1651
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Alkafeef SS, Lane S, Yu C, Zhou T, Solis NV, Filler SG, Huang L, Liu H. Proteomic profiling of the monothiol glutaredoxin Grx3 reveals its global role in the regulation of iron dependent processes. PLoS Genet 2020; 16:e1008881. [PMID: 32525871 PMCID: PMC7319344 DOI: 10.1371/journal.pgen.1008881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/26/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Iron is an essential nutrient required as a cofactor for many biological processes. As a fungal commensal-pathogen of humans, Candida albicans encounters a range of bioavailable iron levels in the human host and maintains homeostasis with a conserved regulatory circuit. How C. albicans senses and responds to iron availability is unknown. In model yeasts, regulation of the iron homeostasis circuit requires monothiol glutaredoxins (Grxs), but their functions beyond the regulatory circuit are unclear. Here, we show Grx3 is required for virulence and growth on low iron for C. albicans. To explore the global roles of Grx3, we applied a proteomic approach and performed in vivo cross-linked tandem affinity purification coupled with mass spectrometry. We identified a large number of Grx3 interacting proteins that function in diverse biological processes. This included Fra1 and Bol2/Fra2, which function with Grxs in intracellular iron trafficking in other organisms. Grx3 interacts with and regulates the activity of Sfu1 and Hap43, components of the C. albicans iron regulatory circuit. Unlike the regulatory circuit, which determines expression or repression of target genes in response to iron availability, Grx3 amplifies levels of gene expression or repression. Consistent with the proteomic data, the grx3 mutant is sensitive to heat shock, oxidative, nitrosative, and genotoxic stresses, and shows growth dependence on histidine, leucine, and tryptophan. We suggest Grx3 is a conserved global regulator of iron-dependent processes occurring within the cell. Mammalian pathogens occupy a diverse set of niches within the host organism. These niches vary in iron and oxygen availability. As a commensal and pathogen of humans, its ability to regulate iron uptake and utilization in response to bioavailable iron level is critical for its survival in different host environments encompassing a broad range of iron levels. This study aims to understand how C. albicans senses and responds to iron level to regulate multiple aspects of its biology. The cytosolic monothiol glutaredoxin Grx3 is a critical regulator of C. albicans iron homeostasis and virulence. Taking a proteomic approach, we identified a large list of Grx3 associated proteins of diverse functions, including iron-sulfur trafficking, iron homeostasis, metabolism redox homeostasis, protein translation, DNA maintenance and repair. In support of these protein associations, Grx3 is important for all these processes. Thus, Grx3 is a global regulator of iron homeostasis and other iron dependent cellular processes.
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Affiliation(s)
- Selma S Alkafeef
- Department of Biological Chemistry, University of California, Irvine, California, United States of America.,Department of Biochemistry, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Shelley Lane
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, California, United States of America
| | - Tingting Zhou
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Norma V Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Scott G Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America.,David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, California, United States of America
| | - Haoping Liu
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
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1652
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Lee JJ, Kopetz S, Vilar E, Shen JP, Chen K, Maitra A. Relative Abundance of SARS-CoV-2 Entry Genes in the Enterocytes of the Lower Gastrointestinal Tract. Genes (Basel) 2020; 11:E645. [PMID: 32545271 PMCID: PMC7349178 DOI: 10.3390/genes11060645] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/01/2020] [Accepted: 06/09/2020] [Indexed: 01/08/2023] Open
Abstract
There is increasing evidence of gastrointestinal (GI) infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We surveyed the co-expression of SARS-CoV-2 entry genes ACE2 and TMPRSS2 throughout the GI tract to assess potential sites of infection. Publicly available and in-house single-cell RNA-sequencing datasets from the GI tract were queried. Enterocytes from the small intestine and colonocytes showed the highest proportions of cells co-expressing ACE2 and TMPRSS2. Therefore, the lower GI tract represents the most likely site of SARS-CoV-2 entry leading to GI infection.
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Affiliation(s)
- Jaewon J. Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research and the Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.K.); (E.V.); (J.P.S.)
| | - Eduardo Vilar
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.K.); (E.V.); (J.P.S.)
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (S.K.); (E.V.); (J.P.S.)
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research and the Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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1653
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Jelcic M, Wang K, Hui KL, Cai XC, Enyedi B, Luo M, Niethammer P. A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. Cell Chem Biol 2020; 27:1073-1083.e12. [PMID: 32521230 DOI: 10.1016/j.chembiol.2020.05.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/13/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
ATP is an important energy metabolite and allosteric signal in health and disease. ATP-interacting proteins, such as P2 receptors, control inflammation, cell death, migration, and wound healing. However, identification of allosteric ATP sites remains challenging, and our current inventory of ATP-controlled pathways is likely incomplete. Here, we develop and verify mipATP as a minimally invasive photoaffinity probe for ATP-interacting proteins. Its N6 functionalization allows target enrichment by UV crosslinking and conjugation to reporter tags by "click" chemistry. The additions are compact, allowing mipATP to completely retain the calcium signaling responses of native ATP in vitro and in vivo. mipATP specifically enriched for known nucleotide binders in A549 cell lysates and membrane fractions. In addition, it retrieved unannotated ATP interactors, such as the FAS receptor, CD44, and various SLC transporters. Thus, mipATP is a promising tool to identify allosteric ATP sites in the proteome.
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Affiliation(s)
- Mark Jelcic
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ke Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - King Lam Hui
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiao-Chuan Cai
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Balázs Enyedi
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary; MTA-SE Lendület Tissue Damage Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary; HCEMM-SE Inflammatory Signaling Research Group, Department of Physiology, Semmelweis University, Budapest, Hungary
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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1654
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Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. J Biol Chem 2020; 295:11435-11454. [PMID: 32518159 DOI: 10.1074/jbc.ra120.013426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022] Open
Abstract
mRNA levels are determined by the balance between mRNA synthesis and decay. Protein factors that mediate both processes, including the 5'-3' exonuclease Xrn1, are responsible for a cross-talk between the two processes that buffers steady-state mRNA levels. However, the roles of these proteins in transcription remain elusive and controversial. Applying native elongating transcript sequencing (NET-seq) to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator and that its disruption manifests as a reduction of RNA polymerase II (Pol II) occupancy downstream of transcription start sites. By combining our sequencing data and mathematical modeling of transcription, we found that Xrn1 modulates transcription initiation and elongation of its target genes. Furthermore, Pol II occupancy markedly increased near cleavage and polyadenylation sites in xrn1Δ cells, whereas its activity decreased, a characteristic feature of backtracked Pol II. We also provide indirect evidence that Xrn1 is involved in transcription termination downstream of polyadenylation sites. We noted that two additional decay factors, Dhh1 and Lsm1, seem to function similarly to Xrn1 in transcription, perhaps as a complex, and that the decay factors Ccr4 and Rpb4 also perturb transcription in other ways. Interestingly, the decay factors could differentiate between SAGA- and TFIID-dominated promoters. These two classes of genes responded differently to XRN1 deletion in mRNA synthesis and were differentially regulated by mRNA decay pathways, raising the possibility that one distinction between these two gene classes lies in the mechanisms that balance mRNA synthesis with mRNA decay.
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Affiliation(s)
- Jonathan Fischer
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Chan Zuckerberg BioHub, San Francisco, California, USA
| | - Nir Yosef
- Chan Zuckerberg BioHub, San Francisco, California, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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1655
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Bovo S, Ribani A, Muñoz M, Alves E, Araujo JP, Bozzi R, Charneca R, Di Palma F, Etherington G, Fernandez AI, García F, García-Casco J, Karolyi D, Gallo M, Gvozdanović K, Martins JM, Mercat MJ, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Škrlep M, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. Anim Genet 2020; 51:541-556. [PMID: 32510676 DOI: 10.1111/age.12954] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 02/06/2023]
Abstract
In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed-specific DNA pooling approach (30-35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed-specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.
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Affiliation(s)
- S Bovo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - A Ribani
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Muñoz
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - E Alves
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - J P Araujo
- Centro de Investigação de Montanha, Instituto Politécnico de Viana do Castelo, Escola Superior Agrária, Refóios do Lima, Ponte de Lima, 4990-706, Portugal
| | - R Bozzi
- DAGRI - Animal Science Section, Università di Firenze, Via delle Cascine 5, Firenze, 50144, Italy
| | - R Charneca
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - F Di Palma
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - G Etherington
- Earlham Institute, Norwich Research Park, Colney Lane, Norwich, NR47UZ, UK
| | - A I Fernandez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - F García
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - J García-Casco
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - D Karolyi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska c. 25, Zagreb, 10000, Croatia
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, Roma, 00198, Italy
| | - K Gvozdanović
- Faculty of Agrobiotechnical Sciences Osijek, University of Osijek, Vladimira Preloga 1, Osijek, 31000, Croatia
| | - J M Martins
- MED - Mediterranean Institute for Agriculture, Environment and Development, Universidade de Évora, Pólo da Mitra, Apartado 94, Évora, 7006-554, Portugal
| | - M J Mercat
- IFIP Institut Du Porc, La Motte au Vicomte, BP 35104, Le Rheu Cedex, 35651, France
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - R Quintanilla
- Programa de Genética y Mejora Animal, IRTA, Torre Marimon, Caldes de Montbui, Barcelona, 08140, Spain
| | - Č Radović
- Department of Pig Breeding and Genetics, Institute for Animal Husbandry, Belgrade-Zemun, 11080, Serbia
| | - V Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, Baisogala, 82317, Lithuania
| | - J Riquet
- GenPhySE, INRA, Université de Toulouse, Chemin de Borde-Rouge 24, Auzeville Tolosane, Castanet Tolosan, 31326, France
| | - R Savić
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, Belgrade-Zemun, 11080, Serbia
| | - G Schiavo
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - M Škrlep
- Kmetijski Inštitut Slovenije, Hacquetova 17, Ljubljana, SI-1000, Slovenia
| | - G Usai
- AGRIS SARDEGNA, Loc. Bonassai, Sassari, 07100, Italy
| | - V J Utzeri
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
| | - C Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Haller Str. 20, Wolpertshausen, 74549, Germany
| | - C Ovilo
- Departamento Mejora Genética Animal, INIA, Crta. de la Coruña, km. 7,5, Madrid, 28040, Spain
| | - L Fontanesi
- Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, 40127, Italy
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1656
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Ilyin AA, Stolyarenko AD, Klenov MS, Shevelyov YY. Various modes of HP1a interactions with the euchromatic chromosome arms in Drosophila ovarian somatic cells. Chromosoma 2020; 129:201-214. [PMID: 32500264 DOI: 10.1007/s00412-020-00738-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 05/05/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022]
Abstract
Heterochromatin protein 1a (HP1a) is a well-known component of pericentromeric and telomeric heterochromatin in Drosophila. However, its role and the mechanisms of its binding in the chromosome arms (ChAs) remain largely unclear. Here, we identified HP1a-interacting domains in the somatic cells of Drosophila ovaries using a DamID-seq approach and compared them with insertion sites of transposable elements (TEs) revealed by genome sequencing. Although HP1a domains cover only 13% of ChAs, they non-randomly associate with 42% of TE insertions. Furthermore, HP1a on average propagates at 2-kb distances from the TE insertions. These data confirm the role of TEs in formation of HP1a islands in ChAs. However, only 18% of HP1a domains have adjacent TEs, indicating the existence of other mechanisms of HP1a domain formation besides spreading from TEs. In particular, many TE-independent HP1a domains correspond to the regions attached to the nuclear pore complexes (NPCs) or contain active gene promoters. However, HP1a occupancy on the promoters does not significantly influence expression of corresponding genes. At the same time, the steady-state transcript level of many genes located outside of HP1a domains was altered upon HP1a knockdown in the somatic cells of ovaries, thus pointing to the strong indirect effect of HP1a depletion. Collectively, our results support an existence of at least three different mechanisms of HP1a domain emergence in ChAs: spreading from TE insertions, transient interactions with the chromatin located near NPCs, and targeting to the promoters of moderately expressed genes.
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Affiliation(s)
- Artem A Ilyin
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182
| | - Anastasia D Stolyarenko
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182
| | - Mikhail S Klenov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182.
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, Russia, 123182.
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1657
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Nkya S, Mwita L, Mgaya J, Kumburu H, van Zwetselaar M, Menzel S, Mazandu GK, Sangeda R, Chimusa E, Makani J. Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. BMC MEDICAL GENETICS 2020; 21:125. [PMID: 32503527 PMCID: PMC7275552 DOI: 10.1186/s12881-020-01059-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/24/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Sickle cell disease (SCD) is a blood disorder caused by a point mutation on the beta globin gene resulting in the synthesis of abnormal hemoglobin. Fetal hemoglobin (HbF) reduces disease severity, but the levels vary from one individual to another. Most research has focused on common genetic variants which differ across populations and hence do not fully account for HbF variation. METHODS We investigated rare and common genetic variants that influence HbF levels in 14 SCD patients to elucidate variants and pathways in SCD patients with extreme HbF levels (≥7.7% for high HbF) and (≤2.5% for low HbF) in Tanzania. We performed targeted next generation sequencing (Illumina_Miseq) covering exonic and other significant fetal hemoglobin-associated loci, including BCL11A, MYB, HOXA9, HBB, HBG1, HBG2, CHD4, KLF1, MBD3, ZBTB7A and PGLYRP1. RESULTS Results revealed a range of genetic variants, including bi-allelic and multi-allelic SNPs, frameshift insertions and deletions, some of which have functional importance. Notably, there were significantly more deletions in individuals with high HbF levels (11% vs 0.9%). We identified frameshift deletions in individuals with high HbF levels and frameshift insertions in individuals with low HbF. CHD4 and MBD3 genes, interacting in the same sub-network, were identified to have a significant number of pathogenic or non-synonymous mutations in individuals with low HbF levels, suggesting an important role of epigenetic pathways in the regulation of HbF synthesis. CONCLUSIONS This study provides new insights in selecting essential variants and identifying potential biological pathways associated with extreme HbF levels in SCD interrogating multiple genomic variants associated with HbF in SCD.
