1
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Kopczynski D, Hoffmann N, Troppmair N, Coman C, Ekroos K, Kreutz MR, Liebisch G, Schwudke D, Ahrends R. LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies. Anal Chem 2023; 95:15236-15244. [PMID: 37792961 PMCID: PMC10585661 DOI: 10.1021/acs.analchem.3c02449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/09/2023] [Indexed: 10/06/2023]
Abstract
Lipid analysis gained significant importance due to the enormous range of lipid functions, e.g., energy storage, signaling, or structural components. Whole lipidomes can be quantitatively studied in-depth thanks to recent analytical advancements. However, the systematic comparison of thousands of distinct lipidomes remains challenging. We introduce LipidSpace, a standalone tool for analyzing lipidomes by assessing their structural and quantitative differences. A graph-based comparison of lipid structures is the basis for calculating structural space models and subsequently computing lipidome similarities. When adding study variables such as body weight or health condition, LipidSpace can determine lipid subsets across all lipidomes that describe these study variables well by utilizing machine-learning approaches. The user-friendly GUI offers four built-in tutorials and interactive visual interfaces with pdf export. Many supported data formats allow an efficient (re)analysis of data sets from different sources. An integrated interactive workflow guides the user through the quality control steps. We used this suite to reanalyze and combine already published data sets (e.g., one with about 2500 samples and 576 lipids in one run) and made additional discoveries to the published conclusions with the potential to fill gaps in the current lipid biology understanding. LipidSpace is available for Windows or Linux (https://lifs-tools.org).
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Affiliation(s)
- Dominik Kopczynski
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Nils Hoffmann
- Forschungszentrum
Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), Jülich 52428, Germany
| | - Nina Troppmair
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Cristina Coman
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Kim Ekroos
- Lipidomics
Consulting Ltd., Esbo 02230, Finland
| | - Michael R. Kreutz
- Leibniz
Group “Dendritic Organelles and Synaptic Function” University
Medical Center Hamburg-Eppendorf, Center
for Molecular Neurobiology, ZMNH, Hamburg 20251, Germany
- RG
Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Gerhard Liebisch
- Institute
of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg 93053, Germany
| | - Dominik Schwudke
- German
Center for Infection Research (DZIF), Site
Hamburg-Lübeck-Borstel-Riems, Hamburg 22297, Germany
- Airway
Research Center North (ARCN), German Center
for Lung Research (DZL), Grosshansdorf 22927, Germany
- Bioanalytical
Chemistry, Research Center Borstel, Borstel 23845, Germany
| | - Robert Ahrends
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
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2
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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians. Nat Commun 2022; 13:6044. [PMID: 36229545 PMCID: PMC9561172 DOI: 10.1038/s41467-022-33782-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
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3
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Lysophosphatidylcholine: Potential Target for the Treatment of Chronic Pain. Int J Mol Sci 2022; 23:ijms23158274. [PMID: 35955410 PMCID: PMC9368269 DOI: 10.3390/ijms23158274] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 12/26/2022] Open
Abstract
The bioactive lipid lysophosphatidylcholine (LPC), a major phospholipid component of oxidized low-density lipoprotein (Ox-LDL), originates from the cleavage of phosphatidylcholine by phospholipase A2 (PLA2) and is catabolized to other substances by different enzymatic pathways. LPC exerts pleiotropic effects mediated by its receptors, G protein-coupled signaling receptors, Toll-like receptors, and ion channels to activate several second messengers. Lysophosphatidylcholine (LPC) is increasingly considered a key marker/factor positively in pathological states, especially inflammation and atherosclerosis development. Current studies have indicated that the injury of nervous tissues promotes oxidative stress and lipid peroxidation, as well as excessive accumulation of LPC, enhancing the membrane hyperexcitability to induce chronic pain, which may be recognized as one of the hallmarks of chronic pain. However, findings from lipidomic studies of LPC have been lacking in the context of chronic pain. In this review, we focus in some detail on LPC sources, biochemical pathways, and the signal-transduction system. Moreover, we outline the detection methods of LPC for accurate analysis of each individual LPC species and reveal the pathophysiological implication of LPC in chronic pain, which makes it an interesting target for biomarkers and the development of medicine regarding chronic pain.
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4
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Luo H, Shen T, Xie X. Stochastic simulation of enzymatic kinetics for 13C isotope labeling at the single-cell scale. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-022-02262-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Pan H, Tan PF, Lim IY, Huan J, Teh AL, Chen L, Gong M, Tin F, Mir SA, Narasimhan K, Chan JKY, Tan KH, Kobor MS, Meikle PJ, Wenk MR, Chong YS, Eriksson JG, Gluckman PD, Karnani N. Integrative Multi-Omics database (iMOMdb) of Asian Pregnant Women. Hum Mol Genet 2022; 31:3051-3067. [PMID: 35445712 PMCID: PMC9476622 DOI: 10.1093/hmg/ddac079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/20/2022] [Accepted: 04/03/2022] [Indexed: 11/14/2022] Open
Abstract
Asians are underrepresented across many omics databases, thereby limiting the potential of precision medicine in nearly 60% of the global population. As such, there is a pressing need for multi-omics derived quantitative trait loci (QTLs) to fill the knowledge gap of complex traits in populations of Asian ancestry. Here, we provide the first blood-based multi-omics analysis of Asian pregnant women, constituting high-resolution genotyping (N = 1079), DNA methylation (N = 915) and transcriptome profiling (N = 238). Integrative omics analysis identified 219 154 CpGs associated with cis-DNA methylation QTLs (meQTLs) and 3703 RNAs associated with cis-RNA expression QTLs (eQTLs). Ethnicity was the largest contributor of inter-individual variation across all omics datasets, with 2561 genes identified as hotspots of this variation; 395 of these hotspot genes also contained both ethnicity-specific eQTLs and meQTLs. Gene set enrichment analysis of these ethnicity QTL hotspots showed pathways involved in lipid metabolism, adaptive immune system and carbohydrate metabolism. Pathway validation by profiling the lipidome (~480 lipids) of antenatal plasma (N = 752) and placenta (N = 1042) in the same cohort showed significant lipid differences among Chinese, Malay and Indian women, validating ethnicity-QTL gene effects across different tissue types. To develop deeper insights into the complex traits and benefit future precision medicine research in Asian pregnant women, we developed iMOMdb, an open-access database.
