1
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Ong SLM, Baelde HJ, van IJzendoorn DGP, Bovée JVMG, Szuhai K. Identification of stable housekeeping genes for induced pluripotent stem cells and -derived endothelial cells for drug testing. Sci Rep 2022; 12:16160. [PMID: 36171445 PMCID: PMC9519970 DOI: 10.1038/s41598-022-20435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
There are no validated housekeeping genes in induced pluripotent stem cells (iPSC) and derived endothelial iPSC (iPSC-EC). Thus a comparison of gene expression levels is less reliable, especially during drug treatments. Here, we utilized transcriptome sequencing data of iPSC and iPSC-EC with or without CRISPR-Cas9 induced translocation to identify a panel of 15 candidate housekeeping genes. For comparison, five commonly used housekeeping genes (B2M, GAPDH, GUSB, HMBS, and HPRT1) were included in the study. The panel of 20 candidate genes were investigated for their stability as reference genes. This panel was analyzed and ranked based on stability using five algorithms, delta-Ct, bestkeeper, geNorm, Normfinder, and Reffinder. Based on the comprehensive ranking of Reffinder, the stability of the top two genes—RPL36AL and TMBIM6, and the bottom two genes—UBA1 and B2M, were further studied in iPSC-EC with and without genetic manipulation, and after treatment with telatinib. Using quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR), it was shown that gene expression of the top two housekeeping genes, RPL36AL and TMBIM6, remained stable during drug treatment. We identified a panel of housekeeping genes that could be utilized in various conditions using iPSC and iPSC-derived endothelial cells as well as genetically modified iPSC for drug treatment.
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Affiliation(s)
- Sheena L M Ong
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans J Baelde
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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2
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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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3
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Passeron T, Malmqvst VEA, Bzioueche H, Marchetti S, Rocchi S, Tulic MK. Increased Activation of Innate Immunity and Pro-Apoptotic CXCR3B in Normal-Appearing Skin on the Lesional Site of Patients with Segmental Vitiligo. J Invest Dermatol 2021; 142:480-483.e2. [PMID: 34343558 DOI: 10.1016/j.jid.2021.07.157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Thierry Passeron
- Mediterranean Centre for Molecular Medicine (C3M), Team 12, INSERM U1065, Université Côte d'Azur, Nice, France; Department of Dermatology, University Hospital of Nice, Côte d'Azur University, Nice, France.
| | - Valentina E A Malmqvst
- Department is Dermatology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Hanene Bzioueche
- Mediterranean Centre for Molecular Medicine (C3M), Team 12, INSERM U1065, Université Côte d'Azur, Nice, France
| | - Sandrine Marchetti
- Mediterranean Centre for Molecular Medicine (C3M), Team 3, INSERM U1065, Université Côte d'Azur, Nice, France
| | - Stephane Rocchi
- Mediterranean Centre for Molecular Medicine (C3M), Team 12, INSERM U1065, Université Côte d'Azur, Nice, France
| | - Meri K Tulic
- Mediterranean Centre for Molecular Medicine (C3M), Team 12, INSERM U1065, Université Côte d'Azur, Nice, France
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Chang KV, Chen YC, Wu WT, Shen HJ, Huang KC, Chu HP, Han DS. Expression of Telomeric Repeat-Containing RNA Decreases in Sarcopenia and Increases after Exercise and Nutrition Intervention. Nutrients 2020; 12:nu12123766. [PMID: 33302352 PMCID: PMC7762552 DOI: 10.3390/nu12123766] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023] Open
Abstract
Sarcopenia is defined as aging-related loss of muscle mass and function. Telomere length in chromosomes shortens with age and is modulated by telomeric repeat-containing RNA (TERRA). This study aimed to explore the impact of aging and sarcopenia on telomere length and TERRA expression, and changes following strengthening exercise and nutrition intervention (supplement of branched-chain amino acids, calcium and vitamin D3) for 12 weeks in the sarcopenic population. Older adults (≥65 years old) were divided into non-sarcopenic controls (n = 36) and sarcopenic individuals (n = 36) after measurement of grip strength and body composition. The relative telomere length of leukocytes in all research participants was evaluated using the T/S ratio (telomere/single copy gene), and relative TERRA expression of leukocytes was determined by reverse-transcription qPCR (RT-qPCR). Generalized estimating equation (GEE) was used to analyze the influence of sarcopenia and intervention on the outcomes. There was no significant difference in telomere length between control subjects and participants with sarcopenia. TERRA expression was lower in sarcopenic participants compared to that in non-sarcopenic controls (5.18 ± 2.98 vs. 2.51 ± 1.89; p < 0.001). In the sarcopenic group, intervention significantly increased TERRA expression, but not telomere length. The GEE analysis demonstrated that TERRA expression was negatively associated with sarcopenia (β coefficient = −2.705, p < 0.001) but positively associated with intervention (β coefficient = 1.599, p = 0.023). Sarcopenia is associated with a decrease in TERRA expression in leukocytes. Rebound TERRA expression (returning to the level similar to the non-sarcopenic controls) was observed in the sarcopenic group after exercise and nutrition intervention. Future studies are warranted to examine the potential of TERRA as a biomarker for sarcopenia and its subsequent responses to intervention.
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Affiliation(s)
- Ke-Vin Chang
- Department of Physical Medicine and Rehabilitation, National Taiwan University Hospital, Bei-Hu Branch, Taipei 100, Taiwan; (K.-V.C.); (W.-T.W.)
- Community and Geriatric Medicine Research Center, National Taiwan University Hospital, Bei-Hu Branch, Taipei 108, Taiwan;
- Department of Physical Medicine and Rehabilitation, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Yu-Chen Chen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan; (Y.-C.C.); (H.-J.S.)
| | - Wei-Ting Wu
- Department of Physical Medicine and Rehabilitation, National Taiwan University Hospital, Bei-Hu Branch, Taipei 100, Taiwan; (K.-V.C.); (W.-T.W.)
| | - Hong-Jhin Shen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan; (Y.-C.C.); (H.-J.S.)
| | - Kuo-Chin Huang
- Community and Geriatric Medicine Research Center, National Taiwan University Hospital, Bei-Hu Branch, Taipei 108, Taiwan;
- Department of Family Medicine, National Taiwan University College of Medicine, Taipei 100, Taiwan
| | - Hsueh-Ping Chu
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei 106, Taiwan; (Y.-C.C.); (H.-J.S.)
- Correspondence: (H.-P.C.); (D.-S.H.); Tel.: +886-233-662487 (H.-P.C.); +886-223-717101(ext. 5001) (D.-S.H.)
| | - Der-Sheng Han
- Department of Physical Medicine and Rehabilitation, National Taiwan University Hospital, Bei-Hu Branch, Taipei 100, Taiwan; (K.-V.C.); (W.-T.W.)
