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Kovacik M, Nowicka A, Zwyrtková J, Strejčková B, Vardanega I, Esteban E, Pasha A, Kaduchová K, Krautsova M, Červenková M, Šafář J, Provart NJ, Simon R, Pecinka A. The transcriptome landscape of developing barley seeds. Plant Cell 2024:koae095. [PMID: 38635902 DOI: 10.1093/plcell/koae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
Cereal grains are an important source of food and feed. To provide comprehensive spatiotemporal information about biological processes in developing seeds of cultivated barley (Hordeum vulgare L. subsp. vulgare), we performed a transcriptomic study of the embryo, endosperm, and seed maternal tissues collected from grains 4-32 days after pollination. Weighted gene co-expression network and motif enrichment analyses identified specific groups of genes and transcription factors (TFs) potentially regulating barley seed tissue development. We defined a set of tissue-specific marker genes and families of TFs for functional studies of the pathways controlling barley grain development. Assessing selected groups of chromatin regulators revealed that epigenetic processes are highly dynamic and likely play a major role during barley endosperm development. The repressive H3K27me3 modification is globally reduced in endosperm tissues and at specific genes related to development and storage compounds. Altogether, this atlas uncovers the complexity of developmentally regulated gene expression in developing barley grains.
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Affiliation(s)
- Martin Kovacik
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
| | - Anna Nowicka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Niezapominajek 21, 30 239 Kraków, Poland
| | - Jana Zwyrtková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Beáta Strejčková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Isaia Vardanega
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Kateřina Kaduchová
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Maryna Krautsova
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Marie Červenková
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Jan Šafář
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine-University, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Ales Pecinka
- Institute of Experimental Botany, Czech Acad Sci, Centre of Plant Structural and Functional Genomics, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 779 00 Olomouc, Czech Republic
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2
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Pahari S, Vaid N, Soolanayakanahally R, Kagale S, Pasha A, Esteban E, Provart N, Stobbs JA, Vu M, Meira D, Karunakaran C, Boda P, Prasannakumar MK, Nagaraja A, Jain AK. Nutri-cereal tissue-specific transcriptome atlas during development: Functional integration of gene expression to identify mineral uptake pathways in little millet (Panicum sumatrense). Plant J 2024. [PMID: 38576267 DOI: 10.1111/tpj.16749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/06/2024]
Abstract
Little millet (Panicum sumatrense Roth ex Roem. & Schult.) is an essential minor millet of southeast Asia and Africa's temperate and subtropical regions. The plant is stress-tolerant, has a short life cycle, and has a mineral-rich nutritional profile associated with unique health benefits. We report the developmental gene expression atlas of little millet (genotype JK-8) from ten tissues representing different stages of its life cycle, starting from seed germination and vegetative growth to panicle maturation. The developmental transcriptome atlas led to the identification of 342 827 transcripts. The BUSCO analysis and comparison with the transcriptomes of related species confirm that this study presents high-quality, in-depth coverage of the little millet transcriptome. In addition, the eFP browser generated here has a user-friendly interface, allowing interactive visualizations of tissue-specific gene expression. Using these data, we identified transcripts, the orthologs of which in Arabidopsis and rice are involved in nutrient acquisition, transport, and response pathways. The comparative analysis of the expression levels of these transcripts holds great potential for enhancing the mineral content in crops, particularly zinc and iron, to address the issue of "hidden hunger" and to attain nutritional security, making it a valuable asset for translational research.
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Affiliation(s)
- Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - Miranda Vu
- Canadian Light Source Inc, Saskatoon, Saskatchewan, Canada
| | - Debora Meira
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL, United States
| | | | - Praveen Boda
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | | | - Alur Nagaraja
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
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3
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Fan C, Lyu M, Zeng B, He Q, Wang X, Lu MZ, Liu B, Liu J, Esteban E, Pasha A, Provart NJ, Wang H, Zhang J. Profiling of the gene expression and alternative splicing landscapes of Eucalyptus grandis. Plant Cell Environ 2024; 47:1363-1378. [PMID: 38221855 DOI: 10.1111/pce.14814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024]
Abstract
Eucalyptus is a widely planted hardwood tree species due to its fast growth, superior wood properties and adaptability. However, the post-transcriptional regulatory mechanisms controlling tissue development and stress responses in Eucalyptus remain poorly understood. In this study, we performed a comprehensive analysis of the gene expression profile and the alternative splicing (AS) landscape of E. grandis using strand-specific RNA-Seq, which encompassed 201 libraries including different organs, developmental stages, and environmental stresses. We identified 10 416 genes (33.49%) that underwent AS, and numerous differentially expressed and/or differential AS genes involved in critical biological processes, such as primary-to-secondary growth transition of stems, adventitious root formation, aging and responses to phosphorus- or boron-deficiency. Co-expression analysis of AS events and gene expression patterns highlighted the potential upstream regulatory role of AS events in multiple processes. Additionally, we highlighted the lignin biosynthetic pathway to showcase the potential regulatory functions of AS events in the KNAT3 and IRL3 genes within this pathway. Our high-quality expression atlas and AS landscape serve as valuable resources for unravelling the genetic control of woody plant development, long-term adaptation, and understanding transcriptional diversity in Eucalyptus. Researchers can conveniently access these resources through the interactive ePlant browser (https://bar.utoronto.ca/eplant_eucalyptus).
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Affiliation(s)
- Chunjie Fan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Mingjie Lyu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Bingshan Zeng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Qiang He
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of State Forestry and Grassland Administration on Tropical Forestry, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Bobin Liu
- Jiansu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eddi Esteban
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
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4
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Schnabel E, Thomas J, El-Hawaz R, Gao Y, Poehlman WL, Chavan S, Pasha A, Esteban E, Provart N, Feltus FA, Frugoli J. Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia. Mol Plant Microbe Interact 2023; 36:805-820. [PMID: 37717250 DOI: 10.1094/mpmi-03-23-0029-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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] [Indexed: 09/19/2023]
Abstract
We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Elise Schnabel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Jacklyn Thomas
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Rabia El-Hawaz
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - William L Poehlman
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Sage Bionetworks, Seattle, WA 98121, U.S.A
| | - Suchitra Chavan
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Leidos, Inc., Atlanta, GA 30345, U.S.A
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - F Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, U.S.A
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, U.S.A
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
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5
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Da Ros L, Bollina V, Soolanayakanahally R, Pahari S, Elferjani R, Kulkarni M, Vaid N, Risseuw E, Cram D, Pasha A, Esteban E, Konkin D, Provart N, Nambara E, Kagale S. Multi-omics atlas of combinatorial abiotic stress responses in wheat. Plant J 2023; 116:1118-1135. [PMID: 37248640 DOI: 10.1111/tpj.16332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/10/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Field-grown crops rarely experience growth conditions in which yield can be maximized. Environmental stresses occur in combination, with advancements in crop tolerance further complicated by its polygenic nature. Strategic targeting of causal genes is required to meet future crop production needs. Here, we employed a systems biology approach in wheat (Triticum aestivum L.) to investigate physio-metabolic adjustments and transcriptome reprogramming involved in acclimations to heat, drought, salinity and all combinations therein. A significant shift in magnitude and complexity of plant response was evident across stress scenarios based on the agronomic losses, increased proline concentrations and 8.7-fold increase in unique differentially expressed transcripts (DETs) observed under the triple stress condition. Transcriptome data from all stress treatments were assembled into an online, open access eFP browser for visualizing gene expression during abiotic stress. Weighted gene co-expression network analysis revealed 152 hub genes of which 32% contained the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) transcriptional repression motif. Cross-referencing against the 31 DETs common to all stress treatments isolated TaWRKY33 as a leading candidate for greater plant tolerance to combinatorial stresses. Integration of our findings with available literature on gene functional characterization allowed us to further suggest flexible gene combinations for future adaptive gene stacking in wheat. Our approach demonstrates the strength of robust multi-omics-based data resources for gene discovery in complex environmental conditions. Accessibility of such datasets will promote cross-validation of candidate genes across studies and aid in accelerating causal gene validation for crop resiliency.
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Affiliation(s)
- Letitia Da Ros
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, British Columbia, Canada
| | - Venkatesh Bollina
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Raju Soolanayakanahally
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Shankar Pahari
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Raed Elferjani
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Manoj Kulkarni
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Neha Vaid
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Eddy Risseuw
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, Canada
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6
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Jiang Y, N'Diaye A, Koh CS, Quilichini TD, Shunmugam ASK, Kirzinger MW, Konkin D, Bekkaoui Y, Sari E, Pasha A, Esteban E, Provart NJ, Higgins JD, Rozwadowski K, Sharpe AG, Pozniak CJ, Kagale S. The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat. Plant J 2023; 114:209-224. [PMID: 36710629 DOI: 10.1111/tpj.16125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.
