Ruprecht-Karls-Universität Heidelberg
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Raffel0219 - Scientist (f/m) / PhD position
Project no:
Raffel0219

Project leader:

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

Project description:

Title:
Manipulation of alpha-Ketoglutarate homeostasis to target Acute Myeloid Leukemia Stem Cells
Summary:
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. Targeting aberrant immunophenotypes of LSCs has been the predominant strategy to achieve this. However, the efficacy of this approach may be limited due to the plasticity of LSC phenotypes. Thus, modulating fundamental aspects of LSC biology may represent a more comprehensive and effective type of therapy.
LSC populations are characterized by specific gene expression (Eppert et al., 2011), protein composition (Raffel et al., 2017), epigenetic alterations (Jung et al., 2015) and metabolic properties (Raffel et al., 2017; Jones et al. 2018; Sancho et al., 2016).
We have identified alpha-ketoglutarate (αKG) as a key metabolite regulating stemness in LSCs via epigenetic and posttranslational mechanisms (Raffel et al., 2017). αKG is an essential co-substrate for cellular dioxygenases, which comprise an enzyme family of about 70 members in humans contributing to the control of a broad range of cellular functions (McDonough et al.). For example, we showed that αKG controls the tumor suppressor protein TET2, which modulates the DNA methylome of leukemic stem cells making them more aggressive by blocking their differentiation.
Among others, αKG homeostasis is controlled by the degradation of branched chain amino acids (BCAAs) via the activity of BCAT1. However, a systematic analysis of αKG homeostasis is lacking.

In the proposed project we will determine the key enzymes for cytoplasmic and mitochondrial αKG homeostasis in AML, test the effect of modulation of αKG levels on survival and stemness of AML cell lines and primary AML stem cells as well as healthy hematopoietic stem cells in vitro and in vivo, and conduct a CRISPR screen for synthetic lethality of BCAT1 overexpression. This approach will identify pathways beyond BCAA/BCAT1 to interfere with αKG homeostasis and may open new opportunities for targeted therapy of patients with AML and other malignancies.
References:
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. *equal contribution

McDonough, M. A. et al. Structural studies on human 2-oxoglutarate dependent oxygenases. Curr Opin Struct Biol 20, 659-672 (2010)

Eppert, K. et al. Stem cell gene expression programs influence clinical outcome in human leukemia. Nat Med 17, 1086-1093 (2011).

Jung, N. et al. An LSC epigenetic signature is largely mutation independent and implicates the HOXA cluster in AML pathogenesis. Nat Commun 6, 8489 (2015).

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:
Targeted Metabolomics, RNA/DNA-Seq, CRISPR-Cas9 screens, human-to-mouse xenotransplantation models of primary patient leukemia samples, overexpression/knockdown/knockout of genes, multi-parameter Flow Cytometry (FACS) analyses and cell sorting, clinical translation, and various stem cell and molecular biology techniques including single-cell analyses.
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 metabolism - 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.
Keywords:
Acute Leukemias, Leukemic Stem Cells, Metabolism, alpha-ketoglutarate, single cell technologies, therapy resistance