- Community and Geriatric Medicine Research Center, National Taiwan University Hospital, Bei-Hu Branch, Taipei 108, Taiwan;
- Department of Physical Medicine and Rehabilitation, National Taiwan University College of Medicine, Taipei 100, Taiwan
- Health Science and Wellness Center, National Taiwan University, Taipei 106, Taiwan
- Correspondence: (H.-P.C.); (D.-S.H.); Tel.: +886-233-662487 (H.-P.C.); +886-223-717101(ext. 5001) (D.-S.H.)
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5
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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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Wentling M, Lopez-Gomez C, Park HJ, Amatruda M, Ntranos A, Aramini J, Petracca M, Rusielewicz T, Chen E, Tolstikov V, Kiebish M, Fossati V, Inglese M, Quinzii CM, Katz Sand I, Casaccia P. A metabolic perspective on CSF-mediated neurodegeneration in multiple sclerosis. Brain 2020; 142:2756-2774. [PMID: 31305892 DOI: 10.1093/brain/awz201] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 12/26/2022] Open
Abstract
Multiple sclerosis is an autoimmune demyelinating disorder of the CNS, characterized by inflammatory lesions and an underlying neurodegenerative process, which is more prominent in patients with progressive disease course. It has been proposed that mitochondrial dysfunction underlies neuronal damage, the precise mechanism by which this occurs remains uncertain. To investigate potential mechanisms of neurodegeneration, we conducted a functional screening of mitochondria in neurons exposed to the CSF of multiple sclerosis patients with a relapsing remitting (n = 15) or a progressive (secondary, n = 15 or primary, n = 14) disease course. Live-imaging of CSF-treated neurons, using a fluorescent mitochondrial tracer, identified mitochondrial elongation as a unique effect induced by the CSF from progressive patients. These morphological changes were associated with decreased activity of mitochondrial complexes I, III and IV and correlated with axonal damage. The effect of CSF treatment on the morphology of mitochondria was characterized by phosphorylation of serine 637 on the dynamin-related protein DRP1, a post-translational modification responsible for unopposed mitochondrial fusion in response to low glucose conditions. The effect of neuronal treatment with CSF from progressive patients was heat stable, thereby prompting us to conduct an unbiased exploratory lipidomic study that identified specific ceramide species as differentially abundant in the CSF of progressive patients compared to relapsing remitting multiple sclerosis. Treatment of neurons with medium supplemented with ceramides, induced a time-dependent increase of the transcripts levels of specific glucose and lactate transporters, which functionally resulted in progressively increased glucose uptake from the medium. Thus ceramide levels in the CSF of patients with progressive multiple sclerosis not only impaired mitochondrial respiration but also decreased the bioavailability of glucose by increasing its uptake. Importantly the neurotoxic effect of CSF treatment could be rescued by exogenous supplementation with glucose or lactate, presumably to compensate the inefficient fuel utilization. Together these data suggest a condition of 'virtual hypoglycosis' induced by the CSF of progressive patients in cultured neurons and suggest a critical temporal window of intervention for the rescue of the metabolic impairment of neuronal bioenergetics underlying neurodegeneration in multiple sclerosis patients.
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Affiliation(s)
- Maureen Wentling
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Neuroscience Initiative, Advanced Science Research Center, The Graduate Center at The City University of New York, New York, NY, USA
| | | | - Hye-Jin Park
- Neuroscience Initiative, Advanced Science Research Center, The Graduate Center at The City University of New York, New York, NY, USA
| | - Mario Amatruda
- Neuroscience Initiative, Advanced Science Research Center, The Graduate Center at The City University of New York, New York, NY, USA
| | - Achilles Ntranos
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Corinne Goldsmith Dickinson Center for multiple sclerosis, Mount Sinai Medical Center, New York, NY, USA
| | - James Aramini
- Structural Biology Initiative, Advanced Science Research Center, The Graduate Center at The City University of New York, New York, NY, USA
| | - Maria Petracca
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tom Rusielewicz
- New York Stem Cell Foundation Research Institute, New York, New York, USA
| | | | | | | | - Valentina Fossati
- New York Stem Cell Foundation Research Institute, New York, New York, USA
| | - Matilde Inglese
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ilana Katz Sand
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Corinne Goldsmith Dickinson Center for multiple sclerosis, Mount Sinai Medical Center, New York, NY, USA
| | - Patrizia Casaccia
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Neuroscience Initiative, Advanced Science Research Center, The Graduate Center at The City University of New York, New York, NY, USA
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7
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Feng J, Zhou Q, Gao W, Wu Y, Mu R. Seeking for potential pathogenic genes of major depressive disorder in the Gene Expression Omnibus database. Asia Pac Psychiatry 2020; 12:e12379. [PMID: 31889427 DOI: 10.1111/appy.12379] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/20/2019] [Accepted: 12/14/2019] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Major depressive disorder (MDD) is one of the most common mental disorders worldwide. The aim of this study was to identify potential pathological genes in MDD. METHODS We searched and downloaded gene expression data from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) in MDD. Then, Kyoto Encyclopedia of Genes and Genomes pathway, Gene Ontology analysis, and protein-protein interaction (PPI) network were applied to investigate the biological function of identified DEGs. The quantitative real-time polymerase chain reaction and a published dataset were used to validate the result of bioinformatics analysis. RESULTS A total of 514 DEGs were identified in MDD. In the PPI network, some hub genes with high degrees were identified, such as EEF2, RPL26L1, RPLP0, PRPF8, LSM3, DHX9, RSRC1, and AP2B1. The result of in vitro validation of RPL26L1, RSRC1, TOMM20L, RPLPO, PRPF8, AP2B1, STIP1, and C5orf45 was consistent with the bioinformatics analysis. Electronic validation of C5orf45, STIP1, PRPF8, AP2B1, and SLC35E1 was consistent with the bioinformatics analysis. DISCUSSION The deregulated genes could be used as potential pathological factors of MDD. In addition, EEF2, RPL26L1, RPLP0, PRPF8, LSM3, DHX9, RSRC1, and AP2B1 might be therapeutic targets for MDD.
