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Macías M, Acha B, Corroza J, Urdánoz-Casado A, Roldan M, Robles M, Sánchez-Ruiz de Gordoa J, Erro ME, Jericó I, Blanco-Luquin I, Mendioroz M. Liquid Biopsy in Alzheimer's Disease Patients Reveals Epigenetic Changes in the PRLHR Gene. Cells 2023; 12:2679. [PMID: 38067107 PMCID: PMC10705731 DOI: 10.3390/cells12232679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
In recent years, new DNA methylation variants have been reported in genes biologically relevant to Alzheimer's disease (AD) in human brain tissue. However, this AD-specific epigenetic information remains brain-locked and unreachable during patients' lifetimes. In a previous methylome performed in the hippocampus of 26 AD patients and 12 controls, we found higher methylation levels in AD patients in the promoter region of PRLHR, a gene involved in energy balance regulation. Our aim was to further characterize PRLHR's role in AD and to evaluate if the liquid biopsy technique would provide life access to this brain information in a non-invasive way. First, we extended the methylation mapping of PRLHR and validated previous methylome results via bisulfite cloning sequencing. Next, we observed a positive correlation between PRLHR methylation levels and AD-related neuropathological changes and a decreased expression of PRLHR in AD hippocampus. Then, we managed to replicate the hippocampal methylation differences in plasma cfDNA from an additional cohort of 35 AD patients and 35 controls. The isolation of cfDNA from the plasma of AD patients may constitute a source of potential epigenetic biomarkers to aid AD clinical management.
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Affiliation(s)
- Mónica Macías
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Blanca Acha
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Jon Corroza
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Amaya Urdánoz-Casado
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Miren Roldan
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Maitane Robles
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Javier Sánchez-Ruiz de Gordoa
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - María Elena Erro
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Ivonne Jericó
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
| | - Idoia Blanco-Luquin
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
| | - Maite Mendioroz
- Navarrabiomed, Hospital Universitario de Navarra, Universidad Pública de Navarra, IdiSNA, 31008 Pamplona, Spain; (M.M.); (B.A.); (A.U.-C.); (M.R.); (M.R.); (J.S.-R.d.G.); (M.E.E.); (I.B.-L.)
- Neurology Department, Hospital Universitario de Navarra, IdiSNA, 31008 Pamplona, Spain; (J.C.); (I.J.)
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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Iturria-Medina Y, Adewale Q, Khan AF, Ducharme S, Rosa-Neto P, O’Donnell K, Petyuk VA, Gauthier S, De Jager PL, Breitner J, Bennett DA. Unified epigenomic, transcriptomic, proteomic, and metabolomic taxonomy of Alzheimer's disease progression and heterogeneity. SCIENCE ADVANCES 2022; 8:eabo6764. [PMID: 36399579 PMCID: PMC9674284 DOI: 10.1126/sciadv.abo6764] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) is a heterogeneous disorder with abnormalities in multiple biological domains. In an advanced machine learning analysis of postmortem brain and in vivo blood multi-omics molecular data (N = 1863), we integrated epigenomic, transcriptomic, proteomic, and metabolomic profiles into a multilevel biological AD taxonomy. We obtained a personalized multilevel molecular index of AD dementia progression that predicts severity of neuropathologies, and identified three robust molecular-based subtypes that explain much of the pathologic and clinical heterogeneity of AD. These subtypes present distinct patterns of alteration in DNA methylation, RNA, proteins, and metabolites, identifiable in the brain and subsequently in blood. In addition, the genetic variations that predispose to the various AD subtypes in brain predict distinct spatial patterns of alteration in cell types, suggesting a unique influence of each putative AD variant on neuropathological mechanisms. These observations support that an individually tailored multi-omics molecular taxonomy of AD may represent distinct targets for preventive or treatment interventions.