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Affiliation(s)
- Hong Pan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Pei Fang Tan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Ives Y Lim
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Jason Huan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Min Gong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Felicia Tin
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Sartaj Ahmad Mir
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Kothandaraman Narasimhan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Jerry K Y Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore.,Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore
| | - Kok Hian Tan
- Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore.,Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, Singapore
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Peter J Meikle
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Australia
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Department of Obstetrics and Gynecology and Human Potential Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Johan G Eriksson
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Department of Obstetrics and Gynecology and Human Potential Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Folkhälsan Research Center, Helsinki, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, Finland
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore.,Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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6
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Chen Y, Kassam I, Lau SH, Kooner JS, Wilson R, Peters A, Winkelmann J, Chambers JC, Chow VT, Khor CC, van Dam RM, Teo YY, Loh M, Sim X. Impact of BMI and waist circumference on epigenome-wide DNA methylation and identification of epigenetic biomarkers in blood: an EWAS in multi-ethnic Asian individuals. Clin Epigenetics 2021; 13:195. [PMID: 34670603 PMCID: PMC8527674 DOI: 10.1186/s13148-021-01162-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/29/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The prevalence of obesity and its related chronic diseases have been increasing especially in Asian countries. Obesity-related genetic variants have been identified, but these explain little of the variation in BMI. Recent studies reported associations between DNA methylation and obesity, mostly in non-Asian populations. METHODS We performed an epigenome-wide association study (EWAS) on general adiposity (body mass index, BMI) and abdominal adiposity (waist circumference, WC) in 409 multi-ethnic Asian individuals and replicated BMI and waist-associated DNA methylation CpGs identified in other populations. The cross-lagged panel model and Mendelian randomization were used to assess the temporal relationship between methylation and BMI. The temporal relationship between the identified CpGs and inflammation and metabolic markers was also examined. RESULTS EWAS identified 116 DNA methylation CpGs independently associated with BMI and eight independently associated with WC at false discovery rate PFDR < 0.05 in 409 Asian samples. We replicated 110 BMI-associated CpGs previously reported in Europeans and identified six novel BMI-associated CpGs and two novel WC-associated CpGs. We observed high consistency in association direction of effect compared to studies in other populations. Causal relationship analyses indicated that BMI was more likely to be the cause of DNA methylation alteration, rather than the consequence. The causal analyses using BMI-associated methylation risk score also suggested that higher levels of the inflammation marker IL-6 were likely the consequence of methylation change. CONCLUSION Our study provides evidence of an association between obesity and DNA methylation in multi-ethnic Asians and suggests that obesity can drive methylation change. The results also suggested possible causal influence that obesity-related methylation changes might have on inflammation and lipoprotein levels.
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Affiliation(s)
- Yuqing Chen
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Tahir Foundation Building, Singapore, 117549, Singapore
| | - Irfahan Kassam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Tahir Foundation Building, Singapore, 117549, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Suk Hiang Lau
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Rory Wilson
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Bavaria, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, Munich, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- Lehrstuhl Für Neurogenetik, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology, Munich, Germany
| | - John C Chambers
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Middlesex, UK
- Imperial College Healthcare NHS Trust, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Level 18, Lee Kong Chian Clinical Science Building, Singapore, 308232, Singapore
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Vincent T Chow
- National University Health System Infectious Diseases Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Rob M van Dam
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Tahir Foundation Building, Singapore, 117549, Singapore
- Department of Nutrition and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Tahir Foundation Building, Singapore, 117549, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Level 18, Lee Kong Chian Clinical Science Building, Singapore, 308232, Singapore.
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- National Skin Centre, Singapore, Singapore.
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, 12 Science Drive 2, #10-01, Tahir Foundation Building, Singapore, 117549, Singapore.
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7
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Comparative Genomic Analysis of Extended-spectrum β-lactamase and mcr-1 Positive Escherichia coli from Gut Microbiota of Healthy Singaporeans. Appl Environ Microbiol 2021; 87:e0048821. [PMID: 34347523 DOI: 10.1128/aem.00488-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and six different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analysed the genetic context of the resistance genes and found that composite transposons played important roles in the co-transfer of blaCTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome SNPs shared by these isolates, we identified possible clonal transmission of a MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. Importance The human gut can harbor both antibiotic resistant and virulent E. coli which may subsequently cause infections. In this study, we found that MDR E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes, and are highly diverse to each other. By comparing their genomes with the ESBL-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected a MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.
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8
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Ding Y, Saw WY, Tan LWL, Moong DKN, Nagarajan N, Teo YY, Seedorf H. Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans. J Antimicrob Chemother 2021; 75:3480-3484. [PMID: 32853333 DOI: 10.1093/jac/dkaa372] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/03/2020] [Indexed: 01/01/2023] Open
Abstract
OBJECTIVES The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on isolation and screening of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a cohort of healthy individuals in Singapore. METHODS MinION and Illumina sequencing was performed to obtain the complete genome sequences of Escherichia coli 2EC1-1 and 94EC. Subsequently, 109 human faecal samples were screened retrospectively for eravacycline-resistant Enterobacteriaceae strains, which were further tested for tet(X4) by PCR. The taxonomy of the isolated strains was determined by 16S rRNA gene PCR and Sanger sequencing. RESULTS Comparative genomic analysis of E. coli 2EC1-1 and 94EC revealed that both carry tet(X4), which is encoded by IncI1-type plasmids p2EC1-1 and p94EC-2, respectively. Retrospective screening of faecal samples collected from 109 healthy individuals showed that the faecal carriage rate of Tet(X4)-producing Enterobacteriaceae is 10.1% (95% CI = 5.1%-17.3%), suggesting that tet(X4) is widely distributed in the gut microbiota of healthy individuals in Singapore. CONCLUSIONS To the best of our knowledge, this is the first report on the prevalence of tet(X4) in the gut microbiota of a healthy human cohort, as well as the first description of this resistance mechanism outside of China. Our findings suggest that surveillance of tet(X4) in community settings is vital to monitor the spread of this resistance mechanism.
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Affiliation(s)
- Yichen Ding
- Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore
| | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, 75 Commercial Rd, Melbourne, 3004, Victoria, Australia
| | - Linda Wei Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore, A*STAR, 138672, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 119077, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, 117549, Singapore.,Genome Institute of Singapore, A*STAR, 138672, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 119077, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, 117546, Singapore.,Life Sciences Institute, National University of Singapore, 117456, Singapore
| | - Henning Seedorf
- Temasek Life Sciences Laboratory, 1 Research Link, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, 117558, Singapore
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9
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Zhao X, Kang J, Svetnik V, Warden D, Wilcock G, David Smith A, Savage MJ, Laterza OF. A Machine Learning Approach to Identify a Circulating MicroRNA Signature for Alzheimer Disease. J Appl Lab Med 2021; 5:15-28. [PMID: 31811079 DOI: 10.1373/jalm.2019.029595] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND Accurate diagnosis of Alzheimer disease (AD) involving less invasive molecular procedures and at reasonable cost is an unmet medical need. We identified a serum miRNA signature for AD that is less invasive than a measure in cerebrospinal fluid. METHODS From the Oxford Project to Investigate Memory and Aging (OPTIMA) study, 96 serum samples were profiled by a multiplex (>500 analytes) microRNA (miRNA) reverse transcription quantitative PCR analysis, including 51 controls, 32 samples from patients with AD, and 13 samples from patients with mild cognitive impairment (MCI). Clinical diagnosis of a subset of AD and the controls was confirmed by postmortem (PM) histologic examination of brain tissue. In a machine learning approach, the AD and control samples were split 70:30 as the training and test cohorts. A multivariate random forest statistical analysis was applied to construct and test a miRNA signature for AD identification. In addition, the MCI participants were included in the test cohort to assess whether the signature can identify early AD patients. RESULTS A 12-miRNA signature for AD identification was constructed in the training cohort, demonstrating 76.0% accuracy in the independent test cohort with 90.0% sensitivity and 66.7% specificity. The signature, however, was not able to identify MCI participants. With a subset of AD and control participants with PM-confirmed diagnosis status, a separate 12-miRNA signature was constructed. Although sample size was limited, the PM-confirmed signature demonstrated improved accuracy of 85.7%, largely owing to improved specificity of 80.0% with comparable sensitivity of 88.9%. CONCLUSION Although additional and more diverse cohorts are needed for further clinical validation of the robustness, the miRNA signature appears to be a promising blood test to diagnose AD.
