1
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Oyarbide U, Crane GM, Corey SJ. The metabolic basis of inherited neutropenias. Br J Haematol 2024; 204:45-55. [PMID: 38049194 DOI: 10.1111/bjh.19192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
Neutrophils are the shortest-lived blood cells, which requires a prodigious degree of proliferation and differentiation to sustain physiologically sufficient numbers and be poised to respond quickly to infectious emergencies. More than 107 neutrophils are produced every minute in an adult bone marrow-a process that is tightly regulated by a small group of cytokines and chemical mediators and dependent on nutrients and energy. Like granulocyte colony-stimulating factor, the primary growth factor for granulopoiesis, they stimulate signalling pathways, some affecting metabolism. Nutrient or energy deficiency stresses the survival, proliferation, and differentiation of neutrophils and their precursors. Thus, it is not surprising that monogenic disorders related to metabolism exist that result in neutropenia. Among these are pathogenic mutations in HAX1, G6PC3, SLC37A4, TAFAZZIN, SBDS, EFL1 and the mitochondrial disorders. These mutations perturb carbohydrate, lipid and/or protein metabolism. We hypothesize that metabolic disturbances may drive the pathogenesis of a subset of inherited neutropenias just as defects in DNA damage response do in Fanconi anaemia, telomere maintenance in dyskeratosis congenita and ribosome formation in Diamond-Blackfan anaemia. Greater understanding of metabolic pathways in granulopoiesis will identify points of vulnerability in production and may point to new strategies for the treatment of neutropenias.
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Affiliation(s)
- Usua Oyarbide
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
| | - Genevieve M Crane
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, Ohio, USA
| | - Seth J Corey
- Department of Cancer Biology, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Pediatrics, Cleveland Clinic, Cleveland, Ohio, USA
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2
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Xiao Y, Xie X, Chen Z, Yin G, Kong W, Zhou J. Advances in the roles of ATF4 in osteoporosis. Biomed Pharmacother 2023; 169:115864. [PMID: 37948991 DOI: 10.1016/j.biopha.2023.115864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Osteoporosis (OP) is characterized by reduced bone mass, decreased strength, and enhanced bone fragility fracture risk. Activating transcription factor 4 (ATF4) plays a role in cell differentiation, proliferation, apoptosis, redox balance, amino acid uptake, and glycolipid metabolism. ATF4 induces the differentiation of bone marrow mesenchymal stem cells (BM-MSCs) into osteoblasts, increases osteoblast activity, and inhibits osteoclast formation, promoting bone formation and remodeling. In addition, ATF4 mediates the energy metabolism in osteoblasts and promotes angiogenesis. ATF4 is also involved in the mediation of adipogenesis. ATF4 can selectively accumulate in osteoblasts. ATF4 can directly interact with RUNT-related transcription factor 2 (RUNX2) and up-regulate the expression of osteocalcin (OCN) and osterix (Osx). Several upstream factors, such as Wnt/β-catenin and BMP2/Smad signaling pathways, have been involved in ATF4-mediated osteoblast differentiation. ATF4 promotes osteoclastogenesis by mediating the receptor activator of nuclear factor κ-B (NF-κB) ligand (RANKL) signaling. Several agents, such as parathyroid (PTH), melatonin, and natural compounds, have been reported to regulate ATF4 expression and mediate bone metabolism. In this review, we comprehensively discuss the biological activities of ATF4 in maintaining bone homeostasis and inhibiting OP development. ATF4 has become a therapeutic target for OP treatment.
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Affiliation(s)
- Yaosheng Xiao
- Department of Orthopaetics, First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xunlu Xie
- Department of Pathology, Ganzhou People's Hospital, Ganzhou 341000, China
| | - Zhixi Chen
- Department of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Guoqiang Yin
- Ganzhou Hospital Affiliated to Nanchang University, Ganzhou 341000, China
| | - Weihao Kong
- Department of Joint Surgery, Ganzhou People's Hospital, Ganzhou 341000, China
| | - Jianguo Zhou
- Department of Joint Surgery, Ganzhou People's Hospital, Ganzhou 341000, China.
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3
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Lara-Astiaso D, Goñi-Salaverri A, Mendieta-Esteban J, Narayan N, Del Valle C, Gross T, Giotopoulos G, Beinortas T, Navarro-Alonso M, Aguado-Alvaro LP, Zazpe J, Marchese F, Torrea N, Calvo IA, Lopez CK, Alignani D, Lopez A, Saez B, Taylor-King JP, Prosper F, Fortelny N, Huntly BJP. In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis. Nat Genet 2023; 55:1542-1554. [PMID: 37580596 PMCID: PMC10484791 DOI: 10.1038/s41588-023-01471-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 07/11/2023] [Indexed: 08/16/2023]
Abstract
Cellular differentiation requires extensive alterations in chromatin structure and function, which is elicited by the coordinated action of chromatin and transcription factors. By contrast with transcription factors, the roles of chromatin factors in differentiation have not been systematically characterized. Here, we combine bulk ex vivo and single-cell in vivo CRISPR screens to characterize the role of chromatin factor families in hematopoiesis. We uncover marked lineage specificities for 142 chromatin factors, revealing functional diversity among related chromatin factors (i.e. barrier-to-autointegration factor subcomplexes) as well as shared roles for unrelated repressive complexes that restrain excessive myeloid differentiation. Using epigenetic profiling, we identify functional interactions between lineage-determining transcription factors and several chromatin factors that explain their lineage dependencies. Studying chromatin factor functions in leukemia, we show that leukemia cells engage homeostatic chromatin factor functions to block differentiation, generating specific chromatin factor-transcription factor interactions that might be therapeutically targeted. Together, our work elucidates the lineage-determining properties of chromatin factors across normal and malignant hematopoiesis.