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Affiliation(s)
- Yunfei Jiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Amidou N'Diaye
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Arun S K Shunmugam
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Morgan W Kirzinger
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Ehsan Sari
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - James D Higgins
- Department of Genetics and Genome Biology, University of Leicester, Adrian Building, University Road, Leicester, Leicestershire, LE1 7RH, UK
| | - Kevin Rozwadowski
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Pl., Saskatoon, SK, S7N 0X2, Canada
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Rd., Saskatoon, SK, S7N 4L8, Canada
| | - Curtis J Pozniak
- Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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7
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Gao P, Quilichini TD, Yang H, Li Q, Nilsen KT, Qin L, Babic V, Liu L, Cram D, Pasha A, Esteban E, Condie J, Sidebottom C, Zhang Y, Huang Y, Zhang W, Bhowmik P, Kochian LV, Konkin D, Wei Y, Provart NJ, Kagale S, Smith M, Patterson N, Gillmor CS, Datla R, Xiang D. Evolutionary divergence in embryo and seed coat development of U's Triangle Brassica species illustrated by a spatiotemporal transcriptome atlas. New Phytol 2022; 233:30-51. [PMID: 34687557 DOI: 10.1111/nph.17759] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
The economically valuable Brassica species include the six related members of U's Triangle. Despite the agronomic and economic importance of these Brassicas, the impacts of evolution and relatively recent domestication events on the genetic landscape of seed development have not been comprehensively examined in these species. Here we present a 3D transcriptome atlas for the six species of U's Triangle, producing a unique resource that captures gene expression data for the major subcompartments of the seed, from the unfertilized ovule to the mature embryo and seed coat. This comprehensive dataset for seed development in tetraploid and ancestral diploid Brassicas provides new insights into evolutionary divergence and expression bias at the gene and subgenome levels during the domestication of these valued crop species. Comparisons of gene expression associated with regulatory networks and metabolic pathways operating in the embryo and seed coat during seed development reveal differences in storage reserve accumulation and fatty acid metabolism among the six Brassica species. This study illustrates the genetic underpinnings of seed traits and the selective pressures placed on seed production, providing an immense resource for continued investigation of Brassica polyploid biology, genomics and evolution.
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Affiliation(s)
- Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Hui Yang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kirby T Nilsen
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Li Qin
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Vivijan Babic
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Li Liu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Asher Pasha
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Janet Condie
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Christine Sidebottom
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yan Zhang
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Yi Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Pankaj Bhowmik
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Yangdou Wei
- College of Art & Science, University of Saskatchewan, 9 Campus Dr, Saskatoon, SK, S7N 5A5, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Mark Smith
- Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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8
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Kehelpannala C, Rupasinghe T, Pasha A, Esteban E, Hennessy T, Bradley D, Ebert B, Provart NJ, Roessner U. An Arabidopsis lipid map reveals differences between tissues and dynamic changes throughout development. Plant J 2021; 107:287-302. [PMID: 33866624 PMCID: PMC8361726 DOI: 10.1111/tpj.15278] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/30/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 05/24/2023]
Abstract
Mass spectrometry is the predominant analytical tool used in the field of plant lipidomics. However, there are many challenges associated with the mass spectrometric detection and identification of lipids because of the highly complex nature of plant lipids. Studies into lipid biosynthetic pathways, gene functions in lipid metabolism, lipid changes during plant growth and development, and the holistic examination of the role of plant lipids in environmental stress responses are often hindered. Here, we leveraged a robust pipeline that we previously established to extract and analyze lipid profiles of different tissues and developmental stages from the model plant Arabidopsis thaliana. We analyzed seven tissues at several different developmental stages and identified more than 200 lipids from each tissue analyzed. The data were used to create a web-accessible in silico lipid map that has been integrated into an electronic Fluorescent Pictograph (eFP) browser. This in silico library of Arabidopsis lipids allows the visualization and exploration of the distribution and changes of lipid levels across selected developmental stages. Furthermore, it provides information on the characteristic fragments of lipids and adducts observed in the mass spectrometer and their retention times, which can be used for lipid identification. The Arabidopsis tissue lipid map can be accessed at http://bar.utoronto.ca/efp_arabidopsis_lipid/cgi-bin/efpWeb.cgi.
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Affiliation(s)
- Cheka Kehelpannala
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | | | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Thomas Hennessy
- Agilent Technologies Australia Pty Ltd679 Springvale RoadMulgraveVIC3170Australia
| | - David Bradley
- Agilent Technologies Australia Pty Ltd679 Springvale RoadMulgraveVIC3170Australia
| | - Berit Ebert
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
| | - Nicholas J. Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Ute Roessner
- School of BioSciencesThe University of MelbourneMelbourneVIC3010Australia
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9
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Thiel J, Koppolu R, Trautewig C, Hertig C, Kale SM, Erbe S, Mascher M, Himmelbach A, Rutten T, Esteban E, Pasha A, Kumlehn J, Provart NJ, Vanderauwera S, Frohberg C, Schnurbusch T. Transcriptional landscapes of floral meristems in barley. Sci Adv 2021; 7:eabf0832. [PMID: 33910893 PMCID: PMC8081368 DOI: 10.1126/sciadv.abf0832] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/26/2021] [Indexed: 05/02/2023]
Abstract
Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.
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Affiliation(s)
- J Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - R Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - C Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - C Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S Erbe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - M Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - A Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - T Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - E Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - A Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - J Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - N J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - S Vanderauwera
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - C Frohberg
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - T Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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10
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Gray J, Rodríguez-Abreu D, Powell S, Hochmair M, Gadgeel S, Esteban E, Felip E, Speranza G, De Angelis F, Dómine M, Cheng S, Bischoff H, Peled N, Reck M, Hui R, Garon E, Boyer M, Kurata T, Yang J, Jensen E, Souza F, Garassino M. FP13.02 Pembrolizumab + Pemetrexed-Platinum vs Pemetrexed-Platinum for Metastatic NSCLC: 4-Year Follow-up From KEYNOTE-189. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.141] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Bizouerne E, Buitink J, Vu BL, Vu JL, Esteban E, Pasha A, Provart N, Verdier J, Leprince O. Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour. BMC Plant Biol 2021; 21:124. [PMID: 33648457 PMCID: PMC7923611 DOI: 10.1186/s12870-021-02889-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 07/22/2020] [Accepted: 02/11/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy. RESULTS During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes. CONCLUSION The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.
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Affiliation(s)
- Elise Bizouerne
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Julia Buitink
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Benoît Ly Vu
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Joseph Ly Vu
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Eddi Esteban
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology / Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jérôme Verdier
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Olivier Leprince
- Institut Agro, Univ Angers, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France.
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12
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Rich-Griffin C, Eichmann R, Reitz MU, Hermann S, Woolley-Allen K, Brown PE, Wiwatdirekkul K, Esteban E, Pasha A, Kogel KH, Provart NJ, Ott S, Schäfer P. Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots. Plant Cell 2020; 32:2742-2762. [PMID: 32699170 PMCID: PMC7474276 DOI: 10.1105/tpc.20.00154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/07/2020] [Accepted: 07/20/2020] [Indexed: 05/04/2023]
Abstract
While root diseases are among the most devastating stresses in global crop production, our understanding of root immunity is still limited relative to our knowledge of immune responses in leaves. Considering that root performance is based on the concerted functions of its different cell types, we undertook a cell type-specific transcriptome analysis to identify gene networks activated in epidermis, cortex, and pericycle cells of Arabidopsis (Arabidopsis thaliana) roots challenged with two immunity elicitors, the bacterial flagellin-derived flg22 and the endogenous Pep1 peptide. Our analyses revealed distinct immunity gene networks in each cell type. To further substantiate our understanding of regulatory patterns underlying these cell type-specific immunity networks, we developed a tool to analyze paired transcription factor binding motifs in the promoters of cell type-specific genes. Our study points toward a connection between cell identity and cell type-specific immunity networks that might guide cell types in launching immune response according to the functional capabilities of each cell type.
