KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas
Identifieur interne : 000149 ( Main/Exploration ); précédent : 000148; suivant : 000150KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas
Auteurs : Matthias S. Roost [Pays-Bas] ; Liesbeth Van Iperen [Pays-Bas] ; Yavuz Ariyurek [Pays-Bas] ; Henk P. Buermans [Pays-Bas] ; Wibowo Arindrarto [Pays-Bas] ; Harsha D. Devalla [Pays-Bas] ; Robert Passier [Pays-Bas] ; Christine L. Mummery [Pays-Bas] ; Françoise Carlotti [Pays-Bas] ; Eelco J. P. De Koning [Pays-Bas] ; Erik W. Van Zwet [Pays-Bas] ; Jelle J. Goeman [Pays-Bas] ; Susana M. Chuva De Sousa Lopes [Pays-Bas, Belgique]Source :
- Stem Cell Reports [ 2213-6711 ] ; 2015.
Abstract
Differentiated derivatives of human pluripotent stem cells in culture are generally phenotypically immature compared to their adult counterparts. Their identity is often difficult to determine with certainty because little is known about their human fetal equivalents in vivo. Cellular identity and signaling pathways directing differentiation are usually determined by extrapolating information from either human adult tissue or model organisms, assuming conservation with humans. To resolve this, we generated a collection of human fetal transcriptional profiles at different developmental stages. Moreover, we developed an algorithm, KeyGenes, which uses this dataset to quantify the extent to which next-generation sequencing or microarray data resemble specific cell or tissue types in the human fetus. Using KeyGenes combined with the human fetal atlas, we identified multiple cell and tissue samples unambiguously on a limited set of features. We thus provide a flexible and expandable platform to monitor and evaluate the efficiency of differentiation in vitro.
Url:
DOI: 10.1016/j.stemcr.2015.05.002
PubMed: 26028532
PubMed Central: 4472038
Affiliations:
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<author><name sortKey="Passier, Robert" sort="Passier, Robert" uniqKey="Passier R" first="Robert" last="Passier">Robert Passier</name>
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<author><name sortKey="Mummery, Christine L" sort="Mummery, Christine L" uniqKey="Mummery C" first="Christine L." last="Mummery">Christine L. Mummery</name>
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<author><name sortKey="Carlotti, Francoise" sort="Carlotti, Francoise" uniqKey="Carlotti F" first="Françoise" last="Carlotti">Françoise Carlotti</name>
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<author><name sortKey="De Koning, Eelco J P" sort="De Koning, Eelco J P" uniqKey="De Koning E" first="Eelco J. P." last="De Koning">Eelco J. P. De Koning</name>
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<author><name sortKey="Van Zwet, Erik W" sort="Van Zwet, Erik W" uniqKey="Van Zwet E" first="Erik W." last="Van Zwet">Erik W. Van Zwet</name>
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<wicri:regionArea>Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden</wicri:regionArea>
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<author><name sortKey="Goeman, Jelle J" sort="Goeman, Jelle J" uniqKey="Goeman J" first="Jelle J." last="Goeman">Jelle J. Goeman</name>
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<wicri:regionArea>Department for Health Evidence, Radboud University Medical Center, Geert Grooteplein 21, 6525 EZ Nijmegen</wicri:regionArea>
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<author><name sortKey="Chuva De Sousa Lopes, Susana M" sort="Chuva De Sousa Lopes, Susana M" uniqKey="Chuva De Sousa Lopes S" first="Susana M." last="Chuva De Sousa Lopes">Susana M. Chuva De Sousa Lopes</name>
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<affiliation wicri:level="3"><nlm:aff id="aff8">Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium</nlm:aff>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Department for Reproductive Medicine, Ghent University Hospital, De Pintelaan 185, 9000 Ghent</wicri:regionArea>
