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Chiu KHY, Yip CCY, Poon RWS, Leung KH, Li X, Hung IFN, To KKW, Cheng VCC, Yuen KY. Correlations of Myeloperoxidase (MPO), Adenosine deaminase (ADA), C-C motif chemokine 22 (CCL22), Tumour necrosis factor alpha (TNFα) and Interleukin-6 (IL-6) mRNA expression in the nasopharyngeal specimens with the diagnosis and severity of SARS-CoV-2 infections. Emerg Microbes Infect 2023; 12:2157338. [PMID: 36482706 PMCID: PMC9809351 DOI: 10.1080/22221751.2022.2157338] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytokine dynamics in patients with coronavirus disease 2019 (COVID-19) have been studied in blood but seldomly in respiratory specimens. We studied different cell markers and cytokines in fresh nasopharyngeal swab specimens for the diagnosis and for stratifying the severity of COVID-19. This was a retrospective case-control study comparing Myeloperoxidase (MPO), Adenosine deaminase (ADA), C-C motif chemokine ligand 22 (CCL22), Tumour necrosis factor alpha (TNFα) and Interleukin-6 (IL-6) mRNA expression in 490 (327 patients and 163 control) nasopharyngeal specimens from 317 (154 COVID-19 and 163 control) hospitalized patients. Of the 154 COVID-19 cases, 46 died. Both total and normalized MPO, ADA, CCL22, TNFα, and IL-6 mRNA expression levels were significantly higher in the nasopharyngeal specimens of infected patients when compared with controls, with ADA showing better performance (OR 5.703, 95% CI 3.424-9.500, p < 0.001). Receiver operating characteristics (ROC) curve showed that the cut-off value of normalized ADA mRNA level at 2.37 × 10-3 had a sensitivity of 81.8% and specificity of 83.4%. While patients with severe COVID-19 had more respiratory symptoms, and elevated lactate dehydrogenase, multivariate analysis showed that severe COVID-19 patients had lower CCL22 mRNA (OR 0.211, 95% CI 0.060-0.746, p = 0.016) in nasopharyngeal specimens, while lymphocyte count, C-reactive protein, and viral load in nasopharyngeal specimens did not correlate with disease severity. In summary, ADA appears to be a better biomarker to differentiate between infected and uninfected patients, while CCL22 has the potential in stratifying the severity of COVID-19.
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Affiliation(s)
- Kelvin Hei-Yeung Chiu
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Cyril Chik-Yan Yip
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Rosana Wing-Shan Poon
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kit-Hang Leung
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Xin Li
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ivan Fan-Ngai Hung
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China,Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, , Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region, China
| | - Vincent Chi-Chung Cheng
- Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Disease, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China,Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, , Hong Kong Science and Technology Park, Pak Shek Kok, Hong Kong Special Administrative Region, China, Kwok-Yung Yuen
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2
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Nuñez R, Rodriguez MJ, Palomares F, Gomez F, Jabato FM, Cordoba-Caballero J, Seoane P, Losada J, Rojo J, Torres MJ, Perkins JR, Mayorga C. Transcriptional changes in dendritic cells underlying allergen specific induced tolerance in a mouse model. Sci Rep 2022; 12:2797. [PMID: 35181694 PMCID: PMC8857182 DOI: 10.1038/s41598-022-06186-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
To investigate food allergy-tolerance mechanisms induced through allergen-specific immunotherapy we used RNA-Sequencing to measure gene expression in lymph-node-derived dendritic cells from Pru p 3-anaphylactic mice after immunotherapy with glycodendropeptides at 2 nM and 5 nM, leading to permanent tolerance and short-term desensitization, respectively. Gene expression was also measured in mice receiving no immunotherapy (anaphylaxis); and in which anaphylaxis could never occur (antigen-only). Compared to anaphylaxis, the antigen-only group showed the greatest number of expression-changes (411), followed by tolerant (186) and desensitized (119). Only 29 genes changed in all groups, including Il12b, Cebpb and Ifngr1. The desensitized group showed enrichment for genes related to chronic inflammatory response, secretory granule, and regulation of interleukin-12 production; the tolerant group showed genes related to cytokine receptor activity and glucocorticoid receptor binding, suggesting distinct pathways for similar outcomes. We identified genes and processes potentially involved in the restoration of long-term tolerance via allergen-specific immunotherapy, representing potential prognostic biomarkers.
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Affiliation(s)
- Rafael Nuñez
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
| | - Maria Jose Rodriguez
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
| | - Francisca Palomares
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
| | - Francisca Gomez
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Fernando M Jabato
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
| | | | - Pedro Seoane
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Jorge Losada
- Laboratory of Carbohydrates, Instituto de Investigaciones Químicas (IIQ), CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Javier Rojo
- Laboratory of Carbohydrates, Instituto de Investigaciones Químicas (IIQ), CSIC-Universidad de Sevilla, Sevilla, Spain
| | - Maria Jose Torres
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain
- Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain
- Medicine Department, Universidad de Málaga-UMA, Málaga, Spain
| | - James Richard Perkins
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain
- Department of Molecular Biology and Biochemistry, University of Malaga, Malaga, Spain
- CIBER de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristobalina Mayorga
- Allergy Research Group, Research Laboratory, Allergy Unit, Hospital Regional Universitario de Málaga-IBIMA, Instituto de Investigación Biomédica de Málaga-IBIMA, 29009, Málaga, Spain.
- Allergy Clinical Unit, Hospital Regional Universitario de Málaga, Málaga, Spain.
- Nanostructures for Diagnosing and Treatment of Allergic Diseases Laboratory, Centro Andaluz de Nanomedicina y Biotecnología-BIONAND, Málaga, Spain.
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Liu BHM, Tey SK, Mao X, Ma APY, Yeung CLS, Wong SWK, Ng TH, Xu Y, Yao Y, Fung EYM, Tan KV, Khong P, Ho DW, Ng IO, Tang AHN, Cai SH, Yun JP, Yam JWP. TPI1-reduced extracellular vesicles mediated by Rab20 downregulation promotes aerobic glycolysis to drive hepatocarcinogenesis. J Extracell Vesicles 2021; 10:e12135. [PMID: 34401050 PMCID: PMC8357635 DOI: 10.1002/jev2.12135] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/30/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022] Open
Abstract
Rab GTPases are major mediators that ensure the proper spatiotemporal regulation of intracellular trafficking. Functional impairment and altered expression of Rab proteins have been revealed in various human cancers. There is an emerging evidence about the role of Rab proteins in the biogenesis of extracellular vesicles (EVs). In hepatocellular carcinoma (HCC), using RNA sequencing comparing expression profiles of adjacent non-tumorous tissues and HCC, Rab20 is identified to be the most frequently downregulated Rab member in HCC. Functionally, restoration of Rab20 in metastatic HCC cells results in the release of EVs with a diminished activity to promote cell growth, motility and metastasis. Conversely, EVs released from normal liver cells with Rab20 knockdown loses suppressive effect on HCC cell growth and motility. Proteomic profiling revealed the level of triosephosphate isomerase 1 (TPI1), a glycolytic enzyme, in EVs to be positively associated with Rab20 expression of the releasing cells. TPI1 targeted to be expressed in EVs released by Rab20 knockdown cells compromises the oncogenic activity of EVs. Besides, EVs released by TPI1 knockdown cells recapitulates the promoting effect of EVs derived from HCC cells with Rab20 underexpression. Aerobic glycolysis is beneficial to the survival and proliferation of tumour cells. Here, we observed that the enhanced cell growth and motility are driven by the enhanced aerobic glycolysis induced by EVs with reduced TPI1. The addition of glycolytic inhibitor blocks the promoting effect of EVs with reduced TPI1. Taken together, our study provides a mechanistic link among tumour cell-derived EVs and glucose metabolism in HCC with Rab20 deregulation.
