1
|
Bosman-Schluep D, de Pril R, Verbaken B, Legent A, Stallen J, de Jong EC, Janssen RAJ. siRNA-based identification of IBD-related targets in human monocyte-derived dendritic cells. J Immunol Methods 2021; 494:113058. [PMID: 33891922 DOI: 10.1016/j.jim.2021.113058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/31/2021] [Accepted: 04/16/2021] [Indexed: 01/09/2023]
Abstract
Inflammatory bowel disease (IBD) is thought to be caused by an aberrant host response to the commensal enteric flora in genetically susceptible individuals. Dendritic cells (DCs) play a key role in the regulation of this response as they sample gut commensals. In healthy individuals DCs actively contribute to tolerance upon recognition of these resident bacteria, whereas in individuals with IBD, DCs will initiate an inflammatory response. To mimic the disease response in vitro, human monocyte-derived DCs were matured with E. coli causing the cells to produce high levels of the pro-inflammatory cytokine IL-12/IL-23p40 (p40) and low levels of the anti-inflammatory cytokine IL-10. A siRNA-based screening assay was developed and screened to identify potential therapeutic targets that shift this balance towards an immunosuppressive state with lower levels of p40 and higher levels of IL-10. The screening assay was optimized and quality controlled using non-targeting controls and positive control siRNAs targeting IL12B and TLR4 transcripts. In the primary screen, smartpool siRNAs were screened for reduction in p40 expression, induction of IL-10 levels, or increase in IL-10:p40 ratios without affecting cell viability. All potential targets were taken forward into a confirmation screen in a different DC donor in which four individual siRNAs per target were screened. At least two siRNAs per target should have an effect to be considered a valid target. This screen resulted in a concise list of ten genes, of which their role in DC maturation is currently being investigated.
Collapse
Affiliation(s)
| | | | | | | | | | - Esther C de Jong
- Department of Experimental Immunology, Amsterdam UMC, the Netherlands
| | | |
Collapse
|
2
|
Liu LL, Zhu SG, Jiang XY, Ren J, Lin Y, Zhang NN, Tong ML, Zhang HL, Zheng WH, Fu HJ, Luo HJ, Lin LR, Yan JH, Yang TC. LncRNA Expression in CD4+ T Cells in Neurosyphilis Patients. Front Cell Infect Microbiol 2017; 7:461. [PMID: 29167762 PMCID: PMC5682391 DOI: 10.3389/fcimb.2017.00461] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/18/2017] [Indexed: 12/31/2022] Open
Abstract
Recent studies have shown that several long noncoding RNAs (lncRNAs) are involved in regulating the immune response to cope with pathogenic invasion. To date, the roles of lncRNAs in the CD4+ T cell response to Treponema pallidum (T. pallidum) infection in neurosyphilis patients remain unknown. The mRNA and lncRNA expression profiles of CD4+ T cells that were isolated from neurosyphilis patients and healthy controls were analyzed by microarray. A total of 2258 lncRNAs and 1728 mRNAs were identified as over-expressed or under-expressed, respectively (fold change > 1.5) in the CD4+ T cells of neurosyphilis patients compared to the healthy controls. The lncRNA-mRNA co-expression network showed that 59 lncRNAs showed significant differences along with significantly different mRNAs. Among the 59 gene pairs, the LOC79999 mRNA was positively correlated with the RP11-160E2.16, RP11-160E2.11, and RP11-160E2.19 lncRNAs, and the NKX1-1 mRNA was positively correlated with the RP11-1398P2.1, RP11-160E2.19, and XLOC_003422 lncRNAs. The following five mRNAs were correlated with two differential lncRNAs: DUSP16, AP000349.1, FAM115C, TIMM8A, and SMCHD1. Gene Ontology (GO) analysis revealed that the differentially expressed coding genes were mainly involved in biological processes and the top 4 terms that associated with above-mentioned differentially expressed coding genes were as follows: defense response to fungus, defense response to bacterium, killing of cells of other organism and disruption of cells of another organism. A subsequent pathway analysis was also conducted, and several pathways, including the T cell receptor, MAPK, and TGF-beta signaling pathways, were associated with the differentially expressed mRNAs. This study reveals the differential expression profiles of lncRNAs in the CD4+ T cell response to the T. pallidum infection in neurosyphilis patients. LncRNAs are involved in key biological processes that comprise the CD4+ T cell response to the T. pallidum infection.
Collapse
Affiliation(s)
- Li-Li Liu
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Shao-Gang Zhu
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Xiao-Yong Jiang
- Department of Dermatology, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Jun Ren
- Department of Dermatology, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Yong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Ning-Ning Zhang
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Man-Li Tong
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Hui-Lin Zhang
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Wei-Hong Zheng
- Department of Neurology, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Hua-Jun Fu
- Department of Neurology, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Hai-Juan Luo
- Department of Neurology, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Li-Rong Lin
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| | - Jiang-Hua Yan
- Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Tian-Ci Yang
- Center of Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University, Xiamen, China
| |
Collapse
|
3
|
Abstract
Dendritic cells (DCs) capture HIV particles and transmit them to CD4 T cells. In a recent article published in Cell, Ménager and Littman (2016) perform an shRNA screen in DCs and find that actin nucleation and stabilization regulate HIV uptake and maintain the virus on membrane protrusions for efficient transfer.
