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Koss KM, Son T, Li C, Hao Y, Cao J, Churchward MA, Zhang ZJ, Wertheim JA, Derda R, Todd KG. Toward discovering a novel family of peptides targeting neuroinflammatory states of brain microglia and astrocytes. J Neurochem 2023:10.1111/jnc.15840. [PMID: 37171455 PMCID: PMC10640667 DOI: 10.1111/jnc.15840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
Microglia are immune-derived cells critical to the development and healthy function of the brain and spinal cord, yet are implicated in the active pathology of many neuropsychiatric disorders. A range of functional phenotypes associated with the healthy brain or disease states has been suggested from in vivo work and were modeled in vitro as surveying, reactive, and primed sub-types of primary rat microglia and mixed microglia/astrocytes. It was hypothesized that the biomolecular profile of these cells undergoes a phenotypical change as well, and these functional phenotypes were explored for potential novel peptide binders using a custom 7 amino acid-presenting M13 phage library (SX7) to identify unique peptides that bind differentially to these respective cell types. Surveying glia were untreated, reactive were induced with a lipopolysaccharide treatment, recovery was modeled with a potent anti-inflammatory treatment dexamethasone, and priming was determined by subsequently challenging the cells with interferon gamma. Microglial function was profiled by determining the secretion of cytokines and nitric oxide, and expression of inducible nitric oxide synthase. After incubation with the SX7 phage library, populations of SX7-positive microglia and/or astrocytes were collected using fluorescence-activated cell sorting, SX7 phage was amplified in Escherichia coli culture, and phage DNA was sequenced via next-generation sequencing. Binding validation was done with synthesized peptides via in-cell westerns. Fifty-eight unique peptides were discovered, and their potential functions were assessed using a basic local alignment search tool. Peptides potentially originated from proteins ranging in function from a variety of supportive glial roles, including synapse support and pruning, to inflammatory incitement including cytokine and interleukin activation, and potential regulation in neurodegenerative and neuropsychiatric disorders.
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Affiliation(s)
- K M Koss
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - T Son
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - C Li
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - Y Hao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
| | - J Cao
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - M A Churchward
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biology and Environmental Sciences, Concordia University of Edmonton, Alberta, Edmonton, Canada
| | - Z J Zhang
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
| | - J A Wertheim
- Comprehensive Transplant Center and Department of Surgery, Feinberg School of Medicine, Northwestern University, Illinois, Chicago, USA
- Department of Surgery, University of Arizona College of Medicine, Arizona, Tucson, USA
| | - R Derda
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB T6G 2G2, Canada
- 48Hour Discovery Inc, 11421 Saskatchewan Dr NW, Edmonton, AB T6G 2M9, Canada
| | - K G Todd
- Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Alberta, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Alberta, Edmonton, Canada
- Department of Biomedical Engineering, University of Alberta, Alberta, Edmonton, Canada
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Liang X, Yadav SP, Batz ZA, Nellissery J, Swaroop A. Protein kinase CK2 modulates the activity of Maf-family bZIP transcription factor NRL in rod photoreceptors of mammalian retina. Hum Mol Genet 2023; 32:948-958. [PMID: 36226585 PMCID: PMC9991000 DOI: 10.1093/hmg/ddac256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/21/2022] [Accepted: 10/07/2022] [Indexed: 11/14/2022] Open
Abstract
Maf-family basic motif leucine zipper protein NRL specifies rod photoreceptor cell fate during retinal development and, in concert with homeodomain protein CRX and other regulatory factors, controls the expression of most rod-expressed genes including the visual pigment gene Rhodopsin (Rho). Transcriptional regulatory activity of NRL is modulated by post-translational modifications, especially phosphorylation, and mutations at specific phosphosites can lead to retinal degeneration. During our studies to elucidate NRL-mediated transcriptional regulation, we identified protein kinase CK2 in NRL-enriched complexes bound to Rho promoter-enhancer regions and in NRL-enriched high molecular mass fractions from the bovine retina. The presence of CK2 in NRL complexes was confirmed by co-immunoprecipitation from developing and adult mouse retinal extracts. In vitro kinase assay and bioinformatic analysis indicated phosphorylation of NRL at Ser117 residue by CK2. Co-transfection of Csnk2a1 cDNA encoding murine CK2 with human NRL and CRX reduced the bovine Rho promoter-driven luciferase expression in HEK293 cells and mutagenesis of NRL-Ser117 residue to Ala restored the reporter gene activity. In concordance, overexpression of CK2 in the mouse retina in vivo by electroporation resulted in reduction of Rho promoter-driven DsRed reporter expression as well as the transcript level of many phototransduction genes. Thus, our studies demonstrate that CK2 can phosphorylate Ser117 of NRL. Modulation of NRL activity by CK2 suggests intricate interdependence of transcriptional and signaling pathways in maintaining rod homeostasis.