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Affiliation(s)
| | - Ruth Eichmann
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Institute of Molecular Botany, Ulm University, 89069 Ulm, Germany
| | - Marco U Reitz
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sophie Hermann
- Institute of Phytopathology, Justus Liebig University, 35392 Giessen, Germany
| | | | - Paul E Brown
- Bioinformatics Research Technology Platform, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Kate Wiwatdirekkul
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Justus Liebig University, 35392 Giessen, Germany
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Sascha Ott
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Patrick Schäfer
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Institute of Molecular Botany, Ulm University, 89069 Ulm, Germany
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
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13
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Doll NM, Just J, Brunaud V, Caïus J, Grimault A, Depège-Fargeix N, Esteban E, Pasha A, Provart NJ, Ingram GC, Rogowsky PM, Widiez T. Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. Plant Cell 2020; 32:833-852. [PMID: 32086366 PMCID: PMC7145466 DOI: 10.1105/tpc.19.00756] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/03/2020] [Accepted: 02/20/2020] [Indexed: 05/23/2023]
Abstract
Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm, and maternal tissues). However, the complexity of the kernel makes it difficult to understand intercompartment interactions without access to spatially accurate information. Here, we took advantage of the large size of the maize (Zea mays) kernel to characterize genome-wide expression profiles of tissues at different embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared with whole seed compartments: the scutellar aleurone layer and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 d after pollination and persists for around 11 d, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated and to which additional endosperm cells are recruited as the embryo grows.
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Affiliation(s)
- Nicolas M Doll
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, F-91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, F-91405 Orsay, France
| | - José Caïus
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, F-91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, F-91405 Orsay, France
| | - Aurélie Grimault
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Nathalie Depège-Fargeix
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Gwyneth C Ingram
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
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14
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Ferrari C, Shivhare D, Hansen BO, Pasha A, Esteban E, Provart NJ, Kragler F, Fernie A, Tohge T, Mutwil M. Expression Atlas of Selaginella moellendorffii Provides Insights into the Evolution of Vasculature, Secondary Metabolism, and Roots. Plant Cell 2020; 32:853-870. [PMID: 31988262 PMCID: PMC7145505 DOI: 10.1105/tpc.19.00780] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/08/2020] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
Selaginella moellendorffii is a representative of the lycophyte lineage that is studied to understand the evolution of land plant traits such as the vasculature, leaves, stems, roots, and secondary metabolism. However, only a few studies have investigated the expression and transcriptional coordination of Selaginella genes, precluding us from understanding the evolution of the transcriptional programs behind these traits. We present a gene expression atlas comprising all major organs, tissue types, and the diurnal gene expression profiles for S. moellendorffii We show that the transcriptional gene module responsible for the biosynthesis of lignocellulose evolved in the ancestor of vascular plants and pinpoint the duplication and subfunctionalization events that generated multiple gene modules involved in the biosynthesis of various cell wall types. We demonstrate how secondary metabolism is transcriptionally coordinated and integrated with other cellular pathways. Finally, we identify root-specific genes and show that the evolution of roots did not coincide with an increased appearance of gene families, suggesting that the development of new organs does not coincide with increased fixation of new gene functions. Our updated database at conekt.plant.tools represents a valuable resource for studying the evolution of genes, gene families, transcriptomes, and functional gene modules in the Archaeplastida kingdom.
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Affiliation(s)
- Camilla Ferrari
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Devendra Shivhare
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Bjoern Oest Hansen
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Takayuki Tohge
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Marek Mutwil
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
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15
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Zhang L, Liu M, Long H, Dong W, Pasha A, Esteban E, Li W, Yang X, Li Z, Song A, Ran D, Zhao G, Zeng Y, Chen H, Zou M, Li J, Liang F, Xie M, Hu J, Wang D, Cao H, Provart NJ, Zhang L, Tan X. Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production. Genomics Proteomics Bioinformatics 2020; 17:558-575. [PMID: 32224189 PMCID: PMC7212303 DOI: 10.1016/j.gpb.2019.03.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 12/12/2018] [Accepted: 03/29/2019] [Indexed: 12/05/2022]
Abstract
Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further whole-genome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites; 17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.
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Affiliation(s)
- Lin Zhang
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China; (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
| | - Meilan Liu
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Hongxu Long
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Wei Dong
- (4)State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Asher Pasha
- (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Wenying Li
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Xiaoming Yang
- (5)College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Ze Li
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China
| | - Aixia Song
- (4)State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Duo Ran
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Guang Zhao
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Yanling Zeng
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Hao Chen
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
| | - Ming Zou
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Jingjing Li
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Fan Liang
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Meili Xie
- (6)Nextomics Biosciences Co., Wuhan 430073, China; (7)Oil Crop Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jiang Hu
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Depeng Wang
- (6)Nextomics Biosciences Co., Wuhan 430073, China
| | - Heping Cao
- (8)US Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, New Orleans, LA 70124, USA.
| | - Nicholas J Provart
- (3)Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
| | - Liangsheng Zhang
- (4)State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Xiaofeng Tan
- (1)Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, China; (2)Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China.
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Guitart C, Alejandre C, Torrús I, Balaguer M, Esteban E, Cambra FJ, Jordan I. Impact of a modification of the clinical practice guide of the American Academy of Pediatrics in the management of severe acute bronchiolitis in a pediatric intensive care unit. Med Intensiva 2019; 45:289-297. [PMID: 31892419 PMCID: PMC7115415 DOI: 10.1016/j.medin.2019.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 07/19/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To describe the characteristics and evolution of patients with bronchiolitis admitted to a pediatric intensive care unit, and compare treatment pre- and post-publication of the American Academy of Pediatrics clinical practice guide. DESIGN A descriptive and observational study was carried out between September 2010 and September 2017. SETTING Pediatric intensive care unit. PATIENTS Infants under one year of age with severe bronchiolitis. INTERVENTIONS Two periods were compared (2010-14 and 2015-17), corresponding to before and after modification of the American Academy of Pediatrics guidelines for the management of bronchiolitis in hospital. MAIN VARIABLES Patient sex, age, comorbidities, severity, etiology, administered treatment, bacterial infections, respiratory and inotropic support, length of stay and mortality. RESULTS A total of 706 patients were enrolled, of which 414 (58.6%) males, with a median age of 47 days (IQR 25-100.25). Median bronchiolitis severity score (BROSJOD) upon admission: 9 points (IQR 7-11). Respiratory syncytial virus appeared in 460 (65.16%) patients. The first period (2010-14) included 340 patients and the second period (2015-17) 366 patients. More adrenalin and hypertonic saline nebulizations and more corticosteroid treatment were administered in the second period. More noninvasive ventilation and less conventional mechanical ventilation were used, and less inotropic support was needed, with no significant differences. The antibiotherapy rate decreased significantly (P=.003). CONCLUSIONS Despite the decrease in antibiotherapy, the use of nebulizations and glucocorticoids in these patients should be limited, as recommended by the guide.
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Affiliation(s)
- C Guitart
- Unidad de Cuidados Intensivos Pediátricos (UCIP), Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España
| | - C Alejandre
- Unidad de Cuidados Intensivos Pediátricos (UCIP), Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España.
| | - I Torrús
- Servicio de Pediatría, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España
| | - M Balaguer
- Unidad de Cuidados Intensivos Pediátricos (UCIP), Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España
| | - E Esteban
- Unidad de Cuidados Intensivos Pediátricos (UCIP), Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España
| | - F J Cambra
- Unidad de Cuidados Intensivos Pediátricos (UCIP), Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España
| | - I Jordan
- Unidad de Cuidados Intensivos Pediátricos (UCIP), Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, España
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17
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Gadgeel S, Rodriguez-Abreu D, Felip E, Esteban E, Speranza G, Reck M, Hui R, Boyer M, Garon E, Horinouchi H, Cristescu R, Aurora-Garg D, Lunceford J, Kobie J, Ayers M, Piperdi B, Pietanza M, Garassino M. KRAS mutational status and efficacy in KEYNOTE-189: Pembrolizumab (pembro) plus chemotherapy (chemo) vs placebo plus chemo as first-line therapy for metastatic non-squamous NSCLC. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz453.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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18
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Xiang D, Quilichini TD, Liu Z, Gao P, Pan Y, Li Q, Nilsen KT, Venglat P, Esteban E, Pasha A, Wang Y, Wen R, Zhang Z, Hao Z, Wang E, Wei Y, Cuthbert R, Kochian LV, Sharpe A, Provart N, Weijers D, Gillmor CS, Pozniak C, Datla R. The Transcriptional Landscape of Polyploid Wheats and Their Diploid Ancestors during Embryogenesis and Grain Development. Plant Cell 2019; 31:2888-2911. [PMID: 31628162 PMCID: PMC6925018 DOI: 10.1105/tpc.19.00397] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/07/2019] [Accepted: 10/16/2019] [Indexed: 05/17/2023]
Abstract
Modern wheat production comes from two polyploid species, Triticum aestivum and Triticum turgidum (var durum), which putatively arose from diploid ancestors Triticum urartu, Aegilops speltoides, and Aegilops tauschii How gene expression during embryogenesis and grain development in wheats has been shaped by the differing contributions of diploid genomes through hybridization, polyploidization, and breeding selection is not well understood. This study describes the global landscape of gene activities during wheat embryogenesis and grain development. Using comprehensive transcriptomic analyses of two wheat cultivars and three diploid grasses, we investigated gene expression at seven stages of embryo development, two endosperm stages, and one pericarp stage. We identified transcriptional signatures and developmental similarities and differences among the five species, revealing the evolutionary divergence of gene expression programs and the contributions of A, B, and D subgenomes to grain development in polyploid wheats. The characterization of embryonic transcriptional programming in hexaploid wheat, tetraploid wheat, and diploid grass species provides insight into the landscape of gene expression in modern wheat and its ancestral species. This study presents a framework for understanding the evolution of domesticated wheat and the selective pressures placed on grain production, with important implications for future performance and yield improvements.plantcell;31/12/2888/FX1F1fx1.