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Affiliation(s)
- Jianfei Feng
- Department of Cardiology, Pizhou Dongda Hospital, Pizhou, China
| | - Qing Zhou
- Department of Cardiology, Pizhou Dongda Hospital, Pizhou, China
| | - Wenquan Gao
- Department of Cardiology, Pizhou Dongda Hospital, Pizhou, China
| | - Yanying Wu
- Department of Cardiology, Pizhou Dongda Hospital, Pizhou, China
| | - Ruibin Mu
- Department of Cardiology, Pizhou Dongda Hospital, Pizhou, China
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8
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Miladinovic T, Sharma M, Phan A, Geres H, Ungard RG, Linher-Melville K, Singh G. Activation of hippocampal microglia in a murine model of cancer-induced pain. J Pain Res 2019; 12:1003-1016. [PMID: 30936739 PMCID: PMC6430067 DOI: 10.2147/jpr.s191860] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Introduction Pain is a common and debilitating comorbidity of metastatic breast cancer. The hippocampus has been implicated in nociceptive processing, particularly relating to the subjective aspect of pain. Here, a syngeneic mouse model was used to characterize the effects of peripheral tumors on hippocampal microglial activation in relation to cancer-induced pain (CIP). Materials and methods Mice were systemically treated with the colony-stimulating factor 1 receptor inhibitor Pexidartinib prior to intrafemoral (IF) or subcutaneous 4T1 carcinoma cell inoculation. Spontaneous and evoked nociceptive responses were quantitated throughout tumor development, and contralateral hippocampi were collected via endpoint microdissection for RNA analysis. Additionally, IF tumor-bearing animals were sacrificed on days 5, 10, 15, and 20 post 4T1 cell inoculation, and brain sections were immunofluorescently stained for Iba1, a marker of activated microglia. Results Ablation of these neuroimmune cells with the CSF1R inhibitor Pexidartinib delayed the onset and severity of cancer-induced nociceptive behaviors in IF tumor-bearing animals, adding to the body of literature that demonstrates microglial contribution to the development and maintenance of CIP. Furthermore, in untreated IF tumor-bearing mice, nociceptive behaviors appeared to progress in parallel with microglial activation in hippocampal regions. Immunofluorescent Iba1+ microglia increased in the dentate gyrus and cornu ammonis 1 hippocampal regions in IF tumor-bearing animals over time, which was confirmed at the mRNA level using relevant microglial markers. Conclusion This is the first experimental evidence to demonstrate the effects of peripheral tumor-induced nociception on hippocampal microglial activation. The increase in hippocampal microglia observed in the present study may reflect the emotional and cognitive deficits reported by patients with CIP.
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Affiliation(s)
- Tanya Miladinovic
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
| | - Manu Sharma
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
| | - Andy Phan
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
| | - Hana Geres
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
| | - Robert G Ungard
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
| | - Katja Linher-Melville
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
| | - Gurmit Singh
- Michael G. DeGroote Institute for Pain Research and Care, Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada, .,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4M1, Canada,
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9
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Akhaphong B, Lockridge A, Jo S, Mohan R, Wilcox JA, Wing CR, Regal JF, Alejandro EU. Reduced uterine perfusion pressure causes loss of pancreatic β-cell area but normal function in fetal rat offspring. Am J Physiol Regul Integr Comp Physiol 2018; 315:R1220-R1231. [PMID: 30303709 DOI: 10.1152/ajpregu.00458.2017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Maternal hypertension during pregnancy is a major risk factor for intrauterine growth restriction (IUGR), which increases susceptibility to cardiovascular and metabolic disease in adulthood through unclear mechanisms. The aim of this study was to characterize the pancreatic β-cell area and function in the fetal rat offspring of a reduced uterine perfusion pressure (RUPP) model of gestational hypertension. At embryonic day 19.5, RUPP dams exhibited lower body weight, elevated mean blood pressure, reduced litter size, and higher blood glucose compared with sham-operated controls. In RUPP placental lysates, a nonsignificant change in mammalian target of rapamycin (mTOR) activity markers, phosphorylated S6 at serine 240, and phosphorylated AKT (at S473) was observed. RUPP offspring showed significantly reduced β-cell-to-pancreas area and increased β-cell death but normal insulin levels in serum. Isolated islets had normal insulin content and secretory function in response to glucose and palmitate. Fetal pancreatic lysates showed a tendency for reduced insulin levels, with a significant reduction in total mTOR protein with RUPP surgery. In addition, its downstream complex 2 targets phosphorylation of AKT at S473, and pAKT at Thr308 tended to be reduced in the fetal RUPP pancreas. Altogether, these data show that RUPP offspring demonstrated increased β-cell death, reduced β-cell area, and altered nutrient-sensor mTOR protein level in the pancreas. This could represent a mechanistic foundation in IUGR offspring's risk for enhanced susceptibility to type 2 diabetes and other metabolic vulnerabilities seen in adulthood.
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Affiliation(s)
- Brian Akhaphong
- Department of Integrative Biology & Physiology, University of Minnesota: Twin Cities, Minnesota
| | - Amber Lockridge
- Department of Integrative Biology & Physiology, University of Minnesota: Twin Cities, Minnesota
| | - Seokwon Jo
- Department of Integrative Biology & Physiology, University of Minnesota: Twin Cities, Minnesota
| | - Ramkumar Mohan
- Department of Integrative Biology & Physiology, University of Minnesota: Twin Cities, Minnesota
| | - Jacob A Wilcox
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota
| | - Cameron R Wing
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota
| | - Jean F Regal
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota
| | - Emilyn U Alejandro
- Department of Integrative Biology & Physiology, University of Minnesota: Twin Cities, Minnesota
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10
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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: 35] [Impact Index Per Article: 5.8] [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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11
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Iżykowska K, Przybylski GK, Gand C, Braun FC, Grabarczyk P, Kuss AW, Olek-Hrab K, Bastidas Torres AN, Vermeer MH, Zoutman WH, Tensen CP, Schmidt CA. Genetic rearrangements result in altered gene expression and novel fusion transcripts in Sézary syndrome. Oncotarget 2018; 8:39627-39639. [PMID: 28489605 PMCID: PMC5503638 DOI: 10.18632/oncotarget.17383] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 03/27/2017] [Indexed: 11/25/2022] Open
Abstract
Sézary syndrome (SS) is an aggressive, leukemic cutaneous T-cell lymphoma variant. Molecular pathogenesis of SS is still unclear despite many studies on genetic alterations, gene expression and epigenetic regulations. Through whole genome and transcriptome next generation sequencing nine Sézary syndrome patients were analyzed in terms of copy number variations and rearrangements affecting gene expression. Recurrent copy number variations were detected within 8q (MYC, TOX), 17p (TP53, NCOR1), 10q (PTEN, FAS), 2p (DNMT3A), 11q (USP28), 9p (CAAP1), but no recurrent rearrangements were identified. However, expression of five genes involved in rearrangements (TMEM244, EHD1, MTMR2, RNF123 and TOX) was altered in all patients. Fifteen rearrangements detected in Sézary syndrome patients and SeAx resulted in an expression of new fusion transcripts, nine of them were in frame (EHD1-CAPN12, TMEM66-BAIAP2, MBD4-PTPRC, PTPRC-CPN2, MYB-MBNL1, TFG-GPR128, MAP4K3-FIGLA, DCP1A-CCL27, MBNL1-KIAA2018) and five resulted in ectopic expression of fragments of genes not expressed in normal T-cells (BAIAP2, CPN2, GPR128, CAPN12, FIGLA). Our results not only underscored the genomic complexity of the Sézary cancer cell genome but also showed an unpreceded large variety of novel gene rearrangements resulting in fusions transcripts and ectopically expressed genes.
