151
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Pardo L, Valor LM, Eraso-Pichot A, Barco A, Golbano A, Hardingham GE, Masgrau R, Galea E. CREB Regulates Distinct Adaptive Transcriptional Programs in Astrocytes and Neurons. Sci Rep 2017; 7:6390. [PMID: 28743894 PMCID: PMC5526874 DOI: 10.1038/s41598-017-06231-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 06/12/2017] [Indexed: 01/04/2023] Open
Abstract
The cyclic AMP response element binding protein (CREB) is a primary hub of activity-driven genetic programs in neurons controlling plasticity, neurogenesis and survival. By contrast, the gene networks coordinated by CREB in astrocytes are unknown despite the fact that the astrocytic CREB is also activity-driven and neuroprotective. Herein we identified the transcriptional programs regulated by CREB in astrocytes as compared to neurons using, as study materials, transcriptome databases of astrocyte exposed to well-known activators of CREB-dependent transcription as well as publicly available transcriptomes of neuronal cultures. Functional CREB signatures were extracted from the transcriptomes using Gene Ontology, adult-brain gene lists generated by Translating Ribosome Affinity Purification (TRAP) and CREB-target gene repositories. We found minimal overlap between CREB signatures in astrocytes and neurons. In astrocytes, the top triad of functions regulated by CREB consists of 'Gene expression', 'Mitochondria', and 'Signalling', while in neurons it is 'Neurotransmission', 'Signalling' and 'Gene expression', the latter two being represented by different genes from those in astrocytes. The newly generated databases will provide a tool to explore novel means whereby CREB impinges on brain functions requiring adaptive, long-lasting changes by coordinating transcriptional cascades in astrocytes.
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Affiliation(s)
- Luis Pardo
- Institut de Neurociències and Unitat de Bioquímica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Luis Miguel Valor
- Unidad de Investigación, Hospital Universitario Puerta del Mar, Av. Ana de Viya 21, 11009, Cádiz, Spain
| | - Abel Eraso-Pichot
- Institut de Neurociències and Unitat de Bioquímica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández/Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Arantxa Golbano
- Institut de Neurociències and Unitat de Bioquímica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Giles E Hardingham
- UK Dementia Research Institute at The University of Edinburgh, Edinburgh Medical School, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.,Deanery of Biomedical Sciences, Edinburgh Medical School, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Roser Masgrau
- Institut de Neurociències and Unitat de Bioquímica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Elena Galea
- Institut de Neurociències and Unitat de Bioquímica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. .,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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152
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Lösing P, Niturad CE, Harrer M, Reckendorf CMZ, Schatz T, Sinske D, Lerche H, Maljevic S, Knöll B. SRF modulates seizure occurrence, activity induced gene transcription and hippocampal circuit reorganization in the mouse pilocarpine epilepsy model. Mol Brain 2017; 10:30. [PMID: 28716058 PMCID: PMC5513048 DOI: 10.1186/s13041-017-0310-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/28/2017] [Indexed: 11/10/2022] Open
Abstract
A hallmark of temporal lobe epilepsy (TLE) is hippocampal neuronal demise and aberrant mossy fiber sprouting. In addition, unrestrained neuronal activity in TLE patients induces gene expression including immediate early genes (IEGs) such as Fos and Egr1. We employed the mouse pilocarpine model to analyze the transcription factor (TF) serum response factor (SRF) in epileptogenesis, seizure induced histopathology and IEG induction. SRF is a neuronal activity regulated TF stimulating IEG expression as well as nerve fiber growth and guidance. Adult conditional SRF deficient mice (SrfCaMKCreERT2) were more refractory to initial status epilepticus (SE) acquisition. Further, SRF deficient mice developed more spontaneous recurrent seizures (SRS). Genome-wide transcriptomic analysis uncovered a requirement of SRF for SE and SRS induced IEG induction (e.g. Fos, Egr1, Arc, Npas4, Btg2, Atf3). SRF was required for epilepsy associated neurodegeneration, mossy fiber sprouting and inflammation. We uncovered MAP kinase signaling as SRF target during epilepsy. Upon SRF ablation, seizure evoked induction of dual specific phosphatases (Dusp5 and Dusp6) was reduced. Lower expression of these negative ERK kinase regulators correlated with altered P-ERK levels in epileptic Srf mutant animals. Overall, this study uncovered an SRF contribution to several processes of epileptogenesis in the pilocarpine model.
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Affiliation(s)
- Pascal Lösing
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Cristina Elena Niturad
- Department of Neurology and Epileptology, Hertie-Institute of Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Merle Harrer
- Department of Neurology and Epileptology, Hertie-Institute of Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | | | - Theresa Schatz
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Daniela Sinske
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie-Institute of Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany
| | - Snezana Maljevic
- Department of Neurology and Epileptology, Hertie-Institute of Clinical Brain Research, University of Tübingen, Hoppe-Seyler-Straße 3, 72076, Tübingen, Germany.,Present address: The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville VIC, Melbourne, 3052, Australia
| | - Bernd Knöll
- Institute of Physiological Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
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153
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Kaur H, Carvalho J, Looso M, Singh P, Chennupati R, Preussner J, Günther S, Albarrán-Juárez J, Tischner D, Classen S, Offermanns S, Wettschureck N. Single-cell profiling reveals heterogeneity and functional patterning of GPCR expression in the vascular system. Nat Commun 2017. [PMID: 28621310 PMCID: PMC5481776 DOI: 10.1038/ncomms15700] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
G-protein-coupled receptor (GPCR) expression is extensively studied in bulk cDNA, but heterogeneity and functional patterning of GPCR expression in individual vascular cells is poorly understood. Here, we perform a microfluidic-based single-cell GPCR expression analysis in primary smooth muscle cells (SMC) and endothelial cells (EC). GPCR expression is highly heterogeneous in all cell types, which is confirmed in reporter mice, on the protein level and in human cells. Inflammatory activation in murine models of sepsis or atherosclerosis results in characteristic changes in the GPCR repertoire, and we identify functionally relevant subgroups of cells that are characterized by specific GPCR patterns. We further show that dedifferentiating SMC upregulate GPCRs such as Gpr39, Gprc5b, Gprc5c or Gpr124, and that selective targeting of Gprc5b modulates their differentiation state. Taken together, single-cell profiling identifies receptors expressed on pathologically relevant subpopulations and provides a basis for the development of new therapeutic strategies in vascular diseases. GPCRs are key regulators of vascular functions. By analysing single-cell GPCRs expression in vascular smooth muscle and endothelial cells from healthy and diseased murine vessels, Kaur et al. show that GPCR expression is highly heterogeneous in all cell types and that disease causes GPCR repertoire changes depending on cell type and vascular localization.
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Affiliation(s)
- H Kaur
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - J Carvalho
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - M Looso
- ECCPS Bioinformatics Facility, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - P Singh
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - R Chennupati
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - J Preussner
- ECCPS Bioinformatics Facility, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - S Günther
- ECCPS Deep sequencing platform, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - J Albarrán-Juárez
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - D Tischner
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany
| | - S Classen
- Harvey Vascular Centre, Kerckhoff-Klinik, Benekestraße 2-8, 61231 Bad Nauheim, Germany
| | - S Offermanns
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany.,Medical Faculty, J.W. Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - N Wettschureck
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany.,Medical Faculty, J.W. Goethe University, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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154
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Rozman JZ, Pohar Perme M, Jez M, Malicev E, Krasna M, Vrtovec B, Rozman P. DNA Methylation and Hydroxymethylation Profile of CD34 +-Enriched Cell Products Intended for Autologous CD34 + Cell Transplantation. DNA Cell Biol 2017; 36:737-746. [PMID: 28613929 DOI: 10.1089/dna.2017.3729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Epigenetic dysregulation has been shown to limit functional capacity of aging hematopoietic stem cells, which may contribute to impaired outcome of hematopoietic stem cell-based therapies. The aim of our study was to gain better insight into the epigenetic profile of CD34+-enriched cell products intended for autologous CD34+ cell transplantation in patients with cardiomyopathy. We found global DNA methylation content significantly higher in immunoselected CD34+ cells compared to leukocytes in leukapheresis products (2.33 ± 1.03% vs. 1.84 ± 0.86%, p = 0.04). Global DNA hydroxymethylation content did not differ between CD34+ cells and leukocytes (p = 0.30). By measuring methylation levels of 94 stem cell transcription factors on a ready-to-use array, we identified 15 factors in which average promoter methylation was significantly different between leukocytes and CD34+ cells. The difference was highest for HOXC12 (58.18 ± 6.47% vs. 13.34 ± 24.18%, p = 0.0009) and NR2F2 (51.65 ± 25.89% vs. 7.66 ± 21.43%, p = 0.0045) genes. Our findings suggest that global DNA methylation and hydroxymethylation patterns as well as target methylation profile of selected genes in CD34+-enriched cell products do not differ significantly compared to leukapheresis products and, thus, can tell us little about the functional capacity and regenerative properties of CD34+ cells. Future studies should examine other CD34+ cell graft characteristics, which may serve as prognostic tools for autologous CD34+ cell transplantation.
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Affiliation(s)
| | - Maja Pohar Perme
- 2 Institute for Biostatistics and Medical Informatics , Faculty of Medicine Ljubljana, Ljubljana, Slovenia
| | - Mojca Jez
- 1 Blood Transfusion Centre of Slovenia , Ljubljana, Slovenia
| | - Elvira Malicev
- 1 Blood Transfusion Centre of Slovenia , Ljubljana, Slovenia
| | - Metka Krasna
- 1 Blood Transfusion Centre of Slovenia , Ljubljana, Slovenia
| | - Bojan Vrtovec
- 3 Advanced Heart Failure and Transplantation Center, University Medical Center Ljubljana , Ljubljana, Slovenia
- 4 Stanford Cardiovascular Institute, Stanford University School of Medicine , Stanford, California
| | - Primoz Rozman
- 1 Blood Transfusion Centre of Slovenia , Ljubljana, Slovenia
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155
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Gnesutta N, Kumimoto RW, Swain S, Chiara M, Siriwardana C, Horner DS, Holt BF, Mantovani R. CONSTANS Imparts DNA Sequence Specificity to the Histone Fold NF-YB/NF-YC Dimer. THE PLANT CELL 2017; 29:1516-1532. [PMID: 28526714 PMCID: PMC5502446 DOI: 10.1105/tpc.16.00864] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 04/07/2017] [Accepted: 05/18/2017] [Indexed: 05/19/2023]
Abstract
Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. We term this complex NF-CO. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA. In summary, a unifying molecular mechanism of CO function relates it to the NF-YA paradigm, as part of a trimeric complex imparting sequence specificity to HFD/DNA interactions. It is likely that members of the large CCT family participate in similar complexes with At-NF-YB and At-NF-YC, broadening HFD combinatorial possibilities in terms of trimerization, DNA binding specificities, and transcriptional regulation.
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Affiliation(s)
- Nerina Gnesutta
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Roderick W Kumimoto
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Swadhin Swain
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Chamindika Siriwardana
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - David S Horner
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133, Milano, Italy
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156
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He S, Chen J, Zhang Y, Zhang M, Yang X, Li Y, Sun H, Lin L, Fan K, Liang L, Feng C, Wang F, Zhang X, Guo Y, Pei D, Zheng H. Sequential EMT-MET induces neuronal conversion through Sox2. Cell Discov 2017; 3:17017. [PMID: 28580167 PMCID: PMC5450022 DOI: 10.1038/celldisc.2017.17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/26/2017] [Indexed: 12/20/2022] Open
Abstract
Direct neuronal conversion can be achieved with combinations of small-molecule compounds and growth factors. Here, by studying the first or induction phase of the neuronal conversion induced by defined 5C medium, we show that the Sox2-mediated switch from early epithelial-mesenchymal transition (EMT) to late mesenchymal-epithelial transition (MET) within a high proliferation context is essential and sufficient for the conversion from mouse embryonic fibroblasts (MEFs) to TuJ+ cells. At the early stage, insulin and basic fibroblast growth factor (bFGF)-induced cell proliferation, early EMT, the up-regulation of Stat3 and Sox2, and the subsequent activation of neuron projection. Up-regulated Sox2 then induced MET and directed cells towards a neuronal fate at the late stage. Inhibiting either stage of this sequential EMT-MET impaired the conversion. In addition, Sox2 could replace sequential EMT-MET to induce a similar conversion within a high proliferation context, and its functions were confirmed with other neuronal conversion protocols and MEFs reprogramming. Therefore, the critical roles of the sequential EMT-MET were implicated in direct cell fate conversion in addition to reprogramming, embryonic development and cancer progression.
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Affiliation(s)
- Songwei He
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Jinlong Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Yixin Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Mengdan Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiao Yang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Yuan Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Hao Sun
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Lilong Lin
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Ke Fan
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Lining Liang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Chengqian Feng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Fuhui Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Xiao Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Yiping Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Duanqing Pei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
| | - Hui Zheng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou, China
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157
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Donati G, Rognoni E, Hiratsuka T, Liakath-Ali K, Hoste E, Kar G, Kayikci M, Russell R, Kretzschmar K, Mulder KW, Teichmann SA, Watt FM. Wounding induces dedifferentiation of epidermal Gata6 + cells and acquisition of stem cell properties. Nat Cell Biol 2017; 19:603-613. [PMID: 28504705 DOI: 10.1038/ncb3532] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 04/18/2017] [Indexed: 02/08/2023]
Abstract
The epidermis is maintained by multiple stem cell populations whose progeny differentiate along diverse, and spatially distinct, lineages. Here we show that the transcription factor Gata6 controls the identity of the previously uncharacterized sebaceous duct (SD) lineage and identify the Gata6 downstream transcription factor network that specifies a lineage switch between sebocytes and SD cells. During wound healing differentiated Gata6+ cells migrate from the SD into the interfollicular epidermis and dedifferentiate, acquiring the ability to undergo long-term self-renewal and differentiate into a much wider range of epidermal lineages than in undamaged tissue. Our data not only demonstrate that the structural and functional complexity of the junctional zone is regulated by Gata6, but also reveal that dedifferentiation is a previously unrecognized property of post-mitotic, terminally differentiated cells that have lost contact with the basement membrane. This resolves the long-standing debate about the contribution of terminally differentiated cells to epidermal wound repair.
