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Gustavsen S, Olsson A, Oturai AB, Linnet K, Thomsen R, Rasmussen BS, Jørgensen CF, Langkilde AR, Sorensen PS, Sellebjerg F, Søndergaard HB. The peripheral endocannabinoid system and its association with biomarkers of inflammation in untreated patients with multiple sclerosis. Eur J Neurol 2023; 30:3212-3220. [PMID: 37337838 DOI: 10.1111/ene.15930] [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: 03/20/2023] [Revised: 05/11/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND AND PURPOSE The endocannabinoid system (ECS) has been found altered in patients with multiple sclerosis (MS). However, whether the ECS alteration is present in the early stage of MS remains unknown. First, we aimed to compare the ECS profile between newly diagnosed MS patients and healthy controls (HCs). Next, we explored the association of the ECS, biomarkers of inflammation, and clinical parameters in newly diagnosed MS patients. METHODS Whole blood gene expression of ECS components and levels of endocannabinoids in plasma were measured by real-time quantitative polymerase chain reaction and ultra-high-pressure liquid chromatography-mass spectrometry, respectively, in 66 untreated MS patients and 46 HCs. RESULTS No differences were found in the gene expression or plasma levels of the selected ECS components between newly diagnosed MS patients and HCs. Interferon-γ, encoded by the gene IFNG, correlated positively (ρ = 0.60) with the expression of G protein-coupled receptor 55 (GPR55), and interleukin1β (IL1B) correlated negatively (ρ = -0.50) with cannabinoid receptor 2 (CNR2) in HCs. CONCLUSIONS We found no alteration in the peripheral ECS between untreated patients with MS and HC. Furthermore, our results indicate that the ECS has a minor overall involvement in the early stage of MS on inflammatory markers and clinical parameters when compared with HCs.
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Affiliation(s)
- Stefan Gustavsen
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
| | - Anna Olsson
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
| | - Annette B Oturai
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
| | - Kristian Linnet
- Department of Forensic Medicine, Section of Forensic Chemistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ragnar Thomsen
- Department of Forensic Medicine, Section of Forensic Chemistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brian S Rasmussen
- Department of Forensic Medicine, Section of Forensic Chemistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian F Jørgensen
- Department of Forensic Medicine, Section of Forensic Chemistry, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Annika R Langkilde
- Department of Radiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Per S Sorensen
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Finn Sellebjerg
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Helle B Søndergaard
- Department of Neurology, Danish Multiple Sclerosis Center, Copenhagen University Hospital - Rigshospitalet, Glostrup, Denmark
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Grzybkowska A, Anczykowska K, Antosiewicz J, Olszewski S, Dzitkowska-Zabielska M, Tomczyk M. Identification of Optimal Reference Genes for qRT-PCR Normalization for Physical Activity Intervention and Omega-3 Fatty Acids Supplementation in Humans. Int J Mol Sci 2023; 24:ijms24076734. [PMID: 37047706 PMCID: PMC10094777 DOI: 10.3390/ijms24076734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
The quantitative polymerase chain reaction (qRT-PCR) technique gives promising opportunities to detect and quantify RNA targets and is commonly used in many research fields. This study aimed to identify suitable reference genes for physical exercise and omega-3 fatty acids supplementation intervention. Forty healthy, physically active men were exposed to a 12-week eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) supplementation and standardized endurance training protocol. Blood samples were collected before and after the intervention and mRNA levels of six potential reference genes were tested in the leukocytes of 18 eligible participants using the qRT-PCR method: GAPDH (Glyceraldehyde-3-phosphate dehydrogenase), ACTB (Beta actin), TUBB (Tubulin Beta Class I), RPS18 (Ribosomal Protein S18), UBE2D2 (Ubiquitin-conjugating enzyme E2 D2), and HPRT1 (Hypoxanthine Phosphoribosyltransferase 1). The raw quantification cycle (Cq) values were then analyzed using RefFinder, an online tool that incorporates four different algorithms: NormFinder, geNorm, BestKeeper, and the comparative delta-Ct method. Delta-Ct, NormFinder, BestKeeper, and RefFinder comprehensive ranking have found GAPDH to be the most stably expressed gene. geNorm has identified TUBB and HPRT as the most stable genes. All algorithms have found ACTB to be the least stably expressed gene. A combination of the three most stably expressed genes, namely GAPDH, TUBB, and HPRT, is suggested for obtaining the most reliable results.
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Affiliation(s)
- Agata Grzybkowska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Katarzyna Anczykowska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
| | - Jędrzej Antosiewicz
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Szczepan Olszewski
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdansk, 80-211 Gdansk, Poland
| | - Magdalena Dzitkowska-Zabielska
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
- Center of Translational Medicine, Medical University of Gdansk, 80-952 Gdansk, Poland
| | - Maja Tomczyk
- Faculty of Physical Education, Gdansk University of Physical Education and Sport, 80-336 Gdansk, Poland
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Hazarika A, Nongkhlaw B, Mukhopadhyay A. Identification of stable reference genes in peripheral blood mononuclear cells from type 2 diabetes mellitus patients. Sci Rep 2023; 13:486. [PMID: 36627346 PMCID: PMC9831022 DOI: 10.1038/s41598-023-27460-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
Reference genes are obligatory for accurate normalization of mRNA transcript levels across samples and experimental conditions in Real Time-polymerase chain reaction (qRT-PCR) based quantitative gene expression assays. Selection of stably expressed reference genes is therefore crucial for ensuring reproducibility of such assays. However, there is a complete dearth of data on stability of commonly used reference genes in Peripheral Blood Mononuclear Cells (PBMCs) from Type 2 diabetes mellitus (T2DM) patients. We have evaluated the gene expression stability of 4 widely used reference genes (Beta-actin, ACTB; Peptidylprolyl Isomerase B, PPIB; Tyrosine 3 Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein Zeta, YWHAZ; and Glyceraldehyde-3-Phosphate Dehydrogenase, GAPDH); in PBMCs from 39 T2DM patients and 47 normoglycemic (NGT) subjects. ACTB and YWHAZ were found to be the most stable genes in PBMCs from T2DM patients and therefore, can be recommended as suitable reference genes in similar contexts. GAPDH and PPIB expressions were not stable in PBMCs from T2DM patients. On using ACTB and YWHAZ as reference genes for measuring relative expression of GAPDH and PPIB in these subjects, relative GAPDH expression was found to be significantly lower in female T2DM patients, compared to female NGT subjects [GAPDH relative normalization unit (RNU): female T2DM (n = 19), median (Q1, Q3): 9.0 (8.1, 9.9); female NGT (n = 18): median (Q1, Q3): 10.1 (9.1, 11.0); P = 0.034]. Dysregulation of GAPDH in PBMCs from female T2DM patients could be associated with sex-specific differences in pathogenesis and outcomes of T2DM.
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Affiliation(s)
- Ankita Hazarika
- grid.418280.70000 0004 1794 3160Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Sarjapur Road, Bangalore, India
| | - Bajanai Nongkhlaw
- grid.418280.70000 0004 1794 3160Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Sarjapur Road, Bangalore, India ,grid.464649.d0000 0004 1792 1201Present Address: Department of Pathology, North Eastern Indira Gandhi Regional Institute of Health and Medical Sciences, Shillong, Meghalaya India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Sarjapur Road, Bangalore, India.
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Mikkelsen RB, Arora T, Trošt K, Dmytriyeva O, Jensen SK, Meijnikman AS, Olofsson LE, Lappa D, Aydin Ö, Nielsen J, Gerdes V, Moritz T, van de Laar A, de Brauw M, Nieuwdorp M, Hjorth SA, Schwartz TW, Bäckhed F. Type 2 diabetes is associated with increased circulating levels of 3-hydroxydecanoate activating GPR84 and neutrophil migration. iScience 2022; 25:105683. [PMID: 36561890 PMCID: PMC9763857 DOI: 10.1016/j.isci.2022.105683] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/10/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Obesity and diabetes are associated with inflammation and altered plasma levels of several metabolites, which may be involved in disease progression. Some metabolites can activate G protein-coupled receptors (GPCRs) expressed on immune cells where they can modulate metabolic inflammation. Here, we find that 3-hydroxydecanoate is enriched in the circulation of obese individuals with type 2 diabetes (T2D) compared with nondiabetic controls. Administration of 3-hydroxydecanoate to mice promotes immune cell recruitment to adipose tissue, which was associated with adipose inflammation and increased fasting insulin levels. Furthermore, we demonstrate that 3-hydroxydecanoate stimulates migration of primary human and mouse neutrophils, but not monocytes, through GPR84 and Gαi signaling in vitro. Our findings indicate that 3-hydroxydecanoate is a T2D-associated metabolite that increases inflammatory responses and may contribute to the chronic inflammation observed in diabetes.
