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Transcriptional Biomarkers for Treatment Monitoring of Pulmonary Drug-Resistant Tuberculosis: Protocol for a Prospective Observational Study in Indonesia. Trop Med Infect Dis 2022; 7:tropicalmed7110326. [DOI: 10.3390/tropicalmed7110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022] Open
Abstract
Many blood-based gene expression biomarkers for monitoring tuberculosis (TB) treatment have been suggested so far, but promising biomarker results for drug-resistant TB treatment response have not been studied. This protocol presents a prospective observational study in Indonesia to profile the human blood transcriptome for predicting the response to drug-resistant TB treatment, focusing on pulmonary TB, and to adapt the specific RNA signature to the qRT-PCR platform. Longitudinal blood samples will be collected from 44 subjects with rifampicin resistant TB, confirmed by Xpert MTB/RIF, and 52 healthy controls. RNA-Seq will be performed to identify changes in the transcriptome following TB treatment. A discriminative RNA signature will be chosen and translated into a score for use in a quantitative PCR-based assay. This study will provide crucial information to guide the discovery and design of a clinically implementable tool to monitor the response of TB treatment.
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Kumon H, Yoshino Y, Funahashi Y, Mori H, Ueno M, Ozaki Y, Yamazaki K, Ochi S, Mori T, Iga JI, Nagai M, Nomoto M, Ueno SI. PICALM mRNA Expression in the Blood of Patients with Neurodegenerative Diseases and Geriatric Depression. J Alzheimers Dis 2021; 79:1055-1062. [PMID: 33386803 PMCID: PMC7990403 DOI: 10.3233/jad-201046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Phosphatidylinositol-binding clathrin assembly protein (PICALM) is a validated genetic risk factor for late-onset Alzheimer's disease (AD) and is associated with other neurodegenerative diseases. However, PICALM expression in the blood of neurodegenerative diseases remains elusive. OBJECTIVE This study aimed to assess the usefulness of PICALM expression levels in the blood of patients with AD, Parkinson's disease (PD), dementia with Lewy bodies (DLB), and geriatric major depressive disorder (MDD) as a diagnostic biomarker. METHODS In total, 45, 20, 21, and 19 patients with AD, PD, DLB, and geriatric MDD, respectively, and 54 healthy controls (HCs) were enrolled in the study. Expression data from Gene Expression Omnibus database (GSE97760), (GSE133347) and (GSE98793), (GSE48350), and (GSE144459) were used to validate the ability of biomarkers in the blood of patients with AD, PD, geriatric MDD, and a postmortem human AD brain and animal model of AD (3xTg-AD mouse), respectively. RESULTS PICALM mRNA expression in human blood was significantly increased in patients with AD compared with that in HCs. PICALM mRNA expression and age were negatively correlated only in patients with AD. PICALM mRNA expression in human blood was significantly lower in patients with PD than in HCs. No changes in PICALM mRNA expression were found in patients with DLB and geriatric MDD. CONCLUSION PICALM mRNA expression in blood was higher in patients with AD, but lower in patients with PD, which suggests that PICALM mRNA expression in human blood may be a useful biomarker for differentiating neurodegenerative diseases and geriatric MDD.
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Affiliation(s)
- Hiroshi Kumon
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Yu Funahashi
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Hiroaki Mori
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Mariko Ueno
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Masahiro Nagai
- Department of Neurology and Clinical Pharmacology, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
| | - Masahiro Nomoto
- Department of Neurology and Clinical Pharmacology, Graduate School of Medicine, Ehime University, Toon, Ehime, Japan
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Hieronymus K, Dorschner B, Schulze F, Vora NL, Parker JS, Winkler JL, Rösen-Wolff A, Winkler S. Validation of reference genes for whole blood gene expression analysis in cord blood of preterm and full-term neonates and peripheral blood of healthy adults. BMC Genomics 2021; 22:489. [PMID: 34193041 PMCID: PMC8244134 DOI: 10.1186/s12864-021-07801-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 06/13/2021] [Indexed: 11/16/2022] Open
Abstract
Background Preterm birth is the leading cause of neonatal morbidity and mortality, but research efforts in neonatology are complicated due to the unavailability of large volume blood samples. Whole blood assays can be used to overcome this problem by performing both functional and gene expression studies using small amounts of blood. Gene expression studies using RT-qPCR estimate mRNA-levels of target genes normalized to reference genes. The goal of this study was to identify and validate stable reference genes applicable to cord blood samples obtained from developing neonates of different gestational age groups as well as to adult peripheral blood samples. Eight reference gene candidates (ACTB, B2M, GAPDH, GUSB, HPRT, PPIB, RPLP0, RPL13) were analyzed using the three published software algorithms Bestkeeper, GeNorm and NormFinder. Results A normalization factor consisting of ACTB and PPIB allows for comparative expression analyses of neonatal samples from different gestational age groups. Normalization factors consisting of GAPDH and PPIB or ACTB and GAPDH are suitable when samples from preterm and full-term neonates and adults are compared. However, all candidate reference genes except RPLP0 exhibited significant intergroup gene expression variance and a higher gene expression towards an older age which resulted in a small but statistically significant systematic bias. Systematic analysis of RNA-seq data revealed new reference gene candidates with potentially superior stability. Conclusions The current study identified suitable normalization factors and proposed the use of the additional single gene RPLP0 to avoid systematic bias. This combination will enable comparative analyses not only between neonates of different gestational ages, but also between neonates and adults, as it facilitates more detailed investigations of developmental gene expression changes. The use of software algorithms did not prevent unintended systematic bias. This generally highlights the need for careful validation of such results to prevent false interpretation of potential age-dependent changes in gene expression. To identify the most stable reference genes in the future, RNA-seq based global approaches are recommended. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07801-0.
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Affiliation(s)
- Kristin Hieronymus
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Benjamin Dorschner
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Felix Schulze
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Neeta L Vora
- Department of Obstetrics and Gynecology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jennifer Lucia Winkler
- Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Angela Rösen-Wolff
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Stefan Winkler
- Department of Pediatrics, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
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Grønlien HK, Christoffersen TE, Nystrand CF, Garabet L, Syvertsen T, Moe MK, Olstad OK, Jonassen CM. Cytokine and Gene Expression Profiling in Patients with HFE-Associated Hereditary Hemochromatosis according to Genetic Profile. Acta Haematol 2020; 144:446-457. [PMID: 33326952 DOI: 10.1159/000511551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/12/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Hemochromatosis gene (HFE)-associated hereditary hemochromatosis (HH) is characterized by downregulation of hepcidin synthesis, leading to increased intestinal iron absorption. OBJECTIVES The objectives were to characterize and elucidate a possible association between gene expression profile, hepcidin levels, disease severity, and markers of inflammation in HFE-associated HH patients. METHODS Thirty-nine HFE-associated HH patients were recruited and assigned to 2 groups according to genetic profile: C282Y homozygotes in 1 group and patients with H63D, as homozygote or in combination with C282Y, in the other group. Eleven healthy first-time blood donors were recruited as controls. Gene expression was characterized from peripheral blood cells, and inflammatory cytokines and hepcidin-25 isoform were quantified in serum. Biochemical disease characteristics were recorded. RESULTS Elevated levels of interleukin 8 were observed in a significant higher proportion of patients than controls. In addition, compared to controls, gene expression of ζ-globin was significantly increased among C282Y homozygote patients, while gene expression of matrix metalloproteinase 8, and other neutrophil-secreted proteins, was significantly upregulated in patients with H63D. CONCLUSION Different disease signatures may characterize HH patients according to their HFE genetic profile. Studies on larger populations, including analyses at protein level, are necessary to confirm these findings.
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Affiliation(s)
| | | | | | - Lamya Garabet
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
- Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry, Akershus University Hospital, Lørenskog, Norway
| | - Terje Syvertsen
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway
| | - Morten K Moe
- Department of Multidisciplinary Laboratory Medicine and Medical Biochemistry, Akershus University Hospital, Lørenskog, Norway
| | | | - Christine Monceyron Jonassen
- Center for Laboratory Medicine, Østfold Hospital Trust, Grålum, Norway,
- Department of Chemistry, Biotechnology and Food Sciences, The Norwegian University of Life Sciences, Ås, Norway,
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Yamazaki K, Yoshino Y, Kawabe K, Ibuki T, Ochi S, Mori Y, Ozaki Y, Numata S, Iga JI, Ohmori T, Ueno SI. ABCA7 Gene Expression and Genetic Association Study in Schizophrenia. Neuropsychiatr Dis Treat 2020; 16:441-446. [PMID: 32103964 PMCID: PMC7025661 DOI: 10.2147/ndt.s238471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/25/2020] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Although ATP-binding cassette sub-family A member 7 gene (ABCA7) is known to be associated with Alzheimer's disease, the relationship between ABCA7 and schizophrenia has been unknown. METHODS Schizophrenia patients (n = 50; 24 males, 62.1 ± 0.50 years old) and age- and sex-matched healthy controls (n = 50) were recruited for the mRNA analysis. Additionally, a case-control study for the rs3764650 genotypes was performed with 1308 samples (control subjects; n = 527, schizophrenia patients; n = 781). All participants were Japanese, unrelated to each other, and living in the same area. RESULTS The distributions of the rs3764650 genotypes in schizophrenia patients were not different from that of controls. However, the ABCA7 mRNA expression levels in schizophrenia patients were significantly higher than those in controls by a logistic regression analysis. Additionally, the ABCA7 mRNA expression levels in schizophrenia patients were correlated with the rs3764650 genotypes in a dose-dependent manner. DISCUSSION The ABCA7 mRNA expression levels in peripheral blood with the rs3764650 genotypes may be related to pathological mechanisms in schizophrenia and may be a biological marker for schizophrenia.