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Affiliation(s)
- Giacomo Donati
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK.,Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK.,Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Turin, Italy
| | - Emanuel Rognoni
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Toru Hiratsuka
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Kifayathullah Liakath-Ali
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Esther Hoste
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK.,VIB Center for Inflammation Research, Department of Biomedical Molecular Biology (Ghent University), B-9052 Ghent, Belgium
| | - Gozde Kar
- European Bioinformatics Institute and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Melis Kayikci
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Roslin Russell
- Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK
| | - Kai Kretzschmar
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK.,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, UK.,Hubrecht Institute, KNAW and UMC Utrecht, 3584CT Utrecht, The Netherlands
| | - Klaas W Mulder
- Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK.,Radboud Institute for Molecular Life Sciences, Department of Molecular Developmental Biology, Radboud University, Nijmegen, The Netherlands
| | - Sarah A Teichmann
- European Bioinformatics Institute and Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK
| | - Fiona M Watt
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
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158
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Arifuzzaman S, Das A, Kim SH, Yoon T, Lee YS, Jung KH, Chai YG. Selective inhibition of EZH2 by a small molecule inhibitor regulates microglial gene expression essential for inflammation. Biochem Pharmacol 2017; 137:61-80. [PMID: 28431938 DOI: 10.1016/j.bcp.2017.04.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/13/2017] [Indexed: 12/15/2022]
Abstract
Multiple studies have documented that Enhancer of zeste homolog 2 (EZH2) could play a role in inflammation and a wide range of malignancies; however, the underlying mechanisms remain largely unaddressed. Microglial activation is a key process in the production and release of numerous pro-inflammatory mediators that play important roles in inflammation and neurodegeneration in the central nervous system (CNS). Therefore, our aim was to investigate whether inhibition of EZH2 with the selective small molecule inhibitor EPZ-6438 protects against neonatal microglial activation. First, in mouse primary microglial cells and a microglial cell line, we found that LPS can rapidly increase EZH2 mRNA level and we subsequently performed gene expression profiling and constructed networks in resting, EPZ-6438-treated, LPS-treated and LPS+EPZ-6438-treated primary microglial cells and a microglial cell line using transcriptome RNA sequencing and bioinformatics analyses. By examining the RNA sequencing, we identified EPZ-6438 target genes and co-regulated modules that were critical for inflammation. We also identified unexpected relationships between the inducible transcription factors (TFs), motif strength, and the transcription of key inflammatory mediators. Furthermore, we showed that EPZ-6438 controls important inflammatory gene targets by modulating interferon regulatory factor (IRF) 1, IRF8, and signal transducer and activator of transcription (STAT) 1 levels at their promoter sites. Our unprecedented findings demonstrate that pharmacological interventions built upon EZH2 inhibition by EPZ-6438 could be a useful therapeutic approach for the treatment of neuroinflammatory diseases associated with microglial activation.
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Affiliation(s)
- Sarder Arifuzzaman
- Department of Bionanotechnology, Hanyang University, Seoul 04673, Republic of Korea.
| | - Amitabh Das
- Institute of Natural Science & Technology, Hanyang University, Ansan 15588, Republic of Korea.
| | - Sun Hwa Kim
- Department of Molecular & Life Sciences, Hanyang University, Ansan 15588, Republic of Korea.
| | - Taeho Yoon
- Department of Molecular & Life Sciences, Hanyang University, Ansan 15588, Republic of Korea.
| | - Young Seek Lee
- Department of Molecular & Life Sciences, Hanyang University, Ansan 15588, Republic of Korea.
| | - Kyoung Hwa Jung
- Institute of Natural Science & Technology, Hanyang University, Ansan 15588, Republic of Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul 04673, Republic of Korea; Department of Molecular & Life Sciences, Hanyang University, Ansan 15588, Republic of Korea.
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159
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Das A, Arifuzzaman S, Kim SH, Lee YS, Jung KH, Chai YG. FTY720 (fingolimod) regulates key target genes essential for inflammation in microglial cells as defined by high-resolution mRNA sequencing. Neuropharmacology 2017; 119:1-14. [PMID: 28373076 DOI: 10.1016/j.neuropharm.2017.03.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 12/23/2022]
Abstract
Although microglial cells have an essential role in the host defense of the brain, the abnormal activation of microglia can lead to devastating outcomes, such as neuroinflammation and neurodegeneration. Emerging evidence indicates that FTY720 (fingolimod), an FDA-approved drug, has beneficial effects on brain cells in the central nervous system (CNS) and, more recently, immunosuppressive activities in microglia via modulation of the sphingosine 1 phosphate (S1P) 1 receptor. However, the exact molecular aspects of FTY720 contribution in microglia remain largely unaddressed. To understand the molecular mechanisms underlying the roles of FTY720 in microglia, we performed gene expression profiling in resting, FTY720, LPS and LPS + FTY720 challenged primary microglial (PM) cells isolated from 3-day-old ICR mice, and we identified FTY720 target genes and co-regulated modules that were critical in inflammation. By examining RNA sequencing and binding motif datasets from FTY720 suppressed LPS-induced inflammatory mediators, we also identified unexpected relationships between the inducible transcription factors (TFs), motif strength, and the transcription of key inflammatory mediators. Furthermore, we showed that FTY720 controls important inflammatory genes targets by modulating STAT1 and IRF8 levels at their promoter site. Our unprecedented findings demonstrate that FTY720 could be a useful therapeutic application for neuroinflammatory diseases associated with microglia activation, as well as provide a rich resource and framework for future analyses of FTY720 effects on microglia interaction.
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Affiliation(s)
- Amitabh Das
- Institute of Natural Science & Technology, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Sarder Arifuzzaman
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea.
| | - Sun Hwa Kim
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Young Seek Lee
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Kyoung Hwa Jung
- Institute of Natural Science & Technology, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea; Department of Molecular & Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea.
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160
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Paci P, Colombo T, Fiscon G, Gurtner A, Pavesi G, Farina L. SWIM: a computational tool to unveiling crucial nodes in complex biological networks. Sci Rep 2017; 7:44797. [PMID: 28317894 PMCID: PMC5357943 DOI: 10.1038/srep44797] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/14/2017] [Indexed: 12/14/2022] Open
Abstract
SWItchMiner (SWIM) is a wizard-like software implementation of a procedure, previously described, able to extract information contained in complex networks. Specifically, SWIM allows unearthing the existence of a new class of hubs, called “fight-club hubs”, characterized by a marked negative correlation with their first nearest neighbors. Among them, a special subset of genes, called “switch genes”, appears to be characterized by an unusual pattern of intra- and inter-module connections that confers them a crucial topological role, interestingly mirrored by the evidence of their clinic-biological relevance. Here, we applied SWIM to a large panel of cancer datasets from The Cancer Genome Atlas, in order to highlight switch genes that could be critically associated with the drastic changes in the physiological state of cells or tissues induced by the cancer development. We discovered that switch genes are found in all cancers we studied and they encompass protein coding genes and non-coding RNAs, recovering many known key cancer players but also many new potential biomarkers not yet characterized in cancer context. Furthermore, SWIM is amenable to detect switch genes in different organisms and cell conditions, with the potential to uncover important players in biologically relevant scenarios, including but not limited to human cancer.
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Affiliation(s)
- Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.,SysBio Centre for Systems Biology, Rome, 00185, Italy
| | - Teresa Colombo
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Aymone Gurtner
- Department of Research, Advanced Diagnostics, and Technological Innovation, Translational Research Area, Regina Elena National Cancer Institute, Rome, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, "Sapienza" University, Rome, Italy
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161
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Davegårdh C, Broholm C, Perfilyev A, Henriksen T, García-Calzón S, Peijs L, Hansen NS, Volkov P, Kjøbsted R, Wojtaszewski JFP, Pedersen M, Pedersen BK, Ballak DB, Dinarello CA, Heinhuis B, Joosten LAB, Nilsson E, Vaag A, Scheele C, Ling C. Abnormal epigenetic changes during differentiation of human skeletal muscle stem cells from obese subjects. BMC Med 2017; 15:39. [PMID: 28222718 PMCID: PMC5320752 DOI: 10.1186/s12916-017-0792-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/11/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human skeletal muscle stem cells are important for muscle regeneration. However, the combined genome-wide DNA methylation and expression changes taking place during adult myogenesis have not been described in detail and novel myogenic factors may be discovered. Additionally, obesity is associated with low relative muscle mass and diminished metabolism. Epigenetic alterations taking place during myogenesis might contribute to these defects. METHODS We used Infinium HumanMethylation450 BeadChip Kit (Illumina) and HumanHT-12 Expression BeadChip (Illumina) to analyze genome-wide DNA methylation and transcription before versus after differentiation of primary human myoblasts from 14 non-obese and 14 obese individuals. Functional follow-up experiments were performed using siRNA mediated gene silencing in primary human myoblasts and a transgenic mouse model. RESULTS We observed genome-wide changes in DNA methylation and expression patterns during differentiation of primary human muscle stem cells (myoblasts). We identified epigenetic and transcriptional changes of myogenic transcription factors (MYOD1, MYOG, MYF5, MYF6, PAX7, MEF2A, MEF2C, and MEF2D), cell cycle regulators, metabolic enzymes and genes previously not linked to myogenesis, including IL32, metallothioneins, and pregnancy-specific beta-1-glycoproteins. Functional studies demonstrated IL-32 as a novel target that regulates human myogenesis, insulin sensitivity and ATP levels in muscle cells. Furthermore, IL32 transgenic mice had reduced insulin response and muscle weight. Remarkably, approximately 3.7 times more methylation changes (147,161 versus 39,572) were observed during differentiation of myoblasts from obese versus non-obese subjects. In accordance, DNMT1 expression increased during myogenesis only in obese subjects. Interestingly, numerous genes implicated in metabolic diseases and epigenetic regulation showed differential methylation and expression during differentiation only in obese subjects. CONCLUSIONS Our study identifies IL-32 as a novel myogenic regulator, provides a comprehensive map of the dynamic epigenome during differentiation of human muscle stem cells and reveals abnormal epigenetic changes in obesity.
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Affiliation(s)
- Cajsa Davegårdh
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Christa Broholm
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark
| | - Alexander Perfilyev
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Tora Henriksen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Sonia García-Calzón
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Lone Peijs
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Petr Volkov
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Rasmus Kjøbsted
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Jørgen F P Wojtaszewski
- Department of Exercise and Sports Sciences, Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bente Klarlund Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Dov B Ballak
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, 80309, USA.,Department of Medicine, University of Colorado, Aurora, CO, 80045, USA
| | - Charles A Dinarello
- Department of Medicine, University of Colorado, Aurora, CO, 80045, USA.,Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Bas Heinhuis
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Emma Nilsson
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, 2100, Denmark.,Early Clinical Development, Translational Medical Unit, AstraZeneca, Mölndal, 431 83, Sweden
| | - Camilla Scheele
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Malmö, 205 02, Sweden.
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162
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Baranwal VK, Khurana P. Major intrinsic proteins repertoire of Morus notabilis and their expression profiles in different species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2017; 111:304-317. [PMID: 27988481 DOI: 10.1016/j.plaphy.2016.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 10/27/2016] [Accepted: 12/02/2016] [Indexed: 06/06/2023]
Abstract
Leaf moisture content in Morus is a significant trait regulating the yield of silk production. Studies have shown that fresh leaves or leaves with high water content are preferably eaten by silk worm. Water and certain other molecules transport in plants is known to be regulated by aquaporins or Major Intrinsic Proteins (MIPs). Members of the MIP gene family have also been implicated in plant development and stress responsiveness. To understand how members of MIP gene family are regulated and evolved, we carried out an extensive analysis of the gene family. We identified a total of 36 non redundant MIPs in Morus notabilis genome, belonging to five subfamilies PIPs, TIPs, NIPs, XIPs and SIPs) have been identified. We performed a Gene ontology (GO) term enrichment analysis and looked at distribution of cis elements in their 2K upstream regulatory region to reveal their putative roles in various stresses and developmental aspects. Expression analysis in developmental stages revealed their tissue preferential expression pattern in diverse vegetative and reproductive tissues. Comparison of expression profiles in the leaves of three species including Morus notabilis, Morus serrata and Morus laevigata led to identification of differential expression in these species. In all, this study elaborates a basic insight into the structure, function and evolutionary analysis of MIP gene family in Morus which is hitherto unavailable. Our analysis will provide a ready reference to the mulberry research community involved in the Morus improvement program.
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Affiliation(s)
- Vinay Kumar Baranwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India.
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163
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Wouters J, Kalender Atak Z, Aerts S. Decoding transcriptional states in cancer. Curr Opin Genet Dev 2017; 43:82-92. [PMID: 28129557 DOI: 10.1016/j.gde.2017.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 12/27/2022]
Abstract
Gene regulatory networks determine cellular identity. In cancer, aberrations of gene networks are caused by driver mutations that often affect transcription factors and chromatin modifiers. Nevertheless, gene transcription in cancer follows the same cis-regulatory rules as normal cells, and cancer cells have served as convenient model systems to study transcriptional regulation. Tumours often show regulatory heterogeneity, with subpopulations of cells in different transcriptional states, which has important therapeutic implications. Here, we review recent experimental and computational techniques to reverse engineer cancer gene networks using transcriptome and epigenome data. New algorithms, data integration strategies, and increasing amounts of single cell genomics data provide exciting opportunities to model dynamic regulatory states at unprecedented resolution.