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Affiliation(s)
- Randi Bonke Mikkelsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Tulika Arora
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Kajetan Trošt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Oksana Dmytriyeva
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sune Kjærsgaard Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Abraham Stijn Meijnikman
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Louise Elisabeth Olofsson
- Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Dimitra Lappa
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ömrüm Aydin
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Victor Gerdes
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Thomas Moritz
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Maurits de Brauw
- Department of Surgery, Spaarne Hospital, Hoofddorp, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centre, Amsterdam, the Netherlands
| | - Siv Annegrethe Hjorth
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thue Walter Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Fredrik Bäckhed
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark,Department of Molecular and Clinical Medicine/Wallenberg Laboratory, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden,Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden,Corresponding author
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5
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Selection of species specific panel of reference genes in peripheral blood mononuclear cells of native livestock species adapted to trans-Himalayan region of Leh-Ladakh. Sci Rep 2022; 12:18473. [PMID: 36323741 PMCID: PMC9630269 DOI: 10.1038/s41598-022-22588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat, Double hump cattle and Zanskar ponies were included in this study. The commonly used statistical algorithms such as geNorm, Normfinder, BestKeeper and RefFinder were employed to assess the stability of these RGs in all the livestock species. Our study has identified different panel of reference genes in each species; for example, EEF1A1, RPL4 in Ladakhi cattle; GAPDH, RPS9, ACTB in Ladakhi yak; HPRT1, B2M, ACTB in Ladakhi donkey; HPRT1, B2M, ACTB in Double hump camel, RPS9, HPRT1 in Changthangi goat, HPRT1 and ACTB in Zanskar ponies. To the best of our knowledge, this is the first systematic attempt to identify panel of RGs across different livestock species types adapted to high altitude hypoxia conditions. In future, the findings of the present study would be quite helpful in conducting any transcriptional studies to understand the molecular basis of high altitude adaptation of native livestock population of Leh-Ladakh.
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Guan L, Crasta KC, Maier AB. Assessment of cell cycle regulators in human peripheral blood cells as markers of cellular senescence. Ageing Res Rev 2022; 78:101634. [PMID: 35460888 DOI: 10.1016/j.arr.2022.101634] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 12/12/2022]
Abstract
Cellular senescence has gained increasing interest during recent years, particularly due to causal involvement in the aging process corroborated by multiple experimental findings. Indeed, cellular senescence considered to be one of the hallmarks of aging, is defined as a stable growth arrest predominantly mediated by cell cycle regulators p53, p21 and p16. Senescent cells have frequently been studied in the peripheral blood of humans due to its accessibility. This review summarizes ex vivo studies describing cell cycle regulators as markers of senescence in human peripheral blood cells, along with detection methodologies and associative studies examining demographic and clinical characteristics. The utility of techniques such as the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), microarray, RNA sequencing and nCounter technologies for detection at the transcriptional level, along with Western blotting, enzyme-linked immunosorbent assay and flow cytometry at the translational level, will be brought up at salient points throughout this review. Notably, housekeeping genes or proteins serving as controls such as GAPDH and β-Actin, were found not to be stably expressed in some contexts. As such, optimization and validation of such genes during experimental design were recommended. In addition, the expression of cell cycle regulators was found to vary not only between different types of blood cells such as T cells and B cells but also between stages of cellular differentiation such as naïve T cells and highly differentiated T cells. On the other hand, the associations of the presence of cell cycle regulators with demographics (age, gender, ethnicity, and socioeconomic status), clinical characteristics (body mass index, specific diseases, disease-related parameters) and lifestyle vary in groups of participants. One envisions that increased understanding and insights into the assessment of cell cycle regulators as markers of senescence in human peripheral blood cells will help inform prognostication and clinical intervention in elderly individuals.
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Affiliation(s)
- Lihuan Guan
- Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Victoria, Australia.
| | - Karen C Crasta
- Healthy Longevity Translational Researc h Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Physiology, National University of Singapore, Singapore; NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Agency for Science, Technology & Research (A⁎STAR), Institute of Molecular and Cell Biology (IMCB), Singapore.
| | - Andrea B Maier
- Department of Medicine and Aged Care, @AgeMelbourne, The Royal Melbourne Hospital, The University of Melbourne, Victoria, Australia; Healthy Longevity Translational Researc h Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Centre for Healthy Longevity, @AgeSingapore, National University Health System, Singapore; Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, the Netherlands.
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7
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Bantulà M, Arismendi E, Picado C, Mullol J, Roca-Ferrer J, Tubita V. Reference Gene Validation for RT-qPCR in PBMCs from Asthmatic Patients with or without Obesity. Methods Protoc 2022; 5:35. [PMID: 35645343 PMCID: PMC9149987 DOI: 10.3390/mps5030035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/10/2022] [Accepted: 04/19/2022] [Indexed: 01/26/2023] Open
Abstract
Obesity is known to impair the efficacy of glucocorticoid medications for asthma control. Glucocorticoid-induced gene expression studies may be useful to discriminate those obese asthmatic patients who present a poor response to glucocorticoids. The expression of genes of interest is normalized with respect to reference genes (RGs). Ideally, RGs have a stable expression in different samples and are not affected by experimental conditions. The objective of this work was to analyze suitable RGs to study the role of glucocorticoid-induced genes in obese asthmatic patients in further research. The gene expression of eight potential RGs (GUSB, B2M, POLR2A, PPIA, ACTB, GAPDH, HPRT1, and TBP) was assessed with reverse transcription-quantitative polymerase chain reaction in peripheral blood mononuclear cells (PBMCs) from asthmatic, obese asthmatic, and healthy individuals. Their stability was analyzed using four different algorithms-BestKeeper, ΔCt, geNorm, and NormFinder. geNorm analysis recommended the use of a minimum of three genes for normalization. Moreover, intergroup variation due to the treatment was calculated by NormFinder, which found that B2M was the gene that was least affected by different treatments. Comprehensive rankings indicated GUSB and HPRT1 as the best RGs for qPCR in PBMCs from healthy and asthmatic subjects, while B2M and PPIA were the best for obese asthmatic subjects. Finally, our results demonstrated that B2M and HPRT1 were the most stable RGs among all groups, whereas ACTB, TBP, and GAPDH were the worst shared ones.
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Affiliation(s)
- Marina Bantulà
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
| | - Ebymar Arismendi
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Department of Pneumology, Hospital Clinic, 08036 Barcelona, Spain
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - César Picado
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Department of Pneumology, Hospital Clinic, 08036 Barcelona, Spain
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Joaquim Mullol
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
- Rhinology Unit and Smell Clinic, ENT Department, Hospital Clinic, 08036 Barcelona, Spain
| | - Jordi Roca-Ferrer
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Valeria Tubita
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
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Abstract
Quantification of cell associated HIV RNA (ca-RNA) is one of the most important and commonly used methods to evaluate the performance of latency-reversing agents (LRAs). Copies of HIV RNA measured by qPCR, are often normalized to the input RNA or cell number. However, these could be affected by biological variability and/or technical errors, which can be avoided by using an internal reference gene. To obtain reliable data, it is essential to select stable reference genes (RGs) of which the expression is not influenced by biological variability, the type of cells, or the LRAs used. However, to date, no study has carefully evaluated RG stability following LRA exposure. We analyzed the stability of six widely used RGs (GAPDH, TBP, YWHAZ, UBE2D2, HPRT1 and RPL27A) in human PBMC and CD4+ T cells. LRA exposure significantly influenced the stability of these RGs. Overall, TBP, UBE2D2, and RPL27A were the most stable RGs in all tested conditions. TBP was generally the most stable RG whereas GAPDH varied the most. Finally, we evaluated the impact of applying different RG normalizers to host genes and HIV ca-RNA data. Altered results were observed both in host and HIV gene expression when unstable RGs were used. Our data underline the importance of testing the stability of RGs utilized to evaluate LRA-induced HIV ca-RNA expression. To our knowledge, this is the first careful evaluation of the stability of RGs after LRA exposure and will significantly contribute to the quality of data analysis in regard to gene expression.IMPORTANCELatency-reversing agents (LRAs) are ubiquitously used in the "shock-and-kill" HIV cure strategy and their performance is often evaluated by ex-vivo quantification of cell associated HIV RNA. HIV RNA, measured by qPCR, is often normalized to internal reference genes, but the expression of these genes should not be influenced by the experimental settings. We found that treatment of human PBMC and CD4+ T cells with LRAs significantly altered the expression of several commonly used reference genes, such as GAPDH. Finally, we evaluate the impact of different reference genes on normalization of host genes and HIV cell associated RNA expression and demonstrated that using unstable reference genes dramatically altered experimental outcome. Our data highlight the importance of using reference genes that are unaffected by LRAs under study to correctly evaluate host gene and cell associated HIV RNA expression induced by latency-reversing agents.