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Affiliation(s)
- Xuemei Zhao
- Translational Molecular Biomarkers, MRL, Merck & Co., Kenilworth, NJ
| | - John Kang
- Biometrics, MRL, Merck & Co., Rahway, NJ
| | | | - Donald Warden
- Department of Pharmacology, Oxford University, Oxford, UK
| | - Gordon Wilcock
- Nuffield Department of Clinical Neuroscience, John Radcliffe Hospital, Oxford, UK
| | - A David Smith
- Department of Pharmacology, Oxford University, Oxford, UK
| | - Mary J Savage
- Translational Companion Diagnostics, MRL, Merck & Co., Kenilworth, NJ
| | - Omar F Laterza
- Translational Molecular Biomarkers, MRL, Merck & Co., Kenilworth, NJ
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10
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Lam ATL, Lee AP, Jayaraman P, Tan KY, Raghothaman D, Lim HL, Cheng H, Zhou L, Tan AHM, Reuveny S, Oh S. Multiomics analyses of cytokines, genes, miRNA, and regulatory networks in human mesenchymal stem cells expanded in stirred microcarrier-spinner cultures. Stem Cell Res 2021; 53:102272. [PMID: 33676128 DOI: 10.1016/j.scr.2021.102272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/19/2021] [Accepted: 02/21/2021] [Indexed: 01/09/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are of great clinical interest as a form of allogenic therapy due to their excellent regenerative and immunomodulatory effects for various therapeutic indications. Stirred suspension bioreactors using microcarriers (MC) have been used for large-scale production of MSCs compared to planar cultivation systems. Previously, we have demonstrated that expansion of MSCs in MC-spinner cultures improved chondrogenic, osteogenic, and cell migration potentials as compared to monolayer-static cultures. In this study, we sought to address this by analyzing global gene expression patterns, miRNA profiles and secretome under both monolayer-static and MC-spinner cultures in serum-free medium at different growth phases. The datasets revealed differential expression patterns that correlated with potentially improved MSC properties in cells from MC-spinner cultures compared to those of monolayer-static cultures. Transcriptome analysis identified a unique expression signature for cells from MC-spinner cultures, which correlated well with miRNA expression, and cytokine secretion involved in key MSC functions. Importantly, MC-spinner cultures and conditioned medium showed increased expression of factors that possibly enhance pathways of extracellular matrix dynamics, cellular metabolism, differentiation potential, immunoregulatory function, and wound healing. This systematic analysis provides insights for the efficient optimization of stem cell bioprocessing and infers that MC-based bioprocess manufacturing could improve post-expansion cellular properties for stem cell therapies.
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Affiliation(s)
- Alan Tin-Lun Lam
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Alison P Lee
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Premkumar Jayaraman
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kah Yong Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Deepak Raghothaman
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Hsueh Lee Lim
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - He Cheng
- MiRXES, 2 Tukang Innovation Grove, JTC MedTech Hub, Singapore
| | - Lihan Zhou
- MiRXES, 2 Tukang Innovation Grove, JTC MedTech Hub, Singapore
| | - Andy Hee-Meng Tan
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shaul Reuveny
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Steve Oh
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore.
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11
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Systematic evaluation of multiple qPCR platforms, NanoString and miRNA-Seq for microRNA biomarker discovery in human biofluids. Sci Rep 2021; 11:4435. [PMID: 33627690 PMCID: PMC7904811 DOI: 10.1038/s41598-021-83365-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
Aberrant miRNA expression has been associated with many diseases, and extracellular miRNAs that circulate in the bloodstream are remarkably stable. Recently, there has been growing interest in identifying cell-free circulating miRNAs that can serve as non-invasive biomarkers for early detection of disease or selection of treatment options. However, quantifying miRNA levels in biofluids is technically challenging due to their low abundance. Using reference samples, we performed a cross-platform evaluation in which miRNA profiling was performed on four different qPCR platforms (MiRXES, Qiagen, Applied Biosystems, Exiqon), nCounter technology (NanoString), and miRNA-Seq. Overall, our results suggest that using miRNA-Seq for discovery and targeted qPCR for validation is a rational strategy for miRNA biomarker development in clinical samples that involve limited amounts of biofluids.
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12
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Kassam I, Tan S, Gan FF, Saw WY, Tan LWL, Moong DKN, Soong R, Teo YY, Loh M. Genome-wide identification of cis DNA methylation quantitative trait loci in three Southeast Asian Populations. Hum Mol Genet 2021; 30:603-618. [PMID: 33547791 DOI: 10.1093/hmg/ddab038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 12/12/2022] Open
Abstract
DNA methylation (DNAm) is an epigenetic modification that acts to regulate gene transcription, is essential for cellular processes and plays an important role in complex traits and disease. Variation in DNAm levels is influenced by both genetic and environmental factors. Several studies have examined the extent to which common genetic variation influences DNAm (i.e. mQTLs), however, an improved understanding of mQTLs across diverse human populations is needed to increase their utility in integrative genomic studies in order to further our understanding of complex trait and disease biology. Here, we systematically examine cis-mQTLs in three Southeast Asian populations in the Singapore Integrative Omics (iOmics) Study, comprised of Chinese (n = 93), Indians (n = 83) and Malays (n = 78). A total of 24 851 cis-mQTL probes were associated with at least one SNP in meta- and ethnicity-specific analyses at a stringent significance level. These cis-mQTL probes show significant differences in local SNP heritability between the ethnicities, enrichment in functionally relevant regions using data from the Roadmap Epigenomics Mapping Consortium and are associated with nearby genes and complex traits due to pleiotropy. Importantly, DNAm prediction performance and the replication of cis-mQTLs both within iOmics and between two independent mQTL studies in European and Bangladeshi individuals is best when the genetic distance between the ethnicities is small, with differences in cis-mQTLs likely due to differences in allele frequency and linkage disequilibrium. This study highlights the importance of, and opportunities from, extending investigation of the genetic control of DNAm to Southeast Asian populations.