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Affiliation(s)
- Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Kentaro Kawabe
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Tomomasa Ibuki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Shusuke Numata
- Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, the University of Tokushima Graduate School, Tokushima 770-8503, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Course of Integrated Brain Sciences, Medical Informatics, Institute of Health Biosciences, the University of Tokushima Graduate School, Tokushima 770-8503, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
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Gautam A, Donohue D, Hoke A, Miller SA, Srinivasan S, Sowe B, Detwiler L, Lynch J, Levangie M, Hammamieh R, Jett M. Investigating gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple collection and processing methods. PLoS One 2019; 14:e0225137. [PMID: 31809517 PMCID: PMC6897427 DOI: 10.1371/journal.pone.0225137] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 10/29/2019] [Indexed: 01/07/2023] Open
Abstract
Gene expression profiling using blood samples is a valuable tool for biomarker discovery in clinical studies. Different whole blood RNA collection and processing methods are highly variable and might confound comparisons of results across studies. The main aim of the current study is to compare how blood storage, extraction methodologies, and the blood components themselves may influence gene expression profiling. Whole blood and peripheral blood mononuclear cell (PBMC) samples were collected in triplicate from five healthy donors. Whole blood was collected in RNAgard® and PAXgene® Blood RNA Tubes, as well as in collection tubes with anticoagulants such as dipotassium ethylenediaminetetraacetic acid (K2EDTA) and Acid Citrate Dextrose Solution A (ACD-A). PBMCs were separated using sodium citrate Cell Preparation Tubes (CPT™), FICOLL™, magnetic separation, and the LeukoLOCK™ methods. After blood collection, the LeukoLOCK™, K2EDTA and ACD-A blood tubes were shipped overnight using cold conditions and samples from the rest of the collection were immediately frozen with or without pre-processing. The RNA was isolated from whole blood and PBMCs using a total of 10 different experimental conditions employing several widely utilized RNA isolation methods. The RNA quality was assessed by RNA Integrity Number (RIN), which showed that all PBMC procedures had the highest RIN values when blood was stabilized in TRIzol® Reagent before RNA extraction. Initial data analysis showed that human blood stored and shipped at 4°C overnight performed equally well when checked for quality using RNA integrity number when compared to frozen stabilized blood. Comparisons within and across donor/method replicates showed signal-to-noise patterns which were not captured by RIN value alone. Pathway analysis using the top 1000 false discovery rate (FDR) corrected differentially expressed genes (DEGs) showed frozen vs. cold shipping conditions greatly impacted gene expression patterns in whole blood. However, the top 1000 FDR corrected DEGs from PBMCs preserved after frozen vs. cold shipping conditions (LeukoLOCK™ preserved in RNAlater®) revealed no significantly affected pathways. Our results provide novel insight into how RNA isolation, various storage, handling, and processing methodologies can influence RNA quality and apparent gene expression using blood samples. Careful consideration is necessary to avoid bias resulting from downstream processing. Better characterization of the effects of collection method idiosyncrasies will facilitate further research in understanding the effect of gene expression variability in human sample types.
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Affiliation(s)
- Aarti Gautam
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Duncan Donohue
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Allison Hoke
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Stacy Ann Miller
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Seshamalini Srinivasan
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Bintu Sowe
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Leanne Detwiler
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Jesse Lynch
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Oak Ridge Institute for Science and Education, Fort Detrick, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Michael Levangie
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Rasha Hammamieh
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Marti Jett
- US Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
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Donohue DE, Gautam A, Miller SA, Srinivasan S, Abu-Amara D, Campbell R, Marmar CR, Hammamieh R, Jett M. Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods. PLoS One 2019; 14:e0223065. [PMID: 31600258 PMCID: PMC6786555 DOI: 10.1371/journal.pone.0223065] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/12/2019] [Indexed: 11/18/2022] Open
Abstract
Peripheral Blood gene expression is widely used in the discovery of biomarkers and development of therapeutics. Recently, a spate of commercial blood collection and preservation systems have been introduced with proprietary variations that may differentially impact the transcriptomic profiles. Comparative analysis of these collection platforms will help optimize protocols to detect, identify, and reproducibly validate true biological variance among subjects. In the current study, we tested two recently introduced whole blood collection methods, RNAgard® and PAXgene® RNA, in addition to the traditional method of peripheral blood mononuclear cells (PBMCs) separated from whole blood and preserved in Trizol reagent. Study results revealed striking differences in the transcriptomic profiles from the three different methods that imply ex vivo changes in gene expression occurred during the blood collection, preservation, and mRNA extraction processes. When comparing the ability of the three preservation methods to accurately capture individuals’ expression differences, RNAgard® outperformed PAXgene® RNA, and both showed better individual separation of transcriptomic profiles than PBMCs. Hence, our study recommends using a single blood collection platform, and strongly cautions against combining methods during the course of a defined study.
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Affiliation(s)
- Duncan E. Donohue
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Fort Detrick, MD, United States of America
| | - Aarti Gautam
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Stacy-Ann Miller
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Fort Detrick, MD, United States of America
| | - Seshamalini Srinivasan
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- The Geneva Foundation, Fort Detrick, MD, United States of America
| | - Duna Abu-Amara
- Steven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury, Department of Psychiatry, NYU School of Medicine, New York, NY, United States of America
| | - Ross Campbell
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- Advanced Biomedical Computing Center, Frederick, MD, United States of America
| | - Charles R. Marmar
- Steven and Alexandra Cohen Veterans Center for the Study of Posttraumatic Stress and Traumatic Brain Injury, Department of Psychiatry, NYU School of Medicine, New York, NY, United States of America
| | - Rasha Hammamieh
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
| | - Marti Jett
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, MD, United States of America
- * E-mail:
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Tang R, She Q, Lu Y, Yin R, Zhu P, Zhu L, Zhou M, Zheng C. Quality Control of RNA Extracted from PAXgene Blood RNA Tubes After Different Storage Periods. Biopreserv Biobank 2019; 17:477-482. [PMID: 31343263 DOI: 10.1089/bio.2019.0029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Rong Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qinying She
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ling Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Minlin Zhou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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9
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Sao T, Yoshino Y, Yamazaki K, Ozaki Y, Mori Y, Ochi S, Yoshida T, Mori T, Iga JI, Ueno SI. TREM1 mRNA Expression in Leukocytes and Cognitive Function in Japanese Patients with Alzheimer's Disease. J Alzheimers Dis 2019; 64:1275-1284. [PMID: 30010135 DOI: 10.3233/jad-180418] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Triggering receptor expressed on myeloid cells 2 (TREM2) activates the innate immune system, promotes phagocytosis by microglia, and is associated with Alzheimer's disease (AD). The possible role of a related molecule, TREM1, in AD remains unknown. OBJECTIVE We investigated a possible role for TREM1 in AD by determining the gene expression and methylation levels of TREM1 in leukocytes from AD patients. METHODS Fifty patients with AD and 50 age-matched healthy controls were enrolled. AD patients underwent a battery of neuropsychiatric tests. Peripheral blood samples were obtained from each participant, RNA and DNA were extracted, and samples were assessed for TREM1 mRNA expression and methylation rates at three CpG sites in the TREM1 promoter. RESULTS TREM1 mRNA expression levels in AD patients were significantly higher than those in controls (p = 0.008). TREM1 mRNA expression levels were not correlated with sex, age, duration of illness, APOE genotype, donepezil treatment, or scores of most neuropsychiatric tests. TREM1 mRNA expression levels in AD patients were correlated with the total score of the Montgomery-Åsberg Depression Rating Scale (p = 0.047, r = - 0.344). Methylation rates at the three CpG sites were significantly lower in AD patients than in controls. We also found a significant correlation between TREM1 mRNA expression and TREM1 DNA methylation rates (p < 0.001). CONCLUSION TREM1 may be associated with the immune responses in AD, and along with hypomethylation at CpG sites in the TREM1 promoter, may become part of a biomarker panel for AD pathogenesis.
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Affiliation(s)
- Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
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10
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Yoshino Y, Funahashi Y, Nakata S, Ozaki Y, Yamazaki K, Yoshida T, Mori T, Mori Y, Ochi S, Iga JI, Ueno SI. Ghrelin cascade changes in the peripheral blood of Japanese patients with Alzheimer's disease. J Psychiatr Res 2018; 107:79-85. [PMID: 30366284 DOI: 10.1016/j.jpsychires.2018.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 11/26/2022]
Abstract
The neuroprotective effect of ghrelin has recently been reported in Alzheimer's disease (AD). Ghrelin is converted from des-acyl ghrelin to the activated form, acyl ghrelin, by membrane bound o-acyltransferase 4 (MBOAT4), and then binds to growth hormone secretagogue receptor (GHS-R). We examined the levels of plasma acyl/des-acyl ghrelin in 75 AD subjects and age- and sex-matched controls, as well as the DNA methylation and mRNA expression of MBOAT4 and GHS-R in peripheral leukocytes. The acyl ghrelin concentration was significantly higher in AD subjects than in controls (2.18 ± 1.25 vs. 1.49 ± 2.3, p = 0.001). The methylation rate of MBOAT4 CpG 2 was significantly lower in AD subjects than in controls (4.0 ± 0.9 vs. 4.7 ± 1.2, p < 0.001). The mRNA expression levels of MBOAT4 and GHS-R1b were significantly higher in AD subjects than in controls (MBOAT4: 1.10 ± 0.48 vs. 1.0 ± 0.55, p = 0.049; GHS-R1b: 1.76 ± 3.18 vs. 1.0 ± 1.56, p = 0.030). These changes in the ghrelin cascade in peripheral blood may reflect those in the brain, and may be a neuroprotective biomarker in AD.