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Affiliation(s)
| | | | - Claudia Gand
- Clinic for Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Floriane C Braun
- Clinic for Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Piotr Grabarczyk
- Clinic for Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
| | - Andreas W Kuss
- Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Karolina Olek-Hrab
- Department of Dermatology, Karol Marcinkowski University of Medical Sciences, Poznan, Poland
| | | | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Willem H Zoutman
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelis P Tensen
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Christian A Schmidt
- Clinic for Internal Medicine C, University Medicine Greifswald, Greifswald, Germany
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12
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Zhang P, Zeng D, Yi YL, Tang YY, Zou W, Yang XF, Wang CY, Tang XQ. β2-microglobulin induces depressive- and anxiety-like behaviors in rat. PLoS One 2018; 13:e0198027. [PMID: 29795686 PMCID: PMC5968416 DOI: 10.1371/journal.pone.0198027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 05/11/2018] [Indexed: 11/27/2022] Open
Abstract
β2-microglobulin (B2M), the light chain of major histocompatibility complex class I (MHC I) molecules, has been found to impair hippocampal neurogenesis. Based on the crucial role of hippocampal neurogenesis disturbance in the process of depression and anxiety, the aim of the present study is to investigate whether B2M leads to depressive- and anxiety-like behaviors. We found that 6 days after intracerebroventricular injection with B2M (0.3 μg), the immobility times of rats in the tail suspension test and the forced swimming test were increased, the swimming and climbing time in the forced swimming test was decreased, and the latency to feed in the novelty-suppressed feeding test was increased, indicating that B2M induces depressive-like behaviors. In addition, in the elevated plus maze test, B2M-treated rats displayed obvious decline in the number of entries into and the proportion of time spent in the open arm, while the number of total arm entries was no change, which indicated that B2M induces anxiety-like behaviors. Our present findings suggest that target B2M might represent a novel approach for treatment of depression and anxiety.
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Affiliation(s)
- Ping Zhang
- Department of Neurology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China.,Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China
| | - Dan Zeng
- Department of Neurology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China.,Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China
| | - Yi-Li Yi
- Department of Neurology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China.,Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China
| | - Yi-Yun Tang
- Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China.,Department of Physiology, Medical College, University of South China, Hengyang, Hunan, China
| | - Wei Zou
- Department of Neurology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China.,Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China
| | - Xue-Feng Yang
- Department of Gastroenterology, Affiliated Nanhua Hospital, University of South China, Hengyang, Hunan, China
| | - Chun-Yan Wang
- Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China.,Department of Pathophysiology, Medical College, University of South China, Hengyang, Hunan, China
| | - Xiao-Qing Tang
- Institute of Neuroscience, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan, China.,Department of Physiology, Medical College, University of South China, Hengyang, Hunan, China
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13
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Chinchilla B, Gomez-Casado E. Identification of the functional regions of the viral haemorrhagic septicaemia virus (VHSV) NV protein: Variants that improve function. FISH & SHELLFISH IMMUNOLOGY 2017; 70:343-350. [PMID: 28882802 DOI: 10.1016/j.fsi.2017.09.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/28/2017] [Accepted: 09/03/2017] [Indexed: 06/07/2023]
Abstract
Non-virion (NV) protein is essential for an efficient replication increasing the pathogenicity of the Salmonid novirhabdovirus (formerly IHNV), Piscine novirhabdovirus (formerly VHSV), and Hirame novirhabdovirus (HIRV). The interferon system, apoptosis, and other immune-related genes are modulated by NV to finally induce a deficient antiviral state in the cell. However, little is known about the VHSV NV regions involved in function and location. Here, eight different NV 07.71 fragments and eleven NV 07.71 mutants derived from the region between the two first α-helices have been studied in order to establish the mx and il8 transcript levels in ZF4 cells and the subcellular location. As a result, we determined that the N-terminal part of NV preserves the same ability as the wild-type (wt) NV in mx/il8 modulation and it also shares the subcellular location. Among NV mutants, some induced mx upregulation (N34A, C35A, D38A, and S40A) but maintained the il8 levels stable when compared to wt-NV in ZF4. Four NV mutants (D28A, N31A, L33A, and F37A) were not affected by the mutation and showed mx and il8 transcript levels similar to wt-NV. Surprisingly, mutants D36A, R39A, and D41A induced a stronger downregulation of both mx and il8 transcript levels than wt-NV, suggesting that a more stable structure and an improved interaction with ligands could be achieved through these mutations. Amino acids at positions 36 and 39 are conserved among known VHSV NV proteins whereas at position 41 two different amino acids have been described. To date, no natural NV proteins with alanine at positions 36, 39, and 41 have been found. In addition, wt-NV, all NV mutants, and one N-terminal NV fragment were located at cytoplasm with a characteristic pattern, which might support that cytoplasm is the site for interaction with candidate ligands such as PPM1Bb. Taken together, the data presented in this work indicated that NV function relies on the first part of the molecule and is dependent on tertiary structure rather than on the linear one. This study could lead to a better knowledge of VHSV escape from fish antiviral mechanisms as well as to future studies on immune targets.
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Affiliation(s)
- Blanca Chinchilla
- Department of Biotechnology, INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain
| | - Eduardo Gomez-Casado
- Department of Biotechnology, INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, 28040 Madrid, Spain.
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14
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Activation of IGF1 Signaling in the Cochlea Induces the Transcription of Its Mediators During the Protection of Cochlear Hair Cells Against Aminoglycoside. Otol Neurotol 2017; 38:278-282. [PMID: 27846039 DOI: 10.1097/mao.0000000000001276] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
HYPOTHESIS Transcription of the Erk and Akt genes and phosphorylation of their products are promoted by insulin-like growth factor 1 (IGF1) during hair cell protection. BACKGROUND IGF1 protects mammalian hair cells in animal models from various types of damage, including aminoglycoside. Moreover, clinical trials have revealed that IGF1 was effective for idiopathic sudden sensorineural hearing loss. In this process, activation of the downstream of IGF1 signaling, including the phosphorylation of extracellular signal-regulated kinase (ERK) and AKT proteins, is involved. However, the regulation of IGF1 signaling mediators at the transcriptional level has not been studied. METHODS We used a neomycin damage model on neonatal mouse cochlear explant culture. Explants established from neonatal mice were treated with either neomycin alone or neomycin and IGF1. The expression levels of IGF1 signaling mediator genes, Akt1, Mapk3, and Mapk1, in the explants were compared using quantitative reverse transcriptase-polymerase chain reaction at several time points. Inhibitors of IGF1 signaling were added to confirm that this observation was dependent on IGF1 signaling. RESULTS The expression levels of all genes tested were significantly upregulated in neomycin+IGF1 treatment samples (p < 0.0001, analysis of variance [ANOVA]). Addition of inhibitors of IGF1 signaling significantly attenuated the upregulation of expression (p < 0.0001, ANOVA). CONCLUSIONS IGF1 treatment upregulates the expression of its mediator genes during the protection of hair cells against aminoglycoside. The regulation of mediator gene expression may serve as a novel treatment for sensorineural hearing loss.
