Ruprecht-Karls-Universität Heidelberg
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Raffel0119 - Scientist (f/m) / PhD position
Project no:

Project leader:

Project supervisor:
Raffel, Simon
Application deadline:
30. Jun 2019
Start of PhD project:
1. Jul 2019

Project description:

Single-cell metabolism, transcriptomics and function of Acute Myeloid Leukemia Stem Cells
Acute Myeloid Leukemia (AML) is an aggressive hematologic malignancy with poor overall survival (Dohner et al, 2015). While classic chemotherapy regimens lead to remission in the majority of patients, relapse rates are very high. Relapse and therapy resistance are caused by the hierarchical organization of AML with a minor fraction of leukemic stem cells (LSCs) at the apex generating leukemic progeny, which make up the majority of leukemic cells. The cancer stem cell model implies that in order to eradicate the disease and achieve long-term remissions, treatment courses must eliminate the LSC population. There is increasing evidence that LSCs harbor specific metabolic properties (Raffel et al., 2017; Jones et al, 2018, Sancho et al., 2016). We have recently shown that branched chain amino acid (BCAA) metabolism is essential for stemness in LSCs. Mechanistically, branched-chain amino acid transaminase 1 (BCAT1) regulates intracellular alpha-ketoglutarate (aKG) levels. aKG controls the activity of the tumor suppressor protein TET2, which modulates the DNA methylome of leukemic stem cells. Our work directly links metabolic changes to long-term reorganization of chromatin activity in leukemic stem cells (Raffel et al., 2017).

Due to previous technological limitations, the majority of studies in the hematology field are based on assays that require pooling thousands of cells. Hence, cellular heterogeneity and clonal composition as important drivers of leukemogenesis and therapy resistance cannot be resolved within these populations. Only single-cell approaches have the potential to overcome these limitations. We have developed a combined transcriptomic and functional single cell approach to study hematopoiesis at the single cell level (Velten et al., 2017). As this technology is able to link transcriptome and function of individual single cells it confers a substantial advantage over commercial single cell analysis platforms (e.g. 10x genomics or fluidigm).

In the proposed project we will expand this technology to simultaneously monitor key metabolic features, gene expression, genomic mutations and functional properties of primary AML cells at the single-cell level. This will allow us to de-convolute heterogeneity within the leukemic clone, detect and define metabolic vulnerabilities of functional LSCs, and identify putative therapeutic targets to overcome therapy resistance and improve the survival of AML patients.
Raffel, S. et al. (2017). BCAT1 restricts alphaKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation. Nature 551, 384-388.

Velten, L*., Haas, S. F*., Raffel, S*. et al. (2017). Human haematopoietic stem cell lineage commitment is a continuous process. Nat Cell Biol 19, 271-281.

Sancho, P. et al. Hallmarks of cancer stem cell metabolism. Br J Cancer 114, 1305-1312 (2016).

Jones, C. L. et al. Inhibition of Amino Acid Metabolism Selectively Targets Human Leukemia Stem Cells. Cancer Cell 34, 724-740 e724 (2018).

Dohner, H. et al. Acute Myeloid Leukemia. N Engl J Med 373, 1136-1152 (2015).
Methods that will be used:
Single-cell technologies (RNA-Seq, Index FACS sort, metabolic profiling, bioinformatics, etc.) human-to-mouse xenotransplantation models of primary patient leukemia samples, overexpression/knockdown/knockout of genes, multi-parameter Flow Cytometry (FACS) analyses, clinical translation, and various stem cell and molecular biology (i.e. CRISPR-Cas9) techniques.
Cooperation partners:
Prof. Andreas Trumpp, DFKZ, HI-STEM, Heidelberg
Dr. Simon Haas, DKFZ, HI-STEM, Heidelberg
Dr. Lars Velten, EMBL, Heidelberg
Prof. Carsten Müller-Tidow, Heidelberg University Hospital
Personal qualifications:
We are looking for a highly motivated PhD student with a background in molecular cell biology and a strong interest in single-cell technologies - an interest in bioinformatics analysis would be a plus. You will become a member of the Emmy Noether-Group “Metabolic Vulnerabilities of Acute Myeloid Leukemia Stem Cells” recently established at Heidelberg University Hospital, Department of Hematology, Oncology and Rheumatology (Director: Prof. Dr. C. Müller-Tidow). You will participate in the Blood Club and the Heidelberg Leukemia Network (HeLeNe) that connects hematology labs across the Heidelberg. In addition, you will closely interact with our collaboration partners at DKFZ, HI-STEM and EMBL. All this will provide you with the opportunity to acquire expertise in cutting-edge molecular stem cell, cancer and translational research.
Acute Leukemias, Leukemic Stem Cells, Metabolism, single cell technologies, therapy resistance