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Affiliation(s)
- Bonnie Hei Man Liu
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Sze Keong Tey
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Xiaowen Mao
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Angel Po Yee Ma
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Cherlie Lot Sum Yeung
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Samuel Wan Ki Wong
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Tung Him Ng
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Yi Xu
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Department of Hepatopancreatobiliary SurgerySecond Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Yue Yao
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- Department of EndocrinologySecond Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Eva Yi Man Fung
- Department of ChemistryState Key Laboratory of Synthetic ChemistryThe University of Hong KongHong KongChina
| | - Kel Vin Tan
- Department of Diagnostic RadiologyQueen Mary Hospitalthe University of Hong KongHong KongChina
| | - Pek‐Lan Khong
- Department of Diagnostic RadiologyQueen Mary Hospitalthe University of Hong KongHong KongChina
| | - Daniel Wai‐Hung Ho
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- State Key Laboratory of Liver Research (The University of Hong Kong)Hong KongChina
| | - Irene Oi‐Lin Ng
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- State Key Laboratory of Liver Research (The University of Hong Kong)Hong KongChina
| | - Alexander Hin Ning Tang
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
| | - Shao Hang Cai
- Department of Infectious DiseasesNanfang HospitalSouthern Medical UniversityGuangzhouChina
| | - Jing Ping Yun
- Department of PathologySun Yat‐sen University Cancer CentreGuangzhouChina
| | - Judy Wai Ping Yam
- Department of PathologyLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongChina
- State Key Laboratory of Liver Research (The University of Hong Kong)Hong KongChina
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4
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Human Monocytes Plasticity in Neurodegeneration. Biomedicines 2021; 9:biomedicines9070717. [PMID: 34201693 PMCID: PMC8301413 DOI: 10.3390/biomedicines9070717] [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: 05/12/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 01/09/2023] Open
Abstract
Monocytes play a crucial role in immunity and tissue homeostasis. They constitute the first line of defense during the inflammatory process, playing a role in the pathogenesis and progression of diseases, making them an attractive therapeutic target. They are heterogeneous in morphology and surface marker expression, which suggest different molecular and physiological properties. Recent evidences have demonstrated their ability to enter the brain, and, as a consequence, their hypothetical role in different neurodegenerative diseases. In this review, we will discuss the current knowledge about the correlation between monocyte dysregulation in the brain and/or in the periphery and neurological diseases in humans. Here we will focus on the most common neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and multiple sclerosis.
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5
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Bruno M, Dewi IM, Matzaraki V, ter Horst R, Pekmezovic M, Rösler B, Groh L, Röring RJ, Kumar V, Li Y, Carvalho A, Netea MG, Latgé JP, Gresnigt MS, van de Veerdonk FL. Comparative host transcriptome in response to pathogenic fungi identifies common and species-specific transcriptional antifungal host response pathways. Comput Struct Biotechnol J 2020; 19:647-663. [PMID: 33510868 PMCID: PMC7817431 DOI: 10.1016/j.csbj.2020.12.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
Candidiasis, aspergillosis, and mucormycosis cause the majority of nosocomial fungal infections in immunocompromised patients. Using an unbiased transcriptional profiling in PBMCs exposed to the fungal species causing these infections, we found a core host response in healthy individuals that may govern effective fungal clearance: it consists of 156 transcripts, involving canonical and non-canonical immune pathways. Systematic investigation of key steps in antifungal host defense revealed fungal-specific signatures. As previously demonstrated, Candida albicans induced type I and Type II interferon-related pathways. In contrast, central pattern recognition receptor, reactive oxygen species production, and host glycolytic pathways were down-regulated in response to Rhizopus oryzae, which was associated with an ER-stress response. TLR5 was identified to be uniquely regulated by Aspergillus fumigatus and to control cytokine release in response to this fungus. In conclusion, our data reveals the transcriptional profiles induced by C. albicans, A. fumigatus, and R. oryzae, and describes both the common and specific antifungal host responses that could be exploited for novel therapeutic strategies.
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Affiliation(s)
- Mariolina Bruno
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Intan M.W. Dewi
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vicky Matzaraki
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob ter Horst
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marina Pekmezovic
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a 07745, Jena, Germany
| | - Berenice Rösler
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laszlo Groh
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rutger J. Röring
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vinod Kumar
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yang Li
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Centre for Individualised Infection Medicine (CiiM) and TWINCORE, Joint Ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B’s – PT Government Associate Laboratory, Guimarães/Braga, Portugal
| | - Mihai G. Netea
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | | | - Mark S. Gresnigt
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
- Junior Research Group Adaptive Pathogenicity Strategies, Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Beutenbergstraße 11a 07745, Jena, Germany
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboudumc Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
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6
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Guo CC, Majewski T, Zhang L, Yao H, Bondaruk J, Wang Y, Zhang S, Wang Z, Lee JG, Lee S, Cogdell D, Zhang M, Wei P, Grossman HB, Kamat A, Duplisea JJ, Ferguson JE, Huang H, Dadhania V, Gao J, Dinney C, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Cell Rep 2020; 27:1781-1793.e4. [PMID: 31067463 DOI: 10.1016/j.celrep.2019.04.048] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/28/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022] Open
Abstract
Sarcomatoid urothelial bladder cancer (SARC) displays a high propensity for distant metastasis and is associated with short survival. We report a comprehensive genomic analysis of 28 cases of SARC and 84 cases of conventional urothelial carcinoma (UC), with the TCGA cohort of 408 muscle-invasive bladder cancers serving as the reference. SARCs show a distinct mutational landscape, with enrichment of TP53, RB1, and PIK3CA mutations. They are related to the basal molecular subtype of conventional UCs and could be divided into epithelial-basal and more clinically aggressive mesenchymal subsets on the basis of TP63 and its target gene expression levels. Other analyses reveal that SARCs are driven by downregulation of homotypic adherence genes and dysregulation of the EMT network, and nearly half exhibit a heavily infiltrated immune phenotype. Our observations have important implications for prognostication and the development of more effective therapies for this highly lethal variant of bladder cancer.
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Affiliation(s)
- Charles C Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Hui Yao
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yan Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shizhen Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - June Goo Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Miao Zhang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - H Barton Grossman
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ashish Kamat
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - James Edward Ferguson
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - He Huang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vipulkumar Dadhania
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N Weinstein
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keith Baggerly
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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7
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Assessment of Luminal and Basal Phenotypes in Bladder Cancer. Sci Rep 2020; 10:9743. [PMID: 32546765 PMCID: PMC7298008 DOI: 10.1038/s41598-020-66747-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/21/2020] [Indexed: 12/11/2022] Open
Abstract
Genomic profiling studies have demonstrated that bladder cancer can be divided into two molecular subtypes referred to as luminal and basal with distinct clinical behaviors and sensitivities to frontline chemotherapy. We analyzed the mRNA expressions of signature luminal and basal genes in bladder cancer tumor samples from publicly available and MD Anderson Cancer Center cohorts. We developed a quantitative classifier referred to as basal to luminal transition (BLT) score which identified the molecular subtypes of bladder cancer with 80–94% sensitivity and 83–93% specificity. In order to facilitate molecular subtyping of bladder cancer in primary care centers, we analyzed the protein expressions of signature luminal (GATA3) and basal (KRT5/6) markers by immunohistochemistry, which identified molecular subtypes in over 80% of the cases. In conclusion, we provide a tool for assessment of molecular subtypes of bladder cancer in routine clinical practice.
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8
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Regulation of Small GTPase Rab20 by Ikaros in B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2020; 21:ijms21051718. [PMID: 32138279 PMCID: PMC7084408 DOI: 10.3390/ijms21051718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/20/2020] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Ikaros is a DNA-binding protein that regulates gene expression and functions as a tumor suppressor in B-cell acute lymphoblastic leukemia (B-ALL). The full cohort of Ikaros target genes have yet to be identified. Here, we demonstrate that Ikaros directly regulates expression of the small GTPase, Rab20. Using ChIP-seq and qChIP we assessed Ikaros binding and the epigenetic signature at the RAB20 promoter. Expression of Ikaros, CK2, and RAB20 was determined by qRT-PCR. Overexpression of Ikaros was achieved by retroviral transduction, whereas shRNA was used to knockdown Ikaros and CK2. Regulation of transcription from the RAB20 promoter was analyzed by luciferase reporter assay. The results showed that Ikaros binds the RAB20 promoter in B-ALL. Gain-of-function and loss-of-function experiments demonstrated that Ikaros represses RAB20 transcription via chromatin remodeling. Phosphorylation by CK2 kinase reduces Ikaros’ affinity toward the RAB20 promoter and abolishes its ability to repress RAB20 transcription. Dephosphorylation by PP1 phosphatase enhances both Ikaros’ DNA-binding affinity toward the RAB20 promoter and RAB20 repression. In conclusion, the results demonstrated opposing effects of CK2 and PP1 on expression of Rab20 via control of Ikaros’ activity as a transcriptional regulator. A novel regulatory signaling network in B-cell leukemia that involves CK2, PP1, Ikaros, and Rab20 is identified.
