conditions. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) analysis revealed significant regulation (p < 0.05) of genes associated with antioxidant systems and energy metabolism. Through gas chromatography-mass spectrometry (GC-MS) analysis, we examined yeast cell metabolites under oxidative stress, uncovering insights into the potential protective role of o-vanillin. This study elucidates the biological mechanisms underlying cellular oxidative stress responses, offering valuable insights into its repercussions. These findings shed light on innovative avenues for addressing neurodegenerative diseases, potentially revolutionizing therapeutic strategies.
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Affiliation(s)
| | | | | | | | | | | | - Heng Cai
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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Lanes Iglesias S, Megido Armada A, Castaño González LA, Menéndez Torre EL, Riaño Galán I. Experience in diagnosis and treatment of prolactinomas in pediatric patients and young adults. ENDOCRINOLOGIA, DIABETES Y NUTRICION 2022; 69:911-913. [PMID: 36446712 DOI: 10.1016/j.endien.2022.11.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/13/2021] [Indexed: 11/27/2022]
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5
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Lanes Iglesias S, Megido Armada A, Castaño González LA, Menéndez Torre EL, Riaño Galán I. Experiencia en el diagnóstico y tratamiento de prolactinomas en pacientes pediátricos y adultos jóvenes. ENDOCRINOL DIAB NUTR 2022. [DOI: 10.1016/j.endinu.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Takács-Vellai K, Farkas Z, Ősz F, Stewart GW. Model systems in SDHx-related pheochromocytoma/paraganglioma. Cancer Metastasis Rev 2021; 40:1177-1201. [PMID: 34957538 PMCID: PMC8825606 DOI: 10.1007/s10555-021-10009-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/04/2021] [Indexed: 11/17/2022]
Abstract
Pheochromocytoma (PHEO) and paraganglioma (PGL) (together PPGL) are tumors with poor outcomes that arise from neuroendocrine cells in the adrenal gland, and sympathetic and parasympathetic ganglia outside the adrenal gland, respectively. Many follow germline mutations in genes coding for subunits of succinate dehydrogenase (SDH), a tetrameric enzyme in the tricarboxylic acid (TCA) cycle that both converts succinate to fumarate and participates in electron transport. Germline SDH subunit B (SDHB) mutations have a high metastatic potential. Herein, we review the spectrum of model organisms that have contributed hugely to our understanding of SDH dysfunction. In Saccharomyces cerevisiae (yeast), succinate accumulation inhibits alpha-ketoglutarate-dependent dioxygenase enzymes leading to DNA demethylation. In the worm Caenorhabditis elegans, mutated SDH creates developmental abnormalities, metabolic rewiring, an energy deficit and oxygen hypersensitivity (the latter is also found in Drosophila melanogaster). In the zebrafish Danio rerio, sdhb mutants display a shorter lifespan with defective energy metabolism. Recently, SDHB-deficient pheochromocytoma has been cultivated in xenografts and has generated cell lines, which can be traced back to a heterozygous SDHB-deficient rat. We propose that a combination of such models can be efficiently and effectively used in both pathophysiological studies and drug-screening projects in order to find novel strategies in PPGL treatment.
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Affiliation(s)
| | - Zsolt Farkas
- Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary
| | - Fanni Ősz
- Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary
| | - Gordon W Stewart
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
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Siddiqui N, Seedat F, Bulbulia S, Mtshali NZ, Botha A, Krause A, Daya R, Bayat Z. SDHB-Associated Paraganglioma Syndrome in Africa-A Need for Greater Genetic Testing. J Endocr Soc 2021; 5:bvab111. [PMID: 34377882 PMCID: PMC8348940 DOI: 10.1210/jendso/bvab111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Indexed: 11/19/2022] Open
Abstract
A germline mutation is identified in almost 40% of pheochromocytoma/paraganglioma (PPGL) syndromes. Genetic testing and counseling are essential for the management of index cases as well as presymptomatic identification and preemptive management of affected family members. Mutations in the genes encoding the mitochondrial enzyme succinate dehydrogenase (SDH) are well described in patients with hereditary PPGL. Among patients of African ancestry, the prevalence, phenotype, germline mutation spectrum, and penetrance of SDH mutations is poorly characterized. We describe a multifocal paraganglioma in a young African male with an underlying missense succinate dehydrogenase subunit B (SDHB) mutation and a history of 3 first-degree relatives who died at young ages from suspected cardiovascular causes. The same SDHB mutation, Class V variant c.724C>A p.(Arg242Ser), was detected in one of his asymptomatic siblings. As there are limited data describing hereditary PPGL syndromes in Africa, this report of an SDHB-associated PPGL is a notable contribution to the literature in this growing field. Due to the noteworthy clinical implications of PPGL mutations, this work highlights the existing need for broader genetic screening among African patients with PPGL despite the limited healthcare resources available in this region.
