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Li G, Zhao C, Xu J, Huang Y, Qiao Y, Li F, Peng G, Zheng S, Zhu L, Yang L, Wang Z, Wu H. Moxibustion alleviates intestinal inflammation in ulcerative colitis rats by modulating long non-coding RNA LOC108352929 and inhibiting Phf11 expression. Heliyon 2024; 10:e26898. [PMID: 38439851 PMCID: PMC10909710 DOI: 10.1016/j.heliyon.2024.e26898] [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: 11/05/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
Long noncoding RNA (lncRNAs) are involved in the pathogenesis of ulcerative colitis (UC). Moxibustion, a traditional Chinese medicine, can improve symptoms in patients with UC and reduce intestinal inflammation in rats with UC. However, it remains unclear whether the ameliorative effect of moxibustion on intestinal mucosal inflammation in UC is related to lncRNAs. Thirty-two rats were randomly assigned to four groups: normal control, UC, moxibustion (MOX), and sulfasalazine (SASP). The UC rat model was induced by administering 4% dextran sulfate sodium (DSS) in drinking water. Rats in the moxibustion group underwent bilateral Tianshu (ST25) moxibustion using the herbs-partition moxibustion method. Rats in the sulfasalazine group received SASP solution via gavage twice daily for seven consecutive days. Our results revealed that, compared with the UC group [2.00 (1.00, 2.50)], the DAI score [0.25 (0.00, 0.50)] was significantly lower in the MOX group (P < 0.05). Compared with the UC group [13.00 (11.25, 14.00)], the histopathological score [5.50 (4.00, 7.75)] was significantly lower in the MOX group (P < 0.05). In addition, the CMDI and macroscopic scores were decreased in the MOX group (P < 0.05). Moxibustion significantly decreased the protein expression of inflammatory factors TNF-α, IFN-γ, and IL-1β in the colonic tissues of UC rats (P <0.05), thereby suppressing the inflammatory response. Moreover, moxibustion exerted a regulatory influence on colon lncRNA and mRNA expression profiles, upregulating LOC108352929 and downregulating Phf11 in rats with UC (P <0.05). Moxibustion also led to a reduction in the expression and colocalization of Phf11 and NF-κB in the colons of UC rats. Moreover, knockdown of LOC108352929 in rat enteric glial cells demonstrated a significant upregulation of TNF-α mRNA expression (P <0.05). In summary, these data illustrate that moxibustion effectively ameliorates DSS-induced colonic injury and inflammation while exerting regulatory control over the lncRNA-mRNA co-expression network in UC rats. Collectively, the in vivo and in vitro studies suggested that LOC108352929-Phf11 may serve as a potential biological marker for moxibustion in the treatment of UC.
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Affiliation(s)
- Guona Li
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- School of Acupuncture-Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chen Zhao
- School of Acupuncture-Moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Jing Xu
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Yan Huang
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Yu Qiao
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Feng Li
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Guangbin Peng
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Shiyu Zheng
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Lu Zhu
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
| | - Ling Yang
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Zhaoqin Wang
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
| | - Huangan Wu
- Yueyang Hospital of Integrative Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200437, China
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200030, China
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Kirkland JM, Patel I, Ardeshna MS, Kopec AM. Microglial synaptic pruning in the nucleus accumbens during adolescence sex-specifically influences splenic immune outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539317. [PMID: 37205376 PMCID: PMC10187280 DOI: 10.1101/2023.05.03.539317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Strong social support promotes a variety of positive health outcomes in humans and rodent models, while social isolation in rodents shortens lifespan, perceived social isolation (i.e. loneliness) can increase mortality by up to 50% in humans. How social relationships lead to these drastic health effects is unclear, but may involve modulation of the peripheral immune system. The reward circuitry of the brain and social behaviors undergo a critical period of development during adolescence. We published that microglia-mediated synaptic pruning occurs in the nucleus accumbens (NAc) reward region during adolescence to mediate social development in male and female rats. We hypothesized that if reward circuitry activity and social relationships directly impact the peripheral immune system, then natural developmental changes in the reward circuitry and social behaviors during adolescence should also directly impact the peripheral immune system. To test this, we inhibited microglial pruning in the NAc during adolescence, and then collected spleen tissue for mass spectrometry proteomic analysis and ELISA validation. We found that the global proteomic consequences of inhibiting microglial pruning in the NAc were similar between the sexes, but target-specific examination suggests that NAc pruning impacts Th1 cell-related immune markers in the spleen in males, but not females, and broad neurochemical systems in the spleen in females, but not males.
