Supplementary Material
tumor, CD8 T-cell infiltration
MINOR, CYTOMEGALOVIRUS, TUMOR
Surgical specimens after neoadjuvant therapy from patients who did not respond to treatment. Color scheme: Yellow: CD8, Red: IgG4, White: CK7, Green: PD-L1, Magenta: PD-1, Blue: DAPI. Staining demonstrates minor CD8 T-cell infiltration within viable tumor tissue, with no detectable PD-1, PD-L1, or IgG4 signal present.Click here for additional data file.Immune cell deconvolution of bulk RNA-seq data. MCPcounter was used to summarize gene expression scores for immune cell populations from bulk RNA-seq expression data across ten cell types. Each point represents one sample, and paired baseline/surgery samples are connected by a line. Individual patients and their responses are indicated by color and point shape.Click here for additional data file.Detection of talimogene laherparepvec (T-VEC) vector reads in case #2. This screenshot from the integrated genomics viewer shows reads aligning to CSF2 (GM-CSF) from the peripheral blood, baseline, and end-of-treatment (EOT) whole exome sequencing (WES) data from the surgical specimen of case #2. The short-clipped ends of the reads at the 5’ end of CSF2 contained the T-VEC cytomegalovirus (CMV) promoter sequence, and reads spanned the exon-exon junctions of the CSF2 transcript. This pattern was not observed in the surgical (EOT) specimens from the other patients or in baseline samples.Click here for additional data file.Representativeness of Study ParticipantsClick here for additional data file.Summary of antibodies, antigen retrieval conditions, incubation conditions, and opal dye labeling for multiplex immunofluorescence experimentsClick here for additional data file.Individual details of baseline patient characteristicsClick here for additional data file.Biopsy samples for analysesClick here for additional data file.