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Affiliation(s)
- Nida Siddiqui
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Helen Joseph Hospital, Johannesburg, 2092, South Africa
| | - Faheem Seedat
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Helen Joseph Hospital, Johannesburg, 2092, South Africa.,Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Saajidah Bulbulia
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Helen Joseph Hospital, Johannesburg, 2092, South Africa.,Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Nompumelelo Z Mtshali
- Division of Anatomical Pathology, Department of Pathology, National Health Laboratory Services & University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Adam Botha
- Division of Anatomical Pathology, Department of Pathology, National Health Laboratory Services & University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Services & School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Reyna Daya
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Helen Joseph Hospital, Johannesburg, 2092, South Africa.,Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Zaheer Bayat
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Helen Joseph Hospital, Johannesburg, 2092, South Africa.,Division of Endocrinology and Metabolism, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
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8
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Aleo SJ, Del Dotto V, Fogazza M, Maresca A, Lodi T, Goffrini P, Ghelli A, Rugolo M, Carelli V, Baruffini E, Zanna C. Drug repositioning as a therapeutic strategy for neurodegenerations associated with OPA1 mutations. Hum Mol Genet 2020; 29:3631-3645. [PMID: 33231680 PMCID: PMC7823107 DOI: 10.1093/hmg/ddaa244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
OPA1 mutations are the major cause of dominant optic atrophy (DOA) and the syndromic form DOA plus, pathologies for which there is no established cure. We used a ‘drug repurposing’ approach to identify FDA-approved molecules able to rescue the mitochondrial dysfunctions induced by OPA1 mutations. We screened two different chemical libraries by using two yeast strains carrying the mgm1I322M and the chim3P646L mutations, identifying 26 drugs able to rescue their oxidative growth phenotype. Six of them, able to reduce the mitochondrial DNA instability in yeast, have been then tested in Opa1 deleted mouse embryonic fibroblasts expressing the human OPA1 isoform 1 bearing the R445H and D603H mutations. Some of these molecules were able to ameliorate the energetic functions and/or the mitochondrial network morphology, depending on the type of OPA1 mutation. The final validation has been performed in patients’ fibroblasts, allowing to select the most effective molecules. Our current results are instrumental to rapidly translating the findings of this drug repurposing approach into clinical trial for DOA and other neurodegenerations caused by OPA1 mutations.
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Affiliation(s)
- Serena J Aleo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna 40126, Italy
| | - Valentina Del Dotto
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna 40139, Italy
| | - Mario Fogazza
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna 40126, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
| | - Tiziana Lodi
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Anna Ghelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna 40126, Italy
| | - Michela Rugolo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna 40126, Italy
| | - Valerio Carelli
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna 40139, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna 40139, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Science and Environmental Sustainability, University of Parma, Parma 43124, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna 40126, Italy
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Moreno C, Santos RM, Burns R, Zhang WC. Succinate Dehydrogenase and Ribonucleic Acid Networks in Cancer and Other Diseases. Cancers (Basel) 2020; 12:cancers12113237. [PMID: 33153035 PMCID: PMC7693138 DOI: 10.3390/cancers12113237] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Although the dysfunction of the succinate dehydrogenase complex in mitochondria leads to cancer and other diseases due to aberrant metabolic reactions and signaling pathways, it is not well known how the succinate dehydrogenase complex is regulated. Our review highlights that non-coding ribonucleic acids (RNAs), RNA editing enzymes, and RNA modifying enzymes regulate expressions and functions of the succinate dehydrogenase complex. This research will provide new strategies for treating succinate dehydrogenase-relevant diseases in a clinic. Abstract Succinate dehydrogenase (SDH) complex connects both the tricarboxylic acid (TCA) cycle and the electron transport chain (ETC) in the mitochondria. However, SDH mutation or dysfunction-induced succinate accumulation results in multiple cancers and non-cancer diseases. The mechanistic studies show that succinate activates hypoxia response and other signal pathways via binding to 2-oxoglutarate-dependent oxygenases and succinate receptors. Recently, the increasing knowledge of ribonucleic acid (RNA) networks, including non-coding RNAs, RNA editors, and RNA modifiers has expanded our understanding of the interplay between SDH and RNA networks in cancer and other diseases. Here, we summarize recent discoveries in the RNA networks and their connections to SDH. Additionally, we discuss current therapeutics targeting SDH in both pre-clinical and clinical trials. Thus, we propose a new model of SDH–RNA network interaction and bring promising RNA therapeutics against SDH-relevant cancer and other diseases.
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Moosavi B, Zhu XL, Yang WC, Yang GF. Molecular pathogenesis of tumorigenesis caused by succinate dehydrogenase defect. Eur J Cell Biol 2020; 99:151057. [DOI: 10.1016/j.ejcb.2019.151057] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/19/2019] [Accepted: 10/29/2019] [Indexed: 12/14/2022] Open
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Ben Aim L, Pigny P, Castro-Vega LJ, Buffet A, Amar L, Bertherat J, Drui D, Guilhem I, Baudin E, Lussey-Lepoutre C, Corsini C, Chabrier G, Briet C, Faivre L, Cardot-Bauters C, Favier J, Gimenez-Roqueplo AP, Burnichon N. Targeted next-generation sequencing detects rare genetic events in pheochromocytoma and paraganglioma. J Med Genet 2019; 56:513-520. [DOI: 10.1136/jmedgenet-2018-105714] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 01/29/2023]
Abstract
BackgroundKnowing the genetic status of patients affected by paragangliomas and pheochromocytomas (PPGL) is important for the guidance of their management and their relatives. Our objective was to improve the diagnostic performances of PPGL genetic testing by next-generation sequencing (NGS).MethodsWe developed a custom multigene panel, which includes 17 PPGL genes and is compatible with both germline and tumour DNA screening. The NGS assay was first validated in a retrospective cohort of 201 frozen tumour DNAs and then applied prospectively to 623 DNAs extracted from leucocytes, frozen or paraffin-embedded PPGL tumours.ResultsIn the retrospective cohort, the sensitivity of the NGS assay was evaluated at 100% for point and indels mutations and 86% for large rearrangements. The mutation rate was re-evaluated from 65% (132/202) to 78% (156/201) after NGS analysis. In the prospective cohort, NGS detected not only germline and somatic mutations but also co-occurring variants and mosaicism. A mutation was identified in 74% of patients for whom both germline and tumour DNA were available.ConclusionThe analysis of 824 DNAs from patients with PPGL demonstrated that NGS assay significantly improves the performances of PPGL genetic testing compared with conventional methods, increasing the rate of identified mutations and identifying rare genetic mechanisms.
