Current lab projects include:

Clonal evolution of cancer

Like most cancers, acute myeloid leukemia (AML) develops through the sequential acquisition of driver mutations by a hematopoietic stem/progenitor cell (HSPC) clone over time. In our previous work, we exploited reprogramming of patient cells to capture distinct stages along the clonal evolution of AML into iPSCs (Clonal Hematopoiesis, low-risk MDS, high-risk MDS and sAML) (Kotini et al. Cell Stem Cell 2017).

In order to study the molecular underpinnings of the progression through these stages, we are now developing “de novo leukemogenesis” models through sequential CRISPR gene editing in human iPSCs. With these isogenic models we seek to identify targets for early targeting or even prevention of disease progression. We are also investigating the underlying principles of mutational order and cooperation in the clonal evolution of cancer.

Figure 1. Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of AML.

Splicing factor mutations in MDS

A major discovery of large-scale sequencing of cancer genomes in the past decade was the finding of frequent mutations in genes encoding splicing factors (SF) in myelodysplastic syndrome (MDS). Despite strong evidence that SF mutations are key to the pathogenesis of MDS and can provide new therapeutic opportunities, there is still limited understanding of the key effects of these mutations in driving MDS. We have used CRISPR gene editing and reprogramming of patient cells to derive isogenic models of the canonical SF mutations (SF3B1, SRSF2 and U2AF1). With our collaborators, Dr. Elli Papaemmanuil (MSKCC) and Dr. Gene Yeo (UCSD) we are performing inter sectional analyses of RNA-Seq, eCLIP and ATAC-Seq data to pinpoint important downstream targets of these mutations with therapeutic implications.

Figure 2. Modeling SF mutations in MDS. Isogenic CRISPR-edited iPSC models of U2AF1 and SRSF2 hotspot mutations capture the altered RNA binding motif preferences of the mutant SFs by transcriptome (b) and eCLIP (c) analyses.

Engraftable hPSC-derived hematopoiesis

The inability to derive engraftable hematopoiesis from human pluripotent stem cells (hPSCs, including ESCs and iPSCs) presents a major roadblock to the translation of stem cell research in hematology and regenerative medicine. We have discovered that iPSCs derived from AML patients give rise to engraftable hematopoiesis (Wesely et al. Cell Reports 2020).

Based on genomics datasets, we are currently performing screens using CRISPR and the Pro-Code/CyTOF platform, developed by our collaborator Dr. Brian Brown to uncover new regulators of HSC self-renewal and engraftment.

Figure 3. Pro-Code/CRISPR screening with CyTOF. a, CRISPR/Pro-Code lentiviral vector containing 8 tags assembled in every possible combination of 3, for a total of 56 unique combinations (Pro-Codes), fused with the reporter dNGFR and paired with a specific gRNA. b, Each ProCode population expresses a unique combination of 3 out of 8 tags (E1-E8). c, viSNE plots of HSC marker expression within each ProCode population.