Ongoing projects include the following and the categories below:
- Studying the role of the genome in complex disease traits, understanding how single genetic variants modulate drug efficacy and toxicity, predicting which patients will experience successful therapy or suffer adverse drug responses, and discovering new drugs to overcome these complications.
- Developing new tools to reprogram, culture, and differentiate iPSC in an efficient and cost-effective manner to improve the use, scale, and ubiquity of these across all areas of research.
- Studying the genomics of arrhythmia and sudden cardiac death and devising precision medicine-led drug discovery.
- The applications of iPSC and direct reprogramming in regenerative medicine, repairing the heart after a heart attack or ameliorating the effects of heart failure.
- How heritable (germline) variation influences cancer progression, oncology drug efficacy, and acquisition of resistance.
- The applications of iPSC-derived cells for cultivated meat.
Cardio-Oncology and Pharmacogenomics
One of our primary interests has been in modeling cancer therapy-induced cardiovascular toxicity. This includes heart failure, atrial fibrillation, and peripheral artery disease. To study this we generate hiPSC-derived cardiomyocytes, endothelial cells, smooth muscle, megakaryocytes, platelets, and fibroblasts. This method allows us to recapitulate a patient's off-target cardiotoxic response to drugs such as anthracyclines, tyrosine kinase inhibitors, and monoclonal antibodies. Major mechanisms we study include transporters, drug metabolism, mitochondrial behavior, reactive oxygen species, DNA damage, calcium handling, and sarcomeric damage.
Arrhythmia and Cardiomyopathies
hiPSC-derived cardiac organoids are unique tools for cardiomyopathy and hypertrophy phenotype screening. Currently, we are researching why some heart failure drugs only work in specific populations (such as BiDil) and novel drugs that inhibit and/or reverse these phenotypes in a genetic variant-specific manner. We are also looking at how hiPSC-CMs can be used in pediatric
We are studying methodologies for directly reprogramming somatic cells into cardiomyocytes for cardiac cell therapy and the fundamental questions of how we can improve the yield, engraftment, survival, and function of these cells. This work involves the study of immunogenicity, in vivo differentiation, methods for direct reprogramming, and the induction of in vivo cell-type-specific proliferation using small molecules.
hiPSC Models of Breast Cancer
hiPSCs are unique as a model for cancer as they offer homogeneous unlimited expansion without the phenotypic drifts seen with patient-derived xenograft (PDX) models and without the inability to model early-stage cancer seen with immortalized cell lines. We are using these cells in a reductionist approach to model the underlying mechanisms of tumorigenesis, germline influence on drug response, and drug resistance.
Our expertise in developing negligible-cost, chemically defined pluripotent culture (Kuo et al., 2020, Fonoudi et al., 2020, Lyra-Leite et al., 2020) and chemically defined cardiac differentiation protocols (Burridge et al., 2014) has provided us with a strong interest in how these types of techniques can be used to further develop skeletal muscle differentiation protocols the cultivated meat industry. This work involves very-large-scale, high-density bioreactor-based culture and differentiation, and edible matrices.
Pluripotent Stem Cell Generation, Culture, and Differentiation
We are actively researching how modifying the pluripotent state can influence subsequent differentiation. This work includes optimization of pluripotent media formulae (Kuo et al., 2020), reprogramming methodologies, synthetic matrices, and the maintenance of proliferative differentiation intermediates. We are working on increasingly refined, simplified, and reproducible methods for producing cells of the cardiovascular lineage along with control of subtype specification and maturation, and
Pharmacogenomics and Bioinformatics
The ability to capture a single human genome in culture as a hiPSC and then differentiate it to any desired cell type holds enormous potential to interrogate the genome. We are interested in how gene expression analysis (RNA-seq) of drug-treated hiPSC-derived cells can be combined with whole-genome association studies (WGAS) to provide differential expression quantitative trait loci (deQTL). In the lab, we sequence hundreds of whole genomes per year. As part of this effort, we are working on numerous tools to enhance
We use a variety of tools for drug testing, including Labcyte Echo 555 and Opentrons liquid handling, automated triple-mode plate readers (VarioSkan), a fully automated Nikon microscope with encoded stage, perfect focus, and high-content software, a Vala Sciences Kinetic Image Cytometer KIC200 for high-throughput calcium and high-content imaging, and a Nanion Syncropatch for automated patch clamp and Cardioexcyte96 for MEA/impedance.
Base Editing and CRISPR-Based Knockout Screening
To functionally validate how SNPs influence drug response, we have developed highly optimized CRISPR-based knockout protocols, AAVS1-based overexpression, and SNP corrections. We are also performing both pooled and arrayed CRISPR-based high-throughput screens to discover further probe mechanisms of action.
As part of our stem cell effort, we are working on the construction of multicellular organoids, organ-on-a-chip systems, and bioreactors to better develop the most accurate cellular models to recapitulate the patient's original drug response.