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Affiliation(s)
- Xulong Liang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Sharda P Yadav
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Zachary A Batz
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Jacob Nellissery
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, MSC0610, Bethesda, MD 20892, USA
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Geng Y, Feng J, Huang H, Wang Y, Yi X, Wei S, Zhang M, Li Z, Wang W, Hu W. Single-cell transcriptome analysis of tumor immune microenvironment characteristics in colorectal cancer liver metastasis. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1170. [PMID: 36467341 PMCID: PMC9708492 DOI: 10.21037/atm-22-5270] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/03/2022] [Indexed: 10/22/2023]
Abstract
BACKGROUND Liver metastasis is the leading cause of death in colorectal cancer (CRC) patients, and the precise mechanisms remain unclear. In this study, single-cell RNA sequencing (scRNA-seq) was used to analyze the cellular and molecular heterogeneity between CRC primary lesion and corresponding liver metastasis, and to clarify the characteristics of the tumor microenvironment (TME) in synchronous liver metastasis of CRC. METHODS A case of microsatellite stable (MSS) sigmoid carcinoma with synchronous liver metastasis was selected, and tissues from the primary tumor and the liver metastasis were collected for scRNA-seq. The EdgeR package software was used to identify the differentially expressed genes between cells. Gene Set Enrichment Analysis (GSEA) was performed and the clusterProfiler R package was used for Gene Ontology (GO) enrichment analysis. The SCENIC and CellphoneDB packages were used to reconstruct the transcriptional regulatory networks and to analyze the intercellular interaction network, respectively. RESULTS Compared to the primary tumor, the proportion of myeloid cells in the metastatic tumor was significantly increased, while B cells and plasma cells were decreased. In the metastatic tumor, the myeloid-derived suppressor cell (MDSC) characteristic gene, mannose receptor C-type 1 (MRC1) and tumor associated macrophage 2 (TAM2)-related gene, were highly expressed. Furthermore, angiogenesis, oxidative phosphorylation, and endothelial mesenchymal transition (EMT) of myeloid cells were also significantly enhanced. There were less myeloid cells in primary tumors, and these were mainly monocytes and TAM1; while the number of TAM2 was significantly upregulated in the metastatic samples. In liver metastasis, the T cell population was exhausted, and this was accompanied by a significant increase in the number of CD4+ T cells and a decrease in the number of CD8+ T cells. Furthermore, some immune checkpoint molecules were highly expressed. Interactions between myeloid cells and other cell populations appeared to be strong. CONCLUSIONS The TME of CRC liver metastasis is significantly immunosuppressed. Interactions between myeloid cells and other cell populations in the TME contribute to the establishment of a pro-metastatic niche that promotes colonization and growth of CRC cells in the liver. TAMs may be a potential immunotherapeutic target for MSS CRC.
