Core A: Single Cell Profiling and Bioinformatics Core

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Project Summary/Abstract The Single Cell Sequencing and Bioinformatics Core (Core A) is designed to support all Program Projects in their studies of how external, modifiable risk factors influence the progression of clonal hematopoiesis to hematologic malignancy in mice and humans. Two major themes of the Program – understanding how cells with specific mutations respond to modifiable stressors and evaluating the impact of individual mutant clones on others in the ecosystem – both depend on single-cell analysis of cells. The mission of this Core is to provide advanced technical and analytical platforms to track and characterize human and murine mutant cells at single- cell resolution, followed by bioinformatics and mathematical analyses necessary to interpret the data. The Core will (1) provide high-throughput single-cell genomic analysis and other advanced sequencing platforms to all Projects; (2) will provide bioinformatics analysis of multi-dimensional datasets and facilitate data sharing; and (3) will develop mathematical modeling based on large-scale molecular data from mice and humans. To support the first aim, the core is equipped with various single-cell genomics platforms such as Chromium (10X Genomics) and Tapestri (Mission Bio), which enable high-throughput single-cell RNA and DNA sequencing, as well as single-cell multi-omics approaches (CITE-seq and simultaneous DNA/protein analysis). Dr. Koichi Takahashi, Leader of the Core, has been on the forefront of use of such technologies in evaluating the evolution of hematologic malignancies, making him ideally suited to lead to this Program-specific Core. In the second aim, the Core will provide necessary bioinformatic support in analyzing large-scale epigenetic and transcriptomic data in response to modifiable extrinsic risk factors (infection and obesity in Project 1; chemotherapy and smoking in Project 2) to understand the biological effects of stress on clonal hematopoiesis and malignant transformation. In the third aim, the Core will utilize broad epidemiologic data to develop a mathematical model to predict the risk that CH progresses to frank hematologic malignancy in individuals based on their genetic variants, clone size (as measured by variant allele frequency), and specific exposures to modifiable external risk factors (e.g. smoking, obesity, infection, chemotherapies). Dr. Marek Kimmel, Co-Leader of the Core, has an extensive background in mathematical modeling of stem cell dynamics and cancer and is well-positioned to lead this aspect of the Core. This Core will coordinate data storage and quality controls (QC) to ensure the rigor and reproducibility of the data and facilitate public data sharing. Overall, Core A will provide cutting-edge technical and analytical support for all three proposed Projects and support statistical rigor and reproducibility, with support from Core B. By centralizing data analysis and storage, this Core will facilitate the integration of datasets and cross-sectional analyses in order to optimize crosstalk between the large-scale mechanistic animal and human epidemiology studies in this Program. The work of this Core is central to the Program’s overall goal of elucidating the mechanisms of clonal dynamics in response to modifiable external stressors.