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Friedel CC, Whisnant AW, Djakovic L, Rutkowski AJ, Friedl MS, Kluge M, Williamson JC, Sai S, Vidal RO, Sauer S, Hennig T, Grothey A, Milić A, Prusty BK, Lehner PJ, Matheson NJ, Erhard F, Dölken L. Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level. J Virol 2021; 95:e01399-20. [PMID: 33148793 PMCID: PMC7925104 DOI: 10.1128/jvi.01399-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 10/23/2020] [Indexed: 02/02/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) induces a profound host shutoff during lytic infection. The virion host shutoff (vhs) protein plays a key role in this process by efficiently cleaving host and viral mRNAs. Furthermore, the onset of viral DNA replication is accompanied by a rapid decline in host transcriptional activity. To dissect relative contributions of both mechanisms and elucidate gene-specific host transcriptional responses throughout the first 8 h of lytic HSV-1 infection, we used transcriptome sequencing of total, newly transcribed (4sU-labeled) and chromatin-associated RNA in wild-type (WT) and Δvhs mutant infection of primary human fibroblasts. Following virus entry, vhs activity rapidly plateaued at an elimination rate of around 30% of cellular mRNAs per hour until 8 h postinfection (p.i.). In parallel, host transcriptional activity dropped to 10 to 20%. While the combined effects of both phenomena dominated infection-induced changes in total RNA, extensive gene-specific transcriptional regulation was observable in chromatin-associated RNA and was surprisingly concordant between WT and Δvhs infections. Both induced strong transcriptional upregulation of a small subset of genes that were poorly expressed prior to infection but already primed by H3K4me3 histone marks at their promoters. Most interestingly, analysis of chromatin-associated RNA revealed vhs-nuclease-activity-dependent transcriptional downregulation of at least 150 cellular genes, in particular of many integrin adhesome and extracellular matrix components. This was accompanied by a vhs-dependent reduction in protein levels by 8 h p.i. for many of these genes. In summary, our study provides a comprehensive picture of the molecular mechanisms that govern cellular RNA metabolism during the first 8 h of lytic HSV-1 infection.IMPORTANCE The HSV-1 virion host shutoff (vhs) protein efficiently cleaves both host and viral mRNAs in a translation-dependent manner. In this study, we model and quantify changes in vhs activity, as well as virus-induced global loss of host transcriptional activity, during productive HSV-1 infection. In general, HSV-1-induced alterations in total RNA levels were dominated by these two global effects. In contrast, chromatin-associated RNA depicted gene-specific transcriptional changes. This revealed highly concordant transcriptional changes in WT and Δvhs infections, confirmed DUX4 as a key transcriptional regulator in HSV-1 infection, and identified vhs-dependent transcriptional downregulation of the integrin adhesome and extracellular matrix components. The latter explained seemingly gene-specific effects previously attributed to vhs-mediated mRNA degradation and resulted in a concordant loss in protein levels by 8 h p.i. for many of the respective genes.