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Affiliation(s)
- Yasser Iturria-Medina
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
| | - Quadri Adewale
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
| | - Ahmed F. Khan
- Neurology and Neurosurgery Department, Montreal Neurological Institute, Montreal, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
| | - Simon Ducharme
- McConnell Brain Imaging Centre, Montreal Neurological Institute, Montreal, Canada
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Canada
| | - Pedro Rosa-Neto
- McGill University Research Centre for Studies in Aging, Douglas Research Centre, Montreal, Canada
| | - Kieran O’Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Montreal, Canada
- Yale School of Medicine, New Haven, CT 06519, USA
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Serge Gauthier
- McGill University Research Centre for Studies in Aging, Douglas Research Centre, Montreal, Canada
| | - Philip L. De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - John Breitner
- Centre for Studies on Prevention of Alzheimer’s Disease (StoP-AD), Douglas Research Centre, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL 60612, USA
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Fan HH, Zheng J, Huang XY, Wu KY, Cui L, Dong HJ, Wang Z, Zhang X, Zhu JH. An antisense Alu transposon insertion/deletion polymorphism of ALDH1A1 may functionally associate with Parkinson's disease. BMC Geriatr 2022; 22:427. [PMID: 35578164 PMCID: PMC9109383 DOI: 10.1186/s12877-022-03132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aldehyde dehydrogenase 1 (encoded by ALDH1A1) has been shown to protect against Parkinson's disease (PD) by reducing toxic metabolites of dopamine. We herein revealed an antisense Alu element insertion/deletion polymorphism in intron 4 of ALDH1A1, and hypothesized that it might play a role in PD. METHODS: A Han Chinese cohort comprising 488 PD patients and 515 controls was recruited to validate the Alu insertion/deletion polymorphism following a previous study of tag-single nucleotide polymorphisms, where rs7043217 was shown to be significantly associated with PD. Functional analyses of the Alu element insertion were performed. RESULTS The Alu element of ALDH1A1 was identified to be a variant of Yb8 subfamily and termed as Yb8c4. The antisense Yb8c4 insertion/deletion polymorphism (named asYb8c4ins and asYb8c4del, respectively) appeared to be in a complete linkage disequilibrium with rs7043217 and was validated to be significantly associated with PD susceptibility with asYb8c4ins serving as a risk allele (P = 0.030, OR = 1.224, 95% CI = 1.020-1.470). Multiple functional analyses including ALDH1A1 mRNA expression in blood cells of carriers, and reporters of EGFP and luciferase showed that the asYb8c4ins had a suppressive activity on gene transcription. Mechanistic explorations suggested that the asYb8c4ins induced no changes in CpG methylation and mRNA splicing of ALDH1A1 and appeared no binding of transcription factors. CONCLUSIONS Our results consolidate an involvement of ALDH1 in PD pathogenesis. The asYb8c4 polymorphism may be a functional output of its linkage disequilibrium-linked single nucleotide polymorphisms.
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Affiliation(s)
- Hui-Hui Fan
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.,Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jing Zheng
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiao-Ya Huang
- Department of Neurology, Wenzhou Central Hospital, Wenzhou, Zhejiang, China
| | - Ke-Yun Wu
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lei Cui
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.,Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Hao-Jia Dong
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zhen Wang
- Department of Neurology, the First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiong Zhang
- Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
| | - Jian-Hong Zhu
- Department of Preventive Medicine, Institute of Nutrition and Diseases, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China. .,Department of Geriatrics and Neurology, the Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
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Abdullah MN, Wah YB, Abdul Majeed AB, Zakaria Y, Shaadan N. Identification of blood-based transcriptomics biomarkers for Alzheimer's disease using statistical and machine learning classifier. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.101083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Finch CE, Haghani A. Gene-Environment Interactions and Stochastic Variations in the Gero-Exposome. J Gerontol A Biol Sci Med Sci 2021; 76:1740-1747. [PMID: 33580247 PMCID: PMC8436990 DOI: 10.1093/gerona/glab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
The limited heritability of human life spans suggests an important role for gene-environment (G × E) interactions across the life span (T), from gametes to geronts. Multilevel G × E × T interactions of aging phenotypes are conceptualized in the Gero-Exposome as Exogenous and Endogenous domains. Stochastic variations in the Endogenous domain contribute to the diversity of aging phenotypes, shown for the diversity of inbred Caenorhabditis elegans life spans in the same culture environment, and for variegated gene expression of somatic cells in nematodes and mammals. These phenotypic complexities can be analyzed as 3-way interactions of gene, environment, and stochastic variations, the Tripartite Phenotype of Aging. Single-cell analyses provide tools to explore this broadening frontier of biogerontology.
