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Amini H, Knepp B, Rodriguez F, Jickling GC, Hull H, Carmona-Mora P, Bushnell C, Ander BP, Sharp FR, Stamova B. Early peripheral blood gene expression associated with good and poor 90-day ischemic stroke outcomes. J Neuroinflammation 2023; 20:13. [PMID: 36691064 PMCID: PMC9869610 DOI: 10.1186/s12974-022-02680-y] [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: 11/01/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND This study identified early immune gene responses in peripheral blood associated with 90-day ischemic stroke (IS) outcomes. METHODS Peripheral blood samples from the CLEAR trial IS patients at ≤ 3 h, 5 h, and 24 h after stroke were compared to vascular risk factor matched controls. Whole-transcriptome analyses identified genes and networks associated with 90-day IS outcome assessed using the modified Rankin Scale (mRS) and the NIH Stroke Scale (NIHSS). RESULTS The expression of 467, 526, and 571 genes measured at ≤ 3, 5 and 24 h after IS, respectively, were associated with poor 90-day mRS outcome (mRS ≥ 3), while 49, 100 and 35 genes at ≤ 3, 5 and 24 h after IS were associated with good mRS 90-day outcome (mRS ≤ 2). Poor outcomes were associated with up-regulated genes or pathways such as IL-6, IL-7, IL-1, STAT3, S100A12, acute phase response, P38/MAPK, FGF, TGFA, MMP9, NF-kB, Toll-like receptor, iNOS, and PI3K/AKT. There were 94 probe sets shared for poor outcomes vs. controls at all three time-points that correlated with 90-day mRS; 13 probe sets were shared for good outcomes vs. controls at all three time-points; and 46 probe sets were shared for poor vs. good outcomes at all three time-points that correlated with 90-day mRS. Weighted Gene Co-Expression Network Analysis (WGCNA) revealed modules significantly associated with 90-day outcome for mRS and NIHSS. Poor outcome modules were enriched with up-regulated neutrophil genes and with down-regulated T cell, B cell and monocyte-specific genes; and good outcome modules were associated with erythroblasts and megakaryocytes. Finally, genes identified by genome-wide association studies (GWAS) to contain significant stroke risk loci or loci associated with stroke outcome including ATP2B, GRK5, SH3PXD2A, CENPQ, HOXC4, HDAC9, BNC2, PTPN11, PIK3CG, CDK6, and PDE4DIP were significantly differentially expressed as a function of stroke outcome in the current study. CONCLUSIONS This study suggests the immune response after stroke may impact functional outcomes and that some of the early post-stroke gene expression markers associated with outcome could be useful for predicting outcomes and could be targets for improving outcomes.
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Affiliation(s)
- Hajar Amini
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Bodie Knepp
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Fernando Rodriguez
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Glen C. Jickling
- grid.17089.370000 0001 2190 316XDivision of Neurology, University of Alberta, Edmonton, AB Canada
| | - Heather Hull
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Paulina Carmona-Mora
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Cheryl Bushnell
- grid.241167.70000 0001 2185 3318Wake Forest University School of Medicine, Winston Salem, NC USA
| | - Bradley P. Ander
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Frank R. Sharp
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
| | - Boryana Stamova
- grid.413079.80000 0000 9752 8549Department of Neurology, University of California at Davis, MIND Institute Biosciences Building Room 2417, 2805 50th Street, Sacramento, CA USA
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Lim EA, Bendell JC, Falchook GS, Bauer TM, Drake CG, Choe JH, George DJ, Karlix JL, Ulahannan S, Sachsenmeier KF, Russell DL, Moorthy G, Sidders BS, Pilling EA, Chen H, Hattersley MM, Das M, Kumar R, Pouliot GP, Patel MR. Phase Ia/b, Open-Label, Multicenter Study of AZD4635 (an Adenosine A2A Receptor Antagonist) as Monotherapy or Combined with Durvalumab, in Patients with Solid Tumors. Clin Cancer Res 2022; 28:4871-4884. [PMID: 36044531 PMCID: PMC9660540 DOI: 10.1158/1078-0432.ccr-22-0612] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/28/2022] [Accepted: 08/29/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE To evaluate AZD4635, an adenosine A2A receptor antagonist, as monotherapy or in combination with durvalumab in patients with advanced solid tumors. PATIENTS AND METHODS In phase Ia (dose escalation), patients had relapsed/refractory solid tumors; in phase Ib (dose expansion), patients had checkpoint inhibitor-naïve metastatic castration-resistant prostate cancer (mCRPC) or colorectal carcinoma, non-small cell lung cancer with prior anti-PD-1/PD-L1 exposure, or other solid tumors (checkpoint-naïve or prior anti-PD-1/PD-L1 exposure). Patients received AZD4635 monotherapy (75-200 mg once daily or 125 mg twice daily) or in combination with durvalumab (AZD4635 75 or 100 mg once daily). The primary objective was safety; secondary objectives included antitumor activity and pharmacokinetics; exploratory objectives included evaluation of an adenosine gene signature in patients with mCRPC. RESULTS As of September 8, 2020, 250 patients were treated (AZD4635, n = 161; AZD4635+durvalumab, n = 89). In phase Ia, DLTs were observed with monotherapy (125 mg twice daily; n = 2) and with combination treatment (75 mg; n = 1) in patients receiving nanosuspension. The most common treatment-related adverse events included nausea, fatigue, vomiting, decreased appetite, dizziness, and diarrhea. The RP2D of the AZD4635 capsule formulation was 75 mg once daily, as monotherapy or in combination with durvalumab. The pharmacokinetic profile was dose-proportional, and exposure was adequate to cover target with 100 mg nanosuspension or 75 mg capsule once daily. In patients with mCRPC receiving monotherapy or combination treatment, tumor responses (2/39 and 6/37, respectively) and prostate-specific antigen responses (3/60 and 10/45, respectively) were observed. High versus low blood-based adenosine signature was associated with median progression-free survival of 21 weeks versus 8.7 weeks. CONCLUSIONS AZD4635 monotherapy or combination therapy was well tolerated. Objective responses support additional phase II combination studies in patients with mCRPC.
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Affiliation(s)
- Emerson A. Lim
- Columbia University Herbert Irving Comprehensive Cancer Center, New York, New York.,Corresponding Author: Emerson A. Lim, Department of Medicine, Division of Hematology/Oncology, Columbia University Herbert Irving Comprehensive Cancer Center, 161 Fort Washington Avenue, 9th Floor, New York, NY 10032. Phone: 212-305-5098; Fax: 212-305-6762; E-mail:
| | - Johanna C. Bendell
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | - Gerald S. Falchook
- Drug Development Unit, Sarah Cannon Research Institute at HealthONE, Denver, Colorado
| | - Todd M. Bauer
- Sarah Cannon Research Institute/Tennessee Oncology, Nashville, Tennessee
| | - Charles G. Drake
- Columbia University Herbert Irving Comprehensive Cancer Center, New York, New York
| | | | | | | | - Susanna Ulahannan
- Sarah Cannon Research Institute/Oklahoma University, Oklahoma City, Oklahoma
| | | | | | - Ganesh Moorthy
- Clinical Pharmacology & Quantitative Pharmacology, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Boston, Massachusetts
| | - Ben S. Sidders
- Oncology Biometrics R&D, AstraZeneca, Cambridge, England, United Kingdom
| | | | - Huifang Chen
- Oncology R&D, AstraZeneca, Boston, Massachusetts
| | | | - Mayukh Das
- Oncology R&D, AstraZeneca, Gaithersburg, Maryland
| | - Rakesh Kumar
- Oncology R&D, AstraZeneca, Gaithersburg, Maryland
| | | | - Manish R. Patel
- Sarah Cannon Research Institute/Florida Cancer Specialists, Sarasota, Florida
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3
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Li H, Fu Q, Philips K, Sun Y, Faurot KR, Gaylord SA, Mann JD. Leukocyte inflammatory phenotype and function in migraine patients compared with matched non-migraine volunteers: a pilot study. BMC Neurol 2022; 22:278. [PMID: 35896985 PMCID: PMC9327171 DOI: 10.1186/s12883-022-02781-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/30/2022] [Indexed: 11/12/2022] Open
Abstract
Background Migraine is a neurological condition characterized by chronic inflammation. However, not much is known about the potential role of peripheral blood immune cells in the pathophysiology of migraine. Methods We investigated the status of peripheral blood immune cells of 15 adults with frequent episodic or chronic migraine recruited chronologically from a randomized clinical trial (RCT) on Nutrition for Migraine (NCCIH 5R01AT007813-05) and 15 non-migraine, healthy volunteers (control) matched by age, gender, and Body Mass Index (BMI). Continuous variables were presented as means ± standard deviationas well as medians, and comparisons between patients and healthy volunteers were performed with non-parametric Wilcoxon signed rank tests. Statistical analysis was performed using Stata (StataCorp. 2019. Stata Statistical Software). Fluorescence-Activated Cell Sorting (FACS) data were processed using FlowJo software (Ashland, OR: Becton, Dickenson and Company; 2019). Results We observed that migraineurs had a significantly lower percentage of non-classical monocytes (CD14+CD16++) in blood circulation, compared to the control group. In addition, Migraineurs also showed a significantly lower percentage of blood CD3+CD4+ helper T cells and CD4+CD25+ regulatory T cells, compared to controls. Differences in leukocyte surface markers between chronic migraine patients and their matched controls were more prominent than those between episodic migraine patients and their matched controls. Conclusions Our results suggest that migraine is associated with dysregulated peripheral immune homeostasis and that inflammation and autoimmunity may play a role in its pathophysiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12883-022-02781-4.
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Affiliation(s)
- Hongtao Li
- Department of Science and Mathematics, Hulman Hall Room116, Saint Mary-of-the-Woods College, 1 St Mary of Woods Coll, IN, 47876, USA. .,Department of Physical Medicine and Rehabilitation Program On Integrative Medicine, University of North Carolina, Chapel Hill, NC, USA.
| | - Qiang Fu
- School of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai, 264003, People's Republic of China
| | - Kamaira Philips
- Division of Comprehensive Oral Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - Yufei Sun
- School of Pharmacology, Institute of Aging Medicine, Binzhou Medical University, Yantai, 264003, People's Republic of China
| | - Keturah R Faurot
- Department of Physical Medicine and Rehabilitation Program On Integrative Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Susan A Gaylord
- Department of Physical Medicine and Rehabilitation Program On Integrative Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - John Douglas Mann
- Department of Physical Medicine and Rehabilitation Program On Integrative Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Neurology, University of North Carolina, Chapel Hill, NC, USA
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Khandare P, Saluja A, Solanki RS, Singh R, Vani K, Garg D, Dhamija RK. Serum S100B and NSE Levels Correlate With Infarct Size and Bladder-Bowel Involvement Among Acute Ischemic Stroke Patients. J Neurosci Rural Pract 2022; 13:218-225. [PMID: 35694066 PMCID: PMC9187393 DOI: 10.1055/s-0042-1743214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abstract
Objectives Stroke is a major global health concern. Due to limited availability of neuroimaging particularly in rural and regional areas in India as well as its limitation, the interest in use of biochemical markers for stroke diagnosis, severity, and prognosis is increasing. Only a handful of studies on stroke biomarkers have been conducted in India. Hence, this study was conducted to investigate the correlation of serum neuron-specific enolase (NSE) and S100 calcium-binding protein B (S100B) levels with stroke severity according to infarct size in acute ischemic stroke patients.
Material and Methods Sixty stroke patients were recruited for the study and were evaluated. Noncontrast computed tomography (CT) scan of the brain was performed for all patients within 48 hours of onset of symptoms. Infarct volume was measured by evaluating dimensions in three planes on CT head. Serum NSE and S100B levels were measured by commercially available immunoassay kits. Continuous data was represented as mean ± standard deviation. Categorical data was expressed in terms of percentages and proportions. Pearson's correlation coefficient was applied to assess correlation between NSE and S100B and infarct size. Infarct size was classified arbitrarily into three groups according to infarct volume (low, moderate, and large) and analysis of variance was applied for comparing mean S100B and NSE levels in the three groups. To assess the independent predictors of infarct size among stroke cases, multivariate logistic regression analysis was used. Association between serum S100B or NSE levels and clinical features was done by the Mann–Whitney U test.
