1
|
Boumajdi N, Bendani H, Kartti S, Alouane T, Belyamani L, Ibrahimi A. A Comprehensive Analysis of 3 Moroccan Genomes Revealed Contributions From Both African and European Ancestries. Evol Bioinform Online 2024; 20:11769343241229278. [PMID: 38327511 PMCID: PMC10848790 DOI: 10.1177/11769343241229278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Genetic variations in the human genome represent the differences in DNA sequence within individuals. This highlights the important role of whole human genome sequencing which has become the keystone for precision medicine and disease prediction. Morocco is an important hub for studying human population migration and mixing history. This study presents the analysis of 3 Moroccan genomes; the variant analysis revealed 6 379 606 single nucleotide variants (SNVs) and 1 050 577 small InDels. Of those identified SNVs, 219 152 were novel, with 1233 occurring in coding regions, and 5580 non-synonymous single nucleotide variants (nsSNP) variants were predicted to affect protein functions. The InDels produced 1055 coding variants and 454 non-3n length variants, and their size ranged from -49 and 49 bp. We further analysed the gene pathways of 8 novel coding variants found in the 3 genomes and revealed 5 genes involved in various diseases and biological pathways. We found that the Moroccan genomes share 92.78% of African ancestry, and 92.86% of Non-Finnish European ancestry, according to the gnomAD database. Then, population structure inference, by admixture analysis and network-based approach, revealed that the studied genomes form a mixed population structure, highlighting the increased genetic diversity in Morocco.
Collapse
Affiliation(s)
- Nasma Boumajdi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
| | - Houda Bendani
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
| | - Souad Kartti
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
| | - Tarek Alouane
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lahcen Belyamani
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
- Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Azeddine Ibrahimi
- Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
- Mohammed VI Center for Research & Innovation (CM6), Rabat, Morocco
- Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| |
Collapse
|
2
|
Liu G, Ni C, Zhan J, Li W, Luo J, Liao Z, Locascio JJ, Xian W, Chen L, Pei Z, Corvol JC, Maple-Grødem J, Campbell MC, Elbaz A, Lesage S, Brice A, Hung AY, Schwarzschild MA, Hayes MT, Wills AM, Ravina B, Shoulson I, Taba P, Kõks S, Beach TG, Cormier-Dequaire F, Alves G, Tysnes OB, Perlmutter JS, Heutink P, van Hilten JJ, Barker RA, Williams-Gray CH, Scherzer CR. Mitochondrial haplogroups and cognitive progression in Parkinson's disease. Brain 2023; 146:42-49. [PMID: 36343661 PMCID: PMC10202390 DOI: 10.1093/brain/awac327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondria are a culprit in the onset of Parkinson's disease, but their role during disease progression is unclear. Here we used Cox proportional hazards models to exam the effect of variation in the mitochondrial genome on longitudinal cognitive and motor progression over time in 4064 patients with Parkinson's disease. Mitochondrial macro-haplogroup was associated with reduced risk of cognitive disease progression in the discovery and replication population. In the combined analysis, patients with the super macro-haplogroup J, T, U# had a 41% lower risk of cognitive progression with P = 2.42 × 10-6 compared to those with macro-haplogroup H. Exploratory analysis indicated that the common mitochondrial DNA variant, m.2706A>G, was associated with slower cognitive decline with a hazard ratio of 0.68 (95% confidence interval 0.56-0.81) and P = 2.46 × 10-5. Mitochondrial haplogroups were not appreciably linked to motor progression. This initial genetic survival study of the mitochondrial genome suggests that mitochondrial haplogroups may be associated with the pace of cognitive progression in Parkinson's disease over time.