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15
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Eghtedardoost M, Hassan ZM, Askari N, Sadeghipour A, Naghizadeh MM, Ghafarpour S, Ghazanfari T. The delayed effect of mustard gas on housekeeping gene expression in lung biopsy of chemical injuries. Biochem Biophys Rep 2017; 11:27-32. [PMID: 28955764 PMCID: PMC5614689 DOI: 10.1016/j.bbrep.2017.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/15/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Objective Sulfur mustard (SM) was used as a chemical weapon in Iraq-Iran war. Exposed people have major complications in important organs such as pulmonary system. Some studies have shown that SM could affect the expression of endogenous genes and non-housekeeping genes, time dependently. To understand the accurate molecular mechanism of the delayed effect of SM, the identification of the gene expression pattern in these patients is essential. Hence, we have evaluated mRNA expression of four common housekeeping genes (ACTIN, PGK1, β2m, GAPDH) in SM-exposed and non-exposed (control) formalin-fixed, paraffin-embedded (FFPE) human lung tissues. Method Paraffin block of lung biopsy of SM-exposed people (11 cases) and people without exposure to SM as control group (9 cases) have been selected. The mRNA expression of four endogenous control genes has been evaluated by qRT-PCR. The stability value of each gene was calculated by different methods. Result It was found that ACTIN mRNA has the highest expression (30.26±2.87) and PGK1 has the lowest standard deviation (SD) (30.885±2.215) between pooled groups. The best correlation was between ACTIN and PGK1 expressions. The M value has shown that ACTIN and then PGK1 are the most stable housekeeping genes among. The results obtained from the GeNorm and NormFinder have indicated that the pair ACTIN- PGK1 is the most suitable choice for endogenous control genes. Conclusion ACTIN and PGK1 genes are stable in studied lung tissues and are the better than two other housekeeping genes. In addition, mustard gas does not affect their expression in long term. Β-actin and PGK1 are most stable housekeeping genes among studied genes in the lung. GAPDH gene has variable expression in the lung tissue. FFPE samples can use instead fresh tissue in gene expression studies.
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Affiliation(s)
- Marzieh Eghtedardoost
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zuhair Mohammad Hassan
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nayereh Askari
- Department of biology, Faculty of Basic Sciences, Shahid Bahonar University, Kerman, Iran
| | - Alireza Sadeghipour
- Pathology Department, Rasoul Akram Medical Complex, Iran University of Medical Sciences, Tehran, Iran
| | | | - Sara Ghafarpour
- Immunoregulation Research Center, Shahed University, Tehran, Iran
| | - Tooba Ghazanfari
- Immunoregulation Research Center, Shahed University, Tehran, Iran
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16
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Eissa N, Kermarrec L, Hussein H, Bernstein CN, Ghia JE. Appropriateness of reference genes for normalizing messenger RNA in mouse 2,4-dinitrobenzene sulfonic acid (DNBS)-induced colitis using quantitative real time PCR. Sci Rep 2017; 7:42427. [PMID: 28186172 PMCID: PMC5301225 DOI: 10.1038/srep42427] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/09/2017] [Indexed: 01/16/2023] Open
Abstract
2,4-Dinitrobenzene sulfonic acid (DNBS)-induced colitis is an experimental model that mimics Crohn's disease. Appropriateness of reference genes is crucial for RT-qPCR. This is the first study to determine the stability of reference gene expression (RGE) in mice treated with DNBS. DNBS experimental Colitis was induced in male C57BL/6 mice. RNA was extracted from colon tissue and comprehensive analysis of 13 RGE was performed according to predefined criteria. Relative colonic TNF-α and IL-1β mRNA levels were calculated. Colitis significantly altered the stability of mucosal RGE. Commonly used glyceraldehyde-3-phosphate dehydrogenase (Gapdh), β-actin (Actb), or β2-microglobulin (β2m) showed the highest fluctuation within the inflamed and control groups. Conversely, ribosomal protein large P0 (Rplp0), non-POU domain containing (Nono), TATA-box-binding protein (Tbp) and eukaryotic translation elongation factor 2 (Eef2) were not affected by inflammation and were the most stable genes. TNF-α and IL-1β mRNA levels was dependent on the reference gene used and varied from significant when the most stable genes were used to non-significant when the least stable genes were used. The appropriate choice of RGE is critical to guarantee satisfactory normalization of RT-qPCR data when using DNBS-Model. We recommend using Rplp0, Nono, Tbp, Hprt and Eef2 instead of common reference genes.
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Affiliation(s)
- Nour Eissa
- Immunology, University of Manitoba, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada
| | | | - Hayam Hussein
- Large Animal Medicine, William R. Pritchard Veterinary Medical Teaching Hospital, School of Veterinary Medicine, University of California Davis, CA, USA
| | - Charles N. Bernstein
- Internal Medicine section of Gastroenterology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Jean-Eric Ghia
- Immunology, University of Manitoba, Winnipeg, MB, Canada
- Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB, Canada
- Internal Medicine section of Gastroenterology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
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17
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Casares FM. A Simple Method for Optimization of Reference Gene Identification and Normalization in DNA Microarray Analysis. Med Sci Monit Basic Res 2016; 22:45-52. [PMID: 27122237 PMCID: PMC4868104 DOI: 10.12659/msmbr.897644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background Comparative DNA microarray analyses typically yield very large gene expression data sets that reflect complex patterns of change. Despite the wealth of information that is obtained, the identification of stable reference genes is required for normalization of disease- or drug-induced changes across tested groups. This is a prerequisite in quantitative real-time reverse transcription-PCR (qRT-PCR) and relative RT-PCR but rare in gene microarray analysis. The goal of the present study was to outline a simple method for identification of reliable reference genes derived from DNA microarray data sets by comparative statistical analysis of software-generated and manually calculated candidate genes. Material/Methods DNA microarray data sets derived from whole-blood samples obtained from 14 Zucker diabetic fatty (ZDF) rats (7 lean and 7 diabetic obese) were used for the method development. This involved the use of software-generated filtering parameters to accomplish the desired signal-to-noise ratios, 75th percentile signal manual normalizations, and the selection of reference genes as endogenous controls for target gene expression normalization. Results The combination of software-generated and manual normalization methods yielded a group of 5 stably expressed, suitable endogenous control genes which can be used in further target gene expression determinations in whole blood of ZDF rats. Conclusions This method can be used to correct for potentially false results and aid in the selection of suitable endogenous control genes. It is especially useful when aimed to aid the software in cases of borderline results, where the expression and/or the fold change values are just beyond the pre-established set of acceptable parameters.
