1
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Deguchi-Horiuchi H, Suzuki S, Lee EY, Miki T, Yamanaka N, Manabe I, Tanaka T, Yokote K. Pancreatic β-cell glutaminase 2 maintains glucose homeostasis under the condition of hyperglycaemia. Sci Rep 2023; 13:7291. [PMID: 37147373 PMCID: PMC10162969 DOI: 10.1038/s41598-023-34336-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023] Open
Abstract
Glutaminase 2 (GLS2), a master regulator of glutaminolysis that is induced by p53 and converts glutamine to glutamate, is abundant in the liver but also exists in pancreatic β-cells. However, the roles of GLS2 in islets associated with glucose metabolism are unknown, presenting a critical issue. To investigate the roles of GLS2 in pancreatic β-cells in vivo, we generated β-cell-specific Gls2 conditional knockout mice (Gls2 CKO), examined their glucose homeostasis, and validated the findings using a human islet single-cell analysis database. GLS2 expression markedly increased along with p53 in β-cells from control (RIP-Cre) mice fed a high-fat diet. Furthermore, Gls2 CKO exhibited significant diabetes mellitus with gluconeogenesis and insulin resistance when fed a high-fat diet. Despite marked hyperglycaemia, impaired insulin secretion and paradoxical glucagon elevation were observed in high-fat diet-fed Gls2 CKO mice. GLS2 silencing in the pancreatic β-cell line MIN6 revealed downregulation of insulin secretion and intracellular ATP levels, which were closely related to glucose-stimulated insulin secretion. Additionally, analysis of single-cell RNA-sequencing data from human pancreatic islet cells also revealed that GLS2 expression was elevated in β-cells from diabetic donors compared to nondiabetic donors. Consistent with the results of Gls2 CKO, downregulated GLS2 expression in human pancreatic β-cells from diabetic donors was associated with significantly lower insulin gene expression as well as lower expression of members of the insulin secretion pathway, including ATPase and several molecules that signal to insulin secretory granules, in β-cells but higher glucagon gene expression in α-cells. Although the exact mechanism by which β-cell-specific GLS2 regulates insulin and glucagon requires further study, our data indicate that GLS2 in pancreatic β-cells maintains glucose homeostasis under the condition of hyperglycaemia.
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Affiliation(s)
- Hanna Deguchi-Horiuchi
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Diabetes, Metabolism and Endocrinology, Chiba University hospital, Chiba, Japan
| | - Sawako Suzuki
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan.
- Department of Diabetes, Metabolism and Endocrinology, Chiba University hospital, Chiba, Japan.
| | - Eun Young Lee
- Department of Medical Physiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takashi Miki
- Department of Medical Physiology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Noriko Yamanaka
- Department of Disease Biology and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Disease Biology and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Diabetes, Metabolism and Endocrinology, Chiba University hospital, Chiba, Japan
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2
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Caratti G, Stifel U, Caratti B, Jamil AJM, Chung KJ, Kiehntopf M, Gräler MH, Blüher M, Rauch A, Tuckermann JP. Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance. Nat Commun 2023; 14:2271. [PMID: 37080971 PMCID: PMC10119112 DOI: 10.1038/s41467-023-37831-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/01/2023] [Indexed: 04/22/2023] Open
Abstract
Insulin resistance (IR) during obesity is linked to adipose tissue macrophage (ATM)-driven inflammation of adipose tissue. Whether anti-inflammatory glucocorticoids (GCs) at physiological levels modulate IR is unclear. Here, we report that deletion of the GC receptor (GR) in myeloid cells, including macrophages in mice, aggravates obesity-related IR by enhancing adipose tissue inflammation due to decreased anti-inflammatory ATM leading to exaggerated adipose tissue lipolysis and severe hepatic steatosis. In contrast, GR deletion in Kupffer cells alone does not alter IR. Co-culture experiments show that the absence of GR in macrophages directly causes reduced phospho-AKT and glucose uptake in adipocytes, suggesting an important function of GR in ATM. GR-deficient macrophages are refractory to alternative ATM-inducing IL-4 signaling, due to reduced STAT6 chromatin loading and diminished anti-inflammatory enhancer activation. We demonstrate that GR has an important function in macrophages during obesity by limiting adipose tissue inflammation and lipolysis to promote insulin sensitivity.
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Affiliation(s)
- Giorgio Caratti
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX37LE, UK
| | - Ulrich Stifel
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Bozhena Caratti
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany
| | - Ali J M Jamil
- Molecular Endocrinology & Stem Cell Research Unit, Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kyoung-Jin Chung
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technical University Dresden, Dresden, Germany
| | - Michael Kiehntopf
- SG Sepsis Research Clinic for Anesthesiology and Intensive Care, Jena University Hospital, Jena, Germany
| | - Markus H Gräler
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
- Center for Molecular Biomedicine (CMB), Jena University Hospital, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Matthias Blüher
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Alexander Rauch
- Molecular Endocrinology & Stem Cell Research Unit, Department of Endocrinology and Metabolism, Odense University Hospital, Odense, Denmark.
