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Wagner M, Jasek M, Karabon L. Immune Checkpoint Molecules-Inherited Variations as Markers for Cancer Risk. Front Immunol 2021; 11:606721. [PMID: 33519815 PMCID: PMC7840570 DOI: 10.3389/fimmu.2020.606721] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
In recent years, immunotherapy has been revolutionized by a new approach that works by blocking receptors called immune checkpoints (IC). These molecules play a key role in maintaining immune homeostasis, mainly by suppressing the immune response and by preventing its overactivation. Since inhibition of the immune response by IC can be used by cancer to avoid recognition and destruction by immune system, blocking them enhances the anti-tumor response. This therapeutic approach has brought spectacular clinical effects. The ICs present heterogeneous expression patterns on immune cells, which may affect the effectiveness of immunotherapy. The inherited genetic variants in regulatory regions of ICs genes can be considered as potential factors responsible for observed inter-individual differences in ICs expression levels on immune cells. Additionally, polymorphism located in exons may introduce changes to ICs amino acid sequences with potential impact on functional properties of these molecules. Since genetic variants may affect both expression and structure of ICs, they are considered as risk factors of cancer development. Inherited genetic markers such as SNPs may also be useful in stratification patients into groups which will benefit from particular immunotherapy. In this review, we have comprehensively summarized the current understanding of the relationship between inherited variations of CTLA-4, PDCD1, PD-L1, BTLA, TIM-3, and LAG-3 genes in order to select SNPs which can be used as predictive biomarkers in personalized evaluation of cancer risk development and outcomes as well as possible response to immunotherapy.
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Affiliation(s)
| | - Monika Jasek
- Laboratory of Genetics and Epigenetics of Human Diseases, Department of Experimental Therapy, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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Analysis of Il36a induction by C/EBPβ via a half-CRE•C/EBP element in murine macrophages in dependence of its CpG methylation level. Genes Immun 2021; 22:313-321. [PMID: 34697411 PMCID: PMC8674125 DOI: 10.1038/s41435-021-00153-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/12/2022]
Abstract
Interleukin-36α is a novel member of the IL-1 cytokine family that is highly expressed in epithelial tissues and several myeloid-derived cell types after induction. The transcription factor (TF) C/EBPβ binds specifically to an essential half-CRE•C/EBP motif in the Il36a promoter to induce Il36a expression upon LPS stimulation. C/EBPs regulate gene expression by binding to recognition sequences that can contain 5'-cytosine-phosphate-guanine-3' dinucleotides (CpG), whose methylation can influence TF binding and gene expression. Herein we show that the half-CRE•C/EBP element in the Il36a promoter is differentially methylated in the murine RAW264.7 macrophage cell line and in primary murine macrophages. We demonstrate that C/EBPβ binding to the half-CRE•C/EBP element in the Il36a promoter following LPS stimulation is insensitive to CpG methylation and that methylation of the CpG in the half-CRE•C/EBP element does not alter LPS-induced Il36a promoter activity which correlated with similar Il36a mRNA copy numbers and pro-IL-36α protein amount in both cell types. Taken together, our data indicate that C/EBPβ binding to the half-CRE•C/EBP element and subsequent gene activation occurs independently of the CpG methylation status of the half-CRE•C/EBP motif and underlines the potential of C/EBPs to recognize methylated as well as unmethylated motifs.
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53
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Milan T, Celton M, Lagacé K, Roques É, Safa-Tahar-Henni S, Bresson E, Bergeron A, Hebert J, Meshinchi S, Cellot S, Barabé F, Wilhelm BT. Epigenetic changes in human model KMT2A leukemias highlight early events during leukemogenesis. Haematologica 2020; 107:86-99. [PMID: 33375773 PMCID: PMC8719083 DOI: 10.3324/haematol.2020.271619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Indexed: 11/26/2022] Open
Abstract
Chromosomal translocations involving the KMT2A gene are among the most common genetic alterations found in pediatric acute myeloid leukemias although the molecular mechanisms that initiate the disease remain incompletely defined. To elucidate these initiating events we used a human model system of acute myeloid leukemia driven by the KMT2A-MLLT3 (KM3) fusion. More specifically, we investigated changes in DNA methylation, histone modifications, and chromatin accessibility at each stage of our model system and correlated these with expression changes. We observed the development of a pronounced hypomethyl - ation phenotype in the early stages of leukemic transformation after KM3 addition along with loss of expression of stem-cell-associated genes and skewed expression of other genes, such as S100A8/9, implicated in leukemogenesis. In addition, early increases in the expression of the lysine demethylase KDM4B was functionally linked to these expression changes as well as other key transcription factors. Remarkably, our ATAC-sequencing data showed that there were relatively few leukemia-specific changes and that the vast majority corresponded to open chromatin regions and transcription factor clusters previously observed in other cell types. Integration of the gene expression and epigenetic changes revealed that the adenylate cyclase gene ADCY9 is an essential gene in KM3-acute myeloid leukemia, and suggested the potential for autocrine signaling through the chemokine receptor CCR1 and CCL23 ligand. Collectively, our results suggest that KM3 induces subtle changes in the epigenome while co-opting the normal transcriptional machinery to drive leukemogenesis.
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Affiliation(s)
- Thomas Milan
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Magalie Celton
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Karine Lagacé
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Élodie Roques
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Safia Safa-Tahar-Henni
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Eva Bresson
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec - Université Laval, Québec City, QC, Canada; CHU de Québec - Université Laval - Hôpital Enfant-Jésus; Québec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC
| | - Anne Bergeron
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec - Université Laval, Québec City, QC, Canada; CHU de Québec - Université Laval - Hôpital Enfant-Jésus; Québec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC
| | - Josée Hebert
- Division of Hematology-Oncology and Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sonia Cellot
- Department of pediatrics, division of Hematology, Ste-Justine Hospital, Montréal, QC
| | - Frédéric Barabé
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec - Université Laval, Québec City, QC, Canada; CHU de Québec - Université Laval - Hôpital Enfant-Jésus; Québec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC
| | - Brian T Wilhelm
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC.
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Lala-Tabbert N, AlSudais H, Marchildon F, Fu D, Wiper-Bergeron N. CCAAT/enhancer-binding protein beta promotes muscle stem cell quiescence through regulation of quiescence-associated genes. Stem Cells 2020; 39:345-357. [PMID: 33326659 DOI: 10.1002/stem.3319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
Abstract
Regeneration of skeletal muscle depends on resident muscle stem cells called satellite cells that in healthy, uninjured muscle remain quiescent (noncycling). After activation and expansion of satellite cells postinjury, satellite cell numbers return to uninjured levels and return to mitotic quiescence. Here, we show that the transcription factor CCAAT/enhancer-binding protein beta (C/EBPβ) is required to maintain quiescence of satellite cells in uninjured muscle. We show that C/EBPβ is expressed in quiescent satellite cells in vivo and upregulated in noncycling myoblasts in vitro. Loss of C/EBPβ in satellite cells promotes their premature exit from quiescence resulting in spontaneous activation and differentiation of the stem cell pool. Forced expression of C/EBPβ in myoblasts inhibits proliferation by upregulation of 28 quiescence-associated genes. Furthermore, we find that caveolin-1 is a direct transcriptional target of C/EBPβ and is required for cell cycle exit in muscle satellite cells expressing C/EBPβ. The induction of mitotic quiescence is considered necessary for the long-term maintenance of adult stem cell populations with dysregulation driving increased differentiation of progenitors and depletion of the stem cell pool. Our findings place C/EBPβ as an important transcriptional regulator of muscle satellite cell quiescence.
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Affiliation(s)
- Neena Lala-Tabbert
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Apoptosis Research Centre, Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - François Marchildon
- Graduate Program in Cellular and Molecular Medicine, Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Laboratory of Molecular Metabolism, The Rockefeller University, New York, New York, USA
| | - Dechen Fu
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Cleveland Clinic, Lerner Research Institute, Cleveland, Ohio, USA
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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The transcription factor C/EBPβ orchestrates dendritic cell maturation and functionality under homeostatic and malignant conditions. Proc Natl Acad Sci U S A 2020; 117:26328-26339. [PMID: 33020261 DOI: 10.1073/pnas.2008883117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Dendritic cell (DC) maturation is a prerequisite for the induction of adaptive immune responses against pathogens and cancer. Transcription factor (TF) networks control differential aspects of early DC progenitor versus late-stage DC cell fate decisions. Here, we identified the TF C/EBPβ as a key regulator for DC maturation and immunogenic functionality under homeostatic and lymphoma-transformed conditions. Upon cell-specific deletion of C/EBPβ in CD11c+MHCIIhi DCs, gene expression profiles of splenic C/EBPβ-/- DCs showed a down-regulation of E2F cell cycle target genes and associated proliferation signaling pathways, whereas maturation signatures were enriched. Total splenic DC cell numbers were modestly increased but differentiation into cDC1 and cDC2 subsets were unaltered. The splenic CD11c+MHCIIhiCD64+ DC compartment was also increased, suggesting that C/EBPβ deficiency favors the expansion of monocytic-derived DCs. Expression of C/EBPβ could be mimicked in LAP/LAP* isoform knockin DCs, whereas the short isoform LIP supported a differentiation program similar to deletion of the full-length TF. In accordance with E2F1 being a negative regulator of DC maturation, C/EBPβ-/- bone marrow-derived DCs matured much faster enabling them to activate and polarize T cells stronger. In contrast to a homeostatic condition, lymphoma-exposed DCs exhibited an up-regulation of the E2F transcriptional pathways and an impaired maturation. Pharmacological blockade of C/EBPβ/mTOR signaling in human DCs abrogated their protumorigenic function in primary B cell lymphoma cocultures. Thus, C/EBPβ plays a unique role in DC maturation and immunostimulatory functionality and emerges as a key factor of the tumor microenvironment that promotes lymphomagenesis.
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56
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Lee G, Jang E, Youn J. CCAAT/enhancer binding protein β Induces Post-Switched B Cells to Produce Blimp1 and Differentiate into Plasma Cells. Immune Netw 2020; 20:e42. [PMID: 33163250 PMCID: PMC7609162 DOI: 10.4110/in.2020.20.e42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 02/08/2023] Open
Abstract
Long-lasting post-switched plasma cells (PCs) arise mainly from germinal center (GC) reactions, but little is known about the mechanism by which GC B cells differentiate into PCs. Based on our observation that the expression of the transcription factor CCAAT/enhancer binding protein β (C/EPBβ) is associated with the emergence of post-switched PCs, we enquired whether a cell-autonomous function of C/EPBβ is involved in the program for PC development. To address this, we generated C/EPBβ-deficient mice in which the Cebpb locus was specifically deleted in B cells after transcription of the Ig γ1 constant gene segment (Cγ1). In response to in vitro stimulation, B cells from these Cebpbfl/flCγ1Cre/+ mice had defects in the induction of B lymphocyte-induced maturation protein 1 (Blimp1) and the formation of IgG1+ PCs, but not in proliferation and survival. At steady state, the Cebpbfl/flCγ1Cre/+ mice had reduced serum IgG1 titers but normal IgG2c and IgM titers. Moreover, upon immunization with T-dependent Ag, the mice produced reduced levels of Ag-specific IgG1 Ab, and were defective in the production of Ag-specific IgG1 Ab-secreting cells. These results suggest that a cell-autonomous function of C/EPBβ is crucial for differentiation of post-switched GC B cells into PCs through a Blimp1-dependent pathway.
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Affiliation(s)
- Geonhee Lee
- Laboratory of Autoimmunology, Department of Anatomy and Cell Biology, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Eunkyeong Jang
- Laboratory of Autoimmunology, Department of Anatomy and Cell Biology, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Jeehee Youn
- Laboratory of Autoimmunology, Department of Anatomy and Cell Biology, College of Medicine, Hanyang University, Seoul 04763, Korea
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57
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Moazzeni H, Khani M, Elahi E. Insights into the regulatory molecules involved in glaucoma pathogenesis. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:782-827. [PMID: 32935930 DOI: 10.1002/ajmg.c.31833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022]
Abstract
Glaucoma is an important cause of irreversible blindness, characterized by optic nerve anomalies. Increased intraocular pressure (IOP) and aging are major risk factors. Retinal ganglion cells and trabecular meshwork cells are certainly involved in the etiology of glaucoma. Glaucoma is usually a complex disease, and various genes and functions may contribute to its etiology. Among these may be genes that encode regulatory molecules. In this review, regulatory molecules including 18 transcription factors (TFs), 195 microRNAs (miRNAs), 106 long noncoding RNAs (lncRNAs), and two circular RNAs (circRNAs) that are reasonable candidates for having roles in glaucoma pathogenesis are described. The targets of the regulators are reported. Glaucoma-related features including apoptosis, stress responses, immune functions, ECM properties, IOP, and eye development are affected by the targeted genes. The targeted genes that are frequently targeted by multiple regulators most often affect apoptosis and the related features of cell death and cell survival. BCL2, CDKN1A, and TP53 are among the frequent targets of three types of glaucoma-relevant regulators, TFs, miRNAs, and lncRNAs. TP53 was itself identified as a glaucoma-relevant TF. Several of the glaucoma-relevant TFs are themselves among frequent targets of regulatory molecules, which is consistent with existence of a complex network involved in glaucoma pathogenesis.