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Affiliation(s)
- Caroline C Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Marie-Sophie Friedl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - James C Williamson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Somesh Sai
- Max Delbrück Center for Molecular Medicine/Berlin Institute of Health, Berlin, Germany
| | - Ramon Oliveira Vidal
- Max Delbrück Center for Molecular Medicine/Berlin Institute of Health, Berlin, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine/Berlin Institute of Health, Berlin, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Arnhild Grothey
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Andrea Milić
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Bhupesh K Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Paul J Lehner
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J Matheson
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, United Kingdom
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Helmholtz Institute for RNA-Based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), Würzburg, Germany
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2
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Grinat J, Heuberger J, Vidal RO, Goveas N, Kosel F, Berenguer-Llergo A, Kranz A, Wulf-Goldenberg A, Behrens D, Melcher B, Sauer S, Vieth M, Batlle E, Stewart AF, Birchmeier W. The epigenetic regulator Mll1 is required for Wnt-driven intestinal tumorigenesis and cancer stemness. Nat Commun 2020; 11:6422. [PMID: 33349639 PMCID: PMC7752919 DOI: 10.1038/s41467-020-20222-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/16/2020] [Indexed: 12/30/2022] Open
Abstract
Wnt/β-catenin signaling is crucial for intestinal carcinogenesis and the maintenance of intestinal cancer stem cells. Here we identify the histone methyltransferase Mll1 as a regulator of Wnt-driven intestinal cancer. Mll1 is highly expressed in Lgr5+ stem cells and human colon carcinomas with increased nuclear β-catenin. High levels of MLL1 are associated with poor survival of colon cancer patients. The genetic ablation of Mll1 in mice prevents Wnt/β-catenin-driven adenoma formation from Lgr5+ intestinal stem cells. Ablation of Mll1 decreases the self-renewal of human colon cancer spheres and halts tumor growth of xenografts. Mll1 controls the expression of stem cell genes including the Wnt/β-catenin target gene Lgr5. Upon the loss of Mll1, histone methylation at the stem cell promoters switches from activating H3K4 tri-methylation to repressive H3K27 tri-methylation, indicating that Mll1 sustains stem cell gene expression by antagonizing gene silencing through polycomb repressive complex 2 (PRC2)-mediated H3K27 tri-methylation. Transcriptome profiling of Wnt-mutated intestinal tumor-initiating cells reveals that Mll1 regulates Gata4/6 transcription factors, known to sustain cancer stemness and to control goblet cell differentiation. Our results demonstrate that Mll1 is an essential epigenetic regulator of Wnt/β-catenin-induced intestinal tumorigenesis and cancer stemness. Intestinal cancer stem cells (CSC) are associated with colon cancer. Here, the authors show that Wnt/beta-catenin signalling in CSC requires the epigenetic regulator Mll1 to promote stemness and tumourigenesis in murine and human colon cancer models.
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Affiliation(s)
- Johanna Grinat
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany
| | - Julian Heuberger
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany. .,Division of Gastroenterology and Hepatology, Medical Department, Charité University Medicine, 13353, Berlin, Germany.
| | - Ramon Oliveira Vidal
- Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine (BIMSB/BIH), 13092, Berlin, Germany
| | - Neha Goveas
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frauke Kosel
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany
| | - Antoni Berenguer-Llergo
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Kranz
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | | | - Diana Behrens
- Experimental Pharmacology & Oncology (EPO), 13125, Berlin, Germany
| | - Bálint Melcher
- Institute for Pathology, Klinikum Bayreuth, 95445, Bayreuth, Germany
| | - Sascha Sauer
- Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine (BIMSB/BIH), 13092, Berlin, Germany
| | - Michael Vieth
- Institute for Pathology, Klinikum Bayreuth, 95445, Bayreuth, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - A Francis Stewart
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Walter Birchmeier
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany.