Collapse
Affiliation(s)
- Ganqiang Liu
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Chunming Ni
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiamin Zhan
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Weimin Li
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Junfeng Luo
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Neurogenomics Lab, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joseph J Locascio
- APDA Center for Advanced Parkinson Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Neurogenomics Lab, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Wenbiao Xian
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ling Chen
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zhong Pei
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jean-Christophe Corvol
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Jodi Maple-Grødem
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, 4068 Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
| | - Meghan C Campbell
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexis Elbaz
- Paris-Saclay University, UVSQ, Inserm, Gustave Roussy, ‘Exposome and Heredity’ Team, CESP, F94805 Villejuif, France
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Albert Y Hung
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael A Schwarzschild
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael T Hayes
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Ira Shoulson
- Department of Neurology, Center for Health and Technology, University of Rochester, Rochester, NY 14642, USA
| | - Pille Taba
- Department of Neurology and Neurosurgery, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | - Sulev Kõks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Florence Cormier-Dequaire
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Guido Alves
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, 4068 Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
- Department of Neurology, Stavanger University Hospital, 4068 Stavanger, Norway
| | - Ole-Bjørn Tysnes
- Department of Neurology, Haukeland University Hospital, 5020 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Joel S Perlmutter
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Departments of Radiology and Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program of Physical Therapy and Program of Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peter Heutink
- German Center for Neurodegenerative diseases (DZNE), 72076 Tübingen, Germany
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Roger A Barker
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
- Wellcome—MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Caroline H Williams-Gray
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Neurogenomics Lab, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| |
Collapse
|
3
|
Caporali L, Fiorini C, Palombo F, Romagnoli M, Baccari F, Zenesini C, Visconti P, Posar A, Scaduto MC, Ormanbekova D, Battaglia A, Tancredi R, Cameli C, Viggiano M, Olivieri A, Torroni A, Maestrini E, Rochat MJ, Bacchelli E, Carelli V, Maresca A. Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder. Front Genet 2022; 13:953762. [PMID: 36419830 PMCID: PMC9676943 DOI: 10.3389/fgene.2022.953762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2023] Open
Abstract
Autism spectrum disorder (ASD) is a clinically heterogeneous class of neurodevelopmental conditions with a strong, albeit complex, genetic basis. The genetic architecture of ASD includes different genetic models, from monogenic transmission at one end, to polygenic risk given by thousands of common variants with small effects at the other end. The mitochondrial DNA (mtDNA) was also proposed as a genetic modifier for ASD, mostly focusing on maternal mtDNA, since the paternal mitogenome is not transmitted to offspring. We extensively studied the potential contribution of mtDNA in ASD pathogenesis and risk through deep next generation sequencing and quantitative PCR in a cohort of 98 families. While the maternally-inherited mtDNA did not seem to predispose to ASD, neither for haplogroups nor for the presence of pathogenic mutations, an unexpected influence of paternal mtDNA, apparently centered on haplogroup U, came from the Italian families extrapolated from the test cohort (n = 74) when compared to the control population. However, this result was not replicated in an independent Italian cohort of 127 families and it is likely due to the elevated paternal age at time of conception. In addition, ASD probands showed a reduced mtDNA content when compared to their unaffected siblings. Multivariable regression analyses indicated that variants with 15%-5% heteroplasmy in probands are associated to a greater severity of ASD based on ADOS-2 criteria, whereas paternal super-haplogroups H and JT were associated with milder phenotypes. In conclusion, our results suggest that the mtDNA impacts on ASD, significantly modifying the phenotypic expression in the Italian population. The unexpected finding of protection induced by paternal mitogenome in term of severity may derive from a role of mtDNA in influencing the accumulation of nuclear de novo mutations or epigenetic alterations in fathers' germinal cells, affecting the neurodevelopment in the offspring. This result remains preliminary and needs further confirmation in independent cohorts of larger size. If confirmed, it potentially opens a different perspective on how paternal non-inherited mtDNA may predispose or modulate other complex diseases.
Collapse
Affiliation(s)
- Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Baccari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Danara Ormanbekova
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Agatino Battaglia
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Raffaella Tancredi
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali Jane Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma Diagnostica Funzionale Neuroradiologica, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| |
Collapse
|
4
|
Pezo P, Orellana-Soto M, de la Fuente C, Leiva X, Herrera L, Flores-Alvarado S, Galimany J, de Saint Pierre M, Bravi C, Moraga M. Native American mitochondrial lineages in admixed populations from Chile: Detecting recent migrations during post-Columbian times using geographically restricted lineages. Am J Biol Anthropol 2022; 178:504-512. [PMID: 36790622 DOI: 10.1002/ajpa.24513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/02/2022] [Accepted: 02/22/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVES To analyze the mitochondrial diversity in three admixed populations and evaluate the historical migration effect of native southern population movement to Santiago (capital of Chile). The intensity of migration was quantified using three mitochondrial lineages restricted to South-Central native groups. METHODS D-loop sequences were genotyped in 550 unrelated individuals from San Felipe-Los Andes (n = 108), Santiago (n = 217), and Concepción (n = 225). Sequence processing, alignment, and haplogroup inference were carried out, and different genetic structure analyses were performed for haplogroup frequencies and D-loop sequences. RESULTS The Native lineages B2i2, C1b13, and D1g were the most frequent haplogroups, especially in Santiago (71.8%). Despite the distance, this city showed a high-genetic affinity with southern populations, including Concepción (~500 km distant) and native groups, rather than with those from San Felipe-Los Andes (<100 km distant). In fact, there was a negative correlation between geographical and genetic distance among these cities (r corr = -0.5593, p value = 0.8387). Network analysis revealed shared haplotypes between Santiago, Concepción, and other southern populations. Finally, we found lineages from Concepción acting as ancestral nodes in the northern clade. CONCLUSIONS Considering the geographic distances from these cities, the results were not consistent with a model of genetic isolation by geographic distance, revealing the effects of a historical migration process from the south to the capital. We also show evidence of possible north-to-south migration during admixture onset in Concepción and in addition, we were able to identify previously unreported mitochondrial diversity in urban populations that became lost in Native groups post-European contact.