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Affiliation(s)
- Siana Nkya
- Department of Biological Sciences, Dar es Salaam University College of Education, Dar es Salaam, Tanzania. .,Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - Liberata Mwita
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Josephine Mgaya
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Happiness Kumburu
- Department of Biotechnology Laboratory, Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Marco van Zwetselaar
- Department of Biotechnology Laboratory, Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Stephan Menzel
- Department of Molecular Hematology, King's College of London, London, UK
| | - Gaston Kuzamunu Mazandu
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa. .,Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Observatory, 7925, South Africa. .,African Institute for Mathematical Sciences, Muizenberg, Cape Town, 7945, South Africa.
| | - Raphael Sangeda
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Department of Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Emile Chimusa
- Department of Pathology, Division of Human Genetics, University of Cape Town, IDM, Cape Town, South Africa
| | - Julie Makani
- Sickle Cell Program, Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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1658
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Beacon TH, Xu W, Davie JR. Genomic landscape of transcriptionally active histone arginine methylation marks, H3R2me2s and H4R3me2a, relative to nucleosome depleted regions. Gene 2020; 742:144593. [DOI: 10.1016/j.gene.2020.144593] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/10/2020] [Accepted: 03/14/2020] [Indexed: 02/06/2023]
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1659
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Shin J, Ma S, Hofer E, Patel Y, Vosberg DE, Tilley S, Roshchupkin GV, Sousa AMM, Jian X, Gottesman R, Mosley TH, Fornage M, Saba Y, Pirpamer L, Schmidt R, Schmidt H, Carrion-Castillo A, Crivello F, Mazoyer B, Bis JC, Li S, Yang Q, Luciano M, Karama S, Lewis L, Bastin ME, Harris MA, Wardlaw JM, Deary IE, Scholz M, Loeffler M, Witte AV, Beyer F, Villringer A, Armstrong NJ, Mather KA, Ames D, Jiang J, Kwok JB, Schofield PR, Thalamuthu A, Trollor JN, Wright MJ, Brodaty H, Wen W, Sachdev PS, Terzikhan N, Evans TE, Adams HHHH, Ikram MA, Frenzel S, van der Auwera-Palitschka S, Wittfeld K, Bülow R, Grabe HJ, Tzourio C, Mishra A, Maingault S, Debette S, Gillespie NA, Franz CE, Kremen WS, Ding L, Jahanshad N, Sestan N, Pausova Z, Seshadri S, Paus T. Global and Regional Development of the Human Cerebral Cortex: Molecular Architecture and Occupational Aptitudes. Cereb Cortex 2020; 30:4121-4139. [PMID: 32198502 PMCID: PMC7947185 DOI: 10.1093/cercor/bhaa035] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have carried out meta-analyses of genome-wide association studies (GWAS) (n = 23 784) of the first two principal components (PCs) that group together cortical regions with shared variance in their surface area. PC1 (global) captured variations of most regions, whereas PC2 (visual) was specific to the primary and secondary visual cortices. We identified a total of 18 (PC1) and 17 (PC2) independent loci, which were replicated in another 25 746 individuals. The loci of the global PC1 included those associated previously with intracranial volume and/or general cognitive function, such as MAPT and IGF2BP1. The loci of the visual PC2 included DAAM1, a key player in the planar-cell-polarity pathway. We then tested associations with occupational aptitudes and, as predicted, found that the global PC1 was associated with General Learning Ability, and the visual PC2 was associated with the Form Perception aptitude. These results suggest that interindividual variations in global and regional development of the human cerebral cortex (and its molecular architecture) cascade-albeit in a very limited manner-to behaviors as complex as the choice of one's occupation.
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Affiliation(s)
- Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, M5G 0A4 ON, M5G 0A4, Canada
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Shaojie Ma
- Department of Genetics, Yale University School of Medicine, New Haven, 06510 CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, 06510 CT, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, 8036 Graz, Austria
| | - Yash Patel
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Daniel E Vosberg
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Steven Tilley
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
| | - Gennady V Roshchupkin
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Medical Informatics, Erasmus MC, 3015 Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - André M M Sousa
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, 06510 CT, USA
| | - Xueqiu Jian
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, 77030 Houston, 77030 TX, USA
| | | | - Thomas H Mosley
- University of Mississippi Medical Center, Jackson, 39216 MS, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, 77030 Houston, 77030 TX, USA
| | - Yasaman Saba
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8036 Graz, Austria
| | - Lukas Pirpamer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
| | - Helena Schmidt
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, 8036 Graz, Austria
| | - Amaia Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, 6525 Nijmegen, The Netherlands
| | - Fabrice Crivello
- Groupe d’Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, et Université de Bordeaux, F-33000 Bordeaux, France
| | - Bernard Mazoyer
- Groupe d’Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, et Université de Bordeaux, F-33000 Bordeaux, France
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, 98101 WA, USA
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, 02118, MA, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, 02118, MA, USA
| | - Michelle Luciano
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
- Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Sherif Karama
- Montreal Neurological Institute, McGill University, H3A 2B4 Montreal, QC, Canada
| | - Lindsay Lewis
- Montreal Neurological Institute, McGill University, H3A 2B4 Montreal, QC, Canada
| | - Mark E Bastin
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, EH8 9YL Edinburgh, UK
| | - Mathew A Harris
- Centre for Clinical Brain Sciences, University of Edinburgh, EH8 9YL Edinburgh, UK
- Division of Psychiatry, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Joanna M Wardlaw
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Ian E Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, EH8 9YL Edinburgh, UK
- Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04109 Leipzig, Germany
- LIFE Research Center for Civilization Diseases, 04103 Leipzig, Germany
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04109 Leipzig, Germany
- LIFE Research Center for Civilization Diseases, 04103 Leipzig, Germany
| | - A Veronica Witte
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
- Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, 04109 Leipzig, Germany
- Day Clinic for Cognitive Neurology, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Frauke Beyer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
- Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, 04109 Leipzig, Germany
| | - Arno Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, 04103 Leipzig, Germany
- Faculty of Medicine, CRC 1052 Obesity Mechanisms, University of Leipzig, 04109 Leipzig, Germany
- Day Clinic for Cognitive Neurology, University Hospital Leipzig, 04103 Leipzig, Germany
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, 6150 Perth, WA, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
- Neuroscience Research Australia, 2031 Sydney, NSW, Australia
| | - David Ames
- National Ageing Research Institute, Royal Melbourne Hospital, 3052 Melbourne, VIC, Australia
- Academic Unit for Psychiatry of Old Age, St. Vincent's Health, The University of Melbourne, 3010 Melbourne, VIC, Australia
| | - Jiyang Jiang
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
| | - John B Kwok
- Brain and Mind Centre, The University of Sydney, 2050 Sydney, NSW, Australia
- School of Medical Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, 2031 Sydney, NSW, Australia
- School of Medical Sciences, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Julian N Trollor
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
- Department of Developmental Disability Neuropsychiatry, School of Psychiatry, University of New South Wales, 2031 Sydney, NSW, Australia
| | - Margaret J Wright
- Queensland Brain Institute, The University of Queensland, 4072 St Lucia, QLD, Australia
- Centre for Advanced Imaging, The University of Queensland, 4072 St Lucia, QLD, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
- Dementia Centre for Research Collaboration, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Wei Wen
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, 2052 Sydney, NSW, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, 2031 Sydney, NSW, Australia
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Tavia E Evans
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - Hieab H H H Adams
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus University Medical Center, 3015 Rotterdam, The Netherlands
- Department of Neurology, Erasmus MC University Medical Centre, 3015 Rotterdam, The Netherlands
| | - Stefan Frenzel
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Sandra van der Auwera-Palitschka
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, 37075, Germany
| | - Katharina Wittfeld
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, 37075, Germany
| | - Robin Bülow
- Institute for Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Hans Jörgen Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Rostock/Greifswald, Greifswald, 37075, Germany
| | - Christophe Tzourio
- Inserm, Bordeaux Population Health Research Center, University of Bordeaux, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France
- Department of Neurology, CHU de Bordeaux, F-33000 Bordeaux, France
| | - Aniket Mishra
- Inserm, Bordeaux Population Health Research Center, University of Bordeaux, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France
| | - Sophie Maingault
- Institut des Maladies Neurodégénratives, UMR 5293, CEA, CNRS, University of Bordeaux, Ubordeaux, F-33000 Bordeaux, France
| | - Stephanie Debette
- Inserm, Bordeaux Population Health Research Center, University of Bordeaux, Team VINTAGE, UMR 1219, F-33000 Bordeaux, France
- Department of Neurology, CHU de Bordeaux, F-33000 Bordeaux, France
- Department of Neurology, Boston University School of Medicine, Boston, 02118 MA, USA
| | - Nathan A Gillespie
- Virginia Institute for Psychiatric and Behavioural Genetics, Virginia Commonwealth University, Richmond, 23284 VA, USA
| | - Carol E Franz
- Department of Psychiatry, University of California, San Diego, 92093 CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, 92093 CA, USA
| | - William S Kremen
- Department of Psychiatry, University of California, San Diego, 92093 CA, USA
- Center for Behavior Genetics of Aging, University of California, San Diego, 92093 CA, USA
- VA San Diego Center of Excellence for Stress and Mental Health, San Diego, 92161 CA, USA
| | - Linda Ding
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, 90033 CA, USA
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, 90033 CA, USA
| | | | - Nenad Sestan
- Department of Genetics, Yale University School of Medicine, New Haven, 06510 CT, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, 06510 CT, USA
| | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, M5G 0A4 ON, M5G 0A4, Canada
- Department of Physiology, University of Toronto, Toronto, M5S 1A8 ON, Canada
- Department of Nutritional Sciences, University of Toronto, Toronto, M5S 1A8 ON, Canada
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, 02118 MA, USA
- Department of Epidemiology and Biostatistics, Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, 78229 TX, USA
| | - Tomas Paus
- Holland Bloorview Kids Rehabilitation Hospital, Bloorview Research Institute, University of Toronto, Toronto, M4G 1R8 ON, Canada
- Department of Psychology, University of Toronto, Toronto, M5S 3G3 ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, M5T 1R8 ON, Canada
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1660
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Ranjani TS, Pitchika GK, Yedukondalu K, Gunavathi Y, Daveedu T, Sainath SB, Philip GH, Pradeepkiran JA. Phenotypic and transcriptomic changes in zebrafish (Danio rerio) embryos/larvae following cypermethrin exposure. CHEMOSPHERE 2020; 249:126148. [PMID: 32062212 DOI: 10.1016/j.chemosphere.2020.126148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Cypermethrin is one of the widely used type-II pyrethroid and the indiscriminate use of this pesticide leads to life threatening effects and in particular showed developmental effects in sensitive populations such as children and pregnant woman. However, the molecular mechanisms underlying cypermethrin-induced development toxicity is not well defined. To address this gap, the present study was designed to investigate the phenotypic and transcriptomic (next generation RNA-Seq method) impact of cypermethrin in zebrafish embryos as a model system. Zebrafish embryos at two time points, 24 h postfertilization (hpf) and 48 hpf were exposed to cypermethrin at a concentration of 10 μg/L. Respective control groups were maintained. Cypermethrin induced both phenotypic and transcriptomic changes in zebrafish embryos at 48 hpf. The phenotypic anomalies such as delayed hatching rate, increased heartbeat rate and deformed axial spinal curvature in cypermethrin exposed zebrafish embryos at 48 hpf as compared to its respective controls. Transcriptomic analysis indicated that cypermethrin exposure altered genes associated with visual/eye development and gene functional profiling also revealed that cypermethrin stress over a period of 48 h disrupts phototransduction pathway in zebrafish embryos. Interestingly, cypermethrin exposure resulted in up regulation of only one gene, tnnt3b, fast muscle troponin isoform 3T in 24 hpf embryos as compared to its respective controls. The present model system, cypermethrin exposed zebrafish embryos elaborates the toxic consequences of cypermethrin exposure during developmental stages, especially in fishes. The present findings paves a way to understand the visual impairment in sensitive populations such as children exposed to cypermethrin during their embryonic period and further research is warranted.
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Affiliation(s)
- T Sri Ranjani
- Department of Zoology, Sri Krishnadevaraya University, Anantapuramu, 515003, India; Department of Zoology, D.K. Govt. Degree College for Women (Autonomous), Dargamitta, Nellore, 524003, India
| | - Gopi Krishna Pitchika
- Department of Zoology, Vikrama Simhapuri University Post-Graduation Centre, Kavali, 524201, India
| | - K Yedukondalu
- Department of Zoology, Vikrama Simhapuri University Post-Graduation Centre, Kavali, 524201, India
| | - Y Gunavathi
- Department of Zoology, Vikrama Simhapuri University Post-Graduation Centre, Kavali, 524201, India
| | - T Daveedu
- Department of Biotechnology, Vikrama Sihapuri University, Nellore, 524320, India
| | - S B Sainath
- Department of Biotechnology, Vikrama Sihapuri University, Nellore, 524320, India.
| | - G H Philip
- Department of Zoology, Sri Krishnadevaraya University, Anantapuramu, 515003, India.
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1661
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Gangras P, Gallagher TL, Parthun MA, Yi Z, Patton RD, Tietz KT, Deans NC, Bundschuh R, Amacher SL, Singh G. Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3'UTR intron-containing NMD targets. PLoS Genet 2020; 16:e1008830. [PMID: 32502192 PMCID: PMC7310861 DOI: 10.1371/journal.pgen.1008830] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 06/23/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
Many post-transcriptional mechanisms operate via mRNA 3'UTRs to regulate protein expression, and such controls are crucial for development. We show that homozygous mutations in two zebrafish exon junction complex (EJC) core genes rbm8a and magoh leads to muscle disorganization, neural cell death, and motor neuron outgrowth defects, as well as dysregulation of mRNAs subjected to nonsense-mediated mRNA decay (NMD) due to translation termination ≥ 50 nts upstream of the last exon-exon junction. Intriguingly, we find that EJC-dependent NMD also regulates a subset of transcripts that contain 3'UTR introns (3'UI) < 50 nts downstream of a stop codon. Some transcripts containing such stop codon-proximal 3'UI are also NMD-sensitive in cultured human cells and mouse embryonic stem cells. We identify 167 genes that contain a conserved proximal 3'UI in zebrafish, mouse and humans. foxo3b is one such proximal 3'UI-containing gene that is upregulated in zebrafish EJC mutant embryos, at both mRNA and protein levels, and loss of foxo3b function in EJC mutant embryos significantly rescues motor axon growth defects. These data are consistent with EJC-dependent NMD regulating foxo3b mRNA to control protein expression during zebrafish development. Our work shows that the EJC is critical for normal zebrafish development and suggests that proximal 3'UIs may serve gene regulatory function in vertebrates.
