Extended Data Fig. 10: On-treatment immunohistochemistry for CD45 predicts pathologic complete response.
a. Summary of the clinical characteristics of cohort used to evaluate IHC CD45 percent positive cells within tumor enriched regions as a biomarker. These features include pathologic complete response (pCR), estrogen receptor (ER) status, and PAM50 status. b. Correlation plot comparing the normalized on-treatment CD45 DSP protein values with the paired on-treatment CD45 % positive derived from IHC. The grey shading indicates the 95% confidence interval of the correlation coefficient. P value is assessed via a one-sided t-test (correlation coefficient not equal to 0) using n = 28 tumors with paired data. c. Boxplots showing DSP on-treatment CD45 levels (n = 53 biologically independent tumors), on-treatment stromal tumor infiltrating lymphocyte (TILs) score (n = 31 biologically independent tumors), and on-treatment tumor cellularity (n = 47 biologically independent tumors) stratified by pCR utilizing all available data where these features were measured across the discovery and validation cohorts. P-values were derived using the two-sided Wilcoxon rank-sum test. For each boxplot, the colored box represents the interquartile range and the black lines extending from the box represent 1.5X the interquartile range. d. For both the CD45 on-treatment IHC data (n = 28 patients) and the normalized CD45 on-treatment DSP data (n = 24 patients in the discovery cohort, n = 29 patients in the validation cohort), thresholds were defined to predict pCR vs non-pCR cases. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) are shown for such thresholds.