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Affiliation(s)
- Hamidreza Moazzeni
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Marzieh Khani
- School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Elahe Elahi
- School of Biology, College of Science, University of Tehran, Tehran, Iran
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Chopra A, Cho WC, Willmore WG, Biggar KK. Hypoxia-Inducible Lysine Methyltransferases: G9a and GLP Hypoxic Regulation, Non-histone Substrate Modification, and Pathological Relevance. Front Genet 2020; 11:579636. [PMID: 33088284 PMCID: PMC7495024 DOI: 10.3389/fgene.2020.579636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 12/29/2022] Open
Abstract
Oxygen sensing is inherent among most animal lifeforms and is critical for organism survival. Oxygen sensing mechanisms collectively trigger cellular and physiological responses that enable adaption to a reduction in ideal oxygen levels. The major mechanism by which oxygen-responsive changes in the transcriptome occur are mediated through the hypoxia-inducible factor (HIF) pathway. Upon reduced oxygen conditions, HIF activates hypoxia-responsive gene expression programs. However, under normal oxygen conditions, the activity of HIF is regularly suppressed by cellular oxygen sensors; prolyl-4 and asparaginyl hydroxylases. Recently, these oxygen sensors have also been found to suppress the function of two lysine methyltransferases, G9a and G9a-like protein (GLP). In this manner, the methyltransferase activity of G9a and GLP are hypoxia-inducible and thus present a new avenue of low-oxygen signaling. Furthermore, G9a and GLP elicit lysine methylation on a wide variety of non-histone proteins, many of which are known to be regulated by hypoxia. In this article we aim to review the effects of oxygen on G9a and GLP function, non-histone methylation events inflicted by these methyltransferases, and the clinical relevance of these enzymes in cancer.
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Affiliation(s)
- Anand Chopra
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - William G Willmore
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
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Liu B, Liu GD, Guo HY, Zhu KC, Guo L, Zhang N, Liu BS, Jiang SG, Zhang DC. Characterization and functional analysis of liver-expressed antimicrobial peptide-2 (LEAP-2) from golden pompano Trachinotus ovatus (Linnaeus 1758). FISH & SHELLFISH IMMUNOLOGY 2020; 104:419-430. [PMID: 32562868 DOI: 10.1016/j.fsi.2020.06.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
The liver-expressed antimicrobial peptide-2 (LEAP-2) is an important component of the innate immune defense system and plays an important role in resisting the invasion of pathogenic microorganisms. In this study, LEAP-2 from golden pompano (Trachinotus ovatus) was characterized and its expression in response to Photobacterium damselae was investigated. The full-length LEAP-2 cDNA was 1758 bp, which comprised a 5'-UTR of 250 bp, an ORF of 321 bp, and a 3'-UTR of 1187 bp, encoding 106 amino acids. LEAP-2 consisted of a conserved saposin B domain and four conserved cysteines that formed two pairs of disulphide bonds. The genomic organization of LEAP-2 was also determined and shown to consisted of three introns and two exons. The predicted promoter region of ToLEAP-2 contained several putative transcription factor binding sites. Quantitative real-time (qRT-PCR) analysis indicated that LEAP-2 was ubiquitously expressed in all examined tissues, with higher mRNA levels observed in the muscle, liver, spleen, and kidney. After P. damselae stimulation, the expression level of LEAP-2 mRNA was significantly upregulated in various tissues of golden pompano. In addition, SDS-PAGE showed that the molecular mass of recombinant LEAP-2 expressed in pET-32a was approximately 23 kDa. The purified recombinant protein showed antibacterial activity against Gram-positive and Gram-negative bacteria. Luciferase reporters were constructed for five deletion fragments of different lengths from the promoter region (-1575 bp to +251 bp), and the results showed that L3 (-659 bp to +251 bp) presented the highest activity, and it was therefore defined as the core region of the LEAP-2 promoter. The seven predicted transcription factor binding sites were deleted by using PCR technology, and the results showed that the mutation of the USF transcription factor binding site caused the activity to significantly decrease. The results indicate that golden pompano LEAP-2 potentially exhibits antimicrobial effects in fish innate immunity.
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Affiliation(s)
- Bo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Guang-Dong Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Hua-Yang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Ke-Cheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China; Sanya Tropical Fisheries Research Institute, Sanya, Hainan Province, China.
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60
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Qie C, Jiang J, Liu W, Hu X, Chen W, Xie X, Liu J. Single-cell RNA-Seq reveals the transcriptional landscape and heterogeneity of skin macrophages in Vsir -/- murine psoriasis. Theranostics 2020; 10:10483-10497. [PMID: 32929361 PMCID: PMC7482809 DOI: 10.7150/thno.45614] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/09/2020] [Indexed: 12/13/2022] Open
Abstract
Rationale: V-domain immunoglobulin suppressor of T cell activation (VISTA) is a novel inhibitory immune checkpoint molecule. Vsir-/- mice have exacerbated psoriasis-like skin inflammation. The immune cell subsets involved in inflammation in Vsir-/- psoriatic mice are largely unknown. We have used scRNA-seq as an unbiased profiling strategy to study the heterogeneity of immune cells at a single cell level in the skin of Vsir-/- psoriatic mice. Methods: In the present study, the right ear and shaved back skin of wild type and Vsir-/- mice were treated with IMQ for 5 consecutive days to induce psoriasis-like dermatitis. Then, the single-cell RNA sequencing analysis of mouse back skin lesions was performed using 10 × Genomics technique. Results: We identified 12 major cell subtypes among 23,258 cells. The major populations of the skin cells included macrophages, dendritic cells and fibroblasts. Macrophages constituted the main immune cell population in the WT (61.29%) and Vsir-/- groups (77.7%). It should be noted that DCs and fibroblasts were expanded in the Vsir-/- psoriatic mice. Furthermore, the gene expression signatures were assessed. We observed that Hspb1 and Cebpb were significantly upregulated in the Vsir-/- psoriatic mice. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these subsets and uncovered putative functions of each cell type. Date analysis resulted in the discovery of a number of novel psoriasis-associated genes in Vsir-/- mice. Conclusion: We present a comprehensive single-cell landscape of the skin immune cells in Vsir-/- psoriatic mice. These unprecedented data uncovered the transcriptional landscape and phenotypic heterogeneity of skin macrophages in psoriasis and identified their gene expression signature suggesting specialized functions in Vsir-/- mice. Our findings will open novel opportunities to investigate the role of VISTA in driving psoriasis.
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All-trans retinoic acid reduces the transcriptional regulation of intestinal sodium-dependent phosphate co-transporter gene (Npt2b). Biochem J 2020; 477:817-831. [PMID: 32016357 DOI: 10.1042/bcj20190716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/13/2020] [Accepted: 02/03/2020] [Indexed: 01/03/2023]
Abstract
Inorganic phosphate (Pi) homeostasis is regulated by intestinal absorption via type II sodium-dependent co-transporter (Npt2b) and by renal reabsorption via Npt2a and Npt2c. Although we previously reported that vitamin A-deficient (VAD) rats had increased urine Pi excretion through the decreased renal expression of Npt2a and Npt2c, the effect of vitamin A on the intestinal Npt2b expression remains unclear. In this study, we investigated the effects of treatment with all-trans retinoic acid (ATRA), a metabolite of vitamin A, on the Pi absorption and the Npt2b expression in the intestine of VAD rats, as well as and the underlying molecular mechanisms. In VAD rats, the intestinal Pi uptake activity and the expression of Npt2b were increased, but were reduced by the administration of ATRA. The transcriptional activity of reporter plasmid containing the promoter region of the rat Npt2b gene was reduced by ATRA in NIH3T3 cells overexpressing retinoic acid receptor (RAR) and retinoid X receptor (RXR). On the other hand, CCAAT/enhancer-binding proteins (C/EBP) induced transcriptional activity of the Npt2b gene. Knockdown of the C/EBP gene and a mutation analysis of the C/EBP responsible element in the Npt2b gene promoter indicated that C/EBP plays a pivotal role in the regulation of Npt2b gene transcriptional activity by ATRA. EMSA revealed that the RAR/RXR complex inhibits binding of C/EBP to Npt2b gene promoter. Together, these results suggest that ATRA may reduce the intestinal Pi uptake by preventing C/EBP activation of the intestinal Npt2b gene.
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Kaiser A, Schmidt M, Huber O, Frietsch JJ, Scholl S, Heidel FH, Hochhaus A, Müller JP, Ernst T. SIRT7: an influence factor in healthy aging and the development of age-dependent myeloid stem-cell disorders. Leukemia 2020; 34:2206-2216. [PMID: 32214204 PMCID: PMC8318878 DOI: 10.1038/s41375-020-0803-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/19/2020] [Accepted: 03/12/2020] [Indexed: 12/22/2022]
Abstract
Molecular alterations within the hematopoietic system influence cellular longevity and development of age-related myeloid stem-cell disorders like acute myeloid leukemia (AML) and chronic myeloid leukemia (CML). A reduced SIRT7-expression in aged murine hematopoietic stem cells (HSC) resulted in reduced longevity and increased proliferation. In this study we investigated age-related changes of SIRT7-expression in healthy humans and relevant pathomechanisms in AML and CML. SIRT7-expression in leukocytes of healthy people decreased in an age-dependent manner. Low SIRT7 mRNA levels were also detected in AML and CML patients. With positive treatment response, SIRT7-expression increased, but showed reduction when patients progressed or relapsed. Pharmacologic inhibition of driver mutations in AML (FLT3-ITD) or CML (BCR-ABL) also restored SIRT7 levels in cell lines and patient samples. Furthermore, SIRT7-expression increased with time during PMA-mediated monocyte differentiation of THP-1 cells. SIRT7-overexpression in THP-1 cells resulted in increased expression of differentiation markers. BCR-ABL, FLT3-ITD, and differentiation-associated SIRT7-expression in general were positively regulated by C/EBPα, -β, and -ε binding to two different C/EBP-binding sites within the SIRT7 promoter. SIRT7 is important in human hematopoietic cell aging and longevity. It might act as tumor suppressor and could potentially serve as general biomarker for monitoring treatment response in myeloid stem-cell disorders.
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MESH Headings
- Adult
- Age Factors
- Aged
- Aged, 80 and over
- CCAAT-Enhancer-Binding Protein-alpha/metabolism
- Cell Differentiation
- Fusion Proteins, bcr-abl/antagonists & inhibitors
- Healthy Aging
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/etiology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/etiology
- Middle Aged
- Mutation
- Sirtuins/genetics
- Sirtuins/physiology
- THP-1 Cells
- fms-Like Tyrosine Kinase 3/genetics
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Affiliation(s)
- Alexander Kaiser
- Klinik für Innere Medizin II, Abteilung Hämatologie und Internistische Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Martin Schmidt
- Institut für Biochemie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität, Jena, Germany
| | - Otmar Huber
- Institut für Biochemie II, Universitätsklinikum Jena, Friedrich-Schiller-Universität, Jena, Germany
| | - Jochen J Frietsch
- Klinik für Innere Medizin II, Abteilung Hämatologie und Internistische Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Sebastian Scholl
- Klinik für Innere Medizin II, Abteilung Hämatologie und Internistische Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Florian H Heidel
- Klinik für Innere Medizin II, Abteilung Hämatologie und Internistische Onkologie, Universitätsklinikum Jena, Jena, Germany
- Leibniz-Institute on Aging (Fritz-Lipmann-Institute), Jena, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Abteilung Hämatologie und Internistische Onkologie, Universitätsklinikum Jena, Jena, Germany
| | - Jörg P Müller
- Institut für Molekulare Zellbiologie, CMB, Universitätsklinikum Jena, Friedrich-Schiller-Universität, Jena, Germany
| | - Thomas Ernst
- Klinik für Innere Medizin II, Abteilung Hämatologie und Internistische Onkologie, Universitätsklinikum Jena, Jena, Germany.
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Chen Z, Miao F, Braffett BH, Lachin JM, Zhang L, Wu X, Roshandel D, Carless M, Li XA, Tompkins JD, Kaddis JS, Riggs AD, Paterson AD, Natarajan R. DNA methylation mediates development of HbA1c-associated complications in type 1 diabetes. Nat Metab 2020; 2:744-762. [PMID: 32694834 PMCID: PMC7590966 DOI: 10.1038/s42255-020-0231-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/29/2020] [Indexed: 01/09/2023]
Abstract
Metabolic memory, the persistent benefits of early glycaemic control on preventing and/or delaying the development of diabetic complications, has been observed in the Diabetes Control and Complications Trial (DCCT) and in the Epidemiology of Diabetes Interventions and Complications (EDIC) follow-up study, but the underlying mechanisms remain unclear. Here, we show the involvement of epigenetic DNA methylation (DNAme) in metabolic memory by examining its associations with preceding glycaemic history, and with subsequent development of complications over an 18-yr period in the blood DNA of 499 randomly selected DCCT participants with type 1 diabetes who are also followed up in EDIC. We demonstrate the associations between DNAme near the closeout of DCCT and mean HbA1c during DCCT (mean-DCCT HbA1c) at 186 cytosine-guanine dinucleotides (CpGs) (FDR < 15%, including 43 at FDR < 5%), many of which were located in genes related to complications. Exploration studies into biological function reveal that these CpGs are enriched in binding sites for the C/EBP transcription factor, as well as enhancer/transcription regions in blood cells and haematopoietic stem cells, and open chromatin states in myeloid cells. Mediation analyses show that, remarkably, several CpGs in combination explain 68-97% of the association of mean-DCCT HbA1c with the risk of complications during EDIC. In summary, DNAme at key CpGs appears to mediate the association between hyperglycaemia and complications in metabolic memory, through modifying enhancer activity at myeloid and other cells.
