DOCSLIB.ORG

The Duck Genome and Transcriptome Provide Insight Into an Avian Influenza Virus Reservoir Species

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Duck Genome and Transcriptome Provide Insight Into an Avian Influenza Virus Reservoir Species ARTICLES OPEN The duck genome and transcriptome provide insight into an avian influenza virus reservoir species Yinhua Huang1,2,20, Yingrui Li3,20, David W Burt2,20, Hualan Chen4, Yong Zhang3, Wubin Qian3, Heebal Kim5, Shangquan Gan1, Yiqiang Zhao1, Jianwen Li3, Kang Yi3, Huapeng Feng4, Pengyang Zhu4, Bo Li3, Qiuyue Liu1, Suan Fairley6, Katharine E Magor7, Zhenlin Du1, Xiaoxiang Hu1, Laurie Goodman3, Hakim Tafer8,9, Alain Vignal10, Taeheon Lee5, Kyu-Won Kim11, Zheya Sheng1, Yang An1, Steve Searle6, Javier Herrero12, Martien A M Groenen13, Richard P M A Crooijmans13, Thomas Faraut10, Qingle Cai3, Robert G Webster14, Jerry R Aldridge14, Wesley C Warren15, Sebastian Bartschat8, Stephanie Kehr8, Manja Marz8, Peter F Stadler8,9, Jacqueline Smith2, Robert H S Kraus16,17, Yaofeng Zhao1, Liming Ren1, Jing Fei1, Mireille Morisson10, Pete Kaiser2, Darren K Griffin18, Man Rao1, Frederique Pitel10, Jun Wang3,19 & Ning Li1 The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A viruses. We present the duck genome sequence and perform deep transcriptome analyses to investigate immune-related genes. Our data indicate that the duck possesses a contractive immune gene repertoire, as in chicken and zebra finch, and this repertoire has been shaped through lineage-specific duplications. We identify genes that are responsive to influenza A viruses using the lung transcriptomes of control ducks and ones that were infected with either a highly pathogenic (A/duck/Hubei/49/05) or a weakly pathogenic (A/goose/Hubei/65/05) H5N1 virus. Further, we show how the duck’s defense mechanisms against influenza infection have been optimized through the diversification of its b-defensin and butyrophilin-like repertoires. These analyses, in combination with the genomic and transcriptomic data, provide a resource for characterizing the interaction between host and influenza viruses. Birds are distinct from other vertebrates in many characteristics, both in these areas. Ducks diverged from the related chicken and turkey 4 © 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature morphological (for example, feathers and eggs) and physiological (for and zebra finch approximately 90–100 million years ago . The duck example, their lightweight skeletons and high metabolic rates). Birds is also one of the most economically important waterfowl as a source occupy habitats from the Arctic to the Antarctic, and they have body of meat, eggs and feathers. size ranging from 5 cm to 2.8 m. The diversity found in birds inspires Of special interest to medicine and agriculture is the fact that ducks npg us to investigate the genomic differences underlying their phenotypic serve as the principal natural reservoir for influenza A viruses and differences from mammals and the variation within the avian class. harbor all 16 hemagglutinin (HA) and 9 neuraminidase (NA) subtypes The sequencing of the chicken genome1 provided the first insight into that are currently known5,6, with the exception of the H13 and H16 the evolutionary events between birds and other vertebrates. Avian subtypes7. Often, influenza strains cause the duck no harm. However, evolutionary events have subsequently been elucidated with the recent the long-standing equilibrium between influenza A viruses and the availability of the zebra finch and turkey genomes2,3. Additional avian duck has been disrupted with the emergence of H5N1 viruses8. H5N1 genomes, however, are needed to provide more detailed evolution- strains have caused unprecedented outbreaks in poultry in more than ary information and insight into adaptation mechanisms. The duck 60 countries and have caused 622 human infections (as of March (A. platyrhynchos) is particularly well suited for further exploration 2013), with an overall fatality rate of 59% in humans. Recently, it was 1State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, China. 