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Affiliation(s)
- Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yu Funahashi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Shunsuke Nakata
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan.
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
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11
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Heng Z, Ruan L, Gan R. Three Methods to Purify Leukocytes and RNA Quality Assessment. Biopreserv Biobank 2018; 16:434-438. [PMID: 30379576 DOI: 10.1089/bio.2018.0058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Leukocytes function as central effectors in innate immunity (such as phagocytosis) as well as adaptive immunity (e.g., antigen-dependent T cell activation), and serve as an important resource in the fields of translational medicine, precision medicine, and cell therapy. Isolation of leukocytes from whole blood is necessary for high-quality RNA and downstream research. This process is susceptible to the variability of many factors, such as blood collection, isolation reagents, and extraction methods. In this study, three methods were applied for leukocytes separation, followed by RNA extraction and quality testing to evaluate the methods. Results showed that leukocytes were purified using lymphocyte separation medium (LSM), optimized LSM method, or red blood cell lysis buffer (RBC lysis), and RNA quality met the basic requirements for downstream studies. Although considering the simplicity of the procedure and RNA quality from donated samples, the RBC lysis method should be recommended to biobanks for further research.
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Affiliation(s)
- Zhang Heng
- Shanghai Clinical Research Center, Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
| | - Liangliang Ruan
- Shanghai Clinical Research Center, Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
| | - Rongxing Gan
- Shanghai Clinical Research Center, Shanghai, China.,Shanghai Engineering Research Center of Biobank, Shanghai, China
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12
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Li Q, Wang X, Li X, He X, Wan Q, Yin J, Sun J, Yang X, Chen Q, Miao X. Obtaining High-Quality Blood Specimens for Downstream Applications: A Review of Current Knowledge and Best Practices. Biopreserv Biobank 2018; 16:411-418. [PMID: 30383403 DOI: 10.1089/bio.2018.0052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Blood is a biological fluid that contains multiple blood fraction and cellular components. High-quality blood specimens are essential prerequisites for various downstream applications such as molecular epidemiology studies, genomics, and proteomics studies. Currently, protocols and research publications concerning the collection, handling, preservation, and stability of blood or blood fractions are constantly emerging. Moreover, standardized guidelines are a requirement for biorepositories to tightly control preanalytical variables originating from these procedures and obtain high-quality blood specimen for downstream analyses. In this review article, we summarize the best practices and fit-for-purpose protocols regarding blood collection, processing, storage, and stability. In addition, we present some typical quality biomarkers, which could be used to evaluate the integrity of blood specimens.
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Affiliation(s)
- Qiyuan Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xian Wang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xue Li
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xuheng He
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qian Wan
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jiefang Yin
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jianbo Sun
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xiaoping Yang
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qiaohong Chen
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xinyuan Miao
- China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
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13
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Mise A, Yoshino Y, Yamazaki K, Ozaki Y, Sao T, Yoshida T, Mori T, Mori Y, Ochi S, Iga JI, Ueno SI. TOMM40 and APOE Gene Expression and Cognitive Decline in Japanese Alzheimer's Disease Subjects. J Alzheimers Dis 2018; 60:1107-1117. [PMID: 28984592 DOI: 10.3233/jad-170361] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND TOMM40 is located on chromosome 19, is in linkage disequilibrium with apolipoprotein E (APOE), andis reported in several genome-wide association studies to be associated with Alzheimer's disease (AD). OBJECTIVE Assess APOE and TOM40 and mitochondrial genes as blood biomarkers for AD. METHODS We examined TOMM40, PTEN-induced putative kinase 1 (PINK1), Parkin RBR E3 ubiquitin protein ligase (PARK2), and APOE mRNA expression in relation to the methylation rates of CpG sites in the upstream region of TOMM40exon 1 in peripheral leukocytes and TOMM40523 polyT genotypes in 60 AD and age- and sex-matched control subjects. RESULTS TOMM40 mRNA expression was significantly lower in AD subjects (0.87±0.18 versus 1.0±0.23, p = 0.005), and PINK1 mRNA expression was higher in AD subjects (1.5±0.61 versus 1.0±0.52, p < 0.001). TOMM40 mRNA expression was significantly correlated with the Mini-Mental State Examination total score (r = 0.290, p = 0.027). There was no expressional change in peripheral APOE mRNA in either AD or control subjects (p = 0.32). Methylation rates in the upstream region of TOMM40exon 1 were not different between AD and control subjects (average rate: 1.37±0.99 versus 1.39±1.20, p = 0.885), and TOMM40523 polyT genotypes were also not different between AD and control subjects (p = 0.67). CONCLUSION TOMM40 mRNA expression was lower in AD subjects and was correlated with cognitive decline. Significant changes in both TOMM40 and PINK1 mRNA may be related to mitochondrial dysfunction.
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Affiliation(s)
- Ayano Mise
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime, Japan
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14
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Böck J, Appenzeller S, Haertle L, Schneider T, Gehrig A, Schröder J, Rost S, Wolf B, Bartram CR, Sutter C, Haaf T. Single CpG hypermethylation, allele methylation errors, and decreased expression of multiple tumor suppressor genes in normal body cells of mutation-negative early-onset and high-risk breast cancer patients. Int J Cancer 2018; 143:1416-1425. [PMID: 29659014 PMCID: PMC6099327 DOI: 10.1002/ijc.31526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/28/2018] [Indexed: 01/01/2023]
Abstract
To evaluate the role of constitutive epigenetic changes in normal body cells of BRCA1/BRCA2-mutation negative patients, we have developed a deep bisulfite sequencing assay targeting the promoter regions of 8 tumor suppressor (TS) genes (BRCA1, BRCA2, RAD51C, ATM, PTEN, TP53, MLH1, RB1) and the estrogene receptor gene (ESR1), which plays a role in tumor progression. We analyzed blood samples of two breast cancer (BC) cohorts with early onset (EO) and high risk (HR) for a heterozygous mutation, respectively, along with age-matched controls. Methylation analysis of up to 50,000 individual DNA molecules per gene and sample allowed quantification of epimutations (alleles with >50% methylated CpGs), which are associated with epigenetic silencing. Compared to ESR1, which is representative for an average promoter, TS genes were characterized by a very low (< 1%) average methylation level and a very low mean epimutation rate (EMR; < 0.0001% to 0.1%). With exception of BRCA1, which showed an increased EMR in BC (0.31% vs. 0.06%), there was no significant difference between patients and controls. One of 36 HR BC patients exhibited a dramatically increased EMR (14.7%) in BRCA1, consistent with a disease-causing epimutation. Approximately one third (15 of 44) EO BC patients exhibited increased rates of single CpG methylation errors in multiple TS genes. Both EO and HR BC patients exhibited global underexpression of blood TS genes. We propose that epigenetic abnormalities in normal body cells are indicative of disturbed mechanisms for maintaining low methylation and appropriate expression levels and may be associated with an increased BC risk.
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Affiliation(s)
- Julia Böck
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | | | - Larissa Haertle
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Tamara Schneider
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Andrea Gehrig
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Jörg Schröder
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Simone Rost
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Beat Wolf
- University of Applied Sciences Western Switzerland, Fribourg, Switzerland.,Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Claus R Bartram
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, University Hospital, Heidelberg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
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15
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Sao T, Yoshino Y, Yamazaki K, Ozaki Y, Mori Y, Ochi S, Yoshida T, Mori T, Iga JI, Ueno SI. MEF2C mRNA expression and cognitive function in Japanese patients with Alzheimer's disease. Psychiatry Clin Neurosci 2018; 72:160-167. [PMID: 29112298 DOI: 10.1111/pcn.12618] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/12/2017] [Accepted: 10/30/2017] [Indexed: 12/15/2022]
Abstract
AIM Despite continuing research into Alzheimer's disease (AD), its pathological mechanisms and modulating factors remain unknown. Several genes influence AD pathogenesis by affecting inflammatory pathways. Myocyte-enhancer factor 2C (MEF2C) is one such candidate gene for AD. METHODS We examined MEF2C mRNA expression levels and methylation rates of CpG on its promoter region in peripheral leukocytes from Japanese AD patients compared with age- and sex-matched control subjects. RESULTS In peripheral leukocytes, MEF2C mRNA expression levels in AD subjects were significantly lower than those in control subjects (0.86 ± 0.25 vs 0.99 ± 0.27, respectively, P = 0.007) and were correlated with the Alzheimer's Disease Assessment Scale (r = -0.345, P = 0.049) and the Mini Mental State Examination (r = 0.324, P = 0.02). No significant differences were found in methylation rates between AD and control subjects. CONCLUSION MEF2C mRNA expression in leukocytes may be a biological marker for cognitive decline in AD.