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Del Dotto V, Fogazza M, Musiani F, Maresca A, Aleo SJ, Caporali L, La Morgia C, Nolli C, Lodi T, Goffrini P, Chan D, Carelli V, Rugolo M, Baruffini E, Zanna C. Deciphering OPA1 mutations pathogenicity by combined analysis of human, mouse and yeast cell models. Biochim Biophys Acta Mol Basis Dis 2018; 1864:3496-3514. [PMID: 30293569 DOI: 10.1016/j.bbadis.2018.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/24/2018] [Accepted: 08/01/2018] [Indexed: 11/19/2022]
Abstract
OPA1 is the major gene responsible for Dominant Optic Atrophy (DOA) and the syndromic form DOA "plus". Over 370 OPA1 mutations have been identified so far, although their pathogenicity is not always clear. We have analyzed one novel and a set of known OPA1 mutations to investigate their impact on protein functions in primary skin fibroblasts and in two "ad hoc" generated cell systems: the MGM1/OPA1 chimera yeast model and the Opa1-/- MEFs model expressing the mutated human OPA1 isoform 1. The yeast model allowed us to confirm the deleterious effects of these mutations and to gain information on their dominance/recessivity. The MEFs model enhanced the phenotypic alteration caused by mutations, nicely correlating with the clinical severity observed in patients, and suggested that the DOA "plus" phenotype could be induced by the combinatorial effect of mitochondrial network fragmentation with variable degrees of mtDNA depletion. Overall, the two models proved to be valuable tools to functionally assess and define the deleterious mechanism and the pathogenicity of novel OPA1 mutations, and useful to testing new therapeutic interventions.
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Affiliation(s)
- Valentina Del Dotto
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, 40139 Bologna, Italy
| | - Mario Fogazza
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Alessandra Maresca
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, 40139 Bologna, Italy
| | - Serena J Aleo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Leonardo Caporali
- IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, 40139 Bologna, Italy
| | - Chiara La Morgia
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, 40139 Bologna, Italy; IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, 40139 Bologna, Italy
| | - Cecilia Nolli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Tiziana Lodi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - David Chan
- Division of Biology and Biological Engineering, California Institute of Technology (CALTECH), Pasadena, CA 91125, USA
| | - Valerio Carelli
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, 40139 Bologna, Italy; IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, 40139 Bologna, Italy
| | - Michela Rugolo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy.
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Andrews KA, Ascher DB, Pires DEV, Barnes DR, Vialard L, Casey RT, Bradshaw N, Adlard J, Aylwin S, Brennan P, Brewer C, Cole T, Cook JA, Davidson R, Donaldson A, Fryer A, Greenhalgh L, Hodgson SV, Irving R, Lalloo F, McConachie M, McConnell VPM, Morrison PJ, Murday V, Park SM, Simpson HL, Snape K, Stewart S, Tomkins SE, Wallis Y, Izatt L, Goudie D, Lindsay RS, Perry CG, Woodward ER, Antoniou AC, Maher ER. Tumour risks and genotype-phenotype correlations associated with germline variants in succinate dehydrogenase subunit genes SDHB, SDHC and SDHD. J Med Genet 2018; 55:384-394. [PMID: 29386252 PMCID: PMC5992372 DOI: 10.1136/jmedgenet-2017-105127] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Germline pathogenic variants in SDHB/SDHC/SDHD are the most frequent causes of inherited phaeochromocytomas/paragangliomas. Insufficient information regarding penetrance and phenotypic variability hinders optimum management of mutation carriers. We estimate penetrance for symptomatic tumours and elucidate genotype-phenotype correlations in a large cohort of SDHB/SDHC/SDHD mutation carriers. METHODS A retrospective survey of 1832 individuals referred for genetic testing due to a personal or family history of phaeochromocytoma/paraganglioma. 876 patients (401 previously reported) had a germline mutation in SDHB/SDHC/SDHD (n=673/43/160). Tumour risks were correlated with in silico structural prediction analyses. RESULTS Tumour risks analysis provided novel penetrance estimates and genotype-phenotype correlations. In addition to tumour type susceptibility differences for individual genes, we confirmed that the SDHD:p.Pro81Leu mutation has a distinct phenotype and identified increased age-related tumour risks with highly destabilising SDHB missense mutations. By Kaplan-Meier analysis, the penetrance (cumulative risk of clinically apparent tumours) in SDHB and (paternally inherited) SDHD mutation-positive non-probands (n=371/67 with detailed clinical information) by age 60 years was 21.8% (95% CI 15.2% to 27.9%) and 43.2% (95% CI 25.4% to 56.7%), respectively. Risk of malignant disease at age 60 years in non-proband SDHB mutation carriers was 4.2%(95% CI 1.1% to 7.2%). With retrospective cohort analysis to adjust for ascertainment, cumulative tumour risks for SDHB mutation carriers at ages 60 years and 80 years were 23.9% (95% CI 20.9% to 27.4%) and 30.6% (95% CI 26.8% to 34.7%). CONCLUSIONS Overall risks of clinically apparent tumours for SDHB mutation carriers are substantially lower than initially estimated and will improve counselling of affected families. Specific genotype-tumour risk associations provides a basis for novel investigative strategies into succinate dehydrogenase-related mechanisms of tumourigenesis and the development of personalised management for SDHB/SDHC/SDHD mutation carriers.
