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Cortes-Figueiredo F, Asseyer S, Chien C, Zimmermann HG, Ruprecht K, Schmitz-Hübsch T, Bellmann-Strobl J, Paul F, Morais VA. CD4 + T cell mitochondrial genotype in Multiple Sclerosis: a cross-sectional and longitudinal analysis. Sci Rep 2024; 14:7507. [PMID: 38553515 PMCID: PMC10980703 DOI: 10.1038/s41598-024-57592-z] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Multiple Sclerosis (MS) is a chronic autoimmune demyelinating disease of the central nervous system (CNS), with a largely unknown etiology, where mitochondrial dysfunction likely contributes to neuroaxonal loss and brain atrophy. Mirroring the CNS, peripheral immune cells from patients with MS, particularly CD4+ T cells, show inappropriate mitochondrial phenotypes and/or oxidative phosphorylation (OxPhos) insufficiency, with a still unknown contribution of mitochondrial DNA (mtDNA). We hypothesized that mitochondrial genotype in CD4+ T cells might influence MS disease activity and progression. Thus, we performed a retrospective cross-sectional and longitudinal study on patients with a recent diagnosis of either Clinically Isolated Syndrome (CIS) or Relapsing-Remitting MS (RRMS) at two timepoints: 6 months (VIS1) and 36 months (VIS2) after disease onset. Our primary outcomes were the differences in mtDNA extracted from CD4+ T cells between: (I) patients with CIS/RRMS (PwMS) at VIS1 and age- and sex-matched healthy controls (HC), in the cross-sectional analysis, and (II) different diagnostic evolutions in PwMS from VIS1 to VIS2, in the longitudinal analysis. We successfully performed mtDNA whole genome sequencing (mean coverage: 2055.77 reads/base pair) in 183 samples (61 triplets). Nonetheless, mitochondrial genotype was not associated with a diagnosis of CIS/RRMS, nor with longitudinal diagnostic evolution.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susanna Asseyer
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Claudia Chien
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Hanna G Zimmermann
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center Digital Future, Berlin, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tanja Schmitz-Hübsch
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Judith Bellmann-Strobl
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friedemann Paul
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany.
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Vanessa A Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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Cortes-Figueiredo F, Carvalho FS, Fonseca AC, Paul F, Ferro JM, Schönherr S, Weissensteiner H, Morais VA. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. Int J Mol Sci 2021; 22:12031. [PMID: 34769461 PMCID: PMC8584537 DOI: 10.3390/ijms222112031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 02/06/2023] Open
Abstract
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS's variants (TSS found 57.92% of PCP's variants), with a significant correlation between the variant levels of variants found with both pipelines.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Filipa S. Carvalho
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
| | - Ana Catarina Fonseca
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Friedemann Paul
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - José M. Ferro
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Vanessa A. Morais
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
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Cortes-Figueiredo F, Nielsen NM, Stenager E, Paul F, Hallas J, Kristensen KB. Retinoids are not linked to risk of multiple sclerosis: A Danish nationwide cohort study. Eur J Neurol 2021; 29:247-256. [PMID: 34536255 DOI: 10.1111/ene.15116] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/02/2021] [Accepted: 09/10/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND PURPOSE Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system with an undetermined etiology. Retinoids may have immunomodulatory effects that favorably influence MS progression. We aimed to explore the yet unknown relationship between exposure to retinoids and the risk of acquiring MS. METHODS We performed a nationwide cohort study in the Danish population in the period 1998-2016, comparing MS incidence in three groups: users of systemic retinoids; users of topical retinoids (negative control group); and users of non-retinoid acne drugs (control group). We used data from the Danish Multiple Sclerosis Registry (DMSR), the Danish National Prescription Registry and the Danish National Patient Registry. Linkage was obtained through the personal identification number (CPR number). We addressed confounding by three-way propensity score (PS)-matching weights. Additionally, to evaluate a cumulative dose-response effect for systemic retinoids on MS incidence, we conducted a case-control study, nested within the cohort. RESULTS A total of 257,193 users of non-retinoid acne drugs, 130,560 users of topical retinoids, and 75,610 users of systemic retinoids were included. Systemic retinoid use was not associated with a reduced risk of MS compared to non-retinoid acne drug use in crude (hazard ratio [HR] 0.80, 95% confidence interval [CI] 0.61 to 1.05]) and weighted analyses (HR 0.89, 95% CI 0.67 to 1.20). There was no evidence of a cumulative dose-response association between systemic retinoids and MS incidence. CONCLUSIONS Use of systemic retinoids was not associated with a reduced incidence of MS compared to use of non-retinoid acne drugs in this study.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- VMorais Lab - Mitochondria Biology and Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Clinical Pharmacology, Pharmacy and Environmental Medicine, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Nete Munk Nielsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Focused Research Unit in Neurology, Department of Neurology, Hospital of Southern Jutland, University of Southern Denmark, Denmark