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Affiliation(s)
- David Lara-Astiaso
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | | | | | - Nisha Narayan
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Cynthia Del Valle
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - George Giotopoulos
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Tumas Beinortas
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Mar Navarro-Alonso
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Jon Zazpe
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Francesco Marchese
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Natalia Torrea
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Isabel A Calvo
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Cecile K Lopez
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | - Diego Alignani
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Aitziber Lopez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Borja Saez
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | | | - Felipe Prosper
- Centre for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Nikolaus Fortelny
- Department of Biosciences & Medical Biology, University of Salzburg, Salzburg, Austria.
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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4
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Neill G, Masson GR. A stay of execution: ATF4 regulation and potential outcomes for the integrated stress response. Front Mol Neurosci 2023; 16:1112253. [PMID: 36825279 PMCID: PMC9941348 DOI: 10.3389/fnmol.2023.1112253] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
ATF4 is a cellular stress induced bZIP transcription factor that is a hallmark effector of the integrated stress response. The integrated stress response is triggered by phosphorylation of the alpha subunit of the eukaryotic initiation factor 2 complex that can be carried out by the cellular stress responsive kinases; GCN2, PERK, PKR, and HRI. eIF2α phosphorylation downregulates mRNA translation initiation en masse, however ATF4 translation is upregulated. The integrated stress response can output two contradicting outcomes in cells; pro-survival or apoptosis. The mechanism for choice between these outcomes is unknown, however combinations of ATF4 heterodimerisation partners and post-translational modifications have been linked to this regulation. This semi-systematic review article covers ATF4 target genes, heterodimerisation partners and post-translational modifications. Together, this review aims to be a useful resource to elucidate the mechanisms controlling the effects of the integrated stress response. Additional putative roles of the ATF4 protein in cell division and synaptic plasticity are outlined.
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Affiliation(s)
- Graham Neill
- Division of Cellular and Systems Medicine, School of Medicine, University of Dundee, Dundee, United Kingdom
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5
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Adamo A, Chin P, Keane P, Assi SA, Potluri S, Kellaway SG, Coleman D, Ames L, Ptasinska A, Delwel HR, Cockerill PN, Bonifer C. Identification and interrogation of the gene regulatory network of CEBPA-double mutant acute myeloid leukemia. Leukemia 2023; 37:102-112. [PMID: 36333583 PMCID: PMC9883165 DOI: 10.1038/s41375-022-01744-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy caused by mutations in genes encoding transcriptional and epigenetic regulators together with signaling genes. It is characterized by a disturbance of differentiation and abnormal proliferation of hematopoietic progenitors. We have previously shown that each AML subtype establishes its own core gene regulatory network (GRN), consisting of transcription factors binding to their target genes and imposing a specific gene expression pattern that is required for AML maintenance. In this study, we integrate gene expression, open chromatin and ChIP data with promoter-capture Hi-C data to define a refined core GRN common to all patients with CEBPA-double mutant (CEBPAN/C) AML. These mutations disrupt the structure of a major regulator of myelopoiesis. We identify the binding sites of mutated C/EBPα proteins in primary cells, we show that C/EBPα, AP-1 factors and RUNX1 colocalize and are required for AML maintenance, and we employ single cell experiments to link important network nodes to the specific differentiation trajectory from leukemic stem to blast cells. Taken together, our study provides an important resource which predicts the specific therapeutic vulnerabilities of this AML subtype in human cells.
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Affiliation(s)
- Assunta Adamo
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Paulynn Chin
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Peter Keane
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Sophie G Kellaway
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Daniel Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Luke Ames
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - H Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, University of Birmingham, B152TT, Birmingham, UK.
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6
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Park SD, Saunders AS, Reidy MA, Bender DE, Clifton S, Morris KT. A review of granulocyte colony-stimulating factor receptor signaling and regulation with implications for cancer. Front Oncol 2022; 12:932608. [PMID: 36033452 PMCID: PMC9402976 DOI: 10.3389/fonc.2022.932608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/15/2022] [Indexed: 12/29/2022] Open
Abstract
Granulocyte colony-stimulating factor receptor (GCSFR) is a critical regulator of granulopoiesis. Studies have shown significant upregulation of GCSFR in a variety of cancers and cell types and have recognized GCSFR as a cytokine receptor capable of influencing both myeloid and non-myeloid immune cells, supporting pro-tumoral actions. This systematic review aims to summarize the available literature examining the mechanisms that control GCSFR signaling, regulation, and surface expression with emphasis on how these mechanisms may be dysregulated in cancer. Experiments with different cancer cell lines from breast cancer, bladder cancer, glioma, and neuroblastoma are used to review the biological function and underlying mechanisms of increased GCSFR expression with emphasis on actions related to tumor proliferation, migration, and metastasis, primarily acting through the JAK/STAT pathway. Evidence is also presented that demonstrates a differential physiological response to aberrant GCSFR signal transduction in different organs. The lifecycle of the receptor is also reviewed to support future work defining how this signaling axis becomes dysregulated in malignancies.
