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research.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
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<title>Research : Developmental Cancer Genomics @ CCRI</title>
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<div class="site-content">
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<h1 class="site-title">Developmental Cancer Genomics</h1>
<small class="site-description">Taking apart childhood cancer <tt>bit</tt> by <tt>bit</tt></small>
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<nav class="main-navigation">
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<li class="menu-item"><a href="join.html">Join us!</a></li>
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<li class="menu-item current-menu-item"><a href="research.html">Research & Funding</a></li>
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<h2 class="page-title">Research & Funding </h2>
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<main class="main-content">
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<div class="container ystrip">
<h2 class="section-title">Taking apart pediatric cancer <tt>bit</tt> by <tt>bit</tt></h2>
<h2 style="margin-top:72px">Goals</h2>
<p>
It is our goal to understand developmental processes in cancer biology. We track development of cancer cells in tumors, reconstruct these processes in experimental models, and characterize (epi)genomic changes that occur in time and space. With these data, we aim to decipher the syntax and semantics of development by formal abstraction into intelligible models. To this end, we combine developmental and cancer biology with high-throughput functional genomics assays (*-seq) and computational analysis. We like to collaborate and partner with research labs at CCRI and around the world to achieve these aims.
<h1>
<img width="100" style="vertical-align:middle;" src="images/devbio.svg" onerror="this.src='images/devbio.png'"> + <img style="vertical-align:middle;" width="100" src="images/regepi.svg" onerror="this.src='images/regepi.png'"> + <img style="vertical-align:middle;" width="100" src="images/intana.svg" onerror="this.src='images/intana.png'"> = !
</h1>
<h2>Significance</h2>
<p>
Cancer is a disruption of orderly developmental processes – cancerous cells either fail to reach the destination of their developmental circuit or they revert after they had seemingly completed the track. By achieving a thorough understanding in individual cases and abstracting the findings in quantitative models, we help to elucidate new avenues for detecting (diagnosis), projecting (prognosis), and intercepting (therapy) with aberrant development in pediatric cancers.
<p>
</div><br/><br/>
<div class="fullwidth-block">
<div class="container">
<h2>Current funding:</h2>
<div class="project-list">
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://upload.wikimedia.org/wikipedia/en/thumb/4/43/Cancer_Research_UK.svg/1200px-Cancer_Research_UK.svg.png"></figure>
<h3 class="project-title">Cancer Research UK</h3>
<p>We explore the effects of mutations in neuroblastoma. Info/press: <a href="https://ccri.at/fwfs-esprit-program-supports-research-on-%ce%b2-catenin-in-wilms-tumor/">CCRI</a>, <a href="https://www.sheffield.ac.uk/biosciences/news/understanding-genetic-roots-aggressive-childhood-cancer-research-aims-improve-neuroblastoma">Sheffield</a> </p>
<p></P>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.fwf.ac.at/fileadmin/Website/Logos/FWF_Logo_Zusatz_Dunkelblau_RGB_EN.png"></figure>
<h3 class="project-title">FWF (ESPRIT)</h3>
<p>We investigate developmental regulators in pediatric tumors. Info/press: <a href="https://ccri.at/fwfs-esprit-program-supports-research-on-%ce%b2-catenin-in-wilms-tumor/">CCRI</a>, <a href="https://doi.org/10.55776/ESP652">FWF</a> </p>