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Affiliation(s)
- Pooja Gangras
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Thomas L. Gallagher
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Michael A. Parthun
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Zhongxia Yi
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Robert D. Patton
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Physics, The Ohio State University, Ohio, United States of America
| | - Kiel T. Tietz
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Natalie C. Deans
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Ralf Bundschuh
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Physics, The Ohio State University, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Ohio, United States of America
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Ohio, United States of America
| | - Sharon L. Amacher
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Ohio, United States of America
- Center for Muscle Health and Neuromuscular Disorders, The Ohio State University and Nationwide Children’s Hospital, Ohio, United States of America
| | - Guramrit Singh
- Department of Molecular Genetics, The Ohio State University, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
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1662
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Nedoluzhko AV, Slobodova NV, Sharko F, Shalgimbayeva GM, Tsygankova SV, Boulygina ES, Jeney Z, Nguyen VQ, Pham TT, Nguyen ĐT, Volkov AA, Fernandes JM, Rastorguev SM. A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds. Ecol Evol 2020; 10:5431-5439. [PMID: 32607164 PMCID: PMC7319122 DOI: 10.1002/ece3.6286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/28/2022] Open
Abstract
Common carp (Cyprinus carpio) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site-associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto-Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold-resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.
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Affiliation(s)
| | | | - Fedor Sharko
- National Research Center “Kurchatov Institute”MoscowRussia
- Institute of BioengineeringResearch Center of Biotechnology of the Russian Academy of SciencesMoscowRussia
| | | | | | | | - Zsigmond Jeney
- National Agricultural Research and Innovation CenterResearch Institute for Fisheries and Aquaculture (HAKI)SzarvasHungary
| | - Van Q. Nguyen
- Institute of Marine Environment and ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
- Graduate University of Science and TechnologyHanoiVietnam
| | - Thế T. Pham
- Institute of Marine Environment and ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Đức T. Nguyen
- Institute of Marine Environment and ResourcesVietnam Academy of Science and TechnologyHanoiVietnam
| | - Alexander A. Volkov
- Russian Federal Research Institute of Fisheries and OceanographyMoscowRussia
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1663
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Yue L, Wan R, Luan S, Zeng W, Cheung TH. Dek Modulates Global Intron Retention during Muscle Stem Cells Quiescence Exit. Dev Cell 2020; 53:661-676.e6. [DOI: 10.1016/j.devcel.2020.05.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/06/2020] [Accepted: 05/09/2020] [Indexed: 12/21/2022]
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1664
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Xiong J, Xue Y, Xia Y, Zhao J, Wang Y. Identification of key microRNAs of plasma extracellular vesicles and their diagnostic and prognostic significance in melanoma. Open Med (Wars) 2020; 15:464-482. [PMID: 33313406 PMCID: PMC7706137 DOI: 10.1515/med-2020-0111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 03/12/2020] [Accepted: 03/25/2020] [Indexed: 01/23/2023] Open
Abstract
Melanoma is one of the most highly metastatic, aggressive and fatal malignant tumors in skin cancer. This study employs bioinformatics to identify key microRNAs and target genes (TGs) of plasma extracellular vesicles (pEVs) and their diagnostic and prognostic significance in melanoma. The gene expression microarray dataset (GSE100508) was downloaded from the Gene Expression Omnibus database. Differential analysis of miRNAs in pEVs was performed to compare melanoma samples and healthy samples. Then, TGs of the differential miRNAs (DE-miRNAs) in melanoma were selected, and differential genes were analyzed by bioinformatics (including Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, protein–protein interaction network and prognostic analysis). A total of 55 DE-miRNAs were found, and 3,083 and 1,351 candidate TGs were diagnostically correlated with the top ten upregulated DE-miRNAs and all downregulated DE-miRNAs, respectively. Prognostic analysis results showed that high expression levels of hsa-miR-550a-3p, CDK2 and POLR2A and low expression levels of hsa-miR-150-5p in melanoma patients were associated with significantly reduced overall survival. In conclusion, bioinformatics analysis identified key miRNAs and TGs in pEVs of melanoma, which may represent potential biomarkers for the early diagnosis and treatment of this cancer.
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Affiliation(s)
- Jiachao Xiong
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
| | - Yan Xue
- Department of Dermatology, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
| | - Yu Xia
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
| | - Jiayi Zhao
- Department of General Practice, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
| | - Yuchong Wang
- Department of Plastic Surgery, Changhai Hospital, Naval Military Medical University, Shanghai 200433, China
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1665
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Transcriptome analysis of heat stressed seedlings with or without pre-heat treatment in Cryptomeria japonica. Mol Genet Genomics 2020; 295:1163-1172. [PMID: 32472284 DOI: 10.1007/s00438-020-01689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
With global warming as a major environment concern over the coming years, heat tolerance is an important trait for forest tree survival during the predicted future warmer weather conditions. Cryptomeria japonica is a coniferous species widely distributed throughout Japan, and thus, can adapt to a wide range of air temperatures. To elucidate genes involved in heat response in Cryptomeria japonica, transcriptome analysis was conducted for seedlings under heat shock conditions. To test whether heat acclimation affects levels of gene expression, half of the seedlings were pretreated with moderately high temperatures prior to heat shock. De novo assembly of the transcriptome generated 107,924 unigenes and the analysis of differentially expressed genes was conducted using these unigenes. A total of 5217 differentially expressed genes were identified. Most genes upregulated by heat shock, regardless of pre-heat treatment, were conserved to heat response genes of angiosperm species, such as heat shock factors (Hsf) and heat shock proteins (Hsp). Pre-heating of seedlings affected expression levels of several Hsfs and their induction was lower in pre-heated seedlings than in seedlings without pre-heat treatment. This suggests a conserved role of Hsfs in heat response and heat acclimation in seed plants. On the other hand, many unknown genes were upregulated in only seedlings without pre-heat treatment after heat exposure. Notably, expression of gypsy/Ty3 type retrotransposons was dramatically induced. These findings provide valuable information to develop a better understanding of the molecular mechanisms of heat response and acclimation in C. japonica.
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1666
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Kaltenecker D, Spirk K, Ruge F, Grebien F, Herling M, Rupprecht A, Kenner L, Pohl EE, Mueller KM, Moriggl R. STAT5 is required for lipid breakdown and beta-adrenergic responsiveness of brown adipose tissue. Mol Metab 2020; 40:101026. [PMID: 32473405 PMCID: PMC7322099 DOI: 10.1016/j.molmet.2020.101026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/10/2020] [Accepted: 05/23/2020] [Indexed: 12/02/2022] Open
Abstract
Objective Increasing energy expenditure through activation of brown adipose tissue (BAT) thermogenesis is an attractive approach to counteract obesity. It is therefore essential to understand the molecular mechanisms that control BAT functions. Until now several members of the Janus kinase (JAK) - signal transducer and activator of transcription (STAT) pathway have been implicated as being relevant for BAT physiology. However, whether the STAT family member STAT5 is important for the thermogenic property of adipose tissues is unknown. Therefore, we have investigated the role of STAT5 in thermogenic fat in this paper. Methods We performed metabolic and molecular analyses using mice that harbor an adipocyte-specific deletion of Stat5a/b alleles. Results We found that STAT5 is necessary for acute cold-induced temperature maintenance and the induction of lipid mobilization in BAT following β3-adrenergic stimulation. Moreover, mitochondrial respiration of primary differentiated brown adipocytes lacking STAT5 was diminished. Increased sensitivity to cold stress upon STAT5 deficiency was associated with reduced expression of thermogenic markers including uncoupling protein 1 (UCP1), while decreased stimulated lipolysis was linked to decreased protein kinase A (PKA) activity. Additionally, brown remodeling of white adipose tissue was diminished following chronic β3-adrenergic stimulation, which was accompanied by a decrease in mitochondrial performance. Conclusion We conclude that STAT5 is essential for the functionality and the β-adrenergic responsiveness of thermogenic adipose tissue. Impaired temperature maintenance in mice deficient in adipocyte STAT5 after acute cold exposure. Blocked β3-adrenergic induction of lipolysis and PKA activity in BAT upon STAT5 deficiency. Reduced respiratory capacity in primary differentiated brown adipocytes lacking STAT5. Diminished brown remodeling of STAT5 deficient ScWAT after chronic β3-adrenergic stimulation.
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Affiliation(s)
- Doris Kaltenecker
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria; Institute for Diabetes and Cancer (IDC), Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Katrin Spirk
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
| | - Frank Ruge
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
| | - Florian Grebien
- Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria; Institute for Medical Biochemistry, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Marco Herling
- Laboratory of Lymphocyte Signaling and Oncoproteome, Department I of Internal Medicine, CIO Aachen-Bonn-Cologne-Duesseldorf, Excellence Cluster for Cellular Stress Response and Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Anne Rupprecht
- Unit of Physiology and Biophysics, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Lukas Kenner
- Unit of Pathology of Laboratory Animals, University of Veterinary Medicine, Vienna, 1210, Vienna, Austria; Department of Pathology, Medical University Vienna, 1090, Vienna, Austria; Christian Doppler Laboratory for Applied Metabolomics, Medical University Vienna, 1090, Vienna, Austria
| | - Elena E Pohl
- Unit of Physiology and Biophysics, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Kristina M Mueller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria
| | - Richard Moriggl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210, Vienna, Austria; Ludwig Boltzmann Institute for Cancer Research, 1090, Vienna, Austria.
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1667
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High-resolution annotation of the mouse preimplantation embryo transcriptome using long-read sequencing. Nat Commun 2020; 11:2653. [PMID: 32461551 PMCID: PMC7253418 DOI: 10.1038/s41467-020-16444-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
The transcriptome of the preimplantation mouse embryo has been previously annotated by short-read sequencing, with limited coverage and accuracy. Here we utilize a low-cell number transcriptome based on the Smart-seq2 method to perform long-read sequencing. Our analysis describes additional novel transcripts and complexity of the preimplantation transcriptome, identifying 2280 potential novel transcripts from previously unannotated loci and 6289 novel splicing isoforms from previously annotated genes. Notably, these novel transcripts and isoforms with transcription start sites are enriched for an active promoter modification, H3K4me3. Moreover, we generate a more complete and precise transcriptome by combining long-read and short-read data during early embryogenesis. Based on this approach, we identify a previously undescribed isoform of Kdm4dl with a modified mRNA reading frame and a novel noncoding gene designated XLOC_004958. Depletion of Kdm4dl or XLOC_004958 led to abnormal blastocyst development. Thus, our data provide a high-resolution and more precise transcriptome during preimplantation mouse embryogenesis.
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1668
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Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J, Alvarez-Jarreta J, Barba M, Bolser DM, Cambell L, Carbajo M, Chakiachvili M, Christensen M, Cummins C, Cuzick A, Davis P, Fexova S, Gall A, George N, Gil L, Gupta P, Hammond-Kosack KE, Haskell E, Hunt SE, Jaiswal P, Janacek SH, Kersey PJ, Langridge N, Maheswari U, Maurel T, McDowall MD, Moore B, Muffato M, Naamati G, Naithani S, Olson A, Papatheodorou I, Patricio M, Paulini M, Pedro H, Perry E, Preece J, Rosello M, Russell M, Sitnik V, Staines DM, Stein J, Tello-Ruiz MK, Trevanion SJ, Urban M, Wei S, Ware D, Williams G, Yates AD, Flicek P. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Res 2020; 48:D689-D695. [PMID: 31598706 PMCID: PMC6943047 DOI: 10.1093/nar/gkz890] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/29/2019] [Accepted: 10/02/2019] [Indexed: 12/28/2022] Open
Abstract
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of interfaces to genomic data across the tree of life, including reference genome sequence, gene models, transcriptional data, genetic variation and comparative analysis. Data may be accessed via our website, online tools platform and programmatic interfaces, with updates made four times per year (in synchrony with Ensembl). Here, we provide an overview of Ensembl Genomes, with a focus on recent developments. These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants. Finally, we report on our continued deeper integration with the Ensembl project, which forms a key part of our future strategy for dealing with the increasing quantity of available genome-scale data across the tree of life.
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Affiliation(s)
- Kevin L Howe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bruno Contreras-Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nishadi De Silva
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gareth Maslen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Wasiu Akanni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jorge Alvarez-Jarreta
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Barba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dan M Bolser
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Lahcen Cambell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Manuel Carbajo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marc Chakiachvili
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mikkel Christensen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carla Cummins
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Alayne Cuzick
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Paul Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Silvie Fexova
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Astrid Gall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nancy George
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Laurent Gil
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Erin Haskell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sophie H Janacek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul J Kersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Nick Langridge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Uma Maheswari
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark D McDowall
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ben Moore
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthieu Muffato
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mateus Patricio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helder Pedro
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Emily Perry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Marc Rosello
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Matthew Russell
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vasily Sitnik
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Joshua Stein
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | | | - Stephen J Trevanion
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Sharon Wei
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA.,USDA ARS NAA Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, Ithaca, NY 14853, USA
| | - Gary Williams
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew D Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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1669
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Differential Secretome Profiling of Human Osteoarthritic Synoviocytes Treated with Biotechnological Unsulfated and Marine Sulfated Chondroitins. Int J Mol Sci 2020; 21:ijms21113746. [PMID: 32466468 PMCID: PMC7312545 DOI: 10.3390/ijms21113746] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/21/2020] [Accepted: 05/23/2020] [Indexed: 02/07/2023] Open
Abstract
Symptomatic slow-acting drugs (SYSADOA) are increasingly used as effective therapies for osteoarthritis, representing an attractive alternative to analgesics or non-steroidal anti-inflammatory drugs to relieve disease symptoms. Pharmaceutical preparations of chondroitin sulfate, derived from animal sources, alone or in combination with glucosamine sulfate, are widely recognized for their beneficial effect on osteoarthritis treatment. A growing interest has also been devoted to understanding the molecular mechanisms modulated by SYSADOA using -omic strategies, most of which rely on chondrocytes as a model system. In this work, by using an integrated strategy based on unbiased proteomics and targeted cytokine profiling by a multiplexed protein array, we identified differences in the secretomes of human osteoarthritic synoviocytes in response to biotechnological unsulfated, and marine sulfated chondroitins treatments. The combined strategy allowed the identification of candidate proteins showing both common and distinct regulation responses to the two treatments of chondroitins. These molecules, mainly belonging to ECM proteins, enzymes, enzymatic inhibitors and cytokines, are potentially correlated to treatment outcomes. Overall, the present results provide an integrated overview of protein changes in human osteoarthritic synoviocytes secretome associated to different chondroitin treatments, thus improving current knowledge of the biochemical effects driven by these drugs potentially involved in pathways associated to osteoarthritis pathogenesis.
