2013 - 2021

Genome-wide Mutation Discovery and Delineation of the Somatic Aberration Networks in MPN.

The project part leader, Robert Kralovics, did pioneering studies on JAK2 V617F+ MPN, discovered primary lesions and genetic factors in MPN, and is a group leader at CeMM. He established genome-wide screen assays for the detection of mutations and SNP in neoplastic cells. His research is dedicated to classical MPN, including JAK2 V617F-mutated variants. During the preparation for this SFB, Robert studied a large cohort of MPN patients with high-resolution SNP arrays and identified 18 major recurrent chromosomal aberrations potentially involved in disease initiation and/or progression.

The aims in project #02 are to identify relevant genes somatically mutated in ET, PV, and PMF for diagnostic and prognostic applications and to define relevant pathways involved in disease initiation and transformation. Then to functionally evaluate gain-of-function and loss-of-function mutations in vitro and in vivo with an emphasis on the mechanism of action of mutated CALR, and finally to determine the effects of anti-CALR antibodies, pegylated interferon-alpha (IFN-A), and selective small molecule inhibitors on growth and survival of MPN stem- and progenitor cells in vitro and in vivo.

Project #02 contributes substantially to the common goal of this SFB for several reasons: The key expertise team #02 provides to the SFB consortium is: high-throughput analysis of the human genome using microarray, deep sequencing technologies in hematologic disorders, functional analysis of hematopoietic oncogenes and tumor suppressor genes. The PI has assembled a large sample bank derived from over 2,000 patients with Ph− and Ph+ MPN. The genome analysis platform including the bioinformatics infrastructure as well as the MPN sample bank will be shared among various SFB partners. The main strength of #02 is the ability to identify somatic and hereditary mutations in patient samples. The group of the PI has established protocols for DNA variant detection and transcriptome sequencing in small cell populations which will be vital for #02 and #04. We have extensive experience in dissecting the clonal architecture of hematopoietic stem cells in leukemic patients who acquired a number of somatic mutations during the genetic evolution of the malignant stem cells. This analysis pipeline will greatly support the LSC experiments of #04. Functional evaluation of MPN- associated defects and dissection of cellular responses to drugs will play an important role in our SFB. For this purpose RNA expression profiling using deep sequencing will be useful. RNA-seq and the downstream bioinformatics pipeline established by the PI will be made available for all SFB projects.