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Affiliation(s)
- Tomoko Sao
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules, and Function, Ehime University Graduate School of Medicine, Toon, Japan
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16
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Yamazaki K, Yoshino Y, Mori T, Yoshida T, Ozaki Y, Sao T, Mori Y, Ochi S, Iga JI, Ueno SI. Gene Expression and Methylation Analysis of ABCA7 in Patients with Alzheimer's Disease. J Alzheimers Dis 2018; 57:171-181. [PMID: 28222527 DOI: 10.3233/jad-161195] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND/OBJECTIVE The aim of this study was to examine the blood gene expression and methylation of ATP-binding cassette sub-family A member 7 gene (ABCA7) as a biological marker of AD. METHODS AD subjects (n = 50; 11 males, 77.7±6.05 years old) and age- and sex-matched healthy controls (n = 50) were recruited. A single nucleotide polymorphism in ABCA7 (rs3764650), methylation rates of CpG sites in the ABCA7 promoter region, and ABCA7 mRNA expression levels in peripheral blood were examined. RESULTS The distribution of the rs3764650 polymorphism in AD subjects was not different from that of controls. Although the methylation rates of AD subjects were not significantly different from those of controls, the ABCA7 mRNA expression level in AD subjects was significantly higher than that in controls. Additionally, the ABCA7 mRNA expression level in AD subjects was significantly correlated with Mini-Mental State Examination recall, the Alzheimer's Disease Assessment Scale total score, and the Clinical Dementia Rating score. We also found a significant correlation between the ABCA7 mRNA expression level and duration of illness. CONCLUSION The ABCA7 mRNA expression level in peripheral blood may be a marker for early stages of AD and disease progression regardless of rs3764650 and the methylation rate of its promoter.
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17
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Yamazaki K, Yoshino Y, Mori T, Okita M, Yoshida T, Mori Y, Ozaki Y, Sao T, Iga JI, Ueno SI. Association Study and Meta-Analysis of Polymorphisms, Methylation Profiles, and Peripheral mRNA Expression of the Serotonin Transporter Gene in Patients with Alzheimer's Disease. Dement Geriatr Cogn Disord 2018; 41:334-47. [PMID: 27414430 DOI: 10.1159/000447324] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIM The aim of this study was to elucidate the relationship between Alzheimer's disease (AD) and the serotonin transporter gene (SLC6A4). METHODS AD subjects (n = 43) and controls (n = 47) were recruited and evaluated. In leukocytes, we evaluated two polymorphisms in SLC6A4, the serotonin transporter length polymorphic region (5-HTT-LPR) and rs25531, as well as methylation rates of the SLC6A4 promoter region and the SLC6A4 mRNA expression level. We also performed a meta-analysis to examine the relationship between the frequency of the L allele and the risk of AD. RESULTS The distributions of 5-HTT-LPR and rs25531 polymorphisms in AD subjects were not different from those of controls. Although the methylation rates in AD subjects were not significantly different from those of controls, the expression level in AD subjects was significantly higher than in controls. Additionally, the expression level in AD subjects was significantly correlated with apathy. Meta-analysis revealed that the L/L genotype significantly reduced the risk of AD, but only in the Caucasian population. CONCLUSION Higher SLC6A4 mRNA expression in leukocytes in AD was associated with apathy regardless of SLC6A4 genotypes and methylation rates of the promoter region. The L/L genotype may reduce the risk of AD in the Caucasian population.
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Affiliation(s)
- Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Japan
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18
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Yoshino Y, Mori T, Yoshida T, Yamazaki K, Ozaki Y, Sao T, Funahashi Y, Iga JI, Ueno SI. Elevated mRNA Expression and Low Methylation of SNCA in Japanese Alzheimer's Disease Subjects. J Alzheimers Dis 2018; 54:1349-1357. [PMID: 27567856 DOI: 10.3233/jad-160430] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Despite the continuing debate about the amyloid hypothesis in Alzheimer's disease (AD), the precise pathogenesis is still unclear. Mixed pathology is common and multiple different protein aggregates are seen in human postmortem brains. Aggregates consisting of the alpha-synuclein protein encoded by the Synuclein Alpha gene (SCNA) are common in both dementia with Lewy bodies and AD. We examined SNCA mRNA expression and methylation rates of the CpG island at intron 1 of SNCA in peripheral leukocytes in 50 AD and age- and sex-matched control subjects to verify whether alpha-synuclein pathology affects the AD pathogenesis. SNCA mRNA expression in AD subjects was significantly higher than that in control subjects (1.62±0.73 versus 0.98±0.50, p < 0.001). We found significant differences between AD and control subjects at seven CpG sites (average rate; 8.8±2.7 versus 9.5±2.5, respectively: p = 0.027). The methylation rates tended to be lower in AD subjects at all CpG sites. We conclude that mRNA expression and methylation of SNCA intron 1 are altered in AD, which may be caused by Lewy body pathology in AD.
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19
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Ozaki Y, Yoshino Y, Yamazaki K, Sao T, Mori Y, Ochi S, Yoshida T, Mori T, Iga JI, Ueno SI. DNA methylation changes at TREM2 intron 1 and TREM2 mRNA expression in patients with Alzheimer's disease. J Psychiatr Res 2017; 92:74-80. [PMID: 28412600 DOI: 10.1016/j.jpsychires.2017.04.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/23/2017] [Accepted: 04/10/2017] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Recent genome-wide association studies revealed that Triggering receptor expressed on myeloid cells 2 (TREM2) was associated with Alzheimer's disease (AD) and other neurodegenerative diseases. We previously reported that TREM2 mRNA is highly expressed in leukocytes of AD patients compared to those in healthy controls. However, the mechanism of TREM2 expression change is still not known. In this study, we examined the involvement of the DNA methylation status of TREM2 in its high gene expression. MATERIALS AND METHODS Fifty AD subjects and age- and sex-matched control subjects were recruited (25 males, 25 females; 79.9 ± 5.27 and 79.4 ± 3.92 years old, respectively). TREM2 mRNA expression and the percentage of DNA methylation at four CpG sites in intron 1 of TREM2 were studied using their peripheral leukocytes. RESULTS We confirmed that TREM2 mRNA expression in leukocytes was significantly higher in AD patients than in controls (p = 0.007). The percentage methylation at three CpG sites in TREM2 intron 1 was significantly lower in AD subjects than in control: CpG1, 9.4 ± 3.2 vs 11.9 ± 4.0 (p = 0.001); CpG2, 15.4 ± 4.9 vs 19.1 ± 4.8 (p = 0.001); CpG3, 20.8 ± 5.5 vs 25.5 ± 5.4 (p < 0.001); and the average percentage methylation of all CpG sites: 13.5 ± 3.7 vs 16.1 ± 3.8 (p = 0.002), respectively. In addition, there were significant negative correlations between TREM2 mRNA expression and the percentage DNA methylation of each of CpG sites (CpG1, r = -0.416, p < 0.001; CpG2, r = -0.510, p < 0.001; CpG3, r = -0.504, p < 0.001; CpG4, r = -0.356, p < 0.001). CONCLUSIONS Lower DNA methylation at TREM2 intron 1 caused higher TREM2 mRNA expression in the leukocytes of AD subjects versus controls and may be a biomarker for AD.
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Affiliation(s)
- Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Taku Yoshida
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan.
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
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20
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Yoshino Y, Yamazaki K, Ozaki Y, Sao T, Yoshida T, Mori T, Mori Y, Ochi S, Iga JI, Ueno SI. INPP5D mRNA Expression and Cognitive Decline in Japanese Alzheimer’s Disease Subjects. J Alzheimers Dis 2017; 58:687-694. [DOI: 10.3233/jad-161211] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Bailly-Chouriberry L, Baudoin F, Cormant F, Glavieux Y, Loup B, Garcia P, Popot MA, Bonnaire Y. RNA sample preparation applied to gene expression profiling for the horse biological passport. Drug Test Anal 2017; 9:1448-1455. [DOI: 10.1002/dta.2204] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 04/03/2017] [Accepted: 04/03/2017] [Indexed: 01/28/2023]
Affiliation(s)
| | - Florent Baudoin
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Florence Cormant
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Yohan Glavieux
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Benoit Loup
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Patrice Garcia
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Marie-Agnès Popot
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
| | - Yves Bonnaire
- Laboratoire des Courses Hippiques (LCH); 15 rue de Paradis 91370 Verrières-le-Buisson France
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Kulohoma BW, Marriage F, Vasieva O, Mankhambo L, Nguyen K, Molyneux ME, Molyneux EM, Day PJR, Carrol ED. Peripheral blood RNA gene expression in children with pneumococcal meningitis: a prospective case-control study. BMJ Paediatr Open 2017; 1:e000092. [PMID: 29637127 PMCID: PMC5862186 DOI: 10.1136/bmjpo-2017-000092] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Invasive pneumococcal disease (IPD), caused by Streptococcus pneumoniae, is a leading cause of pneumonia, meningitis and septicaemia worldwide, with increased morbidity and mortality in HIV-infected children. OBJECTIVES We aimed to compare peripheral blood expression profiles between HIV-infected and uninfected children with pneumococcal meningitis and controls, and between survivors and non-survivors, in order to provide insight into the host inflammatory response leading to poorer outcomes. DESIGN AND SETTING Prospective case-control observational study in a tertiary hospital in Malawi. PARTICIPANTS Children aged 2 months to 16 years with pneumococcal meningitis or pneumonia. METHODS We used the human genome HGU133A Affymetrix array to explore differences in gene expression between cases with pneumococcal meningitis (n=12) and controls, and between HIV-infected and uninfected cases, and validated gene expression profiles for 34 genes using real-time quantitative PCR (RT-qPCR) in an independent set of cases with IPD (n=229) and controls (n=13). Pathway analysis was used to explore genes differentially expressed. RESULTS Irrespective of underlying HIV infection, cases showed significant upregulation compared with controls of the following: S100 calcium-binding protein A12 (S100A12); vanin-1 (VNN1); arginase, liver (ARG1); matrix metallopeptidase 9 (MMP9); annexin A3 (ANXA3); interleukin 1 receptor, type II (IL1R2); CD177 molecule (CD177); endocytic adaptor protein (NUMB) and S100 calcium-binding protein A9 (S100A9), cytoskeleton-associated protein 4 (CKAP4); and glycogenin 1 (GYG1). RT-qPCR confirmed differential expression in keeping with microarray results. There was no differential gene expression in HIV-infected compared with HIV-uninfected cases, but there was significant upregulation of folate receptor 3 (FOLR3), S100A12 in survivors compared with non-survivors. CONCLUSION Children with IPD demonstrated increased expression in genes regulating immune activation, oxidative stress, leucocyte adhesion and migration, arginine metabolism, and glucocorticoid receptor signalling.
