{"id":36896,"date":"2021-03-04T17:16:23","date_gmt":"2021-03-04T16:16:23","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=36896"},"modified":"2024-07-26T10:07:43","modified_gmt":"2024-07-26T08:07:43","slug":"ipscs-and-disease","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/ipscs-and-disease\/","title":{"rendered":"Induced pluripotent stem cells reveal causes of disease"},"content":{"rendered":"\n<p id=\"en\">Induced pluripotent stem cells (iPSCs) are suitable for discovering the genes that underlie complex and also rare genetic diseases. Scientists from the German Cancer Research Center (DKFZ) and the European Molecular Biology Laboratory (EMBL), together with international partners, have studied genotype\u2013phenotype relationships in iPSCs using data from approximately 1,000 donors.<\/p>\n\n\n\n<p>Tens of thousands of tiny genetic variations (SNPs, single-nucleotide polymorphisms) have been identified in the human genome that are associated with specific diseases. Many of these genetic variants are not located in the protein-coding regions of genes, but affect regulatory sections. Therefore, scientists are trying to find out if and in which tissues these variants can be linked to changes in the activity of specific genes.<\/p>\n\n\n\n<p>Typically, such analyses are performed in blood cells or tissue biopsies, depending on the type of disease. \u201cPluripotent stem cells, however, might be better suited for this purpose in many cases, as they are undifferentiated and therefore reflect the ancestral state of all cells,\u201d says Oliver Stegle, division head at DKFZ and a group leader at EMBL. \u201cStem cells could be particularly relevant when searching for the cause of diseases that occur early in development.\u201d Pluripotent stem cells can be generated in the culture dish from normal body cells obtained from a blood sample, for example. They are referred to as induced pluripotent stem cells, or iPSCs, since they are not naturally occurring stem cells.<\/p>\n\n\n\n<p>Together with scientists from Stanford University and additional international cooperation partners, Oliver Stegle\u2019s team has compiled sequence and transcriptome data on iPSCs from around 1,000 donors. The researchers systematically examined these data to identify correlations between individual genetic variants and altered expression patterns in stem cells. The results have now been published in the journal <em>Nature Genetics<\/em>.<\/p>\n\n\n\n<p>For more than 67% of all genes active in iPSCs, the researchers found differential expression patterns depending on genetic variants. Many of these associations are novel and have not been described in somatic cell types before. For over 4,000 of these associations, it was possible to link the genetic variants responsible for the altered expression patterns to specific diseases. These included, for example, variants associated with coronary heart disease, lipid metabolism disorders, or hereditary cancers.<\/p>\n\n\n\n<p>Stegle and colleagues also investigated whether iPSCs are suitable for identifying the causative genes of rare genetic diseases. They used iPSC lines from 65 patients with various rare diseases, whose causal gene variants were already known through previous analyses. In the transcriptome data of these iPSC lines, the scientists searched for particularly conspicuous outliers in the expression pattern. These analyses reliably led them to trace the genetic basis of the disease. \u201cSuch screenings were previously impossible because there were simply no sufficiently large reference collections of iPSC transcriptomes,\u201d explains Marc Jan Bonder, first author of the study. \u201cWe were surprised to find such a large number of disease-associated genetic variants that are already visible in the expression pattern at the earliest time point of cell differentiation, represented by the iPSCs.\u201d Until now, the relevance of iPSCs for such biomedical analyses has been significantly underestimated.<\/p>\n\n\n\n<p>In a companion paper published in the same issue of <em>Nature Genetics<\/em>, Stegle and colleagues from EMBL\u2019s European Bioinformatics Institute (EMBL-EBI) and the Wellcome Sanger Institute used more than 200 iPSC lines to investigate how genetic variants affect differentiation into neuronal cells.<\/p>\n\n\n\n<p>The scientists performed single-cell RNA sequencing at different time points of neuronal cell differentiation. This allowed them to analyse how genetic variants affect expression patterns in different cellular states, including different neuronal cell types. \u201cThe study demonstrates the power of combining single-cell sequencing with iPSC technologies to dissect the effect of genetic variants in cell types that would otherwise be inaccessible,\u201d Stegle explains.