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Affiliation(s)
- Federico M Casares
- Department of Bioinformatics, Mitogenetics Research Institute, Farmingdale, NY, USA
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18
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Mahakapuge TAN, Scheerlinck JPY, Rojas CAA, Every AL, Hagen J. Assessment of reference genes for reliable analysis of gene transcription by RT-qPCR in ovine leukocytes. Vet Immunol Immunopathol 2016; 171:1-6. [PMID: 26964711 DOI: 10.1016/j.vetimm.2015.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/21/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
With the availability of genetic sequencing data, quantitative reverse transcription PCR (RT-qPCR) is increasingly being used for the quantification of gene transcription across species. Too often there is little regard to the selection of reference genes and the impact that a poor choice has on data interpretation. Indeed, RT-qPCR provides a snapshot of relative gene transcription at a given time-point, and hence is highly dependent on the stability of the transcription of the reference gene(s). Using ovine efferent lymph cells and peripheral blood mono-nuclear cells (PBMCs), the two most frequently used leukocytes in immunological studies, we have compared the stability of transcription of the most commonly used ovine reference genes: YWHAZ, RPL-13A, PGK1, B2M, GAPDH, HPRT, SDHA and ACTB. Using established algorithms for reference gene normalization "geNorm" and "Norm Finder", PGK1, GAPDH and YWHAZ were deemed the most stably transcribed genes for efferent leukocytes and PGK1, YWHAZ and SDHA were optimal in PBMCs. These genes should therefore be considered for accurate and reproducible RT-qPCR data analysis of gene transcription in sheep.
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Affiliation(s)
- T A N Mahakapuge
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia.
| | - J-P Y Scheerlinck
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - C A Alvarez Rojas
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - A L Every
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - J Hagen
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia; Department of Life Sciences, Imperial College London, SW7 2AZ London, UK
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Oturai DB, Søndergaard HB, Börnsen L, Sellebjerg F, Romme Christensen J. Identification of Suitable Reference Genes for Peripheral Blood Mononuclear Cell Subset Studies in Multiple Sclerosis. Scand J Immunol 2015; 83:72-80. [DOI: 10.1111/sji.12391] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/15/2015] [Indexed: 12/19/2022]
Affiliation(s)
- D. B. Oturai
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - H. B. Søndergaard
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - L. Börnsen
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - F. Sellebjerg
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
| | - J. Romme Christensen
- Department of Neurology; Danish Multiple Sclerosis Center; Rigshospitalet; Copenhagen University Hospital; Copenhagen Denmark
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20
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Li X, Yang Q, Bai J, Xuan Y, Wang Y. Evaluation of eight reference genes for quantitative polymerase chain reaction analysis in human T lymphocytes co‑cultured with mesenchymal stem cells. Mol Med Rep 2015; 12:7721-7. [PMID: 26459413 DOI: 10.3892/mmr.2015.4396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 07/23/2015] [Indexed: 11/05/2022] Open
Abstract
Accurate gene expression analysis relies on the selection of a stable reference gene, as unstable reference genes can alter experimental results and conclusions. It is widely‑accepted that reference genes exhibit different expression levels in different types of tissues and cells. Therefore, it is essential to screen for stably‑expressed reference genes in the cells and tissues used for experimental analysis prior to performing reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). In the present study, eight reference genes were screened for their suitability for RT‑qPCR in five T lymphocytes co‑cultured with mesenchymal stem cells from different sources. Using NormFinder, geNorm, and BestKeeper algorithms consistently demonstrated that RPL13A and B2M were the optimal reference genes for the normalization of RT‑qPCR data obtained from T lymphocytes, whereas glyceraldehyde 3‑phosphate dehydrogenase was not a suitable reference gene due to its extensive variability in expression. These findings highlight the importance of evaluating reference genes for RT‑qPCR.
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Affiliation(s)
- Xiuying Li
- The Central Laboratory, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Qiwei Yang
- The Central Laboratory, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
| | - Jinping Bai
- Department of Pathology, The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Yali Xuan
- Princess Margaret Hospital, Toronto, ON M5G2M9, Canada
| | - Yimin Wang
- The Central Laboratory, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
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21
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Gagné-Ouellet V, Guay SP, Boucher-Lafleur AM, Bouchard L, Laprise C. DNA methylation signature of interleukin 1 receptor type II in asthma. Clin Epigenetics 2015; 7:80. [PMID: 26246860 PMCID: PMC4526162 DOI: 10.1186/s13148-015-0114-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/13/2015] [Indexed: 12/25/2022] Open
Abstract
Interleukin 1 and its receptors are associated with allergic diseases such as asthma. In the present study, we measured DNA methylation at the IL1R1 and IL1R2 gene loci and assessed for associations with asthma-related phenotypes and gene expressions. We found that asthmatic and atopic individuals have higher IL1R2 promoter DNA methylation than control subjects. Additionally, we observed a negative correlation between DNA methylation at the IL1R2 promoter and IL1R2 mRNA expression. These results suggest for the first time that IL1R2 promoter DNA methylation is associated with its gene repression in allergic diseases such as asthma.
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Affiliation(s)
- Valérie Gagné-Ouellet
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC Canada
| | - Simon-Pierre Guay
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC Canada ; ECOGENE-21 and Lipid Clinic, Hôpital de Chicoutimi, Saguenay, QC Canada
| | | | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC Canada ; ECOGENE-21 and Lipid Clinic, Hôpital de Chicoutimi, Saguenay, QC Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC Canada
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22
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Kozmus CEP, Potočnik U. Reference genes for real-time qPCR in leukocytes from asthmatic patients before and after anti-asthma treatment. Gene 2015; 570:71-7. [PMID: 26051416 DOI: 10.1016/j.gene.2015.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/27/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022]
Abstract
The aim of this study was to develop a set of reference genes whose expression is stable and suitable for normalization of target gene expression measured in asthma patients during anti-asthmatic treatment. Real-time qPCR was used to determine expression of 7 candidate reference genes (18S rRNA, ACTB, B2M, GAPDH, POLR2A, RPL13A and RPL32) and 7 target genes in leukocytes from asthma patients before and after treatment with inhaled corticosteroids and leukotriene receptor antagonist. Variance of Cq values was analyzed and stability ranking was determined with geNorm. We further investigated how the different normalization strategies affected the consistency of conclusions if the specific investigated target gene is down-regulated or up-regulated after anti-asthmatic therapy. The top-ranking reference genes determined by geNorm, when samples before and after therapy were analyzed (ACTB, B2M and GAPDH) were different from those (POLR2A and B2M) when only samples before treatment were analyzed. Using only a single reference gene for normalization of 7 target gene expression compared to our strategy, there would be as low as 19% of consistency in conclusions. We suggest the use of the geometric mean of ACTB, B2M and GAPDH for normalization of qPCR data of target genes in pharmacogenomics studies in asthma patients before and after anti-asthmatic therapy, however if gene expression is measured only before anti-asthmatic treatment, we recommend the use of the geometric mean of POLR2A and B2M.
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Affiliation(s)
- Carina E P Kozmus
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; Institute for Molecular and Cell Biology, University of Porto, Rua do Campo Alegre 823, 4150 Porto, Portugal.
| | - Uroš Potočnik
- Centre for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Taborska ulica 8, 2000 Maribor, Slovenia; Laboratory for Biochemistry Molecular Biology and Genomics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, 2000 Maribor, Slovenia.