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Affiliation(s)
- Yiting Geng
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jun Feng
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Hao Huang
- Department of Tumor Biological Treatment, The Third Affiliated Hospital of Soochow University, Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Ying Wang
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xing Yi
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Shanshan Wei
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Mingyue Zhang
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Zhong Li
- Department of Gastrointestinal Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Wei Wang
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Wenwei Hu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, China
- Jiangsu Engineering Research Center for Tumor Immunotherapy, The Third Affiliated Hospital of Soochow University, Changzhou, China
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Michée-Cospolite M, Boudigou M, Grasseau A, Simon Q, Mignen O, Pers JO, Cornec D, Le Pottier L, Hillion S. Molecular Mechanisms Driving IL-10- Producing B Cells Functions: STAT3 and c-MAF as Underestimated Central Key Regulators? Front Immunol 2022; 13:818814. [PMID: 35359922 PMCID: PMC8961445 DOI: 10.3389/fimmu.2022.818814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/11/2022] [Indexed: 12/25/2022] Open
Abstract
Regulatory B cells (Bregs) have been highlighted in very different pathology settings including autoimmune diseases, allergy, graft rejection, and cancer. Improving tools for the characterization of Bregs has become the main objective especially in humans. Transitional, mature B cells and plasma cells can differentiate into IL-10 producing Bregs in both mice and humans, suggesting that Bregs are not derived from unique precursors but may arise from different competent progenitors at unrestricted development stages. Moreover, in addition to IL-10 production, regulatory B cells used a broad range of suppressing mechanisms to modulate the immune response. Although Bregs have been consistently described in the literature, only a few reports described the molecular aspects that control the acquisition of the regulatory function. In this manuscript, we detailed the latest reports describing the control of IL-10, TGFβ, and GZMB production in different Breg subsets at the molecular level. We focused on the understanding of the role of the transcription factors STAT3 and c-MAF in controlling IL-10 production in murine and human B cells and how these factors may represent an important crossroad of several key drivers of the Breg response. Finally, we provided original data supporting the evidence that MAF is expressed in human IL-10- producing plasmablast and could be induced in vitro following different stimulation cocktails. At steady state, we reported that MAF is expressed in specific human B-cell tonsillar subsets including the IgD+ CD27+ unswitched population, germinal center cells and plasmablast.
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Affiliation(s)
| | | | | | | | | | | | - Divi Cornec
- U1227, LBAI, Univ Brest, Inserm, and CHU Brest, Brest, France
| | | | - Sophie Hillion
- U1227, LBAI, Univ Brest, Inserm, and CHU Brest, Brest, France
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Peng X, Zhao M, Gao L, Sen R, MacGlashan D. Identifying regulatory pathways of spleen tyrosine kinase expression in human basophils. J Allergy Clin Immunol 2019; 145:947-957. [PMID: 31629804 DOI: 10.1016/j.jaci.2019.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/27/2019] [Accepted: 10/01/2019] [Indexed: 01/30/2023]
Abstract
BACKGROUND Expression levels of spleen tyrosine kinase (SYK), a critical signaling tyrosine kinase in basophils, are uniquely low relative to all other circulating leukocytes, and levels are highly variable in the population. OBJECTIVE We sought to determine whether transcriptional regulation of SYK through unique silencing of the SYK gene determines its basophil-specific expression patterns. METHODS Culture-derived basophils (CD34B cells) were derived from cultures of CD34+ progenitor cells by using 2 methods (G1 or G3). Peripheral blood basophils (PBBs; relative SYK protein level = 1), B cells (SYK = 8), CD34B-G1 cells (SYK = 11), and CD34B-G3 cells (SYK = 5) were examined by using assay for transposase-accessible chromatin sequencing (ATAC-seq) methods. In addition, the transcriptomes of 6 cell types, PBBs, peripheral blood eosinophils (SYK = 11), plasmacytoid dendritic cells (SYK = 30), CD34+ progenitors (SYK = 11), CD34B-G1 cells, and CD34B-G3 cells, were analyzed for patterns that matched patterns of SYK expression in these cells, with a focus on transcription factors. RESULTS ATAC-seq showed that PBBs have multiple open regions in the SYK gene, suggesting a nonsilenced state with 1 region unique to PBBs (low SYK expression), 1 region unique to both PBBs (low SYK expression) and both G1 and G3 CD34B cells (high and moderate SYK expression, respectively), and 5 regions unique to B cells (high SYK expression). SYK expression across the 6 cell types explored showed a unique pattern that was matched to expression patterns of 3 transcription factors: Kruppel-like factor 5 (KLF5), zinc-finger protein 608 (ZNF608), and musculoaponeurotic fibrosarcoma protein (c-MAF). CONCLUSIONS Two new potential regulatory pathways for SYK expression were identified. One appears independent of transcriptional regulation, and one appears to be dependent on transcriptional control in the SYK gene.