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1670
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Bo D, Jiang X, Liu G, Xu F, Hu R, Wassie T, Chong Y, Ahmed S, Liu C, Girmay S. Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats. BMC Genomics 2020; 21:372. [PMID: 32450814 PMCID: PMC7249689 DOI: 10.1186/s12864-020-6767-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/04/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The microscopic process of postnatal testicular development in early-puberty animals is poorly understood. Therefore, in this study, 21 male Yiling goats with average ages of 0, 30, 60, 90, 120, 150 and 180 days old (each age group comprised three goats) were used to study the changes in organs, tissues and transcriptomes during postnatal testicle development to obtain a broad and deep insight into the dynamic process of testicular transition from growth to spermatogenesis in early-puberty animals. RESULTS The inflection point of testicular weight was at 119 days postpartum (dpp), and the testicular weight increased rapidly from 119 dpp to 150 dpp. Spermatozoa were observed in the testis at 90 dpp by using haematoxylin-eosin staining. We found from the transcriptome analysis of testes that the testicular development of Yiling goat from birth to 180 dpp experienced three stages, namely, growth, transition and spermatogenesis stages. The goats in the testicular growth stage (0-60 dpp) showed a high expression of growth-related genes in neurogenesis, angiogenesis and cell junction, and a low expression of spermatogenesis-related genes. The goats aged 60-120 dpp were in the transitional stage which had a gradually decreased growth-related gene transcription levels and increased spermatogenesis-related gene transcription levels. The goats aged 120-180 dpp were in the spermatogenesis stage. At this stage, highly expressed spermatogenesis-related genes, downregulated testicular growth- and immune-related genes and a shift in the focus of testicular development into spermatogenesis were observed. Additionally, we found several novel hub genes, which may play key roles in spermatogenesis, androgen synthesis and secretion, angiogenesis, cell junction and neurogenesis. Moreover, the results of this study were compared with previous studies on goat or other species, and some gene expression patterns shared in early-puberty mammals were discovered. CONCLUSIONS The postnatal development of the testis undergoes a process of transition from organ growth to spermatogenesis. During this process, spermatogenesis-related genes are upregulated, whereas neurogenesis-, angiogenesis-, cell junction-, muscle- and immune-related genes are downregulated. In conclusion, the multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats and may be a common rule shared by mammals.
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Affiliation(s)
- Dongdong Bo
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Wuhan, 430070, People's Republic of China.
| | - Feng Xu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ruixue Hu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Teketay Wassie
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yuqing Chong
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Sohail Ahmed
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chenhui Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shishay Girmay
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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1671
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Lee HO, Hong Y, Etlioglu HE, Cho YB, Pomella V, Van den Bosch B, Vanhecke J, Verbandt S, Hong H, Min JW, Kim N, Eum HH, Qian J, Boeckx B, Lambrechts D, Tsantoulis P, De Hertogh G, Chung W, Lee T, An M, Shin HT, Joung JG, Jung MH, Ko G, Wirapati P, Kim SH, Kim HC, Yun SH, Tan IBH, Ranjan B, Lee WY, Kim TY, Choi JK, Kim YJ, Prabhakar S, Tejpar S, Park WY. Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer. Nat Genet 2020; 52:594-603. [PMID: 32451460 DOI: 10.1038/s41588-020-0636-z] [Citation(s) in RCA: 345] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/28/2020] [Indexed: 12/30/2022]
Abstract
Immunotherapy for metastatic colorectal cancer is effective only for mismatch repair-deficient tumors with high microsatellite instability that demonstrate immune infiltration, suggesting that tumor cells can determine their immune microenvironment. To understand this cross-talk, we analyzed the transcriptome of 91,103 unsorted single cells from 23 Korean and 6 Belgian patients. Cancer cells displayed transcriptional features reminiscent of normal differentiation programs, and genetic alterations that apparently fostered immunosuppressive microenvironments directed by regulatory T cells, myofibroblasts and myeloid cells. Intercellular network reconstruction supported the association between cancer cell signatures and specific stromal or immune cell populations. Our collective view of the cellular landscape and intercellular interactions in colorectal cancer provide mechanistic information for the design of efficient immuno-oncology treatment strategies.
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Affiliation(s)
- Hae-Ock Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Yourae Hong
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Hakki Emre Etlioglu
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Yong Beom Cho
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea.,Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Valentina Pomella
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ben Van den Bosch
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jasper Vanhecke
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sara Verbandt
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Hyekyung Hong
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae-Woong Min
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Nayoung Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Hye Hyeon Eum
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Junbin Qian
- Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Bram Boeckx
- Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Petros Tsantoulis
- Centre d'Oncologie, Hôpitaux Universitaires de Genève, Geneva, Switzerland.,Service d'Oncologie, Hôpitaux Universitaires de Genève, Geneva, Switzerland.,Université de Genève, Geneva, Switzerland
| | - Gert De Hertogh
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium.,Department of Imaging and Pathology, Leuven, Belgium
| | - Woosung Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Taeseob Lee
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Digital Health, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Minae An
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea
| | - Hyun-Tae Shin
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Min-Hyeok Jung
- Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul, Korea
| | - Gunhwan Ko
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | | | - Seok Hyung Kim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Iain Bee Huat Tan
- Division of Medical Oncology, National Cancer Center, Singapore, Singapore.,Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore, Singapore, Singapore.,Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Bobby Ranjan
- Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Tae-You Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Technology, Yonsei University, Seoul, Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University Graduate School, Seoul, Korea
| | - Shyam Prabhakar
- Systems Biology and Data Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sabine Tejpar
- Molecular Digestive Oncology, Department of Oncology, Katholieke Universiteit Leuven, Leuven, Belgium.
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea. .,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea. .,Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul, Korea.
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1672
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Ochoa S, de Anda-Jáuregui G, Hernández-Lemus E. Multi-Omic Regulation of the PAM50 Gene Signature in Breast Cancer Molecular Subtypes. Front Oncol 2020; 10:845. [PMID: 32528899 PMCID: PMC7259379 DOI: 10.3389/fonc.2020.00845] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/29/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer is a disease that exhibits heterogeneity that goes from the genomic to the clinical levels. This heterogeneity is thought to be captured (at least partially) by the so-called breast cancer molecular subtypes. These molecular subtypes were initially defined based on the unsupervised clustering of gene expression and its correlate with histological, morphological, phenotypic and clinical features already known. Later, a 50-gene signature, PAM50, was defined in order to identify the biological subtype of a given sample within the clinical setting. The PAM50 signature was obtained by the use of unsupervised statistical methods, and therefore no limitation was set on the biological relevance (or lack of) of the selected genes beyond its predictive capacity. An open question that remains is what are the regulatory elements that drive the various expression behaviors of this set of genes in the different molecular subtypes. This question becomes more relevant as the measurement of more biological layers of regulation becomes accessible. In this work, we analyzed the gene expression regulation of the 50 genes in the PAM50 signature, in terms of (a) gene co-expression, (b) transcription factors, (c) micro-RNAs, and (d) methylation. Using data from the Cancer Genome Atlas (TCGA) for the Luminal A and B, Basal, and HER2-enriched molecular subtypes as well as normal tumor adjacent tissue, we identified predictors for gene expression through the use of an elastic net model. We compare and contrast the sets of identified regulators for the gene signature in each molecular subtype, and systematically compare them to current literature. We also identified a unique set of predictors for the expression of genes in the PAM50 signature associated with each of the molecular subtypes. Most selected predictors are exclusive for a PAM50 gene and predictors are not shared across subtypes. There are only 13 coding transcripts and 2 miRNAs selected for the four subtypes. MiR-21 and miR-10b connect almost all the PAM50 genes in all the subtypes and normal tissue, but do it in an exclusive manner, suggesting a cancer switch from miR-10b coordination in normal tissue to miR-21. The PAM50 gene sets of selected predictors that enrich for a function across subtypes, support that different regulatory molecular mechanisms are taking place. With this study we aim to a wider understanding of the regulatory mechanisms that differentiate the expression of the PAM50 signature, which in turn could perhaps help understand the molecular basis of the differences between the molecular subtypes.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Graduate Program in Biomedical Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guillermo de Anda-Jáuregui
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Cátedras Conacyt para Jóvenes Investigadores', National Council on Science and Technology, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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1673
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Riedel R, Addo R, Ferreira-Gomes M, Heinz GA, Heinrich F, Kummer J, Greiff V, Schulz D, Klaeden C, Cornelis R, Menzel U, Kröger S, Stervbo U, Köhler R, Haftmann C, Kühnel S, Lehmann K, Maschmeyer P, McGrath M, Naundorf S, Hahne S, Sercan-Alp Ö, Siracusa F, Stefanowski J, Weber M, Westendorf K, Zimmermann J, Hauser AE, Reddy ST, Durek P, Chang HD, Mashreghi MF, Radbruch A. Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. Nat Commun 2020; 11:2570. [PMID: 32444631 PMCID: PMC7244721 DOI: 10.1038/s41467-020-16464-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/03/2020] [Indexed: 12/15/2022] Open
Abstract
At present, it is not clear how memory B lymphocytes are maintained over time, and whether only as circulating cells or also residing in particular tissues. Here we describe distinct populations of isotype-switched memory B lymphocytes (Bsm) of murine spleen and bone marrow, identified according to individual transcriptional signature and B cell receptor repertoire. A population of marginal zone-like cells is located exclusively in the spleen, while a population of quiescent Bsm is found only in the bone marrow. Three further resident populations, present in spleen and bone marrow, represent transitional and follicular B cells and B1 cells, respectively. A population representing 10-20% of spleen and bone marrow memory B cells is the only one qualifying as circulating. In the bone marrow, all cells individually dock onto VCAM1+ stromal cells and, reminiscent of resident memory T and plasma cells, are void of activation, proliferation and mobility.
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Affiliation(s)
- René Riedel
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Evolutionary Genomics Group, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
| | - Richard Addo
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Marta Ferreira-Gomes
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Gitta Anne Heinz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Frederik Heinrich
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Jannis Kummer
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Victor Greiff
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH Zürich), CH-4058, Basel, Switzerland
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, 0424, Oslo, Norway
| | - Daniel Schulz
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Cora Klaeden
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Rebecca Cornelis
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Ulrike Menzel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH Zürich), CH-4058, Basel, Switzerland
| | - Stefan Kröger
- Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, 12489, Berlin, Germany
- Department of Infectious Disease Epidemiology, Robert Koch Institute, 13353, Berlin, Germany
| | - Ulrik Stervbo
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Ralf Köhler
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Claudia Haftmann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Institute of Experimental Immunology, Universitätsspital Zürich, 8057, Zürich, Switzerland
| | - Silvia Kühnel
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Katrin Lehmann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Patrick Maschmeyer
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Mairi McGrath
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Sandra Naundorf
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Stefanie Hahne
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Özen Sercan-Alp
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- R&D, TA Immunology & Inflammation Research, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926, Frankfurt am Main, Germany
| | - Francesco Siracusa
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Jonathan Stefanowski
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Melanie Weber
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Kerstin Westendorf
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Jakob Zimmermann
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Department for BioMedical Research (DBMR), University of Bern, 3008, Bern, Switzerland
| | - Anja E Hauser
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH Zürich), CH-4058, Basel, Switzerland
| | - Pawel Durek
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany
| | - Mir-Farzin Mashreghi
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany.
- BCRT/DRFZ Single-Cell Laboratory for Advanced Cellular Therapies - Brandenburg Center for Regenerative Therapies (BCRT), 13353, Berlin, Germany.
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum (DRFZ), an Institute of the Leibniz Association, 10117, Berlin, Germany.
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1674
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Murro V, Mucciolo DP, Giorgio D, Sodi A, Boraldi F, Quaglino D, Virgili G, Giansanti F. Pattern dystrophy-like changes and coquille d'oeuf atrophy in elderly patients affected by pseudoxanthoma elasticum. Graefes Arch Clin Exp Ophthalmol 2020; 258:1881-1892. [PMID: 32445016 DOI: 10.1007/s00417-020-04748-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 12/14/2022] Open
Abstract
PURPOSE To evaluate the retinal features of elderly patients affected by pseudoxanthoma elasticum (PXE). MATERIALS AND METHODS This is a retrospective case series of 62 eyes of 31 elderly PXE patients (age > 50 years). Clinical data, ultra-widefield fundus imaging (color, red-free (RF), infra-red imaging (IR), fundus autofluorescence (FAF)), and OCT examinations were collected. Diagnosis was confirmed by genetic testing or skin biopsy. RESULTS Thirty-one patients (10 males and 21 females (mean age 61.3 years, range 50-74 years)) were included in our study. Visual acuity ranged from 20/20 Snellen equivalent to 20/200. The mean follow-up was 66.4 ± 20.7 months (range 10-88). Pattern dystrophy-like changes (PD) (52 eyes of 26 patients, 83.8%) and atrophy resembling the "diffuse trickling" pattern described in geographic atrophy were present in the majority of patients. Twenty-three eyes of 12 patients (67.6%) had peripapillary atrophy, 9 eyes of 5 patients (26.4%) macular atrophy, 6 eyes of 3 patients (17.6%) displayed posterior pole atrophy and in 6 eyes of 3 patients (17.6%), atrophy could be detected beyond the vascular arcades (mid-peripheral atrophy). End-stage atrophy covered the entire area indicated as "coquille d'oeuf" (eggshell). Choroidal neovascularization occurred in 49 eyes of 26 patients (94.2%) with PD and in 6 eyes of 3 patients (60%) without PD. Genetic examinations were available for 29 patients (29/31, 93.5%). CONCLUSIONS The elderly PXE patients were characterized by pattern dystrophy-like changes with more or less extensive atrophy, progressive over time, which in some cases affected the whole area of the coquille d'oeuf during the course of the disease.