| | - Egon Stenager
- MS-clinic of Southern Jutland (Sønderborg, Esbjerg, Kolding), Department of Neurology, Hospital of Southern Jutland, Sønderborg, Denmark.,Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Friedemann Paul
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Berlin, Germany.,Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Jesper Hallas
- Clinical Pharmacology, Pharmacy and Environmental Medicine, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kasper Bruun Kristensen
- Clinical Pharmacology, Pharmacy and Environmental Medicine, Department of Public Health, University of Southern Denmark, Odense, Denmark
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Carmona-Fernandes D, Barreira SC, Leonardo N, Casimiro RI, Castro AM, Santos PO, Fernandes AN, Cortes-Figueiredo F, Gonçalves CA, Cruz R, Fernandes ML, Ivo M, Pedro LM, Canhão H, Fonseca JE, Santos MJ. Atherosclerosis and Bone Loss in Humans-Results From Deceased Donors and From Patients Submitted to Carotid Endarterectomy. Front Med (Lausanne) 2021; 8:672496. [PMID: 34095177 PMCID: PMC8172790 DOI: 10.3389/fmed.2021.672496] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/19/2021] [Indexed: 12/25/2022] Open
Abstract
Background and Aims: Atherosclerosis and osteoporosis share common risk factors, as well as inflammatory mechanisms. Our aim was to understand how atherosclerotic lesions are related with disturbances in bone. Methods: Gene expression of pro-inflammatory and bone metabolism related proteins (IL-1β, IL-6, IL-17A, TNF, RANKL, OPG, COL1, CTSK, OCL, TRAP, CBFA1, DKK1, SOST, ADIPOQ, and ADIPOR1) were analyzed in arteries and bones from 45 deceased donors and adipose tissue was used as control. Additionally, in 139 patients with advanced atherosclerosis submitted to carotid endarterectomy we compared calcium content (Alizarin red) and plaque inflammatory scores (CD3+, CD68+, and adiponectin) of patients with normal bone mineral density (BMD) with those with low BMD and explored the associations between gene expression in atherosclerotic plaques and BMD. Serum levels of pro-inflammatory and bone related proteins were measured both in donors and patients. Associations were investigated by the Pearson or Spearman correlation tests, and multivariate regression analyzes were performed when justified. Results: Gene expression of bone remodeling and pro-inflammatory proteins correlated positively in bone and aorta, independently of age and sex of donors, but not in adipose tissue. The expression of bone formation genes was significantly higher in atheroma plaques from endarterectomized patients with normal vs. low BMD as well as inflammatory CD68+ scores, regardless of patients' age and sex, but not of body mass index. No relationship was observed between serum levels and gene expression levels of pro-inflammatory or bone remodeling proteins. Conclusions: Our results suggest that the relationship between bones and vessels in the context of atherosclerotic disease and osteoporosis may rely on the intrinsic connection between the tissues involved, independently of disease stage. Serum measurements of pro-inflammatory and bone-remodeling proteins do not accurately translate tissue pathologic processes.
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Affiliation(s)
- Diana Carmona-Fernandes
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Sofia C Barreira
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal.,Rheumatology Department, Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisboa, Portugal
| | - Natacha Leonardo
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Renata I Casimiro
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Alice M Castro
- Rheumatology Department, Hospital Garcia de Orta, Almada, Portugal
| | | | - António N Fernandes
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Filipe Cortes-Figueiredo
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Carolina A Gonçalves
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Rafael Cruz
- Pathology Department, Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisboa, Portugal.,Faculdade de Medicina da Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Instituto de Histologia e Biologia do Desenvolvimento, Lisboa, Portugal
| | - Mariana L Fernandes
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Margarida Ivo
- Transplantation Department, Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Luis M Pedro
- Vascular Surgery Department, Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Helena Canhão
- EpiDoC Unit-CEDOC, Comprehensive Health Research Center-CHRC, NOVA Medical School, Universidade NOVA de Lisboa, Lisboa, Portugal.,Rheumatology Unit, Centro Hospitalar Universitario Lisboa Central, Lisboa, Portugal
| | - João Eurico Fonseca
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal.,Rheumatology Department, Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisboa, Portugal
| | - Maria José Santos
- Rheumatology Research Unit, Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Centro Académico de Medicina de Lisboa, Lisboa, Portugal.,Rheumatology Department, Hospital Garcia de Orta, Almada, Portugal
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