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3
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Watanabe Costa R, Batista MF, Meneghelli I, Vidal RO, Nájera CA, Mendes AC, Andrade-Lima IA, da Silveira JF, Lopes LR, Ferreira LRP, Antoneli F, Bahia D. Comparative Analysis of the Secretome and Interactome of Trypanosoma cruzi and Trypanosoma rangeli Reveals Species Specific Immune Response Modulating Proteins. Front Immunol 2020; 11:1774. [PMID: 32973747 PMCID: PMC7481403 DOI: 10.3389/fimmu.2020.01774] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/02/2020] [Indexed: 12/04/2022] Open
Abstract
Chagas disease, a zoonosis caused by the flagellate protozoan Trypanosoma cruzi, is a chronic and systemic parasitic infection that affects ~5–7 million people worldwide, mainly in Latin America. Chagas disease is an emerging public health problem due to the lack of vaccines and effective treatments. According to recent studies, several T. cruzi secreted proteins interact with the human host during cell invasion. Moreover, some comparative studies with T. rangeli, which is non-pathogenic in humans, have been performed to identify proteins directly involved in the pathogenesis of the disease. In this study, we present an integrated analysis of canonical putative secreted proteins (PSPs) from both species. Additionally, we propose an interactome with human host and gene family clusters, and a phylogenetic inference of a selected protein. In total, we identified 322 exclusively PSPs in T. cruzi and 202 in T. rangeli. Among the PSPs identified in T. cruzi, we found several trans-sialidases, mucins, MASPs, proteins with phospholipase 2 domains (PLA2-like), and proteins with Hsp70 domains (Hsp70-like) which have been previously characterized and demonstrated to be related to T. cruzi virulence. PSPs found in T. rangeli were related to protozoan metabolism, specifically carboxylases and phosphatases. Furthermore, we also identified PSPs that may interact with the human immune system, including heat shock and MASP proteins, but in a lower number compared to T. cruzi. Interestingly, we describe a hypothetical hybrid interactome of PSPs which reveals that T. cruzi secreted molecules may be down-regulating IL-17 whilst T. rangeli may enhance the production of IL-15. These results will pave the way for a better understanding of the pathophysiology of Chagas disease and may ultimately lead to the identification of molecular targets, such as key PSPs, that could be used to minimize the health outcomes of Chagas disease by modulating the immune response triggered by T. cruzi infection.
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Affiliation(s)
- Renata Watanabe Costa
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marina Ferreira Batista
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Isabela Meneghelli
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ramon Oliveira Vidal
- The Berlin Institute for Medical Systems Biology-Max Delbrück Center for Molecular Medicine in the Helmholtz Association in Berlin, Berlin, Germany.,Laboratorio Nacional de Biociências (LNBio), Campinas, São Paulo, Brazil
| | - Carlos Alcides Nájera
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Clara Mendes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Izabela Augusta Andrade-Lima
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - José Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Luciano Rodrigo Lopes
- Departamento de Informática em Saúde, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ludmila Rodrigues Pinto Ferreira
- RNA Systems Biology Lab (RSBL), Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernando Antoneli
- Departamento de Informática em Saúde, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Diana Bahia
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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4
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Zhu Q, Fang L, Heuberger J, Kranz A, Schipper J, Scheckenbach K, Vidal RO, Sunaga-Franze DY, Müller M, Wulf-Goldenberg A, Sauer S, Birchmeier W. The Wnt-Driven Mll1 Epigenome Regulates Salivary Gland and Head and Neck Cancer. Cell Rep 2020; 26:415-428.e5. [PMID: 30625324 DOI: 10.1016/j.celrep.2018.12.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/13/2018] [Accepted: 12/12/2018] [Indexed: 12/29/2022] Open
Abstract
We identified a regulatory system that acts downstream of Wnt/β-catenin signaling in salivary gland and head and neck carcinomas. We show in a mouse tumor model of K14-Cre-induced Wnt/β-catenin gain-of-function and Bmpr1a loss-of-function mutations that tumor-propagating cells exhibit increased Mll1 activity and genome-wide increased H3K4 tri-methylation at promoters. Null mutations of Mll1 in tumor mice and in xenotransplanted human head and neck tumors resulted in loss of self-renewal of tumor-propagating cells and in block of tumor formation but did not alter normal tissue homeostasis. CRISPR/Cas9 mutagenesis and pharmacological interference of Mll1 at sequences that inhibit essential protein-protein interactions or the SET enzyme active site also blocked the self-renewal of mouse and human tumor-propagating cells. Our work provides strong genetic evidence for a crucial role of Mll1 in solid tumors. Moreover, inhibitors targeting specific Mll1 interactions might offer additional directions for therapies to treat these aggressive tumors.
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Affiliation(s)
- Qionghua Zhu
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Liang Fang
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany; Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China; Medi-X Institute, SUSTech Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Julian Heuberger
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Andrea Kranz
- Biotechnology Center, Technical University, 01307 Dresden, Germany
| | - Jörg Schipper
- Department of Head and Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Kathrin Scheckenbach
- Department of Head and Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Ramon Oliveira Vidal
- Systems Biology Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Daniele Yumi Sunaga-Franze
- Systems Biology Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Marion Müller
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | | | - Sascha Sauer
- Systems Biology Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany
| | - Walter Birchmeier
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125 Berlin, Germany.