<p></P>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.fwf.ac.at/fileadmin/Website/Logos/FWF_Logo_Zusatz_Dunkelblau_RGB_EN.png"></figure>
<h3 class="project-title">FWF</h3>
<p>We study prerequisites for tumorigenesis in embryonal cancers. Info/press: <a href="https://ccri.at/investigating-the-origins-of-neuroblastoma-and-nephroblastoma/">CCRI</a>, <a href="https://doi.org/10.55776/PAT1300223">FWF</a></p>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.fwf.ac.at/fileadmin/Website/Logos/FWF_Logo_Zusatz_Dunkelblau_RGB_EN.png"></figure>
<h3 class="project-title">FWF (1000 Ideas)</h3>
<p>We develop new ways to direct cellular differentiation. Info/press: <a href="https://doi.org/10.55776/TAI732">FWF</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.alexslemonade.org/sites/default/files/crazy8_logo-01.png"></figure>
<h3 class="project-title">ALSF (Crazy 8 Intiative)</h3>
<p>We aim to discover the origins of bone sarcomas and develop tumor models. Info/press: <a href="https://www.alexslemonade.org/crazy-8-initiative-projects">ALSF</a>, <a href="https://www.ccri.at/2021/03/16/alexs-lemonade-stand-foundation-crazy-8-initiative-award-goes-to-vienna-tracking-the-tumor-origin-to-cure-childhood-cancer/">CCRI</a>, <a href="https://wien.orf.at/stories/3095146/">ORF (in German)</a>.</p>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://api.impactory.org/storage/causes/May2019/PZbG5jnHlIhU99wdh2iE-cropped.png"></figure>
<h3 class="project-title">St. Anna Kinderkrebsforschung</h3>
<p>We investigate the development of pediatric solid tumors and hematopoietic malginancies.</p>
</div>
</div>
</div>
</div>
</div>
<div class="fullwidth-block">
<div class="container">
<h2>Examples of past projects:</h2>
<div class="project-list">
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fs41467-024-47945-7/MediaObjects/41467_2024_47945_Fig1_HTML.png?as=webp"></figure>
<h3 class="project-title">Copy number alterations (CNAs) in neuroblastoma</h3>
<p>Many pediatric cancers are associated with large CNAs. Making use of the <a href="https://www.tsakiridislab.com/">Tsakiridis lab</a>'s stem cell model of the trunk neural crest, we investigated their role in neuroblastoma tumorigenesis.</p>
<a href="https://doi.org/10.1038/s41467-024-47945-7" class="button">Read the paper</a> <a href="https://github.com/cancerbits/saldana_montano2024_ncnb" class="button">Get the code / data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fs41467-024-45802-1/MediaObjects/41467_2024_45802_Fig3_HTML.png?as=webp"></figure>
<h3 class="project-title">Neutrophil maturation across species</h3>
<p>Neutrophils are multifunctional immune cells involved in health and disease. Together with the Distel lab at CCRI we juxtaposed neutrophil maturation in zebrafish, mice, and humans.</p>
<a href="https://doi.org/10.1038/s41467-024-45802-1" class="button">Read the paper</a> <a href="https://github.com/cancerbits/Kirchberger_Shoeb2024_neut" class="button">Get the code / data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://media.springernature.com/lw685/springer-static/image/art%3A10.1038%2Fs43018-024-00879-x/MediaObjects/43018_2024_879_Fig3_HTML.png?as=webp"></figure>
<h3 class="project-title">Oncolytic viruses in skin cancer</h3>
<p>Basal cell carcinoma is the most common cancer worlwide. We participated in the analysis of data from a clinical trial organized by the Hoeller lab at the Medical University of Vienna.</p>
<a href="https://doi.org/10.1038/s43018-024-00879-x" class="button">Read the paper</a> <a href="https://github.com/cancerbits/ressler2024_neobcc" class="button">Get the code / data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.science.org/cms/10.1126/sciimmunol.abg6461/asset/b9f726ae-294e-45f9-bf66-8b7f6ebd203e/assets/graphic/abg6461-f4.jpeg"></figure>
<h3 class="project-title">SARS-CoV-2 mutations</h3>