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Wang T, Ji YL, Yang YY, Xiong XY, Wang IM, Sandford AJ, Liang ZA, He JQ. Transcriptomic profiling of peripheral blood CD4⁺ T-cells in asthmatics with and without depression. Gene 2015; 565:282-7. [PMID: 25871513 DOI: 10.1016/j.gene.2015.04.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 03/29/2015] [Accepted: 04/08/2015] [Indexed: 02/05/2023]
Abstract
BACKGROUND Cumulative studies have shown that asthma is associated with depression but the underlying mechanisms are poorly understood. This study aimed to determine whether asthma with depression is characterized by unique pathophysiological pathways by analyzing the global gene expression patterns of CD4(+) T-cells from asthmatics with or without depression. MATERIALS AND METHODS Four groups of subjects (non-depressive asthmatics, depressive asthmatics, depression patients, and healthy controls) consisting of 6 participants in each group were studied. Peripheral CD4(+) T-cells were isolated and the global transcriptomic profiles were defined by using the Agilent SurePrint G3 Human GE 8x60K microarray. The differences in transcriptomic profiles between asthma with or without depression, depression patients and healthy controls were examined. Pathway enrichment analyses of differentially expressed genes were performed using the Ingenuity Pathway Analysis. Selected genes were verified and correlated to the clinical characteristics. RESULTS A total of 1448 differentially expressed transcripts were identified in any of the non-depressive asthma vs. healthy control, depressive asthma vs. healthy control, or depression vs. healthy control comparisons after correction for multiple comparisons. Among these, 156 were demonstrated as differentially expressed genes only in depressive asthma vs. healthy control. Twenty significant biological pathways were identified and were involved in inflammation, metabolism, immunity, tumor and cell cycle. Increased expression of phosphoinositide-3-kinase, regulatory subunit 1 (alpha) was confirmed in depressive asthmatics and it was inversely correlated with lung function (FEV1/FVC%). CONCLUSIONS Asthmatics with depression exhibit unique pathophysiological pathways and this result may provide clues for specific molecular mechanisms underlying asthma with depression.
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Affiliation(s)
- Ting Wang
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Chengdu, Sichuan Province, PR China
| | - Yu-Lin Ji
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Chengdu, Sichuan Province, PR China
| | - Yin-Yin Yang
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Chengdu, Sichuan Province, PR China
| | - Xing-Yu Xiong
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Chengdu, Sichuan Province, PR China
| | - I-Ming Wang
- Informatics and Analysis, Merck and Co. Inc., West Point, PA, USA
| | - Andrew J Sandford
- Centre for Heart Lung Innovation, University of British Columbia and St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Zong-An Liang
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Chengdu, Sichuan Province, PR China.
| | - Jian-Qing He
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Chengdu, Sichuan Province, PR China.
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Peripheral blood mononuclear cell gene expression profile in obese boys who followed a moderate energy-restricted diet: differences between high and low responders at baseline and after the intervention. Br J Nutr 2014; 113:331-42. [DOI: 10.1017/s0007114514003584] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The present study analyses the gene expression profile of peripheral blood mononuclear cells (PBMC) from obese boys. The aims of the present study were to identify baseline differences between low responders (LR) and high responders (HR) after 10 weeks of a moderate energy-restricted dietary intervention, and to compare the gene expression profile between the baseline and the endpoint of the nutritional intervention. Spanish obese boys (age 10–14 years) were advised to follow a 10-week moderate energy-restricted diet. Participants were classified into two groups based on the association between the response to the nutritional intervention and the changes in BMI standard deviation score (BMI-SDS): HR group (n 6), who had a more decreased BMI-SDS; LR group (n 6), who either maintained or had an even increased BMI-SDS. The expression of 28 869 genes was analysed in PBMC from both groups at baseline and after the nutritional intervention, using the Affymetrix Human Gene 1.1 ST 24-Array plate microarray. At baseline, the HR group showed a lower expression of inflammation and immune response-related pathways, which suggests that the LR group could have a more developed pro-inflammatory phenotype. Concomitantly, LEPR and SIRPB1 genes were highly expressed in the LR group, indicating a tendency towards an impaired immune response and leptin resistance. Moreover, the moderate energy-restricted diet was able to down-regulate the inflammatory ‘mitogen-activated protein kinase signalling pathway’ in the HR group, as well as some inflammatory genes (AREG and TNFAIP3). The present study confirms that changes in the gene expression profile of PBMC in obese boys may help to understand the weight-loss response. However, further research is required to confirm these findings.
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25
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Zhao Y, Ren Y, Zhang X, Zhao P, Tao W, Zhong J, Li Q, Zhang XL. Ficolin-2 inhibits hepatitis C virus infection, whereas apolipoprotein E3 mediates viral immune escape. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2014; 193:783-96. [PMID: 24928988 DOI: 10.4049/jimmunol.1302563] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human ficolin-2 (L-ficolin/p35) is a lectin-complement pathway activator that is present in normal human plasma and is associated with infectious diseases; however, little is known regarding the roles and mechanisms of ficolin-2 during chronic hepatitis C virus (HCV) infection. In this study, we found that ficolin-2 inhibits the entry of HCV at an early stage of viral infection, regardless of the viral genotype. Ficolin-2 neutralized and inhibited the initial attachment and infection of HCV by binding to the HCV envelope surface glycoproteins E1 and E2, blocking HCV attachment to low-density lipoprotein receptor (LDLR) and scavenger receptor B1, and weakly interfering with CD81 receptor attachment. However, no interference with claudin-1 and occludin receptor attachment was observed. The C-terminal fibrinogen domain (201-313 aa) of ficolin-2 was identified as the critical binding region for the HCV-E1-E2 N-glycans, playing a critical role in the anti-HCV activity. More importantly, we found that apolipoprotein E (ApoE)3, which is enriched in the low-density fractions of HCV RNA-containing particles, promotes HCV infection and inhibits ficolin-2-mediated antiviral activity. ApoE3, but not ApoE2 and ApoE4, blocked the interaction between ficolin-2 and HCV-E2. Our data suggest that the HCV entry inhibitor ficolin-2 is a novel and promising antiviral innate immune molecule, whereas ApoE3 blocks the effect of ficolin-2 and mediates an immune escape mechanism during chronic HCV infection. HCV may be neutralized using compounds directed against the lipoprotein moiety of the viral particle, and ApoE3 may be a new target to combat HCV infection.