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<settlement type="city">Gand</settlement>
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<series><title level="j">Stem Cell Reports</title>
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<front><div type="abstract" xml:lang="en"><title>Summary</title>
<p>Differentiated derivatives of human pluripotent stem cells in culture are generally phenotypically immature compared to their adult counterparts. Their identity is often difficult to determine with certainty because little is known about their human fetal equivalents in vivo. Cellular identity and signaling pathways directing differentiation are usually determined by extrapolating information from either human adult tissue or model organisms, assuming conservation with humans. To resolve this, we generated a collection of human fetal transcriptional profiles at different developmental stages. Moreover, we developed an algorithm, KeyGenes, which uses this dataset to quantify the extent to which next-generation sequencing or microarray data resemble specific cell or tissue types in the human fetus. Using KeyGenes combined with the human fetal atlas, we identified multiple cell and tissue samples unambiguously on a limited set of features. We thus provide a flexible and expandable platform to monitor and evaluate the efficiency of differentiation in vitro.</p>
</div>
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<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Annilo, T" uniqKey="Annilo T">T. Annilo</name>
</author>
<author><name sortKey="Kepp, K" uniqKey="Kepp K">K. Kepp</name>
</author>
<author><name sortKey="Laan, M" uniqKey="Laan M">M. Laan</name>
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<biblStruct><analytic><author><name sortKey="Bardou, P" uniqKey="Bardou P">P. Bardou</name>
</author>
<author><name sortKey="Mariette, J" uniqKey="Mariette J">J. Mariette</name>
</author>
<author><name sortKey="Escudie, F" uniqKey="Escudie F">F. Escudié</name>
</author>
<author><name sortKey="Djemiel, C" uniqKey="Djemiel C">C. Djemiel</name>
</author>
<author><name sortKey="Klopp, C" uniqKey="Klopp C">C. Klopp</name>
</author>
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<biblStruct><analytic><author><name sortKey="Bock, C" uniqKey="Bock C">C. Bock</name>
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<author><name sortKey="Kiskinis, E" uniqKey="Kiskinis E">E. Kiskinis</name>
</author>
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<author><name sortKey="Van Handel, B" uniqKey="Van Handel B">B. Van Handel</name>
</author>
<author><name sortKey="Mikkola, H K" uniqKey="Mikkola H">H.K. Mikkola</name>
</author>
<author><name sortKey="Lowry, W E" uniqKey="Lowry W">W.E. Lowry</name>
</author>
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<biblStruct><analytic><author><name sortKey="Rahier, J" uniqKey="Rahier J">J. Rahier</name>
</author>
<author><name sortKey="Wallon, J" uniqKey="Wallon J">J. Wallon</name>
</author>
<author><name sortKey="Henquin, J C" uniqKey="Henquin J">J.C. Henquin</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robinson, M D" uniqKey="Robinson M">M.D. Robinson</name>
</author>
<author><name sortKey="Smyth, G K" uniqKey="Smyth G">G.K. Smyth</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robinson, M D" uniqKey="Robinson M">M.D. Robinson</name>
</author>
<author><name sortKey="Mccarthy, D J" uniqKey="Mccarthy D">D.J. McCarthy</name>
</author>
<author><name sortKey="Smyth, G K" uniqKey="Smyth G">G.K. Smyth</name>
</author>
</analytic>
</biblStruct>
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</author>
<author><name sortKey="Habener, J F" uniqKey="Habener J">J.F. Habener</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
