Integrative Analysis & Developmental Cancer Genomics(Details)

Integrative Analysis & Developmental Cancer Genomics

Dr. Florian Halbritter (PhD)

Email: florian.halbritter(at)ccri.at

Team Integrative Analysis & Developmental Cancer Genomics

Research Focus

Our goal is to understand how dysregulated development of progenitor cells results in childhood cancers.

Cancer and development

Cancer is a disastrous growth of cells in the body. In the most common types of cancer, this growth is brought on by a series of many mutations – accumulated throughout life and possibly influence by extrinsic factors. Childhood cancers are different. In young age, cells have not usually attained many mutations yet, but rather there are individual catastrophic events that occur in undifferentiated cells during the orderly growth of the organism. These singular mutations throw developing cells of their designated path and result in malignancies. However, for most pediatric cancers, the exact histogenesis is not fully understood. Insight into how mutations affect development will ultimately elucidate new avenues for detecting (diagnosis), projecting (prognosis), and interfering (therapy) with aberrant development in childhood cancers.

 

Our research: Taking apart pediatric cancer bit by bit

We are a team of computational biologists approaching childhood cancer development with a scientist’s curiosity in three facets:

  • Developmental biology: We chart cellular plasticity in tumors and trace it back to normal development in time and space.
  • Regulatory epigenomics: We map the regulatory networks that shape cell identity and identify they role of key regulators.
  • Integrative analysis: We develop and apply computational tools that connect pieces of data into knowledge.

Our research combines analysis of clinical samples as well as in vitro and in vivo models with computational, statistical, and machine learning methods to dissect the molecular framework of pediatric cancers. To this end, we apply and develop high-throughput functional genomics technologies (single-cell RNA-seq, ATAC-seq, ChIP-seq, RRBS/WGBS, lineage tracing) and often work in close collaboration with experimental and clinical scientists in the institute and worldwide.

There are three aspects of development that are currently at the heart of our interest: Intra-tumor plasticity, the influence of non-tumor cells on plasticity, and the impact of chromatin state on the receptiveness of cells for developmental changes. We study these using primarily pediatric sarcomas, blastomas, and leukemia as model systems.

Further information and news on our lab website.

Interested in joining the team? Please check the list of current vacancies and/or get in touch stating your research interests and background.

Selected Articles

Halbritter F*, Farlik M*, Schwentner R, Jug G, Fortelny N, Schnöller T, Pisa H, Schuster LC, Reinprecht A, Czech T, Gojo J, Holter W, Minkov M, Bauer W, Simonitsch-Klupp I, Bock C, Hutter C. (2019) Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis. Cancer Discovery 9(10), 1406-1421

Barakat TS*, Halbritter F*, Zhang M, Rendeiro AR, Bock C & Chambers I. (2018) Functional dissection of the enhancer repertoire in human embryonic stem cells. Cell Stem Cell 23, 1-13

Farlik M*, Halbritter F*, Müller F*, Choudry FA, Ebert P, Klughammer J, Farrow S, Santoro A, Ciaurro V, Mathur A, Uppal R, Stunnenberg HG, Ouwehand WH, Laurenti E, Lengauer T, Frontini M & Bock C. (2016) DNA methylation dynamics of human hematopoietic stem cell differentiation. Cell Stem Cell 19 (6), 808-822

Mass E*, Ballesteros I*, Farlik M*, Halbritter F*, Günther P*, Crozet L, Jacome-Galarza CE, Händler K, Klughammer K, Kobayashi Y, Gomez-Perdiguero E, Schultze JL, Beyer M, Bock C & Geissmann F. (2016) Specification of tissue-resident macrophages during organogenesis. Science 353 (6304), aaf4238

Bock C, Halbritter F, & The BLUEPRINT Consortium (2016) Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nature Biotechnology 34 (6), 726-737

Halbritter F, Vaidya H & Tomlinson SR. (2011) GeneProf: analysis of high-throughput sequencing experiments. Nature Methods 9, 7-8

Team Integrative Analysis

Dr. Florian Halbritter (PhD)

Dr. Florian Halbritter (PhD)

Group Leader

florian.halbritter(at)ccri.at +43 1 40470 4058

Mohamed Shoeb, BSc

Mohamed Shoeb, BSc

PhD Student

mohamed.shoeb(at)ccri.at +43 1 40470 4058

Katja Nettermann, BSc

Katja Nettermann, BSc

Master Student

Katja.nettermann(at)ccri.at +43 1 40470 4058

Martin Koban, BSc

Martin Koban, BSc

Master Student

martin.koban(at)ccri.at +43 1 40470 4058