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5
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Haage V, Semtner M, Vidal RO, Hernandez DP, Pong WW, Chen Z, Hambardzumyan D, Magrini V, Ly A, Walker J, Mardis E, Mertins P, Sauer S, Kettenmann H, Gutmann DH. Correction to: Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma. Acta Neuropathol Commun 2020; 8:1. [PMID: 31915069 PMCID: PMC6947830 DOI: 10.1186/s40478-019-0875-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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6
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Haage V, Semtner M, Vidal RO, Hernandez DP, Pong WW, Chen Z, Hambardzumyan D, Magrini V, Ly A, Walker J, Mardis E, Mertins P, Sauer S, Kettenmann H, Gutmann DH. Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma. Acta Neuropathol Commun 2019; 7:20. [PMID: 30764877 PMCID: PMC6376799 DOI: 10.1186/s40478-019-0665-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/22/2019] [Indexed: 12/21/2022] Open
Abstract
Monocytes/macrophages have begun to emerge as key cellular modulators of brain homeostasis and central nervous system (CNS) disease. In the healthy brain, resident microglia are the predominant macrophage cell population; however, under conditions of blood-brain barrier leakage, peripheral monocytes/macrophages can infiltrate the brain and participate in CNS disease pathogenesis. Distinguishing these two populations is often challenging, owing to a paucity of universally accepted and reliable markers. To identify discriminatory marker sets for microglia and peripheral monocytes/macrophages, we employed a large meta-analytic approach using five published murine transcriptional datasets. Following hierarchical clustering, we filtered the top differentially expressed genes (DEGs) through a brain cell type-specific sequencing database, which led to the identification of eight microglia and eight peripheral monocyte/macrophage markers. We then validated their differential expression, leveraging a published single cell RNA sequencing dataset and quantitative RT-PCR using freshly isolated microglia and peripheral monocytes/macrophages from two different mouse strains. We further verified the translation of these DEGs at the protein level. As top microglia DEGs, we identified P2ry12, Tmem119, Slc2a5 and Fcrls, whereas Emilin2, Gda, Hp and Sell emerged as the best DEGs for identifying peripheral monocytes/macrophages. Lastly, we evaluated their utility in discriminating monocyte/macrophage populations in the setting of brain pathology (glioma), and found that these DEG sets distinguished glioma-associated microglia from macrophages in both RCAS and GL261 mouse models of glioblastoma. Taken together, this unbiased bioinformatic approach facilitated the discovery of a robust set of microglia and peripheral monocyte/macrophage expression markers to discriminate these monocyte populations in both health and disease.
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7
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Streckfuss-Bömeke K, Tiburcy M, Fomin A, Luo X, Li W, Fischer C, Özcelik C, Perrot A, Sossalla S, Haas J, Vidal RO, Rebs S, Khadjeh S, Meder B, Bonn S, Linke WA, Zimmermann WH, Hasenfuss G, Guan K. Severe DCM phenotype of patient harboring RBM20 mutation S635A can be modeled by patient-specific induced pluripotent stem cell-derived cardiomyocytes. J Mol Cell Cardiol 2017; 113:9-21. [PMID: 28941705 DOI: 10.1016/j.yjmcc.2017.09.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 09/01/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
Abstract
The ability to generate patient-specific induced pluripotent stem cells (iPSCs) provides a unique opportunity for modeling heart disease in vitro. In this study, we generated iPSCs from a patient with dilated cardiomyopathy (DCM) caused by a missense mutation S635A in RNA-binding motif protein 20 (RBM20) and investigated the functionality and cell biology of cardiomyocytes (CMs) derived from patient-specific iPSCs (RBM20-iPSCs). The RBM20-iPSC-CMs showed abnormal distribution of sarcomeric α-actinin and defective calcium handling compared to control-iPSC-CMs, suggesting disorganized myofilament structure and altered calcium machinery in CMs of the RBM20 patient. Engineered heart muscles (EHMs) from RBM20-iPSC-CMs showed that not only active force generation was impaired in RBM20-EHMs but also passive stress of the tissue was decreased, suggesting a higher visco-elasticity of RBM20-EHMs. Furthermore, we observed a reduced titin (TTN) N2B-isoform expression in RBM20-iPSC-CMs by demonstrating a reduction of exon skipping in the PEVK region of TTN and an inhibition