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Olsson A, Gustavsen S, Nguyen TD, Nyman M, Langkilde AR, Hansen TH, Sellebjerg F, Oturai AB, Bach Søndergaard H. Serum Short-Chain Fatty Acids and Associations With Inflammation in Newly Diagnosed Patients With Multiple Sclerosis and Healthy Controls. Front Immunol 2021; 12:661493. [PMID: 34025661 PMCID: PMC8134701 DOI: 10.3389/fimmu.2021.661493] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic immune-mediated disease characterized by demyelination and neuroaxonal damage in the central nervous system. The etiology is complex and is still not fully understood. Accumulating evidence suggests that our gut microbiota and its metabolites influence the MS pathogenesis. Short-chain fatty acids (SCFAs), such as acetate, propionate and butyrate, are metabolites produced by gut microbiota through fermentation of indigestible carbohydrates. SCFAs and kynurenine metabolites have been shown to have important immunomodulatory properties, and propionate supplementation in MS patients has been associated with long-term clinical improvement. However, the underlying mechanisms of action and its importance in MS remain incompletely understood. We analyzed serum levels of SCFAs and performed targeted metabolomics in relation to biomarkers of inflammation, and clinical and MRI measures in newly diagnosed patients with relapsing-remitting MS before their first disease modifying therapy and healthy controls (HCs). We demonstrated that serum acetate levels were nominally reduced in MS patients compared with HCs. The ratios of acetate/butyrate and acetate/(propionate + butyrate) were significantly lower in MS patients in a multivariate analysis (orthogonal partial least squares discriminant analysis; OPLS-DA). The mentioned ratios and acetate levels correlated negatively with the pro-inflammatory biomarker IFNG, indicating an inverse relation between acetate and inflammation. In contrast, the proportion of butyrate was found higher in MS patients in the multivariate analysis, and both butyrate and valerate correlated positively with proinflammatory cytokines (IFNG and TNF), suggesting complex bidirectional regulatory properties of SCFAs. Branched SCFAs were inversely correlated with clinical disability, at a nominal significance level. Otherwise SCFAs did not correlate with clinical variables or MRI measures. There were signs of an alteration of the kynurenine pathway in MS, and butyrate was positively correlated with the immunomodulatory metabolite 3-hydroxyanthranilic acid. Other variables that influenced the separation between MS and HCs were NfL, ARG1 and IL1R1, D-ribose 5-phosphate, pantothenic acid and D-glucuronic acid. In conclusion, we provide novel results in this rapidly evolving field, emphasizing the complexity of the interactions between SCFAs and inflammation; therefore, further studies are required to clarify these issues before supplementation of SCFAs can be widely recommended.
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Affiliation(s)
- Anna Olsson
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Stefan Gustavsen
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Thao Duy Nguyen
- Department of Food Technology, Engineering and Nutrition, Kemicentrum, Lund University, Lund, Sweden
| | - Margareta Nyman
- Department of Food Technology, Engineering and Nutrition, Kemicentrum, Lund University, Lund, Sweden
| | - Annika R Langkilde
- Department of Radiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Finn Sellebjerg
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Annette B Oturai
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Helle Bach Søndergaard
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
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Gu YH, Cui XW, Ren JY, Long MM, Wang W, Wei CJ, Aimaier R, Li YH, Chung MH, Gu B, Li QF, Wang ZC. Selection of internal references for RT-qPCR assays in Neurofibromatosis type 1 (NF1) related Schwann cell lines. PLoS One 2021; 16:e0241821. [PMID: 33630851 PMCID: PMC7906369 DOI: 10.1371/journal.pone.0241821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/02/2021] [Indexed: 11/20/2022] Open
Abstract
Real-time quantitative PCR (RT-qPCR) has been widely applied in uncovering disease mechanisms and screening potential biomarkers. Internal reference gene selection determines the accuracy and reproducibility of data analyses. The aim of this study was to identify the optimal reference genes for the relative quantitative analysis of RT-qPCR in fourteen NF1 related cell lines, including non-tumor, benign and malignant Schwann cell lines. The expression characteristics of eleven candidate reference genes (RPS18, ACTB, B2M, GAPDH, PPIA, HPRT1, TBP, UBC, RPLP0, TFRC and RPL32) were screened and analyzed by four software programs: geNorm, NormFinder, BestKeeper and RefFinder. Results showed that GAPDH, the most frequently used internal reference gene, was significantly unstable between various cell lines. The combinational use of two reference genes (PPIA and TBP) was optimal in malignant Schwann cell lines and the use of single reference genes (PPIA or PRLP0) alone or in combination was optimal in benign Schwann cell lines. These recommended internal reference gene selections may improve the accuracy and reproducibility of RT-qPCR in gene expression analyses of NF1 related tumors.
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Affiliation(s)
- Yi-Hui Gu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-Wei Cui
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie-Yi Ren
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Man-Mei Long
- Department of Pathology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cheng-Jiang Wei
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rehanguli Aimaier
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue-Hua Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Man-Hon Chung
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Gu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing-Feng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (QFL); (ZCW)
| | - Zhi-Chao Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (QFL); (ZCW)
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11
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Søndergaard HB, Airas L, Christensen JR, Nielsen BR, Börnsen L, Oturai A, Sellebjerg F. Pregnancy-Induced Changes in microRNA Expression in Multiple Sclerosis. Front Immunol 2021; 11:552101. [PMID: 33584638 PMCID: PMC7876450 DOI: 10.3389/fimmu.2020.552101] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 11/30/2020] [Indexed: 12/17/2022] Open
Abstract
Pregnancy affects the disease course in multiple sclerosis (MS), particularly in the third trimester, where the relapse rate is reduced by as much as two thirds. This study aimed at identifying changes in microRNA (miRNA) and immune cell phenotypes in pregnant MS patients. Discovery and validation studies to detect differentially expressed miRNAs were performed with quantitative real-time PCR on peripheral blood mononuclear cells (PBMC). Flow cytometry analysis was performed on PBMC stained with antibodies directed against surface markers of antigen presenting cells (APCs), NK-cells, NKT cells, CD4+ and CD8+ T cells and subsets of these cell types, including PDL1 and PDL2 expressing subsets. RNA was extracted from whole blood, monocytes, and NK-cells to investigate expression and correlation between regulated miRNAs and mRNAs. In total, 15 miRNAs were validated to be differentially expressed between third trimester pregnant and postpartum MS patients (Benjamini-Hochberg false discovery rate from p = 0.03–0.00004). Of these, 12 miRNAs were downregulated in pregnancy and 6 of the 15 miRNAs were altered by more than ±2-fold (+2.99- to -6.38-fold). Pregnant MS patients had a highly significant increase in the percentage of monocytes and a decrease of NK-cells and myeloid dendritic cells compared to non-pregnant MS patients. We confirm previous reports of a relative increase in CD56-bright NK-cells and a decrease in CD56-dim NK-cells in third trimester of pregnancy and report an increase in non-committed follicular helper cells. PDL1 and PDL2 expression was increased in pregnant patients together with IL10. Also, in monocytes IL10, PDL1, and PDL2 were upregulated whereas miR-1, miR-20a, miR-28, miR-95, miR-146a, miR-335, and miR-625 were downregulated between pregnant and untreated MS patients. IL10, PDL1, and PDL2 were predicted targets of MS pregnancy-changed miRNAs, further supported by their negative correlations. Additionally, previously identified pregnancy-regulated mRNAs were identified as predicted targets of the miRNAs. PDL1 and PDL2 bind PD-1 expressed on T cells with an inhibitory effect on T-cell proliferation and increase in IL10 production. These results indicate that some of the effects behind the disease-ameliorating third trimester of pregnancy might be caused by changed expression of miRNAs and immunoregulatory molecules in monocytes.