2The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK. 3BGI-Shenzhen, Shenzhen, China. 4National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Harbin, China. 5Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea. 6Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. 7Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada. 8Department of Computer Science, University of Leipzig, Leipzig, Germany. 9Department of Theoretical Chemistry, University of Vienna, Vienna, Austria. 10Laboratoire de Génétique Cellulaire, Institut National de la Recherche Agronomique (INRA), Castanet-Tolosan, France. 11Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea. 12European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. 13Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands. 14Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA. 15The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA. 16Resource Ecology Group, Wageningen University, Wageningen, The Netherlands. 17Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum, Gelnhausen, Germany. 18Genetics School of Biosciences, University of Kent, Kent, UK. 19Department of Biology, University of Copenhagen, Copenhagen, Denmark. 20These authors contributed equally to this work. Correspondence should be addressed to J.W. ([email protected]) or N.L. ([email protected]). Received 16 December 2012; accepted 8 May 2013; published online 9 June 2013; doi:10.1038/ng.2657 776 VOLUME 45 | NUMBER 7 | JULY 2013 NATURE GENETICS ARTICLES Table 1 Number and length of reads and number of genes detected using RNA sequencing in control and H5N1 virus–infected ducks Number of DEGs Number of uniquely Number of DEGs and PSGsa and PSGsa (versus Number of mapped reads (versus control) GS/65-infected ducks) Total length of expressed Frequency Frequency Group Total reads reads (bp) genes Genome Gene DEGs of PSGs DEG set DEGs of PSGs DEG set Control 146,618,064 13,195,625,760 18,181 84,895,562 72,455,573 DK/49 (day 1) 116,561,634 10,490,547,060 18,276 60,873,691 49,811,986 2,257 63/957 1,506 38/624 DK/49 (day 2) 133,943,194 12,054,887,460 18,233 73,475,680 59,066,187 3,101 89/1,413 1,436 44/654 DK/49 (day 3) 136,923,500 12,323,115,000 17,951 81,116,464 65,172,557 3,066 86/1,383 5,038 1,396 44/625 3,232 GS/65 (day 1) 138,642,320 12,477,808,800 18,135 81,176,979 66,830,938 916 20/367 GS/65 (day 2) 127,576,536 11,481,888,240 18,140 72,750,242 58,940,732 2,060 58/918 GS/65 (day 3) 116,267,820 10,464,103,800 17,983 69,337,186 56,072,340 1,251 29/538 2,741 aDEGs are genes that showed significantly different expression with FDR≤ 0.001 and fold change ≥2. PSGs are genes that are predicted to be under positive selection with FDR <0.05. The numerator and denominator for the frequencies of PSGs are the number of positively selected genes and genes where a likelihood ratio test was performed for PSGs, respectively. reported that an engineered influenza virus encoding hemagglutinin aligned to the duck assembly. We further aligned the duck and chicken from the highly pathogenic avian H5N1 influenza A strains can be assemblies to the human using Narcisse. This effort showed that the transmitted between ferrets9, emphasizing the potential for a human coverage of the two avian assemblies of the human genome (GRCh37) pandemic to emerge from birds. Furthermore, weakly pathogenic was similar, indicating that the quality of the duck and chicken assem- avian influenza A viruses, such as H9N2 (ref. 10) and H7N2 (ref. 11) blies was comparable. In addition, in aligning the duck assembly onto strains, have caused transient infections in humans12. The exceptional the chicken genome sequence using GLINT software with its default virulence of avian influenza viruses in humans, in combination with parameters18, only 41 of the 78,847 duck scaffolds were identified their ongoing evolution in birds, motivates us to better understand as possible chimeras when applying the criterion that they contain host immune