of TTN isoform switch. In contrast, in control-iPSC-CMs both TTN isoforms N2B and N2BA were expressed, indicating that the TTN isoform switch occurs already during early cardiogenesis. Using next generation RNA sequencing, we mapped transcriptome and splicing target profiles of RBM20-iPSC-CMs and identified different cardiac gene networks in response to the analyzed RBM20 mutation in cardiac-specific processes. These findings shed the first light on molecular mechanisms of RBM20-dependent pathological cardiac remodeling leading to DCM. Our data demonstrate that iPSC-CMs coupled with EHMs provide a powerful tool for evaluating disease-relevant functional defects and for a deeper mechanistic understanding of alternative splicing-related cardiac diseases.
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Affiliation(s)
- Katrin Streckfuss-Bömeke
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany
| | - Malte Tiburcy
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany; Institute of Pharmacology and Toxicology, Universitätsmedizin Göttingen, Germany
| | - Andrey Fomin
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany; Department of Cardiovascular Physiology, Ruhr University Bochum, Germany
| | - Xiaojing Luo
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, Germany
| | - Wener Li
- Institute of Pharmacology and Toxicology, Technische Universität Dresden, Germany
| | - Claudia Fischer
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany
| | - Cemil Özcelik
- Cardiovascular Genetics, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, Germany; Medizinischen Klinik I Kardiologie, Gastroenterologie und Diabetologie, Knappschaftskrankenhaus Recklingshausen, Germany
| | - Andreas Perrot
- Cardiovascular Genetics, Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin, Germany
| | - Samuel Sossalla
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany; Department of Internal Medicine 2 - Cardiology, University Medical Center Regensburg, Germany
| | - Jan Haas
- Department of Cardiology, University of Heidelberg, Germany; DZHK, Partner Site Heidelberg, Germany
| | | | - Sabine Rebs
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany
| | - Sara Khadjeh
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany
| | - Benjamin Meder
- Department of Cardiology, University of Heidelberg, Germany; DZHK, Partner Site Heidelberg, Germany
| | - Stefan Bonn
- German Center for Neurodegenerative Diseases, Göttingen and Tübingen, Germany; Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfgang A Linke
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany; Department of Cardiovascular Physiology, Ruhr University Bochum, Germany
| | - Wolfram-Hubertus Zimmermann
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany; Institute of Pharmacology and Toxicology, Universitätsmedizin Göttingen, Germany
| | - Gerd Hasenfuss
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Germany
| | - Kaomei Guan
- Department of Cardiology and Pneumology, Universitätsmedizin Göttingen, Germany; Institute of Pharmacology and Toxicology, Technische Universität Dresden, Germany.
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8
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Lima GC, Vieira VCC, Cazarin CBB, Ribeiro RDR, Junior SB, de Albuquerque CL, Vidal RO, Netto CC, Yamada ÁT, Augusto F, Maróstica Junior MR. Fructooligosaccharide intake promotes epigenetic changes in the intestinal mucosa in growing and ageing rats. Eur J Nutr 2017; 57:1499-1510. [PMID: 28324207 DOI: 10.1007/s00394-017-1435-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/06/2017] [Indexed: 01/16/2023]
Abstract
PURPOSE The aim of this study was to investigate the relationship between fructooligosaccharide (FOS) intake at different life stages of Wistar rats and its stimulatory effects on intestinal parameters. METHODS Recently weaned and ageing female rats were divided into growing and ageing treatments, which were fed diets that partially replaced sucrose with FOS for 12 weeks. RESULTS Dietary FOS intake induced a significant increase in the numbers of Bifidobacterium and Lactobacillus in growing rats. FOS intake was associated with increased butyric acid levels and a reduced pH of the caecal contents at both ages. Differential gene expression patterns were observed by microarray analysis of growing and ageing animals fed the FOS diet. A total of 133 genes showed detectable changes in expression in the growing rats, while there were only 19 gene expression changes in ageing rats fed with FOS. CONCLUSION These results suggest that dietary FOS intake may be beneficial for some parameters of intestinal health in growing rats.