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Affiliation(s)
- Sungjin David Park
- Department of Surgery, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - Apryl S. Saunders
- Department of Surgery, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - Megan A. Reidy
- Department of Surgery, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - Dawn E. Bender
- Department of Surgery, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - Shari Clifton
- Department of Information Management, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
| | - Katherine T. Morris
- Department of Surgery, University of Oklahoma Health Science Center, Oklahoma City, OK, United States
- *Correspondence: Katherine T. Morris,
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7
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Ebert SM, Rasmussen BB, Judge AR, Judge SM, Larsson L, Wek RC, Anthony TG, Marcotte GR, Miller MJ, Yorek MA, Vella A, Volpi E, Stern JI, Strub MD, Ryan Z, Talley JJ, Adams CM. Biology of Activating Transcription Factor 4 (ATF4) and Its Role in Skeletal Muscle Atrophy. J Nutr 2022; 152:926-938. [PMID: 34958390 PMCID: PMC8970988 DOI: 10.1093/jn/nxab440] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/17/2021] [Accepted: 12/23/2021] [Indexed: 12/30/2022] Open
Abstract
Activating transcription factor 4 (ATF4) is a multifunctional transcription regulatory protein in the basic leucine zipper superfamily. ATF4 can be expressed in most if not all mammalian cell types, and it can participate in a variety of cellular responses to specific environmental stresses, intracellular derangements, or growth factors. Because ATF4 is involved in a wide range of biological processes, its roles in human health and disease are not yet fully understood. Much of our current knowledge about ATF4 comes from investigations in cultured cell models, where ATF4 was originally characterized and where further investigations continue to provide new insights. ATF4 is also an increasingly prominent topic of in vivo investigations in fully differentiated mammalian cell types, where our current understanding of ATF4 is less complete. Here, we review some important high-level concepts and questions concerning the basic biology of ATF4. We then discuss current knowledge and emerging questions about the in vivo role of ATF4 in one fully differentiated cell type, mammalian skeletal muscle fibers.
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Affiliation(s)
- Scott M Ebert
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
- Emmyon, Inc., Rochester, MN, USA
| | - Blake B Rasmussen
- Emmyon, Inc., Rochester, MN, USA
- Department of Nutrition, Metabolism and Rehabilitation Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew R Judge
- Emmyon, Inc., Rochester, MN, USA
- Department of Physical Therapy, University of Florida, Gainesville, FL, USA
| | - Sarah M Judge
- Department of Physical Therapy, University of Florida, Gainesville, FL, USA
| | - Lars Larsson
- Department of Physiology and Pharmacology, Karolinska, Stockholm, Sweden
| | - Ronald C Wek
- Department of Biochemistry and Molecular Biology, Indiana University, Indianapolis, IN, USA
| | - Tracy G Anthony
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ, USA
| | - George R Marcotte
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Matthew J Miller
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Mark A Yorek
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
- Department of Internal Medicine, Iowa City VA Medical Center, Iowa City, IA, USA
| | - Adrian Vella
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
- Emmyon, Inc., Rochester, MN, USA
| | - Elena Volpi
- Department of Nutrition, Metabolism and Rehabilitation Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Jennifer I Stern
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - Matthew D Strub
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
| | - Zachary Ryan
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
| | | | - Christopher M Adams
- Department of Internal Medicine, Division of Endocrinology, Diabetes, Metabolism and Nutrition, Mayo Clinic, Rochester, MN, USA
- Emmyon, Inc., Rochester, MN, USA
- Department of Internal Medicine, Iowa City VA Medical Center, Iowa City, IA, USA
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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9
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Xie SZ, Garcia-Prat L, Voisin V, Ferrari R, Gan OI, Wagenblast E, Kaufmann KB, Zeng AGX, Takayanagi SI, Patel I, Lee EK, Jargstorf J, Holmes G, Romm G, Pan K, Shoong M, Vedi A, Luberto C, Minden MD, Bader GD, Laurenti E, Dick JE. Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal. Cell Stem Cell 2019; 25:639-653.e7. [PMID: 31631013 PMCID: PMC6838675 DOI: 10.1016/j.stem.2019.09.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/09/2019] [Accepted: 09/23/2019] [Indexed: 12/30/2022]
Abstract
Cellular stress responses serve as crucial decision points balancing persistence or culling of hematopoietic stem cells (HSCs) for lifelong blood production. Although strong stressors cull HSCs, the linkage between stress programs and self-renewal properties that underlie human HSC maintenance remains unknown, particularly at quiescence exit when HSCs must also dynamically shift metabolic state. Here, we demonstrate distinct wiring of the sphingolipidome across the human hematopoietic hierarchy and find that genetic or pharmacologic modulation of the sphingolipid enzyme DEGS1 regulates lineage differentiation. Inhibition of DEGS1 in hematopoietic stem and progenitor cells during the transition from quiescence to cellular activation with N-(4-hydroxyphenyl) retinamide activates coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs to maintain immunophenotypic and functional HSCs. Thus, our work identifies a linkage between sphingolipid metabolism, proteostatic quality control systems, and HSC self-renewal and provides therapeutic targets for improving HSC-based cellular therapeutics.