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Smith HG, Mansfield D, Roulstone V, Kyula-Currie JN, McLaughlin M, Patel RR, Bergerhoff KF, Paget JT, Dillon MT, Khan A, Melcher A, Thway K, Harrington KJ, Hayes AJ. PD-1 Blockade Following Isolated Limb Perfusion with Vaccinia Virus Prevents Local and Distant Relapse of Soft-tissue Sarcoma. Clin Cancer Res 2019; 25:3443-3454. [PMID: 30885937 DOI: 10.1158/1078-0432.ccr-18-3767] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/16/2019] [Accepted: 03/08/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE The prevention and treatment of metastatic sarcoma are areas of significant unmet need. Immune checkpoint inhibitor monotherapy has shown little activity in sarcoma and there is great interest in identifying novel treatment combinations that may augment responses. In vitro and in vivo, we investigated the potential for an oncolytic vaccinia virus (GLV-1h68) delivered using isolated limb perfusion (ILP) to promote antitumor immune responses and augment response to PD-1 blockade in sarcoma.Experimental Design: In an established animal model of extremity sarcoma, we evaluated the potential of locoregional delivery of a vaccinia virus (GLV-1h68) alongside biochemotherapy (melphalan/TNFα) in ILP. Complementary in vitro assays for markers of immunogenic cell death were performed in sarcoma cell lines. RESULTS PD-1 monotherapy had minimal efficacy in vivo, mimicking the clinical scenario. Pretreatment with GLV-1h68 delivered by ILP (viral ILP) significantly improved responses. Furthermore, when performed prior to surgery and radiotherapy, viral ILP and PD-1 blockade prevented both local and distant relapse, curing a previously treatment-refractory model. Enhanced therapy was associated with marked modulation of the tumor microenvironment, with an increase in the number and penetrance of intratumoral CD8+ T cells and expansion and activation of dendritic cells. GLV-1h68 was capable of inducing markers of immunogenic cell death in human sarcoma cell lines. CONCLUSIONS Viral ILP augments the response to PD-1 blockade, transforming this locoregional therapy into a potentially effective systemic treatment for sarcoma and warrants translational evaluation.
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Affiliation(s)
- Henry G Smith
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
- The Sarcoma Unit, Department of Academic Surgery, The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - David Mansfield
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Victoria Roulstone
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Joan N Kyula-Currie
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Martin McLaughlin
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Radhika R Patel
- Flow Cytometry and Light Microscopy Facility, The Institute of Cancer Research, London, United Kingdom
| | | | - James T Paget
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Magnus T Dillon
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Aadil Khan
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Alan Melcher
- Translational Immunotherapy Team, The Institute of Cancer Research, London, United Kingdom
| | - Khin Thway
- The Sarcoma Unit, Department of Academic Surgery, The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
| | - Kevin J Harrington
- Targeted Therapy Team, The Institute of Cancer Research, London, United Kingdom.
| | - Andrew J Hayes
- The Sarcoma Unit, Department of Academic Surgery, The Royal Marsden Hospital NHS Foundation Trust, London, United Kingdom
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10
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Cooles FAH, Anderson AE, Skelton A, Pratt AG, Kurowska-Stolarska MS, McInnes I, Hilkens CMU, Isaacs JD. Phenotypic and Transcriptomic Analysis of Peripheral Blood Plasmacytoid and Conventional Dendritic Cells in Early Drug Naïve Rheumatoid Arthritis. Front Immunol 2018; 9:755. [PMID: 29867920 PMCID: PMC5968398 DOI: 10.3389/fimmu.2018.00755] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 03/27/2018] [Indexed: 12/27/2022] Open
Abstract
Objective Dendritic cells (DCs) are key orchestrators of immune function. To date, rheumatoid arthritis (RA) researchers have predominantly focused on a potential pathogenic role for CD1c+ DCs. In contrast, CD141+ DCs and plasmacytoid DCs (pDCs) have not been systematically examined, at least in early RA. In established RA, the role of pDCs is ambiguous and, since disease duration and treatment both impact RA pathophysiology, we examined pDCs, and CD1c+ and CD141+ conventional DCs (cDCs), in early, drug-naïve RA (eRA) patients. Methods We analyzed the frequency and phenotype of pDCs, CD1c+, and CD141+ DCs from eRA patients and compared findings with healthy controls. In parallel, we performed transcriptional analysis of >600 immunology-related genes (Nanostring) from peripheral blood pDCs, CD1c+ DCs, B cells, T cells, and monocytes. Results All DC subsets were reduced in eRA (n = 44) compared with healthy controls (n = 30) and, for pDCs, this was most marked in seropositive patients. CD141+ and CD1c+ DCs, but not pDCs, had a comparatively activated phenotype at baseline (increased CD86) and CD1c+ DC frequency inversely associated with disease activity. All DC frequencies remained static 12 months after initiation of immunomodulatory therapy despite a fall in activation markers (e.g., HLA-DR, CD40). There was no association between the whole blood interferon gene signature (IGS) and pDC or CD1c+ DC parameters but an inverse association between CD141+ DC frequency and IGS was noted. Furthermore, IFN-I and IFN-III mRNA transcripts were comparable between eRA pDC and other leukocyte subsets (B cells, CD4+, and CD8+ T cells and monocytes) with no obvious circulating cellular source of IFN-I or IFN-III. Transcriptomic analysis suggested increased pDC and CD1c+ DC proliferation in eRA; pDC differentially expressed genes also suggested enhanced tolerogenic function, whereas for CD1c+ DCs, pro-inflammatory transcripts were upregulated. Discussion This is the first detailed examination of DC subsets in eRA peripheral blood. Compared with CD1c+ DCs, pDCs are less activated and may be skewed toward tolerogenic functions. CD141+ DCs may be implicated in RA pathophysiology. Our findings justify further investigation of early RA DC biology.
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Affiliation(s)
- Faye A H Cooles
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amy E Anderson
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew Skelton
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Arthur G Pratt
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mariola S Kurowska-Stolarska
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), University of Glasgow, Glasgow, United Kingdom
| | - Iain McInnes
- Institute of Infection, Immunity and Inflammation, University of Glasgow, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), University of Glasgow, Glasgow, United Kingdom
| | - Catharien M U Hilkens
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John D Isaacs
- Institute of Cellular Medicine, Newcastle University and National Institute for Health Research Newcastle Biomedical Research Centre at Newcastle upon Tyne Hospitals NHS Foundation Trust and Newcastle University, Newcastle upon Tyne, United Kingdom.,Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence (RACE), Newcastle University, Newcastle upon Tyne, United Kingdom
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11
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Vendelova E, Ashour D, Blank P, Erhard F, Saliba AE, Kalinke U, Lutz MB. Tolerogenic Transcriptional Signatures of Steady-State and Pathogen-Induced Dendritic Cells. Front Immunol 2018. [PMID: 29541071 PMCID: PMC5835767 DOI: 10.3389/fimmu.2018.00333] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dendritic cells (DCs) are key directors of tolerogenic and immunogenic immune responses. During the steady state, DCs maintain T cell tolerance to self-antigens by multiple mechanisms including inducing anergy, deletion, and Treg activity. All of these mechanisms help to prevent autoimmune diseases or other hyperreactivities. Different DC subsets contribute to pathogen recognition by expression of different subsets of pattern recognition receptors, including Toll-like receptors or C-type lectins. In addition to the triggering of immune responses in infected hosts, most pathogens have evolved mechanisms for evasion of targeted responses. One such strategy is characterized by adopting the host’s T cell tolerance mechanisms. Understanding these tolerogenic mechanisms is of utmost importance for therapeutic approaches to treat immune pathologies, tumors and infections. Transcriptional profiling has developed into a potent tool for DC subset identification. Here, we review and compile pathogen-induced tolerogenic transcriptional signatures from mRNA profiling data of currently available bacterial- or helminth-induced transcriptional signatures. We compare them with signatures of tolerogenic steady-state DC subtypes to identify common and divergent strategies of pathogen induced immune evasion. Candidate molecules are discussed in detail. Our analysis provides further insights into tolerogenic DC signatures and their exploitation by different pathogens.