<\/p>\n\n\n\n<p>This article was originally published by <a href=\"https:\/\/www.dkfz.de\/en\/presse\/pressemitteilungen\/2021\/dkfz-pm-21-14-Induced-pluripotent-stem-cells-reveal-causes-of-disease.php\" target=\"_blank\" rel=\"noreferrer noopener\">DKFZ<\/a>.<\/p>\n\n\n<hr class=\"vf-divider\"\/>\n\n\n<h1 class=\"wp-block-heading\" id=\"de\">Induzierte pluripotente Stammzellen verraten Krankheitsursachen<\/h1>\n\n\n\n<h2 class=\"wp-block-heading\">Forscher identifizieren tausende genetische Varianten, von denen viele mit bestimmten Krankheiten in Verbindung gebracht werden k\u00f6nnen<\/h2>\n\n\n\n<p>Induzierte pluripotente Stammzellen (iPSCs) sind geeignet, um die verantwortlichen Gene zu entdecken, die komplexen und auch seltenen genetischen Erkrankungen zugrunde liegen. Dies konnten Wissenschaftler vom Deutschen Krebsforschungszentrum (DKFZ) und vom Europ\u00e4ischen Laboratorium f\u00fcr Molekularbiologie (EMBL) gemeinsam mit internationalen Partnern erstmals mit einer Untersuchung an iPSC-Zelllinien von fast tausend Spendern zeigen.<\/p>\n\n\n\n<p>Im menschlichen Erbgut sind bis heute Zehntausende von winzigen Bauplan-Abweichungen (SNPs, single-nuceotide polymorphisms) identifiziert, die mit bestimmten Erkrankungen im Zusammenhang stehen. Viele dieser genetischen Varianten liegen nicht in den proteinkodierenden Bereichen der Gene, sondern betreffen regulatorische Abschnitte des Erbguts. Deshalb suchen Wissenschaftler, ob und in welchen Geweben diese Mini-Varianten mit Ver\u00e4nderungen in der Aktivit\u00e4t bestimmter Gene in Verbindung gebracht werden k\u00f6nnen.<\/p>\n\n\n\n<p>\u00dcblicherweise werden solche Analysen \u2013 je nach Art der Erkrankung &#8211; an Blutzellen oder an Gewebebiopsien durchgef\u00fchrt. \u201ePluripotente Stammzellen k\u00f6nnten aber in vielen F\u00e4llen besser daf\u00fcr geeignet sein, da sie undifferenziert sind und quasi den Ursprungszustand aller Zellen wiederspiegeln\u201d, sagt Oliver Stegle, Abteilungsleiter am DKFZ und Gruppenleiter am EMBL. \u201eStammzellen k\u00f6nnten besonders relevant sein, wenn nach der Ursache von Erkrankungen gesucht wird, die bereits fr\u00fch in der Entwicklung auftreten.\u201d Pluripotente Stammzellen lassen sich in der Kulturschale aus normalen K\u00f6rperzellen generieren, die beispielsweise einer Blutprobe gewonnen werden. Da es sich dabei nicht um nat\u00fcrlich vorliegende Stammzellen handelt, spricht man von induzierten pluripotenten Stammzellen, kurz iPSCs.<\/p>\n\n\n\n<p>Das Team von Oliver Stegle hat zusammen mit Forschern der Stanford University und weiteren internationalen Kooperationspartnern Sequenz- sowie Transkriptomdaten von iPSCs von rund 1000 Spendern in einer Referenzdatenbank zusammengetragen. Diese Daten untersuchten die Forscher nun systematisch auf Zusammenh\u00e4nge zwischen einzelnen Erbgutvarianten und ver\u00e4nderten Expressionsmustern in Stammzellen. Die Ergebnisse wurden nun in der Zeitschrift <em>Nature Genetics<\/em> ver\u00f6ffentlicht.<\/p>\n\n\n\n<p>Bei \u00fcber 67% aller Gene, die in den iPSCs aktiv sind, fanden die Forscher unterschiedliche Expressionsmuster in Abh\u00e4ngigkeit von genetischen Varianten. Viele dieser Zusammenh\u00e4nge konnten in somatischen K\u00f6rperzellen bisher noch nicht beschrieben werden. F\u00fcr \u00fcber 4000 dieser Assoziationen konnten die Erbgutvarianten, die f\u00fcr die ge\u00e4nderten Expressionsmuster verantwortlich sind, mit bestimmten Krankheiten in Verbindung gebracht werden. Darunter waren beispielsweise Varianten, die mit koronaren Herzerkrankungen, Fettstoffwechselst\u00f6rungen oder vererbbarem Krebs in Verbindung stehen.<\/p>\n\n\n\n<p>Die Forscher untersuchten au\u00dferdem, ob sich iPSCs daf\u00fcr eignen, die urs\u00e4chlichen Gene seltener genetischer Krankheiten zu identifizieren. Dazu nutzten sie iPSC-Linien von 65 Patienten, die an verschiedenen seltenen Erkrankungen litten, deren kausale Gendefekte durch vorherige Analysen bereits bekannt waren. In den Transkriptomdaten dieser iPSC-Linien fahndeten die Wissenschaftler nach besonders auff\u00e4lligen \u201aAusrei\u00dfern\u2018 im Expressionsmuster. Diese Analysen f\u00fchrten zuverl\u00e4ssig auf die Spur der genetischen Grundlage der Erkrankung. \u201eSolche Untersuchengen waren bisher unm\u00f6glich, weil einfach keine ausreichend gro\u00dfen Referenzsammlungen von iPSC-Transkriptomen vorlagen,\u201d erkl\u00e4rt Marc Jan Bonder, Erstautor der Studie. \u201eWir waren \u00fcberrascht, wie viele genetische Varianten bereits zum fr\u00fchesten Zeitpunkt der Zelldifferenzierung, den die iPSCs repr\u00e4sentieren, im Expressionsmuster sichtbar sind.