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Affiliation(s)
- Vittoria Murro
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Dario Pasquale Mucciolo
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy. .,Careggi Teaching Hospital, Florence, Italy.
| | - Dario Giorgio
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Andrea Sodi
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Federica Boraldi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Daniela Quaglino
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Gianni Virgili
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
| | - Fabrizio Giansanti
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Florence, Italy
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1675
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Commer B, Schultzhaus Z, Shaw BD. Localization of NPFxD motif-containing proteins in Aspergillus nidulans. Fungal Genet Biol 2020; 141:103412. [PMID: 32445863 DOI: 10.1016/j.fgb.2020.103412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 12/28/2022]
Abstract
During growth, filamentous fungi produce polarized cells called hyphae. It is generally presumed that polarization of hyphae is dependent upon secretion through the Spitzenkörper, as well as a mechanism called apical recycling, which maintains a balance between the tightly coupled processes of endocytosis and exocytosis. Endocytosis predominates in an annular domain called the sub-apical endocytic collar, which is located in the region of plasma membrane 1-5 μm distal to the Spitzenkörper. It has previously been proposed that one function of the sub-apical endocytic collar is to maintain the apical localization of polarization proteins. These proteins mark areas of polarization at the apices of hyphae. However, as hyphae grow, these proteins are displaced along the membrane and some must then be removed at the sub-apical endocytic collar in order to maintain the hyphoid shape. While endocytosis is fairly well characterized in yeast, comparatively little is known about the process in filamentous fungi. Here, a bioinformatics approach was utilized to identify 39 Aspergillus nidulans proteins that are predicted to be cargo of endocytosis based on the presence of an NPFxD peptide motif. This motif is a necessary endocytic signal sequence first established in Saccharomyces cerevisiae, where it marks proteins for endocytosis through an interaction with the adapter protein Sla1p. It is hypothesized that some proteins that contain this NPFxD peptide sequence in A. nidulans will be potential targets for endocytosis, and therefore will localize either to the endocytic collar or to more proximal polarized regions of the cell, e.g. the apical dome or the Spitzenkörper. To test this, a subset of the motif-containing proteins in A. nidulans was tagged with GFP and the dynamic localization was evaluated. The documented localization patterns support the hypothesis that the motif marks proteins for localization to the polarized cell apex in growing hyphae.
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Affiliation(s)
- Blake Commer
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, USA.
| | - Zachary Schultzhaus
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, USA.
| | - Brian D Shaw
- Department of Plant Pathology and Microbiology, Texas A&M University, 2132 TAMU, College Station, TX 77843, USA.
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1676
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Qin X, Song Y. Bioinformatics Analysis Identifies the Estrogen Receptor 1 (ESR1) Gene and hsa-miR-26a-5p as Potential Prognostic Biomarkers in Patients with Intrahepatic Cholangiocarcinoma. Med Sci Monit 2020; 26:e921815. [PMID: 32435051 PMCID: PMC7257878 DOI: 10.12659/msm.921815] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Intrahepatic cholangiocarcinoma arises from the epithelial cells of the bile ducts and is associated with poor prognosis. This study aimed to use bioinformatics analysis to identify molecular biomarkers of intrahepatic cholangiocarcinoma and their potential mechanisms. Material/Methods MicroRNA (miRNA) and mRNA microarrays from GSE53870 and GSE32879 were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEMs) associated with prognosis were identified using limma software and Kaplan-Meier survival analysis. Predictive target genes of the DEMs were identified using miRWalk, miRTarBase, miRDB, and TargetScan databases of miRNA-binding sites and targets. Target genes underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Hub genes were analyzed by constructing the protein-protein interaction (PPI) network using Cytoscape. DEMs validated the hub genes, followed by construction of the miRNA-gene regulatory network. Results Twenty-five DEMs were identified. Fifteen DEMs were upregulated, and ten were down-regulated. Kaplan-Meier survival analysis identified seven upregulated DEMs and nine down-regulated DEMs that were associated with the overall survival (OS), and 130 target genes were selected. GO analysis showed that target genes were mainly enriched for metabolism and development processes. KEGG analysis showed that target genes were mainly enriched for cancer processes and some signaling pathways. Fourteen hub genes identified from the PPI network were associated with the regulation of cell proliferation. The overlap between hub genes and DEMs identified the estrogen receptor 1 (ESR1) gene and hsa-miR-26a-5p. Conclusions Bioinformatics analysis identified ESR1 and hsa-miR-26a-5p as potential prognostic biomarkers for intrahepatic cholangiocarcinoma.
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Affiliation(s)
- Xianzheng Qin
- Queen Mary School of Nanchang University, Nanchang, Jiangxi, China (mainland)
| | - Yuning Song
- Queen Mary School of Nanchang University, Nanchang, Jiangxi, China (mainland)
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1677
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Paranjapye A, Mutolo MJ, Ebron JS, Leir SH, Harris A. The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 2020; 319:L126-L136. [PMID: 32432922 DOI: 10.1152/ajplung.00023.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The differentiated functions of the human airway epithelium are coordinated by a complex network of transcription factors. These include the pioneer factors Forkhead box A1 and A2 (FOXA1 and FOXA2), which are well studied in several tissues, but their role in airway epithelial cells is poorly characterized. Here, we define the cistrome of FOXA1 and FOXA2 in primary human bronchial epithelial (HBE) cells by chromatin immunoprecipitation with deep-sequencing (ChIP-seq). Next, siRNA-mediated depletion of each factor is used to investigate their transcriptome by RNA-seq. We found that, as predicted from their DNA-binding motifs, genome-wide occupancy of the two factors showed substantial overlap; however, their global impact on gene expression differed. FOXA1 is an abundant transcript in HBE cells, while FOXA2 is expressed at low levels, and both these factors likely exhibit autoregulation and cross-regulation. FOXA1 regulated loci are involved in cell adhesion and the maintenance of epithelial cell identity, particularly through repression of genes associated with epithelial to mesenchymal transition (EMT). FOXA1 also directly targets other transcription factors with a known role in the airway epithelium such as SAM-pointed domain-containing Ets-like factor (SPDEF). The intersection of the cistrome and transcriptome for FOXA1 revealed enrichment of genes involved in epithelial development and tissue morphogenesis. Moreover, depletion of FOXA1 was shown to reduce the transepithelial resistance of HBE cells, confirming the role of this factor in maintaining epithelial barrier integrity.
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Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Michael J Mutolo
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Jey Sabith Ebron
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
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1678
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Maitra N, He C, Blank HM, Tsuchiya M, Schilling B, Kaeberlein M, Aramayo R, Kennedy BK, Polymenis M. Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. eLife 2020; 9:53127. [PMID: 32432546 PMCID: PMC7263821 DOI: 10.7554/elife.53127] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 05/20/2020] [Indexed: 12/12/2022] Open
Abstract
A long-standing problem is how cells that lack one of the highly similar ribosomal proteins (RPs) often display distinct phenotypes. Yeast and other organisms live longer when they lack specific ribosomal proteins, especially of the large 60S subunit of the ribosome. However, longevity is neither associated with the generation time of RP deletion mutants nor with bulk inhibition of protein synthesis. Here, we queried actively dividing RP mutants through the cell cycle. Our data link transcriptional, translational, and metabolic changes to phenotypes associated with the loss of paralogous RPs. We uncovered translational control of transcripts encoding enzymes of methionine and serine metabolism, which are part of one-carbon (1C) pathways. Cells lacking Rpl22Ap, which are long-lived, have lower levels of metabolites associated with 1C metabolism. Loss of 1C enzymes increased the longevity of wild type cells. 1C pathways exist in all organisms and targeting the relevant enzymes could represent longevity interventions.
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Affiliation(s)
- Nairita Maitra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Chong He
- Buck Institute for Research on Aging, Novato, United States
| | - Heidi M Blank
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Mitsuhiro Tsuchiya
- Department of Pathology, University of Washington, Seattle, United States
| | | | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, United States
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, United States
| | - Brian K Kennedy
- Buck Institute for Research on Aging, Novato, United States.,Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Centre for Healthy Ageing, National University of Singapore, National University Health System, Singapore, Singapore
| | - Michael Polymenis
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
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1679
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Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. The reactome pathway knowledgebase. Nucleic Acids Res 2020; 48:D498-D503. [PMID: 31691815 PMCID: PMC7145712 DOI: 10.1093/nar/gkz1031] [Citation(s) in RCA: 1139] [Impact Index Per Article: 284.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/20/2022] Open
Abstract
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consistent data model, an extended version of a classic metabolic map. Reactome functions both as an archive of biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. To extend our ability to annotate human disease processes, we have implemented a new drug class and have used it initially to annotate drugs relevant to cardiovascular disease. Our annotation model depends on external domain experts to identify new areas for annotation and to review new content. New web pages facilitate recruitment of community experts and allow those who have contributed to Reactome to identify their contributions and link them to their ORCID records. To improve visualization of our content, we have implemented a new tool to automatically lay out the components of individual reactions with multiple options for downloading the reaction diagrams and associated data, and a new display of our event hierarchy that will facilitate visual interpretation of pathway analysis results.
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Affiliation(s)
- Bijay Jassal
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | | | - Guilherme Viteri
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Chuqiao Gong
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Pascual Lorente
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Antonio Fabregat
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Konstantinos Sidiropoulos
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Justin Cook
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Marc Gillespie
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.,College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA
| | - Robin Haw
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Fred Loney
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Bruce May
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Marija Milacic
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Karen Rothfels
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Cristoffer Sevilla
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | | | - Solomon Shorser
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Thawfeek Varusai
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Joel Weiser
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada
| | - Guanming Wu
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Lincoln Stein
- Ontario Institute for Cancer Research, Toronto, ON M5G0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.,National Center for Protein Sciences, Beijing, China
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1680
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Silzer TK, Pathak GA, Phillips NR. Mitochondrial tRNA methylation in Alzheimer's disease and progressive supranuclear palsy. BMC Med Genomics 2020; 13:71. [PMID: 32429992 PMCID: PMC7236490 DOI: 10.1186/s12920-020-0727-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/29/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylation of mitochondrial tRNAs (mt-tRNA) at the 9th position ("p9 site") is known to impact translational efficiency and downstream mitochondrial function; however, direct assessment of mt-RNA methylation is challenging. Recent RNA sequence-based methods have been developed to reliably identify post-transcriptional methylation. Though p9 methylation has been studied in healthy human populations and in the context of cancer, it has not yet been analyzed in neurodegenerative disease, where mitochondrial dysfunction is a prominent and early hallmark of disease progression. METHODS Mitochondrial p9 methylation was inferred from multi-allelic calls in RNA-seq data. Gene-based association studies were performed in FUMA. Correlations between nuclear gene expression and p9 methylation were tested using Spearman's rho. Fisher's Exact test was used in PANTHER and IPA to test for overrepresentation and enrichment of biological processes and pathways in the top nuclear genes correlated with p9 methylation. RESULTS Variable methylation was observed at 11 p9 sites in post-mortem cerebellar tissue of elderly subjects who were either healthy or diagnosed with Alzheimer's disease (AD), progressive supranuclear palsy (PSP) or pathological aging (PA). Similarities in degree of methylation were observed between AD and PSP. Certain nuclear encoded genes were identified as significantly associated with p9 methylation. Expression of 5300 nuclear encoded genes was significantly correlated with p9 methylation, with AD and PSP subjects exhibiting similar expression profiles. Overrepresentation and enrichment testing using the top transcripts revealed enrichment for a number of molecular processes, terms and pathways including many of which that were mitochondrial-related. CONCLUSION With mitochondrial dysfunction being an established hallmark of neurodegenerative disease pathophysiology, this work sheds light on the potential molecular underpinnings of this dysfunction. Here we show overlap in cerebellar pathophysiology between common tauopathies such as Alzheimer's disease and progressive supranuclear palsy. Whether p9 hypermethylation is a cause or consequence of pathology remains an area of focus.
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Affiliation(s)
- Talisa K Silzer
- Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Gita A Pathak
- Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA
| | - Nicole R Phillips
- Department of Microbiology, Immunology and Genetics; Graduate School of Biomedical Science, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, USA.
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1681
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Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res 2020; 48:D127-D131. [PMID: 31504780 PMCID: PMC6943051 DOI: 10.1093/nar/gkz757] [Citation(s) in RCA: 1595] [Impact Index Per Article: 398.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/02/2019] [Accepted: 08/27/2019] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that act as master regulators in many biological processes. miRNAs function mainly by downregulating the expression of their gene targets. Thus, accurate prediction of miRNA targets is critical for characterization of miRNA functions. To this end, we have developed an online database, miRDB, for miRNA target prediction and functional annotations. Recently, we have performed major updates for miRDB. Specifically, by employing an improved algorithm for miRNA target prediction, we now present updated transcriptome-wide target prediction data in miRDB, including 3.5 million predicted targets regulated by 7000 miRNAs in five species. Further, we have implemented the new prediction algorithm into a web server, allowing custom target prediction with user-provided sequences. Another new database feature is the prediction of cell-specific miRNA targets. miRDB now hosts the expression profiles of over 1000 cell lines and presents target prediction data that are tailored for specific cell models. At last, a new web query interface has been added to miRDB for prediction of miRNA functions by integrative analysis of target prediction and Gene Ontology data. All data in miRDB are freely accessible at http://mirdb.org.