<p>Our small contribution to the pandemic: We teamed up with researchers at <a href="https://cemm.at/research/groups/andreas-bergthaler-group/">CeMM</a> and the Medical University of Vienna to investigate the effect of SARS-CoV-2 mutations on CD8<sup>+</sup> T cell immunity.</p>
<a href="https://doi.org/10.1126/sciimmunol.abg6461" class="button">Read the paper</a> <a href="https://github.com/cancerbits/agerer2021_covid_epitopes" class="button">Get the code / data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://aacr.silverchair-cdn.com/aacr/content_public/journal/cancerdiscovery/9/10/10.1158_2159-8290.cd-19-0138/10/m_1406fig7.jpeg?Expires=1716967890&Signature=EAhqdtLr8Sn1KIXdKCTCbSWoouY7dIEiFWwlla8XCx8t9Yrqoj-x7Z5-w4MBhVLTzPvAsNSRojAOy0NmE5MV51VlGy6A0JDlUVIs0QOlEueY8aHzVrhfpdmGQE0L-1oXXttAzA0TND4SX0NvuHf1dvbq0JlDOgiGKGvUEA7ZHmMOqmXvIvPcIEnhw8aecfO1IMwyjMHbC1UKGHNU2hyDKG9s-T73HRursaZGsjOza7bThBPKO6uMwKiPS~B3hCsKVGxcLVFhSl-LJuuHynkMTiB6YFe2tgw8QvCZbIrRHyZBalI0p1vgPIZ1OBJjmCWawxq5XTbP8M8IPYHNNG1N9w__&Key-Pair-Id=APKAIE5G5CRDK6RD3PGA"></figure>
<h3 class="project-title">Intra-tumor plasticity in Langerhans cell histiocytosis</h3>
<p>Langerhans cell histiocytosis is an enigmatic neoplasm with highly variable clinical presentation. Together with <a href="https://cemm.at/research/groups/christoph-bock-group/">CeMM</a>, we charted LCH at single-cell resolution and unraveled an unexpected hierarchy.</p>
<a href="https://doi.org/10.1158/2159-8290.CD-19-0138" class="button">Read the paper</a> <a href="http://lch-hierarchy.computational-epigenetics.org/" class="button">Get the code / data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.cell.com/cms/attachment/94c7d545-2d52-4b8e-a903-7009a3573322/fx1.jpg"></figure>
<h3 class="project-title">Finding enhancers</h3>
<p>Enhancers are genetic elements that regulate gene expression. Our study in collaboration with <a href="http://www.crm.ed.ac.uk/research/group/embryonic-stem-cell-biology">Edinburgh</a> and <a href="https://www.erasmusmc.nl/klinische_genetica/research/introduction/stefan-barakat/?lang=en">Rotterdam</a> used a genome-wide assay to explore enhancer activity in pluripotent stem cells.</p>
<a href="https://doi.org/10.1016/j.stem.2018.06.014" class="button">Read the paper</a> <a href="http://hesc-enhancers.computational-epigenetics.org/" class="button">Get the code / data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.cell.com/cms/attachment/22d07242-eb1d-40e6-8e9d-7bbc0cc8bf9b/fx1.jpg"></figure>
<h3 class="project-title">Kinases & blood</h3>
<p>Cells are shaped by the enzymatic activity of kinases. Two of our recent contributions implicate MAPK in blood stem cell activation, and JAK and Aurora kinases in mutant immune cells -- with impacts on the transcriptome and epigenome.</p>
<a href="https://doi.org/10.1016/j.stem.2018.05.003" class="button">MEKi & HSCs</a>
<a href="https://doi.org/10.1172/JCI94509" class="button">STAT5 Neoplasia</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.cell.com/cms/attachment/1b7f4028-28a2-4033-befa-e8c28d0a1a67/fx1.jpg"></figure>
<h3 class="project-title">Epigenetics of hematopoiesis</h3>
<p>The hierarchical development of the human blood system is a highly intricate and fascinating process. Within the <a href="http://www.blueprint-epigenome.eu/">Blueprint Consortium</a>, we mapped epigenetic changes during hematopoiesis using DNA methylation profiling.</p>
<a href="http://dx.doi.org/10.1016/j.stem.2016.10.019" class="button">Read the paper</a> <a href="http://blueprint-methylomes.computational-epigenetics.org/" class="button">Get the data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.researchgate.net/profile/Elvira-Mass/publication/305883959/figure/fig1/AS:558509357637632@1510170415010/Specification-of-tissue-resident-macrophages-Erythro-myeloid-progenitors-EMP-from-the.png"></figure>