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Affiliation(s)
- Xia Peng
- Asthma and Allergy Center, Johns Hopkins University, Baltimore, Md; Department of Laboratory Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
| | - Mingming Zhao
- Laboratory of Molecular Biology and Immunology, Biomedical Research Center, National Institutes of Health/National Institute on Aging, Baltimore, Md
| | - Li Gao
- Asthma and Allergy Center, Johns Hopkins University, Baltimore, Md
| | - Ranjan Sen
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China
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Zarobkiewicz MK, Kowalska W, Slawinski M, Rolinski J, Bojarska-Junak A. The role of interleukin 22 in multiple sclerosis and its association with c-Maf and AHR. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2019; 163:200-206. [PMID: 31162488 DOI: 10.5507/bp.2019.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/24/2019] [Indexed: 02/07/2023] Open
Abstract
The aim of this paper was to summarise knowledge of IL-22 involvement in multiple sclerosis (MS) and the possible link between IL-22 and two transcription factors - AHR and c-Maf. The conclusion is that despite numerous studies, the exact role of IL-22 in the pathogenesis of MS is still unknown. The expression and function of c-Maf in MS have not been studied. It seems that the functions of c-Maf and AHR are at least partly connected with IL-22, as both directly or indirectly influence the regulation of IL-22 expression. This possible connection has never been studied in MS.
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Affiliation(s)
| | - Wioleta Kowalska
- Chair and Department of Clinical Immunology, Medical University of Lublin, Lublin, Poland
| | - Miroslaw Slawinski
- Chair and Department of Histology and Embryology with Experimental Cytology Unit, Medical University of Lublin, Lublin, Poland
| | - Jacek Rolinski
- Chair and Department of Clinical Immunology, Medical University of Lublin, Lublin, Poland
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Ou DL, Lin YY, Hsu CL, Lin YY, Chen CW, Yu JS, Miaw SC, Hsu PN, Cheng AL, Hsu C. Development of a PD-L1-Expressing Orthotopic Liver Cancer Model: Implications for Immunotherapy for Hepatocellular Carcinoma. Liver Cancer 2019; 8:155-171. [PMID: 31192153 PMCID: PMC6547269 DOI: 10.1159/000489318] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/17/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Anti-programmed cell death-1(anti-PD1) treatment has shown promising antitumor efficacy in patients with advanced hepatocellular carcinoma (HCC). This study sought to explore the functional significance of programmed death ligand-1 (PD-L1) expression in tumor cells in the tumor microenvironment. METHODS The mouse liver cancer cell line BNL-MEA was transfected with PD-L1 plasmids and stable clones expressing PD-L1 were selected. An orthotopic HCC model was generated by implanting the cells into the subcapsular space of BALB/c mice. Cell growth features were measured by proliferation assay, colony formation, flow cytometry (in vitro), ultrasonography, and animal survival (in vivo). The changes in T-cell function were examined by cytokine assay, expression of T-cell related genes, and flow cytometry. The efficacy of anti-PD1 therapy was compared between the parental and PD-L1-expressing tumors. RESULTS PD-L1 expression did not affect growth characteristics of BNL-MEA cells but downregulated the expression of genes related to T-cell activation in the tumor microenvironment. Co-culture of PD-L1-expressing BNL-MEA cells with CD8+ T cells reduced T-cell proliferation and expression of cytokines IFNγ and TNFα. Tumors with PD-L1 expression showed better response to anti-PD1 therapy and depletion of CD8+ T cells abolished the antitumor effect. The difference in treatment response between parental and PD-L1-expressing tumors disappeared when a combination of anti-PD1 and sorafenib was given. CONCLUSIONS PD-L1 expression in HCC cells may inhibit T-cell function in the liver tumor microenvironment. Anti-PD1 therapy appeared more effective in PD-L1-expressing than nonexpressing tumors, but the difference was diminished by the addition of sorafenib.
