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Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Canterbury JD, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A Framework for Quality Control in Quantitative Proteomics. J Proteome Res 2024. [PMID: 39248652 DOI: 10.1021/acs.jproteome.4c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow, from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at the protein and peptide levels allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and ProteomeXchange under the identifier PXD051318.
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Affiliation(s)
- Kristine A Tsantilas
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Gennifer E Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Julia E Robbins
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Deanna L Plubell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Jesse D Canterbury
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Josh Eckels
- LabKey, 500 Union St #1000, Seattle, Washington 98101, United States
| | - Christine C Wu
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Michael S Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607, United States
| | - Sandra E Spencer
- Canada's Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
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Varzieva VG, Mesonzhnik NV, Ilgisonis IS, Belenkov YN, Kozhevnikova MV, Appolonova SA. Metabolomic biomarkers of multiple myeloma: A systematic review. Biochim Biophys Acta Rev Cancer 2024; 1879:189151. [PMID: 38986721 DOI: 10.1016/j.bbcan.2024.189151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Multiple myeloma (MM) is an incurable malignancy of clonal plasma cells. Various diagnostic methods are used in parallel to accurately determine stage and severity of the disease. Identifying a biomarker or a panel of biomarkers could enhance the quality of medical care that patients receive by adopting a more personalized approach. Metabolomics utilizes high-throughput analytical platforms to examine the levels and quantities of biochemical compounds in biosamples. The aim of this review was to conduct a systematic literature search for potential metabolic biomarkers that may aid in the diagnosis and prognosis of MM. The review was conducted in accordance with PRISMA recommendations and was registered in PROSPERO. The systematic search was performed in PubMed, CINAHL, SciFinder, Scopus, The Cochrane Library and Google Scholar. Studies were limited to those involving people with clinically diagnosed MM and healthy controls as comparators. Articles had to be published in English and had no restrictions on publication date or sample type. The quality of articles was assessed according to QUADOMICS criteria. A total of 709 articles were collected during the literature search. Of these, 436 were excluded based on their abstract, with 26 more removed after a thorough review of the full text. Finally, 16 articles were deemed relevant and were subjected to further analysis of their data. A number of promising candidate biomarkers was discovered. Follow-up studies with large sample sizes are needed to determine their suitability for clinical applications.
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Affiliation(s)
- Valeria G Varzieva
- Department of Pharmacology, Sechenov First Moscow State Medical University (Sechenov University), Vernadskogo pr., 96, 119571 Moscow, Russia; Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia.
| | - Natalia V Mesonzhnik
- Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia.
| | - Irina S Ilgisonis
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Yuri N Belenkov
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Maria V Kozhevnikova
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Svetlana A Appolonova
- Department of Pharmacology, Sechenov First Moscow State Medical University (Sechenov University), Vernadskogo pr., 96, 119571 Moscow, Russia; Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia
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Kiuchi S, Nakaya K, Cooray U, Takeuchi K, Motoike IN, Nakaya N, Taki Y, Koshiba S, Mugikura S, Osaka K, Hozawa A. A principal component analysis of metabolome and cognitive decline among Japanese older adults: cross-sectional analysis using Tohoku Medical Megabank Cohort Study. J Epidemiol 2024:JE20240099. [PMID: 38972731 DOI: 10.2188/jea.je20240099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
BackgroundDementia is the leading cause of disability and imposes a significant burden on society. Previous studies have suggested an association between metabolites and cognitive decline. Although the metabolite composition differs between Western and Asian populations, studies targeting Asian populations remain scarce.MethodsThis cross-sectional study used data from a cohort survey of community-dwelling older adults aged ≥ 60 years living in Miyagi, Japan, conducted by Tohoku Medical Megabank Organization between 2013 and 2016. Forty-three metabolite variables quantified using nuclear magnetic resonance spectroscopy were used as explanatory variables. Dependent variable was the presence of cognitive decline (≤ 23 points), assessed by the Mini-Mental State Examination. Principal component (PC) analysis was performed to reduce the dimensionality of metabolite variables, followed by logistic regression analysis to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for cognitive decline.ResultsA total of 2,940 participants were included (men: 49.0%, mean age: 67.6 years). Among them, 1.9% showed cognitive decline. The first 12 PC components (PC1-PC12) accounted for 71.7% of the total variance. Multivariate analysis showed that PC1, which mainly represented essential amino acids, was associated with lower odds of cognitive decline (OR = 0.89; 95% CI, 0.80-0.98). PC2, which mainly included ketone bodies, was associated with cognitive decline (OR = 1.29; 95% CI, 1.11-1.51). PC3, which included amino acids, was associated with lower odds of cognitive decline (OR = 0.81; 95% CI, 0.66-0.99).ConclusionAmino acids are protectively associated with cognitive decline, whereas ketone metabolites are associated with higher odds of cognitive decline.