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Affiliation(s)
- J. M. Kirkland
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College
| | - Ishan Patel
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College
| | - Monali S. Ardeshna
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College
| | - Ashley M. Kopec
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College
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3
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Mészárosová M, Mészáros G, Moravčíková N, Pavlík I, Margetín M, Kasarda R. Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep. Animals (Basel) 2022; 12:ani12111346. [PMID: 35681809 PMCID: PMC9179888 DOI: 10.3390/ani12111346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
This study explored the genomic diversity and selection signatures in two Slovakian national breeds, the Original Valachian and the Improved Valachian sheep. As they are an important animal genetic resource within the country, but with decreasing population size, our aim is to identify potentially valuable genomic regions. A total of 97 sheep (18 male and 79 female) from the Original Valachian, and 69 sheep (25 male and 44 female) from the Improved Valachian populations were genotyped using the GeneSeek GGP Ovine 50 K chip. The inbreeding levels were assessed with runs of homozygosity (ROH). The selection signatures within breeds were identified based on the top 1% of most homozygous regions within the breed, the so-called ROH islands. The selection signatures between breeds were assessed based on variance in linkage disequilibrium. Overall, we have identified selection signatures with quantitative trait loci (QTL) and genes pointing towards all three production purposes of the Valachian sheep, milk, meat, and wool, including their quality characteristics. Another group with apparent large importance was the various traits related to health and resistance to parasites, which is well in line with the sturdy nature of this breed.
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Affiliation(s)
- Mária Mészárosová
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
| | - Gábor Mészáros
- Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Gregor-Mendel-Straße 33, 1180 Vienna, Austria;
| | - Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
- Correspondence:
| | - Ivan Pavlík
- Research Institute of Animal Production—NPPC Slovakia, Hlohovecká 2, 95141 Nitra—Lužianky, Slovakia;
| | - Milan Margetín
- Faculty of Agrobiology and Food Resources, Institute of Animal Science, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Institute of Nutrition and Genomics, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (M.M.); (R.K.)
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4
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Genetic Exchange of Lung-Derived Exosome to Brain Causing Neuronal Changes on COVID-19 Infection. Mol Neurobiol 2021; 58:5356-5368. [PMID: 34312772 PMCID: PMC8313419 DOI: 10.1007/s12035-021-02485-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023]
Abstract
The pandemic of novel coronavirus 2 (SARS-CoV-2) has made global chaos for normal human living. Despite common COVID-19 symptoms, variability in clinical phenotypes was reported worldwide. Reports on SARS-CoV-2 suggest causing neurological manifestation. In addition, the susceptibility of SARS-CoV-2 in patients with neurodegenerative diseases and its complexity are largely unclear. Here, we aimed to demonstrate the possible transport of exosome from SARS-CoV-2-infected lungs to the brain regions associated with neurodegenerative diseases using multiple transcriptome datasets of SARS-CoV-2-infected lungs, RNA profiles from lung exosome, and gene expression profiles of the human brain. Upon transport, the transcription factors localized in the exosome regulate genes at lateral substantia nigra, medial substantia nigra, and superior frontal gyrus regions of Parkinson's disease (PD) and frontal cortex, hippocampus, and temporal cortex of Alzheimer's disease (AD). On SARS-CoV-2 infection, BCL3, JUND, MXD1, IRF2, IRF9, and STAT1 transcription factors in the exosomes influence the neuronal gene regulatory network and accelerate neurodegeneration. STAT1 transcription factor regulates 64 PD genes at lateral substantia nigra, 65 at superior frontal gyrus, and 19 at medial substantia nigra. Similarly, in AD, STAT1 regulates 74 AD genes at the temporal cortex, 40 genes at the hippocampus, and 16 genes at the frontal cortex. We further demonstrate that dysregulated neuronal genes showed involvement in immune response, signal transduction, apoptosis, and stress response process. In conclusion, SARS-CoV-2 may dysregulate neuronal gene regulatory network through exosomes that attenuate disease severity of neurodegeneration.
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Kane M, Mele V, Liberatore RA, Bieniasz PD. Inhibition of spumavirus gene expression by PHF11. PLoS Pathog 2020; 16:e1008644. [PMID: 32678836 PMCID: PMC7390438 DOI: 10.1371/journal.ppat.1008644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/29/2020] [Accepted: 05/19/2020] [Indexed: 01/05/2023] Open
Abstract
The foamy viruses (FV) or spumaviruses are an ancient subfamily of retroviruses that infect a variety of vertebrates. FVs are endemic, but apparently apathogenic, in modern non-human primates. Like other retroviruses, FV replication is inhibited by type-I interferon (IFN). In a previously described screen of IFN-stimulated genes (ISGs), we identified the macaque PHD finger domain protein-11 (PHF11) as an inhibitor of prototype foamy virus (PFV) replication. Here, we show that human and macaque PHF11 inhibit the replication of multiple spumaviruses, but are inactive against several orthoretroviruses. Analysis of other mammalian PHF11 proteins revealed that antiviral activity is host species dependent. Using multiple reporter viruses and cell lines, we determined that PHF11 specifically inhibits a step in the replication cycle that is unique to FVs, namely basal transcription from the FV internal promoter (IP). In so doing, PHF11 prevents expression of the viral transactivator Tas and subsequent activation of the viral LTR promoter. These studies reveal a previously unreported inhibitory mechanism in mammalian cells, that targets a family of ancient viruses and may promote viral latency.