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Affiliation(s)
- Jasper Wouters
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium
| | - Zeynep Kalender Atak
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for Brain & Disease Research, Leuven, Belgium; Department of Human Genetics, KU Leuven (University of Leuven), Leuven, Belgium.
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164
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Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic-Specific Genes. PLoS Genet 2017; 13:e1006541. [PMID: 28068333 PMCID: PMC5261807 DOI: 10.1371/journal.pgen.1006541] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 01/24/2017] [Accepted: 12/15/2016] [Indexed: 11/19/2022] Open
Abstract
Bromodomain and Extra-terminal motif (BET) proteins play a central role in transcription regulation and chromatin signalling pathways. They are present in unicellular eukaryotes and in this study, the role of the BET protein Bdf1 has been explored in Saccharomyces cerevisiae. Mutation of Bdf1 bromodomains revealed defects on both the formation of spores and the meiotic progression, blocking cells at the exit from prophase, before the first meiotic division. This phenotype is associated with a massive deregulation of the transcription of meiotic genes and Bdf1 bromodomains are required for appropriate expression of the key meiotic transcription factor NDT80 and almost all the Ndt80-inducible genes, including APC complex components. Bdf1 notably accumulates on the promoter of Ndt80 and its recruitment is dependent on Bdf1 bromodomains. In addition, the ectopic expression of NDT80 during meiosis partially bypasses this dependency. Finally, purification of Bdf1 partners identified two independent complexes with Bdf2 or the SWR complex, neither of which was required to complete sporulation. Taken together, our results unveil a new role for Bdf1 –working independently from its predominant protein partners Bdf2 and the SWR1 complex–as a regulator of meiosis-specific genes. Chromatin modifying proteins play a central role in transcription regulation and chromatin signalling. In this study we investigated the functional role of the bromodomains of the chromatin protein Bdf1 during yeast gametogenesis. Our results show that the bromodomains of Bdf1 are essential for meiotic progression and the formation of mature spores. Bdf1 bromodomains are required for the expression of key meiotic genes and the master regulator NDT80. Forced expression of NDT80 can partially rescue the formation of spores when Bdf1 bromodomains are mutated. The results presented here indicate that Bdf1 forms two exclusive complexes, with Bdf2 or with the SWR complex. However, none of these complexes are required for sporulation progression. To conclude, our findings suggest that Bdf1 is a new regulator of the meiotic transcription program and of the expression of the master regulator NDT80.
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165
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DNA methylation patterns associated with oxidative stress in an ageing population. BMC Med Genomics 2016; 9:72. [PMID: 27884142 PMCID: PMC5123374 DOI: 10.1186/s12920-016-0235-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 11/14/2016] [Indexed: 02/06/2023] Open
Abstract
Background Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease. Methods To investigate the role of epigenetic variation in oxidative stress marker levels and subsequent development of CVD and T2D, we performed analyses of genome-wide DNA methylation in blood, ten markers of oxidative stress (total glutathione [TGSH], reduced glutathione [GSH], oxidised glutathione [GSSG], GSSG to GSH ratio, homocysteine [HCY], oxidised low-density lipoprotein (oxLDL), antibodies against oxLDL [OLAB], conjugated dienes [CD], baseline conjugated dienes [BCD]-LDL and total antioxidant capacity [TAOC]) and incident disease in up to 966 age-matched individuals. Results In total, we found 66 cytosine-guanine (CpG) sites associated with one or more oxidative stress markers (false discovery rate [FDR] <0.05). These sites were enriched in regulatory regions of the genome. Genes annotated to CpG sites showed enrichment in annotation clusters relating to phospho-metabolism and proteins with pleckstrin domains. We investigated the contribution of oxidative stress-associated CpGs to development of cardiometabolic disease. Methylation variation at CpGs in the 3'-UTR of HIST1H4D (cg08170869; histone cluster 1, H4d) and in the body of DVL1 (cg03465880; dishevelled-1) were associated with incident T2D events during 10 years of follow-up (all permutation p-values <0.01), indicating a role of epigenetic regulation in oxidative stress processes leading to development or progression of diabetes. Methylation QTL (meQTL) analysis showed significant associations with genetic sequence variants in cis at 28 (42%) of oxidative stress phenotype-associated sites (FDR < 0.05). Integrating cis-meQTLs with genotype-phenotype associations indicated that genetic effects on oxidative stress phenotype at one locus (cg07547695; BCL2L11) may be mediated through DNA methylation. Conclusions In conclusion, we report novel associations of DNA methylation with oxidative stress, some of which also show evidence of a relation with T2D incidence. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0235-0) contains supplementary material, which is available to authorized users.
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166
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Srinivasan N, Gordon O, Ahrens S, Franz A, Deddouche S, Chakravarty P, Phillips D, Yunus AA, Rosen MK, Valente RS, Teixeira L, Thompson B, Dionne MS, Wood W, Reis e Sousa C. Actin is an evolutionarily-conserved damage-associated molecular pattern that signals tissue injury in Drosophila melanogaster. eLife 2016; 5:e19662. [PMID: 27871362 PMCID: PMC5138034 DOI: 10.7554/elife.19662] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022] Open
Abstract
Damage-associated molecular patterns (DAMPs) are molecules released by dead cells that trigger sterile inflammation and, in vertebrates, adaptive immunity. Actin is a DAMP detected in mammals by the receptor, DNGR-1, expressed by dendritic cells (DCs). DNGR-1 is phosphorylated by Src-family kinases and recruits the tyrosine kinase Syk to promote DC cross-presentation of dead cell-associated antigens. Here we report that actin is also a DAMP in invertebrates that lack DCs and adaptive immunity. Administration of actin to Drosophila melanogaster triggers a response characterised by selective induction of STAT target genes in the fat body through the cytokine Upd3 and its JAK/STAT-coupled receptor, Domeless. Notably, this response requires signalling via Shark, the Drosophila orthologue of Syk, and Src42A, a Drosophila Src-family kinase, and is dependent on Nox activity. Thus, extracellular actin detection via a Src-family kinase-dependent cascade is an ancient means of detecting cell injury that precedes the evolution of adaptive immunity.
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Affiliation(s)
- Naren Srinivasan
- Immunobiology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Oliver Gordon
- Immunobiology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Susan Ahrens
- Immunobiology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Anna Franz
- Department of Biochemistry, Biomedical Sciences, University Walk, University of Bristol, Bristol, United Kingdom
| | - Safia Deddouche
- Immunobiology Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - David Phillips
- Genomics-Equipment Park, The Francis Crick Institute, London, United Kingdom
| | - Ali A Yunus
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael K Rosen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | | | | | - Barry Thompson
- Epithelial Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Marc S Dionne
- Department of Life Sciences and MRC Centre for Molecular Bacteriology and Infection, South Kensington Campus, Imperial College London, London, United Kingdom
| | - Will Wood
- Department of Cellular and Molecular Medicine, Biomedical Sciences, University of Bristol, Bristol, United Kingdom
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167
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Yalamanchili N, Kriete A, Alfego D, Danowski KM, Kari C, Rodeck U. Distinct Cell Stress Responses Induced by ATP Restriction in Quiescent Human Fibroblasts. Front Genet 2016; 7:171. [PMID: 27757122 PMCID: PMC5047886 DOI: 10.3389/fgene.2016.00171] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/09/2016] [Indexed: 12/22/2022] Open
Abstract
Quiescence is the prevailing state of many cell types under homeostatic conditions. Yet, surprisingly little is known about how quiescent cells respond to energetic and metabolic challenges. To better understand compensatory responses of quiescent cells to metabolic stress, we established, in human primary dermal fibroblasts, an experimental ‘energy restriction’ model. Quiescence was achieved by short-term culture in serum-deprived media and ATP supply restricted using a combination of glucose transport inhibitors and mitochondrial uncouplers. In aggregate, these measures led to markedly reduced intracellular ATP levels while not compromising cell viability over the observation period of 48 h. Analysis of the transcription factor (TF) landscape induced by this treatment revealed alterations in several signal transduction nodes beyond the expected biosynthetic adaptations. These included increased abundance of NF-κB regulated TFs and altered TF subsets regulated by Akt and p53. The observed changes in gene regulation and corresponding alterations in key signaling nodes are likely to contribute to cell survival at intracellular ATP concentrations substantially below those achieved by growth factor deprivation alone. This experimental model provides a benchmark for the investigation of cell survival pathways and related molecular targets that are associated with restricted energy supply associated with biological aging and metabolic diseases.
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Affiliation(s)
- Nirupama Yalamanchili
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia PA, USA
| | - Andres Kriete
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia PA, USA
| | - David Alfego
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia PA, USA
| | - Kelli M Danowski
- Department of Dermatology, St. Joseph Mercy Health System, Michigan State University, East Lansing MI, USA
| | - Csaba Kari
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia PA, USA
| | - Ulrich Rodeck
- Department of Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia PA, USA
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168
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Liu T, Longhurst AD, Talavera-Rauh F, Hokin SA, Barton MK. The Arabidopsis transcription factor ABIG1 relays ABA signaled growth inhibition and drought induced senescence. eLife 2016; 5:e13768. [PMID: 27697148 PMCID: PMC5050019 DOI: 10.7554/elife.13768] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Accepted: 08/31/2016] [Indexed: 01/04/2023] Open
Abstract
Drought inhibits plant growth and can also induce premature senescence. Here we identify a transcription factor, ABA INSENSITIVE GROWTH 1 (ABIG1) required for abscisic acid (ABA) mediated growth inhibition, but not for stomatal closure. ABIG1 mRNA levels are increased both in response to drought and in response to ABA treatment. When treated with ABA, abig1 mutants remain greener and produce more leaves than comparable wild-type plants. When challenged with drought, abig1 mutants have fewer yellow, senesced leaves than wild-type. Induction of ABIG1 transcription mimics ABA treatment and regulates a set of genes implicated in stress responses. We propose a model in which drought acts through ABA to increase ABIG1 transcription which in turn restricts new shoot growth and promotes leaf senescence. The results have implications for plant breeding: the existence of a mutant that is both ABA resistant and drought resistant points to new strategies for isolating drought resistant genetic varieties.
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Affiliation(s)
- Tie Liu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Adam D Longhurst
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Samuel A Hokin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - M Kathryn Barton
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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169
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Jammula S, Pasini D. EpiMINE, a computational program for mining epigenomic data. Epigenetics Chromatin 2016; 9:42. [PMID: 27708717 PMCID: PMC5043526 DOI: 10.1186/s13072-016-0095-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/20/2016] [Indexed: 11/10/2022] Open
Abstract
Background In epigenetic research, both the increasing ease of high-throughput sequencing and a greater interest in genome-wide studies have resulted in an exponential flooding of epigenetic-related data in public domain. This creates an opportunity for exploring data outside the limits of any specific query-centred study. Such data have to undergo standard primary analyses that are accessible with multiple well-stabilized programs. Further downstream analyses, such as genome-wide comparative, correlative and quantitative analyses, are critical in deciphering key biological features. However, these analyses are only accessible for computational researchers and completely lack platforms capable of handling, analysing and linking multiple interdisciplinary datasets with efficient analytical methods. Results Here, we present EpiMINE, a program for mining epigenomic data. It is a user-friendly, stand-alone computational program designed to support multiple datasets, for performing genome-wide correlative and quantitative analysis of ChIP-seq and RNA-seq data. Using data available from the ENCODE project, we illustrated several features of EpiMINE through different biological scenarios to show how easy some known observations can be verified. These results highlight how these approaches can be helpful in identifying novel biological features. Conclusions EpiMINE performs different kinds of genome-wide quantitative and correlative analyses, using ChIP-seq- and RNA-seq-related datasets. Its framework enables it to be used by both experimental and computational researchers. EpiMINE can be downloaded from https://sourceforge.net/projects/epimine/. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0095-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- SriGanesh Jammula
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
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170
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Grinchuk OV, Motakis E, Yenamandra SP, Ow GS, Jenjaroenpun P, Tang Z, Yarmishyn AA, Ivshina AV, Kuznetsov VA. Sense-antisense gene-pairs in breast cancer and associated pathological pathways. Oncotarget 2016; 6:42197-221. [PMID: 26517092 PMCID: PMC4747219 DOI: 10.18632/oncotarget.6255] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 09/30/2015] [Indexed: 01/04/2023] Open
Abstract
More than 30% of human protein-coding genes form hereditary complex genome architectures composed of sense-antisense (SA) gene pairs (SAGPs) transcribing their RNAs from both strands of a given locus. Such architectures represent important novel components of genome complexity contributing to gene expression deregulation in cancer cells. Therefore, the architectures might be involved in cancer pathways and, in turn, be used for novel drug targets discovery. However, the global roles of SAGPs in cancer pathways has not been studied. Here we investigated SAGPs associated with breast cancer (BC)-related pathways using systems biology, prognostic survival and experimental methods. Gene expression analysis identified 73 BC-relevant SAGPs that are highly correlated in BC. Survival modelling and metadata analysis of the 1161 BC patients allowed us to develop a novel patient prognostic grouping method selecting the 12 survival-significant SAGPs. The qRT-PCR-validated 12-SAGP prognostic signature reproducibly stratified BC patients into low- and high-risk prognostic subgroups. The 1381 SAGP-defined differentially expressed genes common across three studied cohorts were identified. The functional enrichment analysis of these genes revealed the GABPA gene network, including BC-relevant SAGPs, specific gene sets involved in cell cycle, spliceosomal and proteasomal pathways. The co-regulatory function of GABPA in BC cells was supported using siRNA knockdown studies. Thus, we demonstrated SAGPs as the synergistically functional genome architectures interconnected with cancer-related pathways and associated with BC patient clinical outcomes. Taken together, SAGPs represent an important component of genome complexity which can be used to identify novel aspects of coordinated pathological gene networks in cancers.