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Affiliation(s)
- Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Ziying Liu
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Peng Gao
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1A 0R6, Canada
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Kirby T Nilsen
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Prakash Venglat
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Shenzhen University, Shenzhen 518060, China
| | - Rui Wen
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Zhongjuan Zhang
- Laboratory of Biochemistry, Wageningen University, 6703HA Wageningen, The Netherlands
| | - Zhaodong Hao
- Laboratory of Biochemistry, Wageningen University, 6703HA Wageningen, The Netherlands
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Yangdou Wei
- College of Art and Science, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A5, Canada
| | - Richard Cuthbert
- Agriculture and Agri-Food Canada, Swift Current, Saskatchewan S9H 3X2, Canada
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada
| | - Andrew Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703HA Wageningen, The Netherlands
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato 36824, México
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
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19
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Gadgeel S, Garassino M, Esteban E, Speranza G, Felip E, Hochmair M, Powell S, Cheng SS, Bischoff H, Peled N, Hui R, Reck M, Kurata T, Garon E, Boyer M, Yang J, Pietanza M, Rodríguez-Abreu D. O.03 KEYNOTE-189: OS Update and Progression After the Next Line of Therapy (PFS2) with Pembrolizumab + Chemotherapy for Metastatic Nonsquamous NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.09.090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Sullivan A, Purohit PK, Freese NH, Pasha A, Esteban E, Waese J, Wu A, Chen M, Chin CY, Song R, Watharkar SR, Chan AP, Krishnakumar V, Vaughn MW, Town C, Loraine AE, Provart NJ. An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data. Plant J 2019; 100:641-654. [PMID: 31350781 PMCID: PMC6899666 DOI: 10.1111/tpj.14468] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 04/09/2019] [Revised: 06/25/2019] [Accepted: 07/02/2019] [Indexed: 05/10/2023]
Abstract
Improvements in next-generation sequencing technologies have resulted in dramatically reduced sequencing costs. This has led to an explosion of '-seq'-based methods, of which RNA sequencing (RNA-seq) for generating transcriptomic data is the most popular. By analysing global patterns of gene expression in organs/tissues/cells of interest or in response to chemical or environmental perturbations, researchers can better understand an organism's biology. Tools designed to work with large RNA-seq data sets enable analyses and visualizations to help generate hypotheses about a gene's function. We present here a user-friendly RNA-seq data exploration tool, called the 'eFP-Seq Browser', that shows the read map coverage of a gene of interest in each of the samples along with 'electronic fluorescent pictographic' (eFP) images that serve as visual representations of expression levels. The tool also summarizes the details of each RNA-seq experiment, providing links to archival databases and publications. It automatically computes the reads per kilobase per million reads mapped expression-level summaries and point biserial correlation scores to sort the samples based on a gene's expression level or by how dissimilar the read map profile is from a gene splice variant, to quickly identify samples with the strongest expression level or where alternative splicing might be occurring. Links to the Integrated Genome Browser desktop visualization tool allow researchers to visualize and explore the details of RNA-seq alignments summarized in eFP-Seq Browser as coverage graphs. We present four cases of use of the eFP-Seq Browser for ABI3, SR34, SR45a and U2AF65B, where we examine expression levels and identify alternative splicing. The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/. OPEN RESEARCH BADGES: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. Tool is at https://bar.utoronto.ca/eFP-Seq_Browser/; RNA-seq data at https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/ and https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/Klepikova/. Code is available at https://github.com/BioAnalyticResource/eFP-Seq-Browser.
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Affiliation(s)
- Alexander Sullivan
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Priyank K. Purohit
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | | | - Asher Pasha
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Eddi Esteban
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Alison Wu
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Michelle Chen
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Chih Y. Chin
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | - Richard Song
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
| | | | | | | | - Matthew W. Vaughn
- Texas Advanced Computing CenterUniversity of Texas at AustinAustinTXUSA
| | | | | | - Nicholas J. Provart
- Department of Cell and Systems Biology/CAGEFUniversity of TorontoTorontoONCanada
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21
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Suarez Rodriguez C, Arranz Arija J, Morales Barrera R, Puente J, Reig O, Faez L, González del Alba A, Valderrama B, Gallardo E, Mellado B, Esteban E, Jimenez J, Vivancos A, Carles J. mTOR mutations are not associated with shorter PFS and OS in patients treated with mTOR inhibitors. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz249.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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22
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Massuti Sureda B, Sanchez Torres J, Cobo Dols M, Moran Bueno M, Gonzalez-Larriba J, Barneto Aranda I, De Castro Carpeno J, Iglesias L, Muñoz M, López Vivanco G, Isla Casado M, López R, de las Penas Bataller R, Rodriguez Abreu D, Artal-Cortes A, Esteban E, Provencio M, Pereira E, Sanchez-Paya J, Rosell R. BRCA1 expression level as prognostic factor for recurrence in resected NSCLC with adjuvant chemotherapy: SCAT Trial. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Garassino M, Rodriguez-Abreu D, Gadgeel S, Esteban E, Felip E, Speranza G, Reck M, Hui R, Boyer M, Cristescu R, Aurora-Garg D, Albright A, Loboda A, Kobie J, Lunceford J, Ayers M, Lubiniecki G, Piperdi B, Pietanza M, Garon E. OA04.06 Evaluation of TMB in KEYNOTE-189: Pembrolizumab Plus Chemotherapy vs Placebo Plus Chemotherapy for Nonsquamous NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.427] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Massuti B, Sanchez J, Cobo M, Moran T, Larriba JG, Barneto I, De Castro Carpeno J, Iglesias L, Muñoz M, López-Vivanco G, Isla D, López R, De Las Penas R, Rodriguez-Abreu D, Artal A, Esteban E, Provencio M, Pereira E, Sanchez-Payá J, Rosell R. MA02.01 Reccurrence Pattern After Adjuvant Customized Chemotherapy Based on BRCA Expression Level (SCAT Trial). J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Grimm MO, Schmidinger M, Duran Martinez I, Schinzari G, Esteban E, Schmitz M, Schumacher U, Baretton G, Barthelemy P, Melichar B, Charnley N, Schrijvers D, Albiges L. Tailored immunotherapy approach with nivolumab in advanced renal cell carcinoma (TITAN-RCC). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz394.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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26
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Yébenes JC, Lorencio C, Esteban E, Espinosa L, Badia JM, Capdevila JA, Cisteró B, Moreno S, Calbo E, Jiménez-Fábrega X, Clèries M, Faixedas MT, Ferrer R, Vela E, Medina C, Rodríguez A, Netto C, Armero E, Solsona M, Lopez R, Granes A, Perez-Claveria V, Artigas A, Estany J. Interhospital Sepsis Code in Catalonia (Spain): Territorial model for initial care of patients with sepsis. Med Intensiva 2019; 44:36-45. [PMID: 31542182 DOI: 10.1016/j.medin.2019.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 04/08/2019] [Revised: 05/10/2019] [Accepted: 05/27/2019] [Indexed: 12/29/2022]
Abstract
Sepsis is a syndromic entity with high prevalence and mortality. The management of sepsis is standardized and exhibits time-dependent efficiency. However, the management of patients with sepsis is complex. The heterogeneity of the forms of presentation can make it difficult to detect and manage such cases, in the same way as differences in training, professional competences or the availability of health resources. The Advisory Commission for Patient Care with Sepsis (CAAPAS), comprising 7 scientific societies, the Emergency Medical System (SEM) and the Catalan Health Service (CatSalut), have developed the Interhospital Sepsis Code (CSI) in Catalonia (Spain). The general objective of the CSI is to increase awareness, promote early detection and facilitate initial care and interhospital coordination to attend septic patients in a homogeneous manner throughout Catalonia.