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Affiliation(s)
- Sakura Kiuchi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
| | - Kumi Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
- Division of Epidemiology, School of Public Health, Graduate School of Medicine, Tohoku University
| | - Upul Cooray
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
- National Dental Research Institute Singapore, National Dental Centre Singapore
| | - Kenji Takeuchi
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
- Division of Statistics and Data Science, Liaison Center for Innovative Dentistry, Tohoku University Graduate School of Dentistry
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
- Division of Health Behavioral Epidemiology, Tohoku University Graduate School of Medicine
| | - Yasuyuki Taki
- Department of Aging Research and Geriatric Medicine, Institute of Development, Aging and Cancer, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | - Shunji Mugikura
- Tohoku Medical Megabank Organization, Tohoku University
- Department of Diagnostic Radiology, Graduate School of Medicine, Tohoku University
| | - Ken Osaka
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University
- Division of Epidemiology, School of Public Health, Graduate School of Medicine, Tohoku University
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Li S, Looby N, Chandran V, Kulasingam V. Challenges in the Metabolomics-Based Biomarker Validation Pipeline. Metabolites 2024; 14:200. [PMID: 38668328 PMCID: PMC11051909 DOI: 10.3390/metabo14040200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As end-products of the intersection between the genome and environmental influences, metabolites represent a promising approach to the discovery of novel biomarkers for diseases. However, many potential biomarker candidates identified by metabolomics studies fail to progress beyond analytical validation for routine implementation in clinics. Awareness of the challenges present can facilitate the development and advancement of innovative strategies that allow improved and more efficient applications of metabolite-based markers in clinical settings. This minireview provides a comprehensive summary of the pre-analytical factors, required analytical validation studies, and kit development challenges that must be resolved before the successful translation of novel metabolite biomarkers originating from research. We discuss the necessity for strict protocols for sample collection, storage, and the regulatory requirements to be fulfilled for a bioanalytical method to be considered as analytically validated. We focus especially on the blood as a biological matrix and liquid chromatography coupled with tandem mass spectrometry as the analytical platform for biomarker validation. Furthermore, we examine the challenges of developing a commercially viable metabolomics kit for distribution. To bridge the gap between the research lab and clinical implementation and utility of relevant metabolites, the understanding of the translational challenges for a biomarker panel is crucial for more efficient development of metabolomics-based precision medicine.