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Affiliation(s)
- Katrina A Andrews
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Cancer Centre and Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Douglas Eduardo Valente Pires
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Daniel R Barnes
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Lindsey Vialard
- West Midlands Regional Genetics service, Birmingham Women's Hospital, Birmingham, UK
| | - Ruth T Casey
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Cancer Centre and Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nicola Bradshaw
- Department of Clinical Genetics, Queen Elizabeth University Hospital, Glasgow, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK
| | - Simon Aylwin
- Department of Endocrinology, King's College Hospital, London, UK
| | - Paul Brennan
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Carole Brewer
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Exeter, UK
| | - Trevor Cole
- West Midlands Regional Genetics service, Birmingham Women's Hospital, Birmingham, UK
| | - Jackie A Cook
- Department of Clinical Genetics, Sheffield Children's Hospital, Sheffield, UK
| | - Rosemarie Davidson
- Department of Clinical Genetics, Queen Elizabeth University Hospital, Glasgow, UK
| | - Alan Donaldson
- Department of Clinical Genetics, St Michael's Hospital, Bristol, UK
| | - Alan Fryer
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Lynn Greenhalgh
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Shirley V Hodgson
- Department of Medical Genetics, St. George's University of London, London, UK
| | - Richard Irving
- Queen Elizabeth Medical Centre, Queen Elizabeth Hospital, Birmingham, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Michelle McConachie
- East of Scotland Regional Genetics Service, Ninewells Hospital and Medical School, Dundee, UK
| | - Vivienne P M McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast, UK
| | - Patrick J Morrison
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast, UK
| | - Victoria Murday
- Department of Clinical Genetics, Queen Elizabeth University Hospital, Glasgow, UK
| | - Soo-Mi Park
- Department of Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Helen L Simpson
- The Wolfson Diabetes and Endocrine Clinic, Institute of Metabolic Science, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katie Snape
- Department of Medical Genetics, St. George's University of London, London, UK
| | - Susan Stewart
- West Midlands Regional Genetics service, Birmingham Women's Hospital, Birmingham, UK
| | - Susan E Tomkins
- Department of Clinical Genetics, St Michael's Hospital, Bristol, UK
| | - Yvonne Wallis
- West Midlands Regional Genetics service, Birmingham Women's Hospital, Birmingham, UK
| | - Louise Izatt
- Department of Clinical Genetics, Guy's Hospital, London, UK
| | - David Goudie
- East of Scotland Regional Genetics Service, Ninewells Hospital and Medical School, Dundee, UK
| | - Robert S Lindsay
- Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, Scotland
| | - Colin G Perry
- Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, Scotland
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Antonis C Antoniou
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and NIHR Cambridge Biomedical Research Centre and Cancer Research UK Cambridge Cancer Centre and Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- The Wolfson Diabetes and Endocrine Clinic, Institute of Metabolic Science, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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14
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Bannon AE, Kent J, Forquer I, Town A, Klug LR, McCann K, Beadling C, Harismendy O, Sicklick JK, Corless C, Shinde U, Heinrich MC. Biochemical, Molecular, and Clinical Characterization of Succinate Dehydrogenase Subunit A Variants of Unknown Significance. Clin Cancer Res 2017; 23:6733-6743. [PMID: 28724664 PMCID: PMC6011831 DOI: 10.1158/1078-0432.ccr-17-1397] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/20/2017] [Accepted: 07/14/2017] [Indexed: 01/14/2023]
Abstract
Purpose: Patients who inherit a pathogenic loss-of-function genetic variant involving one of the four succinate dehydrogenase (SDH) subunit genes have up to an 86% chance of developing one or more cancers by the age of 50. If tumors are identified and removed early in these high-risk patients, they have a higher potential for cure. Unfortunately, many alterations identified in these genes are variants of unknown significance (VUS), confounding the identification of high-risk patients. If we could identify misclassified SDH VUS as benign or pathogenic SDH mutations, we could better select patients for cancer screening procedures and remove tumors at earlier stages.Experimental Design: In this study, we combine data from clinical observations, a functional yeast model, and a computational model to determine the pathogenicity of 22 SDHA VUS. We gathered SDHA VUS from two primary sources: The OHSU Knight Diagnostics Laboratory and the literature. We used a yeast model to identify the functional effect of a VUS on mitochondrial function with a variety of biochemical assays. The computational model was used to visualize variants' effect on protein structure.Results: We were able to draw conclusions on functional effects of variants using our three-prong approach to understanding VUS. We determined that 16 (73%) of the alterations are actually pathogenic, causing loss of SDH function, and six (27%) have no effect upon SDH function.Conclusions: We thus report the reclassification of the majority of the VUS tested as pathogenic, and highlight the need for more thorough functional assessment of inherited SDH variants. Clin Cancer Res; 23(21); 6733-43. ©2017 AACR.