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
- Steno Diabetes Center Odense, Odense, Denmark.
| | - Jan P Tuckermann
- Institute of Comparative Molecular Endocrinology, University of Ulm, Ulm, Germany.
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3
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Koh KD, Bonser LR, Eckalbar WL, Yizhar-Barnea O, Shen J, Zeng X, Hargett KL, Sun DI, Zlock LT, Finkbeiner WE, Ahituv N, Erle DJ. Genomic characterization and therapeutic utilization of IL-13-responsive sequences in asthma. CELL GENOMICS 2023; 3:100229. [PMID: 36777184 PMCID: PMC9903679 DOI: 10.1016/j.xgen.2022.100229] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/02/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
Epithelial responses to the cytokine interleukin-13 (IL-13) cause airway obstruction in asthma. Here we utilized multiple genomic techniques to identify IL-13-responsive regulatory elements in bronchial epithelial cells and used these data to develop a CRISPR interference (CRISPRi)-based therapeutic approach to downregulate airway obstruction-inducing genes in a cell type- and IL-13-specific manner. Using single-cell RNA sequencing (scRNA-seq) and acetylated lysine 27 on histone 3 (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) in primary human bronchial epithelial cells, we identified IL-13-responsive genes and regulatory elements. These sequences were functionally validated and optimized via massively parallel reporter assays (MPRAs) for IL-13-inducible activity. The top secretory cell-selective sequence from the MPRA, a novel, distal enhancer of the sterile alpha motif pointed domain containing E-26 transformation-specific transcription factor (SPDEF) gene, was utilized to drive CRISPRi and knock down SPDEF or mucin 5AC (MUC5AC), both involved in pathologic mucus production in asthma. Our work provides a catalog of cell type-specific genes and regulatory elements involved in IL-13 bronchial epithelial response and showcases their use for therapeutic purposes.
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Affiliation(s)
- Kyung Duk Koh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Luke R. Bonser
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter L. Eckalbar
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ofer Yizhar-Barnea
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jiangshan Shen
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xiaoning Zeng
- Department of Pulmonary & Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kirsten L. Hargett
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dingyuan I. Sun
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorna T. Zlock
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Walter E. Finkbeiner
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nadav Ahituv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David J. Erle
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
- CoLabs, University of California, San Francisco, San Francisco, CA 94143, USA
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4
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Suzuki S, Venkatesh D, Kanda H, Nakayama A, Hosokawa H, Lee E, Miki T, Stockwell BR, Yokote K, Tanaka T, Prives C. GLS2 Is a Tumor Suppressor and a Regulator of Ferroptosis in Hepatocellular Carcinoma. Cancer Res 2022; 82:3209-3222. [PMID: 35895807 PMCID: PMC11057045 DOI: 10.1158/0008-5472.can-21-3914] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/12/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022]
Abstract
Glutamine synthase 2 (GLS2) is a key regulator of glutaminolysis and has been previously implicated in activities consistent with tumor suppression. Here we generated Gls2 knockout (KO) mice that develop late-occurring B-cell lymphomas and hepatocellular carcinomas (HCC). Further, Gls2 KO mice subjected to the hepatocarcinogenic Stelic Animal Model (STAM) protocol produce larger HCC tumors than seen in wild-type (WT) mice. GLS2 has been shown to promote ferroptosis, a form of cell death characterized by iron-dependent accumulation of lipid peroxides. In line with this, GLS2 deficiency, either in cells derived from Gls2 KO mice or in human cancer cells depleted of GLS2, conferred significant resistance to ferroptosis. Mechanistically, GLS2, but not GLS1, increased lipid reactive oxygen species (ROS) production by facilitating the conversion of glutamate to α-ketoglutarate (αKG), thereby promoting ferroptosis. Ectopic expression of WT GLS2 in a human hepatic adenocarcinoma xenograft model significantly reduced tumor size; this effect was nullified by either expressing a catalytically inactive form of GLS2 or by blocking ferroptosis. Furthermore, analysis of cancer patient datasets supported a role for GLS2-mediated regulation of ferroptosis in human tumor suppression. These data suggest that GLS2 is a bona fide tumor suppressor and that its ability to favor ferroptosis by regulating glutaminolysis contributes to its tumor suppressive function. SIGNIFICANCE This study demonstrates that the key regulator of glutaminolysis, GLS2, can limit HCC in vivo by promoting ferroptosis through αKG-dependent lipid ROS, which in turn might lay the foundation for a novel therapeutic approach.