Results Correlation between serum S100B protein levels and NSE with larger infarct volume was highly significant (r(S100B) = 0.611, p (S100B) < 0.0001; r(NSE) = 0.258, p(NSE) = 0.047). Using multivariate regression analysis, bladder and bowel involvement, prior stroke history, and dyslipidemia among stroke patients correlated with a larger infarct size. Mann–Whitney U test showed both NSE and S100B levels were significantly associated with bladder bowel involvement among stroke cases.
Conclusion There was a positive correlation between serum S100B and NSE levels with infarct size. In addition, bladder-bowel involvement among stroke patients was associated with increased S100B levels. Therefore, levels of protein S100B and NSE may serve as indicator of infarct size and may be predictors of severe clinical presentations of acute ischemic stroke.
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Affiliation(s)
- Pravin Khandare
- Department of Medicine, Lady Hardinge Medical College, New Delhi, India
| | - Alvee Saluja
- Department of Neurology, Lady Hardinge Medical College, New Delhi, India
| | - Ravi S. Solanki
- Department of Radiodiagnosis, Lady Hardinge Medical College, New Delhi, India
| | - Ritu Singh
- Department of Biochemistry, Lady Hardinge Medical College, New Delhi, India
| | - Kavita Vani
- Department of Radiodiagnosis, Atal Bihari Vajpayee Institute of Medical Sciences (ABVIMS) and Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Divyani Garg
- Department of Neurology, Lady Hardinge Medical College, New Delhi, India
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Garcia-Bonilla L, Iadecola C, Anrather J. Inflammation and Immune Response. Stroke 2022. [DOI: 10.1016/b978-0-323-69424-7.00010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Nagel S, Meyer C. Establishment of the TBX-code reveals aberrantly activated T-box gene TBX3 in Hodgkin lymphoma. PLoS One 2021; 16:e0259674. [PMID: 34807923 PMCID: PMC8608327 DOI: 10.1371/journal.pone.0259674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/22/2021] [Indexed: 11/23/2022] Open
Abstract
T-box genes encode transcription factors which control basic processes in development of several tissues including cell differentiation in the hematopoietic system. Here, we analyzed the physiological activities of all 17 human T-box genes in early hematopoiesis and in lymphopoiesis including developing and mature B-cells, T-cells, natural killer (NK)-cells and innate lymphoid cells. The resultant expression pattern comprised six genes, namely EOMES, MGA, TBX1, TBX10, TBX19 and TBX21. We termed this gene signature TBX-code which enables discrimination of normal and aberrant activities of T-box genes in lymphoid malignancies. Accordingly, expression analysis of T-box genes in Hodgkin lymphoma (HL) patients using a public profiling dataset revealed overexpression of EOMES, TBX1, TBX2, TBX3, TBX10, TBX19, TBX21 and TBXT while MGA showed aberrant downregulation. Analysis of T-cell acute lymphoid leukemia patients indicated aberrant overexpression of six T-box genes while no deregulated T-box genes were detected in anaplastic large cell lymphoma patients. As a paradigm we focused on TBX3 which was ectopically activated in about 6% of HL patients analyzed. Normally, TBX3 is expressed in tissues like lung, adrenal gland and retina but not in hematopoiesis. HL cell line KM-H2 expressed enhanced TBX3 levels and was used as an in vitro model to identify upstream regulators and downstream targets in this malignancy. Genomic studies of this cell line showed focal amplification of the TBX3 locus at 12q24 which may underlie its aberrant expression. In addition, promoter analysis and comparative expression profiling of HL cell lines followed by knockdown experiments revealed overexpressed transcription factors E2F4 and FOXC1 and chromatin modulator KDM2B as functional activators. Furthermore, we identified repressed target genes of TBX3 in HL including CDKN2A, NFKBIB and CD19, indicating its respective oncogenic function in proliferation, NFkB-signaling and B-cell differentiation. Taken together, we have revealed a lymphoid TBX-code and used it to identify an aberrant network around deregulated T-box gene TBX3 in HL which promotes hallmark aberrations of this disease. These findings provide a framework for future studies to evaluate deregulated T-box genes in lymphoid malignancies.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- * E-mail:
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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CD163 as a Potential Biomarker of Monocyte Activation in Ischemic Stroke Patients. Int J Mol Sci 2021; 22:ijms22136712. [PMID: 34201498 PMCID: PMC8268853 DOI: 10.3390/ijms22136712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 01/14/2023] Open
Abstract
In ischemic stroke patients, a higher monocyte count is associated with disease severity and worse prognosis. The complex correlation between subset phenotypes and functions underscores the importance of clarifying the role of monocyte subpopulations. We examined the subtype-specific distribution of the CD163+ and CD80+ circulating monocytes and evaluated their association with the inflammatory status in 26 ischemic stroke patients and 16 healthy controls. An increased percentage of CD163+/CD16+ and CD163+/CD14++ events occurred 24 and 48 h after a stroke compared to the controls. CD163+ expression was more pronounced in CD16+ non-classical and intermediate monocytes, as compared to CD14+ classical subtype, 24 h after stroke. Conversely, the percentage of CD80+/CD16+ events was unaffected in patients; meanwhile, the percentage of CD80+/CD14+ events significantly increased only 24 h after stroke. Interleukin (IL)-1beta, TNF-alpha, and IL-4 mRNA levels were higher, while IL-10 mRNA levels were reduced in total monocytes from patients versus controls, at either 24 h or 48 h after stroke. The percentage of CD163+/CD16+ events 24 h after stroke was positively associated with NIHSS score and mRS at admission, suggesting that stroke severity and disability are relevant triggers for CD163+ expression in circulating CD16+ monocytes.
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8
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Cerig S, Geyikoglu F. Oxidative stress and cyto-genotoxicity induced by poly-d-glucosamine in human blood cells in vitro. ACTA ACUST UNITED AC 2021; 77:43-55. [PMID: 34036758 DOI: 10.1515/znc-2021-0080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/02/2021] [Indexed: 11/15/2022]
Abstract
Poly-N-acetyl-d-glucosamine (CH; chitin) is the main component of the insect skeleton, fungal cell wall, and many crustaceans, including crab and shrimp. CH is the most abundant in nature after cellulose, and it has a complex and hardly soluble structure. Poly-d-glucosamine (CHO; chitosan) is a soluble derivative of CH produced by deacetylation used in many fields, including human health. This study carried out the cytotoxic, genotoxic, and oxidative effects of CHO on human whole blood (hWB) and lymphocytes (LYMs) in dose ranges 6.25-2000 μg/mL, in vitro. Total antioxidant capacity (TAC) and total oxidant status (TOS) analyzes were performed on plasma to appreciate oxidative stress. 3-(4,5-Dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) assays were applied to understand the cytotoxicity. Chromosomal aberration (CA) and micronucleus (MN) methods were practiced to evaluate genotoxicity. 6.25-150 μg/mL doses increased TAC and decreased TOS. A decreasing and increasing curve from 200 to 2000 μg/mL on TAC and TOS values were determined, respectively. 0-250 μg/mL doses did not provide any cytotoxic data. However, 500-2000 μg/mL doses showed increasing cytotoxicity and genotoxicity. The study results showed that CHO does not pose a toxic risk to human health at low doses but may pose a threat at high doses.
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Affiliation(s)
- Salim Cerig
- First and Emergency Aid Program, Medical Services and Techniques Department, Vocational School of Health Services, Ibrahim Cecen University, Agri, Turkey
| | - Fatime Geyikoglu
- Department of Biology, Faculty of Science, Ataturk University, Erzurum, Turkey
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Nagel S, Pommerenke C, Meyer C, MacLeod RAF, Drexler HG. Establishment of the TALE-code reveals aberrantly activated homeobox gene PBX1 in Hodgkin lymphoma. PLoS One 2021; 16:e0246603. [PMID: 33539429 PMCID: PMC7861379 DOI: 10.1371/journal.pone.0246603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/21/2021] [Indexed: 12/26/2022] Open
Abstract
Homeobox genes encode transcription factors which regulate basic processes in development and cell differentiation and are grouped into classes and subclasses according to sequence similarities. Here, we analyzed the activities of the 20 members strong TALE homeobox gene class in early hematopoiesis and in lymphopoiesis including developing and mature B-cells, T-cells, natural killer (NK)-cells and innate lymphoid cells (ILC). The resultant expression pattern comprised eleven genes and which we termed TALE-code enables discrimination of normal and aberrant activities of TALE homeobox genes in lymphoid malignancies. Subsequent expression analysis of TALE homeobox genes in public datasets of Hodgkin lymphoma (HL) patients revealed overexpression of IRX3, IRX4, MEIS1, MEIS3, PBX1, PBX4 and TGIF1. As paradigm we focused on PBX1 which was deregulated in about 17% HL patients. Normal PBX1 expression was restricted to hematopoietic stem cells and progenitors of T-cells and ILCs but absent in B-cells, reflecting its roles in stemness and early differentiation. HL cell line SUP-HD1 expressed enhanced PBX1 levels and served as an in vitro model to identify upstream regulators and downstream targets in this malignancy. Genomic studies of this cell line therein showed a gain of the PBX1 locus at 1q23 which may underlie its aberrant expression. Comparative expression profiling analyses of HL patients and cell lines followed by knockdown experiments revealed NFIB and TLX2 as target genes activated by PBX1. HOX proteins operate as cofactors of PBX1. Accordingly, our data showed that HOXB9 overexpressed in HL coactivated TLX2 but not NFIB while activating TNFRSF9 without PBX1. Further downstream analyses showed that TLX2 activated TBX15 which operated anti-apoptotically. Taken together, we discovered a lymphoid TALE-code and identified an aberrant network around deregulated TALE homeobox gene PBX1 which may disturb B-cell differentiation in HL by reactivation of progenitor-specific genes. These findings may provide the framework for future studies to exploit possible vulnerabilities of malignant cells in therapeutic scenarios.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A. F. MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans G. Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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10
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Subhi O, Schulten HJ, Bagatian N, Al-Dayini R, Karim S, Bakhashab S, Alotibi R, Al-Ahmadi A, Ata M, Elaimi A, Al-Muhayawi S, Mansouri M, Al-Ghamdi K, Hamour OA, Jamal A, Al-Maghrabi J, Al-Qahtani MH. Genetic relationship between Hashimoto`s thyroiditis and papillary thyroid carcinoma with coexisting Hashimoto`s thyroiditis. PLoS One 2020; 15:e0234566. [PMID: 32603365 PMCID: PMC7326236 DOI: 10.1371/journal.pone.0234566] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/28/2020] [Indexed: 12/30/2022] Open
Abstract
Hashimoto's thyroiditis (HT) is present in the background of around 30% of papillary thyroid carcinomas (PTCs). The genetic predisposition effect of this autoimmune condition is not thoroughly understood. We analyzed the microarray expression profiles of 13 HT, eight PTCs with (w/) coexisting HT, six PTCs without (w/o) coexisting HT, six micro PTCs (mPTCs), and three normal thyroid (TN) samples. Based on a false discovery rate (FDR)-adjusted p-value ≤ 0.05 and a fold change (FC) > 2, four comparison groups were defined, which were HT vs. TN; PTC w/ HT vs. TN; PTC w/o HT vs. TN; and mPTC vs. TN. A Venn diagram displayed 15 different intersecting and non-intersecting differentially expressed gene (DEG) sets, of which a set of 71 DEGs, shared between the two comparison groups HT vs. TN ∩ PTC w/ HT vs. TN, harbored the relatively largest number of genes related to immune and inflammatory functions; oxidative stress and reactive oxygen species (ROS); DNA damage and DNA repair; cell cycle; and apoptosis. The majority of the 71 DEGs were upregulated and the most upregulated DEGs included a number of immunoglobulin kappa variable genes, and other immune-related genes, e.g., CD86 molecule (CD86), interleukin 2 receptor gamma (IL2RG), and interferon, alpha-inducible protein 6 (IFI6). Upregulated genes preferentially associated with other gene ontologies (GO) were, e.g., STAT1, MMP9, TOP2A, and BRCA2. Biofunctional analysis revealed pathways related to immunogenic functions. Further data analysis focused on the set of non-intersecting 358 DEGs derived from the comparison group of HT vs. TN, and on the set of 950 DEGs from the intersection of all four comparison groups. In conclusion, this study indicates that, besides immune/inflammation-related genes, also genes associated with oxidative stress, ROS, DNA damage, DNA repair, cell cycle, and apoptosis are comparably more deregulated in a data set shared between HT and PTC w/ HT. These findings are compatible with the conception of a genetic sequence where chronic inflammatory response is accompanied by deregulation of genes and biofunctions associated with oncogenic transformation. The generated data set may serve as a source for identifying candidate genes and biomarkers that are practical for clinical application.