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Affiliation(s)
- Zhuo Chen
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Feng Miao
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Barbara H Braffett
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - John M Lachin
- The Biostatistics Center, The George Washington University, Rockville, MD, USA
| | - Lingxiao Zhang
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Delnaz Roshandel
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melanie Carless
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Xuejun Arthur Li
- Biostatistics Core, Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Joshua D Tompkins
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - John S Kaddis
- Department of Diabetes Immunology, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
- Department of Diabetes and Cancer Discovery Science, Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Arthur D Riggs
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Andrew D Paterson
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Diabetes Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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64
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Caiment F, Wolters J, Smit E, Schrooders Y, Kleinjans J, van den Beucken T. Valproic acid promotes mitochondrial dysfunction in primary human hepatocytes in vitro; impact of C/EBPα-controlled gene expression. Arch Toxicol 2020; 94:3463-3473. [PMID: 32623605 PMCID: PMC7502062 DOI: 10.1007/s00204-020-02835-x] [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: 04/20/2020] [Accepted: 06/30/2020] [Indexed: 11/29/2022]
Abstract
Valproic acid (VPA) is a frequently prescribed anti-epileptic drug which is known to cause liver toxicity and steatosis through mitochondrial dysfunction. Nevertheless the mechanisms underlying these adverse effects are incompletely understood. In this study, we determined the effect of relatively short (3 h) or prolonged (72 h) exposure to VPA on mitochondrial function in primary human hepatocytes (PHHs). While 3 h VPA exposure did not affect oxygen consumption rates (OCRs) in PHHs, prolonged exposure (24–72 h) significantly reduced basal and maximal OCRs. Given that in particular prolonged VPA exposure is required to cause mitochondrial dysfunction, we investigated gene expression data after VPA exposure for 24, 48, 72 h and 72 h VPA followed by a 72 h washout period. We were able to reduce the comprehensive gene expression changes into a more comprehensible set of 18 TFs that were predicted to be persistently activated after 72 h of VPA exposure. Lentiviral knock-down of one of the candidate TFs, C/EBPα, partly rescued VPA-induced mitochondrial dysfunction. Furthermore, RNA-Seq analysis of shC/EBPα and shGFP control PHHs identified 24 genuine C/EBPα target genes that are regulated in response to prolonged VPA exposure in PHHs. Altogether this provides new insights on the involvement of C/EBPα in driving VPA-induced mitochondrial dysfunction in human liver cells. This hub gene, with its downstream regulators involved in this deregulation, thus represent potential new biomarkers for VPA-induced mitochondrial dysfunction.
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Affiliation(s)
- F Caiment
- Maastricht University, Maastricht, The Netherlands
| | - J Wolters
- Maastricht University, Maastricht, The Netherlands
| | - E Smit
- Maastricht University, Maastricht, The Netherlands
| | - Y Schrooders
- Maastricht University, Maastricht, The Netherlands
| | - J Kleinjans
- Maastricht University, Maastricht, The Netherlands
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65
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Turcas C, Moisoiu V, Stefancu A, Jurj A, Iancu SD, Teodorescu P, Pasca S, Bojan A, Trifa A, Iluta S, Zimta AA, Petrushev B, Zdrenghea M, Bumbea H, Coriu D, Dima D, Leopold N, Tomuleasa C. SERS-Based Assessment of MRD in Acute Promyelocytic Leukemia? Front Oncol 2020; 10:1024. [PMID: 32695677 PMCID: PMC7336895 DOI: 10.3389/fonc.2020.01024] [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: 03/02/2020] [Accepted: 05/22/2020] [Indexed: 12/24/2022] Open
Abstract
Acute promyelocytic leukemia (APL) is characterized by a unique chromosome translocation t(15;17)(q24;q21), which leads to the PML/RARA gene fusion formation. However, it is acknowledged that this rearrangement alone is not able to induce the whole leukemic phenotype. In addition, epigenetic processes, such as DNA methylation, may play a crucial role in leukemia pathogenesis. DNA methylation, catalyzed by DNA methyltransferases (DNMTs), involves the covalent transfer of a methyl group (-CH3) to the fifth carbon of the cytosine ring in the CpG dinucleotide and results in the formation of 5-methylcytosine (5-mC). The aberrant gene promoter methylation can be an alternative mechanism of tumor suppressor gene inactivation. Understanding cancer epigenetics and its pivotal role in oncogenesis, can offer us not only attractive targets for epigenetic treatment but can also provide powerful tools in monitoring the disease and estimating the prognosis. Several genes of interest, such as RARA, RARB, p15, p16, have been studied in APL and their methylation status was correlated with potential diagnostic and prognostic significance. In the present manuscript we comprehensively examine the current knowledge regarding DNA methylation in APL pathogenesis. We also discuss the perspectives of using the DNA methylation patterns as reliable biomarkers for measurable residual disease (MRD) monitoring and as a predictor of relapse. This work also highlights the possibility of detecting aberrant methylation profiles of circulating tumor DNA (ctDNA) through liquid biopsies, using the conventional methods, such as methylation-specific polymerase chain reaction (MS-PCR), sequencing methods, but also revolutionary methods, such as surface-enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- Cristina Turcas
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Vlad Moisoiu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Faculty of Physics, Babeş Bolyai University, Cluj-Napoca, Romania
| | - Andrei Stefancu
- Faculty of Physics, Babeş Bolyai University, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Stefania D Iancu
- Faculty of Physics, Babeş Bolyai University, Cluj-Napoca, Romania
| | - Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Bojan
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Adrian Trifa
- Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Sabina Iluta
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Alina-Andreea Zimta
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bobe Petrushev
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Horia Bumbea
- Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Daniel Coriu
- Department of Hematology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Delia Dima
- Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babeş Bolyai University, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Hematology, "Ion Chiricuta" Institute of Oncology, Cluj-Napoca, Romania.,Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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66
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Liu B, Liu GD, Guo HY, Zhu KC, Guo L, Liu BS, Zhang N, Jiang SG, Zhang DC. Functional characterization of NK-lysin in golden pompano Trachinotus ovatus (Linnaeus 1758). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 107:103658. [PMID: 32087193 DOI: 10.1016/j.dci.2020.103658] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
NK-lysin is an important part of the innate immune defence system and plays an important role in resisting the invasion of pathogenic microorganisms. In this study, NK-lysin from golden pompano (Trachinotus ovatus) was characterized and its expression in response to Photobacterium damselae was investigated. The full-length NK-lysin cDNA was 731 bp, which comprised a 5'-UTR of 63 bp, an ORF of 444 bp, and a 3'-UTR of 224 bp, and encoded 147 amino acids; NK-lysin consisted of a conserved saposin B domain and six conserved cysteines that formed three pairs of disulfide bonds. The genomic organization of NK-lysin was also determined and the gene consisted of four introns and five exons. The predicted promoter region of ToNK-lysin contained several putative transcription factor binding sites. Quantitative real-time (qRT-PCR) analysis indicated that ToNK-lysin was ubiquitously expressed in all examined tissues; the highest mRNA levels were observed in the skin, kidney and intestine, while the lowest expression level was detected in the stomach. After P. damselae stimulation, the expression level of NK-lysin mRNA was significantly upregulated in various tissues of golden pompano. In addition, SDS-PAGE showed that the molecular mass of recombinant NK-lysin expressed in pGEX-6P-1 was approximately 37 kDa. The purified recombinant protein showed antibacterial activity against gram-positive and gram-negative bacteria. The results indicate that golden pompano NK-lysin has potential antimicrobial roles in fish innate immunity.
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Affiliation(s)
- Bo Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Guang-Dong Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China
| | - Hua-Yang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Ke-Cheng Zhu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Liang Guo
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Bao-Suo Liu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Nan Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China
| | - Shi-Gui Jiang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, Guangdong Province, China
| | - Dian-Chang Zhang
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, 510300, Guangzhou, Guangdong Province, China; Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, Guangdong Province, China; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, Guangzhou, Guangdong Province, China.
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67
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Tatosyan KA, Stasenko DV, Koval AP, Gogolevskaya IK, Kramerov DA. TATA-Like Boxes in RNA Polymerase III Promoters: Requirements for Nucleotide Sequences. Int J Mol Sci 2020; 21:ijms21103706. [PMID: 32466110 PMCID: PMC7279448 DOI: 10.3390/ijms21103706] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/03/2020] [Accepted: 05/05/2020] [Indexed: 01/02/2023] Open
Abstract
tRNA and some other non-coding RNA genes are transcribed by RNA polymerase III (pol III), due to the presence of intragenic promoter, consisting of boxes A and B spaced by 30–40 bp. Such pol III promoters, called type 2, are also intrinsic to Short Interspersed Elements (SINEs). The contribution of 5′-flanking sequences to the transcription efficiency of genes containing type 2 promoters is still studied insufficiently. Here, we studied this issue, focusing on the genes of two small non-coding RNAs (4.5SH and 4.5SI), as well as B1 and B2 SINEs from the mouse genome. We found that the regions from position −31 to −24 may significantly influence the transcription of genes and SINEs. We studied the influence of nucleotide substitutions in these sites, representing TATA-like boxes, on transcription of 4.5SH and 4.5SI RNA genes. As a rule, the substitutions of A and T to G or C reduced the transcription level, although the replacement of C with A also lowered it. In 4.5SH gene, five distal nucleotides of −31/−24 box (TTCAAGTA) appeared to be the most important, while in the box −31/−24 of 4.5SI gene (CTACATGA), all nucleotides, except for the first one, contributed significantly to the transcription efficiency. Random sequences occurring at positions −31/−24 upstream of SINE copies integrated into genome, promoted their transcription with different efficacy. In the 5′-flanking sequences of 4.5SH and 4.5SI RNA genes, the recognition sites of CREB, C/EBP, and Sp1 factors were found, and their deletion decreased the transcription.
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68
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Mohd MA, Ahmad Norudin NA, Muhammad TST. Transcriptional regulation of retinol binding protein 4 by Interleukin-6 via peroxisome proliferator-activated receptor α and CCAAT/Enhancer binding proteins. Mol Cell Endocrinol 2020; 505:110702. [PMID: 31927097 DOI: 10.1016/j.mce.2020.110702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 01/17/2023]
Abstract
Interleukin-6 (IL-6) is a major mediator of the acute phase response (APR) that regulates the transcription of acute phase proteins (APPs) in the liver. During APR, the plasma levels of negative APPs including retinol binding protein 4 (RBP4) are reduced. Activation of the IL-6 receptor and subsequent signaling pathways leads to the activation of transcription factors, including peroxisome proliferator-activated receptor alpha (PPARα) and CCAAT/enhancer binding protein (C/EBP), which then modulate APP gene expression. The transcriptional regulation of RBP4 by IL-6 is not fully understood. Therefore, this study aimed to elucidate the molecular mechanisms of PPARα and C/EBP isoforms in mediating IL-6 regulation of RBP4 gene expression. IL-6 was shown to reduce the transcriptional activity of RBP4, and functional dissection of the RBP4 promoter further identified the cis-acting regulatory elements that are responsible in mediating the inhibitory effect of IL-6. The binding sites for PPARα and C/EBP present in the RBP4 promoter were predicted at -1079 bp to -1057 bp and -1460 bp to -1439 bp, respectively. The binding of PPARα and C/EBPs to their respective cis-acting elements may lead to antagonistic interactions that modulate the IL-6 regulation of RBP4 promoter activity. Therefore, this study proposed a new mechanism of interaction involving PPARα and different C/EBP isoforms. This interaction is necessary for the regulation of RBP4 gene expression in response to external stimuli, particularly IL-6, during physiological changes.
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Affiliation(s)
- Muzaida Aminah Mohd
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Terengganu, Malaysia
| | - Nur Adelina Ahmad Norudin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Block 5-A, Halaman Bukit Gambir, 11700, Gelugor, Penang, Malaysia
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69
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Chu PH, Chen G, Kuo D, Braisted J, Huang R, Wang Y, Simeonov A, Boehm M, Gerhold DL. Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells. Chem Res Toxicol 2020; 33:751-763. [PMID: 32119531 DOI: 10.1021/acs.chemrestox.9b00363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To clarify how smoking leads to heart attack and stroke, we developed an endothelial cell model (iECs) generated from human induced Pluripotent Stem Cells (iPSC) and evaluated its responses to tobacco smoke. These iECs exhibited a uniform endothelial morphology, and expressed markers PECAM1/CD31, VWF/ von Willebrand Factor, and CDH5/VE-Cadherin. The iECs also exhibited tube formation and acetyl-LDL uptake comparable to primary endothelial cells (EC). RNA sequencing (RNA-Seq) revealed a robust correlation coefficient between iECs and EC (R = 0.76), whereas gene responses to smoke were qualitatively nearly identical between iECs and primary ECs (R = 0.86). Further analysis of transcriptional responses implicated 18 transcription factors in regulating responses to smoke treatment, and identified gene sets regulated by each transcription factor, including pathways for oxidative stress, DNA damage/repair, ER stress, apoptosis, and cell cycle arrest. Assays for 42 cytokines in HUVEC cells and iECs identified 23 cytokines that responded dynamically to cigarette smoke. These cytokines and cellular stress response pathways describe endothelial responses for lymphocyte attachment, activation of coagulation and complement, lymphocyte growth factors, and inflammation and fibrosis; EC-initiated events that collectively lead to atherosclerosis. Thus, these studies validate the iEC model and identify transcriptional response networks by which ECs respond to tobacco smoke. Our results systematically trace how ECs use these response networks to regulate genes and pathways, and finally cytokine signals to other cells, to initiate the diverse processes that lead to atherosclerosis and cardiovascular disease.