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Affiliation(s)
- Sawako Suzuki
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Divya Venkatesh
- Department of Biological Sciences, Columbia University, New York, USA
| | - Hiroaki Kanda
- Department of Pathology, Saitama Cancer Center, Saitama, Japan
| | - Akitoshi Nakayama
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Hosokawa
- Department of Immunology, Tokai University School of Medicine, Kanagawa, Japan
| | - Eunyoung Lee
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takashi Miki
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Brent R. Stockwell
- Department of Biological Sciences, Columbia University, New York, USA
- Department of Chemistry, Columbia University, New York, USA
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Graduate School of Medicine, Chiba University, Chiba, Japan
- Department of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, USA
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5
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Renfro Z, White BE, Stephens KE. CCAAT enhancer binding protein gamma (C/EBP-γ): An understudied transcription factor. Adv Biol Regul 2022; 84:100861. [PMID: 35121409 PMCID: PMC9376885 DOI: 10.1016/j.jbior.2022.100861] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
The CCAAT enhancer binding protein (C/EBP) family of transcription factors are important transcriptional mediators of a wide range of physiologic processes. C/EBP-γ is the shortest C/EBP protein and lacks a canonical activation domain for the recruitment of transcriptional machinery. Despite its ubiquitous expression and ability to dimerize with other C/EBP proteins, C/EBP-γ has been studied far less than other C/EBP proteins, and, to our knowledge, no review of its functions has been written. This review seeks to integrate the current knowledge about C/EBP-γ and its physiologic roles, especially in cell proliferation, the integrated stress response, oncogenesis, hematopoietic and nervous system development, and metabolism, as well as to identify areas for future research.
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Affiliation(s)
- Zachary Renfro
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
| | - Bryan E White
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
| | - Kimberly E Stephens
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
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6
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Plasmablasts derive from CD23- activated B cells after the extinction of IL-4/STAT6 signaling and IRF4 induction. Blood 2021; 137:1166-1180. [PMID: 33150420 DOI: 10.1182/blood.2020005083] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 10/19/2020] [Indexed: 01/07/2023] Open
Abstract
The terminal differentiation of B cells into antibody-secreting cells (ASCs) is a critical component of adaptive immune responses. However, it is a very sensitive process, and dysfunctions lead to a variety of lymphoproliferative neoplasias including germinal center-derived lymphomas. To better characterize the late genomic events that drive the ASC differentiation of human primary naive B cells, we used our in vitro differentiation system and a combination of RNA sequencing and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC sequencing). We discovered 2 mechanisms that drive human terminal B-cell differentiation. First, after an initial response to interleukin-4 (IL-4), cells that were committed to an ASC fate downregulated the CD23 marker and IL-4 signaling, whereas cells that maintained IL-4 signaling did not differentiate. Second, human CD23- cells also increased IRF4 protein to levels required for ASC differentiation, but they did that independently of the ubiquitin-mediated degradation process previously described in mice. Finally, we showed that CD23- cells carried the imprint of their previous activated B-cell status, were precursors of plasmablasts, and had a phenotype similar to that of in vivo preplasmablasts. Altogether, our results provide an unprecedented genomic characterization of the fate decision between activated B cells and plasmablasts, which provides new insights into the pathological mechanisms that drive lymphoma biology.
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7
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Wang W, Wang L, Zha B. The roles of STAT6 in regulating B cell fate, activation, and function. Immunol Lett 2021; 233:87-91. [PMID: 33662403 DOI: 10.1016/j.imlet.2021.02.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023]
Abstract
Signal transducers and activators of transcription (STATs) family of proteins are the key signal molecules in the JAK-STAT classical activation pathway of cell biology. STAT6, as a member of the STATs family, is principally activated by IL-4 and IL-13. In addition to Th2 cell differentiation, it plays a crucial role in promoting the development, differentiation, and class switching of B cells. STAT6 deficiency leads to impaired immune function, decreased glycolysis, and morphological changes in B cells, which will help develop various diseases. In this review, we will systematically summarize the major findings of how STAT6 regulates B cells to reveal the potential of STAT6 in treating human diseases.
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Affiliation(s)
- Wei Wang
- Department of Endocrinology and Metabolism, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China
| | - Luman Wang
- Department of Endocrinology and Metabolism, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China; Department of Immunology, School of Basic Medical Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Bingbing Zha
- Department of Endocrinology and Metabolism, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200240, China.