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Affiliation(s)
- Irfahan Kassam
- Life Sciences Institute, National University of Singapore, Singapore 117456.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Sili Tan
- KK Research Centre, KK Women's and Children's Hospital, Singapore 229899
| | - Fei Fei Gan
- Department of NUH Tissue Repository, National University Health System, Singapore 119228
| | - Woei-Yuh Saw
- Baker Heart and Diabetes Institute, Melbourne Victoria, Australia 3004
| | - Linda Wei-Lin Tan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Don Kyin Nwe Moong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599
| | - Yik-Ying Teo
- Life Sciences Institute, National University of Singapore, Singapore 117456.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232.,Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom W2 1PG.,Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (ASTAR), Singapore 138648
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13
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Medina J, van der Velpen V, Teav T, Guitton Y, Gallart-Ayala H, Ivanisevic J. Single-Step Extraction Coupled with Targeted HILIC-MS/MS Approach for Comprehensive Analysis of Human Plasma Lipidome and Polar Metabolome. Metabolites 2020; 10:E495. [PMID: 33276464 PMCID: PMC7760228 DOI: 10.3390/metabo10120495] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/21/2020] [Accepted: 11/27/2020] [Indexed: 11/24/2022] Open
Abstract
Expanding metabolome coverage to include complex lipids and polar metabolites is essential in the generation of well-founded hypotheses in biological assays. Traditionally, lipid extraction is performed by liquid-liquid extraction using either methyl-tert-butyl ether (MTBE) or chloroform, and polar metabolite extraction using methanol. Here, we evaluated the performance of single-step sample preparation methods for simultaneous extraction of the complex lipidome and polar metabolome from human plasma. The method performance was evaluated using high-coverage Hydrophilic Interaction Liquid Chromatography-ESI coupled to tandem mass spectrometry (HILIC-ESI-MS/MS) methodology targeting a panel of 1159 lipids and 374 polar metabolites. The criteria used for method evaluation comprised protein precipitation efficiency, and relative MS signal abundance and repeatability of detectable lipid and polar metabolites in human plasma. Among the tested methods, the isopropanol (IPA) and 1-butanol:methanol (BUME) mixtures were selected as the best compromises for the simultaneous extraction of complex lipids and polar metabolites, allowing for the detection of 584 lipid species and 116 polar metabolites. The extraction with IPA showed the greatest reproducibility with the highest number of lipid species detected with the coefficient of variation (CV) < 30%. Besides this difference, both IPA and BUME allowed for the high-throughput extraction and reproducible measurement of a large panel of complex lipids and polar metabolites, thus warranting their application in large-scale human population studies.
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Affiliation(s)
- Jessica Medina
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, CH-1005 Lausanne, Switzerland; (J.M.); (V.v.d.V.); (T.T.)
| | - Vera van der Velpen
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, CH-1005 Lausanne, Switzerland; (J.M.); (V.v.d.V.); (T.T.)
| | - Tony Teav
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, CH-1005 Lausanne, Switzerland; (J.M.); (V.v.d.V.); (T.T.)
| | - Yann Guitton
- Laboratoire d’Etude des Résidus et Contaminants dans les Aliments (LABERCA), Oniris, INRAE, F-44307 Nantes, France;
| | - Hector Gallart-Ayala
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, CH-1005 Lausanne, Switzerland; (J.M.); (V.v.d.V.); (T.T.)
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, CH-1005 Lausanne, Switzerland; (J.M.); (V.v.d.V.); (T.T.)
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14
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Low SYY, Cheng H, Zou R, Ng LP, Kuick CH, Syed Sulaiman NB, Chang KTE, Low DCY, Zhou L, Seow WT. Molecular exploration of paediatric intracranial germinomas from multi-ethnic Singapore. BMC Neurol 2020; 20:415. [PMID: 33187494 PMCID: PMC7666528 DOI: 10.1186/s12883-020-01981-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
Background Germinomas (IG) account for up to 50% of all intracranial germ cell tumours. These tumours are reputed to be more prevalent in Oriental populations in comparison to Western cohorts. Biological characteristics of IG in other ethnic groups are unknown. Singapore is a multi-ethnic country with diverse cultures. Owing to inter-racial heterogeneity, the authors hypothesize there are molecular differences between paediatric IG patients in our local population. The aims of this study are exploratory: firstly, to identify molecular characteristics in this tumour type and circulating CSF unique to different racial cohorts; and next, to corroborate our findings with published literature. Methods This is a single-institution, retrospective study of prospectively collected data. Inclusion criteria encompass all paediatric patients with histologically confirmed IG. Excess CSF and brain tumour tissues are collected for molecular analysis. Tumour tissues are subjected to a next generation sequencing (NGS) targeted panel for KIT and PDGRA. All CSF samples are profiled via a high-throughput miRNA multiplexed workflow. Results are then corroborated with existing literature and public databases. Results In our cohort of 14 patients, there are KIT exon variants in the tumour tissues and CSF miRNAs corroborative with published studies. Separately, there are also KIT exon variants and miRNAs not previously highlighted in IG. A subgroup analysis demonstrates differential CSF miRNAs between Chinese and Malay IG patients. Conclusion This is the first in-depth molecular study of a mixed ethnic population of paediatric IGs from a Southeast Asian cohort. Validation studies are required to assess the relevance of novel findings in our study. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-020-01981-0.
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Affiliation(s)
- Sharon Yin Yee Low
- Neurosurgical Service, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore. .,Department of Neurosurgery, National Neuroscience Institute, Singapore, Singapore. .,SingHealth Duke-NUS Neuroscience Academic Clinical Program, 11 Jalan Tan Tock Seng, Singapore, 30843, Singapore. .,VIVA-KKH Paediatric Brain and Solid Tumours Laboratory, Singapore, Singapore.