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Affiliation(s)
- Yuhao Chen
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA.,Department of Electrical and Systems Engineering, Washington University in St Louis, St Louis, MO, USA
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University School of Medicine, St Louis, MO, USA
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1682
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Knockdown of the Ribosomal Protein eL29 in Mammalian Cells Leads to Significant Changes in Gene Expression at the Transcription Level. Cells 2020; 9:cells9051228. [PMID: 32429214 PMCID: PMC7291024 DOI: 10.3390/cells9051228] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 01/02/2023] Open
Abstract
An imbalance in the synthesis of ribosomal proteins can lead to the disruption of various cellular processes. For mammalian cells, it has been shown that the level of the eukaryote-specific ribosomal protein eL29, also known as the one interacting with heparin/heparan sulfate, substantially affects their growth. Moreover, in animals lacking this protein, a number of anatomical abnormalities have been observed. Here, we applied next-generation RNA sequencing to HEK293 cells transfected with siRNAs specific for the mRNA of eL29 to determine what changes occur in the transcriptome profile with a decrease in the level of the target protein. We showed that an approximately 2.5-fold decrease in the content of eL29 leads to statistically significant changes in the expression of more than a thousand genes at the transcription level, without a noticeable effect on cell viability, rRNA level, and global translation. The set of eL29-dependent genes included both up-regulated and down-regulated ones, among which there are those previously identified as targets for proteins implicated in oncogenesis. Thus, our findings demonstrate that an insufficiency of eL29 in mammalian cells causes a significant reorganization of gene expression, thereby highlighting the relationship between the cellular balance of eL29 and the activities of certain genes.
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1683
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Grankvist R, Chireh A, Sandell M, Mukarram AK, Jaff N, Berggren I, Persson H, Linde C, Arnberg F, Lundberg J, Ugander M, La Manno G, Jonsson S, Daub CO, Holmin S. Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. Sci Rep 2020; 10:8029. [PMID: 32415191 PMCID: PMC7229024 DOI: 10.1038/s41598-020-64900-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/02/2020] [Indexed: 01/09/2023] Open
Abstract
Endomyocardial biopsy is a valuable tool in cardiac diagnostics but is limited by low diagnostic yield and significant complication risks. Meanwhile, recent developments in transcriptomic and proteomic technologies promise a wealth of biological data from minimal tissue samples. To take advantage of the minimal tissue amount needed for molecular analyses, we have developed a sub-millimeter endovascular biopsy device, considerably smaller than current clinical equipment, and devised a low-input RNA-sequencing protocol for analyzing small tissue samples. In in vivo evaluation in swine, 81% of biopsy attempts (n = 157) were successful. High quality RNA-sequencing data was generated from 91% of the sequenced cardiac micro-biopsy samples (n = 32). Gene expression signatures of samples taken with the novel device were comparable with a conventional device. No major complications were detected either during procedures or during 7 days' follow-up, despite acquiring a relatively large number of biopsies (median 30) in each animal. In conclusion, the novel device coupled with RNA-sequencing provides a feasible method to obtain molecular data from the myocardium. The method is less traumatic and has a higher flexibility compared to conventional methods, enabling safer and more targeted sampling from different parts of the myocardium.
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Affiliation(s)
- Rikard Grankvist
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Arvin Chireh
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Mikael Sandell
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden.,Department of Micro and Nanosystems, Royal Institute of Technology, Stockholm, Sweden.,MedTechLabs, Solna, Sweden
| | | | - Nasren Jaff
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
| | - Ingrid Berggren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
| | - Hans Persson
- Department of Clinical Sciences, Danderyd Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Linde
- Department of Medicine, Karolinska Institutet, Solna, Sweden.,Heart and Vascular Theme, Karolina University Hospital, Solna, Sweden
| | - Fabian Arnberg
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden.,Department of Neuroradiology, Karolinska University Hospital, Solna, Sweden
| | - Johan Lundberg
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden.,Department of Neuroradiology, Karolinska University Hospital, Solna, Sweden
| | - Martin Ugander
- Kolling Institute, Royal North Shore Hospital, and Northern Clinical School, Sydney Medical School, University of Sydney, Sydney, Australia.,Department of Clinical Physiology, Karolinska University Hospital and Karolinska Institutet, Solna, Sweden.,Charles Perkins Center, University of Sydney, Sydney, Australia
| | - Gioele La Manno
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefan Jonsson
- Department of Materials Science and Engineering, Royal Institute of Technology, Stockholm, Sweden
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, Solna, Sweden
| | - Staffan Holmin
- Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden. .,Department of Neuroradiology, Karolinska University Hospital, Solna, Sweden.
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1684
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Abou Alezz M, Celli L, Belotti G, Lisa A, Bione S. GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front Genet 2020; 11:488. [PMID: 32499820 PMCID: PMC7242645 DOI: 10.3389/fgene.2020.00488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are recognized as an important class of regulatory molecules involved in a variety of biological functions. However, the regulatory mechanisms of long non-coding genes expression are still poorly understood. The characterization of the genomic features of lncRNAs is crucial to get insight into their function. In this study, we exploited recent annotations by GENCODE to characterize the genomic and splicing features of long non-coding genes in comparison with protein-coding ones, both in human and mouse. Our analysis highlighted differences between the two classes of genes in terms of their gene architecture. Significant differences in the splice sites usage were observed between long non-coding and protein-coding genes (PCG). While the frequency of non-canonical GC-AG splice junctions represents about 0.8% of total splice sites in PCGs, we identified a significant enrichment of the GC-AG splice sites in long non-coding genes, both in human (3.0%) and mouse (1.9%). In addition, we found a positional bias of GC-AG splice sites being enriched in the first intron in both classes of genes. Moreover, a significant shorter length and weaker donor and acceptor sites were found comparing GC-AG introns to GT-AG introns. Genes containing at least one GC-AG intron were found conserved in many species, more prone to alternative splicing and a functional analysis pointed toward their enrichment in specific biological processes such as DNA repair. Our study shows for the first time that GC-AG introns are mainly associated with lncRNAs and are preferentially located in the first intron. Additionally, we discovered their regulatory potential indicating the existence of a new mechanism of non-coding and PCGs expression regulation.
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Affiliation(s)
| | | | | | | | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
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1685
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Haplotype-Based Genome-Wide Association Study and Identification of Candidate Genes Associated with Carcass Traits in Hanwoo Cattle. Genes (Basel) 2020; 11:genes11050551. [PMID: 32423003 PMCID: PMC7290854 DOI: 10.3390/genes11050551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/30/2020] [Accepted: 05/05/2020] [Indexed: 12/20/2022] Open
Abstract
Hanwoo, is the most popular native beef cattle in South Korea. Due to its extensive popularity, research is ongoing to enhance its carcass quality and marbling traits. In this study we conducted a haplotype-based genome-wide association study (GWAS) by constructing haplotype blocks by three methods: number of single nucleotide polymorphisms (SNPs) in a haplotype block (nsnp), length of genomic region in kb (Len) and linkage disequilibrium (LD). Significant haplotype blocks and genes associated with them were identified for carcass traits such as BFT (back fat thickness), EMA (eye Muscle area), CWT (carcass weight) and MS (marbling score). Gene-set enrichment analysis and functional annotation of genes in the significantly-associated loci revealed candidate genes, including PLCB1 and PLCB4 present on BTA13, coding for phospholipases, which might be important candidates for increasing fat deposition due to their role in lipid metabolism and adipogenesis. CEL (carboxyl ester lipase), a bile-salt activated lipase, responsible for lipid catabolic process was also identified within the significantly-associated haplotype block on BTA11. The results were validated in a different Hanwoo population. The genes and pathways identified in this study may serve as good candidates for improving carcass traits in Hanwoo cattle.
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1686
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Aminuddin A, Ng PY, Leong CO, Chua EW. Mitochondrial DNA alterations may influence the cisplatin responsiveness of oral squamous cell carcinoma. Sci Rep 2020; 10:7885. [PMID: 32398775 PMCID: PMC7217862 DOI: 10.1038/s41598-020-64664-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/20/2020] [Indexed: 02/07/2023] Open
Abstract
Cisplatin is the first-line chemotherapeutic agent for the treatment of oral squamous cell carcinoma (OSCC). However, the intrinsic or acquired resistance against cisplatin remains a major obstacle to treatment efficacy in OSCC. Recently, mitochondrial DNA (mtDNA) alterations have been reported in a variety of cancers. However, the role of mtDNA alterations in OSCC has not been comprehensively studied. In this study, we evaluated the correlation between mtDNA alterations (mtDNA content, point mutations, large-scale deletions, and methylation status) and cisplatin sensitivity using two OSCC cell lines, namely SAS and H103, and stem cell-like tumour spheres derived from SAS. By microarray analysis, we found that the tumour spheres profited from aberrant lipid and glucose metabolism and became resistant to cisplatin. By qPCR analysis, we found that the cells with less mtDNA were less responsive to cisplatin (H103 and the tumour spheres). Based on the findings, we theorised that the metabolic changes in the tumour spheres probably resulted in mtDNA depletion, as the cells suppressed mitochondrial respiration and switched to an alternative mode of energy production, i.e. glycolysis. Then, to ascertain the origin of the variation in mtDNA content, we used MinION, a nanopore sequencer, to sequence the mitochondrial genomes of H103, SAS, and the tumour spheres. We found that the lower cisplatin sensitivity of H103 could have been caused by a constellation of genetic and epigenetic changes in its mitochondrial genome. Future work may look into how changes in mtDNA translate into an impact on cell function and therefore cisplatin response.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Apoptosis/drug effects
- Apoptosis/genetics
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Cell Survival/drug effects
- Cell Survival/genetics
- Cisplatin/pharmacology
- DNA, Mitochondrial/drug effects
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Mitochondria/drug effects
- Mitochondria/genetics
- Mitochondria/metabolism
- Mouth Neoplasms/genetics
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/pathology
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
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Affiliation(s)
- Amnani Aminuddin
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia
| | - Pei Yuen Ng
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia
| | - Chee-Onn Leong
- School of Pharmacy, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
- Centre for Cancer and Stem Cell Research, Institute for Research, Development and Innovation, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Eng Wee Chua
- Drug and Herbal Research Centre, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300, Kuala Lumpur, Malaysia.
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1687
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Alonso-Garrido M, Manyes L, Pralea IE, Iuga CA. Mitochondrial proteomics profile points oxidative phosphorylation as main target for beauvericin and enniatin B mixture. Food Chem Toxicol 2020; 141:111432. [PMID: 32407736 DOI: 10.1016/j.fct.2020.111432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 01/01/2023]
Abstract
Beauvericin (BEA) and enniatin B (EN B) are non-legislated Fusarium mycotoxins usually found in cereal and cereal-based products all around the world. By the proteomic analysis of mitochondria enriched extracts from Jurkat cells exposed for 24 h to three concentrations of BEA:EN B (0.01-0.1-0.5 μM), a number of 1821 proteins (202 mitochondrial) were identified and relatively quantified. 340 proteins (59 mitochondrial) were statistically significant altered in our samples (Anova p-value ≤ 0.05 and fold change (FC) ≥1.5). The protein mitochondrial translational release factor 1 like (MTRF1L) was the most abundant protein in the three mycotoxin exposures studied. The mycotoxins mixture exposure induced concentration dependent changes at mitochondrial proteins levels that mainly involve inner and outer membrane complexes, Electron Transport Chain (ETC) and ribosomes. These results showed alteration of proteins levels related to oxidative phosphorylation, metabolic and neurodegenerative diseases related pathways.
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Affiliation(s)
- M Alonso-Garrido
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain.
| | - L Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, University of Valencia, Burjassot, Spain
| | - I E Pralea
- Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - C A Iuga
- Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Pharmaceutical Analysis, Faculty of Pharmacy, "Iuliu Hațieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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1688
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Proteomic Profiling of Small Extracellular Vesicles Secreted by Human Pancreatic Cancer Cells Implicated in Cellular Transformation. Sci Rep 2020; 10:7713. [PMID: 32382024 PMCID: PMC7205864 DOI: 10.1038/s41598-020-64718-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/21/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles secreted from tumor cells are functional vehicles capable of contributing to intercellular communication and metastasis. A growing number of studies have focused on elucidating the role that tumor-derived extracellular vesicles play in spreading pancreatic cancer to other organs, due to the highly metastatic nature of the disease. We recently showed that small extracellular vesicles secreted from pancreatic cancer cells could initiate malignant transformation of healthy cells. Here, we analyzed the protein cargo contained within these vesicles using mass spectrometry-based proteomics to better understand their makeup and biological characteristics. Three different human pancreatic cancer cell lines were compared to normal pancreatic epithelial cells revealing distinct differences in protein cargo between cancer and normal vesicles. Vesicles from cancer cells contain an enrichment of proteins that function in the endosomal compartment of cells responsible for vesicle formation and secretion in addition to proteins that have been shown to contribute to oncogenic cell transformation. Conversely, vesicles from normal pancreatic cells were shown to be enriched for immune response proteins. Collectively, results contribute to what we know about the cargo contained within or excluded from cancer cell-derived extracellular vesicles, supporting their role in biological processes including metastasis and cancer progression.
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1689
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Grønningsæter IS, Reikvam H, Aasebø E, Bartaula-Brevik S, Tvedt TH, Bruserud Ø, Hatfield KJ. Targeting Cellular Metabolism in Acute Myeloid Leukemia and The Role of Patient Heterogeneity. Cells 2020; 9:cells9051155. [PMID: 32392896 PMCID: PMC7290417 DOI: 10.3390/cells9051155] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive blood cancer resulting in accumulation of immature, dysfunctional blood cells in the bone marrow. Changes in cell metabolism are features of many cancers, including AML and this may be exploited as a therapeutic target. In this study we investigated the in vitro antileukemic effects of seven metabolic inhibitors that target different metabolic pathways. The metabolic inhibitors were tested on AML cells derived from 81 patients using proliferation and viability assays; we also compared global gene expression and proteomic profiles for various patient subsets. Metformin, 2DG, 6AN, BPTES and ST1326 had strong antiproliferative and proapoptotic effects for most patients, whereas lonidamine and AZD3965 had an effect only for a minority. Antiproliferative effects on AML cells were additive when combined with the chemotherapeutic agent AraC. Using unsupervised hierarchical clustering, we identified a strong antiproliferative effect on AML cells after treatment with metabolic inhibitors for a subset of 29 patients. Gene expression and proteomic studies suggested that this subset was characterized by altered metabolic and transcriptional regulation. In addition, the Bcl-2 inhibitor venetoclax, in combination with 2DG or 6AN, increased the antiproliferative effects of these metabolic inhibitors on AML cells. Therapeutic targeting of cellular metabolism may have potential in AML, but the optimal strategy will likely differ between patients.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Apoptosis/drug effects
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Differentiation/drug effects
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Cluster Analysis
- Cytarabine/pharmacology
- Deoxyglucose/pharmacology
- Female
- Gene Expression Regulation, Leukemic/drug effects
- Genetic Heterogeneity
- Humans
- Karyotype
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mesenchymal Stem Cells/drug effects
- Middle Aged
- Mutation/genetics
- Nuclear Proteins/genetics
- Nucleophosmin
- Proteomics
- Sulfonamides/pharmacology
- Survival Analysis
- Young Adult
- fms-Like Tyrosine Kinase 3/genetics
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Affiliation(s)
- Ida Sofie Grønningsæter
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Håkon Reikvam
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Elise Aasebø
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
| | - Sushma Bartaula-Brevik
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
| | - Tor Henrik Tvedt
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence: (Ø.B.); (K.J.H); Tel.: +47-55973082 (Ø.B.); +47-55973037 (K.J.H); Fax: +47-55972950 (Ø.B.)
| | - Kimberley Joanne Hatfield
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway; (I.S.G.); (H.R.); (E.A.); (S.B.-B.); (T.H.T.)