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Affiliation(s)
- Benard W Kulohoma
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
| | - Fiona Marriage
- Centre for Integrated Genomic Research, University of Manchester, Manchester, UK
| | - Olga Vasieva
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Limangeni Mankhambo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
| | - Kha Nguyen
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Malcolm E Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
| | - Elizabeth M Molyneux
- Department of Paediatrics, University of Malawi, College of Medicine, Blantyre, Malawi
| | - Philip J R Day
- Centre for Integrated Genomic Research, University of Manchester, Manchester, UK
| | - Enitan D Carrol
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi.,Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.,Department of Paediatrics, University of Malawi, College of Medicine, Blantyre, Malawi
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Funahashi Y, Yoshino Y, Yamazaki K, Mori Y, Mori T, Ozaki Y, Sao T, Ochi S, Iga JI, Ueno SI. DNA methylation changes at SNCA intron 1 in patients with dementia with Lewy bodies. Psychiatry Clin Neurosci 2017; 71:28-35. [PMID: 27685250 DOI: 10.1111/pcn.12462] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/07/2016] [Accepted: 09/22/2016] [Indexed: 12/15/2022]
Abstract
AIM It is difficult to diagnose dementia with Lewy bodies (DLB) because it exhibits clinical and neuropathological overlap with both Alzheimer's disease and Parkinson's disease. The α-synuclein protein is a major component of Lewy bodies, and accumulation of α-synuclein aggregates causes synaptic dysfunction in DLB. Epigenetic changes at the synuclein alpha ( SNCA ) gene may be involved in DLB pathogenesis. METHODS We examined DNA methylation rates at 10 CpG sites located in intron 1 of SNCA and SNCA mRNA expression in peripheral leukocytes to compare DLB patients (n = 20; nine men, 11 women; age = 78.8 ± 7.7 years) with healthy controls (n = 20; eight men, 12 women; age = 77.0 ± 6.9 years). RESULTS The methylation rate at CpG 4 ( P = 0.002) and the overall mean methylation rate at these sites (P < 0.001) were significantly lower in DLB patients than in healthy controls after Bonferroni correction. Although SNCA126 , a partial form of SNCA mRNA expression, was significantly increased in DLB ( P = 0.017), there was no significant difference in total SNCA mRNA expression between DLB patients and healthy controls ( P = 0.165). No correlation was observed between SCNA mRNA expression levels and blood DNA methylation rates in either DLB or healthy controls. CONCLUSION Our findings indicated that lower methylation rates may be a biomarker for DLB.
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Affiliation(s)
- Yu Funahashi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yuta Yoshino
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Kiyohiro Yamazaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yoko Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Takaaki Mori
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Yuki Ozaki
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Tomoko Sao
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shinichiro Ochi
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Jun-Ichi Iga
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shu-Ichi Ueno
- Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, Japan
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Evaluation of mRNA Biomarkers to Identify Risk of Hospital Acquired Infections in Children Admitted to Paediatric Intensive Care Unit. PLoS One 2016; 11:e0152388. [PMID: 27015534 PMCID: PMC4807819 DOI: 10.1371/journal.pone.0152388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/14/2016] [Indexed: 12/29/2022] Open
Abstract
Objectives Hospital-acquired infections (HAI) are associated with significant mortality and morbidity and prolongation of hospital stay, adding strain on limited hospital resources. Despite stringent infection control practices some children remain at high risk of developing HAI. The development of biomarkers which could identify these patients would be useful. In this study our objective was to evaluate mRNA candidate biomarkers for HAI prediction in a pediatric intensive care unit. Design Serial blood samples were collected from patients admitted to pediatric intensive care unit between March and June 2012. Candidate gene expression (IL1B, TNF, IL10, CD3D, BCL2, BID) was quantified using RT-qPCR. Comparisons of relative gene expression between those that did not develop HAI versus those that did were performed using Mann Whitney U-test. Patients Exclusion criteria were: age <28 days or ≥16 years, expected length of stay < 24 hours, expected survival < 28 days, end-stage renal disease and end-stage liver disease. Finally, 45 children were included in this study. Main Results The overall HAI rate was 30% of which 62% were respiratory infections. Children who developed HAI had a three-fold increase in hospital stay compared to those who did not (27 days versus 9 days, p<0.001). An increased expression of cytokine genes (IL1B and IL10) was observed in patients who developed HAI, as well as a pro-apoptosis pattern (higher expression of BID and lower expression of BCL2). CD3D, a key TCR co-factor was also significantly down-modulated in patients who developed HAI. Conclusions To our knowledge, this is the first study of mRNA biomarkers of HAI in the paediatric population. Increased mRNA expressions of anti-inflammatory cytokine and modulation of apoptotic genes suggest the development of immunosuppression in critically ill children. Immune monitoring using a panel of genes may offer a novel stratification tool to identify HAI risk.
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TREM2 mRNA Expression in Leukocytes Is Increased in Alzheimer's Disease and Schizophrenia. PLoS One 2015; 10:e0136835. [PMID: 26332043 PMCID: PMC4557831 DOI: 10.1371/journal.pone.0136835] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 08/10/2015] [Indexed: 12/21/2022] Open
Abstract
TREM2 and TYROBP are causal genes for Nasu–Hakola disease (NHD), a rare autosomal recessive disease characterized by bone lesions and early-onset progressive dementia. TREM2 forms a receptor signaling complex with TYROBP, which triggers the activation of immune responses in macrophages and dendritic cells, and the functional polymorphism of TREM2 is reported to be associated with neurodegenerative disorders such as Alzheimer’s disease (AD). The objective of this study was to reveal the involvement of TYROBP and TREM2 in the pathophysiology of AD and schizophrenia. Methods: We investigated the mRNA expression level of the 2 genes in leukocytes of 26 patients with AD and 24 with schizophrenia in comparison with age-matched controls. Moreover, we performed gene association analysis between these 2 genes and schizophrenia. Results: No differences were found in TYROBP mRNA expression in patients with AD and schizophrenia; however, TREM2 mRNA expression was increased in patients with AD and schizophrenia compared with controls (P < 0.001). There were no genetic associations of either gene with schizophrenia in Japanese patients. Conclusion: TREM2 expression in leukocytes is elevated not only in AD but also in schizophrenia. Inflammatory processes involving TREM2 may occur in schizophrenia, as observed in neurocognitive disorders such as AD. TREM2 expression in leukocytes may be a novel biomarker for neurological and psychiatric disorders.
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Wynn JL, Guthrie SO, Wong HR, Lahni P, Ungaro R, Lopez MC, Baker HV, Moldawer LL. Postnatal Age Is a Critical Determinant of the Neonatal Host Response to Sepsis. Mol Med 2015; 21:496-504. [PMID: 26052715 DOI: 10.2119/molmed.2015.00064] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 06/01/2015] [Indexed: 11/06/2022] Open
Abstract
Neonates manifest a unique host response to sepsis even among other children. Preterm neonates may experience sepsis soon after birth or during often-protracted birth hospitalizations as they attain physiologic maturity. We examined the transcriptome using genome-wide expression profiling on prospectively collected peripheral blood samples from infants evaluated for sepsis within 24 h after clinical presentation. Simultaneous plasma samples were examined for alterations in inflammatory mediators. Group designation (sepsis or uninfected) was determined retrospectively on the basis of clinical exam and laboratory results over the next 72 h from the time of evaluation. Unsupervised analysis showed the major node of separation between groups was timing of sepsis episode relative to birth (early, <3 d, or late, ≥3 d). Principal component analyses revealed significant differences between patients with early or late sepsis despite the presence of similar key immunologic pathway aberrations in both groups. Unique to neonates, the uninfected state and host response to sepsis is significantly affected by timing relative to birth. Future therapeutic approaches may need to be tailored to the timing of the infectious event based on postnatal age.