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Affiliation(s)
- Da-Liang Ou
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Yang Lin
- School of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Yao Lin
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Wei Chen
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jhang-Sian Yu
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Shi-Chuen Miaw
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ping-Ning Hsu
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Ann-Lii Cheng
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan,National Taiwan University Cancer Center, Taipei, Taiwan,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun Hsu
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan,National Taiwan University Cancer Center, Taipei, Taiwan,Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan,*Dr. Chiun Hsu, MD, PhD, or Ann-Lii Cheng, MD, PhD, Department of Oncology, National Taiwan University Hospital, 7 Chung-Shan South Road, Taipei 10002 (Taiwan), E-Mail or
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Magnusson R, Mariotti GP, Köpsén M, Lövfors W, Gawel DR, Jörnsten R, Linde J, Nordling TEM, Nyman E, Schulze S, Nestor CE, Zhang H, Cedersund G, Benson M, Tjärnberg A, Gustafsson M. LASSIM-A network inference toolbox for genome-wide mechanistic modeling. PLoS Comput Biol 2017. [PMID: 28640810 PMCID: PMC5501685 DOI: 10.1371/journal.pcbi.1005608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models with truly systems-level data. We demonstrate the power of this approach by inferring a mechanistically motivated, genome-wide model of the Th2 transcription regulatory system, which plays an important role in several immune related diseases. There are excellent methods to mathematically model time-resolved biological data on a small scale using accurate mechanistic models. Despite the rapidly increasing availability of such data, mechanistic models have not been applied on a genome-wide level due to excessive runtimes and the non-identifiability of model parameters. However, genome-wide, mechanistic models could potentially answer key clinical questions, such as finding the best drug combinations to induce an expression change from a disease to a healthy state. We present LASSIM, which is a toolbox built to infer parameters within mechanistic models on a genomic scale. This is made possible due to a property shared across biological systems, namely the existence of a subset of master regulators, here denoted the core system. The introduction of a core system of genes simplifies the network inference into small solvable sub-problems, and implies that all main regulatory actions on peripheral genes come from a small set of regulator genes. This separation allows substantial parts of computations to be solved in parallel, i.e. permitting the use of a computer cluster, which substantially reduces computation time.
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Affiliation(s)
- Rasmus Magnusson
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Guido Pio Mariotti
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Mattias Köpsén
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - William Lövfors
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Danuta R. Gawel
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Rebecka Jörnsten
- Mathematical Sciences, Chalmers University of Technology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Linde
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Research Group Systems Biology and Bioinformatics, Jena, Germany
- Research Group PiDOMICS, Leibniz Institute for Natural Product Research and Infection Biology -Hans Knöll Institute, Jena, Germany
| | - Torbjörn E. M. Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
- Stockholm Bioinformatics Center, Science for Life Laboratory, Solna, Sweden
| | - Elin Nyman
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Sylvie Schulze
- Leibniz-Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Research Group Systems Biology and Bioinformatics, Jena, Germany
| | - Colm E. Nestor
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Huan Zhang
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Gunnar Cedersund
- Integrative Systems Biology, Department of Biomedical Engineering, Linköping University, Linköping, Sweden
- Cell Biology, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Mikael Benson
- Centre for Personalised Medicine, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Andreas Tjärnberg
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Mika Gustafsson
- Bioinformatics Unit, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
- * E-mail:
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The ubiquitin ligase HERC4 mediates c-Maf ubiquitination and delays the growth of multiple myeloma xenografts in nude mice. Blood 2016; 127:1676-86. [PMID: 26825710 DOI: 10.1182/blood-2015-07-658203] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/18/2015] [Indexed: 01/11/2023] Open
Abstract
The transcription factor c-Maf is extensively involved in the pathophysiology of multiple myeloma (MM), a fatal malignancy of plasma cells. In the present study, affinity chromatography and mass spectrometry were used to identify c-Maf ubiquitination-associated proteins, from which the E3 ligase HERC4 was found to interact with c-Maf and catalyzed its polyubiquitination and subsequent proteasome-mediated degradation. HERC4 mediated polyubiquitination at K85 and K297 in c-Maf, and this polyubiquitination could be prevented by the isopeptidase USP5. Further analysis on the NCI-60 cell line collection revealed that RPMI 8226, a MM-derived cell line, expressed the lowest level of HERC4. Primary bone marrow analysis revealed HERC4 expression was high in normal bone marrow, but was steadily decreased during myelomagenesis. These findings suggested HERC4 played an important role in MM progression. Moreover, ectopic HERC4 expression decreased MM proliferation in vitro, and delayed xenograft tumor growth in vivo. Therefore, modulation of c-Maf ubiquitination by targeting HERC4 may represent a new therapeutic modality for MM.
