Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples.

Animals Cell Line DNA Copy Number Variations Databases, Genetic Fetus Gene Expression Regulation, Developmental Gene Expression Regulation, Neoplastic Humans Mice Neoplasms / genetics Protein Biosynthesis RNA, Messenger / genetics Ribosomal Proteins / genetics Ribosomes / metabolism

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
27 07 2020
Historique:
accepted: 28 05 2020
revised: 20 05 2020
received: 05 11 2019
pubmed: 12 6 2020
medline: 24 9 2020
entrez: 12 6 2020
Statut: ppublish

Résumé

We give results from a detailed analysis of human Ribosomal Protein (RP) levels in normal and cancer samples and cell lines from large mRNA, copy number variation and ribosome profiling datasets. After normalizing total RP mRNA levels per sample, we find highly consistent tissue specific RP mRNA signatures in normal and tumor samples. Multiple RP mRNA-subtypes exist in several cancers, with significant survival and genomic differences. Some RP mRNA variations among subtypes correlate with copy number loss of RP genes. In kidney cancer, RP subtypes map to molecular subtypes related to cell-of-origin. Pan-cancer analysis of TCGA data showed widespread single/double copy loss of RP genes, without significantly affecting survival. In several cancer cell lines, CRISPR-Cas9 knockout of RP genes did not affect cell viability. Matched RP ribosome profiling and mRNA data in humans and rodents stratified by tissue and development stage and were strongly correlated, showing that RP translation rates were proportional to mRNA levels. In a small dataset of human adult and fetal tissues, RP protein levels showed development stage and tissue specific heterogeneity of RP levels. Our results suggest that heterogeneous RP levels play a significant functional role in cellular physiology, in both normal and disease states.

Identifiants

DOI: 10.1093/nar/gkaa485 PMID: 32525984 PMC: PMC7367157
pubmed: 32525984
pii: 5856123
doi: 10.1093/nar/gkaa485
pmc: PMC7367157
doi:

Substances chimiques

RNA, Messenger 0
Ribosomal Proteins 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

7079-7098

Subventions

Organisme : NHGRI NIH HHS
ID : U41 HG001715
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM074024
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA194107
Pays : United States
Organisme : NHGRI NIH HHS
ID : P50 HG004233
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA233662
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA072720
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA226803
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA023100
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA232161
Pays : United States
Organisme : NCI NIH HHS
ID : U01 CA217885
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA202752
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA248457
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA172513
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA220341
Pays : United States
Organisme : NHGRI NIH HHS
ID : R01 HG009285
Pays : United States
Organisme : NIDCR NIH HHS
ID : U01 DE028227
Pays : United States
Organisme : NIDCR NIH HHS
ID : R01 DE026870
Pays : United States
Organisme : NCI NIH HHS
ID : U54 CA209891
Pays : United States