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Affiliation(s)
- Stephanie Z Xie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada.
| | - Laura Garcia-Prat
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Veronique Voisin
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Robin Ferrari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Olga I Gan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Elvin Wagenblast
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Kerstin B Kaufmann
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Andy G X Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Shin-Ichiro Takayanagi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; R&D Division, Kyowa Kirin Co., Ltd., Tokyo 194-8533, Japan
| | - Ishita Patel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Esther K Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Joseph Jargstorf
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Gareth Holmes
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Guy Romm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Kristele Pan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Michelle Shoong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada
| | - Aditi Vedi
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - Chiara Luberto
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Division of Medical Oncology and Hematology, Department of Medicine, University Health Network, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada
| | - Elisa Laurenti
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Department of Haematology, University of Cambridge, Cambridge, UK
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G0A3, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S1A8, Canada.
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10
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Jin B, Gong Y, Li H, Jiao L, Xin D, Gong Y, He Z, Zhou L, Jin Y, Wang X, Zhang Z. C/EBPβ promotes the viability of human bladder cancer cell by contributing to the transcription of bladder cancer specific lncRNA UCA1. Biochem Biophys Res Commun 2018; 506:674-679. [PMID: 30376994 DOI: 10.1016/j.bbrc.2018.10.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 10/23/2018] [Indexed: 01/01/2023]
Abstract
Urothelial Carcinoma Antigen 1 (UCA1) is a cell and tissue specific long non-coding RNA (lncRNA) associated with the tumorigenesis and invasion of bladder cancer. However, the mechanism driving the over-transcription of UCA1 in bladder cancer cells remains unclear. It has been reported that C/EBPβ has a significant role of regulation in tumorigenesis. Here we report that the expression of UCA1 was dramatically inhibited in 5637 cells with C/EBPβ down-regulation. Additionally, the function tests indicated that C/EBPβ could promote 5637 cells growth and colony formation by inducing the expression level of UCA1. These data suggest that C/EBPβ was involved in transcriptional regulation of UCA1 and contributed substantially to its high expression and proliferation promoting in bladder cancer cells.
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Affiliation(s)
- Bo Jin
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, 100034, China
| | - Yanbing Gong
- Department of Central Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Haixia Li
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, 100034, China
| | - Lili Jiao
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, 100034, China
| | - Dianqi Xin
- Department of Urology, Peking University First Hospital & Institute of Urology, Peking University, Beijing, 100034, China
| | - Yanqing Gong
- Department of Urology, Peking University First Hospital & Institute of Urology, Peking University, Beijing, 100034, China
| | - Zhisong He
- Department of Urology, Peking University First Hospital & Institute of Urology, Peking University, Beijing, 100034, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital & Institute of Urology, Peking University, Beijing, 100034, China
| | - Yaqiong Jin
- Biobank for Clinical Data and Samples in Pediatric, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiujuan Wang
- Department of Clinical Laboratory, Shandong Academy of Medical Sciences, Shandong Cancer Hospital Affiliated to Shandong University, Jinan, 250117, Shandong, China
| | - Zheng Zhang
- Department of Urology, Peking University First Hospital & Institute of Urology, Peking University, Beijing, 100034, China.
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11
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Wang Y, Fu L, Sun A, Tang D, Xu Y, Li Z, Chen M, Zhang G. C/EBPβ contributes to transcriptional activation of long non-coding RNA NEAT1 during APL cell differentiation. Biochem Biophys Res Commun 2017; 499:99-104. [PMID: 29111326 DOI: 10.1016/j.bbrc.2017.10.137] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 10/26/2017] [Indexed: 01/30/2023]
Abstract
Emerging evidences have shown that long non-coding RNAs (lncRNAs) play critical roles in cancer development and cancer therapy. LncRNA Nuclear Enriched Abundant Transcript 1 (NEAT1) is indispensable during acute promyelocytic leukemia (APL) cell differentiation induced by all-trans retinoic acid (ATRA). However, the precise mechanism of NEAT1 upregulation has not been fully understood. In this study, we performed chromatin immunoprecipitation and luciferase reporter assays to demonstrate that C/EBP family transcription factor C/EBPβ bind to and transactivate the promoter of lncRNA NEAT1 through the C/EBPβ binding sites both around -54 bp and -1453 bp upstream of the transcription start site. Moreover, the expression of C/EBPβ was increased after ATRA treatment, and the binding of C/EBPβ in the NEAT1 promoter was also dramatically increased. Finally, knockdown of C/EBPβ significantly reduced the ATRA-induced upregulation of NEAT1. In conclusion, C/EBPβ directly activates the expression of NEAT1 through binding to the promoter of NEAT1. Knockdown of C/EBPβ impairs ATRA-induced transcriptional activation of NEAT1. Our data indicate that C/EBPβ contributes to ATRA-induced activation of NEAT1 during APL cell differentiation. Our results enrich our knowledge on the regulation of lncRNAs and the regulatory role of C/EBPβ in APL cell differentiation.