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Affiliation(s)
- Melissa Kane
- Department of Pediatrics, Infectious Diseases Division, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Microbial Pathogenesis, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Vincent Mele
- Department of Pediatrics, Infectious Diseases Division, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Microbial Pathogenesis, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Rachel A. Liberatore
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
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6
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Makinde HM, Winter DR, Procissi D, Mike EV, Stock AD, Kando MJ, Gadhvi GT, Droho S, Bloomfield CL, Dominguez ST, Mayr MG, Lavine JA, Putterman C, Cuda CM. A Novel Microglia-Specific Transcriptional Signature Correlates With Behavioral Deficits in Neuropsychiatric Lupus. Front Immunol 2020; 11:230. [PMID: 32174913 PMCID: PMC7055359 DOI: 10.3389/fimmu.2020.00230] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
Neuropsychiatric symptoms of systemic lupus erythematosus (NP-SLE) affect over one-half of SLE patients, yet underlying mechanisms remain largely unknown. We demonstrate that SLE-prone mice (CReCOM) develop NP-SLE, including behavioral deficits prior to systemic autoimmunity, reduced brain volumes, decreased vascular integrity, and brain-infiltrating leukocytes. NP-SLE microglia exhibit numerical expansion, increased synaptic uptake, and a more metabolically active phenotype. Microglia from multiple SLE-prone models express a "NP-SLE signature" unrelated to type I interferon. Rather, the signature is associated with lipid metabolism, scavenger receptor activity and downregulation of inflammatory and chemotaxis processes, suggesting a more regulatory, anti-inflammatory profile. NP-SLE microglia also express genes associated with disease-associated microglia (DAM), a subset of microglia thought to be instrumental in neurodegenerative diseases. Further, expression of "NP-SLE" and "DAM" signatures correlate with the severity of behavioral deficits in young SLE-prone mice prior to overt systemic disease. Our data are the first to demonstrate the predictive value of our newly identified microglia-specific "NP-SLE" and "DAM" signatures as a surrogate for NP-SLE clinical outcomes and suggests that microglia-intrinsic defects precede contributions from systemic SLE for neuropsychiatric manifestations.
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Affiliation(s)
- Hadijat M Makinde
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Deborah R Winter
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Daniele Procissi
- Department of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Elise V Mike
- Division of Rheumatology, Department of Medicine, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - Ariel D Stock
- Division of Rheumatology, Department of Medicine, Albert Einstein College of Medicine, The Bronx, NY, United States
| | - Mary J Kando
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Gaurav T Gadhvi
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Steven Droho
- Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Christina L Bloomfield
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Salina T Dominguez
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Maximilian G Mayr
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jeremy A Lavine
- Department of Ophthalmology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Chaim Putterman
- Division of Rheumatology, Department of Medicine, Albert Einstein College of Medicine, The Bronx, NY, United States.,Research Division, Azrieli Faculty of Medicine and Galilee Medical Center, Nahariya, Israel
| | - Carla M Cuda
- Division of Rheumatology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
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7
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Zarei Ghobadi M, Mozhgani SH, Farzanehpour M, Behzadian F. Identifying novel biomarkers of the pediatric influenza infection by weighted co-expression network analysis. Virol J 2019; 16:124. [PMID: 31665046 PMCID: PMC6819563 DOI: 10.1186/s12985-019-1231-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022] Open
Abstract
Background Despite the high yearly prevalence of Influenza, the pathogenesis mechanism and involved genes have not been fully known. Finding the patterns and mapping the complex interactions between different genes help us to find the possible biomarkers and treatment targets. Methods Herein, weighted gene co-expression network analysis (WGCNA) was employed to construct a co-expression network among genes identified by microarray analysis of the pediatric influenza-infected samples. Results Three of the 38 modules were found as the most related modules to influenza infection. At a functional level, we found that the genes in these modules regulate the immune responses, protein targeting, and defense to virus. Moreover, the analysis of differentially expressed genes disclosed 719 DEGs between the normal and infected subjects. The comprehensive investigation of genes in the module involved in immune system and viral defense (yellow module) revealed that SP110, HERC5, SAMD9L, RTP4, C19orf66, HELZ2, EPSTI1, and PHF11 which were also identified as DEGs (except C19orf66) have the potential to be as the biomarkers and also drug targeting for the treatment of pediatric influenza. Conclusions The WGCN analysis revealed co-expressed genes which were involved in the innate immune system and defense to virus. The differentially expressed genes in the identified modules can be considered for designing drug targets. Moreover, modules can help to find pathogenesis routes in the future.
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Affiliation(s)
- Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.,Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahdieh Farzanehpour
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran
| | - Farida Behzadian
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, Iran.