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8
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Suzuki M, Saito-Adachi M, Arai Y, Fujiwara Y, Takai E, Shibata S, Seki M, Rokutan H, Maeda D, Horie M, Suzuki Y, Shibata T, Kiyono T, Yachida S. E74-Like Factor 3 Is a Key Regulator of Epithelial Integrity and Immune Response Genes in Biliary Tract Cancer. Cancer Res 2020; 81:489-500. [PMID: 33293429 DOI: 10.1158/0008-5472.can-19-2988] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/28/2020] [Accepted: 11/16/2020] [Indexed: 11/16/2022]
Abstract
The transcription factor E74-like factor 3 (ELF3) is inactivated in a range of cancers, including biliary tract cancer (BTC). Here, we investigated the tumor-suppressive role of ELF3 in bile duct cells by identifying several previously unknown direct target genes of ELF3 that appear to be implicated in biliary duct carcinogenesis. ELF3 directly repressed ZEB2, a key regulator of epithelial-mesenchymal transition, and upregulated the expression of CGN, an integral element in lumen formation. Loss of ELF3 led to decreased cell-cell junctions and enhanced cell motility. ALOX5 and CXCL16 were also identified as additional direct targets of ELF3; their corresponding proteins 5-lipoxygenase and CXCL16 play a role in the immune response. Conditioned medium from cells overexpressing ELF3 significantly enhanced the migration of natural killer cells and CD8+ T cells toward the conditioned medium. Gene expression profiling for BTC expressing high levels of ELF3 revealed significant enrichment of the ELF3-related genes. In a BTC xenograft model, activation of ELF3 increased expression of ELF3-related genes, enhanced the tubular structure of the tumors, and led to a loss of vimentin. Overall, our results indicate that ELF3 is a key regulator of both epithelial integrity and immune responses in BTC. SIGNIFICANCE: Thease finding shows that ELF3 regulates epithelial integrity and host immune responses and functions as a tumor suppressor in biliary tract cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/2/489/F1.large.jpg.
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Affiliation(s)
- Masami Suzuki
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuko Fujiwara
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Erina Takai
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shinsuke Shibata
- Electron Microscope Laboratory, Keio University School of Medicine, Tokyo, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hirofumi Rokutan
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Daichi Maeda
- Department of Clinical Genomics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masafumi Horie
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan.
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan.
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9
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Li F, Kitajima S, Kohno S, Yoshida A, Tange S, Sasaki S, Okada N, Nishimoto Y, Muranaka H, Nagatani N, Suzuki M, Masuda S, Thai TC, Nishiuchi T, Tanaka T, Barbie DA, Mukaida N, Takahashi C. Retinoblastoma Inactivation Induces a Protumoral Microenvironment via Enhanced CCL2 Secretion. Cancer Res 2019; 79:3903-3915. [PMID: 31189648 DOI: 10.1158/0008-5472.can-18-3604] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/27/2019] [Accepted: 06/07/2019] [Indexed: 01/01/2023]
Abstract
Cancer cell-intrinsic properties caused by oncogenic mutations have been well characterized; however, how specific oncogenes and tumor suppressors impact the tumor microenvironment (TME) is not well understood. Here, we present a novel non-cell-autonomous function of the retinoblastoma (RB) tumor suppressor in controlling the TME. RB inactivation stimulated tumor growth and neoangiogenesis in a syngeneic and orthotropic murine soft-tissue sarcoma model, which was associated with recruitment of tumor-associated macrophages (TAM) and immunosuppressive cells such as Gr1+CD11b+ myeloid-derived suppressor cells (MDSC) or Foxp3+ regulatory T cells (Treg). Gene expression profiling and analysis of genetically engineered mouse models revealed that RB inactivation increased secretion of the chemoattractant CCL2. Furthermore, activation of the CCL2-CCR2 axis in the TME promoted tumor angiogenesis and recruitment of TAMs and MDSCs into the TME in several tumor types including sarcoma and breast cancer. Loss of RB increased fatty acid oxidation (FAO) by activating AMP-activated protein kinase that led to inactivation of acetyl-CoA carboxylase, which suppresses FAO. This promoted mitochondrial superoxide production and JNK activation, which enhanced CCL2 expression. These findings indicate that the CCL2-CCR2 axis could be an effective therapeutic target in RB-deficient tumors. SIGNIFICANCE: These findings demonstrate the cell-nonautonomous role of the tumor suppressor retinoblastoma in the tumor microenvironment, linking retinoblastoma loss to immunosuppression.
