Based on deep-sequencing studies the majority of genetic aberrations underlying leukemia development have now been identified. Also, it has now become clear that, rather than following a linear evolution model in which one mutant clone dominates, leukemias are much more complex and often display an architecture in which multiple clones can co-exist. Since these subclones carry distinct combinations of mutations in their DNA, they most likely require specific drugs or therapeutic approaches. A current challenge in the field is that clonal heterogeneity is revealed by sequencing technologies that do not allow the prospective isolation of these subclones as viable cell populations. The availability of such technologies is essential to be able to study the molecular characteristics of genetically distinct subclones such as their transcriptome, proteome and epigenome, as well as their specific drug sensitivities. This is one of the main aims of the current proposal.
In preliminary studies we have hypothesized that genetic and epigenetic differences between subclones within individual patients result in changes in their transcriptome and proteome, and potentially also in specific expression patterns of plasma membrane receptors, as a consequence of specific signaling networks operating in these subclones. Over the past years, by performing extensive transcriptome and quantitative proteome studies. Thus, we have been able to identify and validate a set of leukemia-specific plasma membrane proteins. The biological role of a number of these novel plasma membrane proteins in relation to stem cell fate and leukemic transformation will be investigated. Furthermore, by applying a combinatorial approach in which expression of all PM markers is analyzed simultaneously in a principle component analysis, we have been able to evaluate whether (epi)genetically distinct subpopulations can be identified within individual patients. Using this approach we have indeed observed remarkable heterogeneity in clonal distributions in 30-40% of the cases and importantly, we are now – for the first time - able to prospectively sort (epi)genetically distinct subclones for further in vitro and in vivo studies. Preliminary data indeed indicated that transcriptomes and chromatin accessibility are remarkably different within these sublcones isolated from individual patients.
In the current proposal, we will perform in-depth analyses on the molecular biology and drug sensitivity of these prospectively isolated subclones in a large cohort of patients, including longitudinally obtained samples (from diagnosis to relapse) (WP1). Furthermore, we will determine whether our novel markers, or combinations thereof by using infinicyt-based approaches, can aid in predicting disease progression of AML patients, can aid in detecting minimal residual disease (MRD) after treatment, and can identify the (sub)clones responsible for relapse of disease (WP2).
Your salary is € 2.279,- gross per month in the first year up to a maximum of € 2.919,- gross per month in the last year (scale PhD). In addition, the UMCG will offer you 8% holiday pay, an 8.3% end-of-year bonus and a development budget. The terms of employment comply with the Collective Labour Agreement for Medical Centers (CAO-UMC).
The duration of the project is four years. You will be able to develop your research skills within highly experienced and internationally recognized research groups and in addition will receive education within institute research schools.
Prof. Dr. J.J. Schuringa
Department of Experimental Hematology
The general aims of the division of Experimental Hematology are to obtain detailed knowledge on (molecular) mechanisms that determine hematopoietic stem cell self-renewal and differentiation, with the ultimate goal to deepen our insights in the development of human leukemias. We perform gene-function analyses in human hematopoietic stem and progenitor cells isolated from cordblood and bone marrow utilizing various strategies including optimized retro/lentiviral transduction protocols, CRISP/Cas9 and inducible RNAi approaches. We have a longstanding expertise in using molecular approaches including genome-wide transcriptomics, proteomics and ChIP-seq to further understand processes such as hematopoietic differentiation, proliferation, apoptosis and self-renewal. We utilize a series of cell biological in vitro and in vivo humanized niche xenograft model systems to be able to translate knowledge from our molecular research lines to a more (pre)clinical setting.
Within a recently awarded Dutch Cancer Foundation grant entitled “Using the plasma membrane proteome to dissect clonal heterogeneity and track disease progression in AML” we are currently looking for two talented and highly motivated PhD students.