Sricharan Reddy Varra

Abstract Immune checkpoint inhibition (ICI) benefits only a subset of patients with metastatic triple-negative breast cancer and determinants of response remain unclear. We assembled a longitudinal cohort of 103 female patients from the phase 2 TONIC trial, with samples spanning primary tumors, pretreatment metastases and on-treatment metastases during nivolumab therapy.

Abstract Multiplexed imaging offers a powerful approach to characterize the spatial topography of tissues in both health and disease. To analyze such data, the specific combination of markers that are present in each cell must be enumerated to enable accurate phenotyping, a process that often relies on unsupervised clustering. We constructed the Pan-Multiplex (Pan-M) dataset containing 197 million distinct annotations of marker expression across 15 different cell types.

Ethical statement All samples were acquired, and all experiments were approved by Institutional Review Board (IRB) protocol #46646 “Assessing Normal Expression Patterns of Immune and Non-Immune Markers Across Tissue Types With Multiplexed Ion Beam Imaging” at Stanford University. All experiments followed all relevant guidelines and regulations. Pixel clustering methodology The pixel clustering method in Pixie is illustrated in Supplementary Fig. 2a and described above.