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Affiliation(s)
- Fengkai Li
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Shunsuke Kitajima
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Akiyo Yoshida
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan.,Keiju Medical Center, Nanao, Ishikawa, Japan
| | - Shoichiro Tange
- Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University, Sapporo, Japan
| | - Soichiro Sasaki
- Division of Molecular Bioregulation, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Nobuhiro Okada
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan.,Department of Nano-Biotechnology, Graduate School of Interdisciplinary Science & Engineering in Health Systems, Okayama University, Okayama, Okayama, Japan
| | - Yuuki Nishimoto
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hayato Muranaka
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Naoko Nagatani
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Misa Suzuki
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Sayuri Masuda
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tran C Thai
- Keiju Medical Center, Nanao, Ishikawa, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Chiba University Graduate School of Medicine, Chiba, Japan
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Naofumi Mukaida
- Division of Molecular Bioregulation, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa, Japan.
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10
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Hynds RE, Gowers KHC, Nigro E, Butler CR, Bonfanti P, Giangreco A, Prêle CM, Janes SM. Cross-talk between human airway epithelial cells and 3T3-J2 feeder cells involves partial activation of human MET by murine HGF. PLoS One 2018; 13:e0197129. [PMID: 29771943 PMCID: PMC5957441 DOI: 10.1371/journal.pone.0197129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 04/26/2018] [Indexed: 01/13/2023] Open
Abstract
There is considerable interest in the ex vivo propagation of primary human basal epithelial stem/progenitor cells with a view to their use in drug development, toxicity testing and regenerative medicine. These cells can be expanded in co-culture with mitotically inactivated 3T3-J2 murine embryonic feeder cells but, similar to other epithelial cell culture systems employing 3T3-J2 cells, the aspects of cross-talk between 3T3-J2 cells and human airway basal cells that are critical for their expansion remain largely unknown. In this study, we investigated secreted growth factors that are produced by 3T3-J2 cells and act upon primary human airway basal cells. We found robust production of hepatocyte growth factor (HGF) from fibroblast feeder cells following mitotic inactivation. Consistent with the limited cross-species reactivity of murine HGF on the human HGF receptor (MET; HGFR), MET inhibition did not affect proliferative responses in human airway basal cells and HGF could not replace feeder cells in this culture system. However, we found that murine HGF is not completely inactive on human airway epithelial cells or cancer cell lines but stimulates the phosphorylation of GRB2-associated-binding protein 2 (GAB2) and signal transducer and activator of transcription 6 (STAT6). Although HGF induces phosphorylation of STAT6 tyrosine 641 (Y641), there is no subsequent STAT6 nuclear translocation or STAT6-driven transcriptional response. Overall, these findings highlight the relevance of cross-species protein interactions between murine feeder cells and human epithelial cells in 3T3-J2 co-culture and demonstrate that STAT6 phosphorylation occurs in response to MET activation in epithelial cells. However, STAT6 nuclear translocation does not occur in response to HGF, precluding the transcriptional activity of STAT6.
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Affiliation(s)
- Robert E. Hynds
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Kate H. C. Gowers
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Ersilia Nigro
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
- Dipartimento di Scienze Cardio-Toraciche e Respiratorie, Universita’ degli Studi della Campania “L. Vanvitelli”, Naples, Italy
| | - Colin R. Butler
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Paola Bonfanti
- The Francis Crick Institute, London, United Kingdom
- Stem Cell and Regenerative Medicine Section, UCL Institute of Child Health and Great Ormond Street Hospital, London, United Kingdom
- Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Adam Giangreco
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
| | - Cecilia M. Prêle
- Centre for Cell Therapy and Regenerative Medicine, School of Biomedical Sciences, The University of Western Australia, Perth, Australia
- Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, United Kingdom
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11
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Yoshida A, Kitajima S, Li F, Cheng C, Takegami Y, Kohno S, Wan YS, Hayashi N, Muranaka H, Nishimoto Y, Nagatani N, Nishiuchi T, Thai TC, Suzuki S, Nakao S, Tanaka T, Hirose O, Barbie DA, Takahashi C. MicroRNA-140 mediates RB tumor suppressor function to control stem cell-like activity through interleukin-6. Oncotarget 2017; 8:13872-13885. [PMID: 28099924 PMCID: PMC5355146 DOI: 10.18632/oncotarget.14681] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/03/2017] [Indexed: 12/15/2022] Open
Abstract
We established an in vitro cell culture system to determine novel activities of the retinoblastoma (Rb) protein during tumor progression. Rb depletion in p53-null mouse-derived soft tissue sarcoma cells induced a spherogenic phenotype. Cells retrieved from Rb-depleted spheres exhibited slower proliferation and less efficient BrdU incorporation, however, much higher spherogenic activity and aggressive behavior. We discovered six miRNAs, including mmu-miR-18a, -25, -29b, -140, -337, and -1839, whose expression levels correlated tightly with the Rb status and spherogenic activity. Among these, mmu-miR-140 appeared to be positively controlled by Rb and to antagonize the effect of Rb depletion on spherogenesis and tumorigenesis. Furthermore, among genes potentially targeted by mmu-miR-140, Il-6 was upregulated by Rb depletion and downregulated by mmu-mir-140 overexpression. Altogether, we demonstrate the possibility that mmu-mir-140 mediates the Rb function to downregulate Il-6 by targeting its 3′-untranslated region. Finally, we detected the same relationship among RB, hsa-miR-140 and IL-6 in a human breast cancer cell line MCF-7. Because IL-6 is a critical modulator of malignant features of cancer cells and the RB pathway is impaired in the majority of cancers, hsa-miR-140 might be a promising therapeutic tool that disrupts linkage between tumor suppressor inactivation and pro-inflammatory cytokine response.