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Affiliation(s)
- Ohoud Subhi
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hans-Juergen Schulten
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
| | - Nadia Bagatian
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Roa'a Al-Dayini
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sajjad Karim
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherin Bakhashab
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Innovation in Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Reem Alotibi
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Alaa Al-Ahmadi
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Manar Ata
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Aisha Elaimi
- Center of Innovation in Personalized Medicine, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Saad Al-Muhayawi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Majid Mansouri
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Khalid Al-Ghamdi
- Department of Otolaryngology, Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Osman Abdel Hamour
- Department of Surgery, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Awatif Jamal
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jaudah Al-Maghrabi
- Department of Pathology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Pathology, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Mohammed Hussain Al-Qahtani
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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11
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Iadecola C, Buckwalter MS, Anrather J. Immune responses to stroke: mechanisms, modulation, and therapeutic potential. J Clin Invest 2020; 130:2777-2788. [PMID: 32391806 PMCID: PMC7260029 DOI: 10.1172/jci135530] [Citation(s) in RCA: 329] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Stroke is the second leading cause of death worldwide and a leading cause of disability. Most strokes are caused by occlusion of a major cerebral artery, and substantial advances have been made in elucidating how ischemia damages the brain. In particular, increasing evidence points to a double-edged role of the immune system in stroke pathophysiology. In the acute phase, innate immune cells invade brain and meninges and contribute to ischemic damage, but may also be protective. At the same time, danger signals released into the circulation by damaged brain cells lead to activation of systemic immunity, followed by profound immunodepression that promotes life-threatening infections. In the chronic phase, antigen presentation initiates an adaptive immune response targeted to the brain, which may underlie neuropsychiatric sequelae, a considerable cause of poststroke morbidity. Here, we briefly review these pathogenic processes and assess the potential therapeutic value of targeting immunity in human stroke.
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Affiliation(s)
- Costantino Iadecola
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
| | - Marion S. Buckwalter
- Department of Neurology and Neurological Sciences, Stanford University Medical Center, Stanford, California, USA
| | - Josef Anrather
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York, USA
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12
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Ludhiadch A, Vasudeva K, Munshi A. Establishing molecular signatures of stroke focusing on omic approaches: a narrative review. Int J Neurosci 2020; 130:1250-1266. [PMID: 32075476 DOI: 10.1080/00207454.2020.1732964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Stroke or 'brain attack' is considered to be the major cause of mortality and morbidity worldwide after myocardial infraction. Inspite of the years of research and clinical practice, the pathogenesis of stroke still remains incompletely understood. Omics approaches not only enable the description of a huge number of molecular platforms but also have a potential to recognize new factors associated with various complex disorders including stroke. The most significant development among all other omics technologies over the recent years has been seen by genomics which is a powerful tool for exploring the genetic architecture of stroke. Genomics has decisively established itself in stroke research and by now wealth of data has been generated providing new insights into the physiology and pathophysiology of stroke. However, the efficacy of genomic data is restricted to risk prediction only. Omics approaches not only enable the description of a huge number of molecular platforms but also have a potential to recognize new factors associated with various complex disorders including stroke. The data generated by omics technologies enables clinicians to provide detailed insight into the makeup of stroke in individual patients, which will further help in developing diagnostic procedures to direct therapies. Present review has been compiled with an aim to understand the potential of integrated omics approach to help in characterization of mechanisms leading to stroke, to predict the patient risk of getting stroke by analyzing signature biomarkers and to develop targeted therapeutic strategies.
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Affiliation(s)
- Abhilash Ludhiadch
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab
| | - Kanika Vasudeva
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab
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13
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Ulusoy EK. Correlations between the monocyte to high-density lipoprotein cholesterol ratio and white matter hyperintensities in migraine. Neurol Res 2020; 42:126-132. [DOI: 10.1080/01616412.2019.1710406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ersin Kasım Ulusoy
- Neurology Department, Kayseri Training and Research Hospital, Kayseri, Turkey
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14
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Schrag A, Martino D, Apter A, Ball J, Bartolini E, Benaroya-Milshtein N, Buttiglione M, Cardona F, Creti R, Efstratiou A, Gariup M, Georgitsi M, Hedderly T, Heyman I, Margarit I, Mir P, Moll N, Morer A, Müller N, Müller-Vahl K, Münchau A, Orefici G, Plessen KJ, Porcelli C, Paschou P, Rizzo R, Roessner V, Schwarz MJ, Steinberg T, Tagwerker Gloor F, Tarnok Z, Walitza S, Dietrich A, Hoekstra PJ. European Multicentre Tics in Children Studies (EMTICS): protocol for two cohort studies to assess risk factors for tic onset and exacerbation in children and adolescents. Eur Child Adolesc Psychiatry 2019; 28:91-109. [PMID: 29982875 PMCID: PMC6349795 DOI: 10.1007/s00787-018-1190-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/28/2018] [Indexed: 12/22/2022]
Abstract
Genetic predisposition, autoimmunity and environmental factors [e.g. pre- and perinatal difficulties, Group A Streptococcal (GAS) and other infections, stress-inducing events] might interact to create a neurobiological vulnerability to the development of tics and associated behaviours. However, the existing evidence for this relies primarily on small prospective or larger retrospective population-based studies, and is therefore still inconclusive. This article describes the design and methodology of the EMTICS study, a longitudinal observational European multicentre study involving 16 clinical centres, with the following objectives: (1) to investigate the association of environmental factors (GAS exposure and psychosocial stress, primarily) with the onset and course of tics and/or obsessive-compulsive symptoms through the prospective observation of at-risk individuals (ONSET cohort: 260 children aged 3-10 years who are tic-free at study entry and have a first-degree relative with a chronic tic disorder) and affected individuals (COURSE cohort: 715 youth aged 3-16 years with a tic disorder); (2) to characterise the immune response to microbial antigens and the host's immune response regulation in association with onset and exacerbations of tics; (3) to increase knowledge of the human gene pathways influencing the pathogenesis of tic disorders; and (4) to develop prediction models for the risk of onset and exacerbations of tic disorders. The EMTICS study is, to our knowledge, the largest prospective cohort assessment of the contribution of different genetic and environmental factors to the risk of developing tics in putatively predisposed individuals and to the risk of exacerbating tics in young individuals with chronic tic disorders.
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Affiliation(s)
- Anette Schrag
- 0000000121901201grid.83440.3bDepartment of Clinical Neurosciences, UCL Institute of Neurology, University College London, London, UK
| | - Davide Martino
- 0000 0004 1936 7697grid.22072.35Department of Clinical Neurosciences, University of Calgary, Calgary, Canada
| | - Alan Apter
- 0000 0004 1937 0546grid.12136.37Child and Adolescent Psychiatry Department, Schneider Children’s Medical Center of Israel, Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Petah-Tikva, Israel
| | - Juliane Ball
- 0000 0004 1937 0650grid.7400.3Clinic of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | | | - Noa Benaroya-Milshtein
- 0000 0004 1937 0546grid.12136.37Child and Adolescent Psychiatry Department, Schneider Children’s Medical Center of Israel, Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Petah-Tikva, Israel
| | - Maura Buttiglione
- 0000 0001 0120 3326grid.7644.1Department of Biological Sciences and Human Oncology, Medical School, University of Bari “Aldo Moro”, Bari, Italy
| | - Francesco Cardona
- grid.7841.aDepartment of Human Neurosciences, University La Sapienza of Rome, Rome, Italy
| | - Roberta Creti
- 0000 0000 9120 6856grid.416651.1Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Androulla Efstratiou
- 0000 0004 5909 016Xgrid.271308.fWHO Global Collaborating Centre for Reference and Research on Diphtheria and Streptococcal Infections, Reference Microbiology, Directorate National Infection Service, Public Health England, London, UK
| | - Maria Gariup
- 0000 0004 1937 0247grid.5841.8University of Barcelona, Barcelona, Spain ,Intensive Inpatient Unit, Copenhagen Psychiatric Center, Copenhagen, Denmark
| | - Marianthi Georgitsi
- 0000 0001 2170 8022grid.12284.3dDepartment of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece ,0000000109457005grid.4793.9Department of Medicine, Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Tammy Hedderly
- 0000 0004 5345 7223grid.483570.dEvelina London Children’s Hospital GSTT, Kings Health Partners AHSC, London, UK
| | - Isobel Heyman
- 0000000121901201grid.83440.3bGreat Ormond Street Hospital for Children, UCL Institute of Child Health, London, UK
| | | | - Pablo Mir
- Unidad de Trastornos del Movimiento, Servicio de Neurología y Neurofisiología Clinica, Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocio/CSIC/Universidad de Sevilla, Seville, Spain
| | - Natalie Moll
- 0000 0004 1936 973Xgrid.5252.0Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Astrid Morer
- 0000 0000 9635 9413grid.410458.cDepartment of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic Universitari, Barcelona, Spain ,grid.10403.36Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain ,0000 0000 9314 1427grid.413448.eCentro de Investigacion en Red de Salud Mental (CIBERSAM), Instituto Carlos III, Madrid, Spain
| | - Norbert Müller
- 0000 0004 1936 973Xgrid.5252.0Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany ,Marion von Tessin Memory-Zentrum gGmbH, Munich, Germany
| | - Kirsten Müller-Vahl
- 0000 0000 9529 9877grid.10423.34Clinic of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Alexander Münchau
- 0000 0001 0057 2672grid.4562.5Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Graziella Orefici
- 0000 0000 9120 6856grid.416651.1Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Kerstin J. Plessen
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark and University of Copenhagen, Copenhagen, Denmark ,0000 0001 2165 4204grid.9851.5Service of Child and Adolescent Psychiatry, Department of Psychiatry, University Medical Center, University of Lausanne, Lausanne, Switzerland
| | - Cesare Porcelli
- Azienda Sanitaria Locale di Bari, Mental Health Department, Child and Adolescent Neuropsychiatry Service of Bari Metropolitan Area, Bari, Italy
| | - Peristera Paschou
- 0000 0004 1937 2197grid.169077.eDepartment of Biological Sciences, Purdue University, West Lafayette, USA
| | - Renata Rizzo
- 0000 0004 1757 1969grid.8158.4Child Neuropsychiatry Section, Department of Clinical and Experimental Medicine, School of Medicine, Catania University, Catania, Italy
| | - Veit Roessner
- 0000 0001 2111 7257grid.4488.0Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Markus J. Schwarz
- 0000 0004 1936 973Xgrid.5252.0Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Tamar Steinberg
- 0000 0004 1937 0546grid.12136.37Child and Adolescent Psychiatry Department, Schneider Children’s Medical Center of Israel, Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Petah-Tikva, Israel
| | - Friederike Tagwerker Gloor
- 0000 0004 1937 0650grid.7400.3Clinic of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Susanne Walitza
- 0000 0004 1937 0650grid.7400.3Clinic of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | - Andrea Dietrich
- 0000 0004 0407 1981grid.4830.fDepartment of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Pieter J. Hoekstra
- 0000 0004 0407 1981grid.4830.fDepartment of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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15
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Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Z. Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. Front Mol Neurosci 2018; 11:219. [PMID: 29997476 PMCID: PMC6028693 DOI: 10.3389/fnmol.2018.00219] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/06/2018] [Indexed: 12/23/2022] Open
Abstract
Orofacial pain and headache disorders are among the most debilitating pain conditions. While the pathophysiological basis of these disorders may be diverse, it is generally accepted that a common mechanism behind the arising pain is the sensitization of extra- and intracranial trigeminal primary afferents. In the present study we investigated gene expression changes in the trigeminal ganglia (TRG), trigeminal nucleus caudalis (TNC) and peripheral blood mononuclear cells (PBMC) evoked by Complete Freund's Adjuvant (CFA)-induced orofacial inflammation in rats, as a model of trigeminal sensitization. Microarray analysis revealed 512 differentially expressed genes between the ipsi- and contralateral TRG samples 7 days after CFA injection. Time-dependent expression changes of G-protein coupled receptor 39 (Gpr39), kisspeptin-1 receptor (Kiss1r), kisspeptin (Kiss1), as well as synaptic plasticity-associated Lkaaear1 (Lkr) and Neurod2 mRNA were described on the basis of qPCR results. The greatest alterations were observed on day 3 ipsilaterally, when orofacial mechanical allodynia reached its maximum. This corresponded well with patterns of neuronal (Fosb), microglia (Iba1), and astrocyte (Gfap) activation markers in both TRG and TNC, and interestingly also in PBMCs. This is the first description of up- and downregulated genes both in primary and secondary sensory neurones of the trigeminovascular system that might play important roles in neuroinflammatory activation mechanisms. We are the first to show transcriptomic alterations in the PBMCs that are similar to the neuronal changes. These results open new perspectives and initiate further investigations in the research of trigeminal pain disorders.