Collapse
Affiliation(s)
- Patricio Pezo
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michael Orellana-Soto
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Ximena Leiva
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Luisa Herrera
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Programa de Bioestadística, Instituto de Salud Poblacional, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Jacqueline Galimany
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Claudio Bravi
- CCT La Plata, IMBICE, La Plata, Argentina.,Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| |
Collapse
|
5
|
Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. Am J Phys Anthropol 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
Collapse
Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| |
Collapse
|
6
|
González-Oliver A, Pineda-Vázquez D, Garfias-Morales E, La Cruz-Laina ID, Medrano-González L, Márquez-Morfín L, Ortega-Muñoz A. Genetic Overview of the Maya Populations: Mitochondrial DNA Haplogroups. Hum Biol 2019; 90:281-300. [PMID: 31714695 DOI: 10.13110/humanbiology.90.4.03] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022]
Abstract
We identified mitochondrial DNA haplogroups A, B, C, and D in 75 present-day Maya individuals, 24 Maya individuals of the colonial period, and 1 pre-Columbian Maya individual from Quintana Roo, Mexico. We examined these data together with those of 21 Maya populations reported in the literature, comprising 647 present-day Maya individuals and 71 ancient Maya individuals. A demographic study based on analysis of fertility and endogamy was carried out in two modern Maya populations to identify cultural factors that influence the mitochondrial haplogroup genetic diversity. Most present-day and ancient Maya populations show a distribution pattern of mitochondrial haplogroup frequencies A, C, B, and D in decreasing order, with haplogroup D absent in several populations. Considering only modern Maya populations with at least 50 individuals analyzed, the present-day Tzotzil and Lacandon populations from Chiapas show the highest and lowest genetic diversity, 0.706 and 0.025, respectively. Our results show small genetic differences between the Maya populations, with the exception of the present-day Tojolabal and Lacandon populations from Chiapas. The present-day Lacandon population from Chiapas differs from other Maya populations in showing almost only haplogroup A. This result suggests a long history of isolation and endogamy as well as a possible founder effect inside the Lacandonian rain forest. The contemporary Tojolabal population is the only one with an unusual mitochondrial haplogroup pattern, exhibiting a frequency of haplogroup B higher than A and the absence of haplogroup C. With a small sample size, the pre-Columbian Copán Maya show a high content of haplogroup C and a low frequency of haplogroup D. The genetic homogeneity of the Maya populations is indicative of a common origin and nearly continuous gene flow in the long term within a general isolation of the whole group, in contrast to the Nahua populations that had different origins. Our demographic study showed high fertility rates and high levels of endogamy in the present-day Maya populations from Quintana Roo that are consistent with their general low genetic diversity. We propose that the genetic similarity among ancient and present-day Maya populations persists due to a strong sense of social cohesion and identity that impacts their marriage practices, keeping this cultural group isolated. These factors have constrained gene flow inside the Maya region and have impeded the differentiation among the Maya. Discernment of genetic differentiation within the peninsula is constrained by the lack of sampling documentation in the literature.
Collapse
Affiliation(s)
- Angélica González-Oliver
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México,
| | - Dircé Pineda-Vázquez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ernesto Garfias-Morales
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Isabel De La Cruz-Laina
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Luis Medrano-González
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Lourdes Márquez-Morfín
- Escuela Nacional de Antropología e Historia, Instituto Nacional de Antropología e Historia, Ciudad de México, México
| | | |
Collapse
|
7
|
Zhao D, Ding Y, Lin H, Chen X, Shen W, Gao M, Wei Q, Zhou S, Liu X, He N. Mitochondrial Haplogroups N9 and G Are Associated with Metabolic Syndrome Among Human Immunodeficiency Virus-Infected Patients in China. AIDS Res Hum Retroviruses 2019; 35:536-543. [PMID: 30950284 DOI: 10.1089/aid.2018.0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Increasing evidence shows that mitochondrial DNA (mtDNA) variations have an important effect on metabolic disorders, but such studies have not been conducted in HIV-infected patients in Asia. We investigated the distribution of mtDNA haplogroups and their correlation with metabolic disorders in HIV-infected patients. A cross-sectional survey was performed among 296 HIV patients older than the age of 40 years in a rural prefecture, Eastern China. The entire mtDNA sequence was amplified by polymerase chain reaction using four overlapping pairs of primers that have been standardly used. In this sample, mtDNA haplogroups B, D, M7, and F were the most dominant haplogroups. The overall prevalence of metabolic syndrome (MetS) was 36.1%, and was highest (77.8%) among those with haplogroup G and lowest (21.4%) among those with haplogroup M8. In multivariable analysis, haplogroups G and N9 were significantly associated with the presence of MetS [adjusted odds ratio (aOR) = 13.5, 95% confidence interval (CI): 1.9-94.7; aOR = 8.1, 95% CI: 1.8-36.1; respectively]. Moreover, patients with haplogroup G had increased odds of elevated glycated hemoglobin (HbA1c) (aOR = 10.1, 95% CI: 1.4-71.1), patients with haplogroup N9 had increased odds of elevated triglycerides (aOR = 13.5, 95% CI: 2.4-76.8). No significant association between mtDNA haplogroups and other MetS components was observed. Our data demonstrate the association between mtDNA haplogroups and MetS in HIV-infected patients. The Asian-specific mtDNA haplogroups G and N9 may confer higher risk for the development of MetS in HIV-infected patients, which requires further longitudinal investigation.