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Affiliation(s)
- Yewei Wang
- Department of Hematology/Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China.
| | - Lei Fu
- Department of Hematology/Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China.
| | - Ailian Sun
- Department of Hematology/Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China.
| | - Doudou Tang
- Department of Respiratory Medicine, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China.
| | - Yunxiao Xu
- Department of Hematology/Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China.
| | - Zheyuan Li
- Department of Hematology/Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China; Xiangya School of Medicine, Central South University, No.172 Tongzipo Road, Changsha, Hunan 410013, China.
| | - Mingjie Chen
- Cloud-seq Bio-tech Inc., Building 71, No.1066 North Qinzhou Road, Shanghai 200233, China.
| | - Guangsen Zhang
- Department of Hematology/Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, No.139 Middle Renmin Road, Changsha, Hunan 410011, China.
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12
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Carrillo-de-Santa-Pau E, Juan D, Pancaldi V, Were F, Martin-Subero I, Rico D, Valencia A. Automatic identification of informative regions with epigenomic changes associated to hematopoiesis. Nucleic Acids Res 2017; 45:9244-9259. [PMID: 28934481 PMCID: PMC5716146 DOI: 10.1093/nar/gkx618] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/06/2017] [Indexed: 12/19/2022] Open
Abstract
Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate a chromatin space that allows to classify 42 human healthy blood epigenomes from the BLUEPRINT, NIH ROADMAP and ENCODE consortia by their cell type. This approach let us to distinguish different cells types based on their epigenomic profiles, thus recapitulating important aspects of human hematopoiesis. The analysis of the orthogonal dimension of the chromatin space identify 32,662 chromatin determinant regions (CDRs), genomic regions with different epigenetic characteristics between the cell types. Functional analysis revealed that these regions are linked with cell identities. The inclusion of leukemia epigenomes in the healthy hematological chromatin sample space gives us insights on the healthy cell types that are more epigenetically similar to the disease samples. Further analysis of tumoral epigenetic alterations in hematopoietic CDRs points to sets of genes that are tightly regulated in leukemic transformations and commonly mutated in other tumors. Our method provides an analytical approach to study the relationship between epigenomic changes and cell lineage differentiation. Method availability: https://github.com/david-juan/ChromDet.
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Affiliation(s)
| | - David Juan
- Institut de Biologia Evolutiva, Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, 08003, Spain
| | - Vera Pancaldi
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain
| | - Felipe Were
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Ignacio Martin-Subero
- Institut d'Investigacions Biomédiques August Pi i Sunyer (IDIBAPS), Department of Anatomic Pathology, Pharmacology and Microbiology, University of Barcelona, Barcelona, 08036, Spain
| | - Daniel Rico
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Alfonso Valencia
- Barcelona Supercomputing Centre (BSC), Barcelona, 08034, Spain.,ICREA, Pg. Lluís Companys 23, Barcelona, 08010, Spain
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13
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Wong JJ, Gao D, Nguyen TV, Kwok CT, van Geldermalsen M, Middleton R, Pinello N, Thoeng A, Nagarajah R, Holst J, Ritchie W, Rasko JEJ. Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment. Nat Commun 2017; 8:15134. [PMID: 28480880 DOI: 10.1038/ncomms15134] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 03/02/2017] [Indexed: 01/07/2023] Open
Abstract
While intron retention (IR) is considered a widely conserved and distinct mechanism of gene expression control, its regulation is poorly understood. Here we show that DNA methylation directly regulates IR. We also find reduced occupancy of MeCP2 near the splice junctions of retained introns, mirroring the reduced DNA methylation at these sites. Accordingly, MeCP2 depletion in tissues and cells enhances IR. By analysing the MeCP2 interactome using mass spectrometry and RNA co-precipitation, we demonstrate that decreased MeCP2 binding near splice junctions facilitates IR via reduced recruitment of splicing factors, including Tra2b, and increased RNA polymerase II stalling. These results suggest an association between IR and a slower rate of transcription elongation, which reflects inefficient splicing factor recruitment. In summary, our results reinforce the interdependency between alternative splicing involving IR and epigenetic controls of gene expression. Intron retention is a conserved mechanism that controls gene expression but its regulation is poorly understood. Here, the authors provide evidence that DNA methylation regulates intron retention and find reduced MeCP2 occupancy and splicing factor recruitment near affected splice junctions.