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Affiliation(s)
- Akiyo Yoshida
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.,Deperment of Cellular Transplantation Biology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8641, Japan
| | - Shunsuke Kitajima
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215, USA
| | - Fengkai Li
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Chaoyang Cheng
- DNAFORM Precision Gene Technologies, Yokohama, Kanagawa, 230-0046, Japan
| | - Yujiro Takegami
- DNAFORM Precision Gene Technologies, Yokohama, Kanagawa, 230-0046, Japan
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuan Song Wan
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Naoyuki Hayashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.,Department of Health and Nutrition, Faculty of Human Health Science, Kanazawa Gakuin University, Kanazawa, Ishikawa, 920-1302, Japan
| | - Hayato Muranaka
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Yuuki Nishimoto
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Naoko Nagatani
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Tran C Thai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215, USA
| | - Sawako Suzuki
- Deperment of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8670 Japan
| | - Shinji Nakao
- Deperment of Cellular Transplantation Biology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa 920-8641, Japan
| | - Tomoaki Tanaka
- Deperment of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Chiba 260-8670 Japan
| | - Osamu Hirose
- Division of Electrical Engineering and Computer Science, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - David A Barbie
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215, USA
| | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
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12
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Mokada-Gopal L, Boeser A, Lehmann CHK, Drepper F, Dudziak D, Warscheid B, Voehringer D. Identification of Novel STAT6-Regulated Proteins in Mouse B Cells by Comparative Transcriptome and Proteome Analysis. THE JOURNAL OF IMMUNOLOGY 2017; 198:3737-3745. [DOI: 10.4049/jimmunol.1601838] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/03/2017] [Indexed: 12/13/2022]
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13
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Spatial Interplay between Polycomb and Trithorax Complexes Controls Transcriptional Activity in T Lymphocytes. Mol Cell Biol 2015; 35:3841-53. [PMID: 26324324 DOI: 10.1128/mcb.00677-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/21/2015] [Indexed: 11/20/2022] Open
Abstract
Trithorax group (TrxG) and Polycomb group (PcG) proteins are two mutually antagonistic chromatin modifying complexes, however, how they together mediate transcriptional counter-regulation remains unknown. Genome-wide analysis revealed that binding of Ezh2 and menin, central members of the PcG and TrxG complexes, respectively, were reciprocally correlated. Moreover, we identified a developmental change in the positioning of Ezh2 and menin in differentiated T lymphocytes compared to embryonic stem cells. Ezh2-binding upstream and menin-binding downstream of the transcription start site was frequently found at genes with higher transcriptional levels, and Ezh2-binding downstream and menin-binding upstream was found at genes with lower expression in T lymphocytes. Interestingly, of the Ezh2 and menin cooccupied genes, those exhibiting occupancy at the same position displayed greatly enhanced sensitivity to loss of Ezh2. Finally, we also found that different combinations of Ezh2 and menin occupancy were associated with expression of specific functional gene groups important for T cell development. Therefore, spatial cooperative gene regulation by the PcG and TrxG complexes may represent a novel mechanism regulating the transcriptional identity of differentiated cells.