Collapse
Affiliation(s)
- Dan Zhao
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Health Technology Assessment of Ministry of Health, Fudan University, Shanghai, China
| | - Yingying Ding
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Haijiang Lin
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
- Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Xiaoxiao Chen
- Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Weiwei Shen
- Taizhou City Center for Disease Control and Prevention, Taizhou, China
| | - Meiyang Gao
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Qian Wei
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Sujuan Zhou
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Xing Liu
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
| | - Na He
- School of Public Health, Fudan University, Shanghai, China
- Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China
- Key Laboratory of Health Technology Assessment of Ministry of Health, Fudan University, Shanghai, China
| |
Collapse
|
8
|
Cui QN, Ramakrishnan MS, Gudiseva HV, Collins DW, Pistilli M, Lee R, Chavali VM, Lehman A, Addis VM, O'Brien JM. Mitochondrial haplogroup L1c2 is associated with increased disease severity in African American patients with primary open-angle glaucoma. J Clin Exp Ophthalmol 2019; 10:799. [PMID: 31192031 PMCID: PMC6561505 DOI: 10.4172/2155-9570.1000799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
OBJECTIVE The purpose of this study is to evaluate the role mitochondrial inheritance plays in primary open-angle glaucoma (POAG) characteristics in African Americans. METHODS POAG cases from the L1c2 and L1b mitochondrial haplogroups were compared in a retrospective case-case study. Twenty-six pairs of self-identified African American POAG cases from L1c2 and L1b mitochondrial haplogroups matched on age (mean [SD] = 71.2 [9.6] and 71.3 [9.6] years, respectively; p = 0.97), sex (21 female and 5 male pairs), and family history of glaucoma (positive in 15/26 [58%] pairs) were included. RESULTS L1c2 subjects displayed higher vertical cup-to-disc ratio (0.75 [0.12] and 0.67 [0.16], respectively; p = 0.01, Bonferroni-corrected p = 0.08), worse pattern standard deviation on visual field (VF) testing (5.5 [3.5] and 3.5 [2.7]; p = 0.005, Bonferroni-corrected p = 0.02), and more severe glaucoma based on American Glaucoma Society staging criteria (p = 0.04, Bonferroni-corrected p = 0.32) compared to L1b subjects. L1c2 also trended towards worse mean deviation on VF compared to L1b (-8.2 [7.6] and -5.8 [6.8], respectively, p = 0.17). Best corrected visual acuity, central corneal thickness, maximum intraocular pressure (IOP), and cataract severity were comparable between L1c2 and L1b haplogroups (p ≥ 0.49), as was retinal nerve fiber layer thickness on optical coherence tomography (75.1 [14.1] and 75.1 [13.0]; p = 0.99). CONCLUSION Results demonstrated worse glaucomatous cupping and more severe VF loss in the L1c2 compared to the L1b haplogroup despite comparable IOP. Findings implicate mitochondrial inheritance as a factor affecting POAG severity and may ultimately contribute to stratifying POAG patients into phenotypically and genotypically distinct subgroups.