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Affiliation(s)
- James L Wynn
- Department of Pediatrics, Division of Neonatology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Scott O Guthrie
- Department of Pediatrics, Division of Neonatology, Vanderbilt University, Nashville, Tennessee, United States of America.,Ayers Children's Medical Center, Jackson-Madison County General Hospital, Jackson, Tennessee, United States of America
| | - Hector R Wong
- Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Patrick Lahni
- Cincinnati Children's Hospital Medical Center and Cincinnati Children's Research Foundation, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Ricardo Ungaro
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - M Cecilia Lopez
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Henry V Baker
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida, United States of America
| | - Lyle L Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida, United States of America
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Diakite MLY, Rollin J, Jary D, Berthier J, Mourton-Gilles C, Sauvaire D, Philippe C, Delapierre G, Gidrol X. Point-of-care diagnostics for ricin exposure. LAB ON A CHIP 2015; 15:2308-2317. [PMID: 25892365 DOI: 10.1039/c5lc00178a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A long-sought milestone in the defense against bioterrorism is the development of rapid, simple, and near-patient assays for diagnostic and theranostic purposes. Here, we present a powerful test based on a host response to a biological weapon agent, namely the ricin toxin. A signature for exposure to ricin was extracted and characterized in mice and then integrated into a plastic microfluidic cartridge. This enabled early diagnosis of exposure to ricin in mice using a drop of whole blood in less than 1 h and 30 min. The cartridge stores the reagents and implements all of the steps of the analysis, including mRNA extraction from a drop of blood, followed by tens of parallel RT-qPCR reactions. The simple and low-cost microfluidic cartridge developed here may find other applications in point-of-care diagnostics.
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28
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Tao H, Beineke P, Li B, Alberts W, Rosenberg S, Kvam E, Wingrove JA. Evaluation of a solid matrix for collection and ambient storage of RNA from whole blood. BMC Clin Pathol 2014; 14:22. [PMID: 24855452 PMCID: PMC4030268 DOI: 10.1186/1472-6890-14-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 04/22/2014] [Indexed: 12/04/2022] Open
Abstract
Background Whole blood gene expression-based molecular diagnostic tests are becoming increasingly available. Conventional tube-based methods for obtaining RNA from whole blood can be limited by phlebotomy, volume requirements, and RNA stability during transport and storage. A dried blood spot matrix for collecting high-quality RNA, called RNA Stabilizing Matrix (RSM), was evaluated against PAXgene® blood collection tubes. Methods Whole blood was collected from 25 individuals and subjected to 3 sample storage conditions: 18 hours at either room temperature (baseline arm) or 37°C, and 6 days at room temperature. RNA was extracted and assessed for integrity by Agilent Bioanalyzer, and gene expression was compared by RT-qPCR across 23 mRNAs comprising a clinical test for obstructive coronary artery disease. Results RSM produced RNA of relatively high integrity across the various tested conditions (mean RIN ± 95% CI: baseline arm, 6.92 ± 0.24; 37°C arm, 5.98 ± 0.48; 6-day arm, 6.72 ± 0.23). PAXgene samples showed comparable RNA integrity in both baseline and 37°C arms (8.42 ± 0.17; 7.92 ± 0.1 respectively) however significant degradation was observed in the 6-day arm (3.19 ± 1.32). Gene expression scores on RSM were highly correlated between the baseline and 37°C and 6-day study arms (median r = 0.96, 0.95 respectively), as was the correlation to PAXgene tubes (median r = 0.95, p < 0.001). Conclusion RNA obtained from RSM shows little degradation and comparable RT-qPCR performance to PAXgene RNA for the 23 genes analyzed. Further development of this technology may provide a convenient method for collecting, shipping, and storing RNA for gene expression assays.
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Affiliation(s)
- Heng Tao
- CardioDx, Inc., 2500 Faber Place, Palo Alto, CA 94303, USA
| | - Philip Beineke
- CardioDx, Inc., 2500 Faber Place, Palo Alto, CA 94303, USA
| | - Bing Li
- GE Global Research, One Research Circle, K1 5D29 Niskayuna NY 12309, USA
| | - William Alberts
- GE Global Research, One Research Circle, K1 5D29 Niskayuna NY 12309, USA
| | | | - Erik Kvam
- GE Global Research, One Research Circle, K1 5D29 Niskayuna NY 12309, USA
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Kim JH, Jin HO, Park JA, Chang YH, Hong YJ, Lee JK. Comparison of three different kits for extraction of high-quality RNA from frozen blood. SPRINGERPLUS 2014; 3:76. [PMID: 24567882 PMCID: PMC3925490 DOI: 10.1186/2193-1801-3-76] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 02/05/2014] [Indexed: 02/04/2023]
Abstract
Extraction of high-quality RNA is a crucial step in gene expression profiling. To achieve optimal RNA extraction from frozen blood, the performance of three RNA extraction kits- TRI reagent, PAXgene blood RNA system (PAXgene) and NucleoSpin RNA blood kit (NucleoSpin)- was evaluated. Fifteen blood specimens collected in tubes containing potassium ethylenediaminetetraacetic acid (EDTA) and stored at −80°C for approximately 5 years were randomly selected. The yield and purity of RNA, RIN (RNA integrity number) values and cycle threshold (Ct) values were assessed. Mean RNA yields with TRI reagent, PAXgene and NucleoSpin were 15.6 ± 8.7 μg/ml, 3.1 ± 1.7 μg/ml and 9.0 ± 5.5 μg/ml, respectively. Mean A260/280 ratios of RNA for the three kits were 1.7 ± 0.1, 2.0 ± 0.1, and 2.0 ± 0.0, and mean RIN values recorded as 3.2 ± 0.8, 6.0 ± 1.1, and 6.4 ± 0.9, respectively. The Ct values of housekeeping genes, 18S rRNA, β-actin, RPLP0 and HPRT1, were as follows: TRI reagent (19.2 ± 1.6, 30.6 ± 1.8, 29.9 ± 1.4 and 36.3 ± 1.3), PAXgene 16.6 ± 1.4, 26.4 ± 1.3, 28.2 ± 1.8 and 33.8 ± 1.1), and NucleoSpin (16.3 ± 1.5, 27.2 ± 1.3, 27.0 ± 1.6 and 32.9 ± 1.6). RNA yield using TRI reagent was 1.7 times higher than that with NucleoSpin and 5 times higher than that with PAXgene. However, the purity and integrity of TRI-extracted RNA was lower than that extracted with PAXgene and NucleoSpin. Moreover, the Ct values of housekeeping genes after extraction with TRI reagent were approximately 1.7-3.8 times higher than those obtained with PAXgene and NucleoSpin. The PAXgene and NucleoSpin kits produced similar results in terms of RNA purity and integrity and subsequent gene amplification. However, RNA yields from NucleoSpin were 2.9-fold higher, compared to PAXgene. Based on these findings, we conclude that NucleoSpin is the most effective kit for extraction of abundant and high-quality RNA from frozen blood.
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Affiliation(s)
- Jin-Hee Kim
- KIRAMS Radiation Blood Specimen Biobank, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea
| | - Hyeon-Ok Jin
- KIRAMS Radiation Blood Specimen Biobank, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea
| | - Jin-Ah Park
- KIRAMS Radiation Blood Specimen Biobank, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea
| | - Yoon Hwan Chang
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea
| | - Young Jun Hong
- Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea
| | - Jin Kyung Lee
- KIRAMS Radiation Blood Specimen Biobank, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea ; Department of Laboratory Medicine, Korea Cancer Center Hospital, Korea Institute of Radiological & Medical Sciences, 215-4 Gongneung-dong, Nowon-gu, Seoul, 139-709 Republic of Korea
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Guay SP, Brisson D, Lamarche B, Gaudet D, Bouchard L. Epipolymorphisms within lipoprotein genes contribute independently to plasma lipid levels in familial hypercholesterolemia. Epigenetics 2014; 9:718-29. [PMID: 24504152 DOI: 10.4161/epi.27981] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Gene polymorphisms associated so far with plasma lipid concentrations explain only a fraction of their heritability, which can reach up to 60%. Recent studies suggest that epigenetic modifications (DNA methylation) could contribute to explain part of this missing heritability. We therefore assessed whether the DNA methylation of key lipoprotein metabolism genes is associated with high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C) and triglyceride levels in patients with familial hypercholesterolemia (FH). Untreated FH patients (61 men and 37 women) were recruited for the measurement of blood DNA methylation levels at the ABCG1, LIPC, PLTP and SCARB1 gene loci using bisulfite pyrosequencing. ABCG1, LIPC and PLTP DNA methylation was significantly associated with HDL-C, LDL-C and triglyceride levels in a sex-specific manner (all P<0.05). FH subjects with previous history of coronary artery disease (CAD) had higher LIPC DNA methylation levels compared with FH subjects without CAD (P = 0.02). Sex-specific multivariable linear regression models showed that new and previously reported epipolymorphisms (ABCG1-CpGC3, LIPC-CpGA2, mean PLTP-CpGC, LPL-CpGA3, CETP-CpGA2, and CETP-CpGB2) significantly contribute to variations in plasma lipid levels (all P<0.001 in men and P<0.02 in women), independently of traditional predictors such as age, waist circumference, blood pressure, fasting plasma lipids and glucose levels. These results suggest that epigenetic perturbations of key lipoprotein metabolism genes are associated with plasma lipid levels, contribute to the interindividual variability and might partially explain the missing heritability of plasma lipid levels, at least in FH.