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Affiliation(s)
- Helle Bach Søndergaard
- Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Laura Airas
- Department of Neurology, Turku University Hospital, Turku, Finland
| | - Jeppe Romme Christensen
- Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Birgitte Romme Nielsen
- Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Lars Börnsen
- Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Annette Oturai
- Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Finn Sellebjerg
- Danish Multiple Sclerosis Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
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12
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Casagrande S, Stier A, Monaghan P, Loveland JL, Boner W, Lupi S, Trevisi R, Hau M. Increased glucocorticoid concentrations in early life cause mitochondrial inefficiency and short telomeres. J Exp Biol 2020; 223:jeb222513. [PMID: 32532864 DOI: 10.1242/jeb.222513] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
Telomeres are DNA structures that protect chromosome ends. However, telomeres shorten during cell replication and at critically low lengths can reduce cell replicative potential, induce cell senescence and decrease fitness. Stress exposure, which elevates glucocorticoid hormone concentrations, can exacerbate telomere attrition. This phenomenon has been attributed to increased oxidative stress generated by glucocorticoids ('oxidative stress hypothesis'). We recently suggested that glucocorticoids could increase telomere attrition during stressful periods by reducing the resources available for telomere maintenance through changes in the metabolic machinery ('metabolic telomere attrition hypothesis'). Here, we tested whether experimental increases in glucocorticoid levels affected telomere length and mitochondrial function in wild great tit (Parus major) nestlings during the energy-demanding early growth period. We monitored resulting corticosterone (Cort) concentrations in plasma and red blood cells, telomere lengths and mitochondrial metabolism (metabolic rate, proton leak, oxidative phosphorylation, maximal mitochondrial capacity and mitochondrial inefficiency). We assessed oxidative damage caused by reactive oxygen species (ROS) metabolites as well as the total non-enzymatic antioxidant protection in plasma. Compared with control nestlings, Cort-nestlings had higher baseline corticosterone, shorter telomeres and higher mitochondrial metabolic rate. Importantly, Cort-nestlings showed increased mitochondrial proton leak, leading to a decreased ATP production efficiency. Treatment groups did not differ in oxidative damage or antioxidants. Hence, glucocorticoid-induced telomere attrition is associated with changes in mitochondrial metabolism, but not with ROS production. These findings support the hypothesis that shortening of telomere length during stressful periods is mediated by glucocorticoids through metabolic rearrangements.
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Affiliation(s)
- Stefania Casagrande
- Max Planck Institute for Ornithology, Evolutionary Physiology Group, 82319 Seewiesen, Germany
| | - Antoine Stier
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Pat Monaghan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Jasmine L Loveland
- Max Planck Institute for Ornithology, Behavioural Genetics and Evolutionary Ecology Group, 82319 Seewiesen, Germany
| | - Winifred Boner
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Sara Lupi
- Max Planck Institute for Ornithology, Evolutionary Physiology Group, 82319 Seewiesen, Germany
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, A-1160 Vienna, Austria
| | - Rachele Trevisi
- Max Planck Institute for Ornithology, Evolutionary Physiology Group, 82319 Seewiesen, Germany
| | - Michaela Hau
- Max Planck Institute for Ornithology, Evolutionary Physiology Group, 82319 Seewiesen, Germany
- Department of Biology, University of Konstanz, D-78464 Konstanz, Germany
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13
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Reference Genes for Expression Studies in Human CD8 + Naïve and Effector Memory T Cells under Resting and Activating Conditions. Sci Rep 2020; 10:9411. [PMID: 32523060 PMCID: PMC7286888 DOI: 10.1038/s41598-020-66367-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/15/2020] [Indexed: 12/20/2022] Open
Abstract
Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) is widely used for mRNA quantification. To accurately measure changing gene transcript levels under different experimental conditions, the use of appropriate reference gene transcripts is instrumental. In T cell immunology, suitable reference genes have been reported for bulk CD4+ and CD8+ T cells. However, many CD4+ and CD8+ T cell subsets have been described in the past. Although they respond differently to given activation stimuli, proper validation of suitable reference genes in these subsets is lacking. In this study, we evaluated twelve commonly used reference gene products in human naïve (NV) and effector memory (EM) CD8+ T cells under non-activated and activated (2 h, 10 h and 20 h) conditions. We used five different statistical approaches for data analysis. Our results show that a number of widely used reference transcripts become differentially expressed under activating conditions. Using them as references markedly alters results as exemplified with IFNG mRNA expression. The only candidate reference gene products that remained stable during the activation process were 18S rRNA and SDHA mRNA, encouraging their usage as reference gene products for RT-qPCR experiments, when quantifying mRNA levels in human NV and EM CD8+ T cells.
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14
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Roy JG, McElhaney JE, Verschoor CP. Reliable reference genes for the quantification of mRNA in human T-cells and PBMCs stimulated with live influenza virus. BMC Immunol 2020; 21:4. [PMID: 32005148 PMCID: PMC6995044 DOI: 10.1186/s12865-020-0334-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/20/2020] [Indexed: 12/19/2022] Open
Abstract
Background Quantitative PCR (qPCR) is a powerful tool that is particularly well-suited to measure mRNA levels in clinical samples, especially those with relatively low cell counts. However, a caveat of this approach is that reliable, stably expressed reference (housekeeping) genes are vital in order to ensure reproducibility and appropriate biological inference. In this study, we evaluated the expression stability of six reference genes in peripheral blood mononuclear cells (PBMCs) and isolated CD3+ T-cells from young and old adults (n = 10), following ex vivo stimulation with mock (unstimulated) or live influenza virus. Our genes included: β-actin (ACTB), glyercaldehyde-3-phostphate dehydrogenase (GAPDH), ribosomal protein L13a (RPL13a), ribosomal protein S18 (RPS18), succinate dehydrogenase complex flavoprotein subunit A (SDHA), and ubiquitin-conjugating enzyme E2D2 (UBE2D2). Results Reference gene expression varied significantly depending on cell type and stimulation conditions, but not age. Using the comparative ΔCt method, and the previously published software BestKeeper, NormFinder, and geNorm, we show that in PBMCs and T-cells, UBE2D2 and RPS18 were the most stable reference genes, followed by ACTB; however, the expression of UBE2D2 and RPS18 was found to increase with viral stimulation in isolated T-cells, while ACTB expression did not change significantly. No age-related differences in stability were observed for any gene Conclusions This study suggests the use of a combination of UBE2D2, RPS18, and ACTB for the study of influenza responses in PBMCs and T-cells, although ACTB alone may be the most optimal choice if choosing to compare target gene expression before and after viral stimulation. Both GAPDH and RPL13a were found to be poor reference genes and should be avoided for studies of this nature.
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Affiliation(s)
- Justin G Roy
- Health Sciences North Research Institute, 41 Ramsey Lake Rd, Sudbury, ON, P3E5J1, Canada
| | - Janet E McElhaney
- Health Sciences North Research Institute, 41 Ramsey Lake Rd, Sudbury, ON, P3E5J1, Canada
| | - Chris P Verschoor
- Health Sciences North Research Institute, 41 Ramsey Lake Rd, Sudbury, ON, P3E5J1, Canada.
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15
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Tarlinton R, Wang B, Morandi E, Gran B, Khaiboullin T, Martynova E, Rizvanov A, Khaiboullina S. Differential Expression of HERV-W in Peripheral Blood in Multiple Sclerosis and Healthy Patients in Two Different Ethnic Groups. Front Pharmacol 2020; 10:1645. [PMID: 32076404 PMCID: PMC7002920 DOI: 10.3389/fphar.2019.01645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 12/16/2019] [Indexed: 12/17/2022] Open
Abstract
Overexpression of the Human endogenous retrovirus W (HERV-W) group of inherited retroviruses has been consistently linked with Multiple Sclerosis (MS). However most of the studies on this link have focused on European genetic groups with a very high risk of MS and it is not clear that this relationship holds for all ethnic groups. This study examined via qPCR the RNA expression in peripheral blood of HERV-W (the multiple sclerosis associated retrovirus variant MSRV) of MS patients and healthy controls from two ethnic groups with very different risk rates of MS. Population one was derived from the UK with a Northern European genetic background and an MS risk rate of 108/100,000, population two was derived from the republic of Tatarstan, Russian Federation, with a mixed Russian (Eastern European) and Tartar (Turkic or Volga/Urals) population with an MS risk rate of 21-31/100,000. The Russian population displayed a significantly higher basal level of expression of MSRV in both healthy and MS individuals when compared to the British control population with a trend in the Russian population towards higher expression levels in MS patients than healthy patients.