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Affiliation(s)
- Amber E Bannon
- Department of Cell and Developmental Biology, Heinrich Lab, Oregon Health and Science University, Portland, Oregon.
| | - Jason Kent
- Department of Cell and Developmental Biology, Heinrich Lab, Oregon Health and Science University, Portland, Oregon
| | - Isaac Forquer
- Portland VA Medical Center and Oregon Health and Science University, Portland, Oregon
| | - Ajia Town
- Heinrich Lab, Oregon Health and Science University, Portland, Oregon
| | - Lillian R Klug
- Department of Cancer Biology, Heinrich Lab, Oregon Health and Science University, Portland, Oregon
| | - Kelly McCann
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Carol Beadling
- Department of Pathology, Oregon Health and Science University, Portland, Oregon
| | - Oliver Harismendy
- Division of Biomedical Informatics, Department of Medicine, Moores UCSD Cancer Center, University of California San Diego, La Jolla, California
| | - Jason K Sicklick
- Division of Surgical Oncology, Department of Surgery, Moores UCSD Cancer Center, University of California San Diego, La Jolla, California
| | - Christopher Corless
- Department of Pathology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Ujwal Shinde
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, Oregon
| | - Michael C Heinrich
- Departments of Medicine and Cell, Developmental, and Cancer Biology, Portland VA Health Care System and OHSU Knight Cancer Institute, Portland, Oregon
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15
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Bannon AE, Klug LR, Corless CL, Heinrich MC. Using molecular diagnostic testing to personalize the treatment of patients with gastrointestinal stromal tumors. Expert Rev Mol Diagn 2017; 17:445-457. [PMID: 28317407 DOI: 10.1080/14737159.2017.1308826] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION The diagnosis and treatment of gastrointestinal stromal tumor (GIST) has emerged as a paradigm for modern cancer treatment ('precision medicine'), as it highlights the importance of matching molecular defects with specific therapies. Over the past two decades, the molecular classification and diagnostic work up of GIST has been radically transformed, accompanied by the development of molecular therapies for specific subgroups of GIST. This review summarizes the developments in the field of molecular diagnosis of GIST, particularly as they relate to optimizing medical therapy. Areas covered: Based on an extensive literature search of the molecular and clinical aspects of GIST, the authors review the most important developments in this field with an emphasis on the differential diagnosis of GIST including mutation testing, therapeutic implications of each molecular subtype, and emerging technologies relevant to the field. Expert commentary: The use of molecular diagnostics to classify GIST has been shown to be successful in optimizing patient treatment, but these methods remain under-utilized. In order to facilitate efficient and comprehensive molecular testing, the authors have developed a decision tree to aid clinicians.
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Affiliation(s)
- Amber E Bannon
- a Portland VA Health Care System and OHSU Knight Cancer Institute , Portland , OR , USA
| | - Lillian R Klug
- a Portland VA Health Care System and OHSU Knight Cancer Institute , Portland , OR , USA
| | - Christopher L Corless
- a Portland VA Health Care System and OHSU Knight Cancer Institute , Portland , OR , USA
| | - Michael C Heinrich
- a Portland VA Health Care System and OHSU Knight Cancer Institute , Portland , OR , USA
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16
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Bennedbæk M, Rossing M, Rasmussen ÅK, Gerdes AM, Skytte AB, Jensen UB, Nielsen FC, Hansen TVO. Identification of eight novel SDHB, SDHC, SDHD germline variants in Danish pheochromocytoma/paraganglioma patients. Hered Cancer Clin Pract 2016; 14:13. [PMID: 27279923 PMCID: PMC4898401 DOI: 10.1186/s13053-016-0053-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/01/2016] [Indexed: 12/24/2022] Open
Abstract
Background Germline mutations in the succinate dehydrogenase complex genes SDHB, SDHC, and SDHD predispose to pheochromocytomas and paragangliomas. Here, we examine the SDHB, SDHC, and SDHD mutation spectrum in the Danish population by screening of 143 Danish pheochromocytoma and paraganglioma patients. Methods Mutational screening was performed by Sanger sequencing or next-generation sequencing. The frequencies of variants of unknown clinical significance, e.g. intronic, missense, and synonymous variants, were determined using the Exome Aggregation Consortium database, while the significance of missense mutations was predicted by in silico and loss of heterozygosity analysis when possible. Results We report 18 germline variants; nine in SDHB, six in SDHC, and three in SDHD. Of these 18 variants, eight are novel. We classify 12 variants as likely pathogenic/pathogenic, one as likely benign, and five as variants of unknown clinical significance. Conclusions Identifying and classifying SDHB, SDHC, and SDHD variants present in the Danish population will augment the growing knowledge on variants in these genes and may support future clinical risk assessments.