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Affiliation(s)
- Timea Aczél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | - József Kun
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
| | - Éva Szőke
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
| | - Tibor Rauch
- Section of Molecular Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Sini Junttila
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Attila Gyenesei
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- Bioinformatics and Scientific Computing, Vienna Biocenter Core Facilities, Vienna, Austria
| | - Kata Bölcskei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre and Centre for Neuroscience, University of Pécs, Pécs, Hungary
- MTA-PTE Chronic Pain Research Group, Pécs, Hungary
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16
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A natural killer-dendritic cell axis defines checkpoint therapy-responsive tumor microenvironments. Nat Med 2018; 24:1178-1191. [PMID: 29942093 DOI: 10.1038/s41591-018-0085-8] [Citation(s) in RCA: 650] [Impact Index Per Article: 108.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022]
Abstract
Intratumoral stimulatory dendritic cells (SDCs) play an important role in stimulating cytotoxic T cells and driving immune responses against cancer. Understanding the mechanisms that regulate their abundance in the tumor microenvironment (TME) could unveil new therapeutic opportunities. We find that in human melanoma, SDC abundance is associated with intratumoral expression of the gene encoding the cytokine FLT3LG. FLT3LG is predominantly produced by lymphocytes, notably natural killer (NK) cells in mouse and human tumors. NK cells stably form conjugates with SDCs in the mouse TME, and genetic and cellular ablation of NK cells in mice demonstrates their importance in positively regulating SDC abundance in tumor through production of FLT3L. Although anti-PD-1 'checkpoint' immunotherapy for cancer largely targets T cells, we find that NK cell frequency correlates with protective SDCs in human cancers, with patient responsiveness to anti-PD-1 immunotherapy, and with increased overall survival. Our studies reveal that innate immune SDCs and NK cells cluster together as an excellent prognostic tool for T cell-directed immunotherapy and that these innate cells are necessary for enhanced T cell tumor responses, suggesting this axis as a target for new therapies.
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17
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Kuo CHS, Liu CY, Pavlidis S, Lo YL, Wang YW, Chen CH, Ko HW, Chung FT, Lin TY, Wang TY, Lee KY, Guo YK, Wang TH, Yang CT. Unique Immune Gene Expression Patterns in Bronchoalveolar Lavage and Tumor Adjacent Non-Neoplastic Lung Tissue in Non-Small Cell Lung Cancer. Front Immunol 2018; 9:232. [PMID: 29483918 PMCID: PMC5816075 DOI: 10.3389/fimmu.2018.00232] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022] Open
Abstract
Background The immune cells in the local environments surrounding non-small cell lung cancer (NSCLC) implicate the balance of pro- and antitumor immunity; however, their transcriptomic profiles remain poorly understood. Methods A transcriptomic microarray study of bronchoalveolar lavage (BAL) cells harvested from tumor-bearing lung segments was performed in a discovery group. The findings were validated (1) in published microarray datasets, (2) in an independent group by RT-qPCR, and (3) in non-diseased and tumor adjacent non-neoplastic lung tissue by immunohistochemistry and in BAL cell lysates by immunoblotting. Result The differential expression of 129 genes was identified in the discovery group. These genes revealed functional enrichment in Fc gamma receptor-dependent phagocytosis and circulating immunoglobulin complex among others. Microarray datasets analysis (n = 607) showed that gene expression of BAL cells of tumor-bearing lung segment was also the unique transcriptomic profile of tumor adjacent non-neoplastic lung of early stage NSCLC and a significantly gradient increase of immunoglobulin genes’ expression for non-diseased lungs, tumor adjacent non-neoplastic lungs, and tumors was identified (ANOVA, p < 2 × 10−16). A 53-gene signature was determined with significant correlation with inhibitory checkpoint PDCD1 (r = 0.59, p = 0.0078) among others, where the nine top genes including IGJ and IGKC were RT-qPCR validated with high diagnostic performance (AUC: 0.920, 95% CI: 0.831–0.985, p = 2.98 × 10−7). Increased staining and expression of IGKC revealed by immunohistochemistry and immunoblotting in tumor adjacent non-neoplastic lung tissues (Wilcoxon signed-rank test, p < 0.001) and in BAL cell lysates (p < 0.01) of NSCLC, respectively, were noted. Conclusion The BAL cells of tumor-bearing lung segments and tumor adjacent non-neoplastic lung tissues present a unique gene expression characterized by IGKC in relation to inhibitory checkpoints. Further study of humoral immune responses to NSCLC is warranted.
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Affiliation(s)
- Chih-Hsi Scott Kuo
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan.,Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Chien-Ying Liu
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Stelios Pavlidis
- Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Yu-Lun Lo
- Division of Airway Diseases, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Yen-Wen Wang
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Chih-Hung Chen
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - How-Wen Ko
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Fu-Tsai Chung
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Tin-Yu Lin
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Tsai-Yu Wang
- Division of Airway Diseases, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Kang-Yun Lee
- Division of Thoracic Medicine, Taipei Medical University Shuang Ho Hospital, New Taipei City, Taiwan
| | - Yi-Ke Guo
- Department of Computing, Imperial College London, Data Science Institute, London, United Kingdom
| | - Tzu-Hao Wang
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Cheng-Ta Yang
- Division of Lung Cancer and Interventional Bronchoscopy, Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taipei, Taiwan
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18
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RSK2 phosphorylates T-bet to attenuate colon cancer metastasis and growth. Proc Natl Acad Sci U S A 2017; 114:12791-12796. [PMID: 29133416 DOI: 10.1073/pnas.1710756114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metastasis is a major cause of cancer-related deaths. Approximately 80% of patients with colorectal cancer develop liver metastasis and 20% develop lung metastasis. We found that at different stages of colon cancer, IFNγ secretion from peripheral blood mononuclear cells was decreased compared with healthy controls. The ribosomal S6 kinase (RSK) family of kinases has multiple cellular functions, and we examined their roles in this observed IFNγ decrease. Flow cytometry analysis of wild-type (WT) and RSK2 knockout (KO) mice revealed significantly lower levels of IFNγ in the RSK2 KO mice compared with the WT mice. Since IFNγ is a component of immunity, which contributes to protection against metastatic carcinomas, we conducted a colon cancer liver metastasis experiment. We found significantly greater metastasis in RSK2 KO mice compared with WT mice. Transcription factor T-bet can directly activate Ifnγ gene transcription. In vitro kinase assay results showed that RSK2 phosphorylated T-bet at serines 498 and 502. We show that phosphorylation of T-bet by RSK2 is required for IFNγ expression, because knockdown of RSK2 expression or overexpression of mutant T-bet reduces IFNγ mRNA expression. To verify the function of the phosphorylation sites, we overexpressed a constitutively active mutant T-bet (S498E/S502E) in bone marrow. Mutant T-bet restored the IFNγ mRNA levels and dramatically reduced the metastasis rate in these mice. Overall, these results indicate that phosphorylation of T-bet is required for the inhibition of colon cancer metastasis and growth through a positive regulation of RSK2/T-bet/IFNγ signaling.
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19
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Nagel S, Pommerenke C, Meyer C, Kaufmann M, MacLeod RAF, Drexler HG. NKL homeobox gene MSX1 acts like a tumor suppressor in NK-cell leukemia. Oncotarget 2017; 8:66815-66832. [PMID: 28977998 PMCID: PMC5620138 DOI: 10.18632/oncotarget.18609] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/29/2017] [Indexed: 12/17/2022] Open
Abstract
NKL homeobox gene MSX1 is physiologically expressed in lymphoid progenitors and subsequently downregulated in developing T- and B-cells. In contrast, elevated expression levels of MSX1 persist in mature natural killer (NK)-cells, indicating a functional role in this compartment. While T-cell acute lymphoblastic leukemia (T-ALL) subsets exhibit aberrant overexpression of MSX1, we show here that in malignant NK-cells the level of MSX1 transcripts is aberrantly downregulated. Chromosomal deletions at 4p16 hosting the MSX1 locus have been described in NK-cell leukemia patients. However, NK-cell lines analyzed here showed normal MSX1 gene configurations, indicating that this aberration might be uncommon. To identify alternative MSX1 regulatory mechanisms we compared expression profiling data of primary normal NK-cells and malignant NK-cell lines. This procedure revealed several deregulated genes including overexpressed IRF4, MIR155HG and MIR17HG and downregulated AUTS2, EP300, GATA3 and HHEX. As shown recently, chromatin-modulator AUTS2 is overexpressed in T-ALL subsets where it mediates aberrant transcriptional activation of MSX1. Here, our data demonstrate that in malignant NK-cell lines AUTS2 performed MSX1 activation as well, but in accordance with downregulated MSX1 transcription therein we detected reduced AUTS2 expression, a small genomic deletion at 7q11 removing exons 3 and 4, and truncating mutations in exon 1. Moreover, genomic profiling and chromosomal analyses of NK-cell lines demonstrated amplification of IRF4 at 6p25 and deletion of PRDM1 at 6q21, highlighting their potential oncogenic impact. Functional analyses performed via knockdown or forced expression of these genes revealed regulatory network disturbances effecting downregulation of MSX1 which may underlie malignant development in NK-cells.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Claudia Pommerenke
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Corinna Meyer
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Maren Kaufmann
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
| | - Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ, Braunschweig, Germany
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NKL homeobox gene activities in hematopoietic stem cells, T-cell development and T-cell leukemia. PLoS One 2017; 12:e0171164. [PMID: 28151996 PMCID: PMC5289504 DOI: 10.1371/journal.pone.0171164] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/16/2017] [Indexed: 12/18/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) cells represent developmentally arrested T-cell progenitors, subsets of which aberrantly express homeobox genes of the NKL subclass, including TLX1, TLX3, NKX2-1, NKX2-5, NKX3-1 and MSX1. Here, we analyzed the transcriptional landscape of all 48 members of the NKL homeobox gene subclass in CD34+ hematopoietic stem and progenitor cells (HSPCs) and during lymphopoiesis, identifying activities of nine particular genes. Four of these were expressed in HSPCs (HHEX, HLX1, NKX2-3 and NKX3-1) and three in common lymphoid progenitors (HHEX, HLX1 and MSX1). Interestingly, our data indicated downregulation of NKL homeobox gene transcripts in late progenitors and mature T-cells, a phenomenon which might explain the oncogenic impact of this group of genes in T-ALL. Using MSX1-expressing T-ALL cell lines as models, we showed that HHEX activates while HLX1, NKX2-3 and NKX3-1 repress MSX1 transcription, demonstrating the mutual regulation and differential activities of these homeobox genes. Analysis of a public T-ALL expression profiling data set comprising 117 patient samples identified 20 aberrantly activated members of the NKL subclass, extending the number of known NKL homeobox oncogene candidates. While 7/20 genes were also active during hematopoiesis, the remaining 13 showed ectopic expression. Finally, comparative analyses of T-ALL patient and cell line profiling data of NKL-positive and NKL-negative samples indicated absence of shared target genes but instead highlighted deregulation of apoptosis as common oncogenic effect. Taken together, we present a comprehensive survey of NKL homeobox genes in early hematopoiesis, T-cell development and T-ALL, showing that these genes generate an NKL-code for the diverse stages of lymphoid development which might be fundamental for regular differentiation.