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Affiliation(s)
- J C Yébenes
- Servei de Medicina Intensiva, Hospital de Mataró, Mataró, España.
| | - C Lorencio
- Servei de Medicina Intensiva, Hospital Universitari Dr. Josep Trueta, Girona, España
| | - E Esteban
- Servei de Medicina Intensiva, Hospital Sant Joan de Déu, Barcelona, España
| | - L Espinosa
- Consorci Sanitari de Barcelona, CatSalut-Servei Català de la Salut, Barcelona, España
| | - J M Badia
- Servei de Cirurgia General, Hospital Fundació Asil de Granollers, Granollers, España
| | - J A Capdevila
- Servei de Medicina Interna, Hospital de Mataró, Mataró, España
| | - B Cisteró
- Servei d'Urgències, Corporació Sanitària Parc Taulí, Sabadell, España
| | - S Moreno
- Àrea Bàsica de Salut Gràcia, Barcelona, España
| | - E Calbo
- Servei de Medicina Interna-Malalties Infeccioses, Hospital Mutua de Terrassa, Terrassa, España
| | | | - M Clèries
- Unitat d'Informació i Coneixement, CatSalut-Servei Català de la Salut, Barcelona, España
| | - M T Faixedas
- Oficina Tècnica dels Registres de Codis d'Activació, CatSalut-Servei Català de la Salut, Barcelona, España
| | - R Ferrer
- Servei de Medicina Intensiva, Hospital Universitari Vall d'Hebron, Barcelona, España
| | - E Vela
- Unitat d'Informació i Coneixement, CatSalut-Servei Català de la Salut, Barcelona, España
| | - C Medina
- Oficina Tècnica dels Registres de Codis d'Activació, CatSalut-Servei Català de la Salut, Barcelona, España
| | - A Rodríguez
- Servei de Medicina Intensiva, Hospital Universitari Joan XXIII, Tarragona, España
| | - C Netto
- Servei d'Urgències, Corporació Sanitària Parc Taulí, Sabadell, España
| | - E Armero
- Servei d'Urgències, Hospital Comarcal de Blanes, Blanes, España
| | - M Solsona
- Servei de Medicina Intensiva, Hospital de Mataró, Mataró, España
| | - R Lopez
- Consorci Sanitari de Barcelona, CatSalut-Servei Català de la Salut, Barcelona, España
| | - A Granes
- Sistema d'Emergències Mèdiques (SEM)
| | | | - A Artigas
- Servei de Medicina Intensiva, Corporació Sanitària Parc Taulí, Sabadell, España
| | - J Estany
- Consorci Sanitari de Barcelona, CatSalut-Servei Català de la Salut, Barcelona, España
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27
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Yi F, Gu W, Chen J, Song N, Gao X, Zhang X, Zhou Y, Ma X, Song W, Zhao H, Esteban E, Pasha A, Provart NJ, Lai J. High Temporal-Resolution Transcriptome Landscape of Early Maize Seed Development. Plant Cell 2019; 31:974-992. [PMID: 30914497 PMCID: PMC6533015 DOI: 10.1105/tpc.18.00961] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/06/2019] [Accepted: 03/25/2019] [Indexed: 05/13/2023]
Abstract
The early maize (Zea mays) seed undergoes several developmental stages after double fertilization to become fully differentiated within a short period of time, but the genetic control of this highly dynamic and complex developmental process remains largely unknown. Here, we report a high temporal-resolution investigation of transcriptomes using 31 samples collected at an interval of 4 or 6 h within the first six days of seed development. These time-course transcriptomes were clearly separated into four distinct groups corresponding to the stages of double fertilization, coenocyte formation, cellularization, and differentiation. A total of 22,790 expressed genes including 1415 transcription factors (TFs) were detected in early stages of maize seed development. In particular, 1093 genes including 110 TFs were specifically expressed in the seed and displayed high temporal specificity by expressing only in particular period of early seed development. There were 160, 22, 112, and 569 seed-specific genes predominantly expressed in the first 16 h after pollination, coenocyte formation, cellularization, and differentiation stage, respectively. In addition, network analysis predicted 31,256 interactions among 1317 TFs and 14,540 genes. The high temporal-resolution transcriptome atlas reported here provides an important resource for future functional study to unravel the genetic control of seed development.
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Wei Gu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- China Specialty Maize Research Center (CIMMYT), Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Ning Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiang Gao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingsi Zhou
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuxu Ma
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
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Dong S, Lau V, Song R, Ierullo M, Esteban E, Wu Y, Sivieng T, Nahal H, Gaudinier A, Pasha A, Oughtred R, Dolinski K, Tyers M, Brady SM, Grene R, Usadel B, Provart NJ. Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. Plant Physiol 2019; 179:1893-1907. [PMID: 30679268 PMCID: PMC6446796 DOI: 10.1104/pp.18.01216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/15/2019] [Indexed: 05/04/2023]
Abstract
Determining the complete Arabidopsis (Arabidopsis thaliana) protein-protein interaction network is essential for understanding the functional organization of the proteome. Numerous small-scale studies and a couple of large-scale ones have elucidated a fraction of the estimated 300,000 binary protein-protein interactions in Arabidopsis. In this study, we provide evidence that a docking algorithm has the ability to identify real interactions using both experimentally determined and predicted protein structures. We ranked 0.91 million interactions generated by all possible pairwise combinations of 1,346 predicted structure models from an Arabidopsis predicted "structure-ome" and found a significant enrichment of real interactions for the top-ranking predicted interactions, as shown by cosubcellular enrichment analysis and yeast two-hybrid validation. Our success rate for computationally predicted, structure-based interactions was 63% of the success rate for published interactions naively tested using the yeast two-hybrid system and 2.7 times better than for randomly picked pairs of proteins. This study provides another perspective in interactome exploration and biological network reconstruction using protein structural information. We have made these interactions freely accessible through an improved Arabidopsis Interactions Viewer and have created community tools for accessing these and ∼2.8 million other protein-protein and protein-DNA interactions for hypothesis generation by researchers worldwide. The Arabidopsis Interactions Viewer is freely available at http://bar.utoronto.ca/interactions2/.
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Affiliation(s)
- Shaowei Dong
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Vincent Lau
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Richard Song
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Matthew Ierullo
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Yingzhou Wu
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Teeratham Sivieng
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Hardeep Nahal
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, California 95616
| | - Asher Pasha
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Rose Oughtred
- Institute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
- IBG-2: Plant Sciences, Leo-Brandt-Strasse, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, New Jersey 08544
| | - Kara Dolinski
- Institute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
- IBG-2: Plant Sciences, Leo-Brandt-Strasse, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Washington Road, Princeton, New Jersey 08544
| | - Mike Tyers
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, California 95616
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, 101H Price Hall, Mail Code: 0331, 170 Drillfield Drive, Blacksburg, Virginia 24061
| | - Björn Usadel
- Institute for Biology I/Sammelbau Biologie II, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany
| | - Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., University of Toronto, Toronto, Ontario M5S 3B2, Canada
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Hoopes GM, Hamilton JP, Wood JC, Esteban E, Pasha A, Vaillancourt B, Provart NJ, Buell CR. An updated gene atlas for maize reveals organ-specific and stress-induced genes. Plant J 2019; 97:1154-1167. [PMID: 30537259 PMCID: PMC6850026 DOI: 10.1111/tpj.14184] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [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: 09/05/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 05/09/2023]
Abstract
Maize (Zea mays L.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long-read sequencing and optical mapping technology. To facilitate the use of AGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicated mRNA-sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ-specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co-expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co-expression patterns. Presence-absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ-specific and stress-induced DE genes suggesting that PAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds, PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co-expression network connections suggesting that a subset of PAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data-mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).