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Regulation of IL-4 Expression in Immunity and Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 941:31-77. [PMID: 27734408 DOI: 10.1007/978-94-024-0921-5_3] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IL-4 was first identified as a T cell-derived growth factor for B cells. Studies over the past several decades have markedly expanded our understanding of its cellular sources and function. In addition to T cells, IL-4 is produced by innate lymphocytes, such as NTK cells, and myeloid cells, such as basophils and mast cells. It is a signature cytokine of type 2 immune response but also has a nonimmune function. Its expression is tightly regulated at several levels, including signaling pathways, transcription factors, epigenetic modifications, microRNA, and long noncoding RNA. This chapter will review in detail the molecular mechanism regulating the cell type-specific expression of IL-4 in physiological and pathological type 2 immune responses.
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Zhang C, Guo Z. Multiple functions of Maf in the regulation of cellular development and differentiation. Diabetes Metab Res Rev 2015; 31:773-8. [PMID: 26122665 PMCID: PMC5042042 DOI: 10.1002/dmrr.2676] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/29/2015] [Accepted: 06/24/2015] [Indexed: 11/08/2022]
Abstract
Cellular muscular aponeurotic fibrosarcoma (c-Maf) is a member of the large macrophage-activating factor family. C-Maf plays important roles in the morphogenetic processes and cellular differentiation of the lens, kidneys, liver, T cells and nervous system, and it is particularly important in pancreatic islet and erythroblastic island formation. However, the exact role of c-Maf remains to be elucidated. In this review, we summarize the research to clarify the functions of c-Maf in the cellular development and differentiation. The expression of c-Maf is higher in pancreatic duct cells than in pancreatic islet cells. Therefore, we suggest that pancreatic duct cells may be converted to the functional insulin-secreting cells by regulating c-Maf.
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Affiliation(s)
- Chuan Zhang
- Department of Endocrinology and MetabolismThe Second Hospital of Jilin UniversityChangchunChina
| | - Zhi‐Min Guo
- Department of Experimental MicrobiologyThe First Hospital of Jilin UniversityChangchunChina
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Liu CC, Lai CY, Yen WF, Lin YH, Chang HH, Tai TS, Lu YJ, Tsao HW, Ho IC, Miaw SC. Reciprocal regulation of C-Maf tyrosine phosphorylation by Tec and Ptpn22. PLoS One 2015; 10:e0127617. [PMID: 25993510 PMCID: PMC4439128 DOI: 10.1371/journal.pone.0127617] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 04/16/2015] [Indexed: 02/06/2023] Open
Abstract
C-Maf plays an important role in regulating cytokine production in TH cells. Its transactivation of IL-4 is optimized by phosphorylation at Tyr21, Tyr92, and Tyr131. However, the molecular mechanism regulating its tyrosine phosphorylation remains unknown. In this study, we demonstrate that Tec kinase family member Tec, but not Rlk or Itk, is a tyrosine kinase of c-Maf and that Tec enhances c-Maf-dependent IL-4 promoter activity. This effect of Tec is counteracted by Ptpn22, which physically interacts with and facilitates tyrosine dephosphorylation of c-Maf thereby attenuating its transcriptional activity. We further show that phosphorylation of Tyr21/92/131 of c-Maf is also critical for its recruitment to the IL-21 promoter and optimal production of this cytokine by TH17 cells. Thus, manipulating tyrosine phosphorylation of c-Maf through its kinases and phosphatases can have significant impact on TH cell-mediated immune responses.