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Ponnampalam SN, Kamaluddin NR, Zakaria Z, Matheneswaran V, Ganesan D, Haspani MS, Ryten M, Hardy JA. A blood-based gene expression and signaling pathway analysis to differentiate between high and low grade gliomas. Oncol Rep 2016; 37:10-22. [PMID: 28004117 PMCID: PMC5355666 DOI: 10.3892/or.2016.5285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/15/2016] [Indexed: 01/05/2023] Open
Abstract
The aims of the present study were to undertake gene expression profiling of the blood of glioma patients to determine key genetic components of signaling pathways and to develop a panel of genes that could be used as a potential blood-based biomarker to differentiate between high and low grade gliomas, non-gliomas and control samples. In this study, blood samples were obtained from glioma patients, non-glioma and control subjects. Ten samples each were obtained from patients with high and low grade tumours, respectively, ten samples from non-glioma patients and twenty samples from control subjects. Total RNA was isolated from each sample after which first and second strand synthesis was performed. The resulting cRNA was then hybridized with the Agilent Whole Human Genome (4×44K) microarray chip according to the manufacturer's instructions. Universal Human Reference RNA and samples were labeled with Cy3 CTP and Cy5 CTP, respectively. Microarray data were analyzed by the Agilent Gene Spring 12.1V software using stringent criteria which included at least a 2-fold difference in gene expression between samples. Statistical analysis was performed using the unpaired Student's t-test with a P<0.01. Pathway enrichment was also performed, with key genes selected for validation using droplet digital polymerase chain reaction (ddPCR). The gene expression profiling indicated that were a substantial number of genes that were differentially expressed with more than a 2-fold change (P<0.01) between each of the four different conditions. We selected key genes within significant pathways that were analyzed through pathway enrichment. These key genes included regulators of cell proliferation, transcription factors, cytokines and tumour suppressor genes. In the present study, we showed that key genes involved in significant and well established pathways, could possibly be used as a potential blood-based biomarker to differentiate between high and low grade gliomas, non-gliomas and control samples.
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Affiliation(s)
- Stephen N Ponnampalam
- Cancer Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Nor Rizan Kamaluddin
- Cancer Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Zubaidah Zakaria
- Cancer Research Center, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Vickneswaran Matheneswaran
- Department of Neurosurgery, University Malaya Medical Centre, Jalan Universiti, 50603 Kuala Lumpur, Malaysia
| | - Dharmendra Ganesan
- Department of Neurosurgery, University Malaya Medical Centre, Jalan Universiti, 50603 Kuala Lumpur, Malaysia
| | | | - Mina Ryten
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK
| | - John A Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK
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Rinchai D, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery. F1000Res 2016; 5:291. [PMID: 27158451 DOI: 10.12688/f1000research.8182.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/24/2022] Open
Abstract
Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at http://monocyte.gxbsidra.org/dm3/landing.gsp.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sabri Boughorbel
- Biomedical informatics, Sidra Medical and Research Center, Doha, Qatar
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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Rinchai D, Boughorbel S, Presnell S, Quinn C, Chaussabel D. A curated compendium of monocyte transcriptome datasets of relevance to human monocyte immunobiology research. F1000Res 2016; 5:291. [PMID: 27158452 PMCID: PMC4856112 DOI: 10.12688/f1000research.8182.2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 12/19/2022] Open
Abstract
Systems-scale profiling approaches have become widely used in translational research settings. The resulting accumulation of large-scale datasets in public repositories represents a critical opportunity to promote insight and foster knowledge discovery. However, resources that can serve as an interface between biomedical researchers and such vast and heterogeneous dataset collections are needed in order to fulfill this potential. Recently, we have developed an interactive data browsing and visualization web application, the Gene Expression Browser (GXB). This tool can be used to overlay deep molecular phenotyping data with rich contextual information about analytes, samples and studies along with ancillary clinical or immunological profiling data. In this note, we describe a curated compendium of 93 public datasets generated in the context of human monocyte immunological studies, representing a total of 4,516 transcriptome profiles. Datasets were uploaded to an instance of GXB along with study description and sample annotations. Study samples were arranged in different groups. Ranked gene lists were generated based on relevant group comparisons. This resource is publicly available online at
http://monocyte.gxbsidra.org/dm3/landing.gsp.
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Affiliation(s)
- Darawan Rinchai
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sabri Boughorbel
- Biomedical Informatics Division, Sidra Medical and Research Center, Doha, Qatar
| | - Scott Presnell
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Charlie Quinn
- Benaroya Research Institute at Virginia Mason, Seattle, USA
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
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Fernández-Figueroa EA, Imaz-Rosshandler I, Castillo-Fernández JE, Miranda-Ortíz H, Fernández-López JC, Becker I, Rangel-Escareño C. Down-Regulation of TLR and JAK/STAT Pathway Genes Is Associated with Diffuse Cutaneous Leishmaniasis: A Gene Expression Analysis in NK Cells from Patients Infected with Leishmania mexicana. PLoS Negl Trop Dis 2016; 10:e0004570. [PMID: 27031998 PMCID: PMC4816531 DOI: 10.1371/journal.pntd.0004570] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 03/02/2016] [Indexed: 12/15/2022] Open
Abstract
An important NK-cell inhibition with reduced TNF-α, IFN-γ and TLR2 expression had previously been identified in patients with diffuse cutaneous leishmaniasis (DCL) infected with Leishmania mexicana. In an attempt to pinpoint alterations in the signaling pathways responsible for the NK-cell dysfunction in patients with DCL, this study aimed at identifying differences in the NK-cell response towards Leishmania mexicana lipophosphoglycan (LPG) between patients with localized and diffuse cutaneous leishmaniasis through gene expression profiling. Our results indicate that important genes involved in the innate immune response to Leishmania are down-regulated in NK cells from DCL patients, particularly TLR and JAK/STAT signaling pathways. This down-regulation showed to be independent of LPG stimulation. The study sheds new light for understanding the mechanisms that undermine the correct effector functions of NK cells in patients with diffuse cutaneous leishmaniasis contributing to a better understanding of the pathobiology of leishmaniasis. Leishmaniasis, caused by protozoan parasites is considered a neglected disease. Leishmania mexicana can cause localized or diffuse cutaneous leishmaniasis. Patients with localized cutaneous leishmaniasis contain the parasite within granulomas, whereas patients with diffuse cutaneous leishmaniasis show uncontrolled parasite spread. The cause of this progression remains unknown. However, NK cells have been shown to play an important role since they are among the first to produce cytokines (IFN-γ and TNF-α) that help phagocytic cells to eliminate the intracellular parasite. Previous studies had shown that NK cells of patients with diffuse cutaneous leishmaniasis are unresponsive to Leishmania, yet underlying mechanisms were unknown. The current work aims at understanding how the parasite modulates NK-cell responses through gene expression profiling between patients with localized and diffuse cutaneous leishmaniasis. A highlight of our results is that NK cells of patients with the uncontrolled form of leishmaniasis show down-regulation patterns for genes that regulate the innate immune response through TLR receptors and JAK/STAT signaling pathways at different levels: transcription factors (NF-κB and STAT-1), cytokine receptors (IFN-γR2 and IL-12Rβ2) and cytokines (TNF-α). The alteration of expression levels for genes in immune response signaling pathways could predispose to DCL development and/or be associated with disease severity.
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Affiliation(s)
| | - Iván Imaz-Rosshandler
- Unidad de Investigación en Medicina Experimental, Centro de Medicina Tropical, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida, D.F., México
| | - Juan E. Castillo-Fernández
- Unidad de Investigación en Medicina Experimental, Centro de Medicina Tropical, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida, D.F., México
| | - Haydee Miranda-Ortíz
- Unidad de Investigación en Medicina Experimental, Centro de Medicina Tropical, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida, D.F., México
| | - Juan C. Fernández-López
- Unidad de Investigación en Medicina Experimental, Centro de Medicina Tropical, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida, D.F., México
| | - Ingeborg Becker
- Computational Genomics, Instituto Nacional de Medicina Genómica, Arenal Tepepan, México D.F., México
- * E-mail: (CRE); (IB)
| | - Claudia Rangel-Escareño
- Unidad de Investigación en Medicina Experimental, Centro de Medicina Tropical, Facultad de Medicina, Universidad Nacional Autónoma de México, Avenida, D.F., México
- * E-mail: (CRE); (IB)
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25
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Spinelli L, Carpentier S, Montañana Sanchis F, Dalod M, Vu Manh TP. BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses. BMC Genomics 2015; 16:814. [PMID: 26481321 PMCID: PMC4617899 DOI: 10.1186/s12864-015-2012-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 10/07/2015] [Indexed: 12/21/2022] Open
Abstract
Background Recent advances in the analysis of high-throughput expression data have led to the development of tools that scaled-up their focus from single-gene to gene set level. For example, the popular Gene Set Enrichment Analysis (GSEA) algorithm can detect moderate but coordinated expression changes of groups of presumably related genes between pairs of experimental conditions. This considerably improves extraction of information from high-throughput gene expression data. However, although many gene sets covering a large panel of biological fields are available in public databases, the ability to generate home-made gene sets relevant to one’s biological question is crucial but remains a substantial challenge to most biologists lacking statistic or bioinformatic expertise. This is all the more the case when attempting to define a gene set specific of one condition compared to many other ones. Thus, there is a crucial need for an easy-to-use software for generation of relevant home-made gene sets from complex datasets, their use in GSEA, and the correction of the results when applied to multiple comparisons of many experimental conditions. Result We developed BubbleGUM (GSEA Unlimited Map), a tool that allows to automatically extract molecular signatures from transcriptomic data and perform exhaustive GSEA with multiple testing correction. One original feature of BubbleGUM notably resides in its capacity to integrate and compare numerous GSEA results into an easy-to-grasp graphical representation. We applied our method to generate transcriptomic fingerprints for murine cell types and to assess their enrichments in human cell types. This analysis allowed us to confirm homologies between mouse and human immunocytes. Conclusions BubbleGUM is an open-source software that allows to automatically generate molecular signatures out of complex expression datasets and to assess directly their enrichment by GSEA on independent datasets. Enrichments are displayed in a graphical output that helps interpreting the results. This innovative methodology has recently been used to answer important questions in functional genomics, such as the degree of similarities between microarray datasets from different laboratories or with different experimental models or clinical cohorts. BubbleGUM is executable through an intuitive interface so that both bioinformaticians and biologists can use it. It is available at http://www.ciml.univ-mrs.fr/applications/BubbleGUM/index.html. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2012-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lionel Spinelli
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
| | | | - Frédéric Montañana Sanchis
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
| | - Marc Dalod
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
| | - Thien-Phong Vu Manh
- Centre d'Immunologie, de Marseille-Luminy, Aix Marseille University UM2, Inserm, U1104, CNRS UMR7280, F-13288, Marseille, Cedex 09, France.
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26
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Zhai F, Zhang X, Guan Y, Yang X, Li Y, Song G, Guan L. Expression profiles of microRNAs after focal cerebral ischemia/reperfusion injury in rats. Neural Regen Res 2015; 7:917-23. [PMID: 25722676 PMCID: PMC4341287 DOI: 10.3969/j.issn.1673-5374.2012.12.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 02/24/2012] [Indexed: 11/23/2022] Open
Abstract
Rat models of focal cerebral ischemia/reperfusion injury were established by occlusion of the middle cerebral artery. Microarray analysis showed that 24 hours after cerebral ischemia, there were nine up-regulated and 27 down-regulated microRNA genes in cortical tissue. Bioinformatic analysis showed that bcl-2 was the target gene of microRNA-384-5p and microRNA-494, and caspase-3 was the target gene of microRNA-129, microRNA-320 and microRNA-326. Real-time PCR and western blot analyses showed that 24 hours after cerebral ischemia, bcl-2 mRNA and protein levels in brain tissue were significantly decreased, while caspase-3 mRNA and protein levels were significantly increased. This suggests that following cerebral ischemia, differentially expressed microRNA-384-5p, microRNA-494, microRNA-320, microRNA-129 and microRNA-326 can regulate bcl-2 and caspase-3 expression in brain tissue.
