The primary goal of the research program in the Tothova laboratory is to contribute to our understanding of the biology of benign and malignant hematologic disorders, with a specific focus on the study of mechanisms of leukemogenesis in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Genome compartmentalization mediated by the cohesin complex plays an essential role in genomic integrity and transcriptional regulation in healthy and disease states. Cohesin complex is one of the most recurrently mutated protein complexes in cancer, including MDS and AML. It is not known how presence of a cohesin mutation, a driving event in MDS, affects splicing, topologically associated domain (TAD) boundaries, enhancer-promoter loop formation or formation of phase separated condensates, and we strive to understand its basisbas a driver of leukemogenesis. Therefore, understanding the regulation of gene expression and splicing in the context of 3D chromosome structure will be novel and particularly informative in cohesin mutant MDS and other cohesin mutant human diseases. In addition, such studies may help elucidate the mechanisms of aberrant transcriptional programs that are activated by other mutations in MDS, including mutations in genes encoding epigenetic regulators, splicing factors and transcription factors, with a potential to identify a common pathway of transformation.

We have previously determined the effect of mutations in the most commonly mutated subunit STAG2 on cohesin complex association with chromatin in isogenic AML cell lines and identified a number of differentially regulated genes with aberrant promoter and/ or enhancer cohesin binding. We are interested in defining the alterations in TADs that underlie the effects of cohesin mutations on myeloid transformation, and its effect on phase separated condensates. We employ techniques such as chromatin topology studies Hi-C and super-resolution microscopy to identify oncogene neighborhoods using engineered STAG2 mutant cell lines, primary human hematopoietic stem cells CRISPR engineered with relevant mutations, xenograft models and patient samples. We hypothesize that during the process of disease progression of myeloid malignancies, acquisition of cohesin mutations leads to disruption of critical DNA looping interactions, associated with spatial reorganization of phase separated transcriptional bodies and transcriptional deregulation. If our hypothesis is correct, this could have a profound impact on our understanding not only of novel mechanisms of action of cohesins, but on the molecular pathogenesis of leukemia and other cancers, and added opportunities for therapeutic intervention.