responses to avian influenza viruses. We report here sequences that partially map to two different chicken chromosomes. the duck whole-genome sequence and compared it to the genomes of These data indicate that the duck assembly has good coverage and mammals and other birds. We performed deep transcriptome analyses generally provides a reasonable substrate for the analysis presented of lungs from control ducks and ones that were infected with either a in this study. highly pathogenic (A/duck/Hubei/49/05, DK/49) or a weakly patho- We defined reference gene sets from the duck assembly using the genic (A/goose/Hubei/65/05, GS/65) H5N1 virus13. BGI and Ensembl pipelines (Supplementary Note). For the BGI refer- ence set, we aligned the duck transcriptome data and human (22,232) RESULTS and chicken (16,701) genes to the duck genome assembly, yielding The genome landscape 15,065 predicted protein-coding duck genes. We applied GENSCAN19 We sequenced the genome of a 10-week-old female Beijing duck and Augustus20 with the default parameters and predicted 32,383 using methods similar to those applied to sequence the giant panda and 22,739 protein-coding genes in the duck draft genome for the genome14. In total, we generated 77 Gb of paired-end reads (approxi- respective reference sets (Supplementary Table 6). Finally, we inte- © 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature mately 64-fold coverage of the whole genome) with an average length grated all gene sources and created a reference set containing 19,144 of 50 bp (Supplementary Figs. 1–3 and Supplementary Table 1). genes, constituting approximately 2.3% of the total duck assembly. Of Using SOAPdenovo (Supplementary Note), we combined short reads these 19,144 genes, 9,678 were mapped to categories established by npg to generate a draft assembly, which consisted of 78,487 scaffolds and the Gene Ontology (GO) Project, 14,725 had orthologs in the Kyoto covered 1.1 Gb.
Load more

Recommended publications
  • The Novel Cer-Like Protein Caronte Mediates the Establishment of Embryonic Left±Right Asymmetry
    articles The novel Cer-like protein Caronte mediates the establishment of embryonic left±right asymmetry ConcepcioÂn RodrõÂguez Esteban*², Javier Capdevila*², Aris N. Economides³, Jaime Pascual§,AÂ ngel Ortiz§ & Juan Carlos IzpisuÂa Belmonte* * The Salk Institute for Biological Studies, Gene Expression Laboratory, 10010 North Torrey Pines Road, La Jolla, California 92037, USA ³ Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591, USA § Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA ² These authors contributed equally to this work ............................................................................................................................................................................................................................................................................ In the chick embryo, left±right asymmetric patterns of gene expression in the lateral plate mesoderm are initiated by signals located in and around Hensen's node. Here we show that Caronte (Car), a secreted protein encoded by a member of the Cerberus/ Dan gene family, mediates the Sonic hedgehog (Shh)-dependent induction of left-speci®c genes in the lateral plate mesoderm. Car is induced by Shh and repressed by ®broblast growth factor-8 (FGF-8). Car activates the expression of Nodal by antagonizing a repressive activity of bone morphogenic proteins (BMPs). Our results de®ne a complex network of antagonistic molecular interactions between Activin, FGF-8, Lefty-1, Nodal, BMPs and Car that cooperate to control left±right asymmetry in the chick embryo. Many of the cellular and molecular events involved in the establish- If the initial establishment of asymmetric gene expression in the ment of left±right asymmetry in vertebrates are now understood. LPM is essential for proper development, it is equally important to Following the discovery of the ®rst genes asymmetrically expressed ensure that asymmetry is maintained throughout embryogenesis.
