Figure 3: Melanoma brain metastases are immunosuppressed compared to patient-matched extracranial metastases.

(A) Unsupervised hierarchical clustering of the 500 most variable genes from 35 MBMs and 42 ECMs from 29 melanoma patients. Samples are labeled according to the patient identifier and site. Multiple MBMs or ECMs from the same patient are labeled accordingly. (B) ESTIMATE ImmuneScores of MBMs and patient-matched ECMs (lymph nodes excluded). Lines represent mean ± S.D., and each dot represents the average of all MBM or ECM samples from a single patient. Significance determined by two-sided paired Student’s t-test. (C-E) IHC analysis (CD3, CD8, and PAX5) of patient-matched MBMs and non-LN ECMs. Lines represent mean ± S.D., and each dot represents the average of all MBM or ECM samples from a single patient. Significance determined via one-sided paired Student’s t-test. (F) Pie chart showing concordance and discordance for PD-L1 IHC positivity in patient-matched MBMs and ECMs. Each MBM from a single patient was compared against each ECM from the same patient. (G-H) Mean clonality and observed richness of patient-matched MBMs and ECMs by TCR-seq. Lines represent mean ± S.D., and each dot represents the average of all MBM or ECM samples from a single patient. Significance determined via two-sided paired Student’s t-test. (I) Quantification of T cell clone repertoire overlap between patient-matched MBMs and ECMs with available TCR-seq data. The color scale indicates the Morisita Overlap Index (MOI) between two tumor samples.