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Affiliation(s)
- Pei-Hsuan Chu
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Guibin Chen
- Center for Molecular Medicine, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 10 Center Drive, Bethesda, Maryland 20892, United States
| | - David Kuo
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - John Braisted
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ruili Huang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Yuhong Wang
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Manfred Boehm
- Center for Molecular Medicine, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 10 Center Drive, Bethesda, Maryland 20892, United States
| | - David L Gerhold
- National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Bethesda, Maryland 20892, United States
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Yuan H, Du S, Chen L, Xu X, Wang Y, Ji F. Hypomethylation of nerve growth factor (NGF) promotes binding of C/EBPα and contributes to inflammatory hyperalgesia in rats. J Neuroinflammation 2020; 17:34. [PMID: 31980031 PMCID: PMC6982391 DOI: 10.1186/s12974-020-1711-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/13/2020] [Indexed: 11/11/2022] Open
Abstract
Background Chronic pain usually accompanied by tissue damage and inflammation. However, the pathogenesis of chronic pain remains unclear. Methods We investigated the role of nerve growth factor (NGF) in chronic inflammatory pain induced by complete Freund’s adjuvant (CFA), explored the methylation status of CpG islands in the promoter region of the NGF gene, and clarified the function and mechanism of C/EBPα-NGF signaling pathway from epigenetic perspective in the chronic inflammatory pain model. Results CFA induced significant hyperalgesia and continuous upregulation of NGF mRNA and protein levels in the L4–6 dorsal root ganglions (DRGs) in rats. Hypomethylation of CpG islands occurred in the NGF gene promoter region after CFA treatment. At the same time, the miR-29b expression level was significantly increased, while the DNA methyltransferase 3b (DNMT3b) level reduced significantly. Moreover, CFA treatment promoted binding of C/EBPα to the NGF gene promoter region and C/EBPα siRNA treatment obviously decreased expression of NGF levels and also alleviate inflammatory hyperalgesia significantly in rats. Conclusion Collectively, the results indicated that CFA leads to the upregulation of miR-29b level, which represses the expression of DNMT3b, enhances the demethylation of the NGF gene promoter region, and promotes the binding of C/EBPα with the NGF gene promoter, thus results in the upregulation of NGF gene expression and maintenance of chronic inflammatory pain.
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Affiliation(s)
- Hongjie Yuan
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.,Department of Pain Medicine, Nantong Hospital of Traditional Chinese Medicine, Nantong, 226001, Jiangsu, People's Republic of China
| | - Shibin Du
- Department of Anesthesiology, Shenzhen University Clinical Medical Academy, Shenzhen University General Hospital, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Liping Chen
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China
| | - Xiaoqing Xu
- Department of Pain Medicine, Nantong Hospital of Traditional Chinese Medicine, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yufeng Wang
- Department of Radiology, Nantong Hospital of Traditional Chinese Medicine, Nantong, 226001, Jiangsu, People's Republic of China
| | - Fuhai Ji
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.
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Yuan H, Du S, Chen L, Xu X, Wang Y, Ji F. Hypomethylation of nerve growth factor (NGF) promotes binding of C/EBPα and contributes to inflammatory hyperalgesia in rats. J Neuroinflammation 2020. [PMID: 31980031 DOI: hypomethylation of nerve growth factor (ngf) promotes binding of c/ebpα and contributes to inflammatory hyperalgesia in rats] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Chronic pain usually accompanied by tissue damage and inflammation. However, the pathogenesis of chronic pain remains unclear. METHODS We investigated the role of nerve growth factor (NGF) in chronic inflammatory pain induced by complete Freund's adjuvant (CFA), explored the methylation status of CpG islands in the promoter region of the NGF gene, and clarified the function and mechanism of C/EBPα-NGF signaling pathway from epigenetic perspective in the chronic inflammatory pain model. RESULTS CFA induced significant hyperalgesia and continuous upregulation of NGF mRNA and protein levels in the L4-6 dorsal root ganglions (DRGs) in rats. Hypomethylation of CpG islands occurred in the NGF gene promoter region after CFA treatment. At the same time, the miR-29b expression level was significantly increased, while the DNA methyltransferase 3b (DNMT3b) level reduced significantly. Moreover, CFA treatment promoted binding of C/EBPα to the NGF gene promoter region and C/EBPα siRNA treatment obviously decreased expression of NGF levels and also alleviate inflammatory hyperalgesia significantly in rats. CONCLUSION Collectively, the results indicated that CFA leads to the upregulation of miR-29b level, which represses the expression of DNMT3b, enhances the demethylation of the NGF gene promoter region, and promotes the binding of C/EBPα with the NGF gene promoter, thus results in the upregulation of NGF gene expression and maintenance of chronic inflammatory pain.
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Affiliation(s)
- Hongjie Yuan
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.,Department of Pain Medicine, Nantong Hospital of Traditional Chinese Medicine, Nantong, 226001, Jiangsu, People's Republic of China
| | - Shibin Du
- Department of Anesthesiology, Shenzhen University Clinical Medical Academy, Shenzhen University General Hospital, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Liping Chen
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China
| | - Xiaoqing Xu
- Department of Pain Medicine, Nantong Hospital of Traditional Chinese Medicine, Nantong, 226001, Jiangsu, People's Republic of China
| | - Yufeng Wang
- Department of Radiology, Nantong Hospital of Traditional Chinese Medicine, Nantong, 226001, Jiangsu, People's Republic of China
| | - Fuhai Ji
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.
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Ebert SM, Bullard SA, Basisty N, Marcotte GR, Skopec ZP, Dierdorff JM, Al-Zougbi A, Tomcheck KC, DeLau AD, Rathmacher JA, Bodine SC, Schilling B, Adams CM. Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ. J Biol Chem 2020; 295:2787-2803. [PMID: 31953319 PMCID: PMC7049960 DOI: 10.1074/jbc.ra119.012095] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/10/2020] [Indexed: 12/17/2022] Open
Abstract
Skeletal muscle atrophy is a highly-prevalent and debilitating condition that remains poorly understood at the molecular level. Previous work found that aging, fasting, and immobilization promote skeletal muscle atrophy via expression of activating transcription factor 4 (ATF4) in skeletal muscle fibers. However, the direct biochemical mechanism by which ATF4 promotes muscle atrophy is unknown. ATF4 is a member of the basic leucine zipper transcription factor (bZIP) superfamily. Because bZIP transcription factors are obligate dimers, and because ATF4 is unable to form highly-stable homodimers, we hypothesized that ATF4 may promote muscle atrophy by forming a heterodimer with another bZIP family member. To test this hypothesis, we biochemically isolated skeletal muscle proteins that associate with the dimerization- and DNA-binding domain of ATF4 (the bZIP domain) in mouse skeletal muscle fibers in vivo Interestingly, we found that ATF4 forms at least five distinct heterodimeric bZIP transcription factors in skeletal muscle fibers. Furthermore, one of these heterodimers, composed of ATF4 and CCAAT enhancer-binding protein β (C/EBPβ), mediates muscle atrophy. Within skeletal muscle fibers, the ATF4-C/EBPβ heterodimer interacts with a previously unrecognized and evolutionarily conserved ATF-C/EBP composite site in exon 4 of the Gadd45a gene. This three-way interaction between ATF4, C/EBPβ, and the ATF-C/EBP composite site activates the Gadd45a gene, which encodes a critical mediator of muscle atrophy. Together, these results identify a biochemical mechanism by which ATF4 induces skeletal muscle atrophy, providing molecular-level insights into the etiology of skeletal muscle atrophy.
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Affiliation(s)
- Scott M Ebert
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246; Emmyon, Inc., Coralville, Iowa 52241
| | - Steven A Bullard
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Nathan Basisty
- Buck Institute for Research on Aging, Novato, California 94945
| | - George R Marcotte
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Zachary P Skopec
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Jason M Dierdorff
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Asma Al-Zougbi
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Kristin C Tomcheck
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Austin D DeLau
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Jacob A Rathmacher
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246
| | - Sue C Bodine
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Emmyon, Inc., Coralville, Iowa 52241
| | | | - Christopher M Adams
- Departments of Internal Medicine and Molecular Physiology and Biophysics, Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, Iowa 52242; Iowa City Veterans Affairs Medical Center, Iowa City, Iowa 52246; Emmyon, Inc., Coralville, Iowa 52241.
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Raffield LM, Iyengar AK, Wang B, Gaynor SM, Spracklen CN, Zhong X, Kowalski MH, Salimi S, Polfus LM, Benjamin EJ, Bis JC, Bowler R, Cade BE, Choi WJ, Comellas AP, Correa A, Cruz P, Doddapaneni H, Durda P, Gogarten SM, Jain D, Kim RW, Kral BG, Lange LA, Larson MG, Laurie C, Lee J, Lee S, Lewis JP, Metcalf GA, Mitchell BD, Momin Z, Muzny DM, Pankratz N, Park CJ, Rich SS, Rotter JI, Ryan K, Seo D, Tracy RP, Viaud-Martinez KA, Yanek LR, Zhao LP, Lin X, Li B, Li Y, Dupuis J, Reiner AP, Mohlke KL, Auer PL. Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. Am J Hum Genet 2020; 106:112-120. [PMID: 31883642 PMCID: PMC7042494 DOI: 10.1016/j.ajhg.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequencing (WGS) can improve assessment of low-frequency and rare variants, particularly in non-European populations that have been underrepresented in existing genomic studies. The genetic determinants of C-reactive protein (CRP), a biomarker of chronic inflammation, have been extensively studied, with existing genome-wide association studies (GWASs) conducted in >200,000 individuals of European ancestry. In order to discover novel loci associated with CRP levels, we examined a multi-ancestry population (n = 23,279) with WGS (∼38× coverage) from the Trans-Omics for Precision Medicine (TOPMed) program. We found evidence for eight distinct associations at the CRP locus, including two variants that have not been identified previously (rs11265259 and rs181704186), both of which are non-coding and more common in individuals of African ancestry (∼10% and ∼1% minor allele frequency, respectively, and rare or monomorphic in 1000 Genomes populations of East Asian, South Asian, and European ancestry). We show that the minor (G) allele of rs181704186 is associated with lower CRP levels and decreased transcriptional activity and protein binding in vitro, providing a plausible molecular mechanism for this African ancestry-specific signal. The individuals homozygous for rs181704186-G have a mean CRP level of 0.23 mg/L, in contrast to individuals heterozygous for rs181704186 with mean CRP of 2.97 mg/L and major allele homozygotes with mean CRP of 4.11 mg/L. This study demonstrates the utility of WGS in multi-ethnic populations to drive discovery of complex trait associations of large effect and to identify functional alleles in noncoding regulatory regions.
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Affiliation(s)
- Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Apoorva K Iyengar
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Biqi Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - Madeline H Kowalski
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Shabnam Salimi
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Linda M Polfus
- Department of Preventive Medicine, Center for Genetic Epidemiology, University of Southern California, Los Angeles, CA 90089, USA
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Joshua C Bis
- Department of Medicine, Cardiovascular Health Research Unit, University of Washington, Seattle, WA 98101, USA
| | - Russell Bowler
- Department of Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, National Jewish Health, Denver, CO 80206, USA
| | - Brian E Cade
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alejandro P Comellas
- Department of Medicine, Division of Pulmonary and Critical Care, University of Iowa, Iowa City, IA 52242, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Pedro Cruz
- Illumina Laboratory Services, Illumina Inc., San Diego, CA 92122, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Peter Durda
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | | | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | | | - Brian G Kral
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Cardiology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Leslie A Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Martin G Larson
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Cecelia Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jiwon Lee
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Joshua P Lewis
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Braxton D Mitchell
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Stephen S Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Kathleen Ryan
- Department of Medicine, Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Russell P Tracy
- Department of Pathology & Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA; Department of Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT 05446, USA
| | | | - Lisa R Yanek
- GeneSTAR Research Program, Division of General Internal Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lue Ping Zhao
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA 01702, USA
| | - Alexander P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53205, USA.