| | - He Cheng
- Bioprocessing Technology Institute, A*STAR, Singapore, Singapore.,MiRXES Pte Ltd, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Ruiyang Zou
- Bioprocessing Technology Institute, A*STAR, Singapore, Singapore.,MiRXES Pte Ltd, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Lee Ping Ng
- Neurosurgical Service, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore
| | - Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore
| | - Nurfarhanah Bte Syed Sulaiman
- Department of Neurosurgery, National Neuroscience Institute, Singapore, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumours Laboratory, Singapore, Singapore
| | - Kenneth Tou En Chang
- VIVA-KKH Paediatric Brain and Solid Tumours Laboratory, Singapore, Singapore.,Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore
| | - David Chyi Yeu Low
- Neurosurgical Service, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.,Department of Neurosurgery, National Neuroscience Institute, Singapore, Singapore.,SingHealth Duke-NUS Neuroscience Academic Clinical Program, 11 Jalan Tan Tock Seng, Singapore, 30843, Singapore
| | - Lihan Zhou
- Bioprocessing Technology Institute, A*STAR, Singapore, Singapore.,MiRXES Pte Ltd, 10 Biopolis Road, Chromos, Singapore, 138670, Singapore
| | - Wan Tew Seow
- Neurosurgical Service, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.,Department of Neurosurgery, National Neuroscience Institute, Singapore, Singapore.,SingHealth Duke-NUS Neuroscience Academic Clinical Program, 11 Jalan Tan Tock Seng, Singapore, 30843, Singapore
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15
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Determination of one year stability of lipid plasma profile and comparison of blood collection tubes using UHPSFC/MS and HILIC-UHPLC/MS. Anal Chim Acta 2020; 1137:74-84. [DOI: 10.1016/j.aca.2020.08.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/24/2020] [Accepted: 08/29/2020] [Indexed: 01/27/2023]
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16
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Li Y, Yan H, Zhang Y, Li Q, Yu L, Li Q, Liu C, Xie Y, Chen K, Ye F, Wang K, Chen L, Ding Y. Alterations of the Gut Microbiome Composition and Lipid Metabolic Profile in Radiation Enteritis. Front Cell Infect Microbiol 2020; 10:541178. [PMID: 33194790 PMCID: PMC7609817 DOI: 10.3389/fcimb.2020.541178] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Radiation enteritis (RE) is a common complication in cancer patients receiving radiotherapy. Although studies have shown the changes of this disease at clinical, pathological and other levels, the dynamic characteristics of local microbiome and metabolomics are hitherto unknown. We aimed to examine the multi-omics features of the gut microecosystem, determining the functional correlation between microbiome and lipid metabolites during RE activity. By delivering single high-dose irradiation, a RE mouse model was established. High-throughput 16S rDNA sequencing and global lipidomics analysis were performed to examine microbial and lipidomic profile changes in the gut microecosystem. Spearman correlation analysis was used to determine the functional correlation between bacteria and metabolites. Clinical samples were collected to validate the above observations. During RE activity, the intestinal inflammation of the mice was confirmed by typical signs, symptoms, imaging findings and pathological evidences. 16S datasets revealed that localized irradiation dramatically altered the gut microbial composition, resulting in a decrease ratio of Bacteroidetes to Firmicutes. Lipidomics analysis indicated the remarkable lipidomic profile changes in enteric epithelial barrier, determining that glycerophospholipids metabolism was correlated to RE progression with the highest relevance. Spearman correlation analysis identified that five bacteria-metabolite pairs showed the most significant functional correlation in RE, including Alistipes-PC(36:0e), Bacteroides-DG(18:0/20:4), Dubosiella-PC(35:2), Eggerthellaceae-PC(35:6), and Escherichia-Shigella-TG(18:2/18:2/20:4). These observations were partly confirmed in human specimens. Our study provided a comprehensive description of microbiota dysbiosis and lipid metabolic disorders in RE, suggesting strategies to change local microecosystem to relieve radiation injury and maintain homeostasis.
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Affiliation(s)
- Yiyi Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongmei Yan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yaowei Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qingping Li
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lu Yu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Qianyu Li
- Medical Imaging Specialty, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Cuiting Liu
- Central Laboratory, Southern Medical University, Guangzhou, China
| | - Yuwen Xie
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Keli Chen
- HuiQiao Medical Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kai Wang
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Longhua Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Ding
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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17
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Development of a serum miRNA panel for detection of early stage non-small cell lung cancer. Proc Natl Acad Sci U S A 2020; 117:25036-25042. [PMID: 32943537 DOI: 10.1073/pnas.2006212117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Minimally invasive testing for early detection of lung cancer to improve patient survival is a major unmet clinical need. This study aimed to develop and validate a serum multi-microRNA (multimiR) panel as a minimally invasive test for early detection of nonsmall cell lung cancer (NSCLC) regardless of smoking status, gender, and ethnicity. Our study included 744 NSCLC cases and 944 matched controls, including smokers and nonsmokers, male and female, with Asian and Caucasian subjects. Using RT-qPCR and a tightly controlled workflow, we quantified the absolute expression of 520 circulating microRNAs (miRNAs) in a Chinese cohort of 180 early stage NSCLC cases and 216 healthy controls (male smokers). Candidate biomarkers were verified in two case-control cohorts of 432 Chinese and 218 Caucasians, respectively (including females and nonsmokers). A multimiR panel for NSCLC detection was developed using a twofold cross-validation and validated in three additional Asian cohorts comprising 642 subjects. We discovered 35 candidate miRNA biomarkers, verified 22 of them, and developed a five-miR panel that detected NSCLC with area under curve (AUC) of 0.936-0.984 in the discovery and verification cohorts. The panel was validated in three independent cohorts with AUCs of 0.973, 0.916, and 0.917. The sensitivity of five-miR test was 81.3% for all stages, 82.9% for stages I and II, and 83.0% for stage I NSCLC, when the specificity is at 90.7%. We developed a minimally invasive five-miR serum test for detecting early stage NSCLC and validated its performance in multiple patient cohorts independent of smoking status, gender, and ethnicity.
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18
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Wong MWK, Thalamuthu A, Braidy N, Mather KA, Liu Y, Ciobanu L, Baune BT, Armstrong NJ, Kwok J, Schofield P, Wright MJ, Ames D, Pickford R, Lee T, Poljak A, Sachdev PS. Genetic and environmental determinants of variation in the plasma lipidome of older Australian twins. eLife 2020; 9:e58954. [PMID: 32697195 PMCID: PMC7394543 DOI: 10.7554/elife.58954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/20/2020] [Indexed: 12/11/2022] Open
Abstract
The critical role of blood lipids in a broad range of health and disease states is well recognised but less explored is the interplay of genetics and environment within the broader blood lipidome. We examined heritability of the plasma lipidome among healthy older-aged twins (75 monozygotic/55 dizygotic pairs) enrolled in the Older Australian Twins Study (OATS) and explored corresponding gene expression and DNA methylation associations. 27/209 lipids (13.3%) detected by liquid chromatography-coupled mass spectrometry (LC-MS) were significantly heritable under the classical ACE twin model (h2 = 0.28-0.59), which included ceramides (Cer) and triglycerides (TG). Relative to non-significantly heritable TGs, heritable TGs had a greater number of associations with gene transcripts, not directly associated with lipid metabolism, but with immune function, signalling and transcriptional regulation. Genome-wide average DNA methylation (GWAM) levels accounted for variability in some non-heritable lipids. We reveal a complex interplay of genetic and environmental influences on the ageing plasma lipidome.
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Affiliation(s)
- Matthew WK Wong
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- Neuroscience Research AustraliaSydneyAustralia
| | - Yue Liu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
| | - Liliana Ciobanu
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- The University of Adelaide, Adelaide Medical School, Discipline of PsychiatryAdelaideAustralia
| | - Bernhardt T Baune
- The University of Adelaide, Adelaide Medical School, Discipline of PsychiatryAdelaideAustralia
- Department of Psychiatry, University of MünsterMünsterGermany
- Department of Psychiatry, Melbourne Medical School, The University of MelbourneMelbourneAustralia
- The Florey Institute of Neuroscience and Mental Health, The University of MelbourneMelbourneAustralia
| | | | - John Kwok
- Brain and Mind Centre, The University of SydneySydneyAustralia
| | - Peter Schofield
- Neuroscience Research AustraliaSydneyAustralia
- School of Medical Sciences, University of New South WalesSydneyAustralia
| | - Margaret J Wright
- Queensland Brain Institute, University of QueenslandBrisbaneAustralia
- Centre for Advanced Imaging, University of QueenslandBrisbaneAustralia
| | - David Ames
- University of Melbourne Academic Unit for Psychiatry of Old AgeKewAustralia
- National Ageing Research InstituteParkvilleAustralia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South WalesSydneyAustralia
| | - Teresa Lee
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales HospitalSydneyAustralia
| | - Anne Poljak
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- School of Medical Sciences, University of New South WalesSydneyAustralia
- Bioanalytical Mass Spectrometry Facility, University of New South WalesSydneyAustralia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South WalesSydneyAustralia
- Neuropsychiatric Institute, Euroa Centre, Prince of Wales HospitalSydneyAustralia
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19
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Peng B, Kopczynski D, Pratt BS, Ejsing CS, Burla B, Hermansson M, Benke PI, Tan SH, Chan MY, Torta F, Schwudke D, Meckelmann SW, Coman C, Schmitz OJ, MacLean B, Manke MC, Borst O, Wenk MR, Hoffmann N, Ahrends R. LipidCreator workbench to probe the lipidomic landscape. Nat Commun 2020; 11:2057. [PMID: 32345972 PMCID: PMC7188904 DOI: 10.1038/s41467-020-15960-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/06/2020] [Indexed: 12/16/2022] Open
Abstract
Mass spectrometry (MS)-based targeted lipidomics enables the robust quantification of selected lipids under various biological conditions but comprehensive software tools to support such analyses are lacking. Here we present LipidCreator, a software that fully supports targeted lipidomics assay development. LipidCreator offers a comprehensive framework to compute MS/MS fragment masses for over 60 lipid classes. LipidCreator provides all functionalities needed to define fragments, manage stable isotope labeling, optimize collision energy and generate in silico spectral libraries. We validate LipidCreator assays computationally and analytically and prove that it is capable to generate large targeted experiments to analyze blood and to dissect lipid-signaling pathways such as in human platelets.