Collapse
Affiliation(s)
- Qi N Cui
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | | | | | - David W Collins
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Maxwell Pistilli
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Roy Lee
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | | | - Amanda Lehman
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Victoria M Addis
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| | - Joan M O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA
| |
Collapse
|
9
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
10
|
May-Panloup P, Boucret L, Chao de la Barca JM, Desquiret-Dumas V, Ferré-L'Hotellier V, Morinière C, Descamps P, Procaccio V, Reynier P. Ovarian ageing: the role of mitochondria in oocytes and follicles. Hum Reprod Update 2016; 22:725-743. [PMID: 27562289 DOI: 10.1093/humupd/dmw028] [Citation(s) in RCA: 301] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/15/2016] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND There is a great inter-individual variability of ovarian ageing, and almost 20% of patients consulting for infertility show signs of premature ovarian ageing. This feature, taken together with delayed childbearing in modern society, leads to the emergence of age-related ovarian dysfunction concomitantly with the desire for pregnancy. Assisted reproductive technology is frequently inefficacious in cases of ovarian ageing, thus raising the economic, medical and societal costs of the procedures. OBJECTIVE AND RATIONAL Ovarian ageing is characterized by quantitative and qualitative alteration of the ovarian oocyte reserve. Mitochondria play a central role in follicular atresia and could be the main target of the ooplasmic factors determining oocyte quality adversely affected by ageing. Indeed, the oocyte is the richest cell of the body in mitochondria and depends largely on these organelles to acquire competence for fertilization and early embryonic development. Moreover, the oocyte ensures the uniparental transmission and stability of the mitochondrial genome across the generations. This review focuses on the role played by mitochondria in ovarian ageing and on the possible consequences over the generations. SEARCH METHODS PubMed was used to search the MEDLINE database for peer-reviewed original articles and reviews concerning mitochondria and ovarian ageing, in animal and human species. Searches were performed using keywords belonging to three groups: 'mitochondria' or 'mitochondrial DNA'; 'ovarian reserve', 'oocyte', 'ovary' or 'cumulus cells'; and 'ageing' or 'ovarian ageing'. These keywords were combined with other search phrases relevant to the topic. References from these articles were used to obtain additional articles. OUTCOMES There is a close relationship, in mammalian models and humans, between mitochondria and the decline of oocyte quality with ageing. Qualitatively, ageing-related mitochondrial (mt) DNA instability, which leads to the accumulation of mtDNA mutations in the oocyte, plays a key role in the deterioration of oocyte quality in terms of competence and of the risk of transmitting mitochondrial abnormalities to the offspring. In contrast, some mtDNA haplogroups are protective against the decline of ovarian reserve. Quantitatively, mitochondrial biogenesis is crucial during oogenesis for constituting a mitochondrial pool sufficiently large to allow normal early embryonic development and to avoid the untimely activation of mitochondrial biogenesis. Ovarian ageing also seriously affects the dynamic nature of mitochondrial biogenesis in the surrounding granulosa cells that may provide interesting alternative biomarkers of oocyte quality. WIDER IMPLICATIONS A fuller understanding of the involvement of mitochondria in cases of infertility linked to ovarian ageing would contribute to a better management of the disorder in the future.
Collapse
Affiliation(s)
- Pascale May-Panloup
- Laboratoire de Biologie de la Reproduction, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France .,PREMMi/Pôle de Recherche et d'Enseignement en Médecine Mitochondriale, Institut MITOVASC, CNRS 6214, INSERM U1083, Université d'Angers, Angers, France
| | - Lisa Boucret
- Laboratoire de Biologie de la Reproduction, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France.,PREMMi/Pôle de Recherche et d'Enseignement en Médecine Mitochondriale, Institut MITOVASC, CNRS 6214, INSERM U1083, Université d'Angers, Angers, France
| | - Juan-Manuel Chao de la Barca
- PREMMi/Pôle de Recherche et d'Enseignement en Médecine Mitochondriale, Institut MITOVASC, CNRS 6214, INSERM U1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| | - Valérie Desquiret-Dumas
- PREMMi/Pôle de Recherche et d'Enseignement en Médecine Mitochondriale, Institut MITOVASC, CNRS 6214, INSERM U1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| | - Véronique Ferré-L'Hotellier
- Laboratoire de Biologie de la Reproduction, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| | - Catherine Morinière
- Service de Gynécologie-Obstétrique, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| | - Philippe Descamps
- Service de Gynécologie-Obstétrique, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| | - Vincent Procaccio
- PREMMi/Pôle de Recherche et d'Enseignement en Médecine Mitochondriale, Institut MITOVASC, CNRS 6214, INSERM U1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| | - Pascal Reynier
- PREMMi/Pôle de Recherche et d'Enseignement en Médecine Mitochondriale, Institut MITOVASC, CNRS 6214, INSERM U1083, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, Centre Hospitalier Universitaire d'Angers, 49933 Angers Cedex 9, France
| |
Collapse
|
11
|
Li M, Foli Y, Liu Z, Wang G, Hu Y, Lu Q, Selvaraj S, Lam W, Paintsil E. High frequency of mitochondrial DNA mutations in HIV-infected treatment-experienced individuals. HIV Med 2016; 18:45-55. [PMID: 27328746 PMCID: PMC5132110 DOI: 10.1111/hiv.12390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2016] [Indexed: 01/11/2023]
Abstract
OBJECTIVES We recently observed a decrease in deoxyribonucleotide (dNTP) pools in HIV-infected individuals on antiretroviral therapy (ART). Alterations in dNTPs result in mutations in mitochondrial DNA (mtDNA) in cell culture and animal models. Therefore, we investigated whether ART is associated with mitochondrial genome sequence variation in peripheral blood mononuclear cells (PBMCs) of HIV-infected treatment-experienced individuals. METHODS In this substudy of a case-control study, 71 participants were included: 22 'cases', who were HIV-infected treatment-experienced patients with mitochondrial toxicity, 25 HIV-infected treatment-experienced patients without mitochondrial toxicity, and 24 HIV-uninfected controls. Total DNA was extracted from PBMCs and purified polymerase chain reaction (PCR) products were subjected to third-generation sequencing using the PacBio Single Molecule Real-Time (SMRT) sequencing technology. The sequences were aligned against the revised Cambridge reference sequence for human mitochondrial DNA (NC_012920.1) for detection of variants. RESULTS We identified a total of 123 novel variants, 39 of them in the coding region. HIV-infected treatment-experienced patients with and without toxicity had significantly higher average numbers of mitochondrial variants per participant than HIV-uninfected controls. We observed a higher burden of mtDNA large-scale deletions in HIV-infected treatment-experienced patients with toxicity compared with HIV-uninfected controls (P = 0.02). The frequency of mtDNA molecules containing a common deletion (mt.δ4977) was higher in HIV-infected treatment-experienced patients with toxicity compared with HIV-uninfected controls (P = 0.06). There was no statistically significant difference in mtDNA variants between HIV-infected treatment-experienced patients with and without toxicity. CONCLUSIONS The frequency of mtDNA variants (mutations and large-scale deletions) was higher in HIV-infected treatment-experienced patients with or without ART-induced toxicity than in uninfected controls.