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Affiliation(s)
- Fengguo Zhai
- Department of Pharmacology, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
| | - Xiuping Zhang
- Department of Pharmacology, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
| | - Yue Guan
- Department of Endocrinology, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
| | - Xudong Yang
- Department of Pharmacology, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
| | - Yang Li
- Department of Thoracic Surgery, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
| | - Gaochen Song
- Department of Biochemistry, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
| | - Lixin Guan
- Department of Pharmacology, Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang Province, China
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Wang F, Tian Z, Wei H. Genomic expression profiling of NK cells in health and disease. Eur J Immunol 2014; 45:661-78. [PMID: 25476835 DOI: 10.1002/eji.201444998] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/01/2014] [Accepted: 12/01/2014] [Indexed: 12/15/2022]
Abstract
NK cells are important components of innate and adaptive immunity. Functionally, they play key roles in host defense against tumors and infectious pathogens. Within the past few years, genomic-scale experiments have provided us with a plethora of gene expression data that reveal an extensive molecular and biological map underlying gene expression programs. In order to better explore and take advantage of existing datasets, we review here the genomic expression profiles of NK cells and their subpopulations in resting or stimulated states, in diseases, and in different organs; moreover, we contrast these expression data to those of other lymphocytes. We have also compiled a comprehensive list of genomic profiling studies of both human and murine NK cells in this review.
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Affiliation(s)
- Fuyan Wang
- Institute of Immunology, School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China; Diabetes Center, School of Medicine, Ningbo University, Ningbo, China
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Pullagurla SR, Witek MA, Jackson JM, Lindell MAM, Hupert ML, Nesterova IV, Baird AE, Soper SA. Parallel affinity-based isolation of leukocyte subsets using microfluidics: application for stroke diagnosis. Anal Chem 2014; 86:4058-65. [PMID: 24650222 PMCID: PMC4004188 DOI: 10.1021/ac5007766] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
We report the design and performance
of a polymer microfluidic
device that can affinity select multiple types of biological cells
simultaneously with sufficient recovery and purity to allow for the
expression profiling of mRNA isolated from these cells. The microfluidic
device consisted of four independent selection beds with curvilinear
channels that were 25 μm wide and 80 μm deep and were
modified with antibodies targeting antigens specifically expressed
by two different cell types. Bifurcated and Z-configured device geometries
were evaluated for cell selection. As an example of the performance
of these devices, CD4+ T-cells and neutrophils were selected from
whole blood as these cells are known to express genes found in stroke-related
expression profiles that can be used for the diagnosis of this disease.
CD4+ T-cells and neutrophils were simultaneously isolated with purities
>90% using affinity-based capture in cyclic olefin copolymer (COC)
devices with a processing time of ∼3 min. In addition, sufficient
quantities of the cells could be recovered from a 50 μL whole
blood input to allow for reverse transcription-polymerase chain reaction
(RT-PCR) following cell lysis. The expression of genes from isolated
T-cells and neutrophils, such as S100A9, TCRB, and FPR1, was evaluated using RT-PCR.
The modification and isolation procedures demonstrated here can also
be used to analyze other cell types as well where multiple subsets
must be interrogated.
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Affiliation(s)
- Swathi R Pullagurla
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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Rao P, Benito E, Fischer A. MicroRNAs as biomarkers for CNS disease. Front Mol Neurosci 2013; 6:39. [PMID: 24324397 PMCID: PMC3840814 DOI: 10.3389/fnmol.2013.00039] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/31/2013] [Indexed: 01/23/2023] Open
Abstract
For many neurological diseases, the efficacy and outcome of treatment depend on early detection. Diagnosis is currently based on the detection of symptoms and neuroimaging abnormalities, which appear at relatively late stages in the pathogenesis. However, the underlying molecular responses to genetic and environmental insults begin much earlier and non-coding RNA networks are critically involved in these cellular regulatory mechanisms. Profiling RNA expression patterns could thus facilitate presymptomatic disease detection. Obtaining indirect readouts of pathological processes is particularly important for brain disorders because of the lack of direct access to tissue for molecular analyses. Living neurons and other CNS cells secrete microRNA and other small non-coding RNA into the extracellular space packaged in exosomes, microvesicles, or lipoprotein complexes. This discovery, together with the rapidly evolving massive sequencing technologies that allow detection of virtually all RNA species from small amounts of biological material, has allowed significant progress in the use of extracellular RNA as a biomarker for CNS malignancies, neurological, and psychiatric diseases. There is also recent evidence that the interactions between external stimuli and brain pathological processes may be reflected in peripheral tissues, facilitating their use as potential diagnostic markers. In this review, we explore the possibilities and challenges of using microRNA and other small RNAs as a signature for neurodegenerative and other neuropsychatric conditions.
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Affiliation(s)
- Pooja Rao
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen Göttingen, Germany
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30
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Adamski MG, Li Y, Wagner E, Yu H, Seales-Bailey C, Soper SA, Murphy M, Baird AE. Next-generation qPCR for the high-throughput measurement of gene expression in multiple leukocyte subsets. ACTA ACUST UNITED AC 2013; 18:1008-17. [PMID: 23690294 DOI: 10.1177/1087057113489882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Clinical studies of gene expression are increasingly using the whole blood, peripheral blood mononuclear cells, and leukocyte subsets involved in the innate and adaptive immune responses. However, the small amount of RNA available in the clinical setting is a limitation for commonly used methods such as quantitative polymerase chain reactions (qPCR) and microarrays. Our aim was to design 96 gene assays to simultaneously measure gene expression in the whole blood and seven leukocyte subsets using a new-generation qPCR method--high-throughput nanofluidic reverse transcription qPCR (HT RT-qPCR). The leukocyte subset purity was 94% to 98% for seven subsets and was less for the γδ T-cell receptor subset (80%). The HT RT-qPCR replicate sample measurements were highly reproducible (r = 0.997, p < 2.2 × 10(-16)), and the ΔΔCt values from HT RT-qPCR correlated significantly with those from qPCR. The control genes were differentially expressed across the eight leukocyte subsets in the control subjects (p = 1.3 × 10(-5), analysis of variance). Two analytical methods, absolute and relative, gave concordant results and were significantly correlated (p = 1.9 × 10(-9)). HT RT-qPCR permits the rapid, reproducible, and quantitative measurement of multiple transcripts using minimal sample amounts. The protocol described yielded leukocyte subsets of high purity and identified two analytic methods for use.
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Affiliation(s)
- Mateusz G Adamski
- 1Department of Neurology, SUNY Downstate Medical Center, Brooklyn, NY, USA
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Chen S, Fan Q, Gao X, Wang X, Huang R, Laties AM, Zhang X. Increased expression of the transient receptor potential cation channel 6 gene in patients with primary open-angle glaucoma. Clin Exp Ophthalmol 2013; 41:753-60. [PMID: 23566105 DOI: 10.1111/ceo.12111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 02/22/2013] [Indexed: 12/19/2022]
Abstract
BACKGROUND The result of primary open-angle glaucoma is the loss of retinal ganglion cells. Transient receptor potential cation channel 6 is a pressure-related channel that may function in the survival of retinal ganglion cells. The purpose of this study was to evaluate the expression levels of the transient receptor potential cation channel 6 gene in patients with primary open-angle glaucoma. DESIGN Randomization study at Zhongshan Ophthalmic Center in China. PARTICIPANTS 80 primary open-angle glaucoma patients and 75 cataract patients recruited from Zhongshan Ophthalmic Center. METHODS Total RNA was extracted from the leukocytes of the peripheral blood collected. The levels of transient receptor potential cation channel 6-messenger RNA were determined by real-time polymerase chain reaction. Related factors including age, intraocular pressure, optic cup-to-disc ratio and visual field defect were analysed accordingly. MAIN OUTCOME MEASURES Clinical examination and the messenger RNA level. RESULTS The expression level of the transient receptor potential cation channel 6 gene in the leukocytes of primary open-angle glaucoma patients was two times higher when compared with control cataract patients. The gene expression level was also correlated with intraocular pressure and cup-to-disc ratio. Treatment with different anti-glaucoma drugs did not affect the gene expression. CONCLUSIONS Increasing expression levels of the transient receptor potential cation channel 6 gene in the blood accompanies chronic elevation of intraocular pressure in primary open-angle glaucoma and may serve as a genetic biomarker for primary open-angle glaucoma.
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Affiliation(s)
- Shida Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
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Satpathy AT, KC W, Albring JC, Edelson BT, Kretzer NM, Bhattacharya D, Murphy TL, Murphy KM. Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages. ACTA ACUST UNITED AC 2012; 209:1135-52. [PMID: 22615127 PMCID: PMC3371733 DOI: 10.1084/jem.20120030] [Citation(s) in RCA: 454] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The zinc finger transcription factor Zbtb46 specifically marks cDCs and their committed precursors and, when overexpressed in BM progenitors, promotes cDC development at the expense of granulocytes. Distinguishing dendritic cells (DCs) from other cells of the mononuclear phagocyte system is complicated by the shared expression of cell surface markers such as CD11c. In this study, we identified Zbtb46 (BTBD4) as a transcription factor selectively expressed by classical DCs (cDCs) and their committed progenitors but not by plasmacytoid DCs (pDCs), monocytes, macrophages, or other lymphoid or myeloid lineages. Using homologous recombination, we replaced the first coding exon of Zbtb46 with GFP to inactivate the locus while allowing detection of Zbtb46 expression. GFP expression in Zbtb46gfp/+ mice recapitulated the cDC-specific expression of the native locus, being restricted to cDC precursors (pre-cDCs) and lymphoid organ– and tissue-resident cDCs. GFP+ pre-cDCs had restricted developmental potential, generating cDCs but not pDCs, monocytes, or macrophages. Outside the immune system, Zbtb46 was expressed in committed erythroid progenitors and endothelial cell populations. Zbtb46 overexpression in bone marrow progenitor cells inhibited granulocyte potential and promoted cDC development, and although cDCs developed in Zbtb46gfp/gfp (Zbtb46 deficient) mice, they maintained expression of granulocyte colony-stimulating factor and leukemia inhibitory factor receptors, which are normally down-regulated in cDCs. Thus, Zbtb46 may help enforce cDC identity by restricting responsiveness to non-DC growth factors and may serve as a useful marker to identify rare cDC progenitors and distinguish between cDCs and other mononuclear phagocyte lineages.
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Affiliation(s)
- Ansuman T Satpathy
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
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Oh SH, Kim OJ, Shin DA, Song J, Yoo H, Kim YK, Kim JK. Alteration of immunologic responses on peripheral blood in the acute phase of ischemic stroke: blood genomic profiling study. J Neuroimmunol 2012; 249:60-5. [PMID: 22591946 DOI: 10.1016/j.jneuroim.2012.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/15/2012] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Peripheral blood cells and inflammatory mediators have a detrimental effect on brain during cerebral ischemia. We investigated the immunologic changes on peripheral blood in the acute phase of ischemic stroke using RNA microarray. METHODS mRNA microarray and real time-polymerase chain reaction (RT-PCR) for genes of interest in microarray data were analyzed in 12 stroke patients and 12 controls. Plasma matrix metalloproteinase-9 (MMP-9) concentrations were measured in 120 stroke patients and 82 controls. RESULTS In microarray analysis, a total of 11 genes of interest showed different expression in patients with ischemic stroke. The three most highly expressed genes were C19orf59 (chromosome 19 open reading frame 59), MMP9 and IL18RAP (interleukin-18 receptor accessory protein), whereas gene with the lowest expression was GNLY (granulysin). The expression patterns of three selected genes (MMP9, IL18RAP and GNLY) were validated by RT-PCR. The plasma concentration of MMP-9 was significantly elevated in the stroke patients, and showed a weakly positive correlation with infarct volume. Gene set enrichment analysis (GSEA) showed that gene sets related to immunity and defense, signal transduction, transport and cell adhesion were significant in acute ischemic stroke. CONCLUSIONS In the peripheral blood, numerous genes of inflammatory mediators, including MMP9, IL18RAP and GNLY, are altered in the acute phase of ischemic stroke. This stroke-specific gene expression profiling provides valuable information about the role of peripheral inflammation to the pathophysiological mechanism of ischemic stroke.
