Longitudinal tissue analysis reveals microenvironmental changes correlate with combined immunotherapy and targeted therapy response in metastatic breast cancer

The ability to interrogate changes within the tumor microenvironment (TME) before, during and following therapeutic intervention could yield important understanding of treatment response and causes for disease progression. Yet, the role of investigational tissue analysis faces key challenges in the clinical setting and the value of integrating longitudinal biopsies with emerging multimodal molecular analyses ("Multi-omics") remains to be defined. In this study, we conducted a multicenter phase 2 clinical trial examining the effect of a novel cytotoxic T-lymphocyte-associated protein 4/programmed death-ligand 1 bispecific antibody in combination with a dual-epitope blocking anti-human epidermal growth factor receptor 2 antibody in treatment-resistant metastatic breast cancer. We performed longitudinal sampling of patient tumor tissues before and following treatment. Single-cell RNA and T cell receptor sequencing from 334,183 cells from site-matched tumors reveals significant temporal shift of various immune cell populations and phenotypes within the TME associated with treatment responses. Conversely, regulatory T cells were activated while effector T cells, natural killer cells, and dendritic cells were significantly depleted in non-responding tumors. Taken together, these results support that longitudinal analysis of TME to generate multiomics data that can lead to rich insight into disease process and to provide clinical value in evaluating treatment responses. <b>Trial registration number</b> NCT04521179.