    [Show full text]
  • Transforming Growth Factor-Β, MAPK and Wnt Signaling Interactions In
    EuPA Open Proteomics 8 (2015) 104–115 Contents lists available at ScienceDirect EuPA Open Proteomics journal homepage: www.elsevier.com/locate/euprot Transforming growth factor-b, MAPK and Wnt signaling interactions in colorectal cancer Harish R. Cherukua, Abidali Mohamedalib, David I. Cantora, Sock Hwee Tanc, Edouard C. Niced, Mark S. Bakera,* a Department of Biomedical Sciences, Faculty of Health and Medical Sciences, Macquarie University, New South Wales 2109, Australia b Faculty of Science, Macquarie University, New South Wales 2109, Australia c National University Heart Centre, National University of Singapore, Singapore d Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia ARTICLE INFO ABSTRACT Article history: In non-cancerous cells, transforming growth factor-b (TGFb) regulates cellular responses primarily Received 27 February 2015 through Smad signaling. However, during cancer progression (including colorectal) TGFb promotes Received in revised form 15 June 2015 tumoral growth via Smad-independent mechanisms and is involved in crosstalk with various pathways Accepted 16 June 2015 like the mitogen-activated protein kinases (MAPK) and Wnt. Crosstalk between these pathways Available online 2 July 2015 following activation by TGFb and subsequent downstream signaling activity can be referred to as a crosstalk signaling signature. This review highlights the progress in understanding TGFb signaling Keywords: crosstalk involving various MAPK pathway members (e.g., extracellular signal-regulated kinase (Erk) 1/2, Transforming growth factor-b Ras, c-Jun N-terminal kinases (JNK) and p38) and the Wnt signaling pathway. Colorectal cancer ã TGFb crosstalk 2015 The Authors. Published by Elsevier GmbH. This is an open access article under the CC BY-NC-ND MAPK pathways license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
    [Show full text]
  • Cerberus–Nodal–Lefty–Pitx Signaling Cascade Controls Left–Right Asymmetry in Amphioxus
    Cerberus–Nodal–Lefty–Pitx signaling cascade controls left–right asymmetry in amphioxus Guang Lia,1, Xian Liua,1, Chaofan Xinga, Huayang Zhanga, Sebastian M. Shimeldb,2, and Yiquan Wanga,2 aState Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; and bDepartment of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom Edited by Marianne Bronner, California Institute of Technology, Pasadena, CA, and approved February 21, 2017 (received for review December 14, 2016) Many bilaterally symmetrical animals develop genetically pro- Several studies have sought to dissect the evolutionary history of grammed left–right asymmetries. In vertebrates, this process is un- Nodal signaling and its regulation of LR asymmetry. Notably, der the control of Nodal signaling, which is restricted to the left side asymmetric expression of Nodal and Pitx in gastropod mollusc by Nodal antagonists Cerberus and Lefty. Amphioxus, the earliest embryos plays a role in the development of LR asymmetry, in- diverging chordate lineage, has profound left–right asymmetry as cluding the coiling of the shell (5, 6). Asymmetric expression of alarva.WeshowthatCerberus, Nodal, Lefty, and their target Nodal and/or Pitx has also been reported in some other lopho- transcription factor Pitx are sequentially activated in amphioxus trochozoans, including Pitx in a brachiopod and an annelid and embryos. We then address their function by transcription activa- Nodal in a brachiopod (7, 8). These data can be interpreted to tor-like effector nucleases (TALEN)-based knockout and heat-shock suggest an ancestral role for Nodal and Pitx in regulating bilat- promoter (HSP)-driven overexpression.