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Amon L, Lehmann CHK, Baranska A, Schoen J, Heger L, Dudziak D. Transcriptional control of dendritic cell development and functions. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2019; 349:55-151. [PMID: 31759434 DOI: 10.1016/bs.ircmb.2019.10.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dendritic cells (DCs) are major regulators of adaptive immunity, as they are not only capable to induce efficient immune responses, but are also crucial to maintain peripheral tolerance and thereby inhibit autoimmune reactions. DCs bridge the innate and the adaptive immune system by presenting peptides of self and foreign antigens as peptide MHC complexes to T cells. These properties render DCs as interesting target cells for immunomodulatory therapies in cancer, but also autoimmune diseases. Several subsets of DCs with special properties and functions have been described. Recent achievements in understanding transcriptional programs on single cell level, together with the generation of new murine models targeting specific DC subsets, advanced our current understanding of DC development and function. Thus, DCs arise from precursor cells in the bone marrow with distinct progenitor cell populations splitting the monocyte populations and macrophage populations from the DC lineage, which upon lineage commitment can be separated into conventional cDC1, cDC2, and plasmacytoid DCs (pDCs). The DC populations harbor intrinsic programs enabling them to react for specific pathogens in dependency on the DC subset, and thereby orchestrate T cell immune responses. Similarities, but also varieties, between human and murine DC subpopulations are challenging, and will require further investigation of human specimens under consideration of the influence of the tissue micromilieu and DC subset localization in the future.
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Affiliation(s)
- Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Baranska
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Janina Schoen
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
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Lu YC, Jia L, Zheng Z, Tran E, Robbins PF, Rosenberg SA. Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy. Cancer Immunol Res 2019; 7:1824-1836. [PMID: 31484655 PMCID: PMC6825592 DOI: 10.1158/2326-6066.cir-19-0299] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 06/24/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022]
Abstract
Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TIL) can mediate responses in some patients with metastatic epithelial cancer. Identifying gene signatures associated with successful ACT might enable the development of improved therapeutic approaches. The persistence of transferred T cells in the peripheral blood is one indication of clinical effectiveness, but many T-cell and host factors may influence T-cell persistence. To limit these variables, we previously studied a patient with metastatic colorectal cancer treated with polyclonal TILs targeting the KRAS(G12D) hotspot mutation, who experienced a partial response for 9 months. Three dominant clonotypes specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after ACT. Because of these findings, in this study, we performed the single-cell transcriptome analysis of the infused TILs. The analysis revealed a total of 472 genes that were differentially expressed between clonotypes 9.1-NP and 9.2-P single cells, and 528 genes between 9.1-NP and 10-P. Following these clonotypes in the peripheral blood after ACT, the gene expression patterns changed, but IL7R, ITGB1, KLF2, and ZNF683 remained expressed in the persistent 9.2-P and 10-P cells, compared with the nonpersistent 9.1-NP cells. In addition, four autologous TILs, which were used for treatment but persisted poorly 1 month after ACT, did not express the gene profiles associated with persistence. These results suggest that certain TIL populations possess a unique gene expression profile that can lead to the persistence of T cells. Thus, this single-patient study provides insight into how to improve ACT for solid cancer.
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Affiliation(s)
- Yong-Chen Lu
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Li Jia
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Zhili Zheng
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eric Tran
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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AlSudais H, Wiper-Bergeron N. Contaminating reactivity of a monoclonal CCAAT/Enhancer Binding Protein β antibody in differentiating myoblasts. BMC Res Notes 2019; 12:717. [PMID: 31672165 PMCID: PMC6824081 DOI: 10.1186/s13104-019-4749-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/18/2019] [Indexed: 11/10/2022] Open
Abstract
Objective CCAAT/Enhancer Binding proteins (C/EBPs) are transcription factors involved in the regulation of a variety of cellular processes. We used the Abcam Recombinant Anti-C/EBP beta antibody (E299) to detect C/EBPβ expression during myogenesis. Though the antibody is monoclonal, and the immunogen used is highly specific to C/EBPβ, we identified an intense band at 23 kDa on western blot that did not correspond to any of the known isoforms of C/EBPβ, or family members predicted to cross-react. Absent in myoblast cells overexpressing C/EBPβ, the band was present when C/EBPβ was knocked down, confirming specificity for a protein other than C/EBPβ. The objective of this work was to identify the contaminating reactivity. Results We performed immunoprecipitation followed by mass spectrometry to identified myosin light chain 4 (MYL4) as the unknown band, suggesting that the Abcam monoclonal antibody directed against C/EBPβ is not pure, but contains a contaminating antibody against MYL4. Caution should be used when working in cells lines that express MYL4 to not confound the detection of MYL4 with that of C/EBPβ isoforms.
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Affiliation(s)
- Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Rm 3106, K1H 8M5, Ottawa, ON, Canada
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Rm 2539, K1H 8M5, Ottawa, ON, Canada.
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Tian Y, Li G, Shen J, Tao Z, Chen L, Zeng T, Lu L. Molecular cloning, characterisation, and expression patterns of pigeon CCAAT/enhancer binding protein-α and -β genes. Br Poult Sci 2019; 60:347-356. [PMID: 31064204 DOI: 10.1080/00071668.2019.1614530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
1. CCAAT/enhancer binding proteins (C/EBPs), as a family of transcription factors, consists of six functionally and structurally related proteins which share a conserved basic leucine zipper (bZIP) DNA-binding domain. The aim of this study was to clone the full-length coding sequences (CDS) of C/EBP-α and -β genes, and determine the abundance of these two genes in various tissues of white king pigeon (C. livia). 2. The complete cDNA sequences of C/EBP-α and -β genes were cloned from pigeons by using PCR combined with rapid amplification of cDNA ends (RACE). The sequences were bioinformatically analysed, and the tissue distribution determined by quantitative real-time RT-PCR (qRT-PCR). 3. The results showed that the full-length cDNA sequences of pigeon C/EBP-α and -β genes were 2,807bp and 1,778bp, respectively. The open reading frames of C/EBP-α (978 bp) and -β (987bp) encoded 325 amino acids and 328 amino acids, respectively. The pigeon C/EBP-α and C/EBP-β proteins were predicted to have a conserved basic leucine zipper (bZIP) domain, which is a common structure feature of the C/EBP family. Multiple sequence alignments indicated that pigeon C/EBP-α and -β shared more than 90% amino-acid identity with their corresponding homologues in other avian species. Phylogenetic analysis revealed that these two proteins were highly conserved across different species and evolutionary processes. QRT-PCR results indicated that the pigeon C/EBP-α and -β mRNA transcripts were expressed in all investigated organs. The mRNA expression levels of pigeon C/EBP-α in descending order, were in spleen, heart, liver, lung, kidney and muscle. The pigeon C/EBP-β gene had the most abundant expression in lung, followed by the kidney, with minimal expression detected in muscle. 4. This study investigated the full-length cDNA sequences, genetic characteristics and tissue distribution of pigeon C/EBP-α and -β genes and found that they may have functions in various tissues of pigeon. This provides a foundation for further study for regulatory mechanisms of these two genes in birds.
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Affiliation(s)
- Y Tian
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China.,b Key Laboratory of Information Traceability for Agricultural Products , Ministry of Agriculture of China , Hangzhou , China
| | - G Li
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China.,b Key Laboratory of Information Traceability for Agricultural Products , Ministry of Agriculture of China , Hangzhou , China
| | - J Shen
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China
| | - Z Tao
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China
| | - L Chen
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China
| | - T Zeng
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China.,b Key Laboratory of Information Traceability for Agricultural Products , Ministry of Agriculture of China , Hangzhou , China
| | - L Lu
- a Zhejiang Academy of Agricultural Sciences , Institute of Animal Husbandry and Veterinary Science , Hangzhou , China.,b Key Laboratory of Information Traceability for Agricultural Products , Ministry of Agriculture of China , Hangzhou , China
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78
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Salotti J, Johnson PF. Regulation of senescence and the SASP by the transcription factor C/EBPβ. Exp Gerontol 2019; 128:110752. [PMID: 31648009 DOI: 10.1016/j.exger.2019.110752] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022]
Abstract
Oncogene-induced senescence (OIS) serves as an important barrier to tumor progression in cells that have acquired activating mutations in RAS and other oncogenes. Senescent cells also produce a secretome known as the senescence-associated secretory phenotype (SASP) that includes pro-inflammatory cytokines and chemokines. SASP factors reinforce and propagate the senescence program and identify senescent cells to the immune system for clearance. The OIS program is executed by several transcriptional effectors that include p53, RB, NF-κB and C/EBPβ. In this review, we summarize the critical role of C/EBPβ in regulating OIS and the SASP. Post-translational modifications induced by oncogenic RAS signaling control C/EBPβ activity and dimerization, and these alterations switch C/EBPβ to a pro-senescence form during OIS. In addition, C/EBPβ is regulated by a unique 3'UTR-mediated mechanism that restrains its activity in tumor cells to facilitate senescence bypass and suppression of the SASP.
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Affiliation(s)
- Jacqueline Salotti
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Peter F Johnson
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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79
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Pirie E, Cauntay P, Fu W, Ray S, Pan C, Lusis AJ, Hsiao J, Burel SA, Narayanan P, Crooke RM, Lee RG. Hybrid Mouse Diversity Panel Identifies Genetic Architecture Associated with the Acute Antisense Oligonucleotide-Mediated Inflammatory Response to a 2'- O-Methoxyethyl Antisense Oligonucleotide. Nucleic Acid Ther 2019; 29:266-277. [PMID: 31368839 PMCID: PMC6765210 DOI: 10.1089/nat.2019.0797] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/04/2019] [Indexed: 01/04/2023] Open
Abstract
Although antisense oligonucleotides (ASOs) are well tolerated preclinically and in the clinic, some sequences of ASOs can trigger an inflammatory response leading to B cell and macrophage activation in rodents. This prompted our investigation into the contribution of genetic architecture to the ASO-mediated inflammatory response. Genome-wide association (GWA) and transcriptomic analysis in a hybrid mouse diversity panel (HMDP) were used to identify and validate novel genes involved in the acute and delayed inflammatory response to a single 75 mg/kg dose of an inflammatory 2'-O-methoxyethyl (2'MOE) modified ASO. The acute response was measured 6 h after ASO administration, via evaluation for increased plasma production of interleukin 6 (IL6), IL10, monocyte chemoattractant protein 1 (MCP-1) and macrophage inflammatory protein-1β (MIP-1β). Delayed inflammation was evaluated by spleen weight increases after 96 h. We identified single nucleotide polymorphisms (SNPs) on chromosomes 16 and 17 associated with plasma MIP-1β, IL6, and MCP-1 levels, and one on chromosome 8 associated with increases in spleen weight. Systems genetic analysis utilizing transcriptomic data from HMDP strain macrophages determined that the acute inflammatory SNPs were expression quantitative trait locis (eQTLs) for CCAAT/enhancer-binding protein beta (Cebpb) and salt inducible kinase 1 (Sik1). The delayed inflammatory SNP was an eQTL for Rho guanine nucleotide exchange factor 10 (Arhgef10). In vitro assays in mouse primary cells and human cell lines have confirmed the HMDP finding that lower Sik1 expression increases the acute inflammatory response. Our results demonstrate the utility of using mouse GWA study (GWAS) and the HMDP for detecting genes modulating the inflammatory response to pro-inflammatory ASOs in a pharmacological setting.
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Affiliation(s)
- Elaine Pirie
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, California
| | - Patrick Cauntay
- Preclinical Development, Ionis Pharmaceuticals, Carlsbad, California
| | - Wuxia Fu
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, California
| | - Shayoni Ray
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, California
| | - Calvin Pan
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
| | - Aldonis J. Lusis
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
| | - Jill Hsiao
- Preclinical Development, Ionis Pharmaceuticals, Carlsbad, California
| | | | - Padma Narayanan
- Preclinical Development, Ionis Pharmaceuticals, Carlsbad, California
| | - Rosanne M. Crooke
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, California
| | - Richard G. Lee
- Cardiovascular Antisense Drug Discovery Group, Ionis Pharmaceuticals, Carlsbad, California
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80
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Kusama K, Tamura K, Bai H, Sakurai T, Nishi H, Isaka K, Imakawa K, Yoshie M. Exchange protein directly activated by cAMP (EPAC) promotes transcriptional activation of the decidual prolactin gene via CCAAT/enhancer-binding protein in human endometrial stromal cells. Reprod Fertil Dev 2019; 30:1454-1461. [PMID: 29735004 DOI: 10.1071/rd17483] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 04/10/2018] [Indexed: 11/23/2022] Open
Abstract
Protein kinase A (PKA) signalling accompanies elevated intracellular cAMP levels during endometrial stromal cell (ESC) decidualisation. Exchange protein directly activated by cAMP (EPAC), an alternate mediator of cAMP signalling, promotes PKA analogue-induced decidualisation; however, the precise mechanism by which EPAC and PKA co-operatively stimulate decidualisation has not been characterised. To examine the role of CCAAT/enhancer-binding protein (C/EBP) in EPAC- and PKA-mediated decidualisation of primary human ESCs, a reporter plasmid containing the 332bp region upstream from the transcription initiation site of the decidual prolactin (dPRL) gene was generated and the promoter activity was evaluated using a luciferase assay. The dPRL promoter activity was increased by treatment of transfected ESCs with the PKA-selective cAMP analogue N6-phenyl-cAMP (Phe) and enhanced further by co-treatment with the EPAC-selective cAMP analogue 8-(4-chlorophenyltio)-2'-O-methyl cAMP (CPT). Treatment with forskolin, an adenylyl cyclase activator, had a similar effect on reporter activity. Site-directed mutagenesis of the C/EBPβ- and/or C/EBPδ-binding site in the dPRL promoter abolished Phe/CPT-mediated elevation of the reporter activity. EPAC2 knockdown markedly reduced Phe-stimulated C/EBPβ and C/EBPδ mRNA levels, as well as forkhead box O1 (FOXO1) protein levels. These results suggest that EPAC signalling enhances PKA-mediated dPRL expression in ESCs by acting on C/EBP response elements in the promoter region of the gene.