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Affiliation(s)
- Emilia Vendelova
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Diyaaeldin Ashour
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Patrick Blank
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | | | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Manfred B Lutz
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
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12
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Sander J, Schultze JL, Yosef N. ImpulseDE: detection of differentially expressed genes in time series data using impulse models. Bioinformatics 2018; 33:757-759. [PMID: 27797772 DOI: 10.1093/bioinformatics/btw665] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
Summary Perturbations in the environment lead to distinctive gene expression changes within a cell. Observed over time, those variations can be characterized by single impulse-like progression patterns. ImpulseDE is an R package suited to capture these patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes across time points from a single or between two time courses from two experiments. To optimize running time, the code uses clustering and multi-threading. By applying ImpulseDE , we demonstrate its power to represent underlying biology of gene expression in microarray and RNA-Seq data. Availability and Implementation ImpulseDE is available on Bioconductor ( https://bioconductor.org/packages/ImpulseDE/ ). Contact niryosef@berkeley.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jil Sander
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, 53115, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, 53115, Germany.,Single Cell Genomics and Epigenomics Unit at the University of Bonn and the German Center for Neurodegenerative Diseases, Bonn, Germany
| | - Nir Yosef
- Electrical Engineering and Computer Science, Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720-1776, USA
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13
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Fumagalli S, Torri A, Papagna A, Citterio S, Mainoldi F, Foti M. IL-22 is rapidly induced by Pathogen Recognition Receptors Stimulation in Bone-Marrow-derived Dendritic Cells in the Absence of IL-23. Sci Rep 2016; 6:33900. [PMID: 27652524 PMCID: PMC5031995 DOI: 10.1038/srep33900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 09/04/2016] [Indexed: 02/08/2023] Open
Abstract
In vertebrates, microorganisms are recognized by pathogen recognition receptors (PRRs). Exposure of immune cells to the ligands of these receptors activates intracellular signaling cascades that rapidly induce the expression of a variety of genes. Within these genes, the cytokines family plays a crucial function because of its role in adaptive immunity induction and in tissue-specific functional regulation, such as tissue repair and tissue homeostasis during steady state conditions. Within the myeloid compartment, dendritic cells (DCs) release a variety of inflammatory cytokines in response to microbes. In this study, we show that BMDCs release IL-22 directly upon PRRs activation without the need of IL-23 signaling as reported for other IL22-producing cells. Moreover, we demonstrate that cytokine IL-22 is rapidly released in a cell-specific manner as macrophages are not able to produce IL-22 through the same PRRs system. In addition, we characterize the intracellular signaling cascade required for IL-22 release in BMDCs. Myd88, MEK1/2, NFkb and AhR, but not p38, NFAT, and RORgt, were found to be involved in IL-22 regulation in DCs. Our study suggests that BMDCs possess a unique intracellular molecular plasticity which, once activated, directs different BMDCs functions in a cell-specific manner.
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Affiliation(s)
- Silvia Fumagalli
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, 20126, Italy
| | - Anna Torri
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, 20126, Italy
| | - Angela Papagna
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, 20126, Italy
| | - Stefania Citterio
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, 20126, Italy
| | - Federica Mainoldi
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, 20126, Italy
| | - Maria Foti
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, 20126, Italy
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14
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Tumor necrosis is an important hallmark of aggressive endometrial cancer and associates with hypoxia, angiogenesis and inflammation responses. Oncotarget 2016; 6:39676-91. [PMID: 26485755 PMCID: PMC4741854 DOI: 10.18632/oncotarget.5344] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/26/2015] [Indexed: 02/01/2023] Open
Abstract
Aims Tumor necrosis is associated with aggressive features of endometrial cancer and poor prognosis. Here, we investigated gene expression patterns and potential treatment targets related to presence of tumor necrosis in primary endometrial cancer lesions. Methods and Results By DNA microarray analysis, expression of genes related to tumor necrosis reflected multiple tumor-microenvironment interactions like tissue hypoxia, angiogenesis and inflammation pathways. A tumor necrosis signature of 38 genes and a related patient cluster (Cluster I, 67% of the cases) were associated with features of aggressive tumors such as type II cancers, estrogen receptor negative tumors and vascular invasion. Further, the tumor necrosis signature was increased in tumor cells grown in hypoxic conditions in vitro. Multiple genes with increased expression are known to be activated by HIF1A and NF-kB. Conclusions Our findings indicate that the presence of tumor necrosis within primary tumors is associated with hypoxia, angiogenesis and inflammation responses. HIF1A, NF-kB and PI3K/mTOR might be potential treatment targets in aggressive endometrial cancers with presence of tumor necrosis.
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15
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Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205. J Immunol Res 2015; 2015:585078. [PMID: 26380324 PMCID: PMC4563097 DOI: 10.1155/2015/585078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
The filamentous bacteriophage fd, codisplaying antigenic determinants and a single chain antibody fragment directed against the dendritic cell receptor DEC-205, is a promising vaccine candidate for its safety and its ability to elicit innate and adaptive immune response in absence of adjuvants. By using a system vaccinology approach based on RNA-Sequencing (RNA-Seq) analysis, we describe a relevant gene modulation in dendritic cells pulsed with anti-DEC-205 bacteriophages fd. RNA-Seq data analysis indicates that the bacteriophage fd virions are sensed as a pathogen by dendritic cells; they activate the danger receptors that trigger an innate immune response and thus confer a strong adjuvanticity that is needed to obtain a long-lasting adaptive immune response.
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16
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Pei G, Schnettger L, Bronietzki M, Repnik U, Griffiths G, Gutierrez MG. Interferon-γ-inducible Rab20 regulates endosomal morphology and EGFR degradation in macrophages. Mol Biol Cell 2015; 26:3061-70. [PMID: 26157167 PMCID: PMC4551319 DOI: 10.1091/mbc.e14-11-1547] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 07/01/2015] [Indexed: 12/22/2022] Open
Abstract
IFN-γ is able to modulate endosome dynamics in myelocytic cells, but the molecular mechanisms behind this process remain to be elucidated. Rab20 is identified as part of the molecular machinery that links immune activation and control of endocytic function in macrophages. Little is known about the molecular players that regulate changes in the endocytic pathway during immune activation. Here we investigate the role of Rab20 in the endocytic pathway during activation of macrophages. Rab20 is associated with endocytic structures, but the function of this Rab GTPase in the endocytic pathway remains poorly characterized. We find that in macrophages, Rab20 expression and endosomal association significantly increase after interferon-γ (IFN-γ) treatment. Moreover, IFN-γ and Rab20 expression induce a dramatic enlargement of endosomes. These enlarged endosomes are the result of homotypic fusion promoted by Rab20 expression. The expression of Rab20 or the dominant-negative mutant Rab20T19N does not affect transferrin or dextran 70 kDa uptake. However, knockdown of Rab20 accelerates epidermal growth factor (EGF) trafficking to LAMP-2–positive compartments and EGF receptor degradation. Thus this work defines a function for Rab20 in the endocytic pathway during immune activation of macrophages.