    [Show full text]
  • The TGF-Β Family in the Reproductive Tract
    Downloaded from http://cshperspectives.cshlp.org/ on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press The TGF-b Family in the Reproductive Tract Diana Monsivais,1,2 Martin M. Matzuk,1,2,3,4,5 and Stephanie A. Pangas1,2,3 1Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030 2Center for Drug Discovery, Baylor College of Medicine, Houston, Texas 77030 3Department of Molecular and Cellular Biology, Baylor College of Medicine Houston, Texas 77030 4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030 5Department of Pharmacology, Baylor College of Medicine, Houston, Texas 77030 Correspondence: [email protected]; [email protected] The transforming growth factor b (TGF-b) family has a profound impact on the reproductive function of various organisms. In this review, we discuss how highly conserved members of the TGF-b family influence the reproductive function across several species. We briefly discuss how TGF-b-related proteins balance germ-cell proliferation and differentiation as well as dauer entry and exit in Caenorhabditis elegans. In Drosophila melanogaster, TGF-b- related proteins maintain germ stem-cell identity and eggshell patterning. We then provide an in-depth analysis of landmark studies performed using transgenic mouse models and discuss how these data have uncovered basic developmental aspects of male and female reproductive development. In particular, we discuss the roles of the various TGF-b family ligands and receptors in primordial germ-cell development, sexual differentiation, and gonadal cell development. We also discuss how mutant mouse studies showed the contri- bution of TGF-b family signaling to embryonic and postnatal testis and ovarian development.
    [Show full text]
  • Determination of Left/Right Asymmetric Expression of Nodal by a Left Side-Specific Enhancer with Sequence Similarity to a Lefty-2 Enhancer
    Downloaded from genesdev.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Determination of left/right asymmetric expression of nodal by a left side-specific enhancer with sequence similarity to a lefty-2 enhancer Hitoshi Adachi, Yukio Saijoh, Kyoko Mochida, Sachiko Ohishi, Hiromi Hashiguchi, Akiko Hirao, and Hiroshi Hamada1 Division of Molecular Biology, Institute for Molecular and Cellular Biology, Osaka University, Suita, Osaka 565, Japan; and Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST) The nodal gene is expressed on the left side of developing mouse embryos and is implicated in left/right (L-R) axis formation. The transcriptional regulatory regions of nodal have now been investigated by transgenic analysis. A node-specific enhancer was detected in the upstream region (−9.5 to −8.7 kb) of the gene. Intron 1 was also shown to contain a left side-specific enhancer (ASE) that was able to direct transgene expression in the lateral plate mesoderm and prospective floor plate on the left side. A 3.5-kb region of nodal that contained ASE responded to mutations in iv, inv, and lefty-1, all genes that act upstream of nodal. The same 3.5- kb region also directed expression in the epiblast and visceral endoderm at earlier stages of development. Characterization of deletion constructs delineated ASE to a 340-bp region that was both essential and sufficient for asymmetric expression of nodal. Several sequence motifs were found to be conserved between the nodal ASE and the lefty-2 ASE, some of which appeared to be essential for nodal ASE activity.
    [Show full text]
  • 6 Signaling and BMP Antagonist Noggin in Prostate Cancer
    [CANCER RESEARCH 64, 8276–8284, November 15, 2004] Bone Morphogenetic Protein (BMP)-6 Signaling and BMP Antagonist Noggin in Prostate Cancer Dominik R. Haudenschild, Sabrina M. Palmer, Timothy A. Moseley, Zongbing You, and A. Hari Reddi Center for Tissue Regeneration and Repair, Department of Orthopedic Surgery, School of Medicine, University of California, Davis, Sacramento, California ABSTRACT antagonists has recently been discovered. These are secreted proteins that bind to BMPs and reduce their bioavailability for interactions It has been proposed that the osteoblastic nature of prostate cancer with the BMP receptors. Extracellular BMP antagonists include nog- skeletal metastases is due in part to elevated activity of bone morphoge- gin, follistatin, sclerostatin, chordin, DCR, BMPMER, cerberus, netic proteins (BMPs). BMPs are osteoinductive morphogens, and ele- vated expression of BMP-6 correlates with skeletal metastases of prostate gremlin, DAN, and others (refs. 11–16; reviewed in ref. 17). There are cancer. In this study, we investigated the expression levels of BMPs and several type I and type II receptors that bind to BMPs with different their modulators in prostate, using microarray analysis of cell cultures affinities. BMP activity is also regulated at the cell membrane level by and gene expression. Addition of exogenous BMP-6 to DU-145 prostate receptor antagonists such as BAMBI (18), which acts as a kinase- cancer cell cultures inhibited their growth by up-regulation of several deficient receptor. Intracellularly, the regulation of BMP activity at cyclin-dependent kinase inhibitors such as p21/CIP, p18, and p19. Expres- the signal transduction level is even more complex. There are inhib- sion of noggin, a BMP antagonist, was significantly up-regulated by itory Smads (Smad-6 and Smad-7), as well as inhibitors of inhibitory BMP-6 by microarray analysis and was confirmed by quantitative reverse Smads (AMSH and Arkadia).