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Affiliation(s)
| | - John P. Hamilton
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Joshua C. Wood
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - Brieanne Vaillancourt
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
| | - Nicholas J. Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and FunctionUniversity of TorontoTorontoOntarioM5S 3B2Canada
| | - C. Robin Buell
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
- Department of Energy Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48824USA
- Plant Resilience InstituteMichigan State UniversityEast LansingMI48824USA
- Michigan State University AgBioResearchEast LansingMI48824USA
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Rodriguez Abreu D, Garassino M, Esteban E, Speranza G, Felip E, Domine M, Hochmair M, Powell S, Cheng SS, Bischoff H, Peled N, Hui R, Reck M, Garon E, Boyer M, Grossi F, Jennens R, Yang J, Pietanza M, Gadgeel S. KEYNOTE-189 study of pembrolizumab (pembro) plus pemetrexed (pem) and platinum vs placebo plus pem and platinum for untreated, metastatic, nonsquamous NSCLC: Does choice of platinum affect outcomes? Ann Oncol 2018. [DOI: 10.1093/annonc/mdy425.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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31
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Rodriguez Abreu D, Garassino M, Esteban E, Speranza G, Felip E, Domine M, Hochmair M, Powell S, Cheng SS, Bischoff H, Peled N, Hui R, Reck M, Garon E, Boyer M, Grossi F, Jennens R, Yang J, Pietanza M, Gadgeel S. KEYNOTE-189 study of pembrolizumab (pembro) plus pemetrexed (pem) and platinum vs placebo plus pem and platinum for untreated, metastatic, nonsquamous NSCLC: Does choice of platinum affect outcomes? Ann Oncol 2018. [DOI: 10.1093/annonc/mdy292.086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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32
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Puente J, Mendez Vidal M, Saez M, Font Pous A, Duran I, Castellano D, Juan Fita M, Santander C, Arranz Arija J, Sanchez-Hernandez A, Mellado B, Alonso T, Gonzalez del Alba Baamonde M, Maroto P, Lazaro M, Esteban E, Cassinello J, Climent Duran M. Preliminary safety results of the randomized phase II ABIDO-SOGUG trial: Toxicity profile of concomitant abiraterone acetate + docetaxel treatment in comparison to docetaxel. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy284.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Garassino M, Rodríguez-Abreu D, Gadgeel S, Esteban E, Felip E, Speranza G, Domine M, Hochmair M, Powell S, Cheng S, Bischoff H, Peled N, Reck M, Hui R, Garon E, Boyer M, Yang J, Burke T, Pietanza M, Gandhi L. PD.1.01 Health-Related Quality of Life with Pembrolizumab or Placebo + Pemetrexed + Platinum in Non-Squamous NSCLC: KEYNOTE-189. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kus S, Coenen M, Simmel S, Esteban E, Kirschneck M, Seyfried F, Bühren V. ICF-basierte Prädiktion des Outcomes in der Rehabilitation nach Trauma (icfPROreha) – Identifizierung potenzieller Prädiktoren sowie von Messverfahren zur Prognose der Arbeitsfähigkeit und Lebensqualität nach schweren muskuloskeletalen Verletzungen. Das Gesundheitswesen 2018. [DOI: 10.1055/s-0038-1667735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- S Kus
- ICF Research Branch, ein Kooperationspartner des WHO Collaborating Centre for the Family of International Classifications in Deutschland (am DIMDI), Nottwil, Schweiz
| | - M Coenen
- Ludwig-Maximilians-Universität München, Lehrstuhl für Public Health und Versorgungsforschung, Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie – IBE, München, Deutschland
- ICF Research Branch, ein Kooperationspartner des WHO Collaborating Centre for the Family of International Classifications in Deutschland (am DIMDI), Nottwil, Schweiz
| | - S Simmel
- Berufsgenossenschaftliche Unfallklinik Murnau, Abteilung BG Rehabilitation, Murnau, Deutschland
| | - E Esteban
- Ludwig-Maximilians-Universität München, Lehrstuhl für Public Health und Versorgungsforschung, Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie – IBE, München, Deutschland
| | - M Kirschneck
- Ludwig-Maximilians-Universität München, Lehrstuhl für Public Health und Versorgungsforschung, Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie – IBE, München, Deutschland
- ICF Research Branch, ein Kooperationspartner des WHO Collaborating Centre for the Family of International Classifications in Deutschland (am DIMDI), Nottwil, Schweiz
| | - F Seyfried
- Ludwig-Maximilians-Universität München, Lehrstuhl für Public Health und Versorgungsforschung, Institut für Medizinische Informationsverarbeitung, Biometrie und Epidemiologie – IBE, München, Deutschland
| | - V Bühren
- Berufsgenossenschaftliche Unfallklinik Murnau, Abteilung BG Rehabilitation, Murnau, Deutschland
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Maroto P, Esteban E, Parra EF, Mendez-Vidal MJ, Domenech M, Pérez-Valderrama B, Calderero V, Pérez-Gracia JL, Grande E, Algaba F. HIF pathway and c-Myc as biomarkers for response to sunitinib in metastatic clear-cell renal cell carcinoma. Onco Targets Ther 2017; 10:4635-4643. [PMID: 29033582 PMCID: PMC5614781 DOI: 10.2147/ott.s137677] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Clear-cell renal cell carcinoma (ccRCC) is a heterogeneous disease with a different clinical behavior and response to targeted therapies. Differences in hypoxia-inducible factor (HIF) expression have been used to classify von Hippel-Lindau gene (VHL)-deficient ccRCC tumors. c-Myc may be driving proliferation in HIF-2α-expressing tumors in a growth factor-independent manner. OBJECTIVE To explore the HIF-1α, HIF-2α and c-Myc baseline expression as potential predictors of sunitinib outcome as well as the effectiveness and safety with sunitinib in patients with metastatic ccRCC in routine clinical practice. METHODS This was an observational and prospective study involving 10 Spanish hospitals. Formalin-fixed, paraffin-embedded primary tumor samples from metastatic ccRCC patients who received sunitinib as first-line treatment were analyzed. Association between biomarker expression and sunitinib treatment outcomes was evaluated. Kaplan-Meier method was applied to measure progression-free survival (PFS) and overall survival. RESULTS Eighty-one patients were included: median PFS was 10.8 months (95% CI: 7.4-13.5 months), median overall survival was 21.8 months (95% CI: 14.7-29.8 months) and objective response rate was 40.7%, with 7.4% of patients achieving a complete response. Molecular marker staining was performed in the 69 available tumor samples. Significant association with lower PFS was identified for double c-Myc/HIF-2α-positive staining tumors (median 4.3 vs 11.5 months, hazard ratio =2.64, 95% CI: 1.03-6.80, P=0.036). A trend toward a lower PFS was found in positive c-Myc tumors (median 5.9 vs 10.9 months, P=0.263). HIF-1α and HIF-2α expression levels were not associated with clinical outcome. CONCLUSION These preliminary results suggest that predictive subgroups might be defined based on biomarkers such as c-Myc/HIF-2α. Further validation with more patients will be needed in order to confirm it. Outcomes with sunitinib in metastatic ccRCC in daily clinical practice resemble those obtained in clinical trials.
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Affiliation(s)
- P Maroto
- Department of Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona
| | - E Esteban
- Department of Oncology, Nuevo HUCA, Oviedo
| | | | | | - M Domenech
- Department of Oncology, Hospital de Althaia Xarxa Asistencial Manresa, Barcelona
| | | | - V Calderero
- Department of Oncology, H. Fundación Miguel Servet, Zaragoza
| | - J L Pérez-Gracia
- Department of Oncology, Clinica Universitaria de Pamplona, Pamplona
| | - E Grande
- Department of Oncology, H. Ramón y Cajal, Madrid
| | - F Algaba
- Pathology Unit, Fundació Puigvert, Universitat Autònoma de Barcelona, Barcelona, Spain
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36
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Revuelta A, Rodríguez Rubí D, Sánchez Lorenzo M, Ruiz Echeverria L, Li W, Solís Hernández M, Fáez García L, Fernández Arrojo S, Iglesias Gómez C, Villanueva Palicio N, Jimenez Fonseca P, Luque Cabal M, Álvarez Fernández C, Izquierdo M, Viéitez J, Esteban E. Experience with the implant of vascular access devices by medical oncologist in a non-surgical scenery. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx388.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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37
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Garcia-Donas J, Lainez N, Santos-Romero M, Puente J, Castellano D, Rodriguez-Moreno J, Esteban E, Grande Pulido E, Fernandez Parra E, Rodriguez Lajusticia L, Domenech M, Gonzalez Billalabeitia E, Sáez M, Gallardo Diaz E, Hernando Polo S, Herrador A, Inglada-Pérez L, Robledo M, Rodriguez-Antona C. Prospective study assessing the expression of angiogenesis-related genes as markers of anti-VEGFR2 response in advanced renal cell carcinoma. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx363.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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38
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Sanmamed MF, Esteban E, Uriol E, Zarate R, Capelan M, Muriel C, Crespo G, Berros JP, Pardo-Coto P, Perez Q, Alvarez-Fernández C, Jiménez Fonseca P, Luque M, Astudillo A. Epidermal growth factor receptor and epididymis invasion as prognostic biomarkers in clinical stage I testicular germ cell tumours. J Transl Med 2017; 15:62. [PMID: 28320414 PMCID: PMC5358043 DOI: 10.1186/s12967-017-1162-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/10/2017] [Indexed: 11/10/2022] Open
Abstract
Background Inguinal orchiectomy is curative in 70–80% of clinical stage I testicular germ cell tumours (CS I TGCT). The identification of patients who are at low risk of relapse is critical to avoid unnecessary treatment. The aim of this study is to explore EGFR, hMLH-1/hMSH-2 and microsatellite instability (MSI) as potential prognostic factors of recurrence in CS I TGCT. Methods Fifty-six CS I TGCT patients who underwent inguinal orchiectomy were included in this study. We analysed the relationship between clinicopathological and molecular factors with survival. Analysis of hMLH1, hMSH2 and EGFR expression was carried out by immunohistochemistry. Methylation status of the hMLH1 promoter was determined by pyrosequencing analysis in selected cases. EGFR exons 19, 20, 21 were analysed by PCR labeled-fragments and MSI status was determined using standard Multiplex MSI assays. Results Classical pathological factors such as lymphovascular invasion, high percentage of embryonal carcinoma, rete testis invasion or tumour size ≥4 cm showed a significant relationship with a higher risk of relapse. Additionally, it was found that an epididymis invasion proved to be a significant independent poor prognostic factor of recurrence (p = 0.001). hMLH1 or hMSH2 expression showed no significant association with risk of relapse and no MSI was found. EGFR expression was observed in 30.4% of samples and its expression was associated with higher risk of relapse (HR 3.5; 95% CI 1.3–9.8; p = 0.016). None of the cases presented EGFR kinase domain mutations. Conclusions Epididymis invasion and EGFR expression, but not hMLH-1/hMSH-2 or MSI, could be potentially useful as new prognostic factors of recurrence for CS I TGCT. Electronic supplementary material The online version of this article (doi:10.1186/s12967-017-1162-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miguel F Sanmamed
- Department of Immunobiology, School of Medicine, Yale University, 300 George Street, Suite 203A, New Haven, CT, 06511, USA. .,Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain.