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Affiliation(s)
- Shenghan Li
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Orthopaedic Surgery, Osteoarthritis Research Program, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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Stevens-Jones O, Mojzisova H, Elisak M, Constantinescu R, Hanzalova J, Axelsson M, Krysl D. Paraneoplastic or not? Sirtuin 2 in anti-N-methyl-d-aspartate receptor encephalitis. Eur J Neurol 2023; 30:3228-3235. [PMID: 37483157 DOI: 10.1111/ene.15987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND AND PURPOSE N-methyl-d-aspartate receptor (NMDAR) and leucine-rich glioma-inactivated protein 1 (LGI1) encephalitis are important types of autoimmune encephalitis (AE) with significant morbidity. In this study, we used a proteomic approach in search of novel clinically relevant biomarkers in these types of encephalitides. METHODS Swedish and Czech tertiary neuroimmunology centers collaborated in this retrospective exploratory study. Fifty-eight cerebrospinal fluid (CSF) samples of 28 patients with AE (14 definite NMDAR, 14 with definite LGI1 encephalitis) and 30 controls were included. CSF samples were analyzed using proximity extension assay technology (Olink Target 96 Inflammation panel). For each CSF sample, 92 proteins were measured. Clinical variables were retrospectively collected, and correlations with protein levels were statistically analyzed. RESULTS Patients and controls differed significantly in the following 18 biomarkers: TNFRSF9, TNFRSF12, TNFRSF14, TNFβ, TNFα, IL7, IL10, IL12B, IFNγ, CD5, CD6, CASP8, MMP1, CXCL8, CXCL10, CXCL11, IL20RA, and sirtuin 2 (SIRT2). In LGI1 encephalitis, no clinically useful association was found between biomarkers and clinical variables. In the NMDAR encephalitis group, SIRT2, TNFβ, and CD5 were significantly associated with ovarian teratoma. For SIRT2, this was true even for the first patients' CSF sample (SIRT2 without vs. with tumor, mean ± SD = 2.2 ± 0.29 vs. 2.88 ± 0.48; p = 0.007, 95% confidence interval = -1.15 to -0.22; r statistic in point-biserial correlation (rpb) = 0.66, p = 0.011). SIRT2 was positively correlated with age (rpb = 0.39, p = 0.018) and total hospital days (r = 0.55, p = <0.001). CONCLUSIONS SIRT2 should be investigated as a biomarker of paraneoplastic etiology in NMDAR encephalitis.
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Affiliation(s)
- Oskar Stevens-Jones
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
| | - Hana Mojzisova
- Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Martin Elisak
- Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Radu Constantinescu
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
| | - Jitka Hanzalova
- Department of Immunology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Markus Axelsson
- Department of Neurology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
| | - David Krysl
- Institute of Neuroscience and Physiology, Sahlgrenska Akademin, Gothenburg University, Gothenburg, Sweden
- Department of Neurology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
- Department of Clinical Neurophysiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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Cai J, Chong CCY, Cheng CY, Lim CC, Sabanayagam C. Circulating Metabolites and Cardiovascular Disease in Asians with Chronic Kidney Disease. Cardiorenal Med 2023; 13:301-309. [PMID: 37669626 PMCID: PMC10664326 DOI: 10.1159/000533741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
INTRODUCTION Chronic kidney disease (CKD) is a growing public health problem, with significant burden of cardiovascular disease and mortality. The risk of cardiovascular disease in CKD is elevated beyond that predicted by traditional cardiovascular risk factors, suggesting that other factors may account for this increased risk. Through metabolic profiling, this study aimed to investigate the associations between serum metabolites and prevalent cardiovascular disease in Asian patients with CKD to provide insights into the complex interactions between metabolism, cardiovascular disease and CKD. METHODS This was a single-center cross-sectional study of 1,122 individuals from three ethnic cohorts in the population-based Singapore Epidemiology of Eye Disease (SEED) study (153 Chinese, 262 Indians, and 707 Malays) aged 40-80 years with CKD (estimated glomerular filtration rate <60 mL/min/1.73 m2). Nuclear magnetic resonance spectroscopy was used to quantify 228 metabolites from the participants' serum or plasma. Prevalent cardiovascular disease was defined as self-reported myocardial infarction, angina, or stroke. Multivariate logistic regression identified metabolites independently associated with cardiovascular disease in each ethnic cohort. Metabolites with the same direction of association with cardiovascular disease in all three cohorts were selected and subjected to meta-analysis. RESULTS Cardiovascular disease was present in 275 (24.5%). Participants with cardiovascular disease tend to be male; of older age; with hypertension, hyperlipidemia, and diabetes; with lower systolic and diastolic blood pressure (BP); lower high-density lipoprotein (HDL) and low-density lipoprotein (LDL) cholesterol than those without cardiovascular disease. After adjusting for age, sex, systolic BP, diabetes, total cholesterol, and HDL cholesterol, 10 lipoprotein subclass ratios and 6 other metabolites were significantly associated with prevalent cardiovascular disease in at least one cohort. Meta-analysis with Bonferroni correction for multiple comparisons found that lower tyrosine, leucine, and valine concentrations and lower cholesteryl esters to total lipid ratio in intermediate-density lipoprotein (IDL) were associated with cardiovascular disease. CONCLUSION In Chinese, Indian, and Malay participants with CKD, prevalent cardiovascular disease was associated with tyrosine, leucine, valine, and cholesteryl esters to total lipid ratios in IDL. Increased cardiovascular risk in CKD patients may be contributed by altered amino acid and lipoprotein metabolism. The presence of CKD and ethnic differences may affect interactions between metabolites in health and disease, hence greater understanding will allow us to better risk stratify patients, and also individualize care with consideration of ethnic disparities.