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Affiliation(s)
- Kazuya Kusama
- Animal Resource Science Centre, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Kazuhiro Tamura
- Department of Endocrine and Neural Pharmacology, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
| | - Hanako Bai
- Laboratory of Animal Genetics and Reproduction, Department of Animal Science, Graduate School of Agriculture, Hokkaido University, Hokkaido, 060-8589, Japan
| | - Toshihiro Sakurai
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Science, Tokyo University of Science, Chiba, 278-8510, Japan
| | - Hirotaka Nishi
- Department of Obstetrics and Gynaecology, Tokyo Medical University, Tokyo, 160-0023, Japan
| | - Keiichi Isaka
- Department of Obstetrics and Gynaecology, Tokyo Medical University, Tokyo, 160-0023, Japan
| | - Kazuhiko Imakawa
- Animal Resource Science Centre, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Mikihiro Yoshie
- Department of Endocrine and Neural Pharmacology, Tokyo University of Pharmacy and Life Sciences, Tokyo, 192-0392, Japan
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81
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Tam HW, Hall JR, Messenger ZJ, Jima DD, House JS, Linder K, Smart RC. C/EBPβ suppresses keratinocyte autonomous type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer. Carcinogenesis 2019; 40:1099-1109. [PMID: 30698678 PMCID: PMC10893916 DOI: 10.1093/carcin/bgz012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 12/14/2022] Open
Abstract
p53 is activated by DNA damage and oncogenic stimuli to regulate senescence, apoptosis and cell-cycle arrest, which are essential to prevent cancer. Here, we utilized UVB radiation, a potent inducer of DNA damage, p53, apoptosis and skin cancer to investigate the mechanism of CCAAT/enhancer binding protein-β (C/EBPβ) in regulating p53-mediated apoptosis in keratinocytes and to test whether the deletion of C/EBPβ in epidermis can protect mice from UVB-induced skin cancer. UVB-treatment of C/EBPβ skin conditional knockout (CKOβ) mice increased p53 protein levels in epidermis and enhanced p53-dependent apoptotic activity 3-fold compared with UVB-treated control mice. UVB increased C/EBPβ levels through a p53-dependent pathway and stimulated the formation of a C/EBPβ-p53 protein complex; knockdown of C/EBPβ increased p53 protein stability in keratinocytes. These results suggest a p53-C/EBPβ feedback loop, whereby C/EBPβ, a transcriptional target of a p53 pathway, functions as a survival factor by negatively regulating p53 apoptotic activity in response to DNA damage. RNAseq analysis of UVB-treated CKOβ epidermis unexpectedly revealed that type 1 interferon (IFN) pathway was the most highly enriched pathway. Numerous pro-apoptotic interferon stimulated genes were upregulated including some known to enhance p53 apoptosis. Our results indicate that p53 and IFN pathways function together in response to DNA damage to result in the activation of extrinsic apoptosis pathways and caspase 8 cleavage. Last, we observed CKOβ mice were resistant to UVB-induced skin cancer. Our results suggest that C/EBPβ represses apoptosis through keratinocyte autonomous suppression of the type 1 IFN response and p53 to increase cell survival and susceptibility to UVB-induced skin cancer.
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Affiliation(s)
- Hann W Tam
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Jonathan R Hall
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | | | - Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John S House
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Keith Linder
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Robert C Smart
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
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82
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Yang J, Horton JR, Wang D, Ren R, Li J, Sun D, Huang Y, Zhang X, Blumenthal RM, Cheng X. Structural basis for effects of CpA modifications on C/EBPβ binding of DNA. Nucleic Acids Res 2019; 47:1774-1785. [PMID: 30566668 PMCID: PMC6393304 DOI: 10.1093/nar/gky1264] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/28/2018] [Accepted: 12/08/2018] [Indexed: 12/30/2022] Open
Abstract
CCAAT/enhancer binding proteins (C/EBPs) regulate gene expression in a variety of cells/tissues/organs, during a range of developmental stages, under both physiological and pathological conditions. C/EBP-related transcription factors have a consensus binding specificity of 5'-TTG-CG-CAA-3', with a central CpG/CpG and two outer CpA/TpG dinucleotides. Methylation of the CpG and CpA sites generates a DNA element with every pyrimidine having a methyl group in the 5-carbon position (thymine or 5-methylcytosine (5mC)). To understand the effects of both CpG and CpA modification on a centrally-important transcription factor, we show that C/EBPβ binds the methylated 8-bp element with modestly-increased (2.4-fold) binding affinity relative to the unmodified cognate sequence, while cytosine hydroxymethylation (particularly at the CpA sites) substantially decreased binding affinity (36-fold). The structure of C/EBPβ DNA binding domain in complex with methylated DNA revealed that the methyl groups of the 5mCpA/TpG make van der Waals contacts with Val285 in C/EBPβ. Arg289 recognizes the central 5mCpG by forming a methyl-Arg-G triad, and its conformation is constrained by Val285 and the 5mCpG methyl group. We substituted Val285 with Ala (V285A) in an Ala-Val dipeptide, to mimic the conserved Ala-Ala in many members of the basic leucine-zipper family of transcription factors, important in gene regulation, cell proliferation and oncogenesis. The V285A variant demonstrated a 90-fold binding preference for methylated DNA (particularly 5mCpA methylation) over the unmodified sequence. The smaller side chain of Ala285 permits Arg289 to adopt two alternative conformations, to interact in a similar fashion with either the central 5mCpG or the TpG of the opposite strand. Significantly, the best-studied cis-regulatory elements in RNA polymerase II promoters and enhancers have variable sequences corresponding to the central CpG or reduced to a single G:C base pair, but retain a conserved outer CpA sequence. Our analyses suggest an important modification-dependent CpA recognition by basic leucine-zipper transcription factors.
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Affiliation(s)
- Jie Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dongxue Wang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ren Ren
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Deqiang Sun
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Xing Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xiaodong Cheng
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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83
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Malinow RA, Ying P, Koorman T, Boxem M, Jin Y, Kim KW. Functional Dissection of C. elegans bZip-Protein CEBP-1 Reveals Novel Structural Motifs Required for Axon Regeneration and Nuclear Import. Front Cell Neurosci 2019; 13:348. [PMID: 31417366 PMCID: PMC6685058 DOI: 10.3389/fncel.2019.00348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/15/2019] [Indexed: 12/02/2022] Open
Abstract
The basic leucine-zipper (bZIP) domain transcription factors CCAAT/enhancer-binding proteins (C/EBP) have a variety of roles in cell proliferation, differentiation, and stress response. In the nervous system, several isoforms of C/EBP function in learning and memory, neuronal plasticity, neuroinflammation, and axon regeneration. We previously reported that the Caenorhabditis elegans C/EBP homolog, CEBP-1, is essential for axon regeneration. CEBP-1 consists of 319 amino acids, with its bZIP domain at the C-terminus and a long N-terminal fragment with no known protein motifs. Here, using forward genetic screening with targeted genome editing, we have identified a unique domain in the N-terminus that is critical for its in vivo function. Additionally, we characterized three nuclear localization signals (NLS) in CEBP-1 that act together to mediate CEBP-1’s nuclear import. Moreover, the Importin-α, IMA-3, can bind to CEBP-1 via one of the NLS. ima-3 is ubiquitously expressed in all somatic cells, and ima-3 null mutants are larval lethal. Using Cre-lox dependent neuron-specific deletion strategy, we show that ima-3 is not critical for axon development, but is required for axon regeneration in adults. Together, these data advance our understanding of CEBP-1’s function, and suggest new regulators that remain to be identified to expand the CEBP-1 protein interactome.
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Affiliation(s)
- Rose Aria Malinow
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Phoenix Ying
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Thijs Koorman
- Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Mike Boxem
- Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Yishi Jin
- Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Kyung Won Kim
- Convergence Program of Material Science for Medicine and Pharmaceutics, Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon, South Korea
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84
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Dias C, Elzein S, Sladek R, Goodyer CG. Sex-specific effects of a microsatellite polymorphism on human growth hormone receptor gene expression. Mol Cell Endocrinol 2019; 492:110442. [PMID: 31063794 DOI: 10.1016/j.mce.2019.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/05/2023]
Abstract
Growth hormone (GH) binds to its specific receptor (GHR) at the surface of target cells activating multiple signaling pathways implicated in growth and metabolism. Dysregulation of GHRs leads to pathophysiological states that most commonly affect stature. We previously showed the association of a polymorphic (n = 15-37) GT microsatellite in the human GHR gene promoter with short stature in a sex-specific manner. In the present study we evaluated the functional relevance of this polymorphism in regulating GHR expression. Using luciferase reporter assays, we found that the GT repeat had a significant cis regulatory effect in response to HIF1α and a potential repressor role following C/EBPβ stimulation. Using a digital PCR application to measure allelic imbalance (AI), we showed a high prevalence of AI (∼76%) at the GHR locus in lymphoblastoid cell lines (LCLs), with a significantly higher degree of imbalance in LCLs derived from males. Examination of expression of GHR as well as other members of the GH-IGF1 axis in the LCLs revealed significant associations of GHR, IGF1 and BCL2 expression with GT genotype in a sex-specific manner. Our results suggest that this GT microsatellite exerts both cis and trans effects in a sex-specific context, revealing a new mechanism by which GHR gene expression is regulated.
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Affiliation(s)
- Christel Dias
- Division of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Samar Elzein
- Division of Experimental Medicine, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Robert Sladek
- Division of Experimental Medicine and Department of Human Genetics, McGill University, Montreal, Quebec, H4A 3J1, Canada
| | - Cynthia Gates Goodyer
- Division of Experimental Medicine and Department of Pediatrics, McGill University, Montreal, Quebec, H4A 3J1, Canada.
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85
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Cohen DM, Lim HW, Won KJ, Steger DJ. Shared nucleotide flanks confer transcriptional competency to bZip core motifs. Nucleic Acids Res 2019; 46:8371-8384. [PMID: 30085281 PMCID: PMC6144830 DOI: 10.1093/nar/gky681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 12/31/2022] Open
Abstract
Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at <1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hee-Woong Lim
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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86
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Muraoka M, Akagi T, Ueda A, Wada T, Koeffler HP, Yokota T, Yachie A. C/EBPε ΔRS derived from a neutrophil-specific granule deficiency patient interacts with HDAC1 and its dysfunction is restored by trichostatin A. Biochem Biophys Res Commun 2019; 516:293-299. [PMID: 31256937 DOI: 10.1016/j.bbrc.2019.06.130] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022]
Abstract
CCAAT/enhancer binding protein epsilon (C/EBPε), a myeloid-specific transcription factor, plays an important role in granulopoiesis. A loss-of-function mutation in this protein can result in an abnormal development of neutrophils and eosinophils, known as neutrophil-specific granule deficiency (SGD). The transcriptional activity of C/EBPε is regulated by interactions with other transcription factors and/or post-translational modification, including acetylation. Previously, we reported a novel SGD patient who had a homozygous mutation for two amino acids, arginine (R247) and serine (S248), which were deleted in the basic leucine zipper domain of C/EBPε (ΔRS) and exhibited loss of transcriptional activity with aberrant protein-protein interactions. In the present study, we found that a single amino acid deletion of either R247 (ΔR) or S248 (ΔS) was sufficient for the loss of C/EBPε transcriptional activity, while an amino acid substitution at S248 to alanine in C/EBPε (SA) had comparable transcriptional activity with the wild-type C/EBPε (WT). Although acetylation at lysine residues (K121 and K198) is indispensable for C/EBPε transcriptional activity, an acetylation mimic form of ΔRS (ΔRS-K121/198Q) did not exhibit the transcriptional activity. Interestingly, we discovered that ΔRS, ΔR, ΔS, and ΔRS-K121/198Q interacted with histone deacetylase 1 (HDAC1), whereas WT and SA did not. Furthermore, the proteoglycan 2/eosinophil major basic protein induction activity of ΔRS, ΔR, and ΔS could be restored by the HDAC inhibitor, trichostatin A (TSA), and protein-protein interactions between ΔRS and Gata1 could also be recovered by TSA treatment. Taken together, our results show that TSA has the potential to restore the transcriptional activity of ΔRS, indicating that the inhibition of HDAC1 could be a molecularly targeted treatment for SGD with ΔRS.