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Affiliation(s)
- Oleg V Grinchuk
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Efthymios Motakis
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore.,Current address: RIKEN, Japan
| | - Surya Pavan Yenamandra
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Ghim Siong Ow
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Piroon Jenjaroenpun
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Zhiqun Tang
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Aliaksandr A Yarmishyn
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Anna V Ivshina
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Vladimir A Kuznetsov
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore.,School of Computing Engineering, Nanyang Technological University, Singapore
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171
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He JJ, Ma J, Elsheikha HM, Song HQ, Huang SY, Zhu XQ. Transcriptomic analysis of mouse liver reveals a potential hepato-enteric pathogenic mechanism in acute Toxoplasma gondii infection. Parasit Vectors 2016; 9:427. [PMID: 27488578 PMCID: PMC4973073 DOI: 10.1186/s13071-016-1716-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/20/2016] [Indexed: 12/12/2022] Open
Abstract
Background Toxoplasma gondii is a worldwide spread pathogen which can infect all tissues of its host. The transcriptomic responses of infected brain and spleen have been reported. However, our knowledge of the global transcriptomic change in infected liver is limited. Additionally, T. gondii infection represents a highly dynamic process involving complex biological responses of the host at many levels. Herein, we describe such processes at a global level by discovering gene expression changes in mouse livers after acute infection with T. gondii ToxoDB#9 strain. Results Global transcriptomic analysis identified 2,758 differentially expressed transcripts in infected liver, of which 1,356 were significantly downregulated and 1,402 upregulated. GO and KEGG database analyses showed that host immune responses were upregulated, while the metabolic-related processes/pathways were downregulated, especially xenobiotic metabolism, fatty acid metabolism, energy metabolism, and bile biosynthesis and secretion. The metabolism of more than 800 chemical compounds including anti-Toxoplasma prescribed medicines were predicted to be modulated during acute T. gondii infection due to the downregulation of enzymes involved in xenobiotic metabolism. Conclusions To the best of our knowledge, this is the first global transcriptomic analysis of mouse liver infected by T. gondii. The present data indicate that during the early stage of liver infection, T. gondii can induce changes in liver xenobiotic metabolism, upregulating inflammatory response and downregulating hepatocellular PPAR signaling pathway, altering host bile biosynthesis and secretion pathway; these changes could enhance host intestinal dysbacteriosis and thus contribute to the pathological changes of both liver and intestine of infected mice. These findings describe the biological changes in infected liver, providing a potential mechanistic pathway that links hepatic and intestinal pathologies to T. gondii infection. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1716-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun-Jun He
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Jun Ma
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China.,College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, 410128, People's Republic of China
| | - Hany M Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Hui-Qun Song
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China
| | - Si-Yang Huang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province, 225009, People's Republic of China.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, 730046, People's Republic of China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province, 225009, People's Republic of China.
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172
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Malusa F, Taranta M, Zaki N, Cinti C, Capobianco E. Time-course gene profiling and networks in demethylated retinoblastoma cell line. Oncotarget 2016; 6:23688-707. [PMID: 26143641 PMCID: PMC4695145 DOI: 10.18632/oncotarget.4644] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/31/2015] [Indexed: 02/06/2023] Open
Abstract
Retinoblastoma, a very aggressive cancer of the developing retina, initiatiates by the biallelic loss of RB1 gene, and progresses very quickly following RB1 inactivation. While its genome is stable, multiple pathways are deregulated, also epigenetically. After reviewing the main findings in relation with recently validated markers, we propose an integrative bioinformatics approach to include in the previous group new markers obtained from the analysis of a single cell line subject to epigenetic treatment. In particular, differentially expressed genes are identified from time course microarray experiments on the WERI-RB1 cell line treated with 5-Aza-2′-deoxycytidine (decitabine; DAC). By inducing demethylation of CpG island in promoter genes that are involved in biological processes, for instance apoptosis, we performed the following main integrative analysis steps: i) Gene expression profiling at 48h, 72h and 96h after DAC treatment; ii) Time differential gene co-expression networks and iii) Context-driven marker association (transcriptional factor regulated protein networks, master regulatory paths). The observed DAC-driven temporal profiles and regulatory connectivity patterns are obtained by the application of computational tools, with support from curated literature. It is worth emphasizing the capacity of networks to reconcile multi-type evidences, thus generating testable hypotheses made available by systems scale predictive inference power. Despite our small experimental setting, we propose through such integrations valuable impacts of epigenetic treatment in terms of gene expression measurements, and then validate evidenced apoptotic effects.
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Affiliation(s)
- Federico Malusa
- Laboratory of Integrative Systems Medicine (LISM), Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Monia Taranta
- Experimental Oncology Unit, Institute of Clinical Physiology, CNR, Siena, Italy
| | - Nazar Zaki
- College of Information Technology (CIT), United Arab Emirates University (UAEU), Al Ain, UAE
| | - Caterina Cinti
- Experimental Oncology Unit, Institute of Clinical Physiology, CNR, Siena, Italy
| | - Enrico Capobianco
- Laboratory of Integrative Systems Medicine (LISM), Institute of Clinical Physiology, CNR, Pisa, Italy.,Center for Computational Science (CCS), University of Miami, Miami, FL, USA
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173
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Lysine-specific histone demethylase 1 inhibition promotes reprogramming by facilitating the expression of exogenous transcriptional factors and metabolic switch. Sci Rep 2016; 6:30903. [PMID: 27481483 PMCID: PMC4969595 DOI: 10.1038/srep30903] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/08/2016] [Indexed: 01/04/2023] Open
Abstract
Lysine-specific histone demethylase 1 (LSD1) regulates histone methylation and influences the epigenetic state of cells during the generation of induced pluripotent stem cells (iPSCs). Here we reported that LSD1 inhibition via shRNA or specific inhibitor, tranylcypromine, promoted reprogramming at early stage via two mechanisms. At early stage of reprogramming, LSD1 inhibition increased the retrovirus-mediated exogenous expression of Oct4, Klf4, and Sox2 by blocking related H3K4 demethylation. Since LSD1 inhibition still promoted reprogramming even when iPSCs were induced with small-molecule compounds in a virus-free system, additional mechanisms should be involved. When RNA-seq was used for analysis, it was found that LSD1 inhibition reversed some gene expression changes induced by OKS, which subsequently promoted reprogramming. For example, by partially rescuing the decreased expression of Hif1α, LSD1 inhibition reversed the up-regulation of genes in oxidative phosphorylation pathway and the down-regulation of genes in glycolysis pathway. Such effects facilitated the metabolic switch from oxidative phosphorylation to glycolysis and subsequently promoted iPSCs induction. In addition, LSD1 inhibition also promoted the conversion from pre-iPSCs to iPSCs by facilitating the similar metabolic switch. Therefore, LSD1 inhibition promotes reprogramming by facilitating the expression of exogenous transcriptional factors and metabolic switch.
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174
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Rai A, Umashankar S, Rai M, Kiat LB, Bing JAS, Swarup S. Coordinate Regulation of Metabolite Glycosylation and Stress Hormone Biosynthesis by TT8 in Arabidopsis. PLANT PHYSIOLOGY 2016; 171:2499-515. [PMID: 27432888 PMCID: PMC4972274 DOI: 10.1104/pp.16.00421] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/21/2016] [Indexed: 05/18/2023]
Abstract
Secondary metabolites play a key role in coordinating ecology and defense strategies of plants. Diversity of these metabolites arises by conjugation of core structures with diverse chemical moieties, such as sugars in glycosylation. Active pools of phytohormones, including those involved in plant stress response, are also regulated by glycosylation. While much is known about the enzymes involved in glycosylation, we know little about their regulation or coordination with other processes. We characterized the flavonoid pathway transcription factor TRANSPARENT TESTA8 (TT8) in Arabidopsis (Arabidopsis thaliana) using an integrative omics strategy. This approach provides a systems-level understanding of the cellular machinery that is used to generate metabolite diversity by glycosylation. Metabolomics analysis of TT8 loss-of-function and inducible overexpression lines showed that TT8 coordinates glycosylation of not only flavonoids, but also nucleotides, thus implicating TT8 in regulating pools of activated nucleotide sugars. Transcriptome and promoter network analyses revealed that the TT8 regulome included sugar transporters, proteins involved in sugar binding and sequestration, and a number of carbohydrate-active enzymes. Importantly, TT8 affects stress response, along with brassinosteroid and jasmonic acid biosynthesis, by directly binding to the promoters of key genes of these processes. This combined effect on metabolite glycosylation and stress hormones by TT8 inducible overexpression led to significant increase in tolerance toward multiple abiotic and biotic stresses. Conversely, loss of TT8 leads to increased sensitivity to these stresses. Thus, the transcription factor TT8 is an integrator of secondary metabolism and stress response. These findings provide novel approaches to improve broad-spectrum stress tolerance.
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Affiliation(s)
- Amit Rai
- Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.)
| | - Shivshankar Umashankar
- Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.)
| | - Megha Rai
- Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.)
| | - Lim Boon Kiat
- Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.)
| | - Johanan Aow Shao Bing
- Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.)
| | - Sanjay Swarup
- Metabolites Biology Lab, Department of Biological Sciences, National University of Singapore, Singapore 117543 (A.R., S.U., M.R., L.B.K., J.A.S.B., S.S.);Synthetic Biology Research Consortium (A.R., S.S.) and Singapore Centre for Environmental Life Science Engineering (S.U., S.S.), National University of Singapore, Singapore 117456;NUS Environmental Research Institute, National University of Singapore, Singapore 117411 (S.U., M.R., L.B.K., S.S.); andSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551 (S.S.)
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175
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Transcriptome sequencing wide functional analysis of human mesenchymal stem cells in response to TLR4 ligand. Sci Rep 2016; 6:30311. [PMID: 27444640 PMCID: PMC4957230 DOI: 10.1038/srep30311] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 06/30/2016] [Indexed: 12/13/2022] Open
Abstract
Due to their multipotentiality and immunomodulation, human mesenchymal stem cells (hMSCs) are widely studied for the treatment of degenerative and inflammatory diseases. Transplantation of hMSCs to damaged tissue is a promising approach for tissue regeneration. However, the physiological mechanisms and regulatory processes of MSC trafficking to injured tissue are largely unexplored. Here, we evaluated the gene expression profile and migratory potential of hMSCs upon stimulation with the TLR4 ligand lipopolysaccharide (LPS). Using RNA sequencing, we identified unique induction patterns of interferon stimulated genes, cytokines and chemokines involved in chemotaxis and homing. The −950 to +50 bp regions of many of these LPS-responsive genes were enriched with putative binding motifs for the transcription factors (TFs) interferon regulatory factor (IRF1) and nuclear factor kappa B (NF-κB1, REL), which were also induced by LPS along with other TFs. Chromatin immunoprecipitation assays showed that IRF1 bound within their target genes promoter region. In addition, IRF1 attenuation significantly down-regulated interferon stimulated genes as well as key cytokines. Furthermore, using pharmacological inhibitors, we showed that the NF-κB and phosphatidylinositol 3-kinase (PI3K) pathways regulate the migratory and cytokines/chemokines response to LPS. These unprecedented data suggest that IRF1 and NF-κB orchestrate the TLR4-primed immunomodulatory response of hMSCs and that this response also involves the PI3K pathway.
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176
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Das A, Kim SH, Arifuzzaman S, Yoon T, Chai JC, Lee YS, Park KS, Jung KH, Chai YG. Transcriptome sequencing reveals that LPS-triggered transcriptional responses in established microglia BV2 cell lines are poorly representative of primary microglia. J Neuroinflammation 2016; 13:182. [PMID: 27400875 PMCID: PMC4940985 DOI: 10.1186/s12974-016-0644-1] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 06/27/2016] [Indexed: 12/22/2022] Open
Abstract
Background Microglia are resident myeloid cells in the CNS that are activated by infection, neuronal injury, and inflammation. Established BV2 microglial cell lines have been the primary in vitro models used to study neuroinflammation for more than a decade because they reduce the requirement of continuously maintaining cell preparations and animal experimentation models. However, doubt has recently been raised regarding the value of BV2 cell lines as a model system. Methods We used triplicate RNA sequencing (RNA-seq) to investigate the molecular signature of primary and BV2 microglial cell lines using two transcriptomic techniques: global transcriptomic biological triplicate RNA-seq and quantitative real-time PCR. We analyzed differentially expressed genes (DEGs) to identify transcription factor (TF) motifs (−950 to +50 bp of the 5′ upstream promoters) and epigenetic mechanisms. Results Sequencing assessment and quality evaluation revealed that primary microglia have a distinct transcriptomic signature and express a unique cluster of transcripts in response to lipopolysaccharide. This microglial signature was not observed in BV2 microglial cell lines. Importantly, we observed that previously unidentified TFs (i.e., IRF2, IRF5, IRF8, STAT1, STAT2, and STAT5A) and the epigenetic regulators KDM1A, NSD3, and SETDB2 were significantly and selectively expressed in primary microglia (PM). Although transcriptomic alterations known to occur in BV2 microglial cell lines were identified in PM, we also observed several novel transcriptomic alterations in PM that are not frequently observed in BV2 microglial cell lines. Conclusions Collectively, these unprecedented findings demonstrate that established BV2 microglial cell lines are probably a poor representation of PM, and we establish a resource for future studies of neuroinflammation. Electronic supplementary material The online version of this article (doi:10.1186/s12974-016-0644-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amitabh Das
- Institute of Natural Science and Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Sun Hwa Kim
- Department of Molecular and Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea
| | - Sarder Arifuzzaman
- Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea
| | - Taeho Yoon
- Department of Molecular and Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea
| | - Jin Choul Chai
- Department of Molecular and Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea
| | - Young Seek Lee
- Department of Molecular and Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea
| | - Kyoung Sun Park
- Institute of Natural Science and Technology, Hanyang University, Ansan, 15588, Republic of Korea
| | - Kyoung Hwa Jung
- Institute of Natural Science and Technology, Hanyang University, Ansan, 15588, Republic of Korea.
| | - Young Gyu Chai
- Department of Molecular and Life Sciences, Hanyang University, Ansan, 15588, Republic of Korea. .,Department of Bionanotechnology, Hanyang University, Seoul, 04673, Republic of Korea.