| | - E Esteban
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - E Uriol
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - R Zarate
- Clinical Genetics Unit, Clínica Universidad de Navarra, Pamplona, Spain
| | - M Capelan
- Breast Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - C Muriel
- Department of Medical Oncology, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - G Crespo
- Department of Medical Oncology, Hospital Universitario de Burgos, Burgos, Spain
| | - J P Berros
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - P Pardo-Coto
- Department of Medical Oncology, Centro Médico de Asturias, Oviedo, Spain
| | - Q Perez
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - C Alvarez-Fernández
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - P Jiménez Fonseca
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - M Luque
- Department of Medical Oncology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - A Astudillo
- Department of Pathology, Hospital Universitario Central de Asturias, Oviedo, Spain
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Gómez J, Yunta F, Esteban E, Carpena RO, Zornoza P. Use of radiometric indices to evaluate Zn and Pb stress in two grass species (Festuca rubra L. and Vulpia myuros L.). Environ Sci Pollut Res Int 2016; 23:23239-23248. [PMID: 27638786 DOI: 10.1007/s11356-016-7546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/29/2016] [Indexed: 05/04/2023]
Abstract
Vegetation indices obtained from radiometric measurements have been used to estimate the stress response of plants grown in contaminated sites. The phytotoxicity of Pb and Zn in Festuca rubra L. and Vulpia myuros L. plants grown under hydroponic conditions was evaluated using vegetation indices obtained from radiometric measurements. The plants were supplied with 3 mM Zn (+Zn), 500 μM Pb (+Pb) and 500 μM Pb with EDTA (+PbEDTA) for 3 months. Significantly higher Zn concentrations in F. rubra shoots compared with V. myuros shoots were detected for Zn and Pb treatments. EDTA increased Pb transport to the shoots for both grasses, while Pb-treated plants retained Pb primarily in the roots. All vegetation indices tested showed the highest differences in F. rubra under +PbEDTA treatment and minor effects under +Zn, whereas the major variations for V. myuros corresponded to +Zn treatment, followed by +PbEDTA. Red edge normalized difference vegetation index, yellowness index and anthocyanin concentration index were the most sensitive indices to report Zn and Pb phytotoxicity in these grasses. According to the results obtained, both metal concentrations and radiometric indices suggested that Pb is more phytotoxic to F. rubra, which tolerates high Zn levels, whereas V. myuros was strongly affected by high Zn levels and markedly tolerant to Pb, even when applied in a mobile form (PbEDTA). Both species could be used in the phytostabilization of Zn- and Pb-contaminated soils. The abilities of F. rubra to accumulate Zn and V. myuros to accumulate Pb in the roots would facilitate a more efficient phytoremediation strategy when used in combination.
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Affiliation(s)
- J Gómez
- Dpto. Química Agrícola y Bromatología. Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - F Yunta
- Dpto. Química Agrícola y Bromatología. Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - E Esteban
- Dpto. Química Agrícola y Bromatología. Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain.
| | - R O Carpena
- Dpto. Química Agrícola y Bromatología. Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
| | - P Zornoza
- Dpto. Química Agrícola y Bromatología. Facultad de Ciencias, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 7, 28049, Madrid, Spain
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40
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Esteban E, Palacio J, Estella R. Deformidad de pie en paciente diabético. Fractura-luxación de Lisfranc: a propósito de un caso. Semergen 2016; 42:336-8. [DOI: 10.1016/j.semerg.2015.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 10/23/2022]
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41
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Calvo Temprano D, Esteban E, Jiménez Fonseca P, Fernández-Mariño B. CT scan prior to radiotherapy in unresectable, locally advanced, non-small cell carcinoma of the lung: is it always necessary? Clin Transl Oncol 2016; 19:105-110. [PMID: 27091132 DOI: 10.1007/s12094-016-1510-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
Abstract
PURPOSE There is broad consensus regarding evaluating response to chemotherapy (CHT) by means of computerized tomography (CT) in patients with localized or locally advanced non-small cell lung carcinoma (NSCLC). We present a study comparing the usefulness of CT versus chest X-ray (XR) and clinical findings when indicating radiotherapy (RT) following CHT. METHODS Ninety-eight of 150 subjects with unresectable locally advanced NSCLC were blindly and independently evaluated by XR and CT, with pairs of chest XR and CT (before and after CHT). A null hypothesis (H0) was established of the conditioned probability of detecting progression by CT and not by XR of 10 % or more, with a statistical power of 80 %. RESULTS Sensitivity, specificity, positive and negative predictive value of XR versus CT were 98, 89, 99, and 80 % respectively. A 4 % (p = 0.0451) probability of improvement of CT versus XR was calculated, enabling the H0 to be ruled out. CONCLUSION The CT failed to prove to be significantly superior to the chest XR + clinical picture in indicating a change in treatment approach in patients with unresectable locally advanced NSCLC after CHT.
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MESH Headings
- Adenocarcinoma/diagnostic imaging
- Adenocarcinoma/pathology
- Adenocarcinoma/radiotherapy
- Adult
- Aged
- Carcinoma, Large Cell/diagnostic imaging
- Carcinoma, Large Cell/pathology
- Carcinoma, Large Cell/radiotherapy
- Carcinoma, Non-Small-Cell Lung/diagnostic imaging
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/radiotherapy
- Carcinoma, Squamous Cell/diagnostic imaging
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/radiotherapy
- Female
- Follow-Up Studies
- Humans
- Lung Neoplasms/diagnostic imaging
- Lung Neoplasms/pathology
- Lung Neoplasms/radiotherapy
- Male
- Middle Aged
- Neoplasm Staging
- Prognosis
- Radiography, Thoracic/methods
- Tomography, X-Ray Computed/methods
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Affiliation(s)
- D Calvo Temprano
- Radiology Service, Hospital Universitario Central de Asturias, Avenida de Roma, s/n, ES-33011, Oviedo, Asturias, Spain.