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Affiliation(s)
- Masahiro Muraoka
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Kanazawa, 920-8641, Japan
| | - Tadayuki Akagi
- Department of Stem Cell Biology, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Kanazawa, 920-8640, Japan.
| | - Atsushi Ueda
- Department of Stem Cell Biology, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Taizo Wada
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Kanazawa, 920-8641, Japan
| | - H Phillip Koeffler
- Division of Hematology and Oncology, Cedars-Sinai Medical Center, University of California Los Angeles School of Medicine, Los Angeles, CA, 90048, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Takashi Yokota
- Department of Stem Cell Biology, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Akihiro Yachie
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, School of Medicine, Kanazawa University, Kanazawa, 920-8641, Japan
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Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, Rödin‐Mörch P, Quintela M, Richter‐Boix A, Höglund J, Laurila A. Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor
C/EBP‐1. Mol Ecol 2019; 28:2786-2801. [DOI: 10.1111/mec.15123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Emilien Luquet
- Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés Université Lyon 1 Villeurbanne France
| | - Fríða Jóhannesdóttir
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York
- Ecology and Genetics Research Unit University of Oulu Oulu Finland
| | - Patrik Rödin‐Mörch
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - María Quintela
- Department of Population Genetics Institute of Marine Research Bergen Norway
| | - Alex Richter‐Boix
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and Genetics Uppsala University Uppsala Sweden
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88
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Guo Q, Hu H, Liu X, Yang D, Yin Y, Zhang B, He H, Oh Y, Wu Q, Liu C, Gu N. C/EBPβ mediates palmitate-induced musclin expression via the regulation of PERK/ATF4 pathways in myotubes. Am J Physiol Endocrinol Metab 2019; 316:E1081-E1092. [PMID: 30964708 DOI: 10.1152/ajpendo.00478.2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Musclin is a muscle-secreted cytokine that disrupts glucose uptake and glycogen synthesis in type 2 diabetes. The purpose of this study was to investigate the mechanisms responsible for the regulation of musclin gene expression in response to treatment with palmitate. RNA sequencing results showed that biological processes activated by palmitate are mainly enriched in endoplasmic reticulum (ER) stress. The protein kinase RNA-like ER kinase (PERK) signaling pathway is involved in the regulation of musclin expression induced by palmitate. Chromatin immunoprecipitation data showed that activating transcription factor 4 (ATF4)-downstream of PERK-bound to the promoter of the C/EBPβ gene. Notably, C/EBPβ also contains a binding site in the region -94~-52 of the musclin gene promoter. Knockdown or knockout of PERK and ATF4 using short hairpin RNA or CRISPR-Cas9 decreased the expression of C/EBPβ and musclin induced by palmitate. Furthermore, knockdown and knockout of C/EBPβ alleviated the high expression of musclin in response to treatment with palmitate. Moreover, CRISPR-Cas9 knockout of the region -94~-52 in which C/EBPβ binds to the promoter of musclin abrogated the induction of high musclin expression caused by palmitate. Collectively, these findings suggest that treatment with palmitate activates the PERK/ATF4 signaling pathway, which in turn increases the expression of C/EBPβ. C/EBPβ binds directly to the promoter of the musclin gene and upregulates its expression.
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Affiliation(s)
- Qian Guo
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Hailong Hu
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Xiaohuan Liu
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - DaQian Yang
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Yao Yin
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Boya Zhang
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Hongjuan He
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Yuri Oh
- Faculty of Education, Wakayama University , Wakayama , Japan
| | - Qiong Wu
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Chuanpeng Liu
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
| | - Ning Gu
- School of Life Science and Technology, Harbin Institute of Technology , Harbin , China
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89
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Guénard F, Jacques H, Gagnon C, Marette A, Vohl MC. Acute Effects of Single Doses of Bonito Fish Peptides and Vitamin D on Whole Blood Gene Expression Levels: A Randomized Controlled Trial. Int J Mol Sci 2019; 20:ijms20081944. [PMID: 31010033 PMCID: PMC6514567 DOI: 10.3390/ijms20081944] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 12/18/2022] Open
Abstract
Fish contains high quality proteins and essential nutrients including 25-hydroxyvitamin D (25(OH)D). Fish peptide consumption can lower cardiovascular disease (CVD) risk factors, and studies have shown an association between 25(OH)D deficiency, CVD and CVD risk factors, such as diabetes. This study investigated acute effects of a single dose of cholecalciferol (VitD3), bonito fish peptide hydrolysate (BPH), or a combination of both on CVD risk factors and whole blood gene expression levels. A randomized, crossover, placebo controlled trial was conducted in 22 adults. They ingested, in random order and at 7-day intervals, 1000 IU of VitD3, 3 g of BPH, a combination of both, or a placebo. A 180 min oral glucose tolerance test was performed. Differences in whole-genome expression levels after versus before each supplementation were computed for 18 subjects. We observed that 16, 1 and 5 transcripts were differentially expressed post- vs. pre-ingestion for VitD3, BPH or VitD3 + BPH treatments, respectively. VitD3-containing treatments affected the expression of the solute carrier family 25 member 20 (SLC25A20) gene involved in fatty acid oxidation, various transcription factors and genes related to glucose metabolism. These results suggest that VitD3 rapidly modulates genes related to CVD risk factors in blood while BPH seems to moderately modulate gene expression levels.
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Affiliation(s)
- Frédéric Guénard
- School of Nutrition, Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- Institute of Nutrition and Functional Food (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Hélène Jacques
- School of Nutrition, Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- Institute of Nutrition and Functional Food (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Claudia Gagnon
- Institute of Nutrition and Functional Food (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- Endocrinology and Nephrology Unit, CHU de Quebec Research Center, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
- Department of Medicine, Laval University, 1050 avenue de la Médecine, Quebec, QC G1V 0A6, Canada.
| | - André Marette
- Institute of Nutrition and Functional Food (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- Quebec Heart and Lung Institute (IUCPQ) Research Center, 2725 chemin Sainte-Foy, Quebec, QC G1V 4G5, Canada.
| | - Marie-Claude Vohl
- School of Nutrition, Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- Institute of Nutrition and Functional Food (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
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Mirisis AA, Carew TJ. The ELAV family of RNA-binding proteins in synaptic plasticity and long-term memory. Neurobiol Learn Mem 2019; 161:143-148. [PMID: 30998973 DOI: 10.1016/j.nlm.2019.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/14/2019] [Accepted: 04/13/2019] [Indexed: 12/26/2022]
Abstract
The mechanisms of de novo gene expression and translation of specific gene transcripts have long been known to support long-lasting changes in synaptic plasticity and behavioral long-term memory. In recent years, it has become increasingly apparent that gene expression is heavily regulated not only on the level of transcription, but also through post-transcriptional gene regulation, which governs the subcellular localization, stability, and likelihood of translation of mRNAs. Specific families of RNA-binding proteins (RBPs) bind transcripts which contain AU-rich elements (AREs) within their 3' UTR and thereby govern their downstream fate. These post-transcriptional gene regulatory mechanisms are coordinated through the same cell signaling pathways that play critical roles in long-term memory formation. In this review, we discuss recent results that demonstrate the roles that these ARE-binding proteins play in LTM formation.
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Affiliation(s)
| | - Thomas J Carew
- Center for Neural Science, New York University, New York, NY 10003, USA.
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91
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Characterization of an HPV33 natural variant with enhanced transcriptional activity suggests a role for C/EBPβ in the regulation of the viral early promoter. Sci Rep 2019; 9:5113. [PMID: 30911096 PMCID: PMC6433916 DOI: 10.1038/s41598-019-41102-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
The Long Control Region (LCR) of the human papillomavirus (HPV) genome encompasses the early promoter (EP) that drives expression of the viral oncogenes in infected cells and HPV-associated cancers. Here, we report on a natural variant of HPV33 that displays higher EP activity than the prototype in transfected C33A and HeLa cervical carcinoma cells, and in the osteosarcoma U2OS cell line which supports replication of HPV episomes. This increased promoter activity was ascribed to a single nucleotide variation in the LCR, T7791C, in a putative binding site for the transcription factor C/EBPβ. T7791C abrogated binding of recombinant C/EBPβ to this site in vitro and stimulated the EP in vivo, suggesting that it abrogates a negatively-acting regulatory element. A second C/EBPβ binding site was identified in vitro that activated the EP in vivo and whose function and location in the epithelial-specific enhancer is shown to be conserved in the highly prevalent HPV18. These results suggest that C/EBPβ is both an activator and a repressor of the HPV33 EP, acting via two distinct binding sites. Prediction of C/EBPβ sites in the LCR of 186 HPV types suggests that C/EBPβ regulation of the EP is common among high‐risk viruses from the α genus.
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92
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Yu S, Lu Y, Zong M, Tan Q, Fan L. Hypoxia-induced miR-191-C/EBPβ signaling regulates cell proliferation and apoptosis of fibroblast-like synoviocytes from patients with rheumatoid arthritis. Arthritis Res Ther 2019; 21:78. [PMID: 30894209 PMCID: PMC6425666 DOI: 10.1186/s13075-019-1861-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/06/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Hypoxia plays an important role in the proliferation of rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS), leading to pathology of RA. This study was conducted to evaluate hypoxia-induced microRNAs (hypoxamiR) in RA-FLS and its role in the function of RA-FLS. METHODS RA-FLS were cultured under normoxia (21% O2) or hypoxia (3% O2) condition, followed by a microRNA (miRNA) array analysis. The upregulation of miR-191 by hypoxia was confirmed in RA-FLS and FLS from osteoarthritis (OA) patients by quantitative real-time polymerase chain reaction (RT-PCR). Transfection of miR-191 mimic and inhibitor was used to investigate the function of miR-191 in RA-FLS. The functional targets of miR-191 were predicted by bioinfomatics and then validated by reporter gene assay. RESULTS A subset of miRNAs was identified to be induced by hypoxia including miR-191. The upregulation of miR-191 was found to be specific in hypoxic RA-FLS, compared to hypoxic OA-FLS. We observed that miR-191 in RA-FLS increased cellular proliferation via promoting G1/S transition of the cell cycle and suppressed cell apoptosis induced by cell starvation. Bioinformatical analysis and experimental assays identified CCAAT/enhancer binding protein β (C/EBPβ) as a target gene of miR-191 in RA-FLS. Enforced expression of C/EBPβ rescued the cellular phenotypes induced by miR-191. In addition, an inverse correlation between the C/EBPβ level and hypoxia stimulation was found in RA-FLS, and overexpression of C/EBPβ could partly rescue the hypoxia-induced cell proliferation. CONCLUSION We demonstrated the miR-191-C/EBPβ signaling pathway mediating the hypoxia-induced cell proliferation in RA.
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Affiliation(s)
- Shanshan Yu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji Mo Road, Shanghai, 200120, People's Republic of China
| | - Ying Lu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji Mo Road, Shanghai, 200120, People's Republic of China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji Mo Road, Shanghai, 200120, People's Republic of China
| | - Ming Zong
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji Mo Road, Shanghai, 200120, People's Republic of China
| | - Qi Tan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji Mo Road, Shanghai, 200120, People's Republic of China
| | - Lieying Fan
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, 150 Ji Mo Road, Shanghai, 200120, People's Republic of China.
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93
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Hamel-Côté G, Lapointe F, Gendron D, Rola-Pleszczynski M, Stankova J. Regulation of platelet-activating factor-induced interleukin-8 expression by protein tyrosine phosphatase 1B. Cell Commun Signal 2019; 17:21. [PMID: 30832675 PMCID: PMC6399872 DOI: 10.1186/s12964-019-0334-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 02/22/2019] [Indexed: 12/21/2022] Open
Abstract
Background Platelet-activating factor (PAF) is a potent lipid mediator whose involvement in the onset and progression of atherosclerosis is mediated by, among others, the modulation of cytokine expression patterns. The presence of multiple potential protein-tyrosine phosphatase (PTP) 1B substrates in PAF receptor signaling pathways brought us to investigate its involvement in PAF-induced cytokine expression in monocyte-derived dendritic cells (Mo-DCs) and to study the pathways involved in this modulation. Methods We used in-vitro-matured human dendritic cells and the HEK-293 cell line in our studies. PTP1B inhibition was though siRNAs and a selective inhibitor. Cytokine expression was studied with RT-PCR, luciferase assays and ELISA. Phosphorylation status of kinases and transcription factors was studied with western blotting. Results Here, we report that PTP1B was involved in the modulation of cytokine expression in PAF-stimulated Mo-DCs. A study of the down-regulation of PAF-induced IL-8 expression, by PTP1B, showed modulation of PAF-induced transactivation of the IL-8 promoter which was dependent on the presence of the C/EBPß -binding site. Results also suggested that PTP1B decreased PAF-induced IL-8 production by a glycogen synthase kinase (GSK)-3-dependent pathway via activation of the Src family kinases (SFK). These kinases activated an unidentified pathway at early stimulation times and the PI3K/Akt signaling pathway in a later phase. This change in GSK-3 activity decreased the C/EBPß phosphorylation levels of the threonine 235, a residue whose phosphorylation is known to increase C/EBPß transactivation potential, and consequently modified IL-8 expression. Conclusion The negative regulation of GSK-3 activity by PTP1B and the consequent decrease in phosphorylation of the C/EBPß transactivation domain could be an important negative feedback loop by which cells control their cytokine production after PAF stimulation. Electronic supplementary material The online version of this article (10.1186/s12964-019-0334-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Geneviève Hamel-Côté
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 4N5, Canada
| | - Fanny Lapointe
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 4N5, Canada
| | - Daniel Gendron
- Agriculture and Agri-Food Canada, Dairy and Swine Research and Development Center, 2000 College Street, Sherbrooke, QC, Canada
| | - Marek Rola-Pleszczynski
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 4N5, Canada
| | - Jana Stankova
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, J1H 4N5, Canada.