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8
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Ward-Caviness CK. A review of gene-by-air pollution interactions for cardiovascular disease, risk factors, and biomarkers. Hum Genet 2019; 138:547-561. [DOI: 10.1007/s00439-019-02004-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/22/2019] [Indexed: 02/07/2023]
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9
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S-allyl cysteine inhibits TNFα-induced skeletal muscle wasting through suppressing proteolysis and expression of inflammatory molecules. Biochim Biophys Acta Gen Subj 2018; 1862:895-906. [DOI: 10.1016/j.bbagen.2017.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/15/2017] [Accepted: 12/26/2017] [Indexed: 12/20/2022]
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10
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Accornero F, Schips TG, Petrosino JM, Gu SQ, Kanisicak O, van Berlo JH, Molkentin JD. BEX1 is an RNA-dependent mediator of cardiomyopathy. Nat Commun 2017; 8:1875. [PMID: 29192139 PMCID: PMC5709413 DOI: 10.1038/s41467-017-02005-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 11/01/2017] [Indexed: 01/29/2023] Open
Abstract
Regulation of mRNA splicing, processing and stability is increasingly recognized as a critical control point in dynamically altering gene expression during stress or disease. Very little is understood of this process in heart failure. Here, we show that BEX1 is a heart failure-induced gene functioning as an mRNA-associated protein that enhances expression of a subset of cardiac disease-promoting genes. Modeling the increase in BEX1 that occurs in disease, cardiac-specific BEX1 transgenic mice show worse cardiac disease with stress stimulation, whereas Bex1 gene-deleted mice are protected from heart failure-promoting insults. Proteomic and interactive screening assays show that BEX1 is part of a large ribonucleoprotein processing complex involved in regulating proinflammatory mRNA expression in the heart. Specifically, induction of BEX1 augments the stability and expression of AU-rich element containing mRNAs typically found within proinflammatory genes. Thus, BEX1 functions as an mRNA-dependent effector that augments pathology-promoting gene expression during heart failure. Little is known about the changes in mRNA splicing, processing and stability that can alter gene expression during heart failure. Here, the authors show that BEX1 is induced during heart failure and is part of a ribonucleoprotein complex enhancing the expression and stability of proinflammatory genes.
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Affiliation(s)
- Federica Accornero
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Dorothy M. Davis Heart and Lung Research Institute, Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, 43210, USA.
| | - Tobias G Schips
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jennifer M Petrosino
- Dorothy M. Davis Heart and Lung Research Institute, Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Shan-Qing Gu
- Dorothy M. Davis Heart and Lung Research Institute, Department of Physiology and Cell Biology, Ohio State University, Columbus, OH, 43210, USA
| | - Onur Kanisicak
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Jop H van Berlo
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.,Department of Medicine, Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jeffery D Molkentin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA. .,Howard Hughes Medical Institute, Cincinnati, OH, 45229, USA.
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11
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Crespi B, Read S, Hurd P. The SETDB2 locus: evidence for a genetic link between handedness and atopic disease. Heredity (Edinb) 2017; 120:77-82. [PMID: 29234167 DOI: 10.1038/s41437-017-0004-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
The gene SETDB2, which mediates aspects of laterality in animal model systems, has recently been linked with human handedness as measured continuously on a scale from strong left to strong right. By contrast, it was marginally associated with a left-right dichotomous measure, and it showed no evidence of association with absolute handedness strength independent of direction. We genotyped the SETDB2 handedness-associated single nucleotide polymorphism, rs4942830, in a large healthy population likewise phenotyped for continuous, absolute, and dichotomous handedness variables. Our results demonstrated significant effects of rs4942830 genotype on continuous handedness, and weaker, marginal effects on dichotomous handedness, but no effects on absolute handedness. These results help to establish the locus marked by the SNP rs4942830 as a strong candidate for mediating human handedness. Intriguingly, rs4942830 is also in complete linkage disequilibrium with rs386770867, a polymorphism recently shown to affect human serum levels of IgE production and other atopic phenotypes. These findings implicate this locus in the longstanding links of handedness with asthma and other atopic diseases.
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Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, 8888 University Drive, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
| | - Silven Read
- Department of Biological Sciences, 8888 University Drive, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Peter Hurd
- Department of Psychology and Centre for Neuroscience, University of Alberta, Edmonton, T6G 2R3, Canada
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12
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Menicucci AR, Versteeg K, Woolsey C, Mire CE, Geisbert JB, Cross RW, Agans KN, Jankeel A, Geisbert TW, Messaoudi I. Transcriptome Analysis of Circulating Immune Cell Subsets Highlight the Role of Monocytes in Zaire Ebola Virus Makona Pathogenesis. Front Immunol 2017; 8:1372. [PMID: 29123522 PMCID: PMC5662559 DOI: 10.3389/fimmu.2017.01372] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 10/05/2017] [Indexed: 12/27/2022] Open
Abstract
Existing models of Ebola virus disease (EVD) suggest antigen-presenting cells are initial targets of Zaire ebolavirus (ZEBOV). In vitro studies have shown that ZEBOV infection of monocytes and macrophages results in the production of inflammatory mediators, which may cause lymphocyte apoptosis. However, these findings have not been corroborated by in vivo studies. In this study, we report the first longitudinal analysis of transcriptional changes in purified monocytes, T-cells, and B-cells isolated from cynomolgus macaques following infection with ZEBOV-Makona. Our data reveal monocytes as one of the major immune cell subsets that supports ZEBOV replication in vivo. In addition, we report a marked increase in the transcription of genes involved in inflammation, coagulation, and vascular disease within monocytes, suggesting that monocytes contribute to EVD manifestations. Further, genes important for antigen presentation and regulation of immunity were downregulated, potentially subverting development of adaptive immunity. In contrast, lymphocytes, which do not support ZEBOV replication, showed transcriptional changes limited to a small number of interferon-stimulated genes (ISGs) and a failure to upregulate genes associated with an antiviral effector immune response. Collectively, these data suggest that ZEBOV-infected monocytes play a significant role in ZEBOV-Makona pathogenesis and strategies to suppress virus replication or modify innate responses to infection in these cells should be a priority for therapeutic intervention.
