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E. Aubrey Thompson, PhD

Mayo Clinic Comprehensive Cancer Center
Jacksonville, Florida

Titles and Affiliations

Professor of Cancer Biology
Co-director, Breast Cancer Translational Genomics Initiative

Research area

Understanding how breast tumor cells and immune cells interact and how this affects response to treatment.


The immune environment within a tumor affects how the tumor responds to chemotherapy and/or targeted treatments. Moreover, the interactions between cancer cells and immune cells also serve as targets for immunotherapies, such as checkpoint inhibitors. Dr. Thompson’s BCRF research is focused on understanding the relationship between response to therapy and the numbers, types, locations, and activities of immune cells in patients with aggressive breast cancers. These studies will provide fundamental new insight in tumor cell-immune cell interaction in high-risk breast cancer subtypes, as well as identify novel biomarkers and potential new therapeutic targets.

Progress Thus Far

Dr. Thompson’s focus over the past year has been on the analysis of early-stage triple-negative breast cancer (TNBC) samples from two patient cohorts. He and his team analyzed the relationship between the immune architecture of TNBC and clinical outcome using emerging spatial biology technology. With this technique, they can map the abundance of immune and other tumor-related proteins within tumor microenvironments. A major focus has been on PD-L1, an immune regulatory protein that is expressed at high levels (PD-L1 positive) in many cancers and blocks the immune system from fighting tumor cells. Dr. Thompson found several key immune features that are associated with PD-L1 positivity and may be used to predict PD-L1 positivity in TNBC. He and his team also analyzed immune features associated with risk of recurrence and generated scores that reflect the level of risk based on immune features.

What’s next

Dr. Thompson will focus on developing a single-cell definition of PD-L1 positivity using state-of-the-art molecular imaging to analyze samples of early-stage TNBC that have been treated with the PD-L1 -targeting drug, pembrolizumab. Their objective is to identify features that can be incorporated into a companion diagnostic tool to predict tumor response to anti-PD-L1 therapy in early-stage TNBC.


Dr. Thomspon’s core expertise is in cancer genomics. He was a project leader on the FDA-funded MAQCIII project. His was one of three laboratories world-wide to be designated as a primary sequencing lab for this international collaborative study. A member of the breast cancer analytical working group of The Cancer Genome Atlas project, Dr. Thompson heads the breast cancer fusion transcript subgroup. For almost 40 years this work has focused on gene structure and function within the context of the malignant phenotype, with an emphasis on breast cancer. As co-director of the Mayo Clinic Breast Cancer Translational Genomics program, Dr. Thompson coordinates the efforts of a team of highly committed individuals with expertise in computation, biostatistics, bioinformatics, functional genomics, database management, and clinical management of breast cancer patients. This team’s work represents a broad range of collaborations, including basic mechanistic studies, clinical translational studies with a strong focus on analysis of clinical samples and practice-changing discoveries, and development of new tools for genomic analysis. Dr. Thompson’s work is highly translational in nature, and he is motivated by the concept that more effective clinical management of breast cancer requires a more detailed understanding of the biology that underlies the disease. A major objective is to define the genomic architecture of HER2-positive breast cancer, to use this genomic information to identify the biological processes that are associated with clinical outcome, and to use these biological processes to elucidate the biological and genomic basis of therapeutic response.

BCRF Investigator Since


Donor Recognition

The Play for P.I.N.K. Delaire Country Club Award