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Affiliation(s)
- Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Belinda Wang
- School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Elena Morandi
- Centre de Physiopathologie de Toulouse Purpan (CPTP), Université de Toulouse, UPS, INSERM, CNRS, Toulouse, France
| | - Bruno Gran
- Clinical Neurology Research Group, Division of Clinical Neuroscience, University of Nottingham School of Medicine, Nottingham, United Kingdom
| | - Timur Khaiboullin
- Republican Research and Clinical Center of Neurology and Neurosurgery, Kazan, Russia
| | - Ekatarina Martynova
- Insitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Albert Rizvanov
- Insitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Svetlana Khaiboullina
- Insitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.,Department of Microbiology and Immunology, University of Nevada, Reno, NV, United States
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16
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Shi D, Han M, Liu W, Tao J, Chen L. Circulating MicroRNAs as Diagnostic Biomarkers of Clinical Cognitive Impairment: A Meta-Analysis. Am J Alzheimers Dis Other Demen 2020; 35:1533317520951686. [PMID: 33094634 PMCID: PMC10624042 DOI: 10.1177/1533317520951686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Minimally invasive diagnostic biomarkers of neurodegenerative diseases such as Alzheimer's disease (AD) facilitate patient selection and cognitive progressive decline monitoring. However, the diagnostic value of circulating microRNAs (miRNAs) for early cognitive impairment and progression to dementia is currently under debate. Thus, this study aimed to assess the diagnostic performance of circulating, cerebrospinal fluid (CSF) and exosomal miRNAs in the detection of clinical cognitive impairment in mild cognitive impairment (MCI), AD, and MCI-AD. METHODS We searched PubMed, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), VIP Chinese Science and Technology Journals Database (CQVIP), and Chinese Medicine Premier (Wanfang) to identify potentially eligible studies related to noncoding RNAs and cognitive dysfunction biomarkers published before November 2018. The quality assessment of the studies was performed according to the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) checklist. Meta-analysis of the literature data was performed using Stata/MP 14.0 software. The corresponding effects models were selected to calculate the summary sensitivity, specificity, positive and negative likelihood ratios (PLR and NLR), and diagnostic odds ratio (DOR) and to plot the summary receiver operating characteristic curves (SROCs) and calculate the areas under the curves (AUCs). RESULTS A total of 18 studies involving 729 patients with AD, 283 patients with MCI, and 15 patients with MCI-AD were pooled. The results revealed that the sensitivity and specificity of miRNAs in the diagnosis of AD were 0.78 and 0.79, respectively, and the area under the summary receiver operating characteristic curve (AUSROC) was 0.90. The sensitivity and specificity of miRNAs in the diagnosis of MCI were 0.89 and 0.85, respectively, and the AUSROC was 0.94. The sensitivity and specificity of microRNAs in the diagnosis of MCI-AD were 0.87 and 0.84, respectively, and the AUSROC was 0.92. CONCLUSION Our study found that miRNAs have certain diagnostic value for cognitive impairment, with high sensitivity and specificity, especially in diagnostics with multiple miRNAs and serum-based miRNA assays.
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Affiliation(s)
- Dan Shi
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Mengyu Han
- National-Local Joint Engineering Research Center of Rehabilitation Medicine Technology, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Weilin Liu
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jing Tao
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lidian Chen
- College of Rehabilitation Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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17
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Wright Muelas M, Mughal F, O'Hagan S, Day PJ, Kell DB. The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data. Sci Rep 2019; 9:17960. [PMID: 31784565 PMCID: PMC6884504 DOI: 10.1038/s41598-019-54288-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/08/2019] [Indexed: 12/13/2022] Open
Abstract
We recently introduced the Gini coefficient (GC) for assessing the expression variation of a particular gene in a dataset, as a means of selecting improved reference genes over the cohort ('housekeeping genes') typically used for normalisation in expression profiling studies. Those genes (transcripts) that we determined to be useable as reference genes differed greatly from previous suggestions based on hypothesis-driven approaches. A limitation of this initial study is that a single (albeit large) dataset was employed for both tissues and cell lines. We here extend this analysis to encompass seven other large datasets. Although their absolute values differ a little, the Gini values and median expression levels of the various genes are well correlated with each other between the various cell line datasets, implying that our original choice of the more ubiquitously expressed low-Gini-coefficient genes was indeed sound. In tissues, the Gini values and median expression levels of genes showed a greater variation, with the GC of genes changing with the number and types of tissues in the data sets. In all data sets, regardless of whether this was derived from tissues or cell lines, we also show that the GC is a robust measure of gene expression stability. Using the GC as a measure of expression stability we illustrate its utility to find tissue- and cell line-optimised housekeeping genes without any prior bias, that again include only a small number of previously reported housekeeping genes. We also independently confirmed this experimentally using RT-qPCR with 40 candidate GC genes in a panel of 10 cell lines. These were termed the Gini Genes. In many cases, the variation in the expression levels of classical reference genes is really quite huge (e.g. 44 fold for GAPDH in one data set), suggesting that the cure (of using them as normalising genes) may in some cases be worse than the disease (of not doing so). We recommend the present data-driven approach for the selection of reference genes by using the easy-to-calculate and robust GC.
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Affiliation(s)
- Marina Wright Muelas
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
| | - Farah Mughal
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Steve O'Hagan
- School of Chemistry, Department of Chemistry, The Manchester Institute of Biotechnology 131, Princess Street, Manchester, M1 7DN, UK
- The Manchester Institute of Biotechnology, 131, Princess Street, Manchester, M1 7DN, UK
| | - Philip J Day
- The Manchester Institute of Biotechnology, 131, Princess Street, Manchester, M1 7DN, UK.
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK.
| | - Douglas B Kell
- Department of Biochemistry, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, 10 Building 220, Kemitorvet, 2800, Kgs. Lyngby, Denmark.
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18
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Ghoveud E, Teimuri S, Vatandoost J, Hosseini A, Ghaedi K, Etemadifar M, Nasr Esfahani MH, Megraw TL. Potential Biomarker and Therapeutic LncRNAs in Multiple Sclerosis Through Targeting Memory B Cells. Neuromolecular Med 2019; 22:111-120. [PMID: 31576494 DOI: 10.1007/s12017-019-08570-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 09/13/2019] [Indexed: 02/07/2023]
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disease that degenerates the central nervous system (CNS). B cells exacerbate the progression of CNS lesions in MS by producing auto-antibodies, pro-inflammatory cytokines, and presenting auto-antigens to activated T cells. Long non-coding RNAs (lncRNAs) play a crucial role in complex biological processes and their stability in body fluids combined with their tissue specificity make these biomolecules promising biomarker candidates for MS diagnosis. In the current study, we investigated memory B cell-specific lncRNAs located, on average, less than 50 kb from differentially expressed protein-coding genes in MS patients compared to healthy individuals. Moreover, we included in our selection criteria lncRNA transcripts predicted to interact with microRNAs with established involvement in MS. To assess the expression levels of lncRNAs and their adjacent protein-coding genes, quantitative reverse transcription PCR was performed on peripheral blood mononuclear cells samples of 50 MS patients compared to 25 controls. Our results showed that in relapsing MS patients, compared to remitting MS patients and healthy controls, lncRNA RP11-530C5.1 was up-regulated while AL928742.12 was down-regulated. Pearson's correlation tests showed positive correlations between the expression levels of RP11-530C5.1 and AL928742.12 with PAWR and IGHA2, respectively. The results of the ROC curve test demonstrated the potential biomarker roles of AL928742.12 and RP11-530C5.1. We conclude that these lncRNAs are potential markers for detection of relapsing MS patients.