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Affiliation(s)
- Gang Pei
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Laura Schnettger
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, United Kingdom
| | - Marc Bronietzki
- Research Group Phagosome Biology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Urska Repnik
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Gareth Griffiths
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
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17
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Plaza-Diaz J, Gomez-Llorente C, Fontana L, Gil A. Modulation of immunity and inflammatory gene expression in the gut, in inflammatory diseases of the gut and in the liver by probiotics. World J Gastroenterol 2014; 20:15632-15649. [PMID: 25400447 PMCID: PMC4229528 DOI: 10.3748/wjg.v20.i42.15632] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/04/2014] [Accepted: 06/23/2014] [Indexed: 02/06/2023] Open
Abstract
The potential for the positive manipulation of the gut microbiome through the introduction of beneficial microbes, as also known as probiotics, is currently an active area of investigation. The FAO/WHO define probiotics as live microorganisms that confer a health benefit to the host when administered in adequate amounts. However, dead bacteria and bacterial molecular components may also exhibit probiotic properties. The results of clinical studies have demonstrated the clinical potential of probiotics in many pathologies, such as allergic diseases, diarrhea, inflammatory bowel disease and viral infection. Several mechanisms have been proposed to explain the beneficial effects of probiotics, most of which involve gene expression regulation in specific tissues, particularly the intestine and liver. Therefore, the modulation of gene expression mediated by probiotics is an important issue that warrants further investigation. In the present paper, we performed a systematic review of the probiotic-mediated modulation of gene expression that is associated with the immune system and inflammation. Between January 1990 to February 2014, PubMed was searched for articles that were published in English using the MeSH terms “probiotics" and "gene expression" combined with “intestines", "liver", "enterocytes", "antigen-presenting cells", "dendritic cells", "immune system", and "inflammation". Two hundred and five original articles matching these criteria were initially selected, although only those articles that included specific gene expression results (77) were later considered for this review and separated into three major topics: the regulation of immunity and inflammatory gene expression in the gut, in inflammatory diseases of the gut and in the liver. Particular strains of Bifidobacteria, Lactobacilli, Escherichia coli, Propionibacterium, Bacillus and Saccharomyces influence the gene expression of mucins, Toll-like receptors, caspases, nuclear factor-κB, and interleukins and lead mainly to an anti-inflammatory response in cultured enterocytes. In addition, the interaction of commensal bacteria and probiotics with the surface of antigen-presenting cells in vitro results in the downregulation of pro-inflammatory genes that are linked to inflammatory signaling pathways, whereas other anti-inflammatory genes are upregulated. The effects of probiotics have been extensively investigated in animal models ranging from fish to mice, rats and piglets. These bacteria induce a tolerogenic and hyporesponsive immune response in which many genes that are related to the immune system, in particular those genes expressing anti-inflammatory cytokines, are upregulated. By contrast, information related to gene expression in human intestinal cells mediated by the action of probiotics is scarce. There is a need for further clinical studies that evaluate the mechanism of action of probiotics both in healthy humans and in patients with chronic diseases. These types of clinical studies are necessary for addressing the influence of these microorganisms in gene expression for different pathways, particularly those that are associated with the immune response, and to better understand the role that probiotics might have in the prevention and treatment of disease.
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18
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Lin J, Yin YY, Qin T, Zhu LQ, Yu QH, Yang Q. Enhanced immune response of BMDCs pulsed with H9N2 AIV and CpG. Vaccine 2014; 32:6783-90. [PMID: 25454862 DOI: 10.1016/j.vaccine.2014.10.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/02/2014] [Accepted: 10/03/2014] [Indexed: 12/25/2022]
Abstract
Dendritic cells (DCs), professional antigen presenting cells, have demonstrated effective in controlling the initial of innate immune, while CpG could improve the performance of immune system. To explore the mechanism of CpG enhancing the immune response, we compared different stimulated mouse DCs with systemic approach microarrays. Analysis revealed 1840 differentially expressed genes in H9N2 stimulated group, more than 1728 altered genes in inactive H9N2 group. Investigation also proved that CpG/inactive H9N2 co-stimulation changed 2140 genes, more than that in H9N2 group, strongly demonstrated that CpG improved the performance of inactive H9N2 vaccination. Pathways analysis founded that DCs response rapid to shift in their maturation state, which involved Toll-like receptor (TLR) pathway significantly. Microarrays results were also verified by qRT-PCR with 14 elected representative genes. Further analysis proved that co-stimulatory molecules (CD40, CD80, CD86 and MHC-II), regulatory protein (IRF-7 and TRAF-6) and pro-inflammatory cytokines (IL-1, IL-6 and IL-12) were all changed and involved in DCs maturation. At last we demonstrated TLR signalling pathway in chicken bone marrow-derived dendritic cells (chBM-DCs) stimulated with CpG. The distinct transcriptional profiles of DCs pulsed with various stimuli expanded our understanding of how DCs respond and recognize influenza.
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Affiliation(s)
- Jian Lin
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, China; Nanjing Agricultural University, Wei gang 1, Jiangsu, PR China
| | - Yin Y Yin
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, China; Nanjing Agricultural University, Wei gang 1, Jiangsu, PR China
| | - Tao Qin
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, China; Nanjing Agricultural University, Wei gang 1, Jiangsu, PR China
| | - Li Q Zhu
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, China; Nanjing Agricultural University, Wei gang 1, Jiangsu, PR China
| | - Qing H Yu
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, China; Nanjing Agricultural University, Wei gang 1, Jiangsu, PR China
| | - Qian Yang
- Key Lab of Animal Physiology and Biochemistry, Ministry of Agriculture, Nanjing Agricultural University, China.
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19
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Goeman F, De Nicola F, D'Onorio De Meo P, Pallocca M, Elmi B, Castrignanò T, Pesole G, Strano S, Blandino G, Fanciulli M, Muti P. VDR primary targets by genome-wide transcriptional profiling. J Steroid Biochem Mol Biol 2014; 143:348-56. [PMID: 24726990 DOI: 10.1016/j.jsbmb.2014.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 03/18/2014] [Accepted: 03/23/2014] [Indexed: 12/14/2022]
Abstract
There is growing evidence that 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) plays a role in breast cancer prevention and survival. It elicits a variety of antitumor activities like controlling cellular differentiation, proliferation and angiogenesis. Most of its biological effects are exerted via its nuclear receptor which acts as a transcriptional regulator. Here, we carried out a genome-wide investigation of the primary transcriptional targets of 1α,25(OH)2D3 in breast epithelial cancer cells using RNA-Seq technology. We identified early transcriptional targets of 1α,25(OH)2D3 involved in adhesion, growth regulation, angiogenesis, actin cytoskeleton regulation, hexose transport, inflammation and immunomodulation, apoptosis, endocytosis and signaling. Furthermore, we found several transcription factors to be regulated by 1α,25(OH)2D3 that subsequently amplify and diversify the transcriptional output driven by 1α,25(OH)2D3 leading finally to a growth arrest of the cells. Moreover, we could show that 1α,25(OH)2D3 elevates the trimethylation of histone H3 lysine 4 at several target gene promoters. Our present transcriptomic analysis of differential expression after 1α,25(OH)2D3 treatment provides a resource of primary 1α,25(OH)2D3 targets that might drive the antiproliferative action in breast cancer epithelial cells.
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Affiliation(s)
- Frauke Goeman
- Translational Oncogenomics Unit, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | - Francesca De Nicola
- Laboratory of Epigenetic, Molecular Medicine Area, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | | | - Matteo Pallocca
- Translational Oncogenomics Unit, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | - Berardino Elmi
- Laboratory of Epigenetic, Molecular Medicine Area, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | | | - Graziano Pesole
- Institute of Biomembranes and Bioenergetics of the National Research Council and Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70125 Bari, Italy.
| | - Sabrina Strano
- Molecular Chemoprevention Unit, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | - Giovanni Blandino
- Translational Oncogenomics Unit, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | - Maurizio Fanciulli
- Laboratory of Epigenetic, Molecular Medicine Area, Italian National Cancer Institute "Regina Elena", 00144 Rome, Italy.
| | - Paola Muti
- Department of Oncology, McMaster University, Main Street West Hamilton, ON L8S 4K1, Canada.
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A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells. PLoS One 2014; 9:e100613. [PMID: 24949855 PMCID: PMC4065045 DOI: 10.1371/journal.pone.0100613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/28/2014] [Indexed: 12/24/2022] Open
Abstract
Dendritic cells (DCs) are critical for regulating CD4 and CD8 T cell immunity, controlling Th1, Th2, and Th17 commitment, generating inducible Tregs, and mediating tolerance. It is believed that distinct DC subsets have evolved to control these different immune outcomes. However, how DC subsets mount different responses to inflammatory and/or tolerogenic signals in order to accomplish their divergent functions remains unclear. Lipopolysaccharide (LPS) provides an excellent model for investigating responses in closely related splenic DC subsets, as all subsets express the LPS receptor TLR4 and respond to LPS in vitro. However, previous studies of the LPS-induced DC transcriptome have been performed only on mixed DC populations. Moreover, comparisons of the in vivo response of two closely related DC subsets to LPS stimulation have not been reported in the literature to date. We compared the transcriptomes of murine splenic CD8 and CD11b DC subsets after in vivo LPS stimulation, using RNA-Seq and systems biology approaches. We identified subset-specific gene signatures, which included multiple functional immune mediators unique to each subset. To explain the observed subset-specific differences, we used a network analysis approach. While both DC subsets used a conserved set of transcription factors and major signalling pathways, the subsets showed differential regulation of sets of genes that ‘fine-tune’ the network Hubs expressed in common. We propose a model in which signalling through common pathway components is ‘fine-tuned’ by transcriptional control of subset-specific modulators, thus allowing for distinct functional outcomes in closely related DC subsets. We extend this analysis to comparable datasets from the literature and confirm that our model can account for cell subset-specific responses to LPS stimulation in multiple subpopulations in mouse and man.