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Affiliation(s)
- Jiashen Cai
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
- Medicine Academic Clinical Programme, SingHealth Duke-NUS, Singapore, Singapore
| | | | - Ching Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Programme, SingHealth Duke-NUS, Singapore, Singapore
| | - Cynthia Ciwei Lim
- Department of Renal Medicine, Singapore General Hospital, Singapore, Singapore
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology and Visual Sciences Academic Clinical Programme, SingHealth Duke-NUS, Singapore, Singapore
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Lou N, Wang G, Wang Y, Xu M, Zhou Y, Tan Q, Zhong Q, Zhang L, Zhang X, Liu S, Luo R, Wang S, Tang L, Yao J, Zhang Z, Shi Y, Yu X, Han X. Proteomics Identifies Circulating TIMP-1 as a Prognostic Biomarker for Diffuse Large B-Cell Lymphoma. Mol Cell Proteomics 2023; 22:100625. [PMID: 37500057 PMCID: PMC10470290 DOI: 10.1016/j.mcpro.2023.100625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 06/24/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease, although disease stratification using in-depth plasma proteomics has not been performed to date. By measuring more than 1000 proteins in the plasma of 147 DLBCL patients using data-independent acquisition mass spectrometry and antibody array, DLBCL patients were classified into four proteomic subtypes (PS-I-IV). Patients with the PS-IV subtype and worst prognosis had increased levels of proteins involved in inflammation, including a high expression of metalloproteinase inhibitor-1 (TIMP-1) that was associated with poor survival across two validation cohorts (n = 180). Notably, the combination of TIMP-1 with the international prognostic index (IPI) identified 64.00% to 88.24% of relapsed and 65.00% to 80.49% of deceased patients in the discovery and two validation cohorts, which represents a 24.00% to 41.67% and 20.00% to 31.70% improvement compared to the IPI score alone, respectively. Taken together, we demonstrate that DLBCL heterogeneity is reflected in the plasma proteome and that TIMP-1, together with the IPI, could improve the prognostic stratification of patients.
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Affiliation(s)
- Ning Lou
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Guibin Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Yanrong Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Meng Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Yu Zhou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Qiaoyun Tan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Qiaofeng Zhong
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Lei Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China
| | - Shuxia Liu
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Rongrong Luo
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Shasha Wang
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Le Tang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Jiarui Yao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Zhishang Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China.
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing, China.
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
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Shields PG. Role of untargeted omics biomarkers of exposure and effect for tobacco research. ADDICTION NEUROSCIENCE 2023; 7:100098. [PMID: 37396411 PMCID: PMC10310069 DOI: 10.1016/j.addicn.2023.100098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Tobacco research remains a clear priority to improve individual and population health, and has recently become more complex with emerging combustible and noncombustible tobacco products. The use of omics methods in prevention and cessation studies are intended to identify new biomarkers for risk, compared risks related to other products and never use, and compliance for cessation and reinitation. to assess the relative effects of tobacco products to each other. They are important for the prediction of reinitiation of tobacco use and relapse prevention. In the research setting, both technical and clinical validation is required, which presents a number of complexities in the omics methodologies from biospecimen collection and sample preparation to data collection and analysis. When the results identify differences in omics features, networks or pathways, it is unclear if the results are toxic effects, a healthy response to a toxic exposure or neither. The use of surrogate biospecimens (e.g., urine, blood, sputum or nasal) may or may not reflect target organs such as the lung or bladder. This review describes the approaches for the use of omics in tobacco research and provides examples of prior studies, along with the strengths and limitations of the various methods. To date, there is little consistency in results, likely due to small number of studies, limitations in study size, the variability in the analytic platforms and bioinformatic pipelines, differences in biospecimen collection and/or human subject study design. Given the demonstrated value for the use of omics in clinical medicine, it is anticipated that the use in tobacco research will be similarly productive.