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Affiliation(s)
- Elahe Ghoveud
- Department of Biology, Hakim Sabzevari University, Sabzevar, Iran
| | - Shohreh Teimuri
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Jafar Vatandoost
- Department of Biology, Hakim Sabzevari University, Sabzevar, Iran.
| | - Aref Hosseini
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan St., Salman St., Khorsagan, Isfahan, 816513-1378, Iran.,Institute of Biochemistry and Molecular Medicine, NCCR TransCure, University of Bern, Bern, Switzerland
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. .,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan St., Salman St., Khorsagan, Isfahan, 816513-1378, Iran.
| | - Masood Etemadifar
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Royan St., Salman St., Khorsagan, Isfahan, 816513-1378, Iran.
| | - Timothy L Megraw
- Department of Biomedical Sciences, Florida State University College of Medicine, West Call Street, Tallahassee, FL, 32306-4300, USA
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19
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Hosseini A, Teimuri S, Ehsani M, Rasa SMM, Etemadifar M, Nasr Esfahani MH, Megraw TL, Ghaedi K. LncRNAs associated with multiple sclerosis expressed in the Th1 cell lineage. J Cell Physiol 2019; 234:22153-22162. [PMID: 31066039 DOI: 10.1002/jcp.28779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/17/2019] [Accepted: 04/22/2019] [Indexed: 12/24/2022]
Abstract
Multiple sclerosis (MS) is a type of inflammatory and demyelinating disorder of the central nervous system in which immune-mediated inflammatory processes are elicited by secreted cytokines from T helper (Th)-1 and Th17 cells. While some protein-coding genes expressed in T cell types have established involvement in MS disease progression, little is understood about the roles of long noncoding RNAs (lncRNAs) within the disease landscape. LncRNAs, noncoding RNAs longer than 200 nucleotides, likely control gene expression and function of Th1 cells, and offer the potential to act as therapeutic and biomarker candidates for MS. We identified lncRNAs in Th1 cells linked to MS. Expression levels of candidate lncRNAs and genes were evaluated in 50 MS patients and 25 healthy controls using quantitative real-time polymerase chain reaction, and their correlations were assessed. LncRNAs encoded by AC007278.2 and IFNG-AS1-001 showed significantly higher expression in relapsing Phase MS patients whereas IFNG-AS1-003 was elevated in patients in the remitting phase compared with relapsing patients. Collectively, these misregulated lncRNAs may provide valuable tools to understand the relationships between lncRNAs and MS, and possibly other related disorders.
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Affiliation(s)
- Aref Hosseini
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Shohreh Teimuri
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute of Biotechnology, ACECR, Isfahan, Iran
| | - Marzieh Ehsani
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Seyed Mohammad Mahdi Rasa
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Masoud Etemadifar
- Department of Neurology and Isfahan Neurosurgery Research Center, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr Esfahani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute of Biotechnology, ACECR, Isfahan, Iran
| | - Timothy L Megraw
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran.,Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute of Biotechnology, ACECR, Isfahan, Iran
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20
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Influence of Magnetite Nanoparticles and Quantum Dots on the Expression of Reference Genes in Peripheral Blood Cells. Bull Exp Biol Med 2018; 166:264-267. [PMID: 30488202 DOI: 10.1007/s10517-018-4329-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Indexed: 01/09/2023]
Abstract
We studied the influence of magnetite nanoparticles (FeO•Fe2O3) and quantum dots (CdSe/ZnS coated with mercaptopropionic acid) on the expression of 5 common reference genes (BA, B2M, PPIA, UBC, and YWHAZ) in peripheral blood cells from 20 volunteers by reverse transcription PCR method. The stability of the expression of reference genes varied depending of the cells type and chemical structure of nanoparticles. The level of YWHAZ mRNA after exposure by nanoparticles demonstrated highest stability in lymphocytes, neutrophils, and monocytes. Stability of YWHAZ expression was confirmed by Western blotting. Our findings suggest that YWHAZ is the most suitable as the reference gene.
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21
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Kaur H, Sehgal R, Kumar A, Sehgal A, Bansal D, Sultan AA. Screening and identification of potential novel biomarker for diagnosis of complicated Plasmodium vivax malaria. J Transl Med 2018; 16:272. [PMID: 30286756 PMCID: PMC6172720 DOI: 10.1186/s12967-018-1646-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background In the recent years Plasmodium vivax has been reported to cause severe infections associated with mortality. Clinical evaluation has limited accuracy for the early identification of the patients progressing towards the fatal condition. Researchers have tried to identify the serum and the plasma-based indicators of the severe malaria. Discovery of MicroRNA (miRNA) has opened up an era of identification of early biomarkers for various infectious and non-infectious diseases. MicroRNAs (miRNA) are the small non-coding RNA molecules of length 19–24 nts and are responsible for the regulation of the majority of human gene expressions at post transcriptional level. Methods We identified the differentially expressed miRNAs by microarray and validated the selected miRNAs by qRT-PCR. We assessed the diagnostic potential of these up-regulated miRNAs for complicated P. vivax malaria. Futher, the bioinformtic analysis was performed to construct protein–protein and mRNA–miRNA networks to identify highly regulated miRNA. Results In the present study, utility of miRNA as potential biomarker of complicated P. vivax malaria was explored. A total of 276 miRNAs were found to be differentially expressed by miRNA microarray and out of which 5 miRNAs (hsa-miR-7977, hsa-miR-28-3p, hsa-miR-378-5p, hsa-miR-194-5p and hsa-miR-3667-5p) were found to be significantly up-regulated in complicated P. vivax malaria patients using qRT-PCR. The diagnostic potential of these 5 miRNAs were found to be significant with sensitivity and specificity of 60–71% and 69–81% respectively and area under curve (AUC) of 0.7 (p < 0.05). Moreover, in silico analysis of the common targets of up-regulated miRNAs revealed UBA52 and hsa-miR-7977 as majorly regulated hubs in the PPI and mRNA–miRNA networks, suggesting their putative role in complicated P. vivax malaria. Conclusion miR-7977 might act as a potential biomarker for differentiating complicated P. vivax malaria from uncomplicated type. The elevated levels of miR-7977 may have a role to play in the disease pathology through UBA52 or TGF-beta signalling pathway. Electronic supplementary material The online version of this article (10.1186/s12967-018-1646-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hargobinder Kaur
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India.
| | - Archit Kumar
- Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Sehgal
- Department of Obstt. & Gynae, Government Medical College and Hospital, Chandigarh, India
| | - Devendra Bansal
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar
| | - Ali A Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine-Qatar, Cornell University, Qatar Foundation-Education City, Doha, Qatar
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22
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Faraldi M, Gomarasca M, Banfi G, Lombardi G. Free Circulating miRNAs Measurement in Clinical Settings: The Still Unsolved Issue of the Normalization. Adv Clin Chem 2018; 87:113-139. [PMID: 30342709 PMCID: PMC7112021 DOI: 10.1016/bs.acc.2018.07.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Circulating molecules that are released into the circulation in response to specific stimuli are considered potential biomarkers for physiological or pathological processes. Their effective usefulness as biomarkers resides in their stability and high availability in all the biological fluids, combined with the limited invasiveness of intervention. Among the circulating molecules, miRNAs represent a novel class of biomarkers as they possess all the required characteristics such as sensitivity, predictivity, specificity, robustness, translatability, and noninvasiveness. miRNAs are small non-coding RNAs, that act as inhibitors of protein translation, and intervene in the complex network of the post-transcriptional mechanisms finely regulating gene expression. The emerging role of miRNAs as potential biomarkers for clinical applications (e.g., cancer and cardiovascular diseases diagnosis and prediction, musculoskeletal disease diagnosis and bone fracture risk prediction), however, requires the standardization of miRNA processing, from sample collection and sample storage, to RNA isolation, RNA reverse-transcription, and data analyses. Normalization is one of the most controversial issues related to quantitative Real-Time PCR data analysis since no universally accepted normalization strategies and reference genes exist, even more importantly, for circulating miRNA quantification. As it is widely demonstrated that the choice of different normalization strategies influences the results of gene expression analysis, it is important to select the most appropriate normalizers for each experimental set. This review discloses on the different strategies adopted in RT-qPCR miRNA normalization and the concerning issues to highlight on the need of a universally accepted methodology to make comparable the results produced by different studies.
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Affiliation(s)
- Martina Faraldi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Marta Gomarasca
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Giuseppe Banfi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry & Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Corresponding author: E-mail:
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23
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Cha L, Jones AP, Trend S, Byrne SN, Fabis-Pedrini MJ, Carroll WM, Lucas RM, Cole JM, Booth DR, Kermode AG, Hart PH. Tryptophan and arginine catabolic enzymes and regulatory cytokines in clinically isolated syndrome and multiple sclerosis. Clin Transl Immunology 2018; 7:e1037. [PMID: 30128151 PMCID: PMC6095938 DOI: 10.1002/cti2.1037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/12/2018] [Accepted: 07/25/2018] [Indexed: 12/27/2022] Open
Abstract
Objectives Clinically isolated syndrome (CIS) is the earliest clinical episode in multiple sclerosis (MS). A study of circulating cells from patients with CIS may help us understand the transition to, and processes associated with, the development of MS. Methods As immune cell activity can be determined by flux through metabolic pathways, the mRNA expression of l‐tryptophan‐ and l‐arginine‐catabolising enzymes, indoleamine 2,3‐dioxygenase (IDO) 1 and IDO2 and arginase (ARG) 1 and ARG2, respectively, was compared between peripheral blood mononuclear cells (PBMCs) from healthy controls, and patients with CIS and definite MS. As one measure of cell function, cytokine mRNA levels were analysed directly ex vivo and in cells after culture for 4 h in the absence of regulatory factors in autologous serum. Results When measured directly ex vivo, the expression of IDO and ARG was greater in cells from patients with CIS and MS than cells from healthy controls. Although not linked to IDO and ARG expression, PBMCs from the CIS patients were characterised by low IL‐10 and TGFB mRNA levels and not by greater expression of proinflammatory cytokines. When the cells were cultured for 4 h without autologous serum, pro‐ and anti‐inflammatory cytokine mRNA levels positively correlated with IDO1 expression, and TGFB mRNA levels correlated with ARG1 expression. Conclusion Higher IDO and ARG expression in CIS and MS provides one sustained homeostatic mechanism to control MS‐associated inflammation. However, potent extrinsic mediators in serum may regulate immune cell function in CIS and associations between IDO, ARG and cytokine expression.
