Top image

HRCMMCalls

Project descriptions JCF call January/February 2014

You will find four (4) projects here.

View application as pdf.

Project 1

Project leader:

Andreas E. Kulozik

Project supervisor:

Madhuri BhuvanagiriA,B, Andreas E. KulozikA,B, Matthias W. HentzeB,C

Affiliation:

A-Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany. Webpage

B-Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany. Webpage

C-European Molecular Biology Laboratory Heidelberg (EMBL), Heidelberg, Germany. Webpage

Start of MD project:

Spring 2014

Project description: 

Title:

Pharmacological modulation of RNA quality control in inherited diseases such as Duchene muscular dystrophy or acquired genetic diseases such as cancer

Summary:

Nonsense mediated decay (NMD) is widely conserved cellular quality control pathway that identifies and degrades mRNA that generate c-terminal truncated pathological proteins (reviewed in Holbrook et al. Nature Genet. 2004, Bhuvanagiri et al Biochemical J 2010). Modulating NMD is of therapeutic value in both inherited diseases such as Duchene muscular dystrophy and acquired genetic diseases such as cancer. We have used a high throughput chemical biology screen to find novel NMD inhibitors which can be clinically developed as potential therapeutic agents. Our screening revealed several small molecules with significant activity on NMD efficiency. The aim of this project is to validate and to analyze the mechanism of action of these putative hit compounds. Technically, the candidate will use a wide range of molecular and cellular biology techniques including northern blots, western blots, Q-PCRs, metabolic labeling, read through assays and mass spectrometric analysis.

MMPU Website:

Research Group Blood Diseases

Contact:

Madhuri.Bhuvanagiri@med.uni-heidelberg.de

Project 2

Project supervisor:

Heiko Runz

Affiliation:

Institute of Human Genetics Webpage

Start of MD project:

Spring 2014

Project description: 

Summary:

Elevated blood cholesterol levels are a causal risk factor for myocardial infarction. Through population-based genetic approaches we and others have identified variants in multiple genes and loci in the human genome as highly associated with blood lipid levels and MI-risk. Yet, despite its immense potential, human genetics alone lacks the possibility to systematically extract functional information from genomic data. Recently, we have pioneered new technology to study gene function in a high-throughput manner by RNA-interference, cell-based assays and automated miscropcopy (Bartz et al., 2009; Blattmann et al., 2013). With the current project we want to apply and extend this technology to score DNA sequence variants identified through exome-sequencing as disease relevant or not. The project promises to improve our understanding of which genes increase the risk for heart attacks and could be a basis for new treatments.

References:

Blattmann P, Schuberth C, Pepperkok R, Runz H. (2013). RNAi-based functional profiling of loci from blood lipid genome-wide association studies identifies genes with cholesterol-regulatory functions. PLOS Genetics, 9:e1003338

Runz,H. (2012). Integrated approaches to functionally characterize novel factors in lipoprotein metabolism. (Review) Current Opinion in Lipidology 23, 104-110

MMPU Website:

Research Group Cholesterol Regulation

Methods:

cDNA-cloning, cell culture, functional cell-based assays, automated microscopy, image analysis, interpretation of next-generation sequencing data

Cooperation partners:

Sekar Kathiresan (Massachusetts General Hospital, Boston)

Personal Qualifications:

strong motivation & commitment

Keywords:

cholesterol, high-throughput functional assays, exome sequencing ,cardiovascular disease

Contact:

Heiko.Runz@med.uni-heidelberg.de

Project 3

Project supervisor:

Joachim Kunz

Affiliation:

Department of Pediatric Oncology, Hematology, Immunology and Pulmonology Webpage

Start of MD project:

Spring 2014

Project description: 

Summary:

Acute T-lymphoblastic leukemia (T-ALL) in childhood is a common malignancy and can be cured with intensive chemotherapy in the majority of patients. However, most patients experiencing a relapse die.

By whole exome sequencing of T-ALL samples from primary disease, remission and relapse we identified several somatic mutations involved in leukemogenesis. Besides known alterations such as in Notch1, Fbxw7 or PHF6 we also found novel alterations to occur repetitively in T-ALL. While some of those mutations occur both in primary disease and in relapse, some appear to be specific for relapse and may confer resistance to treatment with cytostatic agents.