<h3 class="project-title">Macrophage development</h3>
<p>Tissue-resident macrophages are key players in immunity, development, and homeostasis. We teamed up with researchers from <a href="https://www.mskcc.org/research-areas/labs/frederic-geissmann">New York</a> and <a href="https://www.limes-institut-bonn.de/forschung/arbeitsgruppen/unit-2/abteilung-schultze/abt-schultze-startseite/">Bonn</a> to trace the orgin of these cells to embryonic progenitors.</p>
<a href="http://doi.org/10.1126/science.aaf4238" class="button">Read the paper</a> <a href="http://macrophage-development.computational-epigenetics.org/" class="button">Get the data</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="images/bock2016.png"></figure>
<h3 class="project-title">Biomarker benchmark</h3>
<p>DNA methylation is a stable epigenetic mark well suited for biomarker assays. We conducted a large benchmark with 16 labs worldwide to compare platforms for clinical translation.</p>
<a href="https://doi.org/10.1038/nbt.3605" class="button">Read the paper</a> <a href="https://github.com/epigen/methylation-biomarker-benchmark" class="button">Get the code</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.cell.com/cms/attachment/11bc157a-0350-455f-b9b5-a911da0ba48d/gr1.jpg"></figure>
<h3 class="project-title">Regulation of pluripotency</h3>
<p>We have investigated multiple core regulators of mammalian pluripotency to discover what makes ESCs tick.</p>
<a href="https://doi.org/10.1016/j.stem.2012.08.002" class="button">Esrrb</a> <a href="https://doi.org/10.1016/j.stem.2013.04.023" class="button">Oct4/Nanog</a> <a href="https://doi.org/10.15252/embr.201540467" class="button">Sox2/Oct</a> <a href="http://emboj.embopress.org/cgi/pmidlookup?view=long&pmid=23892456" class="button">Sox2/Nanog</a> <a href="https://doi.org/10.7554/eLife.27746" class="button">Sox</a> <a href="https://doi.org/10.15252/embj.201695476" class="button">Esrrb-loss</a>
</div>
</div>
<div class="project">
<div class="project-content">
<figure class="project-image"><img src="https://www.ncbi.nlm.nih.gov/pmc/articles/instance/3965072/bin/gkt966f1p.jpg"></figure>
<h3 class="project-title">Streamlined NGS analysis</h3>
<p>To ease access and reuse of functional genomics data, we developed a web-based software suite and database that streamlines NGS data analysis.</p>
<a href="https://doi.org/10.1038/nmeth.1809" class="button">Read the paper</a> <a href="https://doi.org/10.1093/nar/gkt966" class="button">Read the other paper</a>
</div>
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<h3 class="widget-title">Our address</h3>
<strong>Developmental Cancer Genomics</strong>
<div>Florian Halbritter Lab</div>
<address>St. Anna Children's Cancer Research Institute (CCRI), Zimmermannplatz 10, 1090 Vienna, Austria</address>
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<h3 class="widget-title">Our host</h3>
<a href="https://science.ccri.at/"><img src="images/logo-ccri.gif" alt="Children's Cancer Research Institute"/></a>
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<h3 class="widget-title">On the web</h3>
<p>Other presence of the lab and members.</p>
<div class="social-links">
<a href="https://github.com/cancerbits"><i class="fa fa-github"></i></a>
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<a href="https://www.linkedin.com/pub/florian-halbritter/70/79/4b7"><i class="fa fa-linkedin"></i></a>
<a href="https://orcid.org/0000-0003-2452-4784">iD</a>
<a href="https://www.researchgate.net/profile/Florian_Halbritter">RG</a>
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<p class="colophon">Copyright 2020 Florian Halbritter. Design template by <a href="http://www.vandelaydesign.com/" title="Designed by VandelayDesign.com" target="_blank">VandelayDesign.com</a>. All rights reserved.</p>
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