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Affiliation(s)
- Andrea R Menicucci
- Division of Biomedical Sciences, University of California, Riverside, Riverside, CA, United States
| | - Krista Versteeg
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Courtney Woolsey
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Chad E Mire
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Joan B Geisbert
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Robert W Cross
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Krystle N Agans
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Allen Jankeel
- Department of Molecular Biology and Biochemistry, College of Biological Sciences, University of California, Irvine, Irvine, CA, United States
| | - Thomas W Geisbert
- Galveston National Laboratory, Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, College of Biological Sciences, University of California, Irvine, Irvine, CA, United States
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Muscat P, Mercado K, Payne K, Chahal H, Jones G. PHF11 expression and cellular distribution is regulated by the Toll-Like Receptor 3 Ligand Polyinosinic:Polycytidylic Acid in HaCaT keratinocytes. BMC Immunol 2015; 16:69. [PMID: 26573531 PMCID: PMC4647448 DOI: 10.1186/s12865-015-0131-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 11/05/2015] [Indexed: 11/10/2022] Open
Abstract
Background Inflammatory skin diseases such as atopic dermatitis and psoriasis represent a complex interaction between the skin and infiltrating immune cells, resulting in damage to the skin barrier and increased inflammation. Polymorphisms in PHF11 have been associated with dermatitis and allergy and PHF11 regulates the transcription of T-cell cytokines as well as class switching to IgE in activated B-cells. The importance of skin barrier homeostasis in the context of inflammatory skin diseases, together with reports identifying PHF11 as an interferon-induced gene, have led us to examine its role in the innate immune response of keratinocytes. Results We developed a cell culture model that allowed us to analyze the effects of the double-stranded RNA analogue poly(I:C) on a confluent cell monolayer immediately after a 24-h treatment, as well as three days after withdrawal of treatment. Immediately after treatment with poly(I:C), PHF11, IL8, and interferon-dependent ISG15 RNA expression was increased. This was accompanied by nuclear localization of PHF11 as well the tight junction protein claudin-1. Knock-down of PHF11 resulted in increased interleukin-8 expression and secretion immediately following treatment with poly(I:C), as well as changes in the cellular distribution of membrane-bound and increased nuclear claudin-1 that was observed up to 3 days after the withdrawal of poly(I:C). This was associated with lower cell density and a decrease in the number of cells in the G1 phase of the cell cycle. Conclusions In addition to a role for PHF11 in lymphocyte gene expression, we have now shown that PHF11 was part of the keratinocyte innate immune response by poly(I:C). As knock-down of PHF11 was associated with increased expression of the pro-inflammatory chemokine IL-8 and changes in the cellular distribution of claudin-1, a change normally associated with increased proliferation and migration, we suggest that PHF11 may contribute to epidermal recovery following infection or other damage.
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Affiliation(s)
- Pauline Muscat
- School of Science and Health, Western Sydney University, Locked Bag 1797, 2751, Penrith, NSW, Australia.
| | - Karessa Mercado
- School of Science and Health, Western Sydney University, Locked Bag 1797, 2751, Penrith, NSW, Australia.
| | - Kathryn Payne
- Present address: Garvan Institute for Medical Research, Darlinghurst, NSW, Australia.
| | - Hardip Chahal
- School of Science and Health, Western Sydney University, Locked Bag 1797, 2751, Penrith, NSW, Australia.
| | - Graham Jones
- School of Science and Health, Western Sydney University, Locked Bag 1797, 2751, Penrith, NSW, Australia.
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14
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Qiu X, Wu S, Hilchey SP, Thakar J, Liu ZP, Welle SL, Henn AD, Wu H, Zand MS. Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice. PLoS One 2015; 10:e0138110. [PMID: 26413862 PMCID: PMC4586376 DOI: 10.1371/journal.pone.0138110] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/26/2015] [Indexed: 01/23/2023] Open
Abstract
Current approaches to study transcriptional profiles post influenza infection typically rely on tissue sampling from one or two sites at a few time points, such as spleen and lung in murine models. In this study, we infected female C57/BL6 mice intranasally with mouse-adapted H3N2/Hong Kong/X31 avian influenza A virus, and then analyzed the gene expression profiles in four different compartments (blood, lung, mediastinal lymph nodes, and spleen) over 11 consecutive days post infection. These data were analyzed by an advanced statistical procedure based on ordinary differential equation (ODE) modeling. Vastly different lists of significant genes were identified by the same statistical procedure in each compartment. Only 11 of them are significant in all four compartments. We classified significant genes in each compartment into co-expressed modules based on temporal expression patterns. We then performed functional enrichment analysis on these co-expression modules and identified significant pathway and functional motifs. Finally, we used an ODE based model to reconstruct gene regulatory network (GRN) for each compartment and studied their network properties.