Collapse
Affiliation(s)
- Daniel A Donahue
- Institut Pasteur, Department of Virology, Virus & Immunity Unit, Paris 75015, France; CNRS URA 3015, Paris 75015, France.
| | - Olivier Schwartz
- Institut Pasteur, Department of Virology, Virus & Immunity Unit, Paris 75015, France; CNRS URA 3015, Paris 75015, France; Vaccine Research Institute, Creteil 94010, France.
| |
Collapse
|
4
|
Hotta-Iwamura C, Tarbell KV. Type 1 diabetes genetic susceptibility and dendritic cell function: potential targets for treatment. J Leukoc Biol 2016; 100:65-80. [PMID: 26792821 DOI: 10.1189/jlb.3mr1115-500r] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/21/2015] [Indexed: 12/15/2022] Open
Abstract
Type 1 diabetes is an autoimmune disease that results from the defective induction or maintenance of T cell tolerance against islet β cell self-antigens. Under steady-state conditions, dendritic cells with tolerogenic properties are critical for peripheral immune tolerance. Tolerogenic dendritic cells can induce T cell anergy and deletion and, in some contexts, induce or expand regulatory T cells. Dendritic cells contribute to both immunomodulatory effects and triggering of pathogenesis in type 1 diabetes. This immune equilibrium is affected by both genetic and environmental factors that contribute to the development of type 1 diabetes. Genome-wide association studies and disease association studies have identified >50 polymorphic loci that lend susceptibility or resistance to insulin-dependent diabetes mellitus. In parallel, diabetes susceptibility regions known as insulin-dependent diabetes loci have been identified in the nonobese diabetic mouse, a model for human type 1 diabetes, providing a better understanding of potential immunomodulatory factors in type 1 diabetes risk. Most genetic candidates have annotated immune cell functions, but the focus has been on changes to T and B cells. However, it is likely that some of the genomic susceptibility in type 1 diabetes directly interrupts the tolerogenic potential of dendritic cells in the pathogenic context of ongoing autoimmunity. Here, we will review how gene polymorphisms associated with autoimmune diabetes may influence dendritic cell development and maturation processes that could lead to alterations in the tolerogenic function of dendritic cells. These insights into potential tolerogenic and pathogenic roles for dendritic cells have practical implications for the clinical manipulation of dendritic cells toward tolerance to prevent and treat type 1 diabetes.
Collapse
Affiliation(s)
- Chie Hotta-Iwamura
- Immune Tolerance Section, Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristin V Tarbell
- Immune Tolerance Section, Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
5
|
Gonçalves V, Henriques A, Pereira J, Neves Costa A, Moyer MP, Moita LF, Gama-Carvalho M, Matos P, Jordan P. Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells. RNA 2014; 20:474-82. [PMID: 24550521 PMCID: PMC3964909 DOI: 10.1261/rna.041376.113] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/07/2014] [Indexed: 05/28/2023]
Abstract
The premessenger RNA of the majority of human genes can generate various transcripts through alternative splicing, and different tissues or disease states show specific patterns of splicing variants. These patterns depend on the relative concentrations of the splicing factors present in the cell nucleus, either as a consequence of their expression levels or of post-translational modifications, such as protein phosphorylation, which are determined by signal transduction pathways. Here, we analyzed the contribution of protein kinases to the regulation of alternative splicing variant Rac1b that is overexpressed in certain tumor types. In colorectal cells, we found that depletion of AKT2, AKT3, GSK3β, and SRPK1 significantly decreased endogenous Rac1b levels. Although knockdown of AKT2 and AKT3 affected only Rac1b protein levels suggesting a post-splicing effect, the depletion of GSK3β or SRPK1 decreased Rac1b alternative splicing, an effect mediated through changes in splicing factor SRSF1. In particular, the knockdown of SRPK1 or inhibition of its catalytic activity reduced phosphorylation and subsequent translocation of SRSF1 to the nucleus, limiting its availability to promote the inclusion of alternative exon 3b into the Rac1 pre-mRNA. Altogether, the data identify SRSF1 as a prime regulator of Rac1b expression in colorectal cells and provide further mechanistic insight into how the regulation of alternative splicing events by protein kinases can contribute to sustain tumor cell survival.
Collapse
Affiliation(s)
- Vânia Gonçalves
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Andreia Henriques
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Joana Pereira
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Neves Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | - Luís Ferreira Moita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Margarida Gama-Carvalho
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| |
Collapse
|