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Affiliation(s)
- Bing Peng
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany
| | - Brian S Pratt
- University of Washington, Department of Genome Sciences, WA, 98195, Seattle, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-, 5230, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117, Heidelberg, Germany
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, 117456, Singapore, Singapore
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-, 5230, Odense, Denmark
- Wihuri Research Institute, 00290, Helsinki, Finland
| | - Peter Imre Benke
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore, Singapore
| | - Sock Hwee Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University Hospital, 119228, Singapore, Singapore
- Cardiovascular Research Institute, National University of Singapore, 117599, Singapore, Singapore
| | - Mark Y Chan
- Department of Medicine, Yong Loo Lin School of Medicine, National University Hospital, 119228, Singapore, Singapore
- Cardiovascular Research Institute, National University of Singapore, 117599, Singapore, Singapore
- National University Heart Centre, National University Health System, 117599, Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore, Singapore
| | - Dominik Schwudke
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), 38124, Braunschweig, Germany
- Airway Research Center North Member of the German Center for Lung Research (DZL), 22927, Großhansdorf, Germany
| | - Sven W Meckelmann
- Applied Analytical Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany
- Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria
| | - Oliver J Schmitz
- Applied Analytical Chemistry, University of Duisburg-Essen, 45141, Essen, Germany
| | - Brendan MacLean
- University of Washington, Department of Genome Sciences, WA, 98195, Seattle, USA
| | - Mailin-Christin Manke
- Department of Cardiology and Cardiovascular Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Oliver Borst
- Department of Cardiology and Cardiovascular Medicine, University of Tübingen, 72076, Tübingen, Germany
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, 117456, Singapore, Singapore
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore, Singapore
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139, Dortmund, Germany.
- Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090, Vienna, Austria.
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20
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Tkachev A, Stepanova V, Zhang L, Khrameeva E, Zubkov D, Giavalisco P, Khaitovich P. Differences in lipidome and metabolome organization of prefrontal cortex among human populations. Sci Rep 2019; 9:18348. [PMID: 31797944 PMCID: PMC6893025 DOI: 10.1038/s41598-019-53762-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
Human populations, despite their overwhelming similarity, contain some distinct phenotypic, genetic, epigenetic, and gene expression features. In this study, we explore population differences at yet another level of molecular phenotype: the abundance of non-polar and polar low molecular weight compounds, lipids and metabolites in the prefrontal cortical region of the brain. We assessed the abundance of 1,670 lipids and 258 metabolites in 146 Han Chinese, 97 Western European, and 60 African American individuals of varying ages, covering most of the lifespan. The statistical analysis and logistic regression models both demonstrated extensive lipid and metabolic divergence of the Han Chinese individuals from the other two populations. This divergence was age-dependent, peaking in young adults, and involved metabolites and lipids clustering in specific metabolic pathways.
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Affiliation(s)
- Anna Tkachev
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per. 19/1, 127051, Moscow, Russia
| | - Vita Stepanova
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny Per. 19/1, 127051, Moscow, Russia
| | - Lei Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031, Shanghai, China
| | | | - Dmitry Zubkov
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | - Patrick Giavalisco
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Straße 9B, 50931, Cologne, Germany.
| | - Philipp Khaitovich
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia.
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, 320 Yue Yang Road, 200031, Shanghai, China.
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103, Leipzig, Germany.
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Vvedenskaya O, Wang Y, Ackerman JM, Knittelfelder O, Shevchenko A. Analytical challenges in human plasma lipidomics: A winding path towards the truth. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Wong MWK, Braidy N, Pickford R, Sachdev PS, Poljak A. Comparison of Single Phase and Biphasic Extraction Protocols for Lipidomic Studies Using Human Plasma. Front Neurol 2019; 10:879. [PMID: 31496985 PMCID: PMC6712511 DOI: 10.3389/fneur.2019.00879] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/29/2019] [Indexed: 02/03/2023] Open
Abstract
Lipidomic profiling of plasma is an emerging field, given the importance of lipids in major cellular pathways, and is dependent on efficient lipid extraction protocols. Recent attention has turned to plasma lipidomics as a means to identify potential diagnostic and prognostic biomarkers related to dementia, neuropsychiatric health and disease. Although several solvent-based lipid extraction protocols have been developed and are currently in use, novel and more efficient methods could greatly simplify lipid analysis in plasma and warrant investigation. Human plasma from normolipidemic adult volunteers was collected to evaluate three different solvent extraction protocols, including the classical Folch method, the methanol/tert-butyl methyl ether (MTBE) (Matyash) method, and a recent single-phase methanol/1-butanol (Alshehry) method. Extracted lipids were analyzed using liquid chromatography mass spectrometry (LC-MS) in positive and negative ion mode. Overall, more than 500 different lipids were identified in positive and negative ion mode combined. Our data show that the single phase Alshehry method was as effective as the Folch and Matyash methods in extracting most lipid classes and was more effective in extraction of polar lipids. Normalized peak areas of the Alshehry method were highly and positively correlated with both the Folch and Matyash methods (r 2 = 0.99 and 0.97, respectively). Within- and between- subject correlations were r = 0.99 and 0.96, respectively. Median intra-assay coefficient of variation (CV%) in positive mode was 14.1, 15.1, and 21.8 for the Alshehry, Folch and Matyash methods, respectively. Median Alshehry inter-assay CV (collected over 5 separate days) was 14.4%. In conclusion, the novel Alshehry method was at least as good as, if not better than the established biphasic extraction methods in detecting a wide range of lipid classes, using as little as 10 μL of plasma, and was highly reproducible, safer and more environmentally-friendly as it doesn't require chloroform.