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Affiliation(s)
- Simon-Pierre Guay
- Department of Biochemistry; Université de Sherbrooke; Sherbrooke, QC Canada; ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada
| | - Diane Brisson
- ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada; Department of Medicine; Université de Montréal; Montréal, QC Canada
| | - Benoit Lamarche
- Institute of Nutrition and Functional Foods; Université Laval; Québec, QC Canada
| | - Daniel Gaudet
- ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada; Department of Medicine; Université de Montréal; Montréal, QC Canada
| | - Luigi Bouchard
- Department of Biochemistry; Université de Sherbrooke; Sherbrooke, QC Canada; ECOGENE-21 and Lipid Clinic; Chicoutimi Hospital; Saguenay, QC Canada
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Fang WH, Wang Q, Li HM, Ahmed M, Kumar P, Kumar S. PAX3 in neuroblastoma: oncogenic potential, chemosensitivity and signalling pathways. J Cell Mol Med 2013; 18:38-48. [PMID: 24188742 PMCID: PMC3916116 DOI: 10.1111/jcmm.12155] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 09/05/2013] [Indexed: 11/30/2022] Open
Abstract
Transcription factor PAX3/Pax3 contributes to diverse cell lineages during embryonic development and is important in tumourigenesis. We found that PAX3 is re-expressed in neuroblastoma and malignant neuroblastic (N-type) neuroblastoma cells had significantly higher PAX3 protein expression than their benign substrate-adherent (S-type) counterparts. Knock-down of PAX3 expression by siRNA transfection resulted in persistent cell growth inhibition in both types of neuroblastoma cell, owing to G1 cell cycle arrest and progressive apoptosis. Inhibition of PAX3 expression significantly decreased the attachment of S-type SH-EP1 cells to extra-cellular matrix proteins, fibronectin, laminin and collagen IV. Migration and invasion of both neuroblastoma cell types were markedly reduced after PAX3 down-regulation. PAX3 knock-down significantly augmented the cytotoxic effect of chemotherapeutic agents, etoposide, vincristine and cisplatin, commonly used to treat neuroblastoma. Microarray analyses revealed that particularly signalling pathways involving cell cycle, apoptosis, cell adhesion, cytoskeletal remodelling and development were altered by PAX3 down-regulation. Changes in PAX3 downstream genes identified by microarray analyses were validated in 47 genes by quantitative PCR. These novel findings lead us to propose that PAX3 might contribute to oncogenic characteristics of neuroblastoma cells by regulating a variety of crucial signalling pathways.
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Affiliation(s)
- Wen-Hui Fang
- Institute of Inflammation and Repair, Faculty of Medicine and Human Sciences, The University of Manchester, Manchester, UK
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Nick JA, Sanders LA, Ickes B, Briones NJ, Caceres SM, Malcolm KC, Brayshaw SJ, Chacon CS, Barboa CM, Jones MC, St Clair C, Taylor-Cousar JL, Nichols DP, Sagel SD, Strand M, Saavedra MT. Blood mRNA biomarkers for detection of treatment response in acute pulmonary exacerbations of cystic fibrosis. Thorax 2013; 68:929-37. [DOI: 10.1136/thoraxjnl-2012-202278] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Gillio-Meina C, Cepinskas G, Cecchini EL, Fraser DD. Translational research in pediatrics II: blood collection, processing, shipping, and storage. Pediatrics 2013; 131:754-66. [PMID: 23509173 DOI: 10.1542/peds.2012-1181] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Translational research often involves tissue sampling and analysis. Blood is by far the most common tissue collected. Due to the many difficulties encountered with blood procurement from children, it is imperative to maximize the quality and stability of the collected samples to optimize research results. Collected blood can remain whole or be fractionated into serum, plasma, or cell concentrates such as red blood cells, leukocytes, or platelets. Serum and plasma can be used for analyte studies, including proteins, lipids, and small molecules, and as a source of cell-free nucleic acids. Cell concentrates are used in functional studies, flow cytometry, culture experiments, or as a source for cellular nucleic acids. Before initiating studies on blood, a thorough evaluation of practices that may influence analyte and/or cellular integrity is required. Thus, it is imperative that child health researchers working with human blood are aware of how experimental results can be altered by blood sampling methods, times to processing, container tubes, presence or absence of additives, shipping and storage variables, and freeze-thaw cycles. The authors of this review, in an effort to encourage and optimize translational research using blood from pediatric patients, outline best practices for blood collection, processing, shipment, and storage.
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Drew JE. Cellular defense system gene expression profiling of human whole blood: opportunities to predict health benefits in response to diet. Adv Nutr 2012; 3:499-505. [PMID: 22797985 PMCID: PMC3649718 DOI: 10.3945/an.112.002121] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Diet is a critical factor in the maintenance of human cellular defense systems, immunity, inflammation, redox regulation, metabolism, and DNA repair that ensure optimal health and reduce disease risk. Assessment of dietary modulation of cellular defense systems in humans has been limited due to difficulties in accessing target tissues. Notably, peripheral blood gene expression profiles associated with nonhematologic disease are detectable. Coupled with recent innovations in gene expression technologies, gene expression profiling of human blood to determine predictive markers associated with health status and dietary modulation is now a feasible prospect for nutrition scientists. This review focuses on cellular defense system gene expression profiling of human whole blood and the opportunities this presents, using recent technological advances, to predict health status and benefits conferred by diet.
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Schwochow D, Serieys LEK, Wayne RK, Thalmann O. Efficient recovery of whole blood RNA--a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species. BMC Biotechnol 2012; 12:33. [PMID: 22738215 PMCID: PMC3406948 DOI: 10.1186/1472-6750-12-33] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 06/27/2012] [Indexed: 01/08/2023] Open
Abstract
Background Since the emergence of next generation sequencing platforms, unprecedented opportunities have arisen in the study of natural vertebrate populations. In particular, insights into the genetic and epigenetic mechanisms of adaptation can be revealed through study of the expression profiles of genes. However, as a pre-requisite to expression profiling, care must be taken in RNA preparation as factors like DNA contamination, RNA integrity or transcript abundance can affect downstream applications. Here, we evaluated five commonly used RNA extraction methods using whole blood sampled under varying conditions from 20 wild carnivores. Results Despite the use of minute starting volumes, all methods produced quantifiable RNA extracts (1.4 – 18.4 μg) with varying integrity (RIN 4.6 - 7.7), the latter being significantly affected by the storage and extraction method used. We observed a significant overall effect of the extraction method on DNA contamination. One particular extraction method, the LeukoLOCK™ filter system, yielded high RNA integrity along with low DNA contamination and efficient depletion of hemoglobin transcripts highly abundant in whole blood. In a proof of concept sequencing experiment, we found globin RNA transcripts to occupy up to ¼ of all sequencing reads if libraries were not depleted of hemoglobin prior to sequencing. Conclusion By carefully choosing the appropriate RNA extraction method, whole blood can become a valuable source for high-throughput applications like expression arrays or transcriptome sequencing from natural populations. Additionally, candidate genes showing signs of selection could subsequently be genotyped in large population samples using whole blood as a source for RNA without harming individuals from rare or endangered species.
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Affiliation(s)
- Doreen Schwochow
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA.
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Wahlberg K, Huggett J, Sanders R, Whale AS, Bushell C, Elaswarapu R, Scott DJ, Foy CA. Quality Assessment of Biobanked Nucleic Acid Extracts for Downstream Molecular Analysis. Biopreserv Biobank 2012; 10:266-75. [DOI: 10.1089/bio.2012.0004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tran TM, Samal B, Kirkness E, Crompton PD. Systems immunology of human malaria. Trends Parasitol 2012; 28:248-57. [PMID: 22592005 DOI: 10.1016/j.pt.2012.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/27/2012] [Accepted: 03/27/2012] [Indexed: 12/28/2022]
Abstract
Plasmodium falciparum malaria remains a global public health threat. Optimism that a highly effective malaria vaccine can be developed stems in part from the observation that humans can acquire immunity to malaria through experimental and natural P. falciparum infection. Recent advances in systems immunology could accelerate efforts to unravel the mechanisms of acquired immunity to malaria. Here, we review the tools of systems immunology, their current limitations in the context of human malaria research, and the human 'models' of malaria immunity to which these tools can be applied.