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14
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Lee JE, Oney M, Frizzell K, Phadnis N, Hollien J. Drosophila melanogaster activating transcription factor 4 regulates glycolysis during endoplasmic reticulum stress. G3 (Bethesda) 2015; 5:667-75. [PMID: 25681259 DOI: 10.1534/g3.115.017269] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Endoplasmic reticulum (ER) stress results from an imbalance between the load of proteins entering the secretory pathway and the ability of the ER to fold and process them. The response to ER stress is mediated by a collection of signaling pathways termed the unfolded protein response, which plays important roles in development and disease. Here we show that in Drosophila melanogaster S2 cells, ER stress induces a coordinated change in the expression of genes involved in carbon metabolism. Genes encoding enzymes that carry out glycolysis were up-regulated, whereas genes encoding proteins in the tricarboxylic acid cycle and respiratory chain complexes were down-regulated. The unfolded protein response transcription factor Atf4 was necessary for the up-regulation of glycolytic enzymes and Lactate dehydrogenase (Ldh). Furthermore, Atf4 binding motifs in promoters for these genes could partially account for their regulation during ER stress. Finally, flies up-regulated Ldh and produced more lactate when subjected to ER stress. Together, these results suggest that Atf4 mediates a shift from a metabolism based on oxidative phosphorylation to one more heavily reliant on glycolysis, reminiscent of aerobic glycolysis or the Warburg effect observed in cancer and other proliferative cells.
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15
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Abstract
Immune responses occur in the midst of a variety of cellular stresses that can severely perturb endoplasmic reticulum (ER) function. The unfolded protein response is a three-pronged signaling axis dedicated to preserving ER homeostasis. In this review, we highlight many important and emerging functional roles for ER stress in immunity, focusing on how the bidirectional cross talk between immunological processes and basic cell biology leads to pleiotropic signaling outcomes and enhanced sensitivity to inflammatory stimuli. We also discuss how dysregulated ER stress responses can provoke many diseases, including autoimmunity, firmly positioning the unfolded protein response as a major therapeutic target in human disease.
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Affiliation(s)
- Sarah E Bettigole
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065; ,
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16
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Soda T, Frank C, Ishizuka K, Baccarella A, Park YU, Flood Z, Park SK, Sawa A, Tsai LH. DISC1-ATF4 transcriptional repression complex: dual regulation of the cAMP-PDE4 cascade by DISC1. Mol Psychiatry 2013; 18:898-908. [PMID: 23587879 PMCID: PMC3730299 DOI: 10.1038/mp.2013.38] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 01/12/2013] [Accepted: 01/31/2013] [Indexed: 02/08/2023]
Abstract
Disrupted-In-Schizophrenia 1 (DISC1), a risk factor for major mental illnesses, has been studied extensively in the context of neurodevelopment. However, the role of DISC1 in neuronal signaling, particularly in conjunction with intracellular cascades that occur in response to dopamine, a neurotransmitter implicated in numerous psychiatric disorders, remains elusive. Previous data suggest that DISC1 interacts with numerous proteins that impact neuronal function, including activating transcription factor 4 (ATF4). In this study, we identify a novel DISC1 and ATF4 binding region in the genomic locus of phosphodiesterase 4D (PDE4D), a gene implicated in psychiatric disorders. We found that the loss of function of either DISC1 or ATF4 increases PDE4D9 transcription, and that the association of DISC1 with the PDE4D9 locus requires ATF4. We also show that PDE4D9 is increased by D1-type dopamine receptor dopaminergic stimulation. We demonstrate that the mechanism for this increase is due to DISC1 dissociation from the PDE4D locus in mouse brain. We further characterize the interaction of DISC1 with ATF4 to show that it is regulated via protein kinase A-mediated phosphorylation of DISC1 serine-58. Our results suggest that the release of DISC1-mediated transcriptional repression of PDE4D9 acts as feedback inhibition to regulate dopaminergic signaling. Furthermore, as DISC1 loss-of-function leads to a specific increase in PDE4D9, PDE4D9 itself may represent an attractive target for therapeutic approaches in psychiatric disorders.
