Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer

Abstract

Purpose: Lymphocytic infiltration of tumors predicts improved survival in patients with breast cancer. Previous studies have suggested that this survival benefit is confined predominantly to the basal-like subtype. Immune infiltration in ovarian tumors is also associated with improved prognosis. Currently, it is unclear what aspects of the immune response mediate this improved outcome.

Experimental design: Using The Cancer Genome Atlas mRNA-seq data and a large microarray dataset, we evaluated adaptive immune gene expression by genomic subtype in breast and ovarian cancer. To investigate B-cells observed to be prognostic within specific subtypes, we developed methods to analyze B-cell population diversity and degree of somatic hypermutation (SHM) from B-cell receptor (BCR) sequences in mRNA-seq data.

Results: Improved metastasis-free/progression-free survival was correlated with B-cell gene expression signatures, which were restricted mainly to the basal-like and HER2-enriched breast cancer subtypes and the immunoreactive ovarian cancer subtype. Consistent with a restricted epitope-driven response, a subset of basal-like and HER2-enriched breast tumors and immunoreactive ovarian tumors showed high expression of a low-diversity population of BCR gene segments. More BCR segments showed improved prognosis with increased expression in basal-like breast tumors and immunoreactive ovarian tumors compared with other subtypes. Basal-like and HER2-enriched tumors exhibited more BCR sequence variants in regions consistent with SHM.

Conclusion: Taken together, these data suggest the presence of a productive and potentially restricted antitumor B-cell response in basal-like breast and immunoreactive ovarian cancers. Immunomodulatory therapies that support B-cell responses may be a promising therapeutic approach to targeting these B-cell infiltrated tumors.

Figure 1

A Concordant expression of genes from different immune cell types in a distinct subset of primarily basal-like, HER2-enriched, and normal-like tumors. Unsupervised hierarchical clustering of breast cancer mRNA-seq data (n=728); signatures B_Cell_cluster, CD8_cluster, T_Cell_cluster, CD68_cluster, and MacTh1_cluster are derived from this hierarchical clustering. B Expression of breast cancer-derived gene expression signatures in an ovarian cancer mRNA-seq data set (n=266).

Figure 2

Box plots of expression of IGG_Cluster and CD8 gene expression signatures by subtype, with one-way ANOVA p value, in A, B microarray data from 855 breast tumors C, D mRNA-seq data from 819 breast samples (728 tumor, 91 normal breast) and 266 ovarian tumors E, F mRNA-seq data from 266 ovarian tumors. Expression of immune genes is high in basal-like, claudin-low, and HER2-enriched breast cancer subtypes and the immunoreactive ovarian cancer subtype.

Figure 3

Expression level of all BCR segments across breast cancer subtypes and ovarian cancer. Expression is highest in basal-like and HER2-enriched breast cancer and immunoreactive ovarian cancer subtypes and highly correlated within groups.

Figure 4

Expression level of BCR segments is preferentially predictive of improved overall survival in basal-like breast cancer and progression-free survival in immunoreactive ovarian cancer. A, C Grid of prognostic value of all BCR segments (colored cells represent positively prognostic segments). B, D Prognostic BCR segment distribution across subtypes, with bootstrap confidence intervals (95%). Control value represents 353 random non-BCR genes.

Figure 5

A Basal-like, HER2-enriched, and luminal B tumors show high expression of low-diversity BCR V segment pools (data averaged over top ten highest expressed V segments). B Density of V segment expression in breast cancer. C A subset of predominantly immunoreactive ovarian tumors show high expression of low-diversity BCR V segment pools (data averaged over top ten highest expressed V segments). D Density of V segment expression in ovarian cancer.