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Affiliation(s)
- Lilian Cha
- Telethon Kids Institute University of Western Australia Perth WA Australia
| | - Anderson P Jones
- Telethon Kids Institute University of Western Australia Perth WA Australia
| | - Stephanie Trend
- Telethon Kids Institute University of Western Australia Perth WA Australia
| | - Scott N Byrne
- Faculty of Medicine and Health Westmead Institute for Medical Research University of Sydney Westmead NSW Australia
| | - Marzena J Fabis-Pedrini
- Centre for Neuromuscular and Neurological Disorders Perron Institute for Neurological and Translational Science Sir Charles Gairdner Hospital University of Western Australia Perth WA Australia
| | - William M Carroll
- Centre for Neuromuscular and Neurological Disorders Perron Institute for Neurological and Translational Science Sir Charles Gairdner Hospital University of Western Australia Perth WA Australia
| | - Robyn M Lucas
- National Centre for Epidemiology and Population Health Research School of Population Health Australian National University Canberra ACT Australia
| | | | - David R Booth
- Faculty of Medicine and Health Westmead Institute for Medical Research University of Sydney Westmead NSW Australia
| | - Allan G Kermode
- Centre for Neuromuscular and Neurological Disorders Perron Institute for Neurological and Translational Science Sir Charles Gairdner Hospital University of Western Australia Perth WA Australia.,Institute for Immunology and Infectious Disease Murdoch University Perth WA Australia
| | - Prue H Hart
- Telethon Kids Institute University of Western Australia Perth WA Australia
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24
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Kumar VE, Cherupanakkal C, Catherine M, Kadhiravan T, Parameswaran N, Rajendiran S, Pillai AB. Endogenous gene selection for relative quantification PCR and IL6 transcript levels in the PBMC's of severe and non-severe dengue cases. BMC Res Notes 2018; 11:550. [PMID: 30071880 PMCID: PMC6071388 DOI: 10.1186/s13104-018-3620-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
Objectives Dengue viral infection ranges from dengue fever to dengue haemorrhagic fever and lethal dengue shock syndrome. Currently no means are available to monitor the progression of disease. Real time PCR based gene expression analyses are used to find potential molecular markers for effective prediction of dengue clinical outcome. The accuracy of qPCR analysis is strongly dependent on transcript normalization using stably expressed endogenous genes, which if selected imprecisely can lead to misinterpreted results. We aimed to determine the best fit for endogenous gene among six genes namely COX, ACTB, GAPDH, HMBS, HPRT and B2M for dengue viral infection cases. Gene stability was inferred from qPCR data by normalizing with two algorithms geNorm and Normfinder and the rankings generated were validated by gene expression analysis against target gene IL-6. Results Both the algorithms showed ACTB, HPRT, GAPDH as most stable genes. Normalizing with the stable genes revealed a significant fold change (p < .05) in IL-6 levels of .32, .52, .69, and .62 in non-dengue febrile illness, non severe, severe and All Dengue groups respectively compared to healthy controls. based on our study, we suggest ACTB with HPRT/GAPDH combination for normalization in qPCR for precise quantification of transcripts in dengue infected studies. Electronic supplementary material The online version of this article (10.1186/s13104-018-3620-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vigneshwari Easwar Kumar
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Cleetus Cherupanakkal
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Minna Catherine
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Tamilarasu Kadhiravan
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Narayanan Parameswaran
- Department of Pediatrics, Jawaharlal Institute of, Postgraduate Medical Education and Research, Puducherry, India
| | - Soundravally Rajendiran
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India.
| | - Agieshkumar Balakrishna Pillai
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India.
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25
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Teimuri S, Hosseini A, Rezaenasab A, Ghaedi K, Ghoveud E, Etemadifar M, Nasr-Esfahani MH, Megraw TL. Integrative Analysis of lncRNAs in Th17 Cell Lineage to Discover New Potential Biomarkers and Therapeutic Targets in Autoimmune Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 12:393-404. [PMID: 30195777 PMCID: PMC6128809 DOI: 10.1016/j.omtn.2018.05.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 05/24/2018] [Accepted: 05/24/2018] [Indexed: 11/27/2022]
Abstract
Th17 cells play a critical role in the pathogenesis of autoimmune diseases, including multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, Sjogren's syndrome, and inflammatory bowel disease. Despite the extensive investigation into this T cell lineage, little is understood regarding the role of Th17 lineage-specific lncRNAs (long non-coding RNAs) > 200 nt. lncRNAs may influence disease through a variety of mechanisms; their expression could be regulated by SNPs. lncRNAs can also affect the expression of neighboring genes or complementary miRNAs, and their expression may have lineage-specific patterns. In the system biology study presented here, the effective lncRNAs from different criteria were predicted for each autoimmune disease, and we then evaluated their expression levels in 50 MS patients compared to 25 controls using qRT-PCR. We identified changes in the expression levels of AL450992.2, AC009948.5, and RP11-98D18.3 as potential peripheral blood mononuclear cell (PBMC) biomarkers for MS among our studied lncRNAs in which co-expression analysis of AL450992.2 had the most AUCs, and the relationship to RORC was also assessed. We propose that the recurrently deregulated lncRNAs identified in this report could provide a valuable resource for studies aimed at delineating the relationship between functional lncRNAs and autoimmune disorders.
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Affiliation(s)
- Shohreh Teimuri
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Aref Hosseini
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Ahmad Rezaenasab
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| | - Kamran Ghaedi
- Division of Cellular and Molecular Biology, Department of Biology, Faculty of Sciences, University of Isfahan, Isfahan, Iran; Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Elahe Ghoveud
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Masoud Etemadifar
- Department of Neurology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Hossein Nasr-Esfahani
- Department of Cellular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Timothy L Megraw
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL, USA.
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26
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Royer C, Bégin AAG, Plawinski L, Lévesque L, Durrieu MC, Laroche G. Validation of reference genes for real-time PCR of cord blood mononuclear cells, differentiating endothelial progenitor cells, and mature endothelial cells. Exp Cell Res 2018; 370:389-398. [PMID: 30146063 DOI: 10.1016/j.yexcr.2018.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/06/2018] [Accepted: 07/03/2018] [Indexed: 10/28/2022]
Abstract
In the last ten years, endothelial progenitor cells (EPCs) have gained interest as an attractive cell population in regenerative medicine for vascular applications. This population is defined as the precursor of endothelial mature cells (ECs) through a process of differentiation. To our knowledge, no single marker can be used to discriminate them from mature ECs. To effectively study their differentiation kinetics, gene expression must be assessed. Quantitative real-time PCR (RT-qPCR) is widely used to analyze gene expression. To minimize the impact of variances from RT-qPCR, a rigorous selection of reference genes must be performed prior to any experiments due to variations in experimental conditions. In this study, CD34+ mononuclear cells were extracted from human cord blood and differentiated into EPCs after seeding for a maximum period of 21 days. To choose the best combinations of reference genes, we compared the results of EPCs, CD34+ mononuclear cells, and mature endothelial cells to ensure that the differentiation kinetics did not affect the expression of our selected reference genes. The expression levels of seven genes, namely, YWHAZ, GAPDH, HPRT1, RPLP0, UBC, B2M, and TBP were thus compared. The algorithms geNorm, NormFinder, BestKeeper, and the Comparative ΔCt method were employed to assess the expression of each candidate gene. Overall results reveal that the expression stability of reference genes may differ depending on the statistical program used. YWHAZ, GAPDH, and UBC composed the optimal set of reference genes for the gene expression studies performed by RT-qPCR in our experimental conditions. This work can thus serve as a starting point for the selection of candidate reference genes to normalize the levels of gene expression in endothelial progenitor cell populations.