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Références

Sci Rep. 2017 Jul 18;7(1):5681
pubmed: 28720757
Cell Syst. 2015 Sep 23;1(3):224-37
pubmed: 27135913
Nat Biotechnol. 2016 Feb;34(2):184-191
pubmed: 26780180
Cancer Cell. 2017 Aug 14;32(2):204-220.e15
pubmed: 28810145
Nature. 2015 Sep 24;525(7570):523-7
pubmed: 26399832
Cancer Discov. 2017 Oct;7(10):1069-1087
pubmed: 28923911
Cell. 2015 Nov 5;163(4):1011-25
pubmed: 26544944
Nat Commun. 2017 Aug 4;8(1):199
pubmed: 28775315
Science. 2011 Dec 16;334(6062):1524-9
pubmed: 22096102
Nucleic Acids Res. 2014 Jan;42(Database issue):D574-80
pubmed: 24243843
PLoS One. 2016 Nov 3;11(11):e0166021
pubmed: 27812193
Mol Cell. 2014 Oct 2;56(1):104-15
pubmed: 25263593
Science. 2008 Apr 18;320(5874):362-5
pubmed: 18420932
N Engl J Med. 2016 Jan 14;374(2):135-45
pubmed: 26536169
Genome Biol. 2011;12(4):R41
pubmed: 21527027
Nucleic Acids Res. 2019 Jan 8;47(D1):D230-D234
pubmed: 30335166
Biochem Soc Trans. 2016 Aug 15;44(4):1035-44
pubmed: 27528749
Gigascience. 2019 Jun 1;8(6):
pubmed: 31216036
Nat Biotechnol. 2016 Apr;34(4):410-3
pubmed: 26900662
Cancer Cell. 2014 Sep 8;26(3):319-330
pubmed: 25155756
Nat Biotechnol. 2015 Mar;33(3):306-12
pubmed: 25485619
Database (Oxford). 2018 Jan 1;2018:
pubmed: 30010738
J Mol Biol. 2016 May 22;428(10 Pt B):2186-94
pubmed: 26764228
Nature. 2016 Aug 17;536(7616):285-91
pubmed: 27535533
Elife. 2015 Dec 19;4:e08890
pubmed: 26687005
Genome Res. 2003 Nov;13(11):2498-504
pubmed: 14597658
Cell. 2015 Jun 18;161(7):1681-96
pubmed: 26091043
Nat Genet. 2013 Jun;45(6):580-5
pubmed: 23715323
Nature. 2012 Sep 6;489(7414):57-74
pubmed: 22955616
Cancer Discov. 2012 May;2(5):401-4
pubmed: 22588877
Cell. 2016 Jan 28;164(3):550-63
pubmed: 26824661
BMC Cancer. 2018 Mar 12;18(1):275
pubmed: 29530001
Nature. 2013 Jul 4;499(7456):43-9
pubmed: 23792563
Sci Adv. 2018 Feb 28;4(2):eaao0665
pubmed: 29503865
Cell. 2017 Oct 19;171(3):540-556.e25
pubmed: 28988769
Cell. 2018 Apr 5;173(2):400-416.e11
pubmed: 29625055
Nature. 1961 May 13;190:576-581
pubmed: 20446365
Cell. 2015 Dec 3;163(6):1515-26
pubmed: 26627737
Science. 2015 Oct 2;350(6256):82-7
pubmed: 26430118
Cell. 2011 Apr 29;145(3):383-397
pubmed: 21529712
Nat Genet. 2017 Dec;49(12):1779-1784
pubmed: 29083409
Cell. 2018 Apr 5;173(2):291-304.e6
pubmed: 29625048
Cell Rep. 2015 Nov 3;13(5):865-73
pubmed: 26565899
Nat Biotechnol. 2013 Sep;31(9):822-6
pubmed: 23792628
Sci Signal. 2013 Apr 02;6(269):pl1
pubmed: 23550210
Cell. 2017 Jul 27;170(3):564-576.e16
pubmed: 28753430
Mol Cell. 2017 Jul 6;67(1):71-83.e7
pubmed: 28625553
Blood. 2010 Apr 22;115(16):3196-205
pubmed: 20194897
Genome Biol. 2016 Nov 24;17(1):236
pubmed: 27884178
Mol Cell. 2018 Aug 2;71(3):364-374
pubmed: 30075139
Nature. 2014 May 29;509(7502):575-81
pubmed: 24870542
Cell Syst. 2017 Aug 23;5(2):105-118.e9
pubmed: 28837809
Mol Cell. 2019 Jan 3;73(1):36-47.e10
pubmed: 30503772
Mol Syst Biol. 2014 Jul 01;10:733
pubmed: 24987113

Auteurs

Anshuman Panda (A)

Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.

Anupama Yadav (A)

Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA.
Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

Huwate Yeerna (H)

Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA.

Amartya Singh (A)

Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.

Michael Biehl (M)

Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence, University of Groningen, Nijenborgh 9, NL-9747 AG Groningen, The Netherlands.

Markus Lux (M)

Cognitive Interaction Technology (CITEC), Bielefeld University, Inspiration 1, D-33619 Bielefeld, Germany.

Alexander Schulz (A)

Cognitive Interaction Technology (CITEC), Bielefeld University, Inspiration 1, D-33619 Bielefeld, Germany.

Tyler Klecha (T)

Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ,08854, USA.

Sebastian Doniach (S)

Department of Applied Physics, Stanford University, Palo Alto, CA 94305, USA.

Hossein Khiabanian (H)

Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.

Shridar Ganesan (S)

Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.

Pablo Tamayo (P)

Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA.
School of Medicine, University of California San Diego, La Jolla, CA 92093, USA.

Gyan Bhanot (G)

Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA.
Moores Cancer Center, University of California San Diego, La Jolla, CA 92103, USA.
Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ,08854, USA.
Department of Physics and Astronomy, Rutgers University, Piscataway, NJ 08854, USA.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Cellules › Cellules cultivées › Lignée cellulaire › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Polymorphisme génétique › Variation structurale du génome › Variations de nombre de copies de segment d'ADN › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Structures de l'embryon › Foetus › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes au cours du développement › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Phénomènes génétiques › Régulation de l'expression des gènes › Régulation de l'expression des gènes tumoraux › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Rodentia › Muridae › Murinae › Souris › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Tumeurs › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › Biosynthèse des protéines › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN messager › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéines ribosomiques › Tissue- and development-stage-specific mRNA...
questionsmedicales.fr › Cellules › Structures cellulaires › Espace intracellulaire › Cytoplasme › Structures cytoplasmiques › Organites › Ribosomes › Tissue- and development-stage-specific mRNA...