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177
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Alamri AM, Kang K, Groeneveld S, Wang W, Zhong X, Kallakury B, Hennighausen L, Liu X, Furth PA. Primary cancer cell culture: mammary-optimized vs conditional reprogramming. Endocr Relat Cancer 2016; 23:535-54. [PMID: 27267121 PMCID: PMC4962879 DOI: 10.1530/erc-16-0071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/06/2016] [Indexed: 12/22/2022]
Abstract
The impact of different culture conditions on biology of primary cancer cells is not always addressed. Here, conditional reprogramming (CRC) was compared with mammary-optimized EpiCult-B (EpiC) for primary mammary epithelial cell isolation and propagation, allograft generation, and genome-wide transcriptional consequences using cancer and non-cancer mammary tissue from mice with different dosages of Brca1 and p53 Selective comparison to DMEM was included. Primary cultures were established with all three media, but CRC was most efficient for initial isolation (P<0.05). Allograft development was faster using cells grown in EpiC compared with CRC (P<0.05). Transcriptome comparison of paired CRC and EpiC cultures revealed 1700 differentially expressed genes by passage 20. CRC promoted Trp53 gene family upregulation and increased expression of epithelial differentiation genes, whereas EpiC elevated expression of epithelial-mesenchymal transition genes. Differences did not persist in allografts where both methods yielded allografts with relatively similar transcriptomes. Restricting passage (<7) reduced numbers of differentially expressed genes below 50. In conclusion, CRC was most efficient for initial cell isolation but EpiC was quicker for allograft generation. The extensive culture-specific gene expression patterns that emerged with longer passage could be limited by reducing passage number when both culture transcriptomes were equally similar to that of the primary tissue. Defining impact of culture condition and passage on the transcriptome of primary cells could assist experimental design and interpretation. For example, differences that appear with passage and culture condition are potentially exploitable for comparative studies targeting specific biological networks in different transcriptional environments.
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Affiliation(s)
- Ahmad M Alamri
- Department of OncologyLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA Department of Clinical Laboratory SciencesCollege of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Keunsoo Kang
- Laboratory of Genetics and PhysiologyNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, Maryland, USA Department of MicrobiologyDankook University, Cheonan, Republic of Korea
| | - Svenja Groeneveld
- Department of OncologyLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA Department PharmazieLudwig-Maximilians-Universität München, Munich, Germany
| | - Weisheng Wang
- Department of OncologyLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Xiaogang Zhong
- Department of BiostatisticsBioinformatics and Biomathematics, Georgetown University, Washington, District of Columbia, USA
| | - Bhaskar Kallakury
- Department of PathologyLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and PhysiologyNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, Maryland, USA
| | - Xuefeng Liu
- Department of PathologyLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
| | - Priscilla A Furth
- Department of OncologyLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA Department of MedicineLombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA
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178
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Ben-Shoshan SO, Kagan P, Sultan M, Barabash Z, Dor C, Jacob-Hirsch J, Harmelin A, Pappo O, Marcu-Malina V, Ben-Ari Z, Amariglio N, Rechavi G, Goldstein I, Safran M. ADAR1 deletion induces NFκB and interferon signaling dependent liver inflammation and fibrosis. RNA Biol 2016; 14:587-602. [PMID: 27362366 DOI: 10.1080/15476286.2016.1203501] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Adenosine deaminase acting on RNA (ADAR) 1 binds and edits double-stranded (ds) RNA secondary structures found mainly within untranslated regions of many transcripts. In the current research, our aim was to study the role of ADAR1 in liver homeostasis. As previous studies show a conserved immunoregulatory function for ADAR1 in mammalians, we focused on its role in preventing chronic hepatic inflammation and the associated activation of hepatic stellate cells to produce extracellular matrix and promote fibrosis. We show that hepatocytes specific ADAR1 knock out (KO) mice display massive liver damage with multifocal inflammation and fibrogenesis. The bioinformatics analysis of the microarray gene-expression datasets of ADAR1 KO livers reveled a type-I interferons signature and an enrichment for immune response genes compared to control littermate livers. Furthermore, we found that in vitro silencing of ADAR1 expression in HepG2 cells leads to enhanced transcription of NFκB target genes, foremost of the pro-inflammatory cytokines IL6 and IL8. We also discovered immune cell-independent paracrine signaling among ADAR1-depleted HepG2 cells and hepatic stellate cells, leading to the activation of the latter cell type to adopt a profibrogenic phenotype. This paracrine communication dependent mainly on the production and secretion of the cytokine IL6 induced by ADAR1 silencing in hepatocytes. Thus, our findings shed a new light on the vital regulatory role of ADAR1 in hepatic immune homeostasis, chiefly its inhibitory function on the crosstalk between the NFκB and type-I interferons signaling cascades, restraining the development of liver inflammation and fibrosis.
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Affiliation(s)
- Shirley Oren Ben-Shoshan
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Polina Kagan
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Maya Sultan
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Zohar Barabash
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Chen Dor
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Jasmine Jacob-Hirsch
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,e The Mina and Everard Goodman Faculty of Life Sciences , Bar Ilan University , Ramat Gan , Israel
| | - Alon Harmelin
- f Department of Veterinary Resources , Weizmann Institute of Science , Rehovot , Israel
| | - Orit Pappo
- c Department of Pathology , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Victoria Marcu-Malina
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
| | - Ziv Ben-Ari
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Ninette Amariglio
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,e The Mina and Everard Goodman Faculty of Life Sciences , Bar Ilan University , Ramat Gan , Israel
| | - Gideon Rechavi
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Itamar Goldstein
- a Sheba Cancer Research Center , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel.,d Sackler Faculty of Medicine , Tel Aviv University , Israel
| | - Michal Safran
- b Liver Research Laboratory , Chaim Sheba Academic Medical Center, Tel Hashomer , Israel
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Agirrezabal I, Palacios R, Moreno B, Sepulcre J, Abernathy A, Saiz A, Llufriu S, Comabella M, Montalban X, Martinez A, Arteta D, Villoslada P. Increased expression of dedicator-cytokinesis-10, caspase-2 and Synaptotagmin-like 2 is associated with clinical disease activity in multiple sclerosis. ACTA ACUST UNITED AC 2016. [DOI: 10.1186/s40893-016-0009-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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180
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Inhibition of the hexosamine biosynthetic pathway promotes castration-resistant prostate cancer. Nat Commun 2016; 7:11612. [PMID: 27194471 PMCID: PMC4874037 DOI: 10.1038/ncomms11612] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/13/2016] [Indexed: 01/22/2023] Open
Abstract
The precise molecular alterations driving castration-resistant prostate cancer (CRPC) are not clearly understood. Using a novel network-based integrative approach, here, we show distinct alterations in the hexosamine biosynthetic pathway (HBP) to be critical for CRPC. Expression of HBP enzyme glucosamine-phosphate N-acetyltransferase 1 (GNPNAT1) is found to be significantly decreased in CRPC compared with localized prostate cancer (PCa). Genetic loss-of-function of GNPNAT1 in CRPC-like cells increases proliferation and aggressiveness, in vitro and in vivo. This is mediated by either activation of the PI3K-AKT pathway in cells expressing full-length androgen receptor (AR) or by specific protein 1 (SP1)-regulated expression of carbohydrate response element-binding protein (ChREBP) in cells containing AR-V7 variant. Strikingly, addition of the HBP metabolite UDP-N-acetylglucosamine (UDP-GlcNAc) to CRPC-like cells significantly decreases cell proliferation, both in-vitro and in animal studies, while also demonstrates additive efficacy when combined with enzalutamide in-vitro. These observations demonstrate the therapeutic value of targeting HBP in CRPC. The molecular alterations driving anti-androgen resistance in prostate cancer are unclear. Here, the authors show, using a network-based approach, that inhibition of the hexosamine biosynthetic pathway is necessary to develop resistance and that increasing the activity of the pathway enhances the anti-androgen response.
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181
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Montagner S, Leoni C, Emming S, Della Chiara G, Balestrieri C, Barozzi I, Piccolo V, Togher S, Ko M, Rao A, Natoli G, Monticelli S. TET2 Regulates Mast Cell Differentiation and Proliferation through Catalytic and Non-catalytic Activities. Cell Rep 2016; 15:1566-1579. [PMID: 27160912 DOI: 10.1016/j.celrep.2016.04.044] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 03/08/2016] [Accepted: 04/07/2016] [Indexed: 12/13/2022] Open
Abstract
Dioxygenases of the TET family impact genome functions by converting 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC). Here, we identified TET2 as a crucial regulator of mast cell differentiation and proliferation. In the absence of TET2, mast cells showed disrupted gene expression and altered genome-wide 5hmC deposition, especially at enhancers and in the proximity of downregulated genes. Impaired differentiation of Tet2-ablated cells could be relieved or further exacerbated by modulating the activity of other TET family members, and mechanistically it could be linked to the dysregulated expression of C/EBP family transcription factors. Conversely, the marked increase in proliferation induced by the loss of TET2 could be rescued exclusively by re-expression of wild-type or catalytically inactive TET2. Our data indicate that, in the absence of TET2, mast cell differentiation is under the control of compensatory mechanisms mediated by other TET family members, while proliferation is strictly dependent on TET2 expression.
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Affiliation(s)
- Sara Montagner
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Cristina Leoni
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Stefan Emming
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Giulia Della Chiara
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Chiara Balestrieri
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Iros Barozzi
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Susan Togher
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Myunggon Ko
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; School of Life Sciences, Ulsan National Institute of Science and Technology, UNIST-gil 50, Ulju-gun, Ulsan 689-798, Republic of Korea
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), 20139 Milan, Italy
| | - Silvia Monticelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), 6500 Bellinzona, Switzerland.
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182
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Suurmond J, Habets KLL, Tatum Z, Schonkeren JJ, Hoen PAC', Huizinga TWJ, Laros JFJ, Toes REM, Kurreeman F. Repeated FcεRI triggering reveals modified mast cell function related to chronic allergic responses in tissue. J Allergy Clin Immunol 2016; 138:869-880. [PMID: 27033170 DOI: 10.1016/j.jaci.2016.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 12/18/2015] [Accepted: 01/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Activation of mast cells through FcεRI plays an important role in acute allergic reactions. However, little is known about the function of mast cells in patients with chronic allergic inflammation or the effect of repeated FcεRI triggering occurring in such responses. OBJECTIVE We aimed to identify changes in mast cell function after repeated FcεRI triggering and to correlate these changes to chronic allergic responses in tissue. METHODS Human cord blood-derived mast cells were treated for 2 weeks with anti-IgE. The function of naive or treated mast cells was analyzed by means of RNA sequencing, quantitative RT-PCR, flow cytometry, and functional assays. Protein secretion was measured with ELISAs and multiplex assays. RESULTS We observed several changes in mast cell function after repeated anti-IgE triggering. Although the acute response was dampened, we identified 289 genes significantly upregulated after repeated anti-IgE. Most of these genes (84%) were not upregulated after a single anti-IgE stimulus, indicating a significantly different response mode characterized by increased antigen presentation, response to bacteria, and chemotaxis. Changes in mast cell function were related to changes in expression of the transcription factors RXRA and BATF and others. Importantly, we found a substantial overlap between genes upregulated after repeated anti-IgE triggering and genes upregulated in tissue from patients with chronic allergy, in particular those of patients with chronic rhinosinusitis. CONCLUSION Our study provides evidence for intrinsic modulation of mast cell function on repeated FcεRI-mediated activation. The overlap with gene expression in tissues is suggestive of a direct link between repeated IgE-mediated activation of mast cells and chronic allergy.
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Affiliation(s)
- Jolien Suurmond
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim L L Habets
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joris J Schonkeren
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
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183
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Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection. PLoS One 2016; 11:e0152022. [PMID: 27003162 PMCID: PMC4803215 DOI: 10.1371/journal.pone.0152022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 03/08/2016] [Indexed: 02/05/2023] Open
Abstract
Toxoplasma gondii remains a global public health problem. However, its pathophysiology is still not-completely understood particularly the impact of infection on host liver metabolism. We performed iTRAQ-based proteomic analysis to evaluate early liver protein responses in BALB/c mice following infection with T. gondii PYS strain (genotype ToxoDB#9) infection. Our data revealed modification of protein expression in key metabolic pathways, as indicated by the upregulation of immune response and downregulation of mitochondrial respiratory chain, and the metabolism of fatty acids, lipids and xenobiotics. T. gondii seems to hijack host PPAR signaling pathway to downregulate the metabolism of fatty acids, lipids and energy in the liver. The metabolism of over 400 substances was affected by the downregulation of genes involved in xenobiotic metabolism. The top 10 transcription factors used by upregulated genes were Stat2, Stat1, Irf2, Irf1, Sp2, Egr1, Stat3, Klf4, Elf1 and Gabpa, while the top 10 transcription factors of downregulated genes were Hnf4A, Ewsr1, Fli1, Hnf4g, Nr2f1, Pparg, Rxra, Hnf1A, Foxa1 and Foxo1. These findings indicate global reprogramming of the metabolism of the mouse liver after acute T. gondii infection. Functional characterization of the altered proteins may enhance understanding of the host responses to T. gondii infection and lead to the identification of new therapeutic targets.
