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E. Aubrey Thompson, PhD

Professor of Cancer Biology
Co-director, Breast Cancer Translational Genomics Initiative
Mayo Clinic Comprehensive Cancer Center
Jacksonville, Florida

Current Research

Goal: To understand how breast tumor cells and immune cells interact and how this affects response to treatment.

Impact: Dr. Thompson is studying how the immune landscape of three subtypes of breast cancer—HER2-positive, triple-negative, and hormone receptor (HR)-positive—impacts response to chemotherapy and/or targeted treatments. His work could reveal biomarkers of response and new ways of activating the immune system of patients undergoing chemotherapy and/or immune therapy.

What’s next: He and his team will study the interaction of tumor and immune cells and how they relate to recurrence-free survival in patients with high-risk breast cancers.

Response to targeted therapies and/or chemotherapy appears to be at least partly determined by how tumor cells and immune cells interact. Dr. Thompson is studying these interactions in order to discover biomarkers of treatment response as well as to identify new potential therapeutic targets across breast cancer subtypes. 

Full Research Summary

Research Area: Understanding the role of the tumor-immune landscape in response to cancer therapies and identify new therapeutic and prognostic markers to improve outcomes for patients with aggressive forms of breast cancer. 

Impact: There is now clear evidence for the role of the immune environment within the tumor prior to therapeutic response. 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 prior to initiation of therapy 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.
Current Investigation:
Dr. Thompson’s team is utilizing emerging spatial biology technology to map the immune landscape prior to initiation of both adjuvant and neo-adjuvant therapy. Their goal is to define the baseline immune landscape of aggressive breast cancer and identify the baseline immune features that are associated with durable, recurrence-free survival.

What they’ve learned so far: Dr. Thompson’s team has made significant progress in immune profiling and quantifying clinical/genomic features associated with recurrence in early stage TNBC and HER2-positive breast cancer.

What’s next: They will continue to work towards their goal to define the relationship between clinical/therapeutic outcome and the number, types, activities, and locations of immune cells in high risk breast cancer. Their current focus is on high-risk breast cancer, including TNBC, HER2-positive, and HR-positive/HER2-negative tumors.


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.

Grid Researcher Headshot - Thompson

BCRF Investigator Since


Donor Recognition

The Play for P.I.N.K. Award

Area(s) of Focus