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14
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Maekawa S, Imamachi N, Irie T, Tani H, Matsumoto K, Mizutani R, Imamura K, Kakeda M, Yada T, Sugano S, Suzuki Y, Akimitsu N. Analysis of RNA decay factor mediated RNA stability contributions on RNA abundance. BMC Genomics 2015; 16:154. [PMID: 25879614 PMCID: PMC4359779 DOI: 10.1186/s12864-015-1358-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 02/19/2015] [Indexed: 12/28/2022] Open
Abstract
Background Histone epigenome data determined by chromatin immunoprecipitation sequencing (ChIP-seq) is used in identifying transcript regions and estimating expression levels. However, this estimation does not always correlate with eventual RNA expression levels measured by RNA sequencing (RNA-seq). Part of the inconsistency may arise from the variance in RNA stability, where the transcripts that are more or less abundant than predicted RNA expression from histone epigenome data are inferred to be more or less stable. However, there is little systematic analysis to validate this assumption. Here, we used stability data of whole transcriptome measured by 5′-bromouridine immunoprecipitation chase sequencing (BRIC-seq), which enabled us to determine the half-lives of whole transcripts including lincRNAs, and we integrated BRIC-seq with ChIP-seq to achieve better estimation of the eventual transcript levels and to understand the importance of post-transcriptional regulation that determine the eventual transcript levels. Results We identified discrepancies between the RNA abundance estimated by ChIP-seq and measured RNA expression from RNA-seq; for number of genes and estimated that the expression level of 865 genes was controlled at the level of RNA stability in HeLa cells. ENCODE data analysis supported the idea that RNA stability control aids to determine transcript levels in multiple cell types. We identified UPF1, EXOSC5 and STAU1, well-studied RNA degradation factors, as controlling factors for 8% of cases. Computational simulations reasonably explained the changes of eventual mRNA levels attributable to the changes in the rates of mRNA half-lives. In addition, we propose a feedback circuit that includes the regulated degradation of mRNAs encoding transcription factors to maintain the steady state level of RNA abundance. Intriguingly, these regulatory mechanisms were distinct between mRNAs and lincRNAs. Conclusions Integrative analysis of ChIP-seq, RNA-seq and our BRIC-seq showed that transcriptional regulation and RNA degradation are independently regulated. In addition, RNA stability is an important determinant of eventual transcript levels. RNA binding proteins, such as UPF1, STAU1 and EXOSC5 may play active roles in such controls. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1358-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sho Maekawa
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Naoto Imamachi
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Takuma Irie
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Kyoko Matsumoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Rena Mizutani
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Katsutoshi Imamura
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Miho Kakeda
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan.
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan.
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan. .,Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Nobuyoshi Akimitsu
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
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15
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Suzuki A, Makinoshima H, Wakaguri H, Esumi H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y. Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines. Nucleic Acids Res 2014; 42:13557-72. [PMID: 25378332 PMCID: PMC4267666 DOI: 10.1093/nar/gku885] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Here we conducted an integrative multi-omics analysis to understand how cancers harbor various types of aberrations at the genomic, epigenomic and transcriptional levels. In order to elucidate biological relevance of the aberrations and their mutual relations, we performed whole-genome sequencing, RNA-Seq, bisulfite sequencing and ChIP-Seq of 26 lung adenocarcinoma cell lines. The collected multi-omics data allowed us to associate an average of 536 coding mutations and 13,573 mutations in promoter or enhancer regions with aberrant transcriptional regulations. We detected the 385 splice site mutations and 552 chromosomal rearrangements, representative cases of which were validated to cause aberrant transcripts. Averages of 61, 217, 3687 and 3112 mutations are located in the regulatory regions which showed differential DNA methylation, H3K4me3, H3K4me1 and H3K27ac marks, respectively. We detected distinct patterns of aberrations in transcriptional regulations depending on genes. We found that the irregular histone marks were characteristic to EGFR and CDKN1A, while a large genomic deletion and hyper-DNA methylation were most frequent for CDKN2A. We also used the multi-omics data to classify the cell lines regarding their hallmarks of carcinogenesis. Our datasets should provide a valuable foundation for biological interpretations of interlaced genomic and epigenomic aberrations.
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Affiliation(s)
- Ayako Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hideki Makinoshima
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hiroyuki Wakaguri
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Hiroyasu Esumi
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Tokyo, Japan
| | - Katsuya Tsuchihara
- Division of TR, The Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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16
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Seki M, Masaki H, Arauchi T, Nakauchi H, Sugano S, Suzuki Y. A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells. PLoS One 2014; 9:e95374. [PMID: 24752154 PMCID: PMC3994037 DOI: 10.1371/journal.pone.0095374] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/26/2014] [Indexed: 10/29/2022] Open
Abstract
We detected and characterized the binding sites of the representative Rest complex components Rest, Sin3A, and Lsd1. We compared their binding patterns in mouse embryonic stem (ES) cells and epiblast stem (EpiS) cells. We found few Rest sites unique to the EpiS cells. The ES-unique site features were distinct from those of the common sites, namely, the signal intensities were weaker, and the characteristic gene function categories differed. Our analyses showed that the Rest binding sites do not always overlap with the Sin3A and Lsd1 binding sites. The Sin3A binding pattern differed remarkably between the ES and EpiS cells and was accompanied by significant changes in acetylated-histone patterns in the surrounding regions. A series of transcriptome analyses in the same cell types unexpectedly showed that the putative target gene transcript levels were not dramatically different despite dynamic changes in the Rest complex binding patterns and chromatin statuses, which suggests that Rest is not the sole determinant of repression at its targets. Nevertheless, we identified putative Rest targets with explicitly enhanced transcription upon Rest knock-down in 143 and 60 common and ES-unique Rest target genes, respectively. Among such sites, several genes are involved in ES cell proliferation. In addition, we also found that long, intergenic non-coding RNAs were apparent Rest targets and shared similar features with the protein-coding target genes. Interestingly, such non-coding target genes showed less conservation through evolution than protein-coding targets. As a result of differences in the components and targets of the Rest complex, its functional roles may differ in ES and EpiS cells.