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</author>
<author><name sortKey="Kellis, M" uniqKey="Kellis M">M. Kellis</name>
</author>
<author><name sortKey="Garber, M" uniqKey="Garber M">M. Garber</name>
</author>
</analytic>
</biblStruct>
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</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xie, W" uniqKey="Xie W">W. Xie</name>
</author>
<author><name sortKey="Schultz, M D" uniqKey="Schultz M">M.D. Schultz</name>
</author>
<author><name sortKey="Lister, R" uniqKey="Lister R">R. Lister</name>
</author>
<author><name sortKey="Hou, Z" uniqKey="Hou Z">Z. Hou</name>
</author>
<author><name sortKey="Rajagopal, N" uniqKey="Rajagopal N">N. Rajagopal</name>
</author>
<author><name sortKey="Ray, P" uniqKey="Ray P">P. Ray</name>
</author>
<author><name sortKey="Whitaker, J W" uniqKey="Whitaker J">J.W. Whitaker</name>
</author>
<author><name sortKey="Tian, S" uniqKey="Tian S">S. Tian</name>
</author>
<author><name sortKey="Hawkins, R D" uniqKey="Hawkins R">R.D. Hawkins</name>
</author>
<author><name sortKey="Leung, D" uniqKey="Leung D">D. Leung</name>
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<affiliations><list><country><li>Belgique</li>
<li>Pays-Bas</li>
</country>
<region><li>Province de Flandre-Orientale</li>
</region>
<settlement><li>Gand</li>
</settlement>
</list>
<tree><country name="Pays-Bas"><noRegion><name sortKey="Roost, Matthias S" sort="Roost, Matthias S" uniqKey="Roost M" first="Matthias S." last="Roost">Matthias S. Roost</name>
</noRegion>
<name sortKey="Arindrarto, Wibowo" sort="Arindrarto, Wibowo" uniqKey="Arindrarto W" first="Wibowo" last="Arindrarto">Wibowo Arindrarto</name>
<name sortKey="Ariyurek, Yavuz" sort="Ariyurek, Yavuz" uniqKey="Ariyurek Y" first="Yavuz" last="Ariyurek">Yavuz Ariyurek</name>
<name sortKey="Buermans, Henk P" sort="Buermans, Henk P" uniqKey="Buermans H" first="Henk P." last="Buermans">Henk P. Buermans</name>
<name sortKey="Carlotti, Francoise" sort="Carlotti, Francoise" uniqKey="Carlotti F" first="Françoise" last="Carlotti">Françoise Carlotti</name>
<name sortKey="Chuva De Sousa Lopes, Susana M" sort="Chuva De Sousa Lopes, Susana M" uniqKey="Chuva De Sousa Lopes S" first="Susana M." last="Chuva De Sousa Lopes">Susana M. Chuva De Sousa Lopes</name>
<name sortKey="De Koning, Eelco J P" sort="De Koning, Eelco J P" uniqKey="De Koning E" first="Eelco J. P." last="De Koning">Eelco J. P. De Koning</name>
<name sortKey="De Koning, Eelco J P" sort="De Koning, Eelco J P" uniqKey="De Koning E" first="Eelco J. P." last="De Koning">Eelco J. P. De Koning</name>
<name sortKey="Devalla, Harsha D" sort="Devalla, Harsha D" uniqKey="Devalla H" first="Harsha D." last="Devalla">Harsha D. Devalla</name>
<name sortKey="Goeman, Jelle J" sort="Goeman, Jelle J" uniqKey="Goeman J" first="Jelle J." last="Goeman">Jelle J. Goeman</name>
<name sortKey="Mummery, Christine L" sort="Mummery, Christine L" uniqKey="Mummery C" first="Christine L." last="Mummery">Christine L. Mummery</name>
<name sortKey="Passier, Robert" sort="Passier, Robert" uniqKey="Passier R" first="Robert" last="Passier">Robert Passier</name>
<name sortKey="Van Iperen, Liesbeth" sort="Van Iperen, Liesbeth" uniqKey="Van Iperen L" first="Liesbeth" last="Van Iperen">Liesbeth Van Iperen</name>
<name sortKey="Van Zwet, Erik W" sort="Van Zwet, Erik W" uniqKey="Van Zwet E" first="Erik W." last="Van Zwet">Erik W. Van Zwet</name>
</country>
<country name="Belgique"><region name="Province de Flandre-Orientale"><name sortKey="Chuva De Sousa Lopes, Susana M" sort="Chuva De Sousa Lopes, Susana M" uniqKey="Chuva De Sousa Lopes S" first="Susana M." last="Chuva De Sousa Lopes">Susana M. Chuva De Sousa Lopes</name>
</region>
</country>
</tree>
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</record>
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