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Affiliation(s)
| | | | | | | | | | | | - Ramon Oliveira Vidal
- Sainte-Justine University Hospital Center, Université de Montreal, Montreal, Canada
| | - Claudia Cardoso Netto
- Department of Biochemistry, Biological Sciences and Health Center, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Fabio Augusto
- Institute of Chemistry, University of Campinas, Campinas, São Paulo, Brazil
| | - Mário Roberto Maróstica Junior
- School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil. .,Laboratório de Nutrição e Metabolismo-Departamento de Alimentos e Nutrição, Faculdade de Engenharia de Alimentos, Universidade Estadual de Campinas, R. Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil.
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Mofatto LS, Carneiro FDA, Vieira NG, Duarte KE, Vidal RO, Alekcevetch JC, Cotta MG, Verdeil JL, Lapeyre-Montes F, Lartaud M, Leroy T, De Bellis F, Pot D, Rodrigues GC, Carazzolle MF, Pereira GAG, Andrade AC, Marraccini P. Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars. BMC Plant Biol 2016; 16:94. [PMID: 27095276 PMCID: PMC4837521 DOI: 10.1186/s12870-016-0777-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 04/13/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. CONCLUSIONS The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee.
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Affiliation(s)
- Luciana Souto Mofatto
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Fernanda de Araújo Carneiro
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Natalia Gomes Vieira
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Karoline Estefani Duarte
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Ramon Oliveira Vidal
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Jean Carlos Alekcevetch
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | - Michelle Guitton Cotta
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
| | | | | | | | | | | | - David Pot
- />CIRAD UMR AGAP, F-34398 Montpellier, France
| | - Gustavo Costa Rodrigues
- />Embrapa Informática Agropecuária, UNICAMP, Av. André Tosello n° 209, CP 6041, 13083-886 Campinas, SP Brazil
| | - Marcelo Falsarella Carazzolle
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Gonçalo Amarante Guimarães Pereira
- />Laboratório de Genômica e Expressão (LGE), Departamento de Genética e Evolução, Instituto de Biologia/UNICAMP, Cidade Universitária Zeferino Vaz, 13083-970 Campinas, SP Brazil
| | - Alan Carvalho Andrade
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
- />present address: Embrapa Café, INOVACAFÉ, Campus UFLA, 37200-000 Lavras, MG Brazil
| | - Pierre Marraccini
- />Embrapa Recursos Genéticos e Biotecnologia (LGM-NTBio), Parque Estação Biológica, CP 02372, 70770-917, Brasilia, DF Brazil
- />CIRAD UMR AGAP, F-34398 Montpellier, France
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10
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Carazzolle MF, de Carvalho LM, Slepicka HH, Vidal RO, Pereira GAG, Kobarg J, Vaz Meirelles G. IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools. PLoS One 2014; 9:e100385. [PMID: 24949626 PMCID: PMC4065059 DOI: 10.1371/journal.pone.0100385] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. RESULTS We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. CONCLUSIONS We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.