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184
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RNA Sequencing Reveals the Alteration of the Expression of Novel Genes in Ethanol-Treated Embryoid Bodies. PLoS One 2016; 11:e0149976. [PMID: 26930486 PMCID: PMC4773011 DOI: 10.1371/journal.pone.0149976] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/08/2016] [Indexed: 12/11/2022] Open
Abstract
Fetal alcohol spectrum disorder is a collective term representing fetal abnormalities associated with maternal alcohol consumption. Prenatal alcohol exposure and related anomalies are well characterized, but the molecular mechanism behind this phenomenon is not well characterized. In this present study, our aim is to profile important genes that regulate cellular development during fetal development. Human embryonic carcinoma cells (NCCIT) are cultured to form embryoid bodies and then treated in the presence and absence of ethanol (50 mM). We employed RNA sequencing to profile differentially expressed genes in the ethanol-treated embryoid bodies from NCCIT vs. EB, NCCIT vs. EB+EtOH and EB vs. EB+EtOH data sets. A total of 632, 205 and 517 differentially expressed genes were identified from NCCIT vs. EB, NCCIT vs. EB+EtOH and EB vs. EB+EtOH, respectively. Functional annotation using bioinformatics tools reveal significant enrichment of differential cellular development and developmental disorders. Furthermore, a group of 42, 15 and 35 transcription factor-encoding genes are screened from all of the differentially expressed genes obtained from NCCIT vs. EB, NCCIT vs. EB+EtOH and EB vs. EB+EtOH, respectively. We validated relative gene expression levels of several transcription factors from these lists by quantitative real-time PCR. We hope that our study substantially contributes to the understanding of the molecular mechanism underlying the pathology of alcohol-mediated anomalies and ease further research.
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185
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Tong AJ, Liu X, Thomas BJ, Lissner MM, Baker MR, Senagolage MD, Allred AL, Barish GD, Smale ST. A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation. Cell 2016; 165:165-179. [PMID: 26924576 DOI: 10.1016/j.cell.2016.01.020] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 11/01/2015] [Accepted: 01/13/2016] [Indexed: 01/21/2023]
Abstract
Much has been learned about transcriptional cascades and networks from large-scale systems analyses of high-throughput datasets. However, analysis methods that optimize statistical power through simultaneous evaluation of thousands of ChIP-seq peaks or differentially expressed genes possess substantial limitations in their ability to uncover mechanistic principles of transcriptional control. By examining nascent transcript RNA-seq, ChIP-seq, and binding motif datasets from lipid A-stimulated macrophages with increased attention to the quantitative distribution of signals, we identified unexpected relationships between the in vivo binding properties of inducible transcription factors, motif strength, and transcription. Furthermore, rather than emphasizing common features of large clusters of co-regulated genes, our results highlight the extent to which unique mechanisms regulate individual genes with key biological functions. Our findings demonstrate the mechanistic value of stringent interrogation of well-defined sets of genes as a complement to broader systems analyses of transcriptional cascades and networks.
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Affiliation(s)
- Ann-Jay Tong
- Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xin Liu
- Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Brandon J Thomas
- Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michelle M Lissner
- Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mairead R Baker
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Madhavi D Senagolage
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Amanda L Allred
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Grant D Barish
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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186
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Boeva V. Analysis of Genomic Sequence Motifs for Deciphering Transcription Factor Binding and Transcriptional Regulation in Eukaryotic Cells. Front Genet 2016; 7:24. [PMID: 26941778 PMCID: PMC4763482 DOI: 10.3389/fgene.2016.00024] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/05/2016] [Indexed: 12/27/2022] Open
Abstract
Eukaryotic genomes contain a variety of structured patterns: repetitive elements, binding sites of DNA and RNA associated proteins, splice sites, and so on. Often, these structured patterns can be formalized as motifs and described using a proper mathematical model such as position weight matrix and IUPAC consensus. Two key tasks are typically carried out for motifs in the context of the analysis of genomic sequences. These are: identification in a set of DNA regions of over-represented motifs from a particular motif database, and de novo discovery of over-represented motifs. Here we describe existing methodology to perform these two tasks for motifs characterizing transcription factor binding. When applied to the output of ChIP-seq and ChIP-exo experiments, or to promoter regions of co-modulated genes, motif analysis techniques allow for the prediction of transcription factor binding events and enable identification of transcriptional regulators and co-regulators. The usefulness of motif analysis is further exemplified in this review by how motif discovery improves peak calling in ChIP-seq and ChIP-exo experiments and, when coupled with information on gene expression, allows insights into physical mechanisms of transcriptional modulation.
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Affiliation(s)
- Valentina Boeva
- Centre de Recherche, Institut CurieParis, France; INSERM, U900Paris, France; Mines ParisTechFontainebleau, France; PSL Research UniversityParis, France; Department of Development, Reproduction and Cancer, Institut CochinParis, France; INSERM, U1016Paris, France; Centre National de la Recherche Scientifique UMR 8104Paris, France; Université Paris Descartes UMR-S1016Paris, France
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187
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Pardo L, Schlüter A, Valor LM, Barco A, Giralt M, Golbano A, Hidalgo J, Jia P, Zhao Z, Jové M, Portero-Otin M, Ruiz M, Giménez-Llort L, Masgrau R, Pujol A, Galea E. Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury. Glia 2016; 64:853-74. [PMID: 26880229 DOI: 10.1002/glia.22969] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/07/2023]
Abstract
The clinical challenge in acute injury as in traumatic brain injury (TBI) is to halt the delayed neuronal loss that occurs hours and days after the insult. Here we report that the activation of CREB-dependent transcription in reactive astrocytes prevents secondary injury in cerebral cortex after experimental TBI. The study was performed in a novel bitransgenic mouse in which a constitutively active CREB, VP16-CREB, was targeted to astrocytes with the Tet-Off system. Using histochemistry, qPCR, and gene profiling we found less neuronal death and damage, reduced macrophage infiltration, preserved mitochondria, and rescued expression of genes related to mitochondrial metabolism in bitransgenic mice as compared to wild type littermates. Finally, with meta-analyses using publicly available databases we identified a core set of VP16-CREB candidate target genes that may account for the neuroprotective effect. Enhancing CREB activity in astrocytes thus emerges as a novel avenue in acute brain post-injury therapeutics.
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Affiliation(s)
- Luis Pardo
- Institut De Neurociències and Unitat De Bioquímica, Facultat De Medicina, Universitat Autònoma De Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, L'hospitalet De Llobregat, Barcelona, 08907, Spain
| | - Luis M Valor
- Instituto De Neurociencias De Alicante, Universidad Miguel Hernández/Consejo Superior De Investigaciones Científicas, Sant Joan D'alacant, Alicante, 03550, Spain
| | - Angel Barco
- Instituto De Neurociencias De Alicante, Universidad Miguel Hernández/Consejo Superior De Investigaciones Científicas, Sant Joan D'alacant, Alicante, 03550, Spain
| | - Mercedes Giralt
- Institut De Neurociències and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma, Barcelona, 08193, Spain
| | - Arantxa Golbano
- Institut De Neurociències and Unitat De Bioquímica, Facultat De Medicina, Universitat Autònoma De Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Juan Hidalgo
- Institut De Neurociències and Department of Cellular Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma, Barcelona, 08193, Spain
| | - Peilin Jia
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Mariona Jové
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida, Lleida, 25198, Spain
| | - Manuel Portero-Otin
- Department of Experimental Medicine, University of Lleida-Biomedical Research Institute of Lleida, Lleida, 25198, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, L'hospitalet De Llobregat, Barcelona, 08907, Spain
| | - Lydia Giménez-Llort
- Institut De Neurociènces and Department of Psychiatry and Forensic Medicine, School of Medicine, Universitat Autònoma De Barcelona, Bellaterra, 08193, Spain
| | - Roser Masgrau
- Institut De Neurociències and Unitat De Bioquímica, Facultat De Medicina, Universitat Autònoma De Barcelona, Bellaterra, Barcelona, 08193, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, L'hospitalet De Llobregat, Barcelona, 08907, Spain.,Institució Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | - Elena Galea
- Institut De Neurociències and Unitat De Bioquímica, Facultat De Medicina, Universitat Autònoma De Barcelona, Bellaterra, Barcelona, 08193, Spain.,Institució Catalana De Recerca I Estudis Avançats (ICREA), Barcelona, Spain
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188
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Kananen L, Marttila S, Nevalainen T, Jylhävä J, Mononen N, Kähönen M, Raitakari OT, Lehtimäki T, Hurme M. Aging-associated DNA methylation changes in middle-aged individuals: the Young Finns study. BMC Genomics 2016; 17:103. [PMID: 26861258 PMCID: PMC4746895 DOI: 10.1186/s12864-016-2421-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
Background Chronological aging-associated changes in the human DNA methylome have been studied by multiple epigenome-wide association studies (EWASs). Certain CpG sites have been identified as aging-associated in multiple studies, and the majority of the sites identified in various studies show common features regarding location and direction of the methylation change. However, as a whole, the sets of aging-associated CpGs identified in different studies, even with similar tissues and age ranges, show only limited overlap. In this study, we further explore and characterize CpG sites that show close relationship between their DNA methylation level and chronological age during adulthood and which bear the relationship regardless of blood cell type heterogeneity. Results In this study, with a multivariable regression model adjusted for cell type heterogeneity, we identified 1202 aging-associated CpG sites (a-CpGs, FDR < 5 %), in whole blood in a population with an especially narrow age range (40 - 49 years). Repeatedly reported a-CpGs located in genes ELOVL2, FHL2, PENK and KLF14 were also identified. Regions with aging-associated hypermethylation were enriched regarding several gene ontology (GO) terms (especially in the cluster of developmental processes), whereas hypomethylated sites showed no enrichment. The genes with higher numbers of a-CpG hits were more often hypermethylated with advancing age. The comparison analysis revealed that of the 1202 a-CpGs identified in the present study, 987 were identified as differentially methylated also between nonagenarians and young adults in a previous study (The Vitality 90+ study), and importantly, the directions of changes were identical in the previous and in the present study. Conclusions Here we report that aging-associated DNA methylation features can be identified in a middle-aged population with an age range of only 9 years. A great majority of these sites have been previously reported as aging-associated in a population aged 19 to 90 years. Aging is associated with different types of changes in DNA methylation, clock-like as well as random. We speculate that the a-CpGs identified here in a population with a narrow age-range represent clock-like changes, as they showed concordant methylation behavior in population spanning whole adulthood as well. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2421-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- L Kananen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland. .,Gerontology Research Center, Tampere, Finland.
| | - S Marttila
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland. .,Gerontology Research Center, Tampere, Finland.
| | - T Nevalainen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland. .,Gerontology Research Center, Tampere, Finland.
| | - J Jylhävä
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland. .,Gerontology Research Center, Tampere, Finland.
| | - N Mononen
- Fimlab Laboratories, Tampere, Finland.
| | - M Kähönen
- Departments of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere, Finland.
| | - O T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine and the Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, Finland.
| | - T Lehtimäki
- Fimlab Laboratories, Tampere, Finland. .,Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland.
| | - M Hurme
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland. .,Gerontology Research Center, Tampere, Finland. .,Fimlab Laboratories, Tampere, Finland.
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189
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Diaferia GR, Balestrieri C, Prosperini E, Nicoli P, Spaggiari P, Zerbi A, Natoli G. Dissection of transcriptional and cis-regulatory control of differentiation in human pancreatic cancer. EMBO J 2016; 35:595-617. [PMID: 26769127 DOI: 10.15252/embj.201592404] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/07/2015] [Indexed: 12/29/2022] Open
Abstract
The histological grade of carcinomas describes the ability of tumor cells to organize in differentiated epithelial structures and has prognostic and therapeutic impact. Here, we show that differential usage of the genomic repertoire of transcriptional enhancers leads to grade-specific gene expression programs in human pancreatic ductal adenocarcinoma (PDAC). By integrating gene expression profiling, epigenomic footprinting, and loss-of-function experiments in PDAC cell lines of different grade, we identified the repertoires of enhancers specific to high- and low-grade PDACs and the cognate set of transcription factors acting to maintain their activity. Among the candidate regulators of PDAC differentiation, KLF5 was selectively expressed in pre-neoplastic lesions and low-grade primary PDACs and cell lines, where it maintained the acetylation of grade-specific enhancers, the expression of epithelial genes such as keratins and mucins, and the ability to organize glandular epithelia in xenografts. The identification of the transcription factors controlling differentiation in PDACs will help clarify the molecular bases of its heterogeneity and progression.
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Affiliation(s)
- Giuseppe R Diaferia
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Chiara Balestrieri
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Paola Nicoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
| | - Paola Spaggiari
- Division of Pancreatic Surgery, Humanitas Clinical Institute, Milan, Italy
| | - Alessandro Zerbi
- Division of Pancreatic Surgery, Humanitas Clinical Institute, Milan, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan, Italy
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190
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Nafis S, Ponnusamy K, Husain M, Singh RKB, Bamezai RNK. Identification of key regulators and their controlling mechanism in a combinatorial apoptosis network: a systems biology approach. MOLECULAR BIOSYSTEMS 2016; 12:3357-3369. [DOI: 10.1039/c6mb00526h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
NFKB1, SP1 and hsa-let-7a, were identified as key regulators of apoptosis, by network theory through probability of signal propagation, hub-removal and motif analysis.