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Affiliation(s)
- Marc Bennedbæk
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Maria Rossing
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Åse K Rasmussen
- Department of Medical Endocrinology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Anne-Bine Skytte
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21 C, Aarhus N, 8200 Denmark
| | - Uffe B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21 C, Aarhus N, 8200 Denmark
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
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17
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Nolli C, Goffrini P, Lazzaretti M, Zanna C, Vitale R, Lodi T, Baruffini E. Validation of a MGM1/OPA1 chimeric gene for functional analysis in yeast of mutations associated with dominant optic atrophy. Mitochondrion 2015; 25:38-48. [PMID: 26455272 DOI: 10.1016/j.mito.2015.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 09/24/2015] [Accepted: 10/01/2015] [Indexed: 01/08/2023]
Abstract
Mutations in OPA1 are associated with DOA or DOA plus. Novel mutations in OPA1 are periodically identified, but often the causative effect of the mutation is not demonstrated. A chimeric protein containing the N-terminal region of Mgm1, the yeast orthologue of OPA1, and the C-terminal region of OPA1 was constructed. This chimeric construct can be exploited to evaluate the pathogenicity of most of the missense mutations in OPA1 as well as to determine whether the dominance of the mutation is due to haploinsufficiency or to gain of function.
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Affiliation(s)
- Cecilia Nolli
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Mirca Lazzaretti
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy; IRCCS Institute of Neurological Sciences of Bologna, Bellaria Hospital, Via Altura 3, 40139 Bologna, Italy
| | - Rita Vitale
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy
| | - Tiziana Lodi
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy
| | - Enrico Baruffini
- Department of Life Sciences, University of Parma, Viale delle Scienze 11/A, 43124 Parma, Italy.
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18
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Kim E, Rath EM, Tsang VHM, Duff AP, Robinson BG, Church WB, Benn DE, Dwight T, Clifton-Bligh RJ. Structural and functional consequences of succinate dehydrogenase subunit B mutations. Endocr Relat Cancer 2015; 22:387-97. [PMID: 25972245 DOI: 10.1530/erc-15-0099] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mitochondrial dysfunction, due to mutations of the gene encoding succinate dehydrogenase (SDH), has been implicated in the development of adrenal phaeochromocytomas, sympathetic and parasympathetic paragangliomas, renal cell carcinomas, gastrointestinal stromal tumours and more recently pituitary tumours. Underlying mechanisms behind germline SDH subunit B (SDHB) mutations and their associated risk of disease are not clear. To investigate genotype-phenotype correlation of SDH subunit B (SDHB) variants, a homology model for human SDH was developed from a crystallographic structure. SDHB mutations were mapped, and biochemical effects of these mutations were predicted in silico. Results of structural modelling indicated that many mutations within SDHB are predicted to cause either failure of functional SDHB expression (p.Arg27*, p.Arg90*, c.88delC and c.311delAinsGG), or disruption of the electron path (p.Cys101Tyr, p.Pro197Arg and p.Arg242His). GFP-tagged WT SDHB and mutant SDHB constructs were transfected (HEK293) to determine biological outcomes of these mutants in vitro. According to in silico predictions, specific SDHB mutations resulted in impaired mitochondrial localisation and/or SDH enzymatic activity. These results indicated strong genotype-functional correlation for SDHB variants. This study reveals new insights into the effects of SDHB mutations and the power of structural modelling in predicting biological consequences. We predict that our functional assessment of SDHB mutations will serve to better define specific consequences for SDH activity as well as to provide a much needed assay to distinguish pathogenic mutations from benign variants.
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Affiliation(s)
- E Kim
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - E M Rath
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - V H M Tsang
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - A P Duff
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - B G Robinson
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - W B Church
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - D E Benn
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - T Dwight
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
| | - R J Clifton-Bligh
- Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia Cancer GeneticsKolling Institute of Medical Research, Royal North Shore Hospital, and University of Sydney, Sydney, New South Wales, AustraliaDepartment of EndocrinologyRoyal North Shore Hospital, Sydney, New South Wales, AustraliaFaculty of PharmacyUniversity of Sydney, Sydney, New South Wales, AustraliaAustralian Nuclear Science and Technology OrganisationLucas Heights, New South Wales, Australia
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19
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Alston CL, Ceccatelli Berti C, Blakely EL, Oláhová M, He L, McMahon CJ, Olpin SE, Hargreaves IP, Nolli C, McFarland R, Goffrini P, O'Sullivan MJ, Taylor RW. A recessive homozygous p.Asp92Gly SDHD mutation causes prenatal cardiomyopathy and a severe mitochondrial complex II deficiency. Hum Genet 2015; 134:869-79. [PMID: 26008905 PMCID: PMC4495259 DOI: 10.1007/s00439-015-1568-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/16/2015] [Indexed: 01/15/2023]
Abstract
Succinate dehydrogenase (SDH) is a crucial metabolic enzyme complex that is involved in ATP production, playing roles in both the tricarboxylic cycle and the mitochondrial respiratory chain (complex II). Isolated complex II deficiency is one of the rarest oxidative phosphorylation disorders with mutations described in three structural subunits and one of the assembly factors; just one case is attributed to recessively inherited SDHD mutations. We report the pathological, biochemical, histochemical and molecular genetic investigations of a male neonate who had left ventricular hypertrophy detected on antenatal scan and died on day one of life. Subsequent postmortem examination confirmed hypertrophic cardiomyopathy with left ventricular non-compaction. Biochemical analysis of his skeletal muscle biopsy revealed evidence of a severe isolated complex II deficiency and candidate gene sequencing revealed a novel homozygous c.275A>G, p.(Asp92Gly) SDHD mutation which was shown to be recessively inherited through segregation studies. The affected amino acid has been reported as a Dutch founder mutation p.(Asp92Tyr) in families with hereditary head and neck paraganglioma. By introducing both mutations into Saccharomyces cerevisiae, we were able to confirm that the p.(Asp92Gly) mutation causes a more severe oxidative growth phenotype than the p.(Asp92Tyr) mutant, and provides functional evidence to support the pathogenicity of the patient’s SDHD mutation. This is only the second case of mitochondrial complex II deficiency due to inherited SDHD mutations and highlights the importance of sequencing all SDH genes in patients with biochemical and histochemical evidence of isolated mitochondrial complex II deficiency.