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Affiliation(s)
- Matthew Wai Kin Wong
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Perminder Singh Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Euroa Centre, Prince of Wales Hospital, Neuropsychiatric Institute, Sydney, NSW, Australia
| | - Anne Poljak
- Centre for Healthy Brain Ageing, School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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23
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Ethnic differences in bone mineral density among midlife women in a multi-ethnic Southeast Asian cohort. Arch Osteoporos 2019; 14:80. [PMID: 31324992 DOI: 10.1007/s11657-019-0631-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/07/2019] [Indexed: 02/03/2023]
Abstract
UNLABELLED Chinese Singaporean middle-aged women have significantly lower femoral neck bone mineral density and higher lumbar spine bone mineral density than Malays and Indians, after adjustment for age, body mass index, and height. PURPOSE Information regarding mediators of differences in bone mineral density (BMD) among Asian ethnicities are limited. Since the majority of hip fractures are predicted to be from Asia, differences in BMD in Asian ethnicities require further exploration. We compared BMD among the Chinese, Malay, or Indian ethnicities in Singapore, aiming to identify potential mediators for the observed differences. METHODS BMD of 1201 women aged 45-69 years was measured by dual-energy X-ray absorptiometry. We examined the associations between ethnicity and BMD at both sites, before and after adjusting for potential mediators measured using standardized questionnaires and validated performance tests. RESULTS Chinese women had significantly lower femoral neck BMD than Malay and Indian women. Of the more than 20 variables examined, age, body mass index, and height accounted for almost all the observed ethnic differences in femoral neck BMD between Chinese and Malays. However, Indian women still retained 0.047 g/cm2 (95% CI, 0.024, 0.071) higher femoral neck BMD after adjustment, suggesting that additional factors may contribute to the increased BMD in Indians. Although no crude ethnic differences in lumbar spine BMD were observed, adjusted regression model unmasked ethnic differences, wherein Chinese women had 0.061(95% CI, - 0.095, 0.026) and 0.065 (95% CI, - 0.091, 0.038) g/cm2 higher lumbar spine BMD compared to Malay and Indian women, respectively. CONCLUSION BMD in middle-aged Asian women differ by ethnicity and site. Particular attention should be paid to underweight women of Chinese ethnic origin, who may be at highest risk of osteoporosis at the femoral neck and hence hip fractures.
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24
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Chew WS, Torta F, Ji S, Choi H, Begum H, Sim X, Khoo CM, Khoo EYH, Ong WY, Van Dam RM, Wenk MR, Tai ES, Herr DR. Large-scale lipidomics identifies associations between plasma sphingolipids and T2DM incidence. JCI Insight 2019; 5:126925. [PMID: 31162145 PMCID: PMC6629294 DOI: 10.1172/jci.insight.126925] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/28/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Sphingolipids (SPs) are ubiquitous, structurally diverse molecules that include ceramides, sphingomyelins, and sphingosines. They are involved in various pathologies including obesity and type 2 diabetes mellitus (T2DM). Therefore, it is likely that perturbations in plasma concentrations of SPs are associated with disease. Identifying these associations may reveal useful biomarkers or provide insight into disease processes. METHODS We performed a lipidomics evaluation of molecularly-distinct SPs in the plasma of 2,302 ethnically-Chinese Singaporeans using electrospray ionization mass spectrometry coupled with liquid chromatography. SP profiles were compared to clinical and biochemical characteristics, and subjects were evaluated by follow-up visits for 11 years. RESULTS We found that ceramides correlate positively but hexosylceramides correlate negatively with body mass index (BMI) and homeostatic model assessment of insulin resistance (HOMA-IR). Furthermore, SPs with a d16:1 sphingoid backbone correlate more positively with BMI and HOMA-IR, while d18:2 SPs correlate less positively, relative to canonical d18:1 SPs. We also found that higher concentrations of two distinct sphingomyelins were associated with a higher risk of T2DM (HR 1.45, 95% CI 1.18-1.78 for SM d16:1/C18:0; and HR 1.40, 95% CI 1.17-1.68 for SM d18:1/C18:0). CONCLUSION We identified significant associations between SPs and obesity/T2DM characteristics, specifically, that of hexosylceramides, d16:1 SPs, and d18:2 SPs. This suggests that the balance of SP metabolism, rather than ceramide accumulation, is associated with the pathology of obesity. We further identified two specific SPs that may represent prognostic biomarkers for T2DM. FUNDING Funding sources are listed in the Acknowledgements section.
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Affiliation(s)
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Shanshan Ji
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Hyungwon Choi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National Health System, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Singapore
| | - Husna Begum
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National Health System, Singapore
| | - Eric Yin Hao Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National Health System, Singapore
| | - Wei-Yi Ong
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Rob M. Van Dam
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National Health System, Singapore
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National Health System, Singapore
- Duke-NUS Graduate Medical School, Singapore
| | - Deron R. Herr
- Department of Pharmacology and
- Department of Biology, San Diego State University, San Diego, California, USA
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25
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Yong EL, Ganesan G, Kramer MS, Logan S, Lau TC, Cauley JA, Tan KB. Hip fractures in Singapore: ethnic differences and temporal trends in the new millennium. Osteoporos Int 2019; 30:879-886. [PMID: 30671610 DOI: 10.1007/s00198-019-04839-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
Abstract
UNLABELLED Despite an increase in absolute numbers, the age-standardized incidence of hip fractures in Singapore declined in the period 2000 to 2017. Among the three major ethnic groups, Chinese women had the highest fracture rates but were the only group to show a temporal decline. INTRODUCTION A study published in 2001 predicted a 30-50% increase in Singapore hip fracture incidence rates over the ensuing 30 years. To test that prediction, we examined the incidence of hip fracture in Singapore from 2000 to 2017. METHODS We carried out a population-based study of hip fractures among Singapore residents aged ≥ 50 years. National medical insurance claims data were used to identify admissions with a primary discharge diagnosis of hip fracture. Age-adjusted rates, based on the age distribution of the Singapore population of 2000, were analyzed separately by sex and ethnicity (Chinese, Malay, or Indian). RESULTS Over the 18-year study period, 36,082 first hip fractures were recorded. Total hip fracture admissions increased from 1487 to 2729 fractures/year in the years 2000 to 2017. Despite this absolute increase, age-adjusted fracture rates declined, with an average annual change of - 4.3 (95% CI - 5.0, - 3.5) and - 1.1 (95% CI - 1.7, - 0.5) fractures/100,000/year for women and men respectively. Chinese women had 1.4- and 1.9-fold higher age-adjusted rates than Malay and Indian women: 264 (95% CI 260, 267) versus 185 (95% CI 176, 193) and 141 (95% CI 132, 150) fractures/100,000/year, respectively. Despite their higher fracture rates, Chinese women were the only ethnic group exhibiting a decline, most evident in those ≥ 85 years, in age-adjusted fracture rate of - 5.3 (95% CI - 6.0, - 4.5) fractures/100,000/year. CONCLUSION Although the absolute number of fractures increased, steep drops in elderly Chinese women drove a reduction in overall age-adjusted hip fracture rates. Increases in the older population will lead to a rise in total number of hip fractures, requiring budgetary planning and new preventive strategies.