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Affiliation(s)
- Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
| | - Shuang Wu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
| | - Shannon P. Hilchey
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642 United States of America
| | - Zhi-Ping Liu
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- Department of Biomedical Engineering, Shandong University, Jinan, Shandong, China
| | - Stephen L. Welle
- Functional Genomics Center, University of Rochester, Rochester, NY, 14642, United States of America
| | - Alicia D. Henn
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14642 United States of America
| | - Hulin Wu
- Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, United States of America
- * E-mail: (HW); (MSZ)
| | - Martin S. Zand
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, 14642, United States of America
- * E-mail: (HW); (MSZ)
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15
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Heinonen MT, Laine AP, Söderhäll C, Gruzieva O, Rautio S, Melén E, Pershagen G, Lähdesmäki HJ, Knip M, Ilonen J, Henttinen TA, Kere J, Lahesmaa R. GIMAP GTPase family genes: potential modifiers in autoimmune diabetes, asthma, and allergy. THE JOURNAL OF IMMUNOLOGY 2015; 194:5885-94. [PMID: 25964488 DOI: 10.4049/jimmunol.1500016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 03/30/2015] [Indexed: 12/31/2022]
Abstract
GTPase of the immunity-associated protein (GIMAP) family members are differentially regulated during human Th cell differentiation and have been previously connected to immune-mediated disorders in animal studies. GIMAP4 is believed to contribute to the Th cell subtype-driven immunological balance via its role in T cell survival. GIMAP5 has a key role in BB-DR rat and NOD mouse lymphopenia. To elucidate GIMAP4 and GIMAP5 function and role in human immunity, we conducted a study combining genetic association in different immunological diseases and complementing functional analyses. Single nucleotide polymorphisms tagging the GIMAP haplotype variation were genotyped in Finnish type 1 diabetes (T1D) families and in a prospective Swedish asthma and allergic sensitization birth cohort. Initially, GIMAP5 rs6965571 was associated with risk for asthma and allergic sensitization (odds ratio [OR] 3.74, p = 0.00072, and OR 2.70, p = 0.0063, respectively) and protection from T1D (OR 0.64, p = 0.0058); GIMAP4 rs13222905 was associated with asthma (OR 1.28, p = 0.035) and allergic sensitization (OR 1.27, p = 0.0068). However, after false discovery rate correction for multiple testing, only the associations of GIMAP4 with allergic sensitization and GIMAP5 with asthma remained significant. In addition, transcription factor binding sites surrounding the associated loci were predicted. A gene-gene interaction in the T1D data were observed between the IL2RA rs2104286 and GIMAP4 rs9640279 (OR 1.52, p = 0.0064) and indicated between INS rs689 and GIMAP5 rs2286899. The follow-up functional analyses revealed lower IL-2RA expression upon GIMAP4 knockdown and an effect of GIMAP5 rs2286899 genotype on protein expression. Thus, the potential role of GIMAP4 and GIMAP5 as modifiers of immune-mediated diseases cannot be discarded.
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Affiliation(s)
- Mirkka T Heinonen
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Department of Biology, University of Turku, 20014 Turku, Finland; Turku Doctoral Programme of Molecular Medicine, University of Turku, 20520 Turku Finland
| | - Antti-Pekka Laine
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland
| | - Cilla Söderhäll
- Department of Bioscience and Nutrition and Center for Innovative Medicine, Karolinska Institutet, 141 83 Huddinge, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Sini Rautio
- Department of Information and Computer Science, Aalto University, 02150 Espoo, Finland
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden; Karolinska University Hospital, Astrid Lindgren Children's Hospital, 171 76 Solna, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Harri J Lähdesmäki
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland; Institute of Environmental Medicine, Karolinska Institutet, 171 65 Solna, Stockholm, Sweden
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00029 Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland; Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland; Folkhälsan Research Institute, 00290 Helsinki, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, 20520 Turku, Finland; Department of Clinical Microbiology, University of Eastern Finland, 70211 Kuopio, Finland; and
| | | | - Juha Kere
- Department of Bioscience and Nutrition and Center for Innovative Medicine, Karolinska Institutet, 141 83 Huddinge, Stockholm, Sweden; Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Riitta Lahesmaa
- Turku Centre of Biotechnology, University of Turku and Åbo Akademi University, 20520 Turku, Finland;
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16
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Ikari J, Inamine A, Yamamoto T, Watanabe-Takano H, Yoshida N, Fujimura L, Taniguchi T, Sakamoto A, Hatano M, Tatsumi K, Tokuhisa T, Arima M. Plant homeodomain finger protein 11 promotes class switch recombination to IgE in murine activated B cells. Allergy 2014; 69:223-30. [PMID: 24286306 DOI: 10.1111/all.12328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2013] [Indexed: 01/20/2023]
Abstract