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Affiliation(s)
- Seung-Hun Oh
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
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Tian Y, Stamova B, Jickling GC, Liu D, Ander BP, Bushnell C, Zhan X, Davis RR, Verro P, Pevec WC, Hedayati N, Dawson DL, Khoury J, Jauch EC, Pancioli A, Broderick JP, Sharp FR. Effects of gender on gene expression in the blood of ischemic stroke patients. J Cereb Blood Flow Metab 2012; 32:780-91. [PMID: 22167233 PMCID: PMC3345909 DOI: 10.1038/jcbfm.2011.179] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study examined the effects of gender on RNA expression after ischemic stroke (IS). RNA obtained from blood of IS patients (n=51; 153 samples at < or =3, 5, and 24 hours) and from matched controls (n=52) were processed on Affymetrix microarrays. Analyses of covariance for stroke versus control samples were performed separately for both genders and the regulated genes for females compared with males. In all, 242, 227, and 338 male-specific genes were regulated at < or =3, 5, and 24 hours after IS, respectively, of which 59 were regulated at all time points. Overall, 774, 3,437, and 571 female-specific stroke genes were regulated at < or =3, 5, and 24 hours, respectively, of which 152 were regulated at all time points. Male-specific stroke genes were associated with integrin, integrin-liked kinase, actin, tight junction, Wnt/β-catenin, RhoA, fibroblast growth factors (FGF), granzyme, and tumor necrosis factor receptor (TNFR)2 signaling. Female-specific stroke genes were associated with p53, high-mobility group box-1, hypoxia inducible factor (HIF)1α, interleukin (IL)1, IL6, IL12, IL18, acute-phase response, T-helper, macrophage, and estrogen signaling. Cell death signaling was overrepresented in both genders, although the molecules and pathways differed. Gender affects gene expression in the blood of IS patients, which likely implies gender differences in immune, inflammatory, and cell death responses to stroke.
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Affiliation(s)
- Yingfang Tian
- Department of Neurology, the MIND Institute, University of California at Davis, Sacramento, CA, USA.
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Hershey A, Horn P, Kabbouche M, O'Brien H, Powers S. Genomic expression patterns in menstrual-related migraine in adolescents. Headache 2012; 52:68-79. [PMID: 22220971 PMCID: PMC3265619 DOI: 10.1111/j.1526-4610.2011.02049.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Exacerbation of migraine with menses is common in adolescent girls and women with migraine, occurring in up to 60% of females with migraine. These migraines are oftentimes longer and more disabling and may be related to estrogen levels and hormonal fluctuations. OBJECTIVE This study identifies the unique genomic expression pattern of menstrual-related migraine (MRM) in comparison to migraine occurring outside the menstrual period and headache-free controls. METHODS Whole blood samples were obtained from female subjects having an acute migraine during their menstrual period (MRM) or outside of their menstrual period (non-MRM) and controls (C)--females having a menstrual period without any history of headache. The messenger RNA was isolated from these samples, and genomic profile was assessed. Affymetrix Human Exon ST 1.0 (Affymetrix, Santa Clara, CA, USA) arrays were used to examine the genomic expression pattern differences between these 3 groups. RESULTS Blood genomic expression patterns were obtained on 56 subjects (MRM = 18, non-MRM = 18, and controls = 20). Unique genomic expression patterns were observed for both MRM and non-MRM. For MRM, 77 genes were identified that were unique to MRM, while 61 genes were commonly expressed for MRM and non-MRM, and 127 genes appeared to have a unique expression pattern for non-MRM. In addition, there were 279 genes that differentially expressed for MRM compared to non-MRM that were not differentially expressed for non-MRM. Gene ontology of these samples indicated many of these groups of genes were functionally related and included categories of immunomodulation/inflammation, mitochondrial function, and DNA homeostasis. CONCLUSIONS Blood genomic patterns can accurately differentiate MRM from non-MRM. These results indicate that MRM involves a unique molecular biology pathway that can be identified with a specific biomarker and suggest that individuals with MRM have a different underlying genetic etiology.
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Affiliation(s)
- Andrew Hershey
- Children's Hospital Medical Center, Department of Neurology, Cincinnati, OH 45229-3039, USA.
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A study to evaluate the effect of nootropic drug—Piracetam on DNA damage in leukocytes and macrophages. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2011; 726:66-74. [DOI: 10.1016/j.mrgentox.2011.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 08/01/2011] [Accepted: 08/26/2011] [Indexed: 11/17/2022]
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Sun X, Casbas-Hernandez P, Bigelow C, Makowski L, Joseph Jerry D, Smith Schneider S, Troester MA. Normal breast tissue of obese women is enriched for macrophage markers and macrophage-associated gene expression. Breast Cancer Res Treat 2011; 131:1003-12. [PMID: 22002519 DOI: 10.1007/s10549-011-1789-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 09/15/2011] [Indexed: 12/24/2022]
Abstract
Activation of inflammatory pathways is one plausible mechanism underlying the association between obesity and increased breast cancer risk. However, macrophage infiltration and local biomarkers of inflammation in breast adipose tissue have seldom been studied in association with obesity. Gene expression profiles of normal breast tissue from reduction mammoplasty patients were evaluated by whole genome microarrays to identify patterns associated with obesity status (normal-weight, body mass index (BMI) <25; overweight, BMI 25-29.9; obese, BMI ≥30). The presence of macrophage-enriched inflammatory loci with immunopositivity for CD68 protein was evaluated by immunohistochemistry (IHC). After adjusting for confounding by age, 760 genes were differentially expressed (203 up and 557 down; FDR = 0.026) between normal-weight and obese women. Gene ontology analysis suggested significant enrichment for pathways involving IL-6, IL-8, CCR5 signaling in macrophages and RXRα and PPARα activation, consistent with a pro-inflammatory state and suggestive of macrophage infiltration. Gene set enrichment analysis also demonstrated that the genomic signatures of monocytes and macrophages were over-represented in the obese group with FDR of 0.08 and 0.13, respectively. Increased macrophage infiltration was confirmed by IHC, which showed that the breast adipose tissue of obese women had higher average macrophage counts (mean = 8.96 vs. 3.56 in normal-weight women) and inflammatory foci counts (mean = 4.91 vs. 2.67 in normal-weight women). Obesity is associated with local inflammation and macrophage infiltration in normal human breast adipose tissues. Given the role of macrophages in carcinogenesis, these findings have important implications for breast cancer etiology and progression.
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Affiliation(s)
- Xuezheng Sun
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Abstract
Whole genome expression microarrays can be used to study gene expression in blood, which comes in part from leukocytes, immature platelets, and red blood cells. Since these cells are important in the pathogenesis of stroke, RNA provides an index of these cellular responses to stroke. Our studies in rats have shown specific gene expression changes 24 hours after ischemic stroke, hemorrhage, status epilepticus, hypoxia, hypoglycemia, global ischemia, and following brief focal ischemia that simulated transient ischemic attacks in humans. Human studies show gene expression changes following ischemic stroke. These gene profiles predict a second cohort with >90% sensitivity and specificity. Gene profiles for ischemic stroke caused by large-vessel atherosclerosis and cardioembolism have been described that predict a second cohort with >85% sensitivity and specificity. Atherosclerotic genes were associated with clotting, platelets, and monocytes, and cardioembolic genes were associated with inflammation, infection, and neutrophils. These gene profiles predicted the cause of stroke in 58% of cryptogenic patients. These studies will provide diagnostic, prognostic, and therapeutic markers, and will advance our understanding of stroke in humans. New techniques to measure all coding and noncoding RNAs along with alternatively spliced transcripts will markedly advance molecular studies of human stroke.
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Abstract
This review provides a summary of the protein and RNA biomarkers that have been studied for the diagnosis and assessment of ischemic stroke. Many of the biomarkers identified relate to the pathophysiology of ischemic stroke, including ischemia of CNS tissue, acute thrombosis and inflammatory response. These biomarkers are summarized by their intended clinical application in ischemic stroke including diagnosis, prediction of stroke severity and outcome, and stratification of patients for stroke therapy. Among the biomarkers discussed are recent whole genome studies using RNA expression profiles to diagnose ischemic stroke and stroke etiology. Though many candidate blood based biomarkers for ischemic stroke have been identified, none are currently used in clinical practice. With further well designed study and careful validation, the development of blood biomarkers to improve the care of patients with ischemic stroke may be achieved.
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Affiliation(s)
- Glen C Jickling
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento, CA 95817, USA.
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Mendrick DL. Transcriptional profiling to identify biomarkers of disease and drug response. Pharmacogenomics 2011; 12:235-49. [PMID: 21332316 DOI: 10.2217/pgs.10.184] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The discovery, biological qualification and analytical validation of genomic biomarkers requires extensive collaborations between individuals with expertise in biology, statistics, bioinformatics, chemistry, clinical medicine, regulatory science and so on. For clinical utility, blood-borne biomarkers (e.g., mRNA and miRNA) of organ damage, drug toxicity and/or response would be preferred to those that are tissue based. Currently used biomarkers such as serum creatinine (indicating renal dysfunction) denote organ damage whether caused by disease, physical injury or drugs. Therefore, it is anticipated that studies of disease will discover biomarkers that can also be used to identify drug-induced injury and vice versa. This article describes transcriptomic blood-borne biomarkers that have been reported to be connected with disease and drug toxicity. Much more qualification and validation needs to be carried out before many of these biomarkers can prove useful. Discussed here are some of the lessons learned and roadblocks to success.
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Affiliation(s)
- Donna L Mendrick
- Division of Systems Biology, HFT-230, National Center for Toxicological Research, US FDA, 3900 NCTR Rd, Jefferson, AR 72079-4502, USA.
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Bos-Veneman NG, Olieman R, Tobiasova Z, Hoekstra PJ, Katsovitch L, Bothwell ALM, Leckman JF, Kawikova I. Altered immunoglobulin profiles in children with Tourette syndrome. Brain Behav Immun 2011; 25:532-8. [PMID: 21156204 PMCID: PMC3056238 DOI: 10.1016/j.bbi.2010.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/29/2010] [Accepted: 12/01/2010] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Post-infectious autoimmunity and immune deficiency have been implicated in the pathogenesis of Tourette syndrome (TS). We asked here whether B cell immunity of patients with TS differs from healthy subjects. METHODS In two independent cross-sectional samples, we compared serum levels of IgG1, IgG2, IgG3, IgG4, IgM, IgA, and IgE in 21 patients with TS from Yale University (17 males, 4 females, 8-16 years) versus 21 healthy controls (13 males, 8 females, 7-17 years); and in 53 patients with TS from Groningen University (45 males, 8 females, 6-18 years) versus 53 healthy controls (22 males, 31 females, 6-18 years), respectively. We also investigated correlations between Ig concentrations and symptom severity. In 13 additional patients (9 males, 4 females, age range 9-14), we established Ig profiles at time points before, during, and after symptom exacerbations. RESULTS IgG3 levels were significantly lower in Yale patients compared to healthy children (medians 0.28 versus 0.49 mg/ml, p=.04), while levels of IgG2, IgG4, and IgM in patients were lower at trend-level significance (p≤.10). Decreased IgG3 (medians 0.45 versus 0.52 mg/ml; p=.05) and IgM (medians 0.30 versus 0.38 mg/ml; p=.04) levels were replicated in the Groningen patients. Ig levels did not correlate with symptom severity. There was a trend-level elevation of IgG1 during symptom exacerbations (p=.09). CONCLUSION These pilot data indicate that at least some patients with TS have decreased serum IgG3, and possibly also IgM levels, though only few subjects had fully expressed Ig immunodeficiency. Whether these changes are related to TS pathogenesis needs to be investigated.