\u201c Bislang wurde die Relevanz der iPSCs f\u00fcr solche biomedizinischen Analysen deutlich untersch\u00e4tzt.<\/p>\n\n\n\n<p>In einer weiteren Arbeit, die in derselben <em>Nature Genetics-<\/em>Ausgabe ver\u00f6ffentlichten wurde, hat Stegle zusammen mit Kollegen am European Bioinformatics Institute (EMBL-EBI) und am Wellcome Trust Sanger Institut an \u00fcber 200 iPSC-Linien untersucht, wie sich genetische Varianten auf die Ausdifferenzierung zu neuronalen Zellen auswirken. Dazu f\u00fchrten die Wissenschaftler zu verschiedenen Zeitpunkten der Differenzierung neuronaler Zellen RNA-Einzelzell-Sequenzierungen durch. So konnten sie analysieren, wie genetische Varianten die Expressionsmuster in unterschiedlichen Differenzierungszust\u00e4nden beeinflussen. \u201cAuch hier erwiesen sich die iPSCs als ideal, um Effekte bestimmter Genvarianten in Entwicklungsstadien von neuronalen Zellen zu identifizieren, auf die wir ansonsten keinen Zugriff h\u00e4tten,\u201d erkl\u00e4rt Stegle.<\/p>\n\n\n\n<p>Dieser Artikel wurde urspr\u00fcnglich vom <a href=\"https:\/\/www.dkfz.de\/de\/presse\/pressemitteilungen\/2021\/dkfz-pm-21-14-Induzierte-pluripotente-Stammzellen-verraten-Krankheitsursachen.php\" target=\"_blank\" rel=\"noreferrer noopener\">DKFZ<\/a> ver\u00f6ffentlicht.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Scientists in the Stegle group and colleagues have studied induced pluripotent stem cells from around 1,000 donors to identify correlations between individual genetic variants and altered gene expression. They linked more than 4,000 of the genetic variants responsible for altered expression&hellip;<\/p>\n","protected":false},"author":16,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[1794,1307,183,43,842,5740,5686,491,504,470,118],"embl_taxonomy":[19073,19381],"class_list":["post-36896","post","type-post","status-publish","format-standard","hentry","category-science","category-science-technology","tag-disease","tag-dkfz","tag-gene-expression","tag-heidelberg","tag-hinxton","tag-phenotype","tag-rare-disease","tag-single-cell-genomics","tag-single-cell-sequencing","tag-stegle","tag-stem-cell","embl_taxonomy-oliver-stegle","embl_taxonomy-stegle-group"],"acf":{"featured":true,"show_featured_image":false,"color":"#193f90","link_color":"#fff","article_intro":"<p>Researchers identify thousands of genetic variants, many of which can be linked to specific diseases<\/p>\n","related_links":[{"link_description":"","link_url":""}],"article_sources":[{"source_description":"<p>Marc Jan Bonder, Craig Smail <em>et al<\/em>. (2021) Identification of rare and common disease variants using population-scale transcriptomics of pluripotent cells. <em>Nature Genetics<\/em>, published online 4 March 2021. DOI: 10.1038\/s41588-021-00800-7<\/p>\n","source_link_url":"https:\/\/dx.doi.org\/10.1038\/s41588-021-00800-7"},{"source_description":"<p>Julie Jerber, Daniel D. Seaton, Anna S. E. Cuomo <em>et al<\/em>. (2021) Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation. <em>Nature Genetics<\/em>, published online 4 March 2021. DOI: 10.1038\/s41588-021-00801-6<\/p>\n","source_link_url":"https:\/\/dx.doi.org\/10.1038\/s41588-021-00801-6"}],"in_this_article":[{"heading_description":"","anchor":""},{"heading_description":"","anchor":""}],"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"None","vf_locked":false,"field_target_display":"","source_article":false,"field_article_language":{"value":"english","label":"English"},"article_translations":false,"languages":""},"embl_taxonomy_terms":[{"uuid":"a:2:{i:0;s:36:\"4428d1fd-441a-4d6d-a1c5-5dcf5665f213\";i:1;s:36:\"10139fb7-af24-423a-b26f-fe4543ceccbe\";}","parents":[],"name":["Oliver Stegle"],"slug":"oliver-stegle","description":"Who &gt; Oliver Stegle"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"fe59a59f-fd7d-49b3-b3e4-bdd33a6642c3\";i:2;s:36:\"da015526-b30e-4389-900d-df97a55be4b2\";}","parents":[],"name":["Stegle Group"],"slug":"stegle-group","description":"What &gt; Genome Biology &gt; Stegle Group"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Induced pluripotent stem cells reveal causes of disease | EMBL<\/title>\n<meta name=\"description\" content=\"Scientists have studied induced pluripotent stem cells from around 1,000 donors and linked more than 4,000 genetic variants to specific diseases.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/ipscs-and-disease\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Induced pluripotent stem cells reveal causes of disease | EMBL\" \/>\n<meta property=\"og:description\" content=\"Scientists have studied induced pluripotent stem cells from around 1,000 donors and linked more than 4,000 genetic variants 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