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Affiliation(s)
- Charlotte L Alston
- Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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20
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Nesti C, Meschini MC, Meunier B, Sacchini M, Doccini S, Romano A, Petrillo S, Pezzini I, Seddiki N, Rubegni A, Piemonte F, Donati MA, Brasseur G, Santorelli FM. Additive effect of nuclear and mitochondrial mutations in a patient with mitochondrial encephalomyopathy. Hum Mol Genet 2015; 24:3248-56. [PMID: 25736212 DOI: 10.1093/hmg/ddv078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/26/2015] [Indexed: 12/12/2022] Open
Abstract
We describe the case of a woman in whom combination of a mitochondrial (MT-CYB) and a nuclear (SDHB) mutation was associated with clinical and metabolic features suggestive of a mitochondrial disorder. The mutations impaired overall energy metabolism in the patient's muscle and fibroblasts and increased cellular susceptibility to oxidative stress. To clarify the contribution of each mutation to the phenotype, mutant yeast strains were generated. A significant defect in strains carrying the Sdh2 mutation, either alone or in combination with the cytb variant, was observed. Our data suggest that the SDHB mutation was causative of the mitochondrial disorder in our patient with a possible cumulative contribution of the MT-CYB variant. To our knowledge, this is the first association of bi-genomic variants in the mtDNA and in a nuclear gene encoding a subunit of complex II.
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Affiliation(s)
| | | | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Michele Sacchini
- Metabolic and Neuromuscular Unit, AOU Meyer Hospital, Florence, Italy
| | | | - Alessandro Romano
- Neuropathology Unit, Institute of Experimental Neurology and Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Petrillo
- Unit for Neuromuscular and Neurodegenerative Diseases, "Bambino Gesù" Children's Hospital, Rome, Italy and
| | | | - Nadir Seddiki
- Laboratoire de Chimie Bactérienne, CNRS, 31 ch. J. Aiguier, 13402 Marseilles, France
| | - Anna Rubegni
- Molecular Medicine, IRCCS Stella Maris, Pisa, Italy
| | - Fiorella Piemonte
- Unit for Neuromuscular and Neurodegenerative Diseases, "Bambino Gesù" Children's Hospital, Rome, Italy and
| | - M Alice Donati
- Metabolic and Neuromuscular Unit, AOU Meyer Hospital, Florence, Italy
| | - Gael Brasseur
- Laboratoire de Chimie Bactérienne, CNRS, 31 ch. J. Aiguier, 13402 Marseilles, France
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21
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Chang YL, Hsieh MH, Chang WW, Wang HY, Lin MC, Wang CP, Lou PJ, Teng SC. Instability of succinate dehydrogenase in SDHD polymorphism connects reactive oxygen species production to nuclear and mitochondrial genomic mutations in yeast. Antioxid Redox Signal 2015; 22:587-602. [PMID: 25328978 PMCID: PMC4334101 DOI: 10.1089/ars.2014.5966] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
AIMS Mitochondrial succinate dehydrogenase (SDH) is an essential complex of the electron transport chain and tricarboxylic acid cycle. Mutations in the human SDH subunit D frequently lead to paraganglioma (PGL), but the mechanistic consequences of the majority of SDHD polymorphisms have yet to be unraveled. In addition to the originally discovered yeast SDHD subunit Sdh4, a conserved homolog, Shh4, has recently been identified in budding yeast. To assess the pathogenic significance of SDHD mutations in PGL patients, we performed functional studies in yeast. RESULTS SDHD protein expression was reduced in SDHD-related carotid body tumor tissues. A BLAST search of SDHD to the yeast protein database revealed a novel protein, Shh4, that may have a function similar to human SDHD and yeast Sdh4. The missense SDHD mutations identified in PGL patients were created in Sdh4 and Shh4, and, surprisingly, a severe respiratory incompetence and reduced expression of the mutant protein was observed in the sdh4Δ strain expressing shh4. Although shh4Δ cells showed no respiratory-deficient phenotypes, deletion of SHH4 in sdh4Δ cells further abolished mitochondrial function. Remarkably, sdh4Δ shh4Δ strains exhibited increased reactive oxygen species (ROS) production, nuclear DNA instability, mtDNA mutability, and decreased chronological lifespan. INNOVATION AND CONCLUSION SDHD mutations are associated with protein and nuclear and mitochondrial genomic instability and increase ROS production in our yeast model. These findings reinforce our understanding of the mechanisms underlying PGL tumorigenesis and point to the yeast Shh4 as a good model to investigate the possible pathogenic relevance of SDHD in PGL polymorphisms.
