Supplementary material from Tumor-Infiltrating Plasma Cells Are Associated with Tertiary Lymphoid Structures, Cytolytic T-Cell Responses, and Superior Prognosis in Ovarian Cancer

Abstract

Supplementary methods. Table S1. PC-derived immunoglobulin heavy (IGH) V, D, and J region usage and consensus junction amino acid sequences for distinct VDJ families as determined by Sanger sequencing and IMGT V-QUEST alignment Table S2. Genes with greater than 10-fold differential expression between tumors with high numbers of PC ("PC", n=4) versus no B-lineage cells ("no PC/B cells" n=3), or high numbers of PC versus tumors with CD20+ TIL but without PCs ("B cells", n=2) (based on average transcript counts in NanoString analysis of FFPE tumor tissue). Table S3. Differentiation, overexpressed, and CT antigen genes analyzed for expression in TCGA microarray data. Table S4. List of genes that by hierarchical clustering were differentially expressed in tumors with a PC signature (Fig. S3). Table S5. Clinical characteristics of HGSC patients represented on the 172-case TMA used for survival analysis; P-values refer to results of univariate analyses between the indicated variable and disease-specific survival using one-way ANOVA or chi-squared tests. Table S6. Antibodies used in this study. Fig. S1. Immunoglobulin heavy chain expression in HGSC. Standardized read count (FPKM) data for 9 immunoglobulin heavy chain classes were plotted using TCGA HGSC RNA-seq data. Fig. S2. Lack of association between the PC gene signature and immunogenic mutations, TP53 mutations, and differentiation/overexpressed antigens in HGSC. Fig. S3. Heatmap of CT antigen expression.