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Affiliation(s)
- Marcelo Falsarella Carazzolle
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Unicamp, Campinas, São Paulo, Brazil
| | - Lucas Miguel de Carvalho
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Hugo Henrique Slepicka
- Laboratório Nacional de Luz Síncrotron, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Ramon Oliveira Vidal
- Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Unicamp, Campinas, São Paulo, Brazil
| | | | - Jörg Kobarg
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Gabriela Vaz Meirelles
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
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11
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Rosa-Ribeiro R, Nishan U, Vidal RO, Barbosa GO, Reis LO, Cesar CL, Carvalho HF. Transcription factors involved in prostate gland adaptation to androgen deprivation. PLoS One 2014; 9:e97080. [PMID: 24886974 PMCID: PMC4041569 DOI: 10.1371/journal.pone.0097080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/15/2014] [Indexed: 11/18/2022] Open
Abstract
Androgens regulate prostate physiology, and exert their effects through the androgen receptor. We hypothesized that androgen deprivation needs additional transcription factors to orchestrate the changes taking place in the gland after castration and for the adaptation of the epithelial cells to the androgen-deprived environment, ultimately contributing to the origin of castration-resistant prostate cancer. This study was undertaken to identify transcription factors that regulate gene expression after androgen deprivation by castration (Cas). For the sake of comparison, we extended the analysis to the effects of administration of a high dose of 17β-estradiol (E2) and a combination of both (Cas+E2). We approached this by (i) identifying gene expression profiles and enrichment terms, and by searching for transcription factors in the derived regulatory pathways; and (ii) by determining the density of putative transcription factor binding sites in the proximal promoter of the 10 most up- or down-regulated genes in each experimental group in comparison to the controls Gapdh and Tbp7. Filtering and validation confirmed the expression and localized EVI1 (Mecom), NFY, ELK1, GATA2, MYBL1, MYBL2, and NFkB family members (NFkB1, NFkB2, REL, RELA and RELB) in the epithelial and/or stromal cells. These transcription factors represent major regulators of epithelial cell survival and immaturity as well as an adaptation of the gland as an immune barrier in the absence of functional stimulation by androgens. Elk1 was expressed in smooth muscle cells and was up-regulated after day 4. Evi1 and Nfy genes are expressed in both epithelium and stroma, but were apparently not affected by androgen deprivation.
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Affiliation(s)
- Rafaela Rosa-Ribeiro
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Umar Nishan
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Ramon Oliveira Vidal
- Laboratory of Bioinformatics, National Center for Research on Energy and Materials, Campinas, São Paulo, Brazil
| | - Guilherme Oliveira Barbosa
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | | | - Carlos Lenz Cesar
- Department of Quantum Physics, State University of Campinas, Campinas, São Paulo, Brazil
- National Institute of Photonics Applied to Cell Biology (INFABiC), State University of Campinas, Campinas, São Paulo, Brazil
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
- National Institute of Photonics Applied to Cell Biology (INFABiC), State University of Campinas, Campinas, São Paulo, Brazil
- * E-mail:
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Oblessuc PR, Cardoso Perseguini JMK, Baroni RM, Chiorato AF, Carbonell SAM, Mondego JMC, Vidal RO, Camargo LEA, Benchimol-Reis LL. Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean. Theor Appl Genet 2013; 126:2451-65. [PMID: 23832048 DOI: 10.1007/s00122-013-2146-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 06/14/2013] [Indexed: 05/21/2023]
Abstract
Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2(UC)) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning.
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Affiliation(s)
- Paula Rodrigues Oblessuc
- Departamento de Genética e Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, 13083-970, Brazil,
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13
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Real F, Vidal RO, Carazzolle MF, Mondego JMC, Costa GGL, Herai RH, Würtele M, de Carvalho LM, Carmona e Ferreira R, Mortara RA, Barbiéri CL, Mieczkowski P, da Silveira JF, Briones MRDS, Pereira GAG, Bahia D. The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models. DNA Res 2013; 20:567-81. [PMID: 23857904 PMCID: PMC3859324 DOI: 10.1093/dnares/dst031] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3′-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment.