Collapse
Affiliation(s)
- M Li
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Y Foli
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Z Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - G Wang
- Yale Center for Genome Analysis, Yale School of Medicine, West Haven, CT, USA
| | - Y Hu
- School of Public Health, Yale University, New Haven, CT, USA
| | - Q Lu
- School of Public Health, Yale University, New Haven, CT, USA
| | - S Selvaraj
- Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
| | - W Lam
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| | - E Paintsil
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.,School of Public Health, Yale University, New Haven, CT, USA.,Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
12
|
Hsouna S, Ben Halim N, Lasram K, Meiloud G, Arfa I, Kerkeni E, Romdhane L, Jamoussi H, Bahri S, Ben Ammar S, Abid A, Barakat A, Houmeida A, Abdelhak S, Kefi R. Study of the T16189C variant and mitochondrial lineages in Tunisian and overall Mediterranean region. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:1558-63. [PMID: 25208176 DOI: 10.3109/19401736.2014.953136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The mitochondrial DNA (mtDNA) variant T16189C has been investigated in several metabolic diseases. In this study, we aimed to estimate the frequency of the T16189C variant in Tunisian and other Mediterranean populations and to evaluate the impact of this variant on the phylogeny of Mediterranean populations. Blood sample of 240 unrelated Tunisian subjects were recruited from several Tunisian localities. The hypervariable region 1 of the mtDNA were amplified and sequenced. Additional sequences (N = 4921) from Mediterranean populations were compiled from previous studies. The average frequency of T16189C variant in Tunisia (29%) is similar to that observed in North African and Near Eastern populations. Our findings showed positive correlation of the T16189C variant with Sub-Saharan and North African lineages, while a negative correlation was found with the Eurasian haplogroups, reaching its maximum with the Eurasian haplogroup H. The principal component analyses showed a high internal heterogeneity between Tunisian localities. At the Mediterranean scale, Tunisians are closer to North African (Algerian and Moroccan) and Near Eastern populations (Syrians and Palestinians) than to Europeans.
Collapse
Affiliation(s)
- Sana Hsouna
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Nizar Ben Halim
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Khaled Lasram
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Ghlana Meiloud
- b Laboratoire de Biochimie et Biologie Moléculaire , Faculté des Sciences et Techniques , Nouakchott , Mauritania
| | - Imen Arfa
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Emna Kerkeni
- c Genetics Laboratory, Faculté de Médecine de Monastir , Monastir , Tunisia
| | - Lilia Romdhane
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Henda Jamoussi
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Sonia Bahri
- e Department of Biochemistry , Institut Pasteur de Tunis , Tunis , Tunisia , and
| | - Slim Ben Ammar
- e Department of Biochemistry , Institut Pasteur de Tunis , Tunis , Tunisia , and
| | - Abdelmajid Abid
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia .,d Service de Consultation Externe et Exploration Fonctionnelle, Institut National de Nutrition , Tunis , Tunisia
| | - Abdelhamid Barakat
- f Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique , Institut Pasteur du Maroc , Casablanca , Morocco
| | - Ahmed Houmeida
- b Laboratoire de Biochimie et Biologie Moléculaire , Faculté des Sciences et Techniques , Nouakchott , Mauritania
| | - Sonia Abdelhak
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| | - Rym Kefi
- a Biomedical Genomics and Oncogenetics laboratory (LR 11 IPT 05), Institut Pasteur de Tunis, Université El Manar de Tunis , Tunis , Tunisia
| |
Collapse
|
13
|
Abstract
We investigated whether mitochondrial (mtDNA) haplogroups and maternal family history of diabetes mellitus were associated with vascular diabetes mellitus complications in a population-based cohort of 299 Finnish diabetes mellitus patients with disease onset in young adult age. We found that haplogroup U was more prevalent among patients with no vascular diabetes mellitus complications than among those with at least one complication (p = 0.038). Haplogroup U was also more prevalent among the patients who reported maternal family history of diabetes mellitus than among those who did not (p = 0.0013). Furthermore, haplogroup U was more prevalent among patients with maternal family history of diabetes mellitus but no vascular diabetes mellitus complications than among those with at least one vascular diabetes mellitus complication but no maternal family history of diabetes mellitus (p = 0.0003 for difference). These findings suggest that different mtDNA-related factors may influence the risk of diabetes mellitus per se and the risk of vascular diabetes mellitus complications. Further studies are, however, warranted to replicate and elaborate on these results.