    [Show full text]
  • Activin/Nodal Signalling in Stem Cells Siim Pauklin and Ludovic Vallier*
    © 2015. Published by The Company of Biologists Ltd | Development (2015) 142, 607-619 doi:10.1242/dev.091769 REVIEW Activin/Nodal signalling in stem cells Siim Pauklin and Ludovic Vallier* ABSTRACT organisms. Of particular relevance, genetic studies in the mouse Activin/Nodal growth factors control a broad range of biological have established that Nodal signalling is necessary at the early processes, including early cell fate decisions, organogenesis and epiblast stage during implantation, in which the pathway functions adult tissue homeostasis. Here, we provide an overview of the to maintain the expression of key pluripotency factors as well as to mechanisms by which the Activin/Nodal signalling pathway governs regulate the differentiation of extra-embryonic tissue. Activins, β stem cell function in these different stages of development. dimers of different subtypes of Inhibin , are also expressed in pre- We describe recent findings that associate Activin/Nodal signalling implantation blastocyst but not in the primitive streak (Albano to pathological conditions, focusing on cancer stem cells in et al., 1993; Feijen et al., 1994). However, genetic studies have β tumorigenesis and its potential as a target for therapies. Moreover, shown that Inhibin s are not necessary for early development in the we will discuss future directions and questions that currently remain mouse (Lau et al., 2000; Matzuk, 1995; Matzuk et al., 1995a,b). unanswered on the role of Activin/Nodal signalling in stem cell self- Combined gradients of Nodal and BMP signalling within the renewal, differentiation and proliferation. primitive streak control endoderm and mesoderm germ layer specification and also their subsequent patterning whilst blocking KEY WORDS: Activin, Cell cycle, Differentiation, Nodal, neuroectoderm formation (Camus et al., 2006; Mesnard et al., Pluripotency, Stem cells 2006).
    [Show full text]
  • Lefty a Protein Inhibits TGF-Β1-Mediated Apoptosis in Human Renal Tubular Epithelial Cells
    MOLECULAR MEDICINE REPORTS 8: 621-625, 2013 Lefty A protein inhibits TGF-β1-mediated apoptosis in human renal tubular epithelial cells REN-PING ZHENG1,2*, TAO BAI1*, XIAO-GUANG ZHOU1*, CHANG-GEN XU1, WEI WANG1, MING-WEI XU1 and JIE ZHANG1,3 1Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060; 2First People's Hospital of Jiujiang City, Jiujiang 332000; 3Hubei Key Laboratory of Kidney Disease Pathogenesis and Intervention, Huangshi, Hubei 435003, P.R. China Received December 25, 2012; Accepted May 13, 2013 DOI: 10.3892/mmr.2013.1556 Abstract. This study aimed to examine the effects of Lefty A normal biological functions in vivo, and imbalances between protein on transforming growth factor-β1 (TGF-β1)-mediated cell proliferation and cell death can result in the onset of apoptosis in human renal tubular epithelial cells (HK-2). HK-2 numerous pathophysiological processes leading to a variety cells were transfected with the human Lefty gene to induce the of human diseases (1,2). Excessive apoptosis is important in a secretion of endogenous Lefty A protein. Following exposure number of diseases, including chronic degenerative disease and of the HK-2 cells to recombinant human TGF-β1 (10 ng/ml), acquired immune deficiency syndrome. Similarly, inadequate p-Smad2/3 protein levels were examined by western blot apoptosis contributes to autoimmune disease and cancer (3). analysis, and cellular apoptosis was detected by flow cytometry Uncontrolled apoptosis is also involved in numerous types of 6, 12, 24 and 48 h following TGF-β1 treatment. Coculture of renal disease. Acute renal failure induced by toxic, ischemic renal tubular epithelial cells with TGF-β1 resulted in a signifi- or obstructive injury induces apoptosis and necrosis simulta- cant increase in p-Smad2/3 protein levels and the rate of cell neously in renal tubular epithelial cells (4,5).