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Affiliation(s)
- T Soda
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA,Howard Hughes Medical Institute, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA,Daniel Tosteson Medical Education Center, Boston, MA, USA
| | - C Frank
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA,Howard Hughes Medical Institute, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - K Ishizuka
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Baccarella
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Y-U Park
- Division of Molecular and Life Science, Department of Life Science, Biotechnology Research Center, Pohang University of Science and Technology, Pohang, Korea
| | - Z Flood
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA,Howard Hughes Medical Institute, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - S K Park
- Division of Molecular and Life Science, Department of Life Science, Biotechnology Research Center, Pohang University of Science and Technology, Pohang, Korea
| | - A Sawa
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - L-H Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA,Howard Hughes Medical Institute, Cambridge, MA, USA,Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA,Howard Hughes Medical Institute, 77 Massachusetts Avenue, Room 46-4235, Cambridge, MA 02139, USA. E-mail:
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17
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Örd T, Örd D, Kuuse S, Plaas M, Örd T. Trib3 is regulated by IL-3 and affects bone marrow-derived mast cell survival and function. Cell Immunol 2012; 280:68-75. [DOI: 10.1016/j.cellimm.2012.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/02/2012] [Accepted: 11/09/2012] [Indexed: 11/20/2022]
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18
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Cronin KR, Mangan TP, Carew JA. Upregulation of the coagulation factor VII gene during glucose deprivation is mediated by activating transcription factor 4. PLoS One 2012; 7:e40994. [PMID: 22848420 PMCID: PMC3407153 DOI: 10.1371/journal.pone.0040994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/15/2012] [Indexed: 12/20/2022] Open
Abstract
Background Constitutive production of blood coagulation proteins by hepatocytes is necessary for hemostasis. Stressful conditions trigger adaptive cellular responses and delay processing of most proteins, potentially affecting plasma levels of proteins secreted exclusively by hepatocytes. We examined the effect of glucose deprivation on expression of coagulation proteins by the human hepatoma cell line, HepG2. Methodology/Principal Findings Expression of coagulation factor VII, which is required for initiation of blood coagulation, was elevated by glucose deprivation, while expression of other coagulation proteins decreased. Realtime PCR and ELISA demonstrated that the relative percentage expression +/− SD of steady-state F7 mRNA and secreted factor VII antigen were significantly increased (from 100+/−15% to 188+/−27% and 100+/−8.8% to 176.3+/−17.3% respectively, p<0.001) at 24 hr of treatment. The integrated stress response was induced, as indicated by upregulation of transcription factor ATF4 and of additional stress-responsive genes. Small interfering RNAs directed against ATF4 potently reduced basal F7 expression, and prevented F7 upregulation by glucose deprivation. The response of the endogenous F7 gene was replicated in reporter gene assays, which further indicated that ATF4 effects were mediated via interaction with an amino acid response element in the F7 promoter. Conclusions/Significance Our data indicated that glucose deprivation enhanced F7 expression in a mechanism reliant on prior ATF4 upregulation primarily due to increased transcription from the ATF4 gene. Of five coagulation protein genes examined, only F7 was upregulated, suggesting that its functions may be important in a systemic response to glucose deprivation stress.
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Affiliation(s)
- Katherine R. Cronin
- Department of Research, VA Boston Healthcare System, West Roxbury, Massachusetts, United States of America
| | - Thomas P. Mangan
- Department of Research, VA Boston Healthcare System, West Roxbury, Massachusetts, United States of America
| | - Josephine A. Carew
- Department of Research, VA Boston Healthcare System, West Roxbury, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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19
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Tsukada J, Yoshida Y, Kominato Y, Auron PE. The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation. Cytokine 2011; 54:6-19. [DOI: 10.1016/j.cyto.2010.12.019] [Citation(s) in RCA: 231] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Revised: 12/19/2010] [Accepted: 12/22/2010] [Indexed: 12/18/2022]
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20
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Cai R, Cai X, Chen B, Xu W, Lu J. C/EBPε participates in all-trans retinoic acid induction of PI3Kγ in U937 cells via an intronic matrix attachment region sequence. Mol Biol Rep 2010; 37:3795-800. [PMID: 20661648 DOI: 10.1007/s11033-010-0034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 02/24/2010] [Indexed: 11/29/2022]
Abstract
ATRA (all-trans retinoic acid) regulates gene expression by binding as a ligand to its specific receptors like C/EBPε which is directly induced. In the U937 cell line, PI3Kγ is selectively induced over other PI3Ks by ATRA, although the mechanism is still unclear. Here, we show that C/EBPε and PI3Kγ are induced in U937 cells by ATRA both in levels of mRNA and protein. Reporter gene assay revealed that C/EBPε is able to interact with a previously identified 2 kb MAR (matrix attachment region) sequence in the last intron of PI3Kγ gene, and increases its linked heterogeneous reporter gene expression. ChIP assay showed that induction of endogenous PI3Kγ is at least partially caused by enhanced, direct C/EBPε binding to a 15 bp sequence at nucleotides 1428-1442 within this MAR sequence, and EMSA analysis confirmed this binding in vitro. The results above collectively show that C/EBPε participates in ATRA induction of PI3Kγ.
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Affiliation(s)
- Rong Cai
- Department of Molecular and Cellular Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, 280# Chongqing Road(S), Shanghai, 200025, People's Republic of China
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21
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Kilareski EM, Shah S, Nonnemacher MR, Wigdahl B. Regulation of HIV-1 transcription in cells of the monocyte-macrophage lineage. Retrovirology 2009; 6:118. [PMID: 20030845 PMCID: PMC2805609 DOI: 10.1186/1742-4690-6-118] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Accepted: 12/23/2009] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) has been shown to replicate productively in cells of the monocyte-macrophage lineage, although replication occurs to a lesser extent than in infected T cells. As cells of the monocyte-macrophage lineage become differentiated and activated and subsequently travel to a variety of end organs, they become a source of infectious virus and secreted viral proteins and cellular products that likely initiate pathological consequences in a number of organ systems. During this process, alterations in a number of signaling pathways, including the level and functional properties of many cellular transcription factors, alter the course of HIV-1 long terminal repeat (LTR)-directed gene expression. This process ultimately results in events that contribute to the pathogenesis of HIV-1 infection. First, increased transcription leads to the upregulation of infectious virus production, and the increased production of viral proteins (gp120, Tat, Nef, and Vpr), which have additional activities as extracellular proteins. Increased viral production and the presence of toxic proteins lead to enhanced deregulation of cellular functions increasing the production of toxic cellular proteins and metabolites and the resulting organ-specific pathologic consequences such as neuroAIDS. This article reviews the structural and functional features of the cis-acting elements upstream and downstream of the transcriptional start site in the retroviral LTR. It also includes a discussion of the regulation of the retroviral LTR in the monocyte-macrophage lineage during virus infection of the bone marrow, the peripheral blood, the lymphoid tissues, and end organs such as the brain. The impact of genetic variation on LTR-directed transcription during the course of retrovirus disease is also reviewed.