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Duffy D, Rouilly V, Libri V, Hasan M, Beitz B, David M, Urrutia A, Bisiaux A, Labrie ST, Dubois A, Boneca IG, Delval C, Thomas S, Rogge L, Schmolz M, Quintana-Murci L, Albert ML. Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli. Immunity 2014; 40:436-50. [PMID: 24656047 DOI: 10.1016/j.immuni.2014.03.002] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 01/15/2014] [Indexed: 12/24/2022]
Abstract
Standardization of immunophenotyping procedures has become a high priority. We have developed a suite of whole-blood, syringe-based assay systems that can be used to reproducibly assess induced innate or adaptive immune responses. By eliminating preanalytical errors associated with immune monitoring, we have defined the protein signatures induced by (1) medically relevant bacteria, fungi, and viruses; (2) agonists specific for defined host sensors; (3) clinically employed cytokines; and (4) activators of T cell immunity. Our results provide an initial assessment of healthy donor reference values for induced cytokines and chemokines and we report the failure to release interleukin-1α as a common immunological phenotype. The observed naturally occurring variation of the immune response may help to explain differential susceptibility to disease or response to therapeutic intervention. The implementation of a general solution for assessment of functional immune responses will help support harmonization of clinical studies and data sharing.
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Affiliation(s)
- Darragh Duffy
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France; INSERM U818, 75015 Paris, France; Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Vincent Rouilly
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France; Center for Bioinformatics, Institut Pasteur, 75015 Paris, France
| | - Valentina Libri
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France
| | - Milena Hasan
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France
| | - Benoit Beitz
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France
| | - Mikael David
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France
| | - Alejandra Urrutia
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France; INSERM U818, 75015 Paris, France; Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Aurélie Bisiaux
- INSERM U818, 75015 Paris, France; Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | | | - Annick Dubois
- Center for the Integration of Clinical Research, Institut Pasteur, 75015 Paris, France
| | - Ivo G Boneca
- Laboratory of Biology & Genetics of the Bacterial Cell Wall, Department of Microbiology, Institut Pasteur, 75015 Paris, France; INSERM, Equipe Avenir, 75015 Paris, France
| | - Cécile Delval
- Center for the Integration of Clinical Research, Institut Pasteur, 75015 Paris, France
| | - Stéphanie Thomas
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France; INSERM U818, 75015 Paris, France; Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Lars Rogge
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France; Laboratory of Immunoregulation, Department of Immunology, Institut Pasteur, 75015 Paris, France
| | - Manfred Schmolz
- Myriad Rules Based Medicine, Inc., 72770 Reutlingen, Germany
| | - Lluis Quintana-Murci
- Laboratory of Human Evolutionary Genetics, Department of Genomes & Genetics, Institut Pasteur, 75015 Paris, France; CNRS URA3012, 75015 Paris, France.
| | - Matthew L Albert
- Center for Human Immunology, Institut Pasteur, 75015 Paris, France; INSERM U818, 75015 Paris, France; Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, 75015 Paris, France; INSERM UMS20, 75015 Paris, France.
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Neddylation plays an important role in the regulation of murine and human dendritic cell function. Blood 2013; 122:2062-73. [PMID: 23863900 DOI: 10.1182/blood-2013-02-486373] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Posttranslational protein modifications (PTMs) are necessary for cells to function properly. The role of PTMs in regulating immune responses, specifically those mediated by dendritic cells (DCs), which are critical for both innate and adaptive immunity, is not well understood. Utilizing multiple but complementary approaches, we determined the role of an important but less understood type of PTM, namely, neddylation, in regulating DC functions. Inhibition of neddylation suppressed the release of proinflammatory cytokines by DCs in response to Toll-like receptor, nucleotide oligomerization domain-like receptor, and noninfectious CD40L stimulation. These effects were more profound than those mediated by the proteasome inhibitor bortezomib or a commonly used antiinflammatory agent, dexamethasone. Targeting neddylation also suppressed the ability of DCs to stimulate murine allogeneic T cells in vitro and in vivo and human allogeneic T-cell responses in vitro. Mechanistic studies demonstrated that inhibition of neddylation reduced both canonical and noncanonical nuclear factor-κB (NF-κB) activity. Neddylation inhibition prevented the degradation of inhibitor-κB and thus reduced the translocation and activation of NF-κB, but without perturbation of the mitogen-activated protein kinase/extracellular signal-regulated kinase pathway. Thus, blocking neddylation could be a novel strategy for mitigating immune-mediated disease processes.
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23
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Tavares AH, Derengowski LS, Ferreira KS, Silva SS, Macedo C, Bocca AL, Passos GA, Almeida SR, Silva-Pereira I. Murine dendritic cells transcriptional modulation upon Paracoccidioides brasiliensis infection. PLoS Negl Trop Dis 2012; 6:e1459. [PMID: 22235359 PMCID: PMC3250510 DOI: 10.1371/journal.pntd.0001459] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Accepted: 11/18/2011] [Indexed: 02/02/2023] Open
Abstract
Limited information is available regarding the modulation of genes involved in the innate host response to Paracoccidioides brasiliensis, the etiologic agent of paracoccidioidomycosis. Therefore, we sought to characterize, for the first time, the transcriptional profile of murine bone marrow-derived dendritic cells (DCs) at an early stage following their initial interaction with P. brasiliensis. DCs connect innate and adaptive immunity by recognizing invading pathogens and determining the type of effector T-cell that mediates an immune response. Gene expression profiles were analyzed using microarray and validated using real-time RT-PCR and protein secretion studies. A total of 299 genes were differentially expressed, many of which are involved in immunity, signal transduction, transcription and apoptosis. Genes encoding the cytokines IL-12 and TNF-α, along with the chemokines CCL22, CCL27 and CXCL10, were up-regulated, suggesting that P. brasiliensis induces a potent proinflammatory response in DCs. In contrast, pattern recognition receptor (PRR)-encoding genes, particularly those related to Toll-like receptors, were down-regulated or unchanged. This result prompted us to evaluate the expression profiles of dectin-1 and mannose receptor, two other important fungal PRRs that were not included in the microarray target cDNA sequences. Unlike the mannose receptor, the dectin-1 receptor gene was significantly induced, suggesting that this β-glucan receptor participates in the recognition of P. brasiliensis. We also used a receptor inhibition assay to evaluate the roles of these receptors in coordinating the expression of several immune-related genes in DCs upon fungal exposure. Altogether, our results provide an initial characterization of early host responses to P. brasiliensis and a basis for better understanding the infectious process of this important neglected pathogen. Paracoccidioidomycosis is a systemic disease that has an important mortality and morbidity impact in Latin America, mainly affecting rural workers of Argentina, Colombia, Venezuela and Brazil. Upon host infection, one of the most important aspects contributing to disease outcome is the initial encounter of the Paracoccidioides brasiliensis fungus with dendritic cells. This phagocytic cell is specialized in decoding microbial information and triggering specific immune responses. Thus, using a molecular biology technique to examine the response of thousand of genes, we aimed to identify the ways in which murine dendritic cells interact with P. brasiliensis during an early time point following infection. This approach allowed us to recognize diverse modulated genes, in particular those associated with a proinflamatory response and fungal recognition. Our work provides an initial molecular characterization of early infection process and should promote further investigations into the innate host response to this important fungal pathogen.