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Affiliation(s)
- Masahide Seki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Hideki Masaki
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
| | - Takako Arauchi
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, the University of Tokyo, Minato-ku, Tokyo, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
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17
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Tumes DJ, Onodera A, Suzuki A, Shinoda K, Endo Y, Iwamura C, Hosokawa H, Koseki H, Tokoyoda K, Suzuki Y, Motohashi S, Nakayama T. The polycomb protein Ezh2 regulates differentiation and plasticity of CD4(+) T helper type 1 and type 2 cells. Immunity 2014; 39:819-32. [PMID: 24238339 DOI: 10.1016/j.immuni.2013.09.012] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 09/16/2013] [Indexed: 12/23/2022]
Abstract
After antigen encounter by CD4(+) T cells, polarizing cytokines induce the expression of master regulators that control differentiation. Inactivation of the histone methyltransferase Ezh2 was found to specifically enhance T helper 1 (Th1) and Th2 cell differentiation and plasticity. Ezh2 directly bound and facilitated correct expression of Tbx21 and Gata3 in differentiating Th1 and Th2 cells, accompanied by substantial trimethylation at lysine 27 of histone 3 (H3K27me3). In addition, Ezh2 deficiency resulted in spontaneous generation of discrete IFN-γ and Th2 cytokine-producing populations in nonpolarizing cultures, and under these conditions IFN-γ expression was largely dependent on enhanced expression of the transcription factor Eomesodermin. In vivo, loss of Ezh2 caused increased pathology in a model of allergic asthma and resulted in progressive accumulation of memory phenotype Th2 cells. This study establishes a functional link between Ezh2 and transcriptional regulation of lineage-specifying genes in terminally differentiated CD4(+) T cells.
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Affiliation(s)
- Damon J Tumes
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
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18
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Functionally distinct Gata3/Chd4 complexes coordinately establish T helper 2 (Th2) cell identity. Proc Natl Acad Sci U S A 2013; 110:4691-6. [PMID: 23471993 DOI: 10.1073/pnas.1220865110] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
GATA binding protein 3 (Gata3) is a GATA family transcription factor that controls differentiation of naïve CD4 T cells into T helper 2 (Th2) cells. However, it is unknown how Gata3 simultaneously activates Th2-specific genes while repressing those of other Th lineages. Here we show that chromodomain helicase DNA-binding protein 4 (Chd4) forms a complex with Gata3 in Th2 cells that both activates Th2 cytokine transcription and represses the Th1 cytokine IFN-γ. We define a Gata3/Chd4/p300 transcriptional activation complex at the Th2 cytokine loci and a Gata3/Chd4-nucleosome remodeling histone deacetylase repression complex at the Tbx21 locus in Th2 cells. We also demonstrate a physiological role for Chd4 in Th2-dependent inflammation in an in vivo model of asthmatic inflammation. Thus, Gata3/Chd4 forms functionally distinct complexes, which mediate both positive and negative gene regulation to facilitate Th2 cell differentiation.
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19
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Abstract
UNLABELLED Recent proteomic data have uncovered an interdependence of PI3K and STAT3. In PI3K-tranformed murine cells, STAT3 is phosphorylated on Y705 and activated in a PI3K-dependent manner. Dominant negative STAT3 interferes with PI3K-induced oncogenic transformation. Phosphorylation of STAT3 in PI3K-transformed murine cells is mediated by the TEC kinase BMX. Observations on glioblastoma stem cells reveal similar critical roles for STAT3 and BMX. The new data document an important role of STAT3 in PI3K-driven oncogenic transformation and mark BMX as a promising therapeutic target that could enhance the effectiveness of PI3K inhibitors. SIGNIFICANCE The PI3K–TOR and STAT3 signaling pathways represent two distinct regulatory networks. The discovery of a functional link between these pathways is significant for our understanding of PI3K- and STAT3-driven oncogenic mechanisms and identifies the TEC kinase BMX as a new cancer target.
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Affiliation(s)
- Peter K Vogt
- The Scripps Research Institute, Department of Molecular and Experimental Medicine, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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