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Affiliation(s)
- Chih-Chun Liu
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chen-Yen Lai
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Wei-Feng Yen
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Hsien Lin
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hui-Hsin Chang
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tzong-Shyuan Tai
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yu-Jung Lu
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Hsiao-Wei Tsao
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - I-Cheng Ho
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shi-Chuen Miaw
- Graduate Institute of Immunology, National Taiwan University College of Medicine, Taipei, Taiwan
- * E-mail:
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Kwon SJ, Crespo-Barreto J, Zhang W, Wang T, Kim DS, Krensky A, Clayberger C. KLF13 cooperates with c-Maf to regulate IL-4 expression in CD4+ T cells. THE JOURNAL OF IMMUNOLOGY 2014; 192:5703-9. [PMID: 24821970 DOI: 10.4049/jimmunol.1302830] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Kruppel-like factor (KLF) 13 is a transcription factor that positively regulates expression of the chemokine RANTES 3-5 d after activation of T cells. In this study, we document a key role for KLF13 in the expression of IL-4 in CD4(+) T cells. Gene expression analysis in activated T cells from Klf13(-/-) mice showed that IL-4, along with other Th2 cytokine genes, was downregulated when compared with cells from wild-type mice. The decreased levels of IL-4 were not associated with changes in expression of the Th2-inducing transcription factors GATA3 or c-Maf. Additional analysis revealed that KLF13 directly binds to IL-4 promoter regions and synergizes with c-Maf to positively regulate IL-4 expression. These results indicate that KLF13 is a positive regulator for differentiation of Th2 cells, as part of the transcriptional machinery that regulates IL-4 production in Th2 cells.
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Affiliation(s)
- Seok Joo Kwon
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Juan Crespo-Barreto
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wei Zhang
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tianhong Wang
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Dong Seok Kim
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Alan Krensky
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; and Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Carol Clayberger
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611; and
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Ets-1 facilitates nuclear entry of NFAT proteins and their recruitment to the IL-2 promoter. Proc Natl Acad Sci U S A 2013; 110:15776-81. [PMID: 24019486 DOI: 10.1073/pnas.1304343110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
E26 transformation-specific sequence 1 (Ets-1), the prototype of the ETS family of transcription factors, is critical for the expression of IL-2 by murine Th cells; however, its mechanism of action is still unclear. Here we show that Ets-1 is also essential for optimal production of IL-2 by primary human Th cells. Although Ets-1 negatively regulates the expression of Blimp1, a known suppressor of IL-2 expression, ablation of B lymphocyte-induced maturation protein 1 (Blimp1) does not rescue the expression of IL-2 by Ets-1-deficient Th cells. Instead, Ets-1 physically and functionally interacts with the nuclear factor of activated T-cells (NFAT) and is required for the recruitment of NFAT to the IL-2 promoter. In addition, Ets-1 is located in both the nucleus and cytoplasm of resting Th cells. Nuclear Ets-1 quickly exits the nucleus in response to calcium-dependent signals and competes with NFAT proteins for binding to protein components of noncoding RNA repressor of NFAT complex (NRON), which serves as a cytoplasmic trap for phosphorylated NFAT proteins. This nuclear exit of Ets-1 precedes rapid nuclear entry of NFAT and Ets-1 deficiency results in impaired nuclear entry, but not dephosphorylation, of NFAT proteins. Thus, Ets-1 promotes the expression of IL-2 by modulating the activity of NFAT.
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