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The effects of death and post-mortem cold ischemia on human tissue transcriptomes

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dc.contributor.author Ferreira, Pedro G.
dc.contributor.author Muñoz-Aguirre, Manuel
dc.contributor.author Reverter, Ferran
dc.contributor.author Godinho, Caio P. Sá
dc.contributor.author Sousa, Abel
dc.contributor.author Amadoz, Alicia
dc.contributor.author Sodaei, Reza, 1988-
dc.contributor.author Hidalgo, Marta R.
dc.contributor.author Pervouchine, Dmitri D.
dc.contributor.author Carbonell-Caballero, Jose
dc.contributor.author Nurtdinov, Ramil
dc.contributor.author Breschi, Alessandra, 1988-
dc.contributor.author Amador, Raziel
dc.contributor.author Oliveira, Patrícia
dc.contributor.author Çubut, Cankut
dc.contributor.author Curado, Joao
dc.contributor.author Aguet, François
dc.contributor.author Oliveira, Carla
dc.contributor.author Dopazo, Joaquín
dc.contributor.author Sammeth, Michael
dc.contributor.author Ardlie, Kristin G.
dc.contributor.author Guigó Serra, Roderic
dc.date.accessioned 2018-02-15T08:39:47Z
dc.date.available 2018-02-15T08:39:47Z
dc.date.issued 2018
dc.identifier.citation Ferreira PG, Muñoz-Aguirre M, Reverter F, Sá Godinho CP, Sousa A, Amadoz A et al. The effects of death and post-mortem cold ischemia on human tissue transcriptomes. Nature communications. 2018;(9):490. DOI: 10.1038/s41467-017-02772-x
dc.identifier.issn 2041-1723
dc.identifier.uri http://hdl.handle.net/10230/33915
dc.description.abstract Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.
dc.description.sponsorship This work was supported by the following grants and contracts: 1) From the US NIH: Contract HHSN261200800001E (Leidos Prime contract with NCI); Contracts 10XS170 (NDRI), 10XS171 (Roswell Park Cancer Institute), 10 × 172 (Science Care Inc.), and 12ST1039 (IDOX); Contract 10ST1035 (Van Andel Institute); Contract HHSN268201000029C (Broad Institute); R01 DA006227-17 (U Miami Brain Bank) 2) Ipatimup and i3s are partially funded by the Portuguese Foundation for Science and Technology (FCT); FEDER funds through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalization (POCI), Portugal 2020, and by Portuguese funds through FCT/MCTES in the framework POCI-01-0145-FEDER-007274; 3) NORTE-01-0145-FEDER-000029, supported by NORTE 2020, under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF); 4) FCT Fellowships SFRH/BPD/89764/2012 to PO, PD/BD/128007/2016 to AS; Salary support to PGF by POPH—QREN Type 4.2, European Social Fund and MCTES, program Investigador FCT, IF/01127/2014. 5) BIO2014-57291-R from the Spanish Ministry of Economy and Competitiveness and “Plataforma de Recursos Biomoleculares y Bioinformáticos” PT13/0001/0007 from the ISCIII, and EU H2020-INFRADEV-1-2015-1 ELIXIR-EXCELERATE (ref. 6,676559) Spanish Ministry of Economy and Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013-2017’ and CERCA Programme/Generalitat de Catalunya, 7) Ministerio de Educación, Cultura y Deporte, under the FPU programme (Formación de Profesorado Universitario) with pre-doctoral fellowship FPU15/03635 to MMA. 8) Award Number 1R01MH101814 and 3R01MH101814-03S1 from the National Human Genome Research Institute. European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement RNA-MAPS_294653, Ministerio de Economía, Industria y Competitividad, referencia MEIC BIO2015-70777-P y los Fondos Estructurales de la Unión Europea (FEDER) and ISCIII del Ministerio de Economía y Competitividad, referencia PT13/0001/0021 cofinaciada por el Fondo Europeo de Desarrollo Regional (FEDER). 9) MS received funding from CNPq (grant 310132/2015-0 and 427541/2016-6), and from FAPERJ (grant E_06/2015).
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Nature Publishing Group
dc.relation.ispartof Nature communications. 2018;(9):490
dc.rights © Nature Publishing Group. http://dx.doi.org/10.1038/s41467-017-02772-x. http://creativecommons.org/licenses/by/4.0/
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject.other Mineria de dades
dc.subject.other Expressió gènica
dc.subject.other Genòmica
dc.subject.other Aprenentatge automàtic
dc.title The effects of death and post-mortem cold ischemia on human tissue transcriptomes
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1038/s41467-017-02772-x
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/676559
dc.relation.projectID info:eu-repo/grantAgreement/EC/FP7/294653
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/FPU2015/03635
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2015/70777/P
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BIO2014/57291/R
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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