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Affiliation(s)
- Netty G.P. Bos-Veneman
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Netherlands
| | - Renske Olieman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511
| | - Zuzana Tobiasova
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511
| | - Pieter J. Hoekstra
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Netherlands
| | - Lily Katsovitch
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511
| | - Alfred L. M. Bothwell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511
| | - James F. Leckman
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT 06511
| | - Ivana Kawikova
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06511,Corresponding author: PO Box 207900, Yale University School of Medicine, 230 S Frontage Rd, Room I-382, , New Haven, CT 06519-1124, Tel: 203 7857971,
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van Kol SW, Hendriksen PJ, van Loveren H, Peijnenburg A. The effects of deoxynivalenol on gene expression in the murine thymus. Toxicol Appl Pharmacol 2011; 250:299-311. [DOI: 10.1016/j.taap.2010.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 10/16/2010] [Accepted: 11/02/2010] [Indexed: 10/18/2022]
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Abstract
BACKGROUND Chronic daily headache (CDH) and chronic migraine (CM) are one of the most frequent problems encountered in neurology, are often difficult to treat, and frequently complicated by medication-overuse headache (MOH). Proper recognition of MOH may alter treatment outcome and prevent long term disability. OBJECTIVE This study identifies the unique genomic expression pattern MOH that respond to cessation of the overused medication. METHODS Baseline occurrence of MOH and typical pattern of response to medication cessation were measured from a large database. Whole blood samples from patients with CM with or without MOH were obtained and their genomic profile was assessed. Affymetrix human U133 plus2 arrays were used to examine the genomic expression patterns prior to treatment and 6-12 weeks later. Headache characterisation and response to treatment based on headache frequency and disability were compared. RESULTS Of 1311 patients reporting daily or continuous headaches, 513 (39.1%) reported overusing analgesic medication. At follow-up, 44.5% had a 50% or greater reduction in headache frequency, while 41.6% had no change. Blood genomic expression patterns were obtained on 33 patients with 19 (57.6%) overusing analgesic medication with a unique genomic expression pattern in MOH that responded to cessation of analgesics. Gene ontology of these samples indicated a significant number were involved with brain and immunological tissues, including multiple signalling pathways and apoptosis. CONCLUSIONS Blood genomic patterns can accurately identify MOH patients that respond to medication cessation. These results suggest that MOH involves a unique molecular biology pathway that can be identified with a specific biomarker.
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Jickling GC, Xu H, Stamova B, Ander BP, Zhan X, Tian Y, Liu D, Turner RJ, Mesias M, Verro P, Khoury J, Jauch EC, Pancioli A, Broderick JP, Sharp FR. Signatures of cardioembolic and large-vessel ischemic stroke. Ann Neurol 2010; 68:681-92. [PMID: 21031583 DOI: 10.1002/ana.22187] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The cause of stroke remains unknown or cryptogenic in many patients. We sought to determine whether gene expression signatures in blood can distinguish between cardioembolic and large-vessel causes of stroke, and whether these profiles can predict stroke etiology in the cryptogenic group. METHODS A total of 194 samples from 76 acute ischemic stroke patients were analyzed. RNA was isolated from blood and run on Affymetrix U133 Plus2.0 microarrays. Genes that distinguish large-vessel from cardioembolic stroke were determined at 3, 5, and 24 hours following stroke onset. Predictors were evaluated using cross-validation and a separate set of patients with known stroke subtype. The cause of cryptogenic stroke was predicted based on a model developed from strokes of known cause and identified predictors. RESULTS A 40-gene profile differentiated cardioembolic stroke from large-vessel stroke with >95% sensitivity and specificity. A separate 37-gene profile differentiated cardioembolic stroke due to atrial fibrillation from nonatrial fibrillation causes with >90% sensitivity and specificity. The identified genes elucidate differences in inflammation between stroke subtypes. When applied to patients with cryptogenic stroke, 17% are predicted to be large-vessel and 41% to be cardioembolic stroke. Of the cryptogenic strokes predicted to be cardioembolic, 27% were predicted to have atrial fibrillation. INTERPRETATION Gene expression signatures distinguish cardioembolic from large-vessel causes of ischemic stroke. These gene profiles may add valuable diagnostic information in the management of patients with stroke of unknown etiology though they need to be validated in future independent, large studies.
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Affiliation(s)
- Glen C Jickling
- Department of Neurology and the MIND Institute, University of California at Davis, Sacramento, CA 95817, USA.
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Murphy TK, Kurlan R, Leckman J. The immunobiology of Tourette's disorder, pediatric autoimmune neuropsychiatric disorders associated with Streptococcus, and related disorders: a way forward. J Child Adolesc Psychopharmacol 2010; 20:317-31. [PMID: 20807070 PMCID: PMC4003464 DOI: 10.1089/cap.2010.0043] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Obsessive-compulsive disorder (OCD) and related conditions including Tourette's disorder (TD) are chronic, relapsing disorders of unknown etiology associated with marked impairment and disability. Associated immune dysfunction has been reported and debated in the literature since the late 80s. The immunologic culprit receiving the most interest has been Group A Streptococcus (GAS), which began to receive attention as a potential cause of neuropsychiatric symptoms, following the investigation of the symptoms reported in Sydenham's chorea (SC) and rheumatic fever, such as motor tics, vocal tics, and both obsessive-compulsive and attention deficit/hyperactivity symptoms. Young children have been described as having a sudden onset of these neuropsychiatric symptoms temporally associated with GAS, but without supporting evidence of rheumatic fever. This presentation of OCD and tics has been termed pediatric autoimmune neuropsychiatric disorders associated with Streptococcus (PANDAS). Of note, SC, OCD, and TD often begin in early childhood and share common anatomic areas--the basal ganglia of the brain and the related cortical and thalamic sites--adding support to the possibility that these disorders might share a common immunologic and/or genetic vulnerability. Relevant manuscripts were identified through searches of the PsycINFO and MedLine databases using the following keywords: OCD, immune, PANDAS, Sydenham chorea, Tourette's disorder Group A Streptococcus. Articles were also identified through reference lists from research articles and other materials on childhood OCD, PANDAS, and TD between 1966 and December 2010. Considering the overlap of clinical and neuroanatomic findings among these disorders, this review explores evidence regarding the immunobiology as well as the relevant clinical and therapeutic aspects of TD, OCD, and PANDAS.
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Affiliation(s)
- Tanya K Murphy
- Department of Pediatrics and Psychiatry, University of South Florida, St Petersburg, Florida 33701, USA.
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Crozat K, Guiton R, Contreras V, Feuillet V, Dutertre CA, Ventre E, Vu Manh TP, Baranek T, Storset AK, Marvel J, Boudinot P, Hosmalin A, Schwartz-Cornil I, Dalod M. The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8alpha+ dendritic cells. ACTA ACUST UNITED AC 2010; 207:1283-92. [PMID: 20479118 PMCID: PMC2882835 DOI: 10.1084/jem.20100223] [Citation(s) in RCA: 486] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human BDCA3+ dendritic cells (DCs) were suggested to be homologous to mouse CD8α+ DCs. We demonstrate that human BDCA3+ DCs are more efficient than their BDCA1+ counterparts or plasmacytoid DCs (pDCs) in cross-presenting antigen and activating CD8+ T cells, which is similar to mouse CD8α+ DCs as compared with CD11b+ DCs or pDCs, although with more moderate differences between human DC subsets. Yet, no specific marker was known to be shared between homologous DC subsets across species. We found that XC chemokine receptor 1 (XCR1) is specifically expressed and active in mouse CD8α+, human BDCA3+, and sheep CD26+ DCs and is conserved across species. The mRNA encoding the XCR1 ligand chemokine (C motif) ligand 1 (XCL1) is selectively expressed in natural killer (NK) and CD8+ T lymphocytes at steady-state and is enhanced upon activation. Moreover, the Xcl1 mRNA is selectively expressed at high levels in central memory compared with naive CD8+ T lymphocytes. Finally, XCR1−/− mice have decreased early CD8+ T cell responses to Listeria monocytogenes infection, which is associated with higher bacterial loads early in infection. Therefore, XCR1 constitutes the first conserved specific marker for cell subsets homologous to mouse CD8α+ DCs in higher vertebrates and promotes their ability to activate early CD8+ T cell defenses against an intracellular pathogenic bacteria.
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Affiliation(s)
- Karine Crozat
- Centre d'Immunologie de Marseille-Luminy, Université de la Méditerranée, Parc scientifique et technologique de Luminy, 13288 Marseille, France
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Jickling GC, Zhan X, Ander BP, Turner RJ, Stamova B, Xu H, Tian Y, Liu D, Davis RR, Lapchak PA, Sharp FR. Genome response to tissue plasminogen activator in experimental ischemic stroke. BMC Genomics 2010; 11:254. [PMID: 20406488 PMCID: PMC2875237 DOI: 10.1186/1471-2164-11-254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 04/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tissue plasminogen activator (tPA) is known to have functions beyond fibrinolysis in acute ischemic stroke, such as blood brain barrier disruption. To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke. RESULTS tPA differentially expressed 929 genes in the blood of rats (p <or= 0.05, fold change >or= |1.2|). Genes identified had functions related to modulation of immune cells. tPA gene expression was found to be dependent on the reperfusion status of cerebral vasculature. The majority of genes regulated by tPA were different from genes regulated by ischemic stroke. CONCLUSIONS tPA modulates gene expression in the blood of rats involving immune cells in a manner that is dependent on the status of vascular reperfusion. These non-fibrinolytic activities of tPA in the blood serve to better understand tPA-related complications.
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Affiliation(s)
- Glen C Jickling
- Department of Neurology and M,I,N,D, Institute, University of California at Davis, Sacramento, California 95817, USA.
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Crozat K, Guiton R, Guilliams M, Henri S, Baranek T, Schwartz-Cornil I, Malissen B, Dalod M. Comparative genomics as a tool to reveal functional equivalences between human and mouse dendritic cell subsets. Immunol Rev 2010; 234:177-98. [DOI: 10.1111/j.0105-2896.2009.00868.x] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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King MD, Laird MD, Ramesh SS, Youssef P, Shakir B, Vender JR, Alleyne CH, Dhandapani KM. Elucidating novel mechanisms of brain injury following subarachnoid hemorrhage: an emerging role for neuroproteomics. Neurosurg Focus 2010; 28:E10. [PMID: 20043714 PMCID: PMC3151677 DOI: 10.3171/2009.10.focus09223] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Subarachnoid hemorrhage (SAH) is a devastating neurological injury associated with significant patient morbidity and death. Since the first demonstration of cerebral vasospasm nearly 60 years ago, the preponderance of research has focused on strategies to limit arterial narrowing and delayed cerebral ischemia following SAH. However, recent clinical and preclinical data indicate a functional dissociation between cerebral vasospasm and neurological outcome, signaling the need for a paradigm shift in the study of brain injury following SAH. Early brain injury may contribute to poor outcome and early death following SAH. However, elucidation of the complex cellular mechanisms underlying early brain injury remains a major challenge. The advent of modern neuroproteomics has rapidly advanced scientific discovery by allowing proteome-wide screening in an objective, nonbiased manner, providing novel mechanisms of brain physiology and injury. In the context of neurosurgery, proteomic analysis of patient-derived CSF will permit the identification of biomarkers and/or novel drug targets that may not be intuitively linked with any particular disease. In the present report, the authors discuss the utility of neuroproteomics with a focus on the roles for this technology in understanding SAH. The authors also provide data from our laboratory that identifies high-mobility group box protein-1 as a potential biomarker of neurological outcome following SAH in humans.
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Affiliation(s)
- Melanie D King
- Department of Neurosurgery, Medical College of Georgia, Augusta, Georgia 30809, USA
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Vexler ZS, Yenari MA. Does inflammation after stroke affect the developing brain differently than adult brain? Dev Neurosci 2009; 31:378-93. [PMID: 19672067 DOI: 10.1159/000232556] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 03/03/2009] [Indexed: 12/13/2022] Open
Abstract
The immature brain is prone to hypoxic-ischemic encephalopathy and stroke. The incidence of arterial stroke in newborns is similar to that in the elderly. However, the pathogenesis of ischemic brain injury is profoundly affected by age at the time of the insult. Necrosis is a dominant type of neuronal cell death in adult brain, whereas widespread neuronal apoptosis is unique for the early postnatal synaptogenesis period. The inflammatory response, in conjunction with excitotoxic and oxidative responses, is the major contributor to ischemic injury in both the immature and adult brain, but there are several areas where these responses diverge. We discuss the contribution of various inflammatory mechanisms to injury and repair after cerebral ischemia in the context of CNS immaturity. In particular, we discuss the role of lower expression of selectins, a more limited leukocyte transmigration, undeveloped complement pathways, a more rapid microglial activation, differences in cytokine and chemokine interplay, and a different threshold to oxidative stress in the immature brain. We also discuss differences in activation of intracellular pathways, especially nuclear factor kappaB and mitogen-activated protein kinases. Finally, we discuss emerging data on both the supportive and adverse roles of inflammation in plasticity and repair after stroke.
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Affiliation(s)
- Zinaida S Vexler
- Department of Neurology, University of California, San Francisco, CA 94143-0663, USA.
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