Collapse
Affiliation(s)
- Mika H Martikainen
- Division of Clinical Neurosciences, University of Turku and Turku University Hospital, Turku, Finland
| | - Tapani Rönnemaa
- Division of Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Kari Majamaa
- Department of Clinical Medicine, Neurology, University of Oulu and Oulu University Hospital, Oulu, Finland Medical Research Center Oulu, Oulu, Finland
| |
Collapse
|
14
|
Gonçalves FT, Fridman C, Pinto EM, Guevara-Aguirre J, Shevah O, Rosembloom AL, Hwa V, Cassorla F, Rosenfeld RG, Lins TSS, Damiani D, Arnhold IJP, Laron Z, Jorge AAL. The E180splice mutation in the GHR gene causing Laron syndrome: witness of a Sephardic Jewish exodus from the Iberian Peninsula to the New World? Am J Med Genet A 2014; 164A:1204-8. [PMID: 24664892 DOI: 10.1002/ajmg.a.36444] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Accepted: 12/29/2013] [Indexed: 11/05/2022]
Abstract
Laron syndrome (LS) is a genetic disorder caused by mutations in the growth hormone receptor (GHR) gene. The most frequent GHR mutation is E180splice (rs121909360), which was initially found in an inbred population of Spanish descent in Ecuador and subsequently in Israel, Brazil, Chile, and the United States. The aim of the present study is to determine if the E180splice mutation arose from a common origin. We studied 22 patients with LS from Ecuador, Israel (of Moroccan origin), Brazil, Chile, and the United States (of Mexican origin) who were homozygous for the E180splice mutation and compared them to control individuals for markers surrounding the GHR, intragenic polymorphisms, and Y-chromosome STR. An identical haplotype was found in all but one of the subjects carrying the E180splice mutation: D5S665: 150/150; D5S2082: 192/192; D5S2087: 246/246; rs6179 G/G; and rs6180 C/C. One patient differed from the others only at D5S2082 (168/192). This haplotype is rare (~1%) in control individuals and confirmed that the E180splice-associated haplotype was not derived from independent origins but represented recombination from a common ancestor. The analysis of paternal lineage markers showed that 50% belong to haplogroup R1b (found in Portugal and Spain) and 40% to haplogroups J and E (typical in the Middle East and in Eastern European Jews). The germline E180Splice mutation appears to have originated from a single common ancestor. The presence of Y-chromosome markers associated with Sephardic populations in persons harboring the E180splice mutation provides genetic evidence in support of the historical tracking of the exodus of this specific population.
Collapse
Affiliation(s)
- Fernanda T Gonçalves
- Laboratório de Imunohematologia e Hematologia Forense (LIM40), Departamento de Medicina Legal, Ética Médica e Medicina Social e do Trabalho, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Jiménez-Sousa MA, Tamayo E, Guzmán-Fulgencio M, Fernández-Rodríguez A, Heredia-Rodriguez M, García-Álvarez M, Bermejo-Martin JF, Pineda-Tenor D, Ruiz-Granado P, Alvarez-Fuente E, Gómez-Sanchez E, Gómez-Herreras JI, Resino S. Relationship between European mitochondrial haplogroups and chronic renal allograft rejection in patients with kidney transplant. Int J Med Sci 2014; 11:1129-32. [PMID: 25170295 PMCID: PMC4147638 DOI: 10.7150/ijms.9487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/15/2014] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial DNA variants may contribute to differences in mitochondrial function, leading to an altered immune system. The aim of this study was to analyze the relationship between mtDNA haplogroups and the development of chronic allograft dysfunction in patients with kidney transplant. A retrospective observational study was carried out on 261 patients who received kidney transplant (114 had stable transplant and 147 patients developed chronic allograft dysfunction). DNA samples were genotyped for 14 mtDNA polymorphisms by using Sequenom's MassARRAY platform (San Diego, CA, USA). Only European white patients within the N macro-cluster were included. Patients with haplogroups V (odds ratio (OR)=0.32; p=0.037) and J (OR=0.36; p=0.038) showed lower odds for developing CRAD than patients with haplogroup H. After adjusting for the most significant variables, haplogroups V and J tended to statistical significance (p=0.091 and p=0.067 respectively). This is a preliminary study in which mtDNA haplogroups seem to be implicated in susceptibility or protection for developing chronic allograft dysfunction.