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Affiliation(s)
- Shazia Nafis
- Department of Biotechnology
- Jamia Millia Islamia (Central University)
- New Delhi
- India
- School of Computational and Integrative Sciences
| | - Kalaiarasan Ponnusamy
- National Centre of Applied Human Genetics
- School of Life Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Mohammad Husain
- Department of Biotechnology
- Jamia Millia Islamia (Central University)
- New Delhi
- India
| | - R. K. Brojen Singh
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi
- India
| | - Rameshwar N. K. Bamezai
- School of Computational and Integrative Sciences
- Jawaharlal Nehru University
- New Delhi
- India
- National Centre of Applied Human Genetics
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191
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Verfaillie A, Imrichova H, Janky R, Aerts S. iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment. ACTA ACUST UNITED AC 2015; 52:2.16.1-2.16.39. [PMID: 26678384 DOI: 10.1002/0471250953.bi0216s52] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Gene expression profiling is often used to identify genes that are co-expressed in a biological process or disease. Downstream analyses of co-expressed gene sets using bioinformatics methods can reveal candidate transcription factors (TF) that co-regulate these genes, based on the presence of shared TF binding sites. Drawing gene regulatory networks that connect TFs to their predicted target genes can uncover gene modules that implement a particular function. Here, we describe several protocols to analyze any set of co-expressed genes using iRegulon and i-cisTarget. These tools perform regulatory sequence analysis (motif discovery) and integrate and mine large collections of existing regulatory data, such as ChIP-Seq, DHS-seq, and FAIRE-seq (track discovery). While iRegulon focuses on sets of co-expressed genes, i-cisTarget also analyses genomic regions as input. The following protocols describe how to install and use these tools, how to interpret the obtained results, and will thus help to create meaningful regulatory networks.
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Affiliation(s)
- Annelien Verfaillie
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium
| | - Hana Imrichova
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium
| | - Rekins Janky
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Belgium
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192
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Jagannathan L, Jose CC, Arita A, Kluz T, Sun H, Zhang X, Yao Y, Kartashov AV, Barski A, Costa M, Cuddapah S. Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. J Cell Physiol 2015; 231:1611-20. [PMID: 26588041 DOI: 10.1002/jcp.25262] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/04/2023]
Abstract
Oxygen levels range from 2% to 9% in vivo. Atmospheric O2 levels (21%) are known to induce cell proliferation defects and cellular senescence in primary cell cultures. However, the mechanistic basis of the deleterious effects of higher O2 levels is not fully understood. On the other hand, immortalized cells including cancer cell lines, which evade cellular senescence are normally cultured at 21% O2 and the effects of higher O2 on these cells are understudied. Here, we addressed this problem by culturing immortalized human bronchial epithelial (BEAS-2B) cells at ambient atmospheric, 21% O2 and lower, 10% O2. Our results show increased inflammatory response at 21% O2 but not at 10% O2. We found higher RelA binding at the NF-κB1/RelA target gene promoters as well as upregulation of several pro-inflammatory cytokines in cells cultured at 21% O2. RelA knockdown prevented the upregulation of the pro-inflammatory cytokines at 21% O2, suggesting NF-κB1/RelA as a major mediator of inflammatory response in cells cultured at 21% O2. Interestingly, unlike the 21% O2 cultured cells, exposure of 10% O2 cultured cells to H2O2 did not elicit inflammatory response, suggesting increased ability to tolerate oxidative stress in cells cultured at lower O2 levels.
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Affiliation(s)
- Lakshmanan Jagannathan
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Cynthia C Jose
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Adriana Arita
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Thomas Kluz
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Xiaoru Zhang
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Yixin Yao
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Andrey V Kartashov
- Division of Allergy and Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Artem Barski
- Division of Allergy and Immunology and Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Max Costa
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
| | - Suresh Cuddapah
- Department of Environmental Medicine, New York University School of Medicine, Tuxedo, New York
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193
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Scandaglia M, Benito E, Morenilla-Palao C, Fiorenza A, Del Blanco B, Coca Y, Herrera E, Barco A. Fine-tuned SRF activity controls asymmetrical neuronal outgrowth: implications for cortical migration, neural tissue lamination and circuit assembly. Sci Rep 2015; 5:17470. [PMID: 26638868 PMCID: PMC4671020 DOI: 10.1038/srep17470] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/29/2015] [Indexed: 01/09/2023] Open
Abstract
The stimulus-regulated transcription factor Serum Response Factor (SRF) plays an important role in diverse neurodevelopmental processes related to structural plasticity and motile functions, although its precise mechanism of action has not yet been established. To further define the role of SRF in neural development and distinguish between cell-autonomous and non cell-autonomous effects, we bidirectionally manipulated SRF activity through gene transduction assays that allow the visualization of individual neurons and their comparison with neighboring control cells. In vitro assays showed that SRF promotes survival and filopodia formation and is required for normal asymmetric neurite outgrowth, indicating that its activation favors dendrite enlargement versus branching. In turn, in vivo experiments demonstrated that SRF-dependent regulation of neuronal morphology has important consequences in the developing cortex and retina, affecting neuronal migration, dendritic and axonal arborization and cell positioning in these laminated tissues. Overall, our results show that the controlled and timely activation of SRF is essential for the coordinated growth of neuronal processes, suggesting that this event regulates the switch between neuronal growth and branching during developmental processes.
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Affiliation(s)
- Marilyn Scandaglia
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Eva Benito
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Cruz Morenilla-Palao
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Anna Fiorenza
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Yaiza Coca
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Eloísa Herrera
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant. 03550. Alicante, Spain
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194
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Etard C, Armant O, Roostalu U, Gourain V, Ferg M, Strähle U. Loss of function of myosin chaperones triggers Hsf1-mediated transcriptional response in skeletal muscle cells. Genome Biol 2015; 16:267. [PMID: 26631063 PMCID: PMC4668643 DOI: 10.1186/s13059-015-0825-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/05/2015] [Indexed: 01/03/2023] Open
Abstract
Background Mutations in myosin chaperones Unc45b and Hsp90aa1.1 as well as in the Unc45b-binding protein Smyd1b impair formation of myofibrils in skeletal muscle and lead to the accumulation of misfolded myosin. The concomitant transcriptional response involves up-regulation of the three genes encoding these proteins, as well as genes involved in muscle development. The transcriptional up-regulation of unc45b, hsp90aa1.1 and smyd1b is specific to zebrafish mutants with myosin folding defects, and is not triggered in other zebrafish myopathy models. Results By dissecting the promoter of unc45b, we identify a Heat shock factor 1 (Hsf1) binding element as a mediator of unc45b up-regulation in myofibers lacking myosin folding proteins. Loss-of-function of Hsf1 abolishes unc45b up-regulation in mutants with defects in myosin folding. Conclusions Taken together, our data show that skeletal muscle cells respond to defective myosin chaperones with a complex gene program and suggest that this response is mediated by Hsf1 activation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0825-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christelle Etard
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus Nord, PO box, Karlsruhe, Germany
| | - Olivier Armant
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus Nord, PO box, Karlsruhe, Germany
| | - Urmas Roostalu
- Present address: Institute of Inflammation and Repair, Michael Smith Bldg, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Victor Gourain
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus Nord, PO box, Karlsruhe, Germany
| | - Marco Ferg
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus Nord, PO box, Karlsruhe, Germany
| | - Uwe Strähle
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Campus Nord, PO box, Karlsruhe, Germany.
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195
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Parsons MJ, Brancaccio M, Sethi S, Maywood ES, Satija R, Edwards JK, Jagannath A, Couch Y, Finelli MJ, Smyllie NJ, Esapa C, Butler R, Barnard AR, Chesham JE, Saito S, Joynson G, Wells S, Foster RG, Oliver PL, Simon MM, Mallon AM, Hastings MH, Nolan PM. The Regulatory Factor ZFHX3 Modifies Circadian Function in SCN via an AT Motif-Driven Axis. Cell 2015; 162:607-21. [PMID: 26232227 PMCID: PMC4537516 DOI: 10.1016/j.cell.2015.06.060] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/25/2015] [Accepted: 06/01/2015] [Indexed: 01/17/2023]
Abstract
We identified a dominant missense mutation in the SCN transcription factor Zfhx3, termed short circuit (Zfhx3(Sci)), which accelerates circadian locomotor rhythms in mice. ZFHX3 regulates transcription via direct interaction with predicted AT motifs in target genes. The mutant protein has a decreased ability to activate consensus AT motifs in vitro. Using RNA sequencing, we found minimal effects on core clock genes in Zfhx3(Sci/+) SCN, whereas the expression of neuropeptides critical for SCN intercellular signaling was significantly disturbed. Moreover, mutant ZFHX3 had a decreased ability to activate AT motifs in the promoters of these neuropeptide genes. Lentiviral transduction of SCN slices showed that the ZFHX3-mediated activation of AT motifs is circadian, with decreased amplitude and robustness of these oscillations in Zfhx3(Sci/+) SCN slices. In conclusion, by cloning Zfhx3(Sci), we have uncovered a circadian transcriptional axis that determines the period and robustness of behavioral and SCN molecular rhythms.
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Affiliation(s)
- Michael J Parsons
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Marco Brancaccio
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Siddharth Sethi
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Elizabeth S Maywood
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Rahul Satija
- New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10012, USA
| | - Jessica K Edwards
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Aarti Jagannath
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Yvonne Couch
- Acute Stroke Program, Radcliffe Department of Clinical Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Mattéa J Finelli
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - Nicola J Smyllie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher Esapa
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Rachel Butler
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Alun R Barnard
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Johanna E Chesham
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Shoko Saito
- Department of Genetics, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands; Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8575, Japan
| | - Greg Joynson
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Sara Wells
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Russell G Foster
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Peter L Oliver
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - Michelle M Simon
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Ann-Marie Mallon
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK
| | - Michael H Hastings
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Patrick M Nolan
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, UK.
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196
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Kar SP, Tyrer JP, Li Q, Lawrenson K, Aben KKH, Anton-Culver H, Antonenkova N, Chenevix-Trench G, Baker H, Bandera EV, Bean YT, Beckmann MW, Berchuck A, Bisogna M, Bjørge L, Bogdanova N, Brinton L, Brooks-Wilson A, Butzow R, Campbell I, Carty K, Chang-Claude J, Chen YA, Chen Z, Cook LS, Cramer D, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Dicks E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Easton DF, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goode EL, Goodman MT, Grownwald J, Harrington P, Harter P, Hein A, Heitz F, Hildebrandt MAT, Hillemanns P, Hogdall E, Hogdall CK, Hosono S, Iversen ES, Jakubowska A, Paul J, Jensen A, Ji BT, Karlan BY, Kjaer SK, Kelemen LE, Kellar M, Kelley J, Kiemeney LA, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger L, Matsuo K, McGuire V, McLaughlin JR, McNeish IA, Menon U, Modugno F, Moysich KB, Narod SA, Nedergaard L, Ness RB, Nevanlinna H, Odunsi K, Olson SH, Orlow I, Orsulic S, Weber RP, Pearce CL, Pejovic T, Pelttari LM, Permuth-Wey J, Phelan CM, Pike MC, Poole EM, Ramus SJ, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schildkraut JM, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Sucheston-Campbell LE, Tangen IL, Teo SH, Terry KL, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, van Altena AM, Van Nieuwenhuysen E, Vergote I, Vierkant RA, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Woo YL, Wu X, Wu A, Yang H, Zheng W, Ziogas A, Sellers TA, Monteiro ANA, Freedman ML, Gayther SA, Pharoah PDP. Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. Cancer Epidemiol Biomarkers Prev 2015; 24:1574-84. [PMID: 26209509 PMCID: PMC4592449 DOI: 10.1158/1055-9965.epi-14-1270] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 06/29/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. METHODS We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). RESULTS Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. CONCLUSION We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. IMPACT Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization.
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Affiliation(s)
- Siddhartha P Kar
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom.
