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Elli Papaemmanuil, Ph.D.
Biological Consequences of SF3B1 mutations in MDS

Elli Papaemmanuil, Ph.D.

Memorial Sloan-Kettering Cancer Center

2016 Grant Recipient

Biological Consequences of SF3B1 mutations in MDS

EvansMDS Discovery Research Grant 2016

PROJECT SUMMARY

Myelodysplastic syndromes (MDS) are prevalent blood cancers that affect cells in the bone marrow (BM) called hematopoietic stem cells (HSCs). These cells are required for normal blood formation and as in other cancers, changes in the cell’s DNA called mutations, are the cause of tumorigenesis. Most cancers have 3-7 mutations in genes that regulate normal cell function. Accumulation of these mutations impairs normal blood cell development and results in the development of large cell populations in the bone marrow that fail to develop and function properly, resulting in anemia, frequent infections and often disease progression to more severe and lethal blood cancers. The prevalence of MDS increases with age and overall outcomes for MDS patients remain poor. A better understanding of what causes MDS and how to better treat MDS patients is desperately needed.

In recent years, breakthroughs in technologies for DNA sequencing made the analysis of DNA from a large number of MDS patients possible. More than 80 genes have been identified to contribute to MDS pathogenesis and most patients have on average 2-3 mutations in these genes. These mutations provide important biological insights regarding to disease biology but are also of clinical relevance. For example, certain mutations correlate with mild symptoms and favorable outcomes, manifested by the long-term survival of patients, whereas others associate with aggressive disease and short survival. These new insights give us exciting opportunities to better understand disease development by investigating the effects that these mutations exert on the blood cells, particularly the HSCs. Understanding the biology of MDS is crucial to improve clinical management of MDS patients and importantly develop new and effective therapies.

A major complication in making significant advances in our understanding of how such mutations in unison define disease biology lies in that each patient has a unique combination of gene mutations. Todate the cells involved in MDS development (HSCs) remain difficult to study as they represent a rare cell type that is difficult to manipulate experimentally. Additionally the majority of MDS research focuses on single genes or models of disease biology. Whilst these provide important insights, the relevance of any conclusions is limited because of the restricted genetic (only one mutation) background under investigation or important species differences in physiology and disease presentation between animal models and human disease. Thus, significant advances in our understanding of MDS pathophysiology require research that recapitulates patient relevant models of disease biology.

To address these challenges this proposal unites inter-disciplinary expertise with the aim to develop models of MDS biology that capture disease defining, prognostic and therapy informing models of disease biology. Dr. Papaemmanuil has established a large population based database of molecularly annotated MDS specimens and has developed genome profiling methods to support analysis of single to 100’s of purified cells. Dr. Papapetrou has developed a method to convert patient cells into induced pluripotent stem cells (iPSCs). iPSCs represent a type of cell similar to cells found naturally in early embryonic development and can be guided towards becoming any cell type of the human body, in this case blood cells, and can be expanded to very large numbers. iPSC modeling is an invaluable new technology that allows us to pursue extensive experimentation into the biology and downstream consequences of key mutations in MDS. Dr. Papaemmanuil’s profiling of large (>1000) number of MDS patients has led to the identification of the most common combinations of gene mutations observed in MDS and how these affect clinical presentation, response to therapy and disease progression. By combining the expertise of both laboratories in diverse and complementary research areas, we are tackling the pathogenesis of MDS by focusing on the most frequent subset of MDS patients with mutations in the SF3B1 gene. Consequently, patient samples harboring SF3B1 and significantly co-occurring mutations have been identified and used for the generation of iPSCs. Successfully reprogrammed samples are currently being expanded for characterization, and will eventually be used to study how normal blood production is impaired in patients with MDS enabling research that links the genetic causes to the 2 mechanisms of MDS. At the same time, SF3B1 mutated iPSCs were generated using a newly developed gene editing technology called CRISPR/Cas9. This technology allows for the precise introduction of specific DNA mutations and therefore offers a strategy to study mutations of interest complementary to the generation of iPSCs from patient cells. In parallel, we have demonstrated that we are able to isolate and use low cell numbers, as low as 80 cells, to perform gene expression analyses by RNA-sequencing. This remains an important factor due to the scarcity of HSCs in MDS patients. It will also allow for the correct delimitation of cell populations when comparing samples from patients with different patterns of co-mutations.