    [Show full text]
  • Cerberus Regulates Left–Right Asymmetry of the Embryonic Head and Heart Lei Zhu*†, Martha J
    Research Paper 931 Cerberus regulates left–right asymmetry of the embryonic head and heart Lei Zhu*†, Martha J. Marvin†‡, Aaron Gardiner‡, Andrew B. Lassar‡, Mark Mercola§, Claudio D. Stern* and Michael Levin†§ Background: Most of the molecules known to regulate left–right asymmetry in Addresses: *Department of Genetics and vertebrate embryos are expressed on the left side of the future trunk region of Development, Columbia University, 701 West 168th Street #1602, New York, New York 10032, the embryo. Members of the protein family comprising Cerberus and the putative USA. ‡Department of Biological Chemistry and tumour suppressor Dan have not before been implicated in left–right asymmetry. Molecular Pharmacology and §Department of Cell In Xenopus, these proteins have been shown to antagonise members of the Biology, Harvard Medical School, 240 Longwood transforming growth factor β (TGF-β) and Wnt families of signalling proteins. Avenue, Boston, Massachusetts 02115, USA. Correspondence: Claudio D. Stern Results: Chick Cerberus (cCer) was found to be expressed in the left head E-mail: [email protected] mesenchyme and in the left flank of the embryo. Expression on the left side of † the head was controlled by Sonic hedgehog (Shh) acting through the TGF-β L.Z., M.J.M. and M.L. contributed equally to this work. family member Nodal; in the flank, cCer was also regulated by Shh, but independently of Nodal. Surprisingly, although no known targets of Cerberus Received: 12 April 1999 are expressed asymmetrically on the right side of the embryo at these stages, Revised: 2 July 1999 misexpression of cCer on this side of the embryo led to upregulation of the Accepted: 20 July 1999 transcription factor Pitx2 and reversal of the direction of heart and head turning, Published: 18 August 1999 apparently as independent events.
    [Show full text]
  • Context-Dependent Roles in Cell and Tissue Physiology
    Downloaded from http://cshperspectives.cshlp.org/ on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press TGF-b and the TGF-b Family: Context-Dependent Roles in Cell and Tissue Physiology Masato Morikawa,1 Rik Derynck,2 and Kohei Miyazono3 1Ludwig Cancer Research, Science for Life Laboratory, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden 2Department of Cell and Tissue Biology, University of California at San Francisco, San Francisco, California 94143 3Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan Correspondence: [email protected] The transforming growth factor-b (TGF-b) is the prototype of the TGF-b family of growth and differentiation factors, which is encoded by 33 genes in mammals and comprises homo- and heterodimers. This review introduces the reader to the TGF-b family with its complexity of names and biological activities. It also introduces TGF-b as the best-studied factor among the TGF-b family proteins, with its diversity of roles in the control of cell proliferation and differentiation, wound healing and immune system, and its key roles in pathology, for exam- ple, skeletal diseases, fibrosis, and cancer. lthough initially thought to stimulate cell TGF-b has been well documented in most cell Aproliferation, just like many growth factors, types, and has been best characterized in epithe- it became rapidly accepted that transforming lial cells. The bifunctional and context-depen- growth factor b (TGF-b) is a bifunctional reg- dent nature of TGF-b activities was further con- ulator that either inhibits or stimulates cell pro- firmed in a large variety of cell systems and liferation.