Collapse
Affiliation(s)
- María Angeles Jiménez-Sousa
- 1. Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Spain
| | - Eduardo Tamayo
- 2. Departamento de Anestesiología y Reanimación, Hospital Clínico Universitario, Valladolid, Spain
| | - María Guzmán-Fulgencio
- 1. Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Spain
| | - Amanda Fernández-Rodríguez
- 1. Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Spain
| | - María Heredia-Rodriguez
- 2. Departamento de Anestesiología y Reanimación, Hospital Clínico Universitario, Valladolid, Spain
| | - Mónica García-Álvarez
- 1. Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Spain
| | - Jesús F Bermejo-Martin
- 3. Unidad de Investigación Biomédica. Hospital Clínico Universitario-IECSCYL, Valladolid, Spain
| | - Daniel Pineda-Tenor
- 1. Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Spain
| | - Patricia Ruiz-Granado
- 2. Departamento de Anestesiología y Reanimación, Hospital Clínico Universitario, Valladolid, Spain
| | - Elisa Alvarez-Fuente
- 2. Departamento de Anestesiología y Reanimación, Hospital Clínico Universitario, Valladolid, Spain
| | - Esther Gómez-Sanchez
- 2. Departamento de Anestesiología y Reanimación, Hospital Clínico Universitario, Valladolid, Spain
| | - José I Gómez-Herreras
- 2. Departamento de Anestesiología y Reanimación, Hospital Clínico Universitario, Valladolid, Spain
| | - Salvador Resino
- 1. Unidad de Infección Viral e Inmunidad, Centro Nacional de Microbiología. Instituto de Salud Carlos III, Majadahonda, Spain
| |
Collapse
|
16
|
Soini HK, Moilanen JS, Vilmi-Kerälä T, Finnilä S, Majamaa K. Mitochondrial DNA variant m.15218A > G in Finnish epilepsy patients who have maternal relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus. BMC Med Genet 2013; 14:73. [PMID: 23870133 PMCID: PMC3726289 DOI: 10.1186/1471-2350-14-73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 07/17/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mitochondrial diseases caused by mutations in mitochondrial DNA (mtDNA) affect tissues with high energy demand. Epilepsy is one of the manifestations of mitochondrial dysfunction when the brain is affected. We have studied here 79 Finnish patients with epilepsy and who have maternal first- or second-degree relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus. METHODS The entire mtDNA was studied by using conformation sensitive gel electrophoresis and PCR fragments that differed in mobility were directly sequenced. RESULTS We found a common nonsynonymous variant m.15218A > G (p.T158A, MTCYB) that occurs in haplogroup U5a1 to be more frequent in patients with epilepsy. The m.15218A > G variant was present in five patients with epilepsy and in four out of 403 population controls (p = 0.0077). This variant was present in two branches in the phylogenetic network constructed on the basis of mtDNA variation among the patients. Three algorithms predicted that m.15218A > G is damaging in effect. CONCLUSIONS We suggest that the m.15218A > G variant is mildly deleterious and that mtDNA involvement should be considered in patients with epilepsy and who have a maternal history of epilepsy, sensorineural hearing impairment or diabetes mellitus.
Collapse
Affiliation(s)
- Heidi K Soini
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Jukka S Moilanen
- Department of Clinical Genetics, Oulu University Hospital and University of Oulu P.O. Box 23, FI-90029, OYS, Oulu, Finland
| | - Tiina Vilmi-Kerälä
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Saara Finnilä
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Kari Majamaa
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| |
Collapse
|
17
|
Abstract
Working in the 1660s, William Croone wrote on the nature of connections between nerve and muscle. A previously unknown copy of his essay, wrongly attributed to Thomas Willis, has recently come to light. Croone left the challenges of clinical neurology to his successors. The story of multiple sclerosis begins early in the nineteenth century. Despite much information on the aetiology and pathogenesis, the origins of that disease remain obscure. Here, the hypothesis is advanced--based on the epidemiology, clinical neurology, immunology and genetics of demyelinating disease, linked to European history and population genetics--that multiple sclerosis evolved from a related disorder, neuromyelitis optica (or Devic's disease). Genetic drift and stratification altered the immune response to a common pathogen and changed the disease phenotype. Against this background, the sustained epidemic of multiple sclerosis arose when cultural changes led to a subtle but crucial alteration in the age at which genetically vulnerable individuals are exposed to Epstein Barr infection.
Collapse
Affiliation(s)
- Alastair Compston
- Department of Clinical Neurosciences, University of Cambridge, Addenbrooke's Hospital
| |
Collapse
|