- Department of Immunology and Transfusion Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence: (Ø.B.); (K.J.H); Tel.: +47-55973082 (Ø.B.); +47-55973037 (K.J.H); Fax: +47-55972950 (Ø.B.)
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1690
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Li X, Shi G, Li Y, Zhang X, Xiang Y, Wang T, Li Y, Chen H, Fu Q, Zhang H, Wang B. 15q11.2 deletion is enriched in patients with total anomalous pulmonary venous connection. J Med Genet 2020; 58:jmedgenet-2019-106608. [PMID: 32376791 DOI: 10.1136/jmedgenet-2019-106608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/02/2023]
Abstract
INTRODUCTION CNV is a vital pathogenic factor of congenital heart disease (CHD). However, few CNVs have been reported for total anomalous pulmonary venous connection (TAPVC), which is a rare form of CHD. Using case-control study, we identified 15q11.2 deletion associated with TAPVC. We then used a TAPVC trio as model to reveal possible molecular basis of 15q11.2 microdeletion. METHODS CNVplex and Chromosomal Microarray were used to identify and validate CNVs in samples from 231 TAPVC cases and 200 healthy controls from Shanghai Children's Medical Center. In vitro cardiomyocyte differentiation of induced pluripotent stem cells from peripheral blood mononuclear cells for a TAPVC trio with paternal inherited 15q11.2 deletion was performed to characterise the effect of the deletion on cardiomyocyte differentiation and gene expression. RESULTS The 15q11.2 microdeletion was significantly enriched in patients with TAPVC compared with healthy control (13/231 in patients vs 0/200 in controls, p=5.872×10-2, Bonferroni adjusted) using Fisher's exact test. Induced pluripotent stem cells from the proband could not differentiate into normal cardiomyocyte. Transcriptomic analysis identified a number of differentially expressed genes in the 15q11.2 deletion carriers of the family. TAPVC disease-causing genes such as PITX2, NKX2-5 and ANKRD1 showed significantly higher expression in the proband compared with her healthy mother. Knockdown of TUBGCP5 could lead to abnormal cardiomyocyte differentiation. CONCLUSION We discovered that the 15q11.2 deletion is significantly associated with TAPVC. Gene expression profile that might arise from 15q11.2 deletion for a TAPVC family was characterised using cell experiments.
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Affiliation(s)
- Xiaoliang Li
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guocheng Shi
- Department of Cardiothoracic Surgery, Heart Center, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yang Li
- Department of Hematology & Oncology, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoqing Zhang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Xiang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Teng Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yanxin Li
- Department of Hematology & Oncology, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huiwen Chen
- Department of Cardiothoracic Surgery, Heart Center, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hong Zhang
- Department of Obestetrics and Gynecology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Bo Wang
- Pediatric Translational Medicine Institute, Shanghai Children's Medical Center Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
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1691
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Tripodi IJ, Callahan TJ, Westfall JT, Meitzer NS, Dowell RD, Hunter LE. Applying knowledge-driven mechanistic inference to toxicogenomics. Toxicol In Vitro 2020; 66:104877. [PMID: 32387679 DOI: 10.1016/j.tiv.2020.104877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/13/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023]
Abstract
When considering toxic chemicals in the environment, a mechanistic, causal explanation of toxicity may be preferred over a statistical or machine learning-based prediction by itself. Elucidating a mechanism of toxicity is, however, a costly and time-consuming process that requires the participation of specialists from a variety of fields, often relying on animal models. We present an innovative mechanistic inference framework (MechSpy), which can be used as a hypothesis generation aid to narrow the scope of mechanistic toxicology analysis. MechSpy generates hypotheses of the most likely mechanisms of toxicity, by combining a semantically-interconnected knowledge representation of human biology, toxicology and biochemistry with gene expression time series on human tissue. Using vector representations of biological entities, MechSpy seeks enrichment in a manually curated list of high-level mechanisms of toxicity, represented as biochemically- and causally-linked ontology concepts. Besides predicting the canonical mechanism of toxicity for many well-studied compounds, we experimentally validated some of our predictions for other chemicals without an established mechanism of toxicity. This mechanistic inference framework is an advantageous tool for predictive toxicology, and the first of its kind to produce a mechanistic explanation for each prediction. MechSpy can be modified to include additional mechanisms of toxicity, and is generalizable to other types of mechanisms of human biology.
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Affiliation(s)
- Ignacio J Tripodi
- University of Colorado, Computer Science / Interdisciplinary Quantitative Biology, Boulder, CO 80309, USA.
| | - Tiffany J Callahan
- University of Colorado Anschutz Medical Campus, Computational Bioscience, Denver, CO 80045, USA
| | - Jessica T Westfall
- University of Colorado, Molecular, Cellular and Developmental Biology, Boulder, CO 80309, USA
| | | | - Robin D Dowell
- University of Colorado, Molecular, Cellular and Developmental Biology / Interdisciplinary Quantitative Biology, Boulder, CO 80309, USA
| | - Lawrence E Hunter
- University of Colorado Anschutz Medical Campus, Computational Bioscience / Interdisciplinary Quantitative Biology, Denver, CO 80045, USA
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1692
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Laggner M, Copic D, Nemec L, Vorstandlechner V, Gugerell A, Gruber F, Peterbauer A, Ankersmit HJ, Mildner M. Therapeutic potential of lipids obtained from γ-irradiated PBMCs in dendritic cell-mediated skin inflammation. EBioMedicine 2020; 55:102774. [PMID: 32403085 PMCID: PMC7218268 DOI: 10.1016/j.ebiom.2020.102774] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/15/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Since numerous pathological conditions are evoked by unwanted dendritic cell (DC) activity, therapeutic agents modulating DC functions are of great medical interest. In regenerative medicine, cellular secretomes have gained increasing attention and valuable immunomodulatory properties have been attributed to the secretome of γ-irradiated peripheral blood mononuclear cells (PBMCs). Potential effects of the PBMC secretome (PBMCsec) on key DC functions have not been elucidated so far. METHODS We used a hapten-mediated murine model of contact hypersensitivity (CH) to study the effects of PBMCsec on DCs in vivo. Effects of PBMCsec on human DCs were investigated in monocyte-derived DCs (MoDC) and ex vivo skin cultures. DCs were phenotypically characterised by transcriptomics analyses and flow cytometry. DC function was evaluated by cytokine secretion, antigen uptake, PBMC proliferation and T-cell priming. FINDINGS PBMCsec significantly alleviated tissue inflammation and cellular infiltration in hapten-sensitized mice. We found that PBMCsec abrogated differentiation of MoDCs, indicated by lower expression of classical DC markers CD1a, CD11c and MHC class II molecules. Furthermore, PBMCsec reduced DC maturation, antigen uptake, lipopolysaccharides-induced cytokine secretion, and DC-mediated immune cell proliferation. Moreover, MoDCs differentiated with PBMCsec displayed diminished ability to prime naïve CD4+T-cells into TH1 and TH2 cells. Furthermore, PBMCsec modulated the phenotype of DCs present in the skin in situ. Mechanistically, we identified lipids as the main biomolecule accountable for the observed immunomodulatory effects. INTERPRETATION Together, our data describe DC-modulatory actions of lipids secreted by stressed PBMCs and suggest PBMCsec as a therapeutic option for treatment of DC-mediated inflammatory skin conditions. FUNDING This research project was supported by the Austrian Research Promotion Agency (Vienna, Austria; grant "APOSEC" 862068; 2015-2019) and the Vienna Business Agency (Vienna, Austria; grant "APOSEC to clinic" 2343727).
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Affiliation(s)
- Maria Laggner
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Vienna, Austria; Division of Thoracic Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Dragan Copic
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Vienna, Austria; Division of Thoracic Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Lucas Nemec
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna, Austria
| | - Vera Vorstandlechner
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Vienna, Austria; Division of Thoracic Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Alfred Gugerell
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Vienna, Austria; Division of Thoracic Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria
| | - Florian Gruber
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna, Austria
| | - Anja Peterbauer
- Austrian Red Cross Blood Transfusion Service of Upper Austria, Linz, Austria
| | - Hendrik J Ankersmit
- Laboratory for Cardiac and Thoracic Diagnosis, Regeneration and Applied Immunology, Vienna, Austria; Division of Thoracic Surgery, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria.
| | - Michael Mildner
- Research Division of Biology and Pathobiology of the Skin, Department of Dermatology, Medical University of Vienna, Lazarettgasse 14, 1090 Vienna, Austria.
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1693
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Aggarwal S, Banerjee SK, Talukdar NC, Yadav AK. Post-translational Modification Crosstalk and Hotspots in Sirtuin Interactors Implicated in Cardiovascular Diseases. Front Genet 2020; 11:356. [PMID: 32425973 PMCID: PMC7204943 DOI: 10.3389/fgene.2020.00356] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/24/2020] [Indexed: 01/07/2023] Open
Abstract
Sirtuins are protein deacetylases that play a protective role in cardiovascular diseases (CVDs), as well as many other diseases. Absence of sirtuins can lead to hyperacetylation of both nuclear and mitochondrial proteins leading to metabolic dysregulation. The protein post-translational modifications (PTMs) are known to crosstalk among each other to bring about complex phenotypic outcomes. Various PTM types such as acetylation, ubiquitination, and phosphorylation, and so on, drive transcriptional regulation and metabolism, but such crosstalks are poorly understood. We integrated protein–protein interactions (PPI) and PTMs from several databases to integrate information on 1,251 sirtuin-interacting proteins, of which 544 are associated with cardiac diseases. Based on the ∼100,000 PTM sites obtained for sirtuin interactors, we observed that the frequency of PTM sites (83 per protein), as well as PTM types (five per protein), is higher than the global average for human proteome. We found that ∼60–70% PTM sites fall into ordered regions. Approximately 83% of the sirtuin interactors contained at least one competitive crosstalk (in situ) site, with half of the sites occurring in CVD-associated proteins. A large proportion of identified crosstalk sites were observed for acetylation and ubiquitination competition. We identified 614 proteins containing PTM hotspots (≥5 PTM sites) and 133 proteins containing crosstalk hotspots (≥3 crosstalk sites). We observed that a large proportion of disease-associated sequence variants were found in PTM motifs of CVD proteins. We identified seven proteins (TP53, LMNA, MAPT, ATP2A2, NCL, APEX1, and HIST1H3A) containing disease-associated variants in PTM and crosstalk hotspots. This is the first comprehensive bioinformatics analysis on sirtuin interactors with respect to PTMs and their crosstalks. This study forms a platform for generating interesting hypotheses that can be tested for a deeper mechanistic understanding gained or derived from big-data analytics.
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Affiliation(s)
- Suruchi Aggarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India.,Division of Life Sciences, Institute of Advanced Study in Science and Technology, Guwahati, India.,Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Sanjay K Banerjee
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Narayan Chandra Talukdar
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Guwahati, India.,Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, India
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
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1694
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Identification of Novel Targets of RBM5 in the Healthy and Injured Brain. Neuroscience 2020; 440:299-315. [PMID: 32335213 DOI: 10.1016/j.neuroscience.2020.04.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/20/2022]
Abstract
The tumor suppressor RNA-binding motif 5 (RBM5) regulates the expression levels and cassette exon-definition (i.e. splicing) of a select set of mRNAs in a tissue-specific manner. Most RBM5-regulated targets were identified in oncological investigations and frequently involve genes which mediate apoptotic cell death. Little is known about the role of RBM5 in the brain. Also, it is unclear if a brain injury may be required to detect RBM5 mediated effects on pro-apoptotic genes due to their low expression levels in the healthy adult CNS at baseline. Conditional/floxed (brain-specific) gene deleter mice were generated to elucidate CNS-specific RBM5 mRNA targets. Male/female mice were subjected to a severe controlled cortical impact (CCI) traumatic brain injury (TBI) in order to increase the background expression of pro-death mRNAs and facilitate testing of the hypothesis that RBM5 inhibition decreases post-injury upregulation of caspases/FAS in the CNS. As expected, a CCI increased caspases/FAS mRNA in the injured cortex. RBM5 KO did not affect their levels or splicing. Surprisingly, KO increased the mRNA levels of novel targets including casein kinase 2 alpha prime interacting protein (Csnka2ip/CKT2) - a gene not thought to be expressed in the brain, contrary to findings here. Twenty-two unique splicing events were also detected in KOs including increased block-inclusion of cassette exons 20-22 in regulating synaptic membrane exocytosis 2 (Rims2). In conclusion, here we used genome-wide transcriptomic analysis on healthy and injured RBM5 KO mouse brain tissue to elucidate the first known gene targets of this enigmatic RBP in this CNS.