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MESH Headings
- Apolipoprotein E3/genetics
- Apolipoprotein E3/immunology
- Apolipoprotein E3/metabolism
- Binding, Competitive/immunology
- Blotting, Western
- Cell Line, Tumor
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- HEK293 Cells
- HeLa Cells
- Hepacivirus/genetics
- Hepacivirus/immunology
- Hepacivirus/physiology
- Host-Pathogen Interactions/immunology
- Humans
- Lectins/genetics
- Lectins/immunology
- Lectins/metabolism
- Mannans/immunology
- Mannans/metabolism
- Microscopy, Confocal
- Polysaccharides/immunology
- Polysaccharides/metabolism
- Protein Binding/immunology
- RNA Interference
- Receptors, LDL/genetics
- Receptors, LDL/immunology
- Receptors, LDL/metabolism
- Scavenger Receptors, Class B/genetics
- Scavenger Receptors, Class B/immunology
- Scavenger Receptors, Class B/metabolism
- Tetraspanin 28/genetics
- Tetraspanin 28/immunology
- Tetraspanin 28/metabolism
- Tumor Escape/genetics
- Tumor Escape/immunology
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Viral Envelope Proteins/metabolism
- Ficolins
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Affiliation(s)
- Yinglan Zhao
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, China
| | - Yushan Ren
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, China
| | - Xuping Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, China
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Wanyin Tao
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai 200025, China; and
| | - Jin Zhong
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai 200025, China; and
| | - Qiao Li
- University of Michigan Medical Center, Ann Arbor, MI 48109
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, China;
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Zhan C, Zhang Y, Ma J, Wang L, Jiang W, Shi Y, Wang Q. Identification of reference genes for qRT-PCR in human lung squamous-cell carcinoma by RNA-Seq. Acta Biochim Biophys Sin (Shanghai) 2014; 46:330-7. [PMID: 24457517 DOI: 10.1093/abbs/gmt153] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Although the accuracy of quantitative real-time polymerase chain reaction (qRT-PCR) is highly dependent on the reliable reference genes, many commonly used reference genes are not stably expressed and as such are not suitable for quantification and normalization of qRT-PCR data. The aim of this study was to identify novel reliable reference genes in lung squamous-cell carcinoma. We used RNA sequencing (RNA-Seq) to survey the whole genome expression in 5 lung normal samples and 44 lung squamous-cell carcinoma samples. We evaluated the expression profiles of 15 commonly used reference genes and identified five additional candidate reference genes. To validate the RNA-Seq dataset, we used qRT-PCR to verify the expression levels of these 20 genes in a separate set of 100 pairs of normal lung tissue and lung squamous-cell carcinoma samples, and then analyzed these results using geNorm and NormFinder. With respect to 14 of the 15 common reference genes (B2M, GAPDH, GUSB, HMBS, HPRT1, IPO8, PGK1, POLR2A, PPIA, RPLP0, TBP, TFRC, UBC, and YWHAZ), the expression levels were either too low to be easily detected, or exhibited a high degree of variability either between lung normal and squamous-cell carcinoma samples, or even among samples of the same tissue type. In contrast, 1 of the 15 common reference genes (ACTB) and the 5 additional candidate reference genes (EEF1A1, FAU, RPS9, RPS11, and RPS14) were stably and constitutively expressed at high levels in all the samples tested. ACTB, EEF1A1, FAU, RPS9, RPS11, and RPS14 are ideal reference genes for qRT-PCR analysis of lung squamous-cell carcinoma, while 14 commonly used qRT-PCR reference genes are less appropriate in this context.
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Affiliation(s)
- Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200031, China
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27
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Asthma and depression: the Cooper Center Longitudinal Study. Ann Allergy Asthma Immunol 2014; 112:432-6. [PMID: 24650441 DOI: 10.1016/j.anai.2014.02.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/21/2014] [Accepted: 02/25/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND Prior research suggests a possible association between asthma and depression. OBJECTIVE To examine the association between asthma and depressive symptoms, controlling for asthma medications, lung function, and overall health. METHODS We conducted a cross-sectional study of 12,944 adults who completed physician-based preventive health examinations at the Cooper Clinic from 2000 to 2012. Information on medical histories, including asthma and depression, and medications were collected. Participants reported overall health status, completed spirometry testing, and underwent depression screening using the 10-item Center for Epidemiologic Studies Depression Scale (CES-D). Dependent variables of current depressive symptoms (CES-D scores ≥10) and lifetime history of depression were separately modeled using logistic regression with independent variables, including demographics, spirometry, asthma controller medications, and patient-reported health status. RESULTS The sample was predominantly white and well educated. The prevalence of asthma was 9.0%. Asthma was associated with an odds ratio (OR) of 1.41 (95% CI, 1.16-1.70; P < .001) of current depressive symptoms based on CES-D score. Asthma was also associated with lifetime history of depression (OR, 1.66; 95% CI, 1.40-1.95; P < .001). Neither lung function nor asthma controller medications were significantly associated with depression. CONCLUSION Asthma was associated with increased prevalence of current depressive symptoms and lifetime depression in a large sample of relatively healthy adults. These findings suggest that the increased likelihood of depression among patients with asthma does not appear to be exclusively related to severe or poorly controlled asthma. People with asthma, regardless of severity, may benefit from depression screening in clinical settings.
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28
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D'Souza UM, Powell-Smith G, Haddley K, Powell TR, Bubb VJ, Price T, McGuffin P, Quinn JP, Farmer AE. Allele-specific expression of the serotonin transporter and its transcription factors following lamotrigine treatment in vitro. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:474-83. [PMID: 23765727 DOI: 10.1002/ajmg.b.32178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022]
Abstract
Lamotrigine, a mood stabilizer used clinically in the treatment of bipolar disorder, is thought to exert actions on the serotonin system. However lamotrigine's exact mechanism of action remains unclear. The current study investigated whether lamotrigine might exert its effects through altering the expression of the serotonin transporter (5-HTT) gene and its regulatory transcription factors Y box binding protein 1 (YB-1) and CCCTC-binding factor (CTCF). We further considered whether functional variable number tandem repeat (VNTR) polymorphisms in the promoter region of 5-HTT, (5-HTTLPR) and within intron 2 (Stin2) of the gene, moderated any putative gene expression changes. The study employed an in vitro design carried out in human lymphoblastoid cell lines (LCLs) to investigate the effects of lamotrigine treatment at 0.04, 0.2, and 0.4 mM doses for 24 hr on the mRNA expression of 5-HTT, YB-1, and CTCF. LCLs were selected based on combinations of haplotypes of the two VNTRs in the serotonin transporter gene; creating low-expressing and high-expressing LCL groups. Ubiquitin C (UBC) and topoisomerase I (TOP1) genes were found to be the most stably expressed housekeeping genes in drug-treated LCLs. Subsequently, quantitative PCR revealed that higher doses of lamotrigine significantly lowered 5-HTT expression and increased CTCF expression. Haplotype-specific differences in CTCF expression were found in response to lamotrigine, with strongest expression changes observed in the high-expressing LCLs. These data provide an allele-specific in vitro model for examining the molecular targets of lamotrigine, and support the important role of the serotonin transporter gene in its clinical mechanism of action.
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Affiliation(s)
- Ursula M D'Souza
- MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, Institute of Psychiatry, King's College London, London, United Kingdom
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Willcocks S, Offord V, Seyfert HM, Coffey TJ, Werling D. Species-specific PAMP recognition by TLR2 and evidence for species-restricted interaction with Dectin-1. J Leukoc Biol 2013; 94:449-58. [DOI: 10.1189/jlb.0812390] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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30
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Selection of stable reference genes in heat stressed peripheral blood mononuclear cells of tropically adapted Indian cattle and buffaloes. Mol Cell Probes 2013; 27:140-4. [DOI: 10.1016/j.mcp.2013.02.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 02/26/2013] [Accepted: 02/26/2013] [Indexed: 11/19/2022]
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