BACKGROUND Polymorphisms of the Plant homeodomain finger protein 11 (PHF11) are strongly associated with high serum IgE levels and clinical severity of atopic patients. However, the precise mechanism has not been fully elucidated. We investigated the role of Phf11 in class switch recombination (CSR) to IgE by activated B cells. METHODS We generated Phf11 transgenic (Lckd-Phf11-Tg) mice that express the exogenous murine Phf11 in lymphocytes under the control of distal Lck promoter. We examined IL-4-induced CSR to IgE in activated Lckd-Phf11-Tg B cells in vitro. We analyzed production of ovalbumin (OVA)-specific IgE and nose-scratching symptoms in Lckd-Phf11-Tg mice using an OVA-induced allergic rhinitis model. RESULTS The exogenous Phf11 promoted CSR to IgG1 and IgE in activated B cells with an increase in germ line transcript (GLT) γ1 and GLT ε expression. The exogenous Phf11 augmented transcriptional activity of the GLT γ1 and GLT ε promoters through permissive histone modifications and binding of NF-κB and STAT6. Furthermore, the exogenous Phf11 bound to the GLT ε promoter with increased binding of NF-κB. Silencing of the endogenous Phf11 reduced the frequency of CSR to IgE and GLT ε expression, but not to IgG1 or GLT γ1 expression, in activated B cells. In an allergic rhinitis model, Lckd-Phf11-Tg mice showed a significant increase in the production of OVA-specific IgE and the frequency of nose scratching. CONCLUSION Phf11 accelerates CSR to IgE in activated B cells by increasing the transcriptional activity of GLT ε promoter and contributes to the exacerbation of allergic responses. These findings provide a novel therapeutic target for allergic diseases.
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Affiliation(s)
- J. Ikari
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
- Department of Respirology (B2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - A. Inamine
- Department of Otorhinolaryngology (J2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - T. Yamamoto
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - H. Watanabe-Takano
- Department of Biomedical Science (M14); Graduate School of Medicine; Chiba University; Chiba Japan
| | - N. Yoshida
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - L. Fujimura
- Biomedical Research Center; Chiba University; Chiba Japan
| | - T. Taniguchi
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - A. Sakamoto
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - M. Hatano
- Department of Biomedical Science (M14); Graduate School of Medicine; Chiba University; Chiba Japan
- Biomedical Research Center; Chiba University; Chiba Japan
| | - K. Tatsumi
- Department of Respirology (B2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - T. Tokuhisa
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
| | - M. Arima
- Department of Developmental Genetics (H2); Graduate School of Medicine; Chiba University; Chiba Japan
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17
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Kaur S, Kroczynska B, Sharma B, Sassano A, Arslan AD, Majchrzak-Kita B, Stein BL, McMahon B, Altman JK, Su B, Calogero RA, Fish EN, Platanias LC. Critical roles for Rictor/Sin1 complexes in interferon-dependent gene transcription and generation of antiproliferative responses. J Biol Chem 2014; 289:6581-6591. [PMID: 24469448 DOI: 10.1074/jbc.m113.537852] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We provide evidence that type I IFN-induced STAT activation is diminished in cells with targeted disruption of the Rictor gene, whose protein product is a key element of mTOR complex 2. Our studies show that transient or stable knockdown of Rictor or Sin1 results in defects in activation of elements of the STAT pathway and reduced STAT-DNA binding complexes. This leads to decreased expression of several IFN-inducible genes that mediate important biological functions. Our studies also demonstrate that Rictor and Sin1 play essential roles in the generation of the suppressive effects of IFNα on malignant erythroid precursors from patients with myeloproliferative neoplasms. Altogether, these findings provide evidence for critical functions for Rictor/Sin1 complexes in type I IFN signaling and the generation of type I IFN antineoplastic responses.
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Affiliation(s)
- Surinder Kaur
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Barbara Kroczynska
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Bhumika Sharma
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Antonella Sassano
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Ahmet Dirim Arslan
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Beata Majchrzak-Kita
- Toronto Research Institute, University Health Network and Department of Immunology, University of Toronto, Toronto, Ontario M5S 2J7, Canada
| | - Brady L Stein
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Brandon McMahon
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611
| | - Jessica K Altman
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611; Division of Hematology-Oncology, Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612
| | - Bing Su
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Raffaele A Calogero
- Department of Biotechnology and Health Sciences, University of Turin, 8 Turin, Italy
| | - Eleanor N Fish
- Toronto Research Institute, University Health Network and Department of Immunology, University of Toronto, Toronto, Ontario M5S 2J7, Canada
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center and Division of Hematology-Oncology, Department of Medicine, Northwestern University Medical School, Chicago, Illinois 60611; Division of Hematology-Oncology, Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois 60612.