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Affiliation(s)
- Aldo H. Tavares
- Faculdade de Ceilândia, Universidade de Brasília, Brasília, Brasil
| | | | - Karen S. Ferreira
- Departamento de Ciências Biológicas, Universidade Federal de São Paulo, São Paulo, Brasil
| | - Simoneide S. Silva
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brasil
| | - Cláudia Macedo
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brasil
| | - Anamélia L. Bocca
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brasil
| | - Geraldo A. Passos
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brasil
| | - Sandro R. Almeida
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, Brasil
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Pletinckx K, Stijlemans B, Pavlovic V, Laube R, Brandl C, Kneitz S, Beschin A, De Baetselier P, Lutz MB. Similar inflammatory DC maturation signatures induced by TNF or Trypanosoma brucei antigens instruct default Th2-cell responses. Eur J Immunol 2011; 41:3479-94. [PMID: 21928284 DOI: 10.1002/eji.201141631] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 07/20/2011] [Accepted: 09/15/2011] [Indexed: 12/14/2022]
Abstract
DCs represent the major cell type leading to polarized T-helper (Th) cell responses in vivo. Here, we asked whether the instruction of murine Th2 responses by DCs matured with the proinflammatory cytokine TNF is qualitatively different from maturation by different types of TLR4/MyD88-dependent variant-specific surface glycoproteins (VSGs) of Trypanosoma brucei (T. brucei). The results obtained by analyzing DC surface markers, Notch ligand mRNA, cytokines, asthma, and experimental autoimmune encephalomyelitis (EAE) models as well as performing microarrays indicate that both types of stimuli induce similar inflammatory, semi-mature DC profiles. DCs matured by TNF or VSG treatment expressed a common inflammatory signature of 24 genes correlating with their Th2-polarization capacity. However, the same 24 genes and 4498 additional genes were expressed by DCs treated with LPS that went on to induce Th1 cells. These findings support the concept of a default pathway for Th2-cell induction in DCs matured under suboptimal or inflammatory conditions, independent of the surface receptors and signaling pathways involved. Our data also indicate that quantitative differences in DC maturation might direct Th2- vs Th1-cell responses, since suboptimally matured inflammatory DCs induce default Th2-cell maturation, whereas fully mature DCs induce Th1-cell maturation.
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Affiliation(s)
- Katrien Pletinckx
- Institute of Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany
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25
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Calle ML, Urrea V, Boulesteix AL, Malats N. AUC-RF: a new strategy for genomic profiling with random forest. Hum Hered 2011; 72:121-32. [PMID: 21996641 DOI: 10.1159/000330778] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 07/11/2011] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Genomic profiling, the use of genetic variants at multiple loci simultaneously for the prediction of disease risk, requires the selection of a set of genetic variants that best predicts disease status. The goal of this work was to provide a new selection algorithm for genomic profiling. METHODS We propose a new algorithm for genomic profiling based on optimizing the area under the receiver operating characteristic curve (AUC) of the random forest (RF). The proposed strategy implements a backward elimination process based on the initial ranking of variables. RESULTS AND CONCLUSIONS We demonstrate the advantage of using the AUC instead of the classification error as a measure of predictive accuracy of RF. In particular, we show that the use of the classification error is especially inappropriate when dealing with unbalanced data sets. The new procedure for variable selection and prediction, namely AUC-RF, is illustrated with data from a bladder cancer study and also with simulated data. The algorithm is publicly available as an R package, named AUCRF, at http://cran.r-project.org/.
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Affiliation(s)
- M Luz Calle
- Systems Biology Department, University of Vic, Spain. malu.calle @ uvic.cat
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26
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Porter GW, Yi W, Denzin LK. TLR agonists downregulate H2-O in CD8alpha- dendritic cells. THE JOURNAL OF IMMUNOLOGY 2011; 187:4151-60. [PMID: 21918198 DOI: 10.4049/jimmunol.1003137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Peptide loading of MHC class II (MHCII) molecules is catalyzed by the nonclassical MHCII-related molecule H2-M. H2-O, another MHCII-like molecule, associates with H2-M and modulates H2-M function. The MHCII presentation pathway is tightly regulated in dendritic cells (DCs), yet how the key modulators of MHCII presentation, H2-M and H2-O, are affected in different DC subsets in response to maturation is unknown. In this study, we show that H2-O is markedly downregulated in vivo in mouse CD8α(-) DCs in response to a broad array of TLR agonists. In contrast, CD8α(+) DCs only modestly downregulated H2-O in response to TLR agonists. H2-M levels were slightly downmodulated in both CD8α(-) and CD8α(+) DCs. As a consequence, H2-M/H2-O ratios significantly increased for CD8α(-) but not for CD8α(+) DCs. The TLR-mediated downregulation was DC specific, as B cells did not show significant H2-O and H2-M downregulation. TLR4 signaling was required to mediate DC H2-O downregulation in response to LPS. Finally, our studies showed that the mechanism of H2-O downregulation was likely due to direct protein degradation of H2-O as well as downregulation of H2-O mRNA levels. The differential H2-O and H2-M modulation after DC maturation supports the proposed roles of CD8α(-) DCs in initiating CD4-restricted immune responses by optimal MHCII presentation and of CD8α(+) DCs in promoting immune tolerance via presentation of low levels of MHCII-peptide.
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Affiliation(s)
- Gavin W Porter
- Immunology Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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27
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Sommariva M, De Cecco L, De Cesare M, Sfondrini L, Ménard S, Melani C, Delia D, Zaffaroni N, Pratesi G, Uva V, Tagliabue E, Balsari A. TLR9 agonists oppositely modulate DNA repair genes in tumor versus immune cells and enhance chemotherapy effects. Cancer Res 2011; 71:6382-90. [PMID: 21878529 DOI: 10.1158/0008-5472.can-11-1285] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Synthetic oligodeoxynucleotides expressing CpG motifs (CpG-ODN) are a Toll-like receptor 9 (TLR9) agonist that can enhance the antitumor activity of DNA-damaging chemotherapy and radiation therapy in preclinical mouse models. We hypothesized that the success of these combinations is related to the ability of CpG-ODN to modulate genes involved in DNA repair. We conducted an in silico analysis of genes implicated in DNA repair in data sets obtained from murine colon carcinoma cells in mice injected intratumorally with CpG-ODN and from splenocytes in mice treated intraperitoneally with CpG-ODN. CpG-ODN treatment caused downregulation of DNA repair genes in tumors. Microarray analyses of human IGROV-1 ovarian carcinoma xenografts in mice treated intraperitoneally with CpG-ODN confirmed in silico findings. When combined with the DNA-damaging drug cisplatin, CpG-ODN significantly increased the life span of mice compared with individual treatments. In contrast, CpG-ODN led to an upregulation of genes involved in DNA repair in immune cells. Cisplatin-treated patients with ovarian carcinoma as well as anthracycline-treated patients with breast cancer who are classified as "CpG-like" for the level of expression of CpG-ODN modulated DNA repair genes have a better outcome than patients classified as "CpG-untreated-like," indicating the relevance of these genes in the tumor cell response to DNA-damaging drugs. Taken together, the findings provide evidence that the tumor microenvironment can sensitize cancer cells to DNA-damaging chemotherapy, thereby expanding the benefits of CpG-ODN therapy beyond induction of a strong immune response.
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Affiliation(s)
- Michele Sommariva
- Department of Human Morphology and Biomedical Sciences Città Studi, Università degli Studi di Milano, Italy
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Tuana G, Volpato V, Ricciardi-Castagnoli P, Zolezzi F, Stella F, Foti M. Classification of dendritic cell phenotypes from gene expression data. BMC Immunol 2011; 12:50. [PMID: 21875438 PMCID: PMC3179938 DOI: 10.1186/1471-2172-12-50] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 08/29/2011] [Indexed: 12/31/2022] Open
Abstract
Background The selection of relevant genes for sample classification is a common task in many gene expression studies. Although a number of tools have been developed to identify optimal gene expression signatures, they often generate gene lists that are too long to be exploited clinically. Consequently, researchers in the field try to identify the smallest set of genes that provide good sample classification. We investigated the genome-wide expression of the inflammatory phenotype in dendritic cells. Dendritic cells are a complex group of cells that play a critical role in vertebrate immunity. Therefore, the prediction of the inflammatory phenotype in these cells may help with the selection of immune-modulating compounds. Results A data mining protocol was applied to microarray data for murine cell lines treated with various inflammatory stimuli. The learning and validation data sets consisted of 155 and 49 samples, respectively. The data mining protocol reduced the number of probe sets from 5,802 to 10, then from 10 to 6 and finally from 6 to 3. The performances of a set of supervised classification models were compared. The best accuracy, when using the six following genes --Il12b, Cd40, Socs3, Irgm1, Plin2 and Lgals3bp-- was obtained by Tree Augmented Naïve Bayes and Nearest Neighbour (91.8%). Using the smallest set of three genes --Il12b, Cd40 and Socs3-- the performance remained satisfactory and the best accuracy was with Support Vector Machine (95.9%). These data mining models, using data for the genes Il12b, Cd40 and Socs3, were validated with a human data set consisting of 27 samples. Support Vector Machines (71.4%) and Nearest Neighbour (92.6%) gave the worst performances, but the remaining models correctly classified all the 27 samples. Conclusions The genes selected by the data mining protocol proposed were shown to be informative for discriminating between inflammatory and steady-state phenotypes in dendritic cells. The robustness of the data mining protocol was confirmed by the accuracy for a human data set, when using only the following three genes: Il12b, Cd40 and Socs3. In summary, we analysed the longitudinal pattern of expression in dendritic cells stimulated with activating agents with the aim of identifying signatures that would predict or explain the dentritic cell response to an inflammatory agent.