The relevance of candidate mutations needs to be assessed by a panel of methods. This includes targeted resequencing in a large cohort of patients, resequencing at high depth in selected patient samples, correlation with clinical outcome, functional analysis in cell culture and xenograft mouse models, testing of pharmacologic compounds.

Identification of somatic genetic variants directly involved in leukemogenesis or progression to relapse may allow for individualized targeted treatment. 

References:

NOTCH1 activation clinically antagonizes the unfavorable effect of PTEN inactivation in BFM-treated children with precursor T-cell acute lymphoblastic leukemia. Bandapalli OR, Zimmermann M, Kox C, Stanulla M, Schrappe M, Ludwig WD, Koehler R, Muckenthaler MU, Kulozik AE. Haematologica. 2013 Jun;98(6):928-36

Gain-of-function mutations in interleukin-7 receptor-α (IL7R) in childhood acute lymphoblastic leukemias. Shochat C, Tal N, Bandapalli OR, Palmi C, Ganmore I, te Kronnie G, Cario G, Cazzaniga G, Kulozik AE, Stanulla M, Schrappe M, Biondi A, Basso G, Bercovich D, Muckenthaler MU, Izraeli S. J Exp Med. 2011 May 9;208(5):901-8

Website:

Leukemias

Methods:

Genetics: Whole exome sequencing, Sanger sequencing, copy number assays, reverse genetics, cloning, gene expression in cell culture

Cell biology: Cell culture, microscopy, Western blotting, immunoprecipitation, drug testing

Cooperation partners:

Korbel group, EMBL, Heidelberg

J.P. Bourquin, Zuerich

Keywords:

T-ALL, whole exome sequencing, personalized medicine

Contact:

Joachim.Kunz@med.uni-heidelberg.de

Project 4

Project supervisor: Magnus von Knebel Doeberitz, MD
Affiliation: Department of Applied Tumor Biology Webpage
Start of MD project: Spring 2014

 

Project description: 
Summary:

Genomic changes in cancer cells are either caused by chromosomal instability (CIN), microsatellite instability (MSI) or epigenetic alterations like CpG island promoter methylation phenotype (CIMP). These alterations are not mutually exclusive; colorectal CIMP tumors for example can also be affected by MSI or, less frequently, CIN. Recent studies have demonstrated that epigenetic changes can result from the interaction of eukaryotic cells with bacteria, either as a result of cell-cell interaction or through potential metabolites. Recently, distinct changes of the gut microbiome have been linked by others and us with colorectal carcinogenesis. In frame of the MMPU, our partner group led by Peer Bork demonstrated that the composition of the human gut microbiome reflects presence or absence of colorectal cancer and its precursor lesions. However, it is not known whether epigenetic alterations play a central role in a potential pathway of bacteria-mediated colorectal tumor initiation or progression. Moreover, the potential addiction of CIMP colorectal cancer cell lines to a specific methylation status has not yet been systematically analyzed.

Aims:

The proposed project aims at the in-depth characterization of CIMP colorectal cancers and the question whether reversing the promoter hyper-methylation status of crucial tumor suppressor genes in CIMP colorectal cancers may represent a therapeutic option in CIMP cancer patients.

MMPU Website: Research Group Cancer Early Detection
Methods: Monitoring of colorectal  cancer cell lines (CIMP/MSI, n=4; CIMP/non-MSI, n=4; hereditary MSI, n=2; non-MSI, n=2) after treatment with demethylating agents (5-Aza-2-deoxycitidine) for cell survival (MTT assay), proliferation (BrdU incorporation), apoptosis (Annexin V staining), wound healing (scratch assay).
Genome-wide epigenetic profiling of cell lines before/after treatment with demethylating agents.
Transcriptome profiling of cell lines before/after treatment with demethylating agents.
Detailed monitoring of known CIMP target proteins (measuring re-expression of p16, MLH1).
Cooperation partners:

Peer Bork (EMBL), Neli Ulrich (NCT-Heidelberg), Jan Korbel (EMBL)

Personal Qualifications:

Enthusiastic medical student, in depth interest in scientific work, focused interest in GI oncology

Keywords:

Cancer, microbiome, CpG methylator phenotype

Contact:

knebel@med.uni-heidelberg.de