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18
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The role of Vitamin D level and related single nucleotide polymorphisms in Crohn's disease. Nutrients 2013; 5:3898-909. [PMID: 24084050 PMCID: PMC3820050 DOI: 10.3390/nu5103898] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/19/2013] [Accepted: 09/12/2013] [Indexed: 12/11/2022] Open
Abstract
New Zealand has one of the highest rates of Crohn's Disease (CD) in the world, and there is much speculation as to why this might be. A high risk of CD has been associated with deficient or insufficient levels of Vitamin D (Vit D), lifestyle as well as various genetic polymorphisms. In this study we sought to analyse the relevance of serum Vit D levels, lifestyle and genotype to CD status. Serum samples were analysed for 25-OH-Vitamin D levels. DNA was isolated from blood and cheek-swabs, and Sequenom and ImmunoChip techniques were used for genotyping. Serum Vit D levels were significantly lower in CD patients (mean = 49.5 mg/L) than those found in controls (mean = 58.9 mg/L, p = 4.74 × 10⁻⁶). A total of seven single nucleotide polymorphisms were examined for effects on serum Vit D levels, with adjustment for confounding variables. Two variants: rs731236[A] (VDR) and rs732594[A] (SCUBE3) showed a significant association with serum Vit D levels in CD patients. Four variants: rs7975232[A] (VDR), rs732594[A] (SCUBE3), and rs2980[T] and rs2981[A] (PHF-11) showed a significant association with serum Vit D levels in the control group. This study demonstrates a significant interaction between Vit D levels and CD susceptibility, as well as a significant association between Vit D levels and genotype.
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19
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PKB-mediated PHF20 phosphorylation on Ser291 is required for p53 function in DNA damage. Cell Signal 2013; 25:74-84. [DOI: 10.1016/j.cellsig.2012.09.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2012] [Revised: 08/20/2012] [Accepted: 09/05/2012] [Indexed: 11/18/2022]
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20
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Juhász A, Gell G, Sebestyén E, Haraszi R, Tamás L, Balázs E. Brachypodium distachyon as a model for defining the allergen potential of non-prolamin proteins. Funct Integr Genomics 2012; 12:439-46. [PMID: 22933233 PMCID: PMC3431475 DOI: 10.1007/s10142-012-0294-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/07/2012] [Accepted: 08/09/2012] [Indexed: 01/28/2023]
Abstract
Epitope databases and the protein sequences of published plant genomes are suitable to identify some of the proteins causing food allergies and sensitivities. Brachypodium distachyon, a diploid wild grass with a sequenced genome and low prolamin content, is the closest relative of the allergen cereals, such as wheat or barley. Using the Brachypodium genome sequence, a workflow has been developed to identify potentially harmful proteins which may cause either celiac disease or wheat allergy-related symptoms. Seed tissue-specific expression of the potential allergens has been determined, and intact epitopes following an in silico digestion with several endopeptidases have been identified. Molecular function of allergen proteins has been evaluated using Gene Ontology terms. Biologically overrepresented proteins and potentially allergen protein families have been identified.
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Affiliation(s)
- A Juhász
- Applied Genomics Department, Agricultural Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Brunszvik 2, Martonvásár, Hungary.
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Abstract
PURPOSE OF REVIEW The aim is to update current understanding of the genes identified by the recent genome-wide association studies (GWASs) of asthma and its associated traits. The review also discusses how to dissect the functional roles of novel genes in future research. RECENT FINDINGS More than 10 GWAS aimed at identifying the genes underlying asthma and relevant traits have been published in the past 3 years. The largest of these was from the GABRIEL consortium, which discovered that the IL18R1, IL33, SMAD3, ORMDL3, HLA-DQ and IL2RB loci were all significantly associated with asthma. Many novel asthma genes, including those previously identified by positional cloning, are expressed within the respiratory epithelium, emphasizing the importance of epithelial barriers in causing asthma . The genes controlling IgE levels have surprisingly little overlap with the genes mediating asthma susceptibility, suggesting that atopy is secondary to asthma rather than a primary driver of the disease. The next challenge will be the systematic analysis of the precise functions of these genes in the pathogenesis of asthma. SUMMARY GWAS have uncovered many novel genes underlying asthma and detailed functional dissection of their roles in asthma will point the way to new therapies for the disease.
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Relevance and implication of genetic determinants to asthma pathophysiology. Curr Opin Allergy Clin Immunol 2012; 11:407-13. [PMID: 21822132 DOI: 10.1097/aci.0b013e32834a9540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW The number of single nucleotide polymorphisms (SNPs) found to be associated with asthma and related phenotypes outnumbers those with functional impacts. In this review we briefly described some of the approaches used to investigate functionality of SNPs, and summarized recent findings related to the characterization of functional SNPs in asthma. RECENT FINDINGS For disease-associated SNPs residing in the promoter or 3' untranslated regions, differential protein binding affinity between the major and minor alleles is often the first logical area of investigation. In this review, we described SNPs associated with asthma or related phenotypes in five genes which in the past 12 months have new data implicating potential mechanisms in asthma development. SUMMARY Variability in treatment responses poses a great challenge in asthma management. It is established that the genetic makeup of individuals plays a role in asthma development, yet the mechanisms remain unclear. Investigations on the functional impacts of disease-associated SNPs will help us gain insights into potential disease mechanisms, and ultimately lead to effective therapies for those who suffer from asthma.
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