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94
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Dittmar G, Hernandez DP, Kowenz-Leutz E, Kirchner M, Kahlert G, Wesolowski R, Baum K, Knoblich M, Hofstätter M, Muller A, Wolf J, Reimer U, Leutz A. PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ. iScience 2019; 13:351-370. [PMID: 30884312 PMCID: PMC6424098 DOI: 10.1016/j.isci.2019.02.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/20/2019] [Accepted: 02/23/2019] [Indexed: 12/13/2022] Open
Abstract
CCAAT enhancer-binding protein beta (C/EBPβ) is a pioneer transcription factor that specifies cell differentiation. C/EBPβ is intrinsically unstructured, a molecular feature common to many proteins involved in signal processing and epigenetics. The structure of C/EBPβ differs depending on alternative translation initiation and multiple post-translational modifications (PTM). Mutation of distinct PTM sites in C/EBPβ alters protein interactions and cell differentiation, suggesting that a C/EBPβ PTM indexing code determines epigenetic outcomes. Herein, we systematically explored the interactome of C/EBPβ using an array technique based on spot-synthesized C/EBPβ-derived linear tiling peptides with and without PTM, combined with mass spectrometric proteomic analysis of protein interactions. We identified interaction footprints of ∼1,300 proteins in nuclear extracts, many with chromatin modifying, chromatin remodeling, and RNA processing functions. The results suggest that C/EBPβ acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes directing cell fate and function.
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Affiliation(s)
- Gunnar Dittmar
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg; Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany.
| | - Daniel Perez Hernandez
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Marieluise Kirchner
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; BIH Core Facility Proteomics, Robert-Roessle Strasse 10, 10125 Berlin, Germany
| | - Günther Kahlert
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Radoslaw Wesolowski
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Katharina Baum
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Maria Knoblich
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Maria Hofstätter
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Arnaud Muller
- Proteome and Genome Research Laboratory, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Jana Wolf
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine, Robert-Roessle Strasse 10, 13125 Berlin, Germany; Humboldt-University of Berlin, Institute of Biology, 10115 Berlin, Germany.
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95
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Lopes-Paciencia S, Saint-Germain E, Rowell MC, Ruiz AF, Kalegari P, Ferbeyre G. The senescence-associated secretory phenotype and its regulation. Cytokine 2019; 117:15-22. [PMID: 30776684 DOI: 10.1016/j.cyto.2019.01.013] [Citation(s) in RCA: 258] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/19/2019] [Accepted: 01/27/2019] [Indexed: 12/13/2022]
Abstract
The senescence-associated secretory phenotype (SASP) defines the ability of senescent cells to express and secrete a variety of extracellular modulators that includes cytokines, chemokines, proteases, growth factors and bioactive lipids. The role of the SASP depends on the context. The SASP reinforces the senescent cell cycle arrest, stimulates the immune-mediated clearance of potentially tumorigenic cells, limits fibrosis and promotes wound healing and tissue regeneration. On the other hand, the SASP can mediate chronic inflammation and stimulate the growth and survival of tumor cells. The regulation of the SASP occurs at multiple levels including chromatin remodelling, activation of specific transcription factors such as C/EBP and NF-κB, control of mRNA translation and intracellular trafficking. Several SASP modulators have already been identified setting the stage for future research on their clinical applications.
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Affiliation(s)
- Stéphane Lopes-Paciencia
- Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada; CRCHUM, 900 Saint-Denis - Room R10.432, Montréal, QC H2X 0A9, Canada
| | - Emmanuelle Saint-Germain
- Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada; CRCHUM, 900 Saint-Denis - Room R10.432, Montréal, QC H2X 0A9, Canada
| | - Marie-Camille Rowell
- Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada; CRCHUM, 900 Saint-Denis - Room R10.432, Montréal, QC H2X 0A9, Canada
| | - Ana Fernández Ruiz
- Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada; CRCHUM, 900 Saint-Denis - Room R10.432, Montréal, QC H2X 0A9, Canada
| | - Paloma Kalegari
- Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada; CRCHUM, 900 Saint-Denis - Room R10.432, Montréal, QC H2X 0A9, Canada
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada; CRCHUM, 900 Saint-Denis - Room R10.432, Montréal, QC H2X 0A9, Canada.
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Amaral AJ, Bressan MC, Almeida J, Bettencourt C, Moreira O, Sá J, Gama-Carvalho M, Bessa R, Gama LT. Combining genome-wide association analyses and gene interaction networks to reveal new genes associated with carcass traits, meat quality and fatty acid profiles in pigs. Livest Sci 2019. [DOI: 10.1016/j.livsci.2018.12.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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97
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Sakuranetin downregulates inducible nitric oxide synthase expression by affecting interleukin-1 receptor and CCAAT/enhancer-binding protein β. J Nat Med 2018; 73:353-368. [PMID: 30467676 DOI: 10.1007/s11418-018-1267-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/07/2018] [Indexed: 12/31/2022]
Abstract
Pruni Cortex is a herbal drug from the bark of the Japanese flowering cherries, Prunus jamasakura or Prunus verecunda, and is included in the traditional Japanese herbal (Kampo) formula Jumihaidokuto, which is administered orally to patients suffering from inflammatory skin diseases. The flavanones contained in Pruni Cortex (e.g., sakuranetin and naringenin) have potent anti-inflammatory, anti-allergic, and anti-microbial activities. Although the effects of Pruni Cortex on skin disease have been well studied, reports regarding its pharmacological effects on the liver are limited. In this study, we extracted the bark of Prunus jamasakura and purified it to isolate the pharmacologically active constituents by monitoring nitric oxide (NO) production in rat hepatocytes that were treated with the pro-inflammatory cytokine, interleukin (IL)-1β. Sakuranetin and (-)-naringenin, which were present in an ethyl acetate-soluble fraction of the bark extract, significantly inhibited NO induction and inducible nitric oxide synthase (iNOS) expression. These two flavanones decreased the expression of type 1 IL-1 receptor gene and phosphorylation of Akt, also known as protein kinase B, which is regulated by phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K). Furthermore, sakuranetin decreased the phosphorylation of the activator isoforms of CCAAT/enhancer-binding protein β (C/EBPβ), which synergistically activates the transcription of the iNOS gene with nuclear factor κB (NF-κB). Therefore, sakuranetin inhibited the co-activating activity of C/EBPβ with NF-κB, leading to the suppression of iNOS gene expression in hepatocytes. Taken together, sakuranetin in Pruni Cortex downregulated the iNOS gene by inhibiting PI3K/Akt signal transduction and the phosphorylation of C/EBPβ. These results imply that sakuranetin may be primarily responsible for the anti-inflammatory effects of Pruni Cortex in the liver.
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AlSudais H, Lala-Tabbert N, Wiper-Bergeron N. CCAAT/Enhancer Binding Protein β inhibits myogenic differentiation via ID3. Sci Rep 2018; 8:16613. [PMID: 30413755 PMCID: PMC6226455 DOI: 10.1038/s41598-018-34871-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/18/2018] [Indexed: 12/04/2022] Open
Abstract
Myogenesis is regulated by the coordinated expression of muscle regulatory factors, a family of transcription factors that includes MYOD, MYF5, myogenin and MRF4. Muscle regulatory factors are basic helix-loop-helix transcription factors that heterodimerize with E proteins to bind the regulatory regions of target genes. Their activity can be inhibited by members of the Inhibitor of DNA binding and differentiation (ID) family, which bind E-proteins with high affinity, thereby preventing muscle regulatory factor-dependent transcriptional responses. CCAAT/Enhancer Binding protein beta (C/EBPβ) is a transcription factor expressed in myogenic precursor cells that acts to inhibit myogenic differentiation, though the mechanism remains poorly understood. We identify Id3 as a novel C/EBPβ target gene that inhibits myogenic differentiation. Overexpression of C/EBPβ stimulates Id3 mRNA and protein expression, and is required for C/EBPβ-mediated inhibition of myogenic differentiation. Misexpression of C/EBPβ in myogenic precursors, such as in models of cancer cachexia, prevents the differentiation of myogenic precursors and we show that loss of Id3 rescues differentiation under these conditions, suggesting that the stimulation of Id3 expression by C/EBPβ is an important mechanism by which C/EBPβ inhibits myogenic differentiation.
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Affiliation(s)
- Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Neena Lala-Tabbert
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, K1H 8M5, Canada.
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99
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Pulugulla SH, Workman R, Rutter NW, Yang Z, Adamik J, Lupish B, Macar DA, El Abdouni S, Esposito EX, Galson DL, Camacho CJ, Madura JD, Auron PE. A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription. J Biol Chem 2018; 293:19942-19956. [PMID: 30355733 DOI: 10.1074/jbc.ra118.005627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
We previously reported that transcription of the human IL1B gene, encoding the proinflammatory cytokine interleukin 1β, depends on long-distance chromatin looping that is stabilized by a mutual interaction between the DNA-binding domains (DBDs) of two transcription factors: Spi1 proto-oncogene at the promoter and CCAAT enhancer-binding protein (C/EBPβ) at a far-upstream enhancer. We have also reported that the C-terminal tail sequence beyond the C/EBPβ leucine zipper is critical for its association with Spi1 via an exposed residue (Arg-232) located within a pocket at one end of the Spi1 DNA-recognition helix. Here, combining in vitro interaction studies with computational docking and molecular dynamics of existing X-ray structures for the Spi1 and C/EBPβ DBDs, along with the C/EBPβ C-terminal tail sequence, we found that the tail sequence is intimately associated with Arg-232 of Spi1. The Arg-232 pocket was computationally screened for small-molecule binding aimed at IL1B transcription inhibition, yielding l-arginine, a known anti-inflammatory amino acid, revealing a potential for disrupting the C/EBPβ-Spi1 interaction. As evaluated by ChIP, cultured lipopolysaccharide (LPS)-activated THP-1 cells incubated with l-arginine had significantly decreased IL1B transcription and reduced C/EBPβ's association with Spi1 on the IL1B promoter. No significant change was observed in direct binding of either Spi1 or C/EBPβ to cognate DNA and in transcription of the C/EBPβ-dependent IL6 gene in the same cells. These results support the notion that disordered sequences extending from a leucine zipper can mediate protein-protein interactions and can serve as druggable targets for regulating gene promoter activity.
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Affiliation(s)
- Sree H Pulugulla
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Riley Workman
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Nathan W Rutter
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Zhiyong Yang
- the Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Juraj Adamik
- the Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Brian Lupish
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - David A Macar
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Samir El Abdouni
- the Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | | | - Deborah L Galson
- the Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213,; the Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Carlos J Camacho
- the Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Jeffry D Madura
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282; Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Philip E Auron
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282; the Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219.
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100
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Messenger ZJ, Hall JR, Jima DD, House JS, Tam HW, Tokarz DA, Smart RC. C/EBPβ deletion in oncogenic Ras skin tumors is a synthetic lethal event. Cell Death Dis 2018; 9:1054. [PMID: 30323292 PMCID: PMC6189130 DOI: 10.1038/s41419-018-1103-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Therapeutic targeting of specific genetic changes in cancer has proven to be an effective therapy and the concept of synthetic lethality has emerged. CCAAT/enhancer-binding protein-β (C/EBPβ), a basic leucine zipper transcription factor, has important roles in cellular processes including differentiation, inflammation, survival, and energy metabolism. Using a genetically engineered mouse model, we report that the deletion C/EBPβ in pre-existing oncogenic Ha-Ras mouse skin tumors in vivo resulted in rapid tumor regression. Regressing tumors exhibited elevated levels of apoptosis and p53 protein/activity, while adjacent C/EBPβ-deleted skin did not. These results indicate that the deletion of C/EBPβ de-represses p53 in oncogenic Ras tumors but not in normal wild-type Ras keratinocytes, and that C/EBPβ is essential for survival of oncogenic Ras tumors. Co-deletion of C/EBPβ and p53 in oncogenic Ras tumors showed p53 is required for tumor regression and elevated apoptosis. In tumors, loss of a pathway that confers adaptability to a stress phenotype of cancer/tumorigenesis, such as DNA damage, could result in selective tumor cell killing. Our results show that oncogenic Ras tumors display a significant DNA damage/replicative stress phenotype and these tumors have acquired a dependence on C/EBPβ for their survival. RNAseq data analysis of regressing tumors deleted of C/EBPβ indicates a novel interface between p53, type-1 interferon response, and death receptor pathways, which function in concert to produce activation of extrinsic apoptosis pathways. In summary, the deletion of C/EBPβ in oncogenic Ras skin tumors is a synthetic lethal event, making it a promising target for future potential anticancer therapies.
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Affiliation(s)
| | - Jonathan R Hall
- Toxicology Program, Raleigh, NC, USA. .,Center of Human Health and the Environment, Raleigh, NC, USA. .,Department of Biological Sciences, Raleigh, NC, USA.
| | - Dereje D Jima
- Center of Human Health and the Environment, Raleigh, NC, USA.,Bioinformatics Research Center, Raleigh, NC, USA
| | - John S House
- Center of Human Health and the Environment, Raleigh, NC, USA.,Bioinformatics Research Center, Raleigh, NC, USA
| | | | - Debra A Tokarz
- Center of Human Health and the Environment, Raleigh, NC, USA.,Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Robert C Smart
- Toxicology Program, Raleigh, NC, USA. .,Center of Human Health and the Environment, Raleigh, NC, USA. .,Department of Biological Sciences, Raleigh, NC, USA.
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