Harvard Catalyst Profiles

Genes encoding components of the cohesin complex are commonly mutated in human myeloid diseases, including 11% of patients with MDS and 21% of patients with secondary AML, and are associated with poor overall survival1-4. The biology of these mutations has been unknown, and there are currently no therapies known to have selective efficacy in cohesin-mutant cancers. We have recently developed models of cohesin-mutant AML cell lines and investigated the effect of STAG2 mutations, the most commonly mutated cohesin subunit, on the composition and function of the cohesin complex. The multiple independent approaches we undertook to nterrogate the mechanisms of STAG2 mutations, including quantitative proteomics, genetic dependency screens and chromatin immunoprecipitation studies, converged on identification of a shift from STAG2- to STAG1-containing cohesin complexes with perturbed interaction with, function and dependency on DNA damage repair. Furthermore, we demonstrated that cohesin-mutant AML cells are exquisitely sensitive to PARP inhibition in vitro and in vivo xenograft cell line models. In collaboration with Dr. Jacqueline Garcia at the Dana-Farber Cancer Institute, we have written a Phase 1B protocol entitled: A Pilot Proof-of-Concept Study of Talazoparib for Cohesin-Mutated AML and MDS with Excess Blasts, which is currently enrolling patients at the Dana-Farber Cancer Institute. The goal of this research project is to interrogate the mechanistic basis of the effect of PARP inhibition in combination with hypomethylating agents using primary patient samples from the aforementioned Phase 1B trial using super-resolution microscopy, BH3 profiling and development of new cohesin-mutant AML/MDS patient-derived xenograft (PDX) models to test combination treatment of PARP inhibition with hypomethylating agents. The student will be working closely with a postdoctoral fellow and receive training in super-resolution microscopy, BH3 profiling, flow cytometry, and PDX mouse modeling. After training and depending on the time commitment and interest, the student will have the opportunity to lead a major effort within the project.

MDS and AML are clonal diseases of mutated hematopoietic stem and progenitor cells characterized by abnormal differentiation and proliferative states, and associated with mutations and rearrangements affecting transcription factors, epigenetic regulators, chromatin modifiers and splicing genes. The core components of the cohesin complex STAG2, SMC1, SMC3, RAD21, as well as its modulators PDS5 and NIPBL are collectively mutated in 13% of patients with de novo AML, 21% of patients with secondary AML, and 11% of patients with MDS where they are associated with poor overall survival [6-11]. Mutations in the cohesin genes are nearly always mutually exclusive, heterozygous, predicted loss-of function mutations, which are thought to be acquired early during the progression from clonal hematopoiesis to MDS. Recently, our lab at the Dana-Farber Cancer Institute discovered that cohesin mutations common in myeloid malignancies disrupt RNA splicing and render cells highly sensitive to broad-spectrum splicing inhibitors. In this project, we will use state-of-the-art approaches to characterize nascent transcription, RNA processing and RNA-protein interaction assays to define the aberrant RNA species that mediate this vulnerability and explore sensitivity of primary cohesin-mutant patient samples to splicing modulation. We hypothesize that cohesin complex mutations lead to altered RNA biogenesis and splicing and can serve as a therapeutic vulnerability in patients with cohesin-mutant MDS and AML. The student will be working closely with a postdoctoral fellow and will receive training in molecular biology, primary mouse and human cell work, and gene expression profiling methods.

A mentored opportunity in the Tothova Lab at the Dana-Farber Cancer Institute is available for a student interested in understanding the role of epigenetics during blood cancer development. The primary focus of the Tothova laboratory is investigation of the biology, genetics and treatment of myeloid malignancies, including the premalignant state of clonal hematopoiesis (CHIP), myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Our goal is to contribute to our understanding of the effect of chromatin organization on hematopoietic stem cell (HSC) transformation in the context of mutations in cohesin genes and other epigenetic modulators recurrently mutated in myeloid malignancies. We employ a combination of genomic, genome engineering, mouse modeling as well as classical biochemistry, cellular and molecular biology approaches to answer disease-relevant questions with the goal to identify novel therapeutic targets that can be translated to true patient benefit in the future. Major questions being addressed in the lab include: (1) Role of cohesin in driving inflammation and immune evasion during cohesin-mutant disease initiation and progression; (2) Impact of cohesin mutations on transcriptional regulation and splicing, and mechanisms of sensitivity to splicing modulators, (3) Mechanisms of DNA damage accumulation in cohesin-mutant cancers and contribution of transcriptional stress and replication fork stalling; (4) Modeling disease progression from clonal hematopoiesis of indeterminate potential (CHIP) to MDS/AML using primary mouse and human cells; (5) Therapeutic targeting of cohesin-mutant MDS and AML using PARP inhibition, hypomethylating agents, splicing modulators and novel combination treatments