| | - E Esteban
- Medical Oncology Service, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - P Jiménez Fonseca
- Medical Oncology Service, Hospital Universitario Central de Asturias, Oviedo, Asturias, Spain
| | - B Fernández-Mariño
- Radiology Service, Hospital Universitario Central de Asturias, Avenida de Roma, s/n, ES-33011, Oviedo, Asturias, Spain
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Caipo M, Cahill S, Kenny M, Wachsmuth K, Toyofuku H, Hielm S, Carolissen V, Bruno A, Mulholland C, Kojima M, Esteban E. The development of illustrative examples for the establishment and application of microbiological criteria for foods and their role in international standard development. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.06.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Agámez Medina GL, González-Arévalo A, Gómez-Arnau JI, García del Valle S, Rubio JA, Esteban E, Pérez E. Effects of droperidol and ondansetron on dispersion of ventricular repolarization: A randomized double-blind clinical study in anesthetized adult patients. Rev Esp Anestesiol Reanim 2015; 62:495-501. [PMID: 25887095 DOI: 10.1016/j.redar.2015.01.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Droperidol and ondansetron prolong QT interval, a circumstance that has raised some concerns regarding the possibility of inducing torsades de pointes (TdP). However drug-induced spatial dispersion of ventricular repolarization has been shown to be the principal arrhythmogenic substrate for TdP. The aim of this study is to explore the effects of droperidol and ondansetron on the dispersion of repolarization, measured using the T peak-to-end interval (Tp-e) and Tp-e/QT and Tp-e/RR(1/2) ratios in surgical anesthetized patients. METHODS A randomized, double-blind study carried out on sixty-three adult patients without cardiac disease or factors favoring QT prolongation and undergoing non-cardiac surgery were randomly assigned to the droperidol or ondansetron group. Under propofol anesthesia, a 12-lead EKG was obtained, and 1.25mg droperidol or 4mg ondansetron was injected. Five minutes later, a new 12-lead EKG was recorded. EKG analyses were independently performed by two cardiologists blinded to the state of the traces or group allocation. QT, RR and Tp-e intervals were measured by averaging five successive beats in leadII (QT) or V5 (Tp-e). The mean value for each measurement was calculated for statistical analysis. RESULTS Thirty-two patients (19 women) received droperidol, and 31 (22 women) ondansetron. Droperidol and ondansetron prolonged the QTcF interval (Fridericia formula) by 6.8 and 7.2ms (mean values) respectively, but neither droperidol nor ondansetron increased the Tp-e interval or Tp-e/QT and Tp-e/RR(1/2) ratios. CONCLUSION At antiemetic doses, neither ondansetron (4mg) nor droperidol (1.25mg) increases the dispersion of ventricular repolarization in healthy adult patients anesthetized with propofol.
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Affiliation(s)
- G L Agámez Medina
- Departamento de Anestesiología y Reanimación, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España.
| | - A González-Arévalo
- Departamento de Anestesiología y Reanimación, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España
| | - J I Gómez-Arnau
- Departamento de Anestesiología y Reanimación, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España
| | - S García del Valle
- Departamento de Anestesiología y Reanimación, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España
| | - J A Rubio
- Unidad de Cardiología, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España
| | - E Esteban
- Unidad de Cardiología, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España
| | - E Pérez
- Research Institute, Hospital Universitario Fundación Alcorcón, Alcorcón, Madrid, España
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Angelergues A, Bellmunt J, Efstathiou E, Gonzalez I, Gyftaki R, Delanoy N, Ozguroglu M, Flechon A, Guillot A, Le Moulec S, Castellano D, Esteban E, Munarriz J, Campos Balea B, Ardavanis A, Stefanou D, Oudard S. 2538 Response to cabazitaxel in patients with metastatic castrationresistant prostate cancer (mCRPC) poorly responding to docetaxel. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31357-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Grande E, Pinto A, Dur´n I, López-Criado P, Su´rez C, Gonz´lez-Larriba J, S´nchez-Lorenzo L, Maroto P, L´inez N, Gonz´lez del Alba A, S´ez M, Alonso-Gordoa T, Pérez-Valderrama B, Puente J, Morales R, Esteban E, Manneh R, Benedetti J, Carles-Galcerán J, Castellano D. 2540 Experience with radium-223 as a systemic treatment for patients (pts) with castration-resistant prostate cancer (CRPC) out of a clinical trial in Spain. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31359-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Maroto P, Ruiz A, Esteban E, León L, Munarriz J, Su´rez C, Pinto A, Mellado B, Durán I, García-Carbonero I, Arranz J, Sala N, Fernández O, Lainez N, Peláez I, López A, Viqueira A. 2616 Efficacy and safety of Temsirolimus in patients with metastatic renal cell carcinoma: Final results from the Spanish experience. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31434-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Oudard S, Angelergues A, Efstathiou E, Gonzalez I, Gyftaki R, Delanoy N, Ozguroglu M, Flechon A, Guillot A, Le Moulec S, Castellano D, Esteban E, Munarriz J, Campos Balea B, Ardavanis A, Stefanou D, Bellmunt J. 2541 Updated results of the FLAC European database of metastatic castration resistant prostate cancer (mCRPC) patients (pts) treated with life extending therapies in post-docetaxel (D) setting. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)31360-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Esteban E, Majem M, Martinez Aguillo M, Martinez Banaclocha N, Dómine M, Gómez Aldaravi L, Juan O, Cajal R, Gonzalez Arenas M, Provencio M. Prevalence of EGFR mutations in newly diagnosed locally advanced or metastatic non-small cell lung cancer Spanish patients and its association with histological subtypes and clinical features: The Spanish REASON study. Cancer Epidemiol 2015; 39:291-7. [DOI: 10.1016/j.canep.2015.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 10/23/2022]
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Xu CF, Johnson T, Garcia-Donas J, Choueiri TK, Sternberg CN, Davis ID, Bing N, Deen KC, Xue Z, McCann L, Esteban E, Whittaker JC, Spraggs CF, Rodríguez-Antona C, Pandite LN, Motzer RJ. IL8 polymorphisms and overall survival in pazopanib- or sunitinib-treated patients with renal cell carcinoma. Br J Cancer 2015; 112:1190-8. [PMID: 25695485 PMCID: PMC4385958 DOI: 10.1038/bjc.2015.64] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/15/2015] [Accepted: 01/27/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND We evaluated germline single nucleotide polymorphisms (SNPs) for association with overall survival (OS) in pazopanib- or sunitinib-treated patients with advanced renal cell carcinoma (aRCC). METHODS The discovery analysis tested 27 SNPs within 13 genes from a phase III pazopanib trial (N=241, study 1). Suggestive associations were then pursued in two independent datasets: a phase III trial (COMPARZ) comparing pazopanib vs sunitinib (N=729, study 2) and an observational study of sunitinib-treated patients (N=89, study 3). RESULTS In study 1, four SNPs showed nominally significant association (P≤0.05) with OS; two of these SNPs (rs1126647, rs4073) in IL8 were associated (P≤0.05) with OS in study 2. Because rs1126647 and rs4073 were highly correlated, only rs1126647 was evaluated in study 3, which also showed association (P≤0.05). In the combined data, rs1126647 was associated with OS after conservative multiple-test adjustment (P=8.8 × 10(-5); variant vs reference allele hazard ratio 1.32, 95% confidence interval: 1.15-1.52), without evidence for heterogeneity of effects between studies or between pazopanib- and sunitinib-treated patients. CONCLUSIONS Variant alleles of IL8 polymorphisms are associated with poorer survival outcomes in pazopanib- or sunitinib-treated patients with aRCC. These findings provide insight in aRCC prognosis and may advance our thinking in development of new therapies.
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Affiliation(s)
- C-F Xu
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - T Johnson
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - J Garcia-Donas
- Department of Medical Oncology, Centro Integral Oncológico Clara Campal, Calle de Oña 10, Madrid 28050, Spain
- Spanish Oncology Genitourinary Group (SOGUG), Madrid, Spain
| | - T K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - C N Sternberg
- Department of Medical Oncology, San Camillo and Forlanini Hospitals, Circonvallazione Gianicolense 87, Rome 00152, Italy
| | - I D Davis
- Monash University Eastern Health Clinical School, 5 Arnold Street, Victoria 3128, Australia
| | - N Bing
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA
| | - K C Deen
- GlaxoSmithKline, 250 S. Collegeville Road, Collegeville, PA 19426-0989, USA
| | - Z Xue
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA
| | - L McCann
- GlaxoSmithKline, 250 S. Collegeville Road, Collegeville, PA 19426-0989, USA
| | - E Esteban
- Department of Medical Oncology, Centro Integral Oncológico Clara Campal, Calle de Oña 10, Madrid 28050, Spain
- Hospital Universitario Central de Asturias, Calle Carretera de Rubín, Oviedo 33011, Spain
| | - J C Whittaker
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - C F Spraggs
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - C Rodríguez-Antona
- Spanish National Cancer Research Centre and ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Calle de Melchor Fernández Almagro 3, Madrid 28029, Spain
| | - L N Pandite
- GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA
| | - R J Motzer
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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Oudard S, Angelergues A, Maeso IG, Delanoy N, Flechon A, Özgüroğlu M, Castellano D, Guillot A, Le Moulec S, Esteban E, Munarriz J, Campos B, Bellmunt J. Prognostic Factors for Survival and Sequencing of Life-Extending Therapies in Metastatic Castration Resistant Prostate Cancer (Mcrpc) Patients (Pts) in Post-Docetaxel (D) Setting. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu336.37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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