Breast Cancer

Current Projects
Runmin Wei, PhD

Dr. Wei is focusing on inflammatory breast cancer (IBC), an aggressive disease subtype without known genetic signatures. This suggests that IBC could be highly heterogeneous (the cells within a tumor are genetically diverse), and the tumor microenvironment (the environment surrounding a tumor) may be important for disease progression and therapeutic resistance. He is developing a computational toolkit to characterize the IBC tumor spatial heterogeneity and tumor microenvironment. He will leverage cutting-edge deep learning approaches to associate histopathology findings from tumor samples with single cell spatial sequencing information. This project will provide a better understanding of IBC initiation, progression and therapy responses at a molecular level.

Dr. Wei will use open-access single cell and spatial sequencing data analysis tools, e.g. Seurat and Scanpy to analyze data. He will also use specific computational tools for different analytical purposes, e.g. RNA Velocity and Monocle to infer cell differentiation, CytoTRACE, SCENT to infer cell differentiation potentials, and SCENIC to infer the transcriptional factors and gene regulatory network. Besides, he will develop novel algorithms/computational tools for spatial and single-cell sequencing data analysis.

Project title: "Integrating single cell genomic and spatial information to delineate tumor heterogeneity and microenvironment interactions in inflammatory breast cancer"
Institution: The University of Texas MD Anderson Cancer Center
Award Program: Quantitative Biology Fellow
Sponsor(s) / Mentor(s): Nicholas E. Navin, PhD, and Ken Chen, PhD
Cancer Type: Breast
Research Area: Bioinformatics
Xiphias Ge Zhu, PhD

Many immunotherapy strategies require patient T cells to recognize specific cancer-associated antigens. However, it is unclear what these antigens are and how they contribute to tumor shrinkage during treatment. Dr. Zhu [HHMI Fellow] will use large-scale antigen screening methods to identify cancer-associated antigens recognized by T cells that are activated in breast cancer patients during immunotherapy treatment. Mapping the antigen landscape of breast cancer will identify targetable antigens and improve future immunotherapies. Dr. Zhu received his PhD from The Rockefeller University and his BSc from the National University of Singapore.

Project title: "Charting the tumor antigen landscape of breast cancer"
Institution: Brigham and Women's Hospital
Named Award: HHMI Fellow
Award Program: Fellow
Sponsor(s) / Mentor(s): Stephen J. Elledge, PhD
Cancer Type: Breast
Research Area: Tumor Immunology
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