Ruprecht-Karls-Universität Heidelberg
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Raffel0120 - Scientist (f/m) / PhD position
Project no:

Project leader:

Project supervisor:
Raffel, Simon
Application deadline:
31. Mar 2020
Start of PhD project:
1. May 2020

Project description:

Single-cell metabolism and therapy resistance in 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. While antibody-based therapies suffer from heterogeneity and plasticity of surface antigens expressed on LSCs, there is increasing evidence that LSCs harbor specific metabolic properties. These include oxidative phosphorylation (Lagadinou et al., 2013), amino acid and fatty metabolism (Jones et al., 2018; Ye et al., 2016). We have recently shown that branched chain amino acid (BCAA) metabolism is essential for stemness in LSCs (Raffel et al., 2017).

LSCs are rare, however, 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 (Velten et al., 2017).

In the proposed project we will monitor key metabolic features, clonal heterogeneity and functional properties of primary AML cells at the single-cell level. We will apply FACS-index sorting, patient-specific multiplex mutational targeting strategies and single cell in vitro technologies. By integrating indexed metabolic data, clonogenicity and differentiation as well as mutational status for each cell we will be able to deconvolute clonal hierarchies and link metabolism to function in pre-LSCs and LSCs at single cell level. Furthermore, we will identify metabolic characteristics associated with chemotherapy resistance to drugs, which are used in clinical practice.
The overall goal of this project is to find 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.

Lagadinou, E. D. et al. (2013). BCL-2 inhibition targets oxidative phosphorylation and selectively eradicates quiescent human leukemia stem cells. Cell Stem Cell 12, 329-341.

Jones, C. L. et al. (2019). Inhibition of Amino Acid Metabolism Selectively Targets Human Leukemia Stem Cells. Cancer Cell 35, 333-335.

Dohner, H., Weisdorf, D. J. & Bloomfield, C. D. Acute Myeloid Leukemia. N Engl J Med 373, 1136-1152, doi:10.1056/NEJMra1406184 (2015).

Ye H et al. (2016). Leukemic Stem Cells Evade Chemotherapy by Metabolic Adaptation to an Adipose Tissue Niche. Cell Stem Cell. 2016;19(1):23-37.
Methods that will be used:
Single-cell technologies (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:
Partners within the LeukoSyStem consortium:
• Dr. Simon Haas, DKFZ, HI-STEM, Heidelberg
• Dr. Lars Velten, CRG, Barcelona
• Dr. Laleh Hagverdi, EMBL Heidelberg
Prof. Andreas Trumpp, DKFZ, HI-STEM, 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” at Heidelberg University Hospital, Department of Hematology, Oncology and Rheumatology (Director: Prof. Dr. C. Müller-Tidow). The project is embedded in the LeukoSyStem Junior research alliance funded by the Federal Ministry of Education and Research. You will participate in activities within the LeukoSyStem consortium with the collaboration partner at DKFZ/HI-STEM and EMBL as well as the Blood Club and the Heidelberg Leukemia Network (HeLeNe) that connects hematology labs across the Heidelberg. 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