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Affiliation(s)
- Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA
- Dornsife College, University of Southern California, Los Angeles, CA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
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The emerging roles of absent in melanoma 2 (AIM2) inflammasome in central nervous system disorders. Neurochem Int 2021; 149:105122. [PMID: 34284076 DOI: 10.1016/j.neuint.2021.105122] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 02/08/2023]
Abstract
As a double-stranded DNA (dsDNA) sensor, the PYHIN family member absent in melanoma 2 (AIM2) is an essential component of the inflammasome families. Activation of AIM2 by dsDNA leads to the assembly of cytosolic multimolecular complexes termed the AIM2 inflammasome, resulting in activation of caspase-1, the maturation and secretion of pro-inflammatory cytokines interleukin (IL)-1β and IL-18, and pyroptosis. Multiple central nervous system (CNS) diseases are accompanied by immune responses and inflammatory cascade. As the resident macrophage cells, microglia cells act as the first and main form of active immune defense in the CNS. AIM2 is highly expressed in microglia as well as astrocytes and neurons and is essential in neurodevelopment. In this review, we highlight the recent progress on the role of AIM2 inflammasome in CNS disorders, including cerebral stroke, brain injury, neuropsychiatric disease, neurodegenerative diseases, and glioblastoma.
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La Cognata V, Morello G, Cavallaro S. Omics Data and Their Integrative Analysis to Support Stratified Medicine in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22094820. [PMID: 34062930 PMCID: PMC8125201 DOI: 10.3390/ijms22094820] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Molecular and clinical heterogeneity is increasingly recognized as a common characteristic of neurodegenerative diseases (NDs), such as Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. This heterogeneity makes difficult the development of early diagnosis and effective treatment approaches, as well as the design and testing of new drugs. As such, the stratification of patients into meaningful disease subgroups, with clinical and biological relevance, may improve disease management and the development of effective treatments. To this end, omics technologies-such as genomics, transcriptomics, proteomics and metabolomics-are contributing to offer a more comprehensive view of molecular pathways underlying the development of NDs, helping to differentiate subtypes of patients based on their specific molecular signatures. In this article, we discuss how omics technologies and their integration have provided new insights into the molecular heterogeneity underlying the most prevalent NDs, aiding to define early diagnosis and progression markers as well as therapeutic targets that can translate into stratified treatment approaches, bringing us closer to the goal of personalized medicine in neurology.
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Diniz Pereira J, Gomes Fraga V, Morais Santos AL, Carvalho MDG, Caramelli P, Braga Gomes K. Alzheimer's disease and type 2 diabetes mellitus: A systematic review of proteomic studies. J Neurochem 2020; 156:753-776. [PMID: 32909269 DOI: 10.1111/jnc.15166] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/15/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022]
Abstract
Similar to dementia, the risk for developing type 2 diabetes mellitus (T2DM) increases with age, and T2DM also increases the risk for dementia, particularly Alzheimer's disease (AD). Although T2DM is primarily a peripheral disorder and AD is a central nervous system disease, both share some common features as they are chronic and complex diseases, and both show involvement of oxidative stress and inflammation in their progression. These characteristics suggest that T2DM may be associated with AD, which gave rise to a new term, type 3 diabetes (T3DM). In this study, we searched for matching peripheral proteomic biomarkers of AD and T2DM based in a systematic review of the available literature. We identified 17 common biomarkers that were differentially expressed in both patients with AD or T2DM when compared with healthy controls. These biomarkers could provide a useful workflow for screening T2DM patients at risk to develop AD.
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Affiliation(s)
- Jessica Diniz Pereira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vanessa Gomes Fraga
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Anna Luiza Morais Santos
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Maria das Graças Carvalho
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paulo Caramelli
- Departamento de Clínica Médica, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Karina Braga Gomes
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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