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Affiliation(s)
- Peter G. Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH
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Safari F, Kehelpannala C, Safarchi A, Batarseh AM, Vafaee F. Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis. Cancers (Basel) 2023; 15:2780. [PMID: 37345117 DOI: 10.3390/cancers15102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.
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Affiliation(s)
- Fatemeh Safari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Cheka Kehelpannala
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia
| | - Amani M Batarseh
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia
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Hernandez L, Ward LJ, Arefin S, Barany P, Wennberg L, Söderberg M, Bruno S, Cantaluppi V, Stenvinkel P, Kublickiene K. Blood–Brain Barrier Biomarkers before and after Kidney Transplantation. Int J Mol Sci 2023; 24:ijms24076628. [PMID: 37047601 PMCID: PMC10095132 DOI: 10.3390/ijms24076628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Kidney transplantation (KT) may improve the neurological status of chronic kidney disease (CKD) patients, reflected by the altered levels of circulating BBB-specific biomarkers. This study compares the levels of neuron specific enolase (NSE), brain-derived neurotrophic factor (BDNF), neurofilament light chain (NfL), and circulating plasma extracellular vesicles (EVs) in kidney-failure patients before KT and at a two-year follow up. Using ELISA, NSE, BDNF, and NfL levels were measured in the plasma of 74 living-donor KT patients. Plasma EVs were isolated with ultracentrifugation, and characterized for concentration/size and surface protein expression using flow cytometry from a subset of 25 patients. Lower NSE levels, and higher BDNF and NfL were observed at the two-year follow-up compared to the baseline (p < 0.05). Male patients had significantly higher BDNF levels compared to those of females. BBB biomarkers correlated with the baseline lipid profile and with glucose, vitamin D, and inflammation markers after KT. BBB surrogate marker changes in the microcirculation of early vascular aging phenotype patients with calcification and/or fibrosis were observed only in NSE and BDNF. CD31+ microparticles from endothelial cells expressing inflammatory markers such as CD40 and integrins were significantly reduced after KT. KT may, thus, improve the neurological status of CKD patients, as reflected by changes in BBB-specific biomarkers.
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Affiliation(s)
- Leah Hernandez
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Liam J. Ward
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, 587 58 Linköping, Sweden
| | - Samsul Arefin
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Peter Barany
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Lars Wennberg
- Department of Transplantation Surgery, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Magnus Söderberg
- Department of Pathology, Clinical Pharmacology and Safety Sciences, R&D AstraZeneca, 431 83 Gothenburg, Sweden
| | - Stefania Bruno
- Department of Medical Sciences, University of Torino, 10124 Torino, Italy
| | - Vincenzo Cantaluppi
- Nephrology and Kidney Transplant Unit, Department of Translational Medicine (DIMET), University of Piemonte Orientale (UPO), “Maggiore della Carita” University Hospital, 28100 Novara, Italy
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Karolina Kublickiene
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 171 77 Stockholm, Sweden
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Fu X, Zhang M, Yuan Y, Chen Y, Ou Z, Hashim Z, Hashim JH, Zhang X, Zhao Z, Norbäck D, Sun Y. Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft. Metabolites 2023; 13:343. [PMID: 36984783 PMCID: PMC10058785 DOI: 10.3390/metabo13030343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Passengers are at a higher risk of respiratory infections and chronic diseases due to microbial exposure in airline cabins. However, the presence of virulence factors (VFs), antimicrobial resistance genes (ARGs), metabolites, and chemicals are yet to be studied. To address this gap, we collected dust samples from the cabins of two airlines, one with textile seats (TSC) and one with leather seats (LSC), and analyzed the exposure using shotgun metagenomics and LC/MS. Results showed that the abundances of 17 VFs and 11 risk chemicals were significantly higher in TSC than LSC (p < 0.01). The predominant VFs in TSC were related to adherence, biofilm formation, and immune modulation, mainly derived from facultative pathogens such as Haemophilus parainfluenzae and Streptococcus pneumoniae. The predominant risk chemicals in TSC included pesticides/herbicides (carbofuran, bromacil, and propazine) and detergents (triethanolamine, diethanolamine, and diethyl phthalate). The abundances of these VFs and detergents followed the trend of TSC > LSC > school classrooms (p < 0.01), potentially explaining the higher incidence of infectious and chronic inflammatory diseases in aircraft. The level of ARGs in aircraft was similar to that in school environments. This is the first multi-omic survey in commercial aircraft, highlighting that surface material choice is a potential intervention strategy for improving passenger health.