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Affiliation(s)
- E L Yong
- Department of Obstetrics and Gynecology, National University of Singapore, Singapore, Singapore.
| | - G Ganesan
- Division of Policy, Research and Evaluation, Ministry of Health, Singapore, Singapore
| | - M S Kramer
- Department of Obstetrics and Gynecology, National University of Singapore, Singapore, Singapore
- Departments of Epidemiology, Biostatistics & Occupational Health and of Pediatrics, McGill University Faculty of Medicine, Montreal, Quebec, H3G 1Y6, Canada
| | - S Logan
- Department of Obstetrics and Gynecology, National University of Singapore, Singapore, Singapore
| | - T C Lau
- Department of Medicine, National University Hospital, National University of Singapore, Singapore, 119228, Singapore
| | - J A Cauley
- Graduate School of Public Health, Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - K B Tan
- Division of Policy, Research and Evaluation, Ministry of Health, Singapore, Singapore.
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
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26
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Tan ALM, Langley SR, Tan CF, Chai JF, Khoo CM, Leow MKS, Khoo EYH, Moreno-Moral A, Pravenec M, Rotival M, Sadananthan SA, Velan SS, Venkataraman K, Chong YS, Lee YS, Sim X, Stunkel W, Liu MH, Tai ES, Petretto E. Ethnicity-Specific Skeletal Muscle Transcriptional Signatures and Their Relevance to Insulin Resistance in Singapore. J Clin Endocrinol Metab 2019; 104:465-486. [PMID: 30137523 DOI: 10.1210/jc.2018-00309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/14/2018] [Indexed: 11/19/2022]
Abstract
CONTEXT Insulin resistance (IR) and obesity differ among ethnic groups in Singapore, with the Malays more obese yet less IR than Asian-Indians. However, the molecular basis underlying these differences is not clear. OBJECTIVE As the skeletal muscle (SM) is metabolically relevant to IR, we investigated molecular pathways in SM that are associated with ethnic differences in IR, obesity, and related traits. DESIGN, SETTING, AND MAIN OUTCOME MEASURES We integrated transcriptomic, genomic, and phenotypic analyses in 156 healthy subjects representing three major ethnicities in the Singapore Adult Metabolism Study. PATIENTS This study contains Chinese (n = 63), Malay (n = 51), and Asian-Indian (n = 42) men, aged 21 to 40 years, without systemic diseases. RESULTS We found remarkable diversity in the SM transcriptome among the three ethnicities, with >8000 differentially expressed genes (40% of all genes expressed in SM). Comparison with blood transcriptome from a separate Singaporean cohort showed that >95% of SM expression differences among ethnicities were unique to SM. We identified a network of 46 genes that were specifically downregulated in Malays, suggesting dysregulation of components of cellular respiration in SM of Malay individuals. We also report 28 differentially expressed gene clusters, four of which were also enriched for genes that were found in genome-wide association studies of metabolic traits and disease and correlated with variation in IR, obesity, and related traits. CONCLUSION We identified extensive gene-expression changes in SM among the three Singaporean ethnicities and report specific genes and molecular pathways that might underpin and explain the differences in IR among these ethnic groups.
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Affiliation(s)
- Amelia Li Min Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
| | - Sarah R Langley
- Duke-National University of Singapore Medical School, Singapore
- National Heart Centre Singapore, Singapore
| | - Chee Fan Tan
- Nanyang Institute of Technology in Health and Medicine, Nanyang Technological University, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jin Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Chin Meng Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | - Melvin Khee-Shing Leow
- Duke-National University of Singapore Medical School, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Endocrinology, Tan Tock Seng Hospital, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Eric Yin Hao Khoo
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | | | - Michal Pravenec
- Institute Of Physiology, Czech Academy Of Sciences, Prague, Czech Republic
| | - Maxime Rotival
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Suresh Anand Sadananthan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
| | - S Sendhil Velan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kavita Venkataraman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yung Seng Lee
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Paediatrics Endocrinology, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, National University Health System, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Walter Stunkel
- Experimental Biotherapeutics Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Mei Hui Liu
- Department of Chemistry, Food Science & Technology Programme, National University of Singapore, Singapore
| | - E Shyong Tai
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-National University of Singapore Medical School, Singapore
- Division of Endocrinology, Department of Medicine, National University Health System, Singapore
| | - Enrico Petretto
- Duke-National University of Singapore Medical School, Singapore
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27
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Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J Lipid Res 2018; 59:2001-2017. [PMID: 30115755 PMCID: PMC6168311 DOI: 10.1194/jlr.s087163] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/11/2018] [Indexed: 12/19/2022] Open
Abstract
Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.
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Affiliation(s)
- Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Masanori Arita
- National Institute of Genetics, Shizuoka, Japan and RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Anne K Bendt
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Edward A Dennis
- Departments of Pharmacology and Chemistry and Biochemistry, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies and Department of Medicine-Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Michelle K Lin
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matej Orešič
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland and School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Oswald Quehenberger
- Departments of Pharmacology and Medicine, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Federico Torta
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | | | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
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28
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Koshiba S, Motoike I, Saigusa D, Inoue J, Shirota M, Katoh Y, Katsuoka F, Danjoh I, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Ogishima S, Fuse N, Kure S, Tamiya G, Tanabe O, Yasuda J, Kinoshita K, Yamamoto M. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes Cells 2018; 23:406-417. [PMID: 29701317 DOI: 10.1111/gtc.12588] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 01/05/2023]
Abstract
Population-based prospective cohort studies are indispensable for modern medical research as they provide important knowledge on the influences of many kinds of genetic and environmental factors on the cause of disease. Although traditional cohort studies are mainly conducted using questionnaires and physical examinations, modern cohort studies incorporate omics and genomic approaches to obtain comprehensive physical information, including genetic information. Here, we report the design and midterm results of multi-omics analysis on population-based prospective cohort studies from the Tohoku Medical Megabank (TMM) Project. We have incorporated genomic and metabolomic studies in the TMM cohort study as both metabolome and genome analyses are suitable for high-throughput analysis of large-scale cohort samples. Moreover, an association study between the metabolome and genome show that metabolites are an important intermediate phenotype connecting genetic and lifestyle factors to physical and pathologic phenotypes. We apply our metabolome and genome analyses to large-scale cohort samples in the following studies.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasutake Katoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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29
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Low LA, Tagle DA. ‘You-on-a-chip’ for precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1456333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lucie A. Low
- National Center for Advancing Translational Sciences, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Danilo A. Tagle
- National Center for Advancing Translational Sciences, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
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30
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Tan KHX, Tan LWL, Sim X, Tai ES, Lee JJM, Chia KS, van Dam RM. Cohort Profile: The Singapore Multi-Ethnic Cohort (MEC) study. Int J Epidemiol 2018; 47:699-699j. [PMID: 29452397 DOI: 10.1093/ije/dyy014] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/15/2018] [Accepted: 01/25/2018] [Indexed: 12/11/2022] Open
Affiliation(s)
| | | | | | - E Shyong Tai
- Saw Swee Hock School of Public Health and.,Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
| | | | | | - Rob M van Dam
- Saw Swee Hock School of Public Health and.,Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore
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