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Affiliation(s)
- Ya-Lan Chang
- 1 Department of Microbiology, College of Medicine, National Taiwan University , Taipei, Taiwan
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Lalève A, Fillinger S, Walker AS. Fitness measurement reveals contrasting costs in homologous recombinant mutants of Botrytis cinerea resistant to succinate dehydrogenase inhibitors. Fungal Genet Biol 2014; 67:24-36. [DOI: 10.1016/j.fgb.2014.03.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/20/2014] [Accepted: 03/21/2014] [Indexed: 01/22/2023]
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Montanari A, Francisci S, Fazzi D'Orsi M, Bianchi MM. Strain-specific nuclear genetic background differentially affects mitochondria-related phenotypes in Saccharomyces cerevisiae. Microbiologyopen 2014; 3:288-98. [PMID: 24700775 PMCID: PMC4082703 DOI: 10.1002/mbo3.167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/09/2014] [Accepted: 01/20/2014] [Indexed: 01/18/2023] Open
Abstract
In the course of our studies on mitochondrial defects, we have observed important phenotypic variations in Saccharomyces cerevisiae strains suggesting that a better characterization of the genetic variability will be essential to define the relationship between the mitochondrial efficiency and the presence of different nuclear backgrounds. In this manuscript, we have extended the study of such relations by comparing phenotypic assays related to mitochondrial functions of three wild-type laboratory strains. In addition to the phenotypic variability among the wild-type strains, important differences have been observed among strains bearing identical mitochondrial tRNA mutations that could be related only to the different nuclear background of the cells. Results showed that strains exhibited an intrinsic variability in the severity of the effects of the mitochondrial mutations and that specific strains might be used preferentially to evaluate the phenotypic effect of mitochondrial mutations on carbon metabolism, stress responses, and mitochondrial DNA stability. In particular, while W303-1B and MCC123 strains should be used to study the effect of severe mitochondrial tRNA mutations, D273-10B/A1 strain is rather suitable for studying the effects of milder mutations.
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Affiliation(s)
- Arianna Montanari
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, Piazzale A. Moro 5, Rome, 00185, Italy; Pasteur Institute-Cenci Bolognetti Foundation, Sapienza University of Rome, Piazzale A. Moro 5, Rome, 00185, Italy
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Crona J, Nordling M, Maharjan R, Granberg D, Stålberg P, Hellman P, Björklund P. Integrative genetic characterization and phenotype correlations in pheochromocytoma and paraganglioma tumours. PLoS One 2014; 9:e86756. [PMID: 24466223 PMCID: PMC3899286 DOI: 10.1371/journal.pone.0086756] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 12/13/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND About 60% of Pheochromocytoma (PCC) and Paraganglioma (PGL) patients have either germline or somatic mutations in one of the 12 proposed disease causing genes; SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, EPAS1, RET, NF1, TMEM127, MAX and H-RAS. Selective screening for germline mutations is routinely performed in clinical management of these diseases. Testing for somatic alterations is not performed on a regular basis because of limitations in interpreting the results. AIM The purpose of the study was to investigate genetic events and phenotype correlations in a large cohort of PCC and PGL tumours. METHODS A total of 101 tumours from 89 patients with PCC and PGL were re-sequenced for a panel of 10 disease causing genes using automated Sanger sequencing. Selected samples were analysed with Multiplex Ligation-dependent Probe Amplification and/or SNParray. RESULTS Pathogenic genetic variants were found in tumours from 33 individual patients (37%), 14 (16%) were discovered in constitutional DNA and 16 (18%) were confirmed as somatic. Loss of heterozygosity (LOH) was observed in 1/1 SDHB, 11/11 VHL and 3/3 NF1-associated tumours. In patients with somatic mutations there were no recurrences in contrast to carriers of germline mutations (P = 0.022). SDHx/VHL/EPAS1 associated cases had higher norepinephrine output (P = 0.03) and lower epinephrine output (P<0.001) compared to RET/NF1/H-RAS cases. CONCLUSION Somatic mutations are frequent events in PCC and PGL tumours. Tumour genotype may be further investigated as prognostic factors in these diseases. Growing evidence suggest that analysis of tumour DNA could have an impact on the management of these patients.
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Affiliation(s)
- Joakim Crona
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Margareta Nordling
- Department of Clinical Genetics, Sahlgrenska University Hospital, Göteborg, Sweden
| | - Rajani Maharjan
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Dan Granberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Peter Stålberg
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Per Hellman
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Peyman Björklund
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- * E-mail:
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