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Affiliation(s)
- Xi Fu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of Public Health, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Mei Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yiwen Yuan
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zheyuan Ou
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zailina Hashim
- Department of Environmental and Occupational Health, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Malaysia
| | | | - Xin Zhang
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China
| | - Zhuohui Zhao
- Key Laboratory of Public Health Safety of the Ministry of Education, NHC Key Laboratory of Health Technology Assessment, School of Public Health, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Meteorology and Health, Typhoon Institute/CMA, Shanghai 200030, China
| | - Dan Norbäck
- Occupational and Environmental Medicine, Department of Medical Science, University Hospital, Uppsala University, 75237 Uppsala, Sweden
| | - Yu Sun
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
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12
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Machado-Fragua MD, Landré B, Chen M, Fayosse A, Dugravot A, Kivimaki M, Sabia S, Singh-Manoux A. Circulating serum metabolites as predictors of dementia: a machine learning approach in a 21-year follow-up of the Whitehall II cohort study. BMC Med 2022; 20:334. [PMID: 36163029 PMCID: PMC9513883 DOI: 10.1186/s12916-022-02519-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Age is the strongest risk factor for dementia and there is considerable interest in identifying scalable, blood-based biomarkers in predicting dementia. We examined the role of midlife serum metabolites using a machine learning approach and determined whether the selected metabolites improved prediction accuracy beyond the effect of age. METHODS Five thousand three hundred seventy-four participants from the Whitehall II study, mean age 55.8 (standard deviation (SD) 6.0) years in 1997-1999 when 233 metabolites were quantified using nuclear magnetic resonance metabolomics. Participants were followed for a median 21.0 (IQR 20.4, 21.7) years for clinically-diagnosed dementia (N=329). Elastic net penalized Cox regression with 100 repetitions of nested cross-validation was used to select models that improved prediction accuracy for incident dementia compared to an age-only model. Risk scores reflecting the frequency with which predictors appeared in the selected models were constructed, and their predictive accuracy was examined using Royston's R2, Akaike's information criterion, sensitivity, specificity, C-statistic and calibration. RESULTS Sixteen of the 100 models had a better c-statistic compared to an age-only model and 15 metabolites were selected at least once in all 16 models with glucose present in all models. Five risk scores, reflecting the frequency of selection of metabolites, and a 1-SD increment in all five risk scores was associated with higher dementia risk (HR between 3.13 and 3.26). Three of these, constituted of 4, 5 and 15 metabolites, had better prediction accuracy (c-statistic from 0.788 to 0.796) compared to an age-only model (c-statistic 0.780), all p<0.05. CONCLUSIONS Although there was robust evidence for the role of glucose in dementia, metabolites measured in midlife made only a modest contribution to dementia prediction once age was taken into account.
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Affiliation(s)
- Marcos D Machado-Fragua
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France.
| | - Benjamin Landré
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France
| | - Mathilde Chen
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France
| | - Aurore Fayosse
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France
| | - Aline Dugravot
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France
| | - Mika Kivimaki
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Séverine Sabia
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France.,Department of Epidemiology and Public Health, University College London, London, UK
| | - Archana Singh-Manoux
- Université de Paris, Inserm U1153, Epidemiology of Ageing and Neurodegenerative Diseases, 10 Avenue de Verdun, 75010, Paris, France.,Department of Epidemiology and Public Health, University College London, London, UK
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