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Qiyuan Li
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kate Lawrenson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Katja K H Aben
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Nijmegen, the Netherlands. Comprehensive Cancer Center The Netherlands, Utrecht, the Netherlands
| | - Hoda Anton-Culver
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California
| | - Natalia Antonenkova
- Byelorussian Institute for Oncology and Medical Radiology Aleksandrov N.N., Minsk, Belarus
| | | | - Helen Baker
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Elisa V Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Yukie T Bean
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Matthias W Beckmann
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, North Carolina
| | - Maria Bisogna
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Line Bjørge
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Angela Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada. Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland. Department of Pathology, Helsinki University Central Hospital, Helsinki, Finland
| | - Ian Campbell
- Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Karen Carty
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Jenny Chang-Claude
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Yian Ann Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, Florida
| | - Zhihua Chen
- Department of Biostatistics, Moffitt Cancer Center, Tampa, Florida
| | - Linda S Cook
- Division of Epidemiology and Biostatistics, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico
| | - Daniel Cramer
- Obstetrics and Gynecology Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Agnieszka Dansonka-Mieszkowska
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Ed Dicks
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer A Doherty
- Department of Community and Family Medicine, Section of Biostatistics & Epidemiology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Andreas du Bois
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany. Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Matthias Dürst
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Robert P Edwards
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom. Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Arif B Ekici
- University Hospital Erlangen, Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Peter A Fasching
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany. University of California at Los Angeles, David Geffen School of Medicine, Department of Medicine, Division of Hematology and Oncology, Los Angeles, California
| | - Brooke L Fridley
- Biostatistics and Informatics Shared Resource, University of Kansas Medical Center, Kansas City, Kansas
| | | | - Aleksandra Gentry-Maharaj
- Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - Rosalind Glasspool
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Ellen L Goode
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California. Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jacek Grownwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Patricia Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Philipp Harter
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany. Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | - Alexander Hein
- University Hospital Erlangen, Department of Gynecology and Obstetrics, Friedrich-Alexander-University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Essen, Germany. Department of Gynecology and Gynecologic Oncology, Dr. Horst Schmidt Kliniken Wiesbaden, Wiesbaden, Germany
| | | | - Peter Hillemanns
- Departments of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Estrid Hogdall
- Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark. Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K Hogdall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Satoyo Hosono
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Aichi, Japan
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - James Paul
- Cancer Research UK Clinical Trials Unit, The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Allan Jensen
- Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Bu-Tian Ji
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Susanne K Kjaer
- Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark. Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Melissa Kellar
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Joseph Kelley
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Lambertus A Kiemeney
- Radboud University Medical Centre, Radboud Institute for Health Sciences, Nijmegen, the Netherlands
| | - Camilla Krakstad
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Jolanta Kupryjanczyk
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium. Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Sandrina Lambrechts
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Alice W Lee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Shashi Lele
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Arto Leminen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Jenny Lester
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Douglas A Levine
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dong Liang
- College of Pharmacy and Health Sciences, Texas Southern University, Houston, Texas
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Karen Lu
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Lene Lundvall
- Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Leon Massuger
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Valerie McGuire
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - John R McLaughlin
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Iain A McNeish
- Institute of Cancer Sciences, University of Glasgow, Wolfson Wohl Cancer Research Centre, Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Usha Menon
- Women's Cancer, University College London Elizabeth Garrett Anderson Institute for Women's Health, London, United Kingdom
| | - Francesmary Modugno
- Ovarian Cancer Center of Excellence, University of Pittsburgh, Pittsburgh, Pennsylvania. Women's Cancer Research Program, Magee-Women's Research Institute and University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania. Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania. Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Kirsten B Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, New York
| | - Steven A Narod
- Women's College Research Institute, Toronto, Ontario, Canada
| | - Lotte Nedergaard
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Roberta B Ness
- The University of Texas School of Public Health, Houston, Texas
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | - Kunle Odunsi
- Department of Gynecological Oncology, Roswell Park Cancer Institute, Buffalo, New York
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sandra Orsulic
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Rachel Palmieri Weber
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina
| | - Celeste Leigh Pearce
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Tanja Pejovic
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, Oregon. Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Liisa M Pelttari
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, HUS, Finland
| | | | - Catherine M Phelan
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Malcolm C Pike
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California. Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elizabeth M Poole
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Barry Rosen
- Department of Gynecologic-Oncology, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada. Department of Obstetrics and Gynecology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington, Seattle, Washington
| | - Joseph H Rothstein
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - Anja Rudolph
- German Cancer Research Center (DKFZ), Division of Cancer Epidemiology, Heidelberg, Germany
| | - Ingo B Runnebaum
- Department of Gynecology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Iwona K Rzepecka
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Helga B Salvesen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Joellen M Schildkraut
- Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina. Cancer Control and Population Sciences, Duke Cancer Institute, Durham, North Carolina
| | - Ira Schwaab
- Institut für Humangenetik Wiesbaden, Wiesbaden, Germany
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Yurii B Shvetsov
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Nadeem Siddiqui
- Department of Gynaecological Oncology, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Weiva Sieh
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - Honglin Song
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | - Melissa C Southey
- Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Ingvild L Tangen
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway. Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia. University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Kathryn L Terry
- Obstetrics and Gynecology Center, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Harvard School of Public Health, Boston, Massachusetts
| | - Pamela J Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California. Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Agnieszka Timorek
- Department of Obstetrics, Gynecology, and Oncology, IInd Faculty of Medicine, Warsaw Medical University and Brodnowski Hospital, Warsaw, Poland
| | - Ya-Yu Tsai
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Shelley S Tworoger
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts. Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Anne M van Altena
- Radboud University Medical Centre, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Els Van Nieuwenhuysen
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Ignace Vergote
- Division of Gynecological Oncology, Department of Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Robert A Vierkant
- Department of Health Science Research, Mayo Clinic, Rochester, Minnesota
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Christine Walsh
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Alice S Whittemore
- Department of Health Research and Policy-Epidemiology, Stanford University School of Medicine, Stanford, California
| | - Kristine G Wicklund
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Yin-Ling Woo
- University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia. Department of Obstetrics and Gynaecology, University Malaya Medical Centre, University Malaya, Kuala Lumpur, Malaysia
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anna Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Hannah Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center and Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Argyrios Ziogas
- Department of Epidemiology, Director of Genetic Epidemiology Research Institute, School of Medicine, University of California Irvine, Irvine, California
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | | | - Matthew L Freedman
- Department of Medical Oncology, The Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, United Kingdom
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Das A, Chai JC, Kim SH, Lee YS, Park KS, Jung KH, Chai YG. Transcriptome sequencing of microglial cells stimulated with TLR3 and TLR4 ligands. BMC Genomics 2015; 16:517. [PMID: 26159724 PMCID: PMC4497376 DOI: 10.1186/s12864-015-1728-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 06/26/2015] [Indexed: 01/07/2023] Open
Abstract
Background Resident macrophages in the CNS microglia become activated and produce proinflammatory molecules upon encountering bacteria or viruses. TLRs are a phylogenetically conserved diverse family of sensors that drive innate immune responses following interactions with PAMPs. TLR3 and TLR4 recognize viral dsRNA Poly (I:C) and bacterial endotoxin LPS, respectively. Importantly, these receptors differ in their downstream adaptor molecules. Thus far, only a few studies have investigated the effects of TLR3 and TLR4 in macrophages. However, a genome-wide search for the effects of these TLRs has not been performed in microglia using RNA-seq. Gene expression patterns were determined for the BV-2 microglial cell line when stimulated with viral dsRNA Poly (I:C) or bacterial endotoxin LPS to identify novel transcribed genes, as well as investigate how differences in downstream signaling could influence gene expression in innate immunity. Results Sequencing assessment and quality evaluation revealed that common and unique patterns of proinflammatory genes were significantly up-regulated in response to TLR3 and TLR4 stimulation. However, the IFN/viral response gene showed a stronger response to TLR3 stimulation than to TLR4 stimulation. Unexpectedly, TLR3 and TLR4 stimulation did not activate IFN-ß and IRF3 in BV-2 microglia. Most importantly, we observed that previously unidentified transcription factors (TFs) (i.e., IRF1, IRF7, and IRF9) and the epigenetic regulators KDM4A and DNMT3L were significantly up-regulated in both TLR3- and TLR4-stimulated microglia. We also identified 29 previously unidentified genes that are important in immune regulation. In addition, we confirmed the expressions of key inflammatory genes as well as pro-inflammatory mediators in the supernatants were significantly induced in TLR3-and TLR4-stimulated primary microglial cells. Moreover, transcriptional start sites (TSSs) and isoforms, as well as differential promoter usage, revealed a complex pattern of transcriptional and post-transcriptional gene regulation upon infection with TLR3 and TLR4. Furthermore, TF motif analysis (-950 to +50 bp of the 5′ upstream promoters) revealed that the DNA sequences for NF-κB, IRF1, and STAT1 were significantly enriched in TLR3- and TLR4-stimulated microglia. Conclusions These unprecedented findings not only permit a comparison of TLR3-and TLR4-stimulated genes but also identify new genes that have not been previously implicated in innate immunity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1728-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amitabh Das
- Department of Bionanotechnology, Hanyang University, Seoul, 133-791, Republic of Korea.
| | - Jin Choul Chai
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Sun Hwa Kim
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Young Seek Lee
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Kyoung Sun Park
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
| | - Kyoung Hwa Jung
- Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea. .,Institute of Natural Science & Technology, Hanyang University, Ansan, 426-791, South Korea.
| | - Young Gyu Chai
- Department of Bionanotechnology, Hanyang University, Seoul, 133-791, Republic of Korea. .,Department of Molecular & Life Sciences, Hanyang University, Ansan, 426-791, Republic of Korea.
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Lissner MM, Thomas BJ, Wee K, Tong AJ, Kollmann TR, Smale ST. Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults. PLoS One 2015; 10:e0132061. [PMID: 26147648 PMCID: PMC4493075 DOI: 10.1371/journal.pone.0132061] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/09/2015] [Indexed: 11/18/2022] Open
Abstract
A variety of age-related differences in the innate and adaptive immune systems have been proposed to contribute to the increased susceptibility to infection of human neonates and older adults. The emergence of RNA sequencing (RNA-seq) provides an opportunity to obtain an unbiased, comprehensive, and quantitative view of gene expression differences in defined cell types from different age groups. An examination of ex vivo human monocyte responses to lipopolysaccharide stimulation or Listeria monocytogenes infection by RNA-seq revealed extensive similarities between neonates, young adults, and older adults, with an unexpectedly small number of genes exhibiting statistically significant age-dependent differences. By examining the differentially induced genes in the context of transcription factor binding motifs and RNA-seq data sets from mutant mouse strains, a previously described deficiency in interferon response factor-3 activity could be implicated in most of the differences between newborns and young adults. Contrary to these observations, older adults exhibited elevated expression of inflammatory genes at baseline, yet the responses following stimulation correlated more closely with those observed in younger adults. Notably, major differences in the expression of constitutively expressed genes were not observed, suggesting that the age-related differences are driven by environmental influences rather than cell-autonomous differences in monocyte development.
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Affiliation(s)
- Michelle M. Lissner
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Brandon J. Thomas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Kathleen Wee
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ann-Jay Tong
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
| | - Tobias R. Kollmann
- Division of Infectious and Immunological Diseases, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail: (TRK); (STS)
| | - Stephen T. Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (TRK); (STS)
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Zhang YS, Liu B, Luo XJ, Zhang JJ, Li NS, Ma QL, Jiang JL, Li YJ, Li Q, Peng J. A novel function of nuclear nonmuscle myosin regulatory light chain in promotion of xanthine oxidase transcription after myocardial ischemia/reperfusion. Free Radic Biol Med 2015; 83:115-28. [PMID: 25701432 DOI: 10.1016/j.freeradbiomed.2015.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 02/03/2015] [Accepted: 02/05/2015] [Indexed: 12/12/2022]
Abstract
Nuclear myosin regulates gene transcription and this novel function might be modulated through phosphorylation of the myosin regulatory light chain (p-MLC20). Nonmuscle MLC20 (nmMLC20) is also present in the nuclei of cardiomyocytes and a potential nmMLC20 binding sequence has been identified in the promoter of the xanthine oxidase (XO) gene. Thus, we investigated its function in the regulation of XO transcription after myocardial ischemia/reperfusion (IR). In a rat model of myocardial IR and a cardiomyocyte model of hypoxia/reoxygenation (HR) injury, the cardiac or cell injury, myosin light chain kinase (MLCK) content, XO expression and activity, XO-derived products, and level of nuclear p-nmMLC20 were detected. Coimmunoprecipitation (co-IP), chromatin immunoprecipitation, DNA pull-down, and luciferase reporter gene assays were used to decipher the molecular mechanisms through which nmMLC20 promotes XO expression. IR or HR treatment dramatically elevated nuclear p-nmMLC20 level, accompanied by increased XO expression, activity, and products (H2O2 and uric acid), as well as the IR or HR injury; these effects were ameliorated by inhibition of MLCK or knockdown of nmMLC20. Our findings from these experiments demonstrated that nuclear p-nmMLC20 binds to the consensus sequence GTCGCC in the XO gene promoter, interacts with RNA polymerase II and transcription factor IIB to form a transcription preinitiation complex, and hence activates XO gene transcription. These results suggest that nuclear p-nmMLC20 plays an important role in IR/HR injury by transcriptionally upregulating XO gene expression to increase oxidative stress in myocardium. Our findings demonstrate nuclear nmMLC20 as a potential new therapeutic target to combat cardiac IR injury.
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Affiliation(s)
- Yi-Shuai Zhang
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Bin Liu
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Xiu-Ju Luo
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Jie-Jie Zhang
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Nian-Sheng Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Qi-Lin Ma
- Department of Cardiovascular Medicine, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jun-Lin Jiang
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Yuan-Jian Li
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China
| | - Qingjie Li
- Department of Internal Medicine, The University of Texas Medical Branch, Galveston, TX 77555-1083, USA.
| | - Jun Peng
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China; Hunan Provincial Key Laboratory of Cardiovascular Research, School of Pharmaceutical Sciences, Central South University, Changsha 410078, China.
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McLean CS, Mielke C, Cordova JM, Langlais PR, Bowen B, Miranda D, Coletta DK, Mandarino LJ. Gene and MicroRNA Expression Responses to Exercise; Relationship with Insulin Sensitivity. PLoS One 2015; 10:e0127089. [PMID: 25984722 PMCID: PMC4436215 DOI: 10.1371/journal.pone.0127089] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/10/2015] [Indexed: 02/07/2023] Open
Abstract
Background Healthy individuals on the lower end of the insulin sensitivity spectrum also have a reduced gene expression response to exercise for specific genes. The goal of this study was to determine the relationship between insulin sensitivity and exercise-induced gene expression in an unbiased, global manner. Methods and Findings Euglycemic clamps were used to measure insulin sensitivity and muscle biopsies were done at rest and 30 minutes after a single acute exercise bout in 14 healthy participants. Changes in mRNA expression were assessed using microarrays, and miRNA analysis was performed in a subset of 6 of the participants using sequencing techniques. Following exercise, 215 mRNAs were changed at the probe level (Bonferroni-corrected P<0.00000115). Pathway and Gene Ontology analysis showed enrichment in MAP kinase signaling, transcriptional regulation and DNA binding. Changes in several transcription factor mRNAs were correlated with insulin sensitivity, including MYC, r=0.71; SNF1LK, r=0.69; and ATF3, r= 0.61 (5 corrected for false discovery rate). Enrichment in the 5’-UTRs of exercise-responsive genes suggested regulation by common transcription factors, especially EGR1. miRNA species of interest that changed after exercise included miR-378, which is located in an intron of the PPARGC1B gene. Conclusions These results indicate that transcription factor gene expression responses to exercise depend highly on insulin sensitivity in healthy people. The overall pattern suggests a coordinated cycle by which exercise and insulin sensitivity regulate gene expression in muscle.
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Affiliation(s)
- Carrie S. McLean
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Clinton Mielke
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Jeanine M. Cordova
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Paul R. Langlais
- Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America
| | - Benjamin Bowen
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Danielle Miranda
- Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America
| | - Dawn K. Coletta
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Lawrence J. Mandarino
- School for the Science of Health Care Delivery, Arizona State University, Tempe, Arizona, United States of America
- Mayo Clinic in Arizona, Scottsdale, Arizona, United States of America
- * E-mail:
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