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Affiliation(s)
- Tuan M Tran
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA
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Irwin AD, Marriage F, Mankhambo LA, Jeffers G, Kolamunnage-Dona R, Guiver M, Denis B, Molyneux EM, Molyneux ME, Day PJ, Carrol ED. Novel biomarker combination improves the diagnosis of serious bacterial infections in Malawian children. BMC Med Genomics 2012; 5:13. [PMID: 22559298 PMCID: PMC3528639 DOI: 10.1186/1755-8794-5-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 03/27/2012] [Indexed: 01/07/2023] Open
Abstract
Background High throughput technologies offer insight into disease processes and heightens opportunities for improved diagnostics. Using transcriptomic analyses, we aimed to discover and to evaluate the clinical validity of a combination of reliable and functionally important biomarkers of serious bacterial infection (SBI). Methods We identified three previously reported biomarkers of infection (neutrophil gelatinase-associated lipocalin (NGAL), granulysin and resistin) and measured gene expression using quantitative real-time PCR. Protein products related to the three transcripts were measured by immunoassays. Results Relative gene expression values of NGAL and resistin were significantly increased, and expression of granulysin significantly decreased in cases compared to controls. Plasma concentrations of NGAL and resistin were significantly increased in children with confirmed SBI compared to children with no detectable bacterial infection (NBI), and to controls (287 versus 128 versus 62 ng/ml and 195 versus 90 versus 18 ng/ml, respectively, p < 0.05). Plasma protein concentrations of NGAL and resistin were significantly increased in non-survivors compared to survivors (306 versus 211 and 214 versus 150 ng/ml, p = 0.02). The respective areas under the curve (AUC) for NGAL, resistin and procalcitonin in predicting SBI were 0.79, 0.80 and 0.86, whilst a combination of NGAL, resistin and procalcitonin achieved an AUC of 0.90. Conclusions We have demonstrated a unique combination of diagnostic biomarkers of SBI using transcriptomics, and demonstrated translational concordance with the corresponding protein. The addition of NGAL and resistin protein measurement to procalcitonin significantly improved the diagnosis of SBI.
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Affiliation(s)
- Adam D Irwin
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK.
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Implementation of a proficiency testing for the assessment of the preanalytical phase of blood samples used for RNA based analysis. Clin Chim Acta 2012; 413:779-86. [DOI: 10.1016/j.cca.2012.01.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 01/10/2012] [Accepted: 01/15/2012] [Indexed: 01/24/2023]
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Falkenberg VR, Whistler T, Murray JR, Unger ER, Rajeevan MS. Identification of Phosphoglycerate Kinase 1 (PGK1) as a reference gene for quantitative gene expression measurements in human blood RNA. BMC Res Notes 2011; 4:324. [PMID: 21896205 PMCID: PMC3224551 DOI: 10.1186/1756-0500-4-324] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 09/06/2011] [Indexed: 01/18/2023] Open
Abstract
Background Blood is a convenient sample and increasingly used for quantitative gene expression measurements with a variety of diseases including chronic fatigue syndrome (CFS). Quantitative gene expression measurements require normalization of target genes to reference genes that are stable and independent from variables being tested in the experiment. Because there are no genes that are useful for all situations, reference gene selection is an essential step to any quantitative reverse transcription-PCR protocol. Many publications have described appropriate genes for a wide variety of tissues and experimental conditions, however, reference genes that may be suitable for the analysis of CFS, or human blood RNA derived from whole blood as well as isolated peripheral blood mononuclear cells (PBMCs), have not been described. Findings Literature review and analyses of our unpublished microarray data were used to narrow down the pool of candidate reference genes to six. We assayed whole blood RNA from Tempus tubes and cell preparation tube (CPT)-collected PBMC RNA from 46 subjects, and used the geNorm and NormFinder algorithms to select the most stable reference genes. Phosphoglycerate kinase 1 (PGK1) was one of the optimal normalization genes for both whole blood and PBMC RNA, however, additional genes differed for the two sample types; Ribosomal protein large, P0 (RPLP0) for PBMC RNA and Peptidylprolyl isomerase B (PPIB) for whole blood RNA. We also show that the use of a single reference gene is sufficient for normalization when the most stable candidates are used. Conclusions We have identified PGK1 as a stable reference gene for use with whole blood RNA and RNA derived from PBMC. When stable genes are selected it is possible to use a single gene for normalization rather than two or three. Optimal normalization will improve the ability of results from PBMC RNA to be compared with those from whole blood RNA and potentially allows comparison of gene expression results from blood RNA collected and processed by different methods with the intention of biomarker discovery. Results of this study should facilitate large-scale molecular epidemiologic studies using blood RNA as the target of quantitative gene expression measurements.
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Affiliation(s)
- Virginia R Falkenberg
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control & Prevention, Atlanta, GA, 30333, USA.
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CHIMURA N, SHIBATA S, KIMURA T, KONDO N, MORI T, HOSHINO Y, KAMISHINA H, MAEDA S. Suitable Reference Genes for Quantitative Real-Time RT-PCR in Total RNA Extracted from Canine Whole Blood Using the PAXgene System. J Vet Med Sci 2011; 73:1101-4. [DOI: 10.1292/jvms.11-0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Naoki CHIMURA
- The United Graduate School of Veterinary Sciences, Gifu University
| | - Sanae SHIBATA
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Tsuyoshi KIMURA
- The United Graduate School of Veterinary Sciences, Gifu University
| | - Naho KONDO
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Takashi MORI
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Yuki HOSHINO
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Hiroaki KAMISHINA
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
| | - Sadatoshi MAEDA
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University
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McGlynn OF, Browne JA, Blake CM, Murphy BA. Time of day influences cytokine and clock gene response to immune stimulation in equine whole blood. Anim Genet 2010. [DOI: 10.1111/j.1365-2052.2010.02109.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hinrichs C, Kotsch K, Buchwald S, Habicher M, Saak N, Gerlach H, Volk HD, Keh D. Perioperative gene expression analysis for prediction of postoperative sepsis. Clin Chem 2010; 56:613-22. [PMID: 20133891 DOI: 10.1373/clinchem.2009.133876] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Postoperative sepsis is one of the main causes of death after major abdominal surgery; however, the immunologic factors contributing to the development of sepsis are not completely understood. In this study, we evaluated gene expression in patients who developed postoperative sepsis and in patients with an uncomplicated postoperative course. METHODS We enrolled 220 patients in a retrospective matched-pair, case-control pilot study to investigate the perioperative expression of 23 inflammation-related genes regarding their properties for predicting postoperative sepsis. Twenty patients exhibiting symptoms of sepsis in the first 14 days after surgery (case group) were matched with 20 control patients with an uncomplicated postoperative course. Matching criteria were sex, age, main diagnosis, type of surgery, and concomitant diseases. Blood samples were drawn before surgery and on the first and second postoperative days. Relative gene expression was analyzed with real-time reverse-transcription PCR. RESULTS Significant differences (P < 0.005) in gene expression between the 2 groups were observed for IL1B (interleukin 1, beta), TNF [tumor necrosis factor (TNF superfamily, member 2)], CD3D [CD3d molecule, delta (CD3-TCR complex)], and PRF1 [perforin 1 (pore forming protein)]. Logistic regression analysis and a subsequent ROC curve analysis revealed that the combination of TNF, IL1B, and CD3D expression had a specificity and specificity of 90% and 85%, respectively, and predicted exclusion of postoperative sepsis with an estimated negative predictive value of 98.1%. CONCLUSIONS These data suggest that gene expression analysis may be an effective tool for differentiating patients at high and low risk for sepsis after abdominal surgery.
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Affiliation(s)
- Carl Hinrichs
- Department of Medical Immunology, Charité Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany
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Robison EH, Mondala TS, Williams AR, Head SR, Salomon DR, Kurian SM. Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study. BMC Genomics 2009; 10:617. [PMID: 20017944 PMCID: PMC2811129 DOI: 10.1186/1471-2164-10-617] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 12/17/2009] [Indexed: 11/10/2022] Open
Abstract
Background Whole genome gene expression profiling has revolutionized research in the past decade especially with the advent of microarrays. Recently, there have been significant improvements in whole blood RNA isolation techniques which, through stabilization of RNA at the time of sample collection, avoid bias and artifacts introduced during sample handling. Despite these improvements, current human whole blood RNA stabilization/isolation kits are limited by the requirement of a venous blood sample of at least 2.5 mL. While fingerstick blood collection has been used for many different assays, there has yet to be a kit developed to isolate high quality RNA for use in gene expression studies from such small human samples. The clinical and field testing advantages of obtaining reliable and reproducible gene expression data from a fingerstick are many; it is less invasive, time saving, more mobile, and eliminates the need of a trained phlebotomist. Furthermore, this method could also be employed in small animal studies, i.e. mice, where larger sample collections often require sacrificing the animal. In this study, we offer a rapid and simple method to extract sufficient amounts of high quality total RNA from approximately 70 μl of whole blood collected via a fingerstick using a modified protocol of the commercially available Qiagen PAXgene RNA Blood Kit. Results From two sets of fingerstick collections, about 70 uL whole blood collected via finger lancet and capillary tube, we recovered an average of 252.6 ng total RNA with an average RIN of 9.3. The post-amplification yields for 50 ng of total RNA averaged at 7.0 ug cDNA. The cDNA hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips had an average % Present call of 52.5%. Both fingerstick collections were highly correlated with r2 values ranging from 0.94 to 0.97. Similarly both fingerstick collections were highly correlated to the venous collection with r2 values ranging from 0.88 to 0.96 for fingerstick collection 1 and 0.94 to 0.96 for fingerstick collection 2. Conclusions Our comparisons of RNA quality and gene expression data of the fingerstick method with traditionally processed sample workflows demonstrate excellent RNA quality from the capillary collection as well as very high correlations of gene expression data.
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Affiliation(s)
- Elizabeth H Robison
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA.
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Sun JH, Wang YY, Zhang L, Gao CR, Zhang LZ, Guo Z. Time-dependent expression of skeletal muscle troponin I mRNA in the contused skeletal muscle of rats: a possible marker for wound age estimation. Int J Legal Med 2009; 124:27-33. [DOI: 10.1007/s00414-009-0323-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Accepted: 01/14/2009] [Indexed: 01/05/2023]
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