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Affiliation(s)
- Giacomo Tuana
- Genopolis Consortium, University of Milano-Bicocca, Milan, 20126, Italy
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29
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Toufeer M, Bonnefont CMD, Foulon E, Caubet C, Tasca C, Aurel MR, Robert-Granié C, Rupp R, Foucras G. Gene expression profiling of dendritic cells reveals important mechanisms associated with predisposition to Staphylococcus infections. PLoS One 2011; 6:e22147. [PMID: 21857913 PMCID: PMC3155527 DOI: 10.1371/journal.pone.0022147] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 06/19/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Staphylococcus aureus is a major pathogen of humans and animals and emerging antibiotic-resistant strains have further increased the concern of this health issue. Host genetics influence susceptibility to S. aureus infections, and the genes determining the outcome of infections should be identified to find alternative therapies to treatment with antibiotics. Here, we used outbred animals from a divergent selection based on susceptibility towards Staphylococcus infection to explore host immunogenetics. METHODOLOGY/PRINCIPAL FINDINGS We investigated how dendritic cells respond to heat-inactivated S. aureus and whether dendritic cells from animals showing different degrees of susceptibility had distinct gene expression profiles. We measured gene expression levels of in vitro S. aureus-stimulated bone marrow-derived dendritic cells at three different time points (0, 3 and 8 hrs) by using 15 k ovine Agilent microarrays. Furthermore, differential expression of a selected number of genes was confirmed by RT-qPCR. Gene signatures of stimulated DCs were obtained and showed that genes involved in the inflammatory process and T helper cell polarization were highly up-regulated upon stimulation. Moreover, a set of 204 genes were statistically differentially expressed between susceptible and resistant animals, and grouped them according to their predisposition to staphylococcal infection. Interestingly, over-expression of the C1q and Ido1 genes was observed in the resistant line and suggested a role of classical pathway of complement and early regulation of inflammation pathways, respectively. On the contrary, over expression of genes involved in the IL1R pathway was observed in susceptible animals. Furthermore, the leucocyte extravasation pathway was also found to be dominant in the susceptible line. CONCLUSION/SIGNIFICANCE We successfully obtained Staphylococcus aureus associated gene expression of ovine BM-DC in an 8-hour kinetics experiment. The distinct transcriptional profiles of dendritic cells obtained from resistant and susceptible animals may explain susceptibility towards S. aureus infections in a broader context.
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Affiliation(s)
- Mehdi Toufeer
- Université de Toulouse, INP, ENVT; UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
| | - Cécile M. D. Bonnefont
- Université de Toulouse, INP, ENVT; UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
- INRA, UR631, SAGA, Castanet-Tolosan, France
| | - Eliane Foulon
- Université de Toulouse, INP, ENVT; UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
| | - Cécile Caubet
- Université de Toulouse, INP, ENVT; UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
| | - Christian Tasca
- Université de Toulouse, INP, ENVT; UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
| | | | | | | | - Gilles Foucras
- Université de Toulouse, INP, ENVT; UMR 1225, IHAP, Toulouse, France
- INRA, UMR1225, IHAP, Toulouse, France
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Liu WM, Dennis JL, Fowler DW, Dalgleish AG. The gene expression profile of unstimulated dendritic cells can be used as a predictor of function. Int J Cancer 2011; 130:979-90. [PMID: 21455985 DOI: 10.1002/ijc.26101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 03/23/2011] [Indexed: 11/09/2022]
Abstract
Dendritic cells (DCs) represent a subset of professional antigen presenting cell (APC) whose role is to elicit immune responses against harmful antigens. They have been used in DC vaccines to stimulate the immune system to kill cancer cells. However, successes in clinical trials have been limited, which may be attributed to a lack of appreciation of the quality of DCs used. In the present study, whole human genome microarrays were used to examine alterations in gene expression of monocyte-derived DCs after stimulation with supernatants derived from tumours. Our primary aim was to investigate the possibility of a gene signature for DCs that could be used to forecast responsiveness to tumour stimuli. Results showed that DCs are divided into two groups based on their ability to increase costimulatory markers and to trigger T-cell responses. The gene profiles of the immature DCs from these two groups were distinct, with particular divergence in genes from the interleukin (IL) 8 and thrombospondin-1 hubs. A subpanel of genes was identified, whose signature of expression was capable of predicting DC-stimulatory capacity. Overall, these studies have highlighted a gene-based screen that predicts DC function, which could be used to guide DC-vaccine trials.
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Affiliation(s)
- Wai M Liu
- Department of Oncology, Division of Clinical Sciences, St George's University of London, London, United Kingdom.
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31
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Dose-dependent immunomodulation of human dendritic cells by the probiotic Lactobacillus rhamnosus Lcr35. PLoS One 2011; 6:e18735. [PMID: 21533162 PMCID: PMC3078917 DOI: 10.1371/journal.pone.0018735] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/10/2011] [Indexed: 12/23/2022] Open
Abstract
The response of the immune system to probiotics remains controversial. Some strains modulate the cytokine production of dendritic cells (DCs) in vitro and induce a regulatory response, while others induce conversely a pro-inflammatory response. These strain-dependent effects are thought to be linked to specific interactions between bacteria and pattern recognition receptors. We investigated the effects of a well characterized probiotic strain, Lactobacillus rhamnosus Lcr35, on human monocyte-derived immature DCs, using a wide range of bacterial concentrations (multiplicity of infection, MOI, from 0.01 to 100). DNA microarray and qRT-PCR analysis showed that the probiotic induced a large-scale change in gene expression (nearly 1,700 modulated genes, with 3-fold changes), but only with high doses (MOI, 100). The upregulated genes were mainly involved in immune response and identified a molecular signature of inflammation according to the model of Torri. Flow cytometry analysis also revealed a dose-dependent maturation of the DC membrane phenotype, until DCs reached a semi-mature state, with an upregulation of the membrane expression of CD86, CD83, HLA-DR and TLR4, associated with a down-regulation of DC-SIGN, MR and CD14. Measurement of the DC-secreted cytokines showed that Lcr35 induced a strong dose-dependent increase of the pro-Th1/Th17 cytokine levels (TNFα, IL-1β, IL-12p70, IL-12p40 and IL-23), but only a low increase in IL-10 concentration. The probiotic L. rhamnosus Lcr35 therefore induce a dose-dependent immunomodulation of human DCs leading, at high doses, to the semi-maturation of the cells and to a strong pro-inflammatory effect. These results contribute to a fuller understanding of the mechanism of action of this probiotic, and thus of its potential clinical indications in the treatment of either infectious or IgE-dependent allergic diseases.
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Chen X, Wang M, Zhang H. The use of classification trees for bioinformatics. WILEY INTERDISCIPLINARY REVIEWS. DATA MINING AND KNOWLEDGE DISCOVERY 2011; 1:55-63. [PMID: 22523608 PMCID: PMC3329156 DOI: 10.1002/widm.14] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Classification trees are non-parametric statistical learning methods that incorporate feature selection and interactions, possess intuitive interpretability, are efficient, and have high prediction accuracy when used in ensembles. This paper provides a brief introduction to the classification tree-based methods, a review of the recent developments, and a survey of the applications in bioinformatics and statistical genetics.
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Chen X, Wang M, Zhang H. The use of classification trees for bioinformatics. WILEY INTERDISCIPLINARY REVIEWS. DATA MINING AND KNOWLEDGE DISCOVERY 2011. [PMID: 22523608 DOI: 10.1002/widm.8] [Citation(s) in RCA: 409] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Classification trees are non-parametric statistical learning methods that incorporate feature selection and interactions, possess intuitive interpretability, are efficient, and have high prediction accuracy when used in ensembles. This paper provides a brief introduction to the classification tree-based methods, a review of the recent developments, and a survey of the applications in bioinformatics and statistical genetics.
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