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1695
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Jong CJ, Merrill RA, Wilkerson EM, Herring LE, Graves LM, Strack S. Reduction of protein phosphatase 2A (PP2A) complexity reveals cellular functions and dephosphorylation motifs of the PP2A/B'δ holoenzyme. J Biol Chem 2020; 295:5654-5668. [PMID: 32156701 PMCID: PMC7186168 DOI: 10.1074/jbc.ra119.011270] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/21/2020] [Indexed: 12/17/2022] Open
Abstract
Protein phosphatase 2A (PP2A) is a large enzyme family responsible for most cellular Ser/Thr dephosphorylation events. PP2A substrate specificity, localization, and regulation by second messengers rely on more than a dozen regulatory subunits (including B/R2, B'/R5, and B″/R3), which form the PP2A heterotrimeric holoenzyme by associating with a dimer comprising scaffolding (A) and catalytic (C) subunits. Because of partial redundancy and high endogenous expression of PP2A holoenzymes, traditional approaches of overexpressing, knocking down, or knocking out PP2A regulatory subunits have yielded only limited insights into their biological roles and substrates. To this end, here we sought to reduce the complexity of cellular PP2A holoenzymes. We used tetracycline-inducible expression of pairs of scaffolding and regulatory subunits with complementary charge-reversal substitutions in their interaction interfaces. For each of the three regulatory subunit families, we engineered A/B charge-swap variants that could bind to one another, but not to endogenous A and B subunits. Because endogenous Aα was targeted by a co-induced shRNA, endogenous B subunits were rapidly degraded, resulting in expression of predominantly a single PP2A heterotrimer composed of the A/B charge-swap pair and the endogenous catalytic subunit. Using B'δ/PPP2R5D, we show that PP2A complexity reduction, but not PP2A overexpression, reveals a role of this holoenzyme in suppression of extracellular signal-regulated kinase signaling and protein kinase A substrate dephosphorylation. When combined with global phosphoproteomics, the PP2A/B'δ reduction approach identified consensus dephosphorylation motifs in its substrates and suggested that residues surrounding the phosphorylation site play roles in PP2A substrate specificity.
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Affiliation(s)
- Chian Ju Jong
- Department of Neuroscience and Pharmacology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242
| | - Emily M Wilkerson
- Michael Hooker Proteomics Facility, University of North Carolina, Chapel Hill, North Carolina 27516
| | - Laura E Herring
- Michael Hooker Proteomics Facility, University of North Carolina, Chapel Hill, North Carolina 27516
| | - Lee M Graves
- Michael Hooker Proteomics Facility, University of North Carolina, Chapel Hill, North Carolina 27516
| | - Stefan Strack
- Department of Neuroscience and Pharmacology and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242.
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1696
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Yuan JC, Yogarajah T, Lim SK, Yvonne Tee GB, Khoo BY. Pilot study and bioinformatics analysis of differentially expressed genes in adipose tissues of rats with excess dietary intake. Mol Med Rep 2020; 21:2063-2072. [PMID: 32323762 PMCID: PMC7115215 DOI: 10.3892/mmr.2020.11012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
Excessive adipose tissue accumulation is an increasing health problem worldwide. The present study aimed to determine differentially expressed genes (DEGs) that are associated with the excessive accumulation of adipose tissues by PCR arrays in an excess dietary intake animal model. For this purpose, male Sprague Dawley rats were randomly assigned to 2 groups: Control (given an ordinary diet) and experimental (given twice the amount of the ordinary diet). After 2 months of feeding, the abdominal cavities of the rats from each group were opened, then subcutaneous and visceral adipose tissues were removed. The adipose tissues collected were then used for total RNA extraction and then reverse transcribed to cDNA, which was then used as a template to identify the DEGs of 84 transcripts for rat obesity by RT2 Profiler PCR Arrays. The results showed significant downregulation of bombesin‑like receptor 3 (BRS3) and uncoupling protein 1 (UCP1) in visceral adipose tissues of experimental rats compared with those of the control rats, and differential gene expression analysis showed an association with fat cell differentiation and regulation of triglyceride sequestration, as well as fatty acid binding. The gene expression patterns observed in the present study, which may be associated with peroxisome proliferator‑activated receptor‑γ (PPARG) on excessive visceral adipose tissue accumulation, may be useful in identifying a group of surrogate biomarkers for the early diet‑induced accumulation of visceral adipose tissue detection in humans. The biomarkers can also be the specific targets for drug development to reduce excessive visceral adipose tissue accumulation in the body and its associated diseases.
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Affiliation(s)
- Jun Chao Yuan
- Department of Endocrinology, The First People's Hospital of Yunnan Province, Kunming, Yunnan 650032, P.R. China
| | - Thaneswary Yogarajah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Shern Kwok Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Get Bee Yvonne Tee
- School of Health Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan 16150, Malaysia
| | - Boon Yin Khoo
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia
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1697
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Jia C, Ke-Hong C, Fei X, Huan-Zi D, Jie Y, Li-Ming W, Xiao-Yue W, Jian-Guo Z, Ya-Ni H. Decoy receptor 2 mediation of the senescent phenotype of tubular cells by interacting with peroxiredoxin 1 presents a novel mechanism of renal fibrosis in diabetic nephropathy. Kidney Int 2020; 98:645-662. [PMID: 32739204 DOI: 10.1016/j.kint.2020.03.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 02/20/2020] [Accepted: 03/05/2020] [Indexed: 12/14/2022]
Abstract
Premature senescence of renal tubular epithelial cell (RTEC), which is involved in kidney fibrosis, is a key event in the progression of diabetic nephropathy. However, the underlying mechanism remains unclear. Here we investigated the role and mechanism of decoy receptor 2 (DcR2) in kidney fibrosis and the senescent phenotype of RTEC. DcR2 was specifically expressed in senescent RTEC and associated with kidney fibrosis in patients with diabetic nephropathy and mice with streptozotocin-induced with diabetic nephropathy. Knockdown of DcR2 decreased the expression of α-smooth muscle actin, collagen I, fibronectin and serum creatinine levels in streptozotocin-induced mice. DcR2 knockdown also inhibited the expression of senescent markers p16, p21, senescence-associated beta-galactosidase and senescence-associated heterochromatic foci and promoted the secretion of a senescence-associated secretory phenotype including IL-6, TGF-β1, and matrix metalloproteinase 2 in vitro and in vivo. However, DcR2 overexpression showed the opposite effects. Quantitative proteomics and validation studies revealed that DcR2 interacted with peroxiredoxin 1 (PRDX1), which regulated the cell cycle and senescence. Knockdown of PRDX1 upregulated p16 and cyclin D1 while downregulating cyclin-dependent kinase 6 expression in vitro, resulting in RTEC senescence. Furthermore, PRDX1 knockdown promoted DcR2-induced p16, cyclin D1, IL-6, and TGF-β1 expression, whereas PRDX1 overexpression led to the opposite results. Subsequently, DcR2 regulated PRDX1 phosphorylation, which could be inhibited by the specific tyrosine kinase inhibitor genistein. Thus, DcR2 mediated the senescent phenotype of RTEC and kidney fibrosis by interacting with PRDX1. Hence, DcR2 may act as a potential therapeutic target for the amelioration of diabetic nephropathy progression.
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Affiliation(s)
- Chen Jia
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Chen Ke-Hong
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao Fei
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Dai Huan-Zi
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Yang Jie
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Wang Li-Ming
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Wang Xiao-Yue
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Zhang Jian-Guo
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - He Ya-Ni
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China.
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1698
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Beisaw A, Kuenne C, Guenther S, Dallmann J, Wu CC, Bentsen M, Looso M, Stainier DYR. AP-1 Contributes to Chromatin Accessibility to Promote Sarcomere Disassembly and Cardiomyocyte Protrusion During Zebrafish Heart Regeneration. Circ Res 2020; 126:1760-1778. [PMID: 32312172 DOI: 10.1161/circresaha.119.316167] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
RATIONALE The adult human heart is an organ with low regenerative potential. Heart failure following acute myocardial infarction is a leading cause of death due to the inability of cardiomyocytes to proliferate and replenish lost cardiac muscle. While the zebrafish has emerged as a powerful model to study endogenous cardiac regeneration, the molecular mechanisms by which cardiomyocytes respond to damage by disassembling sarcomeres, proliferating, and repopulating the injured area remain unclear. Furthermore, we are far from understanding the regulation of the chromatin landscape and epigenetic barriers that must be overcome for cardiac regeneration to occur. OBJECTIVE To identify transcription factor regulators of the chromatin landscape, which promote cardiomyocyte regeneration in zebrafish, and investigate their function. METHODS AND RESULTS Using the Assay for Transposase-Accessible Chromatin coupled to high-throughput sequencing (ATAC-Seq), we first find that the regenerating cardiomyocyte chromatin accessibility landscape undergoes extensive changes following cryoinjury, and that activator protein-1 (AP-1) binding sites are the most highly enriched motifs in regions that gain accessibility during cardiac regeneration. Furthermore, using bioinformatic and gene expression analyses, we find that the AP-1 response in regenerating adult zebrafish cardiomyocytes is largely different from the response in adult mammalian cardiomyocytes. Using a cardiomyocyte-specific dominant negative approach, we show that blocking AP-1 function leads to defects in cardiomyocyte proliferation as well as decreased chromatin accessibility at the fbxl22 and ilk loci, which regulate sarcomere disassembly and cardiomyocyte protrusion into the injured area, respectively. We further show that overexpression of the AP-1 family members Junb and Fosl1 can promote changes in mammalian cardiomyocyte behavior in vitro. CONCLUSIONS AP-1 transcription factors play an essential role in the cardiomyocyte response to injury by regulating chromatin accessibility changes, thereby allowing the activation of gene expression programs that promote cardiomyocyte dedifferentiation, proliferation, and protrusion into the injured area.
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Affiliation(s)
- Arica Beisaw
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Guenther
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Julia Dallmann
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Chi-Chung Wu
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mette Bentsen
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- ECCPS Bioinformatics and Deep Sequencing Platform (C.K., S.G., M.B., M.L.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y R Stainier
- From the Department of Developmental Genetics (A.B., J.D., C.-C.W., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.,German Centre for Cardiovascular Research (DZHK) Partner Site Rhine-Main (A.B., S.G., D.Y.R.S.), Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
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1699
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Kulappu Arachchige SN, Young ND, Shil PK, Legione AR, Kanci Condello A, Browning GF, Wawegama NK. Differential Response of the Chicken Trachea to Chronic Infection with Virulent Mycoplasma gallisepticum Strain Ap3AS and Vaxsafe MG (Strain ts-304): a Transcriptional Profile. Infect Immun 2020; 88:e00053-20. [PMID: 32122943 PMCID: PMC7171234 DOI: 10.1128/iai.00053-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 12/29/2022] Open
Abstract
Mycoplasma gallisepticum is the primary etiological agent of chronic respiratory disease in chickens. Live attenuated vaccines are most commonly used in the field to control the disease, but current vaccines have some limitations. Vaxsafe MG (strain ts-304) is a new vaccine candidate that is efficacious at a lower dose than the current commercial vaccine strain ts-11, from which it is derived. In this study, the transcriptional profiles of the trachea of unvaccinated chickens and chickens vaccinated with strain ts-304 were compared 2 weeks after challenge with M. gallisepticum strain Ap3AS during the chronic stage of infection. After challenge, genes, gene ontologies, pathways, and protein classes involved in inflammation, cytokine production and signaling, and cell proliferation were upregulated, while those involved in formation and motor movement of cilia, formation of intercellular junctional complexes, and formation of the cytoskeleton were downregulated in the unvaccinated birds compared to the vaccinated birds, reflecting immune dysregulation and the pathological changes induced in the trachea by infection with M. gallisepticum Vaccination appears to protect the structural and functional integrity of the tracheal mucosa 2 weeks after infection with M. gallisepticum.
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Affiliation(s)
- Sathya N Kulappu Arachchige
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pollob K Shil
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria, Australia
| | - Alistair R Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Anna Kanci Condello
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Nadeeka K Wawegama
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Malo Estepa I, Tinning H, Rosas Vasconcelos EJ, Fernandez-Fuertes B, Sánchez JM, Burns GW, Spencer TE, Lonergan P, Forde N. Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy. Int J Mol Sci 2020; 21:ijms21082870. [PMID: 32325999 PMCID: PMC7215316 DOI: 10.3390/ijms21082870] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 12/24/2022] Open
Abstract
Interferon Tau (IFNT), the conceptus-derived pregnancy recognition signal in cattle, significantly modifies the transcriptome of the endometrium. However, the endometrium also responds to IFNT-independent conceptus-derived products. The aim of this study was to determine what proteins are produced by the bovine conceptus that may facilitate the pregnancy recognition process in cattle. We analysed by mass spectrometry the proteins present in conceptus-conditioned media (CCM) after 6 h culture of Day 16 bovine conceptuses (n = 8) in SILAC media (arginine- and lysine-depleted media supplemented with heavy isotopes) and the protein content of extracellular vesicles (EVs) isolated from uterine luminal fluid (ULF) of Day 16 pregnant (n = 7) and cyclic (n = 6) cross-bred heifers on day 16. In total, 11,122 proteins were identified in the CCM. Of these, 5.95% (662) had peptides with heavy labelled amino acids, i.e., de novo synthesised by the conceptuses. None of these proteins were detected in the EVs isolated from ULF. Pregnancy-associated glycoprotein 11, Trophoblast Kunitz domain protein 1 and DExD-Box Helicase 39A were de novo produced and present in the CCM from all conceptuses and in previously published CCM data following 6 and 24 h. A total of 463 proteins were present in the CCM from all the conceptuses in the present study, and after 6 and 24 h culture in a previous study, while expression of their transcripts was not detected in endometrium indicating that they are likely conceptus-derived. Of the proteins present in the EVs, 67 were uniquely identified in ULF from pregnant heifers; 35 of these had been previously reported in CCM from Day 16 conceptuses. This study has narrowed a set of conceptus-derived proteins that may be involved in EV-mediated IFNT-independent embryo–maternal communication during pregnancy recognition in cattle.
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Affiliation(s)
- Irene Malo Estepa
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, West Yorkshire LS2 9JT, UK; (I.M.E.); (H.T.)
| | - Haidee Tinning
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, West Yorkshire LS2 9JT, UK; (I.M.E.); (H.T.)
| | | | - Beatriz Fernandez-Fuertes
- Department of Biology, Faculty of Sciences, Institute of Food and Agricultural Technology, University of Girona, 17003 Girona, Spain;
| | - José María Sánchez
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; (J.M.S.); (P.L.)
| | - Gregory W. Burns
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (G.W.B.); (T.E.S.)
| | - Thomas E. Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA; (G.W.B.); (T.E.S.)
| | - Pat Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland; (J.M.S.); (P.L.)
| | - Niamh Forde
- Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, West Yorkshire LS2 9JT, UK; (I.M.E.); (H.T.)
- Correspondence:
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