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Affiliation(s)
- Caroline Royer
- Univ. Bordeaux, Chimie et Biologie des Membranes et Nano-Objets (UMR5248 CBMN), Pessac, France; CNRS, CBMN UMR5248, Pessac, France; Bordeaux INP, CBMN UMR5248, Pessac, France; Laboratoire d'Ingénierie de Surface, Centre de recherche du CHU de Québec - Université Laval, Hôpital Saint-François d'Assise, Québec, Canada; Département de Génie des Mines, de la Métallurgie et des Matériaux, Centre de Recherche sur les Matériaux Avancés, Université Laval, Québec, Canada
| | - Andrée-Anne Guay Bégin
- Laboratoire d'Ingénierie de Surface, Centre de recherche du CHU de Québec - Université Laval, Hôpital Saint-François d'Assise, Québec, Canada
| | - Laurent Plawinski
- Univ. Bordeaux, Chimie et Biologie des Membranes et Nano-Objets (UMR5248 CBMN), Pessac, France; CNRS, CBMN UMR5248, Pessac, France; Bordeaux INP, CBMN UMR5248, Pessac, France
| | - Lucie Lévesque
- Laboratoire d'Ingénierie de Surface, Centre de recherche du CHU de Québec - Université Laval, Hôpital Saint-François d'Assise, Québec, Canada
| | - Marie-Christine Durrieu
- Univ. Bordeaux, Chimie et Biologie des Membranes et Nano-Objets (UMR5248 CBMN), Pessac, France; CNRS, CBMN UMR5248, Pessac, France; Bordeaux INP, CBMN UMR5248, Pessac, France
| | - Gaétan Laroche
- Laboratoire d'Ingénierie de Surface, Centre de recherche du CHU de Québec - Université Laval, Hôpital Saint-François d'Assise, Québec, Canada; Département de Génie des Mines, de la Métallurgie et des Matériaux, Centre de Recherche sur les Matériaux Avancés, Université Laval, Québec, Canada.
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Yazdanpanahi N, Etemadifar M, Kardi MT, Shams E, Shahbazi S. Investigation of ERG Gene Expression in Iranian Patients with Multiple Sclerosis. Immunol Invest 2018; 47:351-359. [DOI: 10.1080/08820139.2018.1433203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nasrin Yazdanpanahi
- Department of Genetics, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Masoud Etemadifar
- Department of Neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Elahe Shams
- Young Researchers and Elite Club, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Shirin Shahbazi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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O'Hagan S, Wright Muelas M, Day PJ, Lundberg E, Kell DB. GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles. Cell Syst 2018; 6:230-244.e1. [PMID: 29428416 PMCID: PMC5840522 DOI: 10.1016/j.cels.2018.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/26/2017] [Accepted: 12/30/2017] [Indexed: 01/13/2023]
Abstract
The expression levels of SLC or ABC membrane transporter transcripts typically differ 100- to 10,000-fold between different tissues. The Gini coefficient characterizes such inequalities and here is used to describe the distribution of the expression of each transporter among different human tissues and cell lines. Many transporters exhibit extremely high Gini coefficients even for common substrates, indicating considerable specialization consistent with divergent evolution. The expression profiles of SLC transporters in different cell lines behave similarly, although Gini coefficients for ABC transporters tend to be larger in cell lines than in tissues, implying selection. Transporter genes are significantly more heterogeneously expressed than the members of most non-transporter gene classes. Transcripts with the stablest expression have a low Gini index and often differ significantly from the "housekeeping" genes commonly used for normalization in transcriptomics/qPCR studies. PCBP1 has a low Gini coefficient, is reasonably expressed, and is an excellent novel reference gene. The approach, referred to as GeneGini, provides rapid and simple characterization of expression-profile distributions and improved normalization of genome-wide expression-profiling data.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK
| | - Marina Wright Muelas
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK
| | - Philip J Day
- The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK; Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Emma Lundberg
- Science for Life Laboratory, Royal Institute of Technology (KTH), SE-17121 Solna, Sweden.
| | - Douglas B Kell
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK.
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29
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Ascoli C, Huang Y, Schott C, Turturice BA, Metwally A, Perkins DL, Finn PW. A Circulating MicroRNA Signature Serves as a Diagnostic and Prognostic Indicator in Sarcoidosis. Am J Respir Cell Mol Biol 2018; 58:40-54. [PMID: 28812922 DOI: 10.1165/rcmb.2017-0207oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRNAs) act as post-transcriptional regulators of gene expression. In sarcoidosis, aberrant miRNA expression may enhance immune responses mounted against an unknown antigenic agent. We tested whether a distinct miRNA signature functions as a diagnostic biomarker and explored its role as an immune modulator in sarcoidosis. The expression of miRNAs in peripheral blood mononuclear cells from subjects who met clinical and histopathologic criteria for sarcoidosis was compared with that observed in matched controls in the ACCESS (A Case Controlled Etiologic Study of Sarcoidosis) study. Signature miRNAs were determined by miRNA microarray analysis and validated by quantitative RT-PCR. Microarray analysis identified 54 mature, human feature miRNAs that were differentially expressed between the groups. Significant feature miRNAs that distinguished subjects with sarcoidosis from controls were selected by means of probabilistic models adjusted for clinical variables. Eight signature miRNAs were chosen to verify the diagnosis of sarcoidosis in a validation cohort, and distinguished subjects with sarcoidosis from controls with a positive predictive value of 88%. We identified both novel and previously described genes and molecular pathways associated with sarcoidosis as targets of these signature miRNAs. Additionally, we demonstrate that signature miRNAs (hsa-miR-150-3p and hsa-miR-342-5p) are significantly associated with reduced lymphocytes and airflow limitations, both of which are known markers of a poor prognosis. Together, these findings suggest that a circulating miRNA signature serves as a noninvasive biomarker that supports the diagnosis of sarcoidosis. Future studies will test the miRNA signature as a prognostication tool to identify unfavorable changes associated with poor clinical outcomes in sarcoidosis.
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Affiliation(s)
- Christian Ascoli
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine
| | - Yue Huang
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine
| | - Cody Schott
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
| | - Benjamin A Turturice
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
| | | | - David L Perkins
- Department of Bioengineering.,Division of Nephrology, Department of Medicine, and.,Department of Surgery, University of Illinois at Chicago, Chicago, Illinois
| | - Patricia W Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine.,Department of Microbiology and Immunology
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31
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Usarek E, Barańczyk-Kuźma A, Kaźmierczak B, Gajewska B, Kuźma-Kozakiewicz M. Validation of qPCR reference genes in lymphocytes from patients with amyotrophic lateral sclerosis. PLoS One 2017; 12:e0174317. [PMID: 28328930 PMCID: PMC5362213 DOI: 10.1371/journal.pone.0174317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 03/07/2017] [Indexed: 12/12/2022] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is the most specific and reliable method for determination of mRNA gene expression. Crucial point for its accurate normalization is the choice of appropriate internal control genes (ICGs). In the present work we determined and compare the expression of eight commonly used ICGs in lymphocytes from 26 patients with amyotrophic lateral sclerosis (ALS) and 30 control subjects. Peripheral blood mononuclear cells (PBMCs) before and after immortalization by EBV transfection (lymphoblast cell lines—LCLs) were used for qPCR analysis. LCLs were studied before and after liquid nitrogen cryopreservation and culturing (groups LCL1 and LCL2, respectively). qPCR data of 8 ICGs expression was analyzed by BestKeeper, NormFinder and geNorm methods. All studied genes (18SRNA, ACTB, B2M, GUSB,GAPDH, HPRT1, MT-ATP6 and RPS17) were expressed in PBMCs, whereas only first four in LCLs. LCLs cryopreservation had no effect on ICGs expression. Comprehensive ranking indicated RPS17 with MT-ATP6 as the best ICGs for qPCR in PBMCs of control and ALS subjects, and RPS17 with 18RNA or MT-ATP6 in LCLs from ALS. In PBMCs 18RNA shouldn’t be used as ICG.
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Affiliation(s)
- Ewa Usarek
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
| | - Anna Barańczyk-Kuźma
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
| | - Beata Kaźmierczak
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
| | - Beata Gajewska
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
| | - Magdalena Kuźma-Kozakiewicz
- Neurodegenerative Diseases Research Group, Medical University of Warsaw, Warsaw, Poland
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
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