Claudin-low-like mouse mammary tumors show distinct transcriptomic patterns uncoupled from genomic drivers

Abstract

Background: Claudin-low breast cancer is a molecular subtype associated with poor prognosis and without targeted treatment options. The claudin-low subtype is defined by certain biological characteristics, some of which may be clinically actionable, such as high immunogenicity. In mice, the medroxyprogesterone acetate (MPA) and 7, 12-dimethylbenzanthracene (DMBA)-induced mammary tumor model yields a heterogeneous set of tumors, a subset of which display claudin-low features. Neither the genomic characteristics of MPA/DMBA-induced claudinlow tumors nor those of human claudin-low breast tumors have been thoroughly explored. Methods: The transcriptomic characteristics and subtypes of MPA/DMBA-induced mouse mammary tumors were determined using gene expression microarrays. Somatic mutations and copy number aberrations in MPA/DMBAinduced tumors were identified from whole exome sequencing data. A publicly available dataset was queried to explore the genomic characteristics of human claudin-low breast cancer and to validate findings in the murine tumors. Results: Half of MPA/DMBA-induced tumors showed a claudin-low-like subtype. All tumors carried mutations in known driver genes. While the specific genes carrying mutations varied between tumors, there was a consistent mutational signature with an overweight of T>A transversions in TG dinucleotides. Most tumors carried copy number aberrations with a potential oncogenic driver effect. Overall, several genomic events were observed recurrently; however, none accurately delineated claudin-low-like tumors. Human claudin-low breast cancers carried a distinct set of genomic characteristics, in particular a relatively low burden of mutations and copy number aberrations. The gene expression characteristics of claudin-low-like MPA/DMBA-induced tumors accurately reflected those of human claudin-low tumors, including epithelial-mesenchymal transition phenotype, high level of immune activation, and low degree of differentiation. There was an elevated expression of the immunosuppressive genes PTGS2 (encoding COX-2) and CD274 (encoding PD-L1) in human and murine claudin-low tumors. Conclusions: Our findings show that the claudin-low breast cancer subtype is not demarcated by specific genomic aberrations, but carries potentially targetable characteristics warranting further research.

Re-definition of claudin-low as a breast cancer phenotype

“…While we did not find evidence that claudin-low status affects survival, certain claudin-low characteristics may nonetheless be clinically relevant and/or actionable. For example, claudin-low tumors show high levels of immune cell infiltration (8,12), express high levels of PD-L1 (13), are immunosuppressed by T-regulatory cells (27), and carry low mutational burden (13,14); these factors may all be relevant for the efficacy of immunotherapeutics in claudin-low tumors. The EMT phenotype in claudin-low tumors may in itself be a therapeutic target, and may also have implications for chemoresistance (28).…”

“…Functional studies will also be necessary in order to elucidate the etiology of claudin-low breast tumors, and to test novel therapeutic modalities. Due to the major influence of normal cell infiltration, it is likely that immunocompetent animal models will be of particular importance for such studies (3,13,29,30).…”

“…Claudin-low tumors, as a whole, have previously been reported to have a low mutational burden and low level of genomic instability compared to the other subtypes (13,14). Whole genome copy number data, and sequence data from a panel of 173 cancer-associated genes, was available for the METABRIC cohort (4,5).…”

“…Beyond these