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Affiliation(s)
- Fernando Real
- 1Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo - EPM/UNIFESP, Rua Botucatu 862, 6 andar, 04023-062 São Paulo, Brazil
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14
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Vidal RO, do Nascimento LC, Mondego JMC, Pereira GAG, Carazzolle MF. Identification of SNPs in RNA-seq data of two cultivars of Glycine max (soybean) differing in drought resistance. Genet Mol Biol 2012; 35:331-4. [PMID: 22802718 PMCID: PMC3392885 DOI: 10.1590/s1415-47572012000200014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The legume Glycine max (soybean) plays an important economic role in the international commodities market, with a world production of almost 260 million tons for the 2009/2010 harvest. The increase in drought events in the last decade has caused production losses in recent harvests. This fact compels us to understand the drought tolerance mechanisms in soybean, taking into account its variability among commercial and developing cultivars. In order to identify single nucleotide polymorphisms (SNPs) in genes up-regulated during drought stress, we evaluated suppression subtractive libraries (SSH) from two contrasting cultivars upon water deprivation: sensitive (BR 16) and tolerant (Embrapa 48). A total of 2,222 soybean genes were up-regulated in both cultivars. Our method identified more than 6,000 SNPs in tolerant and sensitive Brazilian cultivars in those drought stress related genes. Among these SNPs, 165 (in 127 genes) are positioned at soybean chromosome ends, including transcription factors (MYB, WRKY) related to tolerance to abiotic stress.
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Affiliation(s)
- Ramon Oliveira Vidal
- Laboratório de Genômica e Expressão, Universidade Estadual de Campinas, Campinas, SP, Brazil
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Nascimento LC, Neto JL, Salaza MM, Camargo ELO, Marques WL, Gonçalves DC, Vidal RO, Pereira GAG, Carazzolle MF. An integrated database of Eucalyptusspp. genome project. BMC Proc 2011. [PMCID: PMC3240020 DOI: 10.1186/1753-6561-5-s7-p170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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16
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Salazar MM, Nascimento LC, Camargo ELO, Vidal RO, Lepikson-Neto J, Goncalves DC, Marques WL, Teixeira PJSL, Pereira GAG. Comparative transcriptome analysis of tree Eucalyptusspecies using RNAseq technology: analysis of genes interfering in wood quality aspects. BMC Proc 2011. [PMCID: PMC3240025 DOI: 10.1186/1753-6561-5-s7-p175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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17
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Vidal RO, Mondego JMC, Pot D, Ambrósio AB, Andrade AC, Pereira LFP, Colombo CA, Vieira LGE, Carazzolle MF, Pereira GAG. A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica. Plant Physiol 2010; 154:1053-66. [PMID: 20864545 PMCID: PMC2971587 DOI: 10.1104/pp.110.162438] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Polyploidization constitutes a common mode of evolution in flowering plants. This event provides the raw material for the divergence of function in homeologous genes, leading to phenotypic novelty that can contribute to the success of polyploids in nature or their selection for use in agriculture. Mounting evidence underlined the existence of homeologous expression biases in polyploid genomes; however, strategies to analyze such transcriptome regulation remained scarce. Important factors regarding homeologous expression biases remain to be explored, such as whether this phenomenon influences specific genes, how paralogs are affected by genome doubling, and what is the importance of the variability of homeologous expression bias to genotype differences. This study reports the expressed sequence tag assembly of the allopolyploid Coffea arabica and one of its direct ancestors, Coffea canephora. The assembly was used for the discovery of single nucleotide polymorphisms through the identification of high-quality discrepancies in overlapped expressed sequence tags and for gene expression information indirectly estimated by the transcript redundancy. Sequence diversity profiles were evaluated within C. arabica (Ca) and C. canephora (Cc) and used to deduce the transcript contribution of the Coffea eugenioides (Ce) ancestor. The assignment of the C. arabica haplotypes to the C. canephora (CaCc) or C. eugenioides (CaCe) ancestral genomes allowed us to analyze gene expression contributions of each subgenome in C. arabica. In silico data were validated by the quantitative polymerase chain reaction and allele-specific combination TaqMAMA-based method. The presence of differential expression of C. arabica homeologous genes and its implications in coffee gene expression, ontology, and physiology are discussed.
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