Evaluating tumor inflammation and PD-L1 expression in sequential biopsies of real-world primary and metastatic breast cancer.
Authors: Wallen Zachary D. , Pabla Sarabjot , Nesline Mary K. , Gao Shuang , Vanroey Erik , DePietro Paul , Conroy Jeffrey M. , Ko Heidi Chwan , Strickland Kyle C. , Previs Rebecca A. , Hastings Stephanie B. , Eisenberg Marcia , Caveney Brian , Severson Eric A. , Ramkissoon Shakti H. 
Published: June 2024

e13035

Background: Biomarkers for measuring immunogenicity of tumors such as PD-L1 immunohistochemistry (IHC), tumor mutational burden (TMB), and immune gene expression have been studied in many cancers including breast cancer. How these biomarkers change over time and how their detection differs with sequential testing in the real-world clinical setting has been studied to a lesser extent but is an important consideration for optimal patient care. Methods: We performed an analysis of 30 patients with primary and metastatic breast cancer sequentially tested by comprehensive genomic and immune profiling (CGIP) at two time points during routine clinical care to observe temporal changes in immunotherapy markers and immune gene expression. Genomic variants and TMB were assessed with DNA-seq, while immune gene expression was assessed with RNA-seq. PD-L1 expression was determined using IHC. Immune gene expression signatures characterizing the tumor microenvironment (TME) were calculated, including tumor inflammation (TIGS), cell proliferation (CP), and cancer testis antigen burden (CTAB). Differences between sequential tests were tested for using linear mixed effect models. Results: Time between biopsies for sequential tests ranged from the same day to 4.5 years, with 40% of specimens being collected within 30 days of the first. Sequential specimens were collected from breast (27%), non-breast (40%), or a mix of breast and non-breast (33%) tissue. Non-breast tissue types included sites from lymph node (18%), GI tract (15%), skin (10%), thorax (7%), and musculoskeletal sites (7%). Overall, TMB, PD-L1 IHC, and gene expression signatures were relatively stable between sequential tests (P > 0.05); however, trends were noted for second tests detecting lower tumor inflammation (TIGS score) and PD-L1 IHC (P = 0.1). Further, second tests detected significantly lower levels of tumor inflammation when both were performed on non-breast tissue (P = 0.04), but not when performed on all breast (P = 0.7) or a mix of breast and non-breast (P = 0.6) tissues. An opposite trend was noted for PD-L1 where second tests detected lower levels of PD-L1 IHC when both tests were performed on breast tissue (P = 0.1), but not when performed on all non-breast (P = 0.4) or a mix of breast and non-breast (P = 0.5) tissue. Tissue-dependent trends were still present even when excluding lymph node specimens (P = 0.1). Conclusions: Changes in immunotherapy markers and immune gene expression signatures, on average, remained relatively stable over time, except for tumor inflammation and PD-L1 IHC when sequentially testing all non-breast or breast tissue, respectively. These observations highlight the utility of clinical CGIP testing in revealing temporal changes of the TME, which may help inform clinical trial or treatment strategies occurring over time for primary and metastatic breast cancer.