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Affiliation(s)
- Evelyn M Kilareski
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, 245 N 15th St, Philadelphia, Pennsylvania 19102, USA
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22
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Pascual M, Gómez-Lechón MJ, Castell JV, Jover R. ATF5 Is a Highly Abundant Liver-Enriched Transcription Factor that Cooperates with Constitutive Androstane Receptor in the Transactivation of CYP2B6: Implications in Hepatic Stress Responses. Drug Metab Dispos 2008; 36:1063-72. [DOI: 10.1124/dmd.107.019380] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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23
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Cai DH, Wang D, Keefer J, Yeamans C, Hensley K, Friedman AD. C/EBP alpha:AP-1 leucine zipper heterodimers bind novel DNA elements, activate the PU.1 promoter and direct monocyte lineage commitment more potently than C/EBP alpha homodimers or AP-1. Oncogene 2008; 27:2772-9. [PMID: 18026136 DOI: 10.1038/sj.onc.1210940] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The basic-region leucine zipper (BR-LZ or bZIP) transcription factors dimerize via their LZ domains to position the adjacent BRs for DNA binding. Members of the C/EBP, AP-1 and CREB/ATF bZIP subfamilies form homodimeric or heterodimeric complexes with other members of the same subset and bind-specific DNA motifs. Here we demonstrate that C/EBPalpha also zippers with AP-1 proteins and that this interaction allows contact with novel DNA elements and induction of monocyte lineage commitment in myeloid progenitors. A leucine zipper swap:gel shift assay demonstrates that C/EBPalpha zippers with c-Jun, JunB or c-Fos, but not with c-Maf or MafB. To evaluate activities of specific homodimers or heterodimers we utilized LZs with acid (LZE) or basic (LZK) residues in their salt bridge positions. C/EBPalphaLZE:C/EBPalphaLZK preferentially binds a C/EBP site, c-JunLZE:c-FosLZK an AP-1 site and C/EBPalphaLZE:c-JunLZK a hybrid element identified as TTGCGTCAT by oligonucleotide selection. In murine myeloid progenitors, C/EBPalpha:c-Jun or C/EBPalpha:c-Fos LZE:LZK heterodimers induce monocyte lineage commitment with markedly increased potency compared with C/EBPalpha or c-Jun homodimers or c-Jun:c-Fos heterodimers, demonstrating a positive functional consequence of C/EBP:AP-1 bZIP subfamily interaction. C/EBPalpha:cJun binds and activates the endogenous PU.1 promoter, providing one mechanism for induction of monopoiesis by this complex.
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Chumakov AM, Silla A, Williamson EA, Koeffler HP. Modulation of DNA binding properties of CCAAT/enhancer binding protein epsilon by heterodimer formation and interactions with NFkappaB pathway. Blood 2007; 109:4209-19. [PMID: 17255362 PMCID: PMC1885488 DOI: 10.1182/blood-2005-09-031963] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
C/EBP epsilon is a transcription factor involved in myeloid cell differentiation. Along with C/EBP-alpha, -beta, -gamma, -delta, and -zeta, C/EBP-epsilon belongs to the family of CCAAT/enhancer binding proteins that are implicated in control of growth and differentiation of several cell lineages in inflammation and stress response. We have previously shown that C/EBP-epsilon preferentially binds DNA as a heterodimer with other C/EBP family members such as C/EBP-delta, CHOP (C/EBP-zeta), and the b-zip family protein ATF4. In this study, we define the consensus binding sites for C/EBP-epsilon dimers and C/EBP-epsilon-ATF4 heterodimers. We show that the activated NFkappaB pathway promotes interaction of the C/EBP-epsilon subunit with its cognate DNA binding site via interaction with RelA. RelA-C/EBP interaction is enhanced by phosphorylation of threonine at amino acid 75 and results in increased DNA binding compared with the wild-type nonphosphorylated C/EBP both in vitro and in vivo. We suggest that interaction of the activated NFkappaB pathway and C/EBP-epsilon may be important in selective activation of a subset of C/EBP-epsilon-responsive genes.
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Affiliation(s)
- Alexey M Chumakov
- Department of Medicine, Cedars-Sinai Medical Center, University of California at Los Angeles, CA 90048, USA.
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