    [Show full text]
  • Canonical TGF Signaling and Its Contribution to Endometrial Cancer
    Journal of Clinical Medicine Review Canonical TGFβ Signaling and Its Contribution to Endometrial Cancer Development and Progression—Underestimated Target of Anticancer Strategies Piotr K. Zakrzewski Department of Cytobiochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; [email protected]; Tel.: +48-42-635-52-99 Abstract: Endometrial cancer is one of the leading gynecological cancers diagnosed among women in their menopausal and postmenopausal age. Despite the progress in molecular biology and medicine, no efficient and powerful diagnostic and prognostic marker is dedicated to endometrial carcinogenesis. The canonical TGFβ pathway is a pleiotropic signaling cascade orchestrating a variety of cellular and molecular processes, whose alterations are responsible for carcinogenesis that originates from different tissue types. This review covers the current knowledge concerning the canonical TGFβ pathway (Smad-dependent) induced by prototypical TGFβ isoforms and the involvement of pathway alterations in the development and progression of endometrial neoplastic lesions. Since Smad-dependent signalization governs opposed cellular processes, such as growth arrest, apoptosis, tumor cells growth and differentiation, as well as angiogenesis and metastasis, TGFβ cascade may act both as a tumor suppressor or tumor promoter. However, the final effect of TGFβ signaling on endometrial cancer cells depends on the cancer disease stage. The multifunctional Citation: Zakrzewski, P.K. Canonical role of the TGFβ pathway indicates the possible utilization of alterations in the TGFβ cascade as a TGFβ Signaling and Its Contribution potential target of novel anticancer strategies. to Endometrial Cancer Development and Progression—Underestimated Keywords: endometrial cancer; TGFβ isoforms; TGFβR1; TGFβR2; Smad proteins; TGFβ co-receptors; Target of Anticancer Strategies.
    [Show full text]
  • In Vivo Functions of the Proprotein Convertase PC5/6 During Mouse Development: Gdf11 Is a Likely Substrate
    In vivo functions of the proprotein convertase PC5/6 during mouse development: Gdf11 is a likely substrate Rachid Essalmani, Ahmed Zaid, Jadwiga Marcinkiewicz, Ann Chamberland, Antonella Pasquato, Nabil G. Seidah, and Annik Prat* Laboratory of Biochemical Neuroendocrinology, Clinical Research Institute of Montreal, 110 Pine Avenue West, Montreal, QC, Canada H2W 1R7 Edited by Donald F. Steiner, University of Chicago, Chicago, IL, and approved January 31, 2008 (received for review October 3, 2007) The proprotein convertase PC5/6 cleaves protein precursors after tions and/or specific laterality defects, such as cyclopia, mislo- basic amino acids and is essential for implantation in CD1/129/Sv/ calization of organs and cardiac malformations (13). Our group C57BL/6 mixed-background mice. Conditional inactivation of Pcsk5 showed that Pcsk5 inactivation, by removal of exon 4 (⌬4) that in the epiblast but not in the extraembryonic tissue bypassed early encodes the catalytic Asp, led to embryonic lethality between embryonic lethality but resulted in death at birth. PC5/6-deficient E4.5 and E7.5 (9). embryos exhibited Gdf11-related phenotypes such as altered an- To bypass the PC5/6Ϫ/Ϫ embryonic lethality at the implanta- teroposterior patterning with extra vertebrae and lack of tail and tion stage and to better define the functions of PC5/6, we decided kidney agenesis. They also exhibited Gdf11-independent pheno- to develop a conditional approach for Pcsk5 inactivation. In situ types, such as a smaller size, multiple hemorrhages, collapsed hybridization studies indicated that PC5/6 was not significantly alveoli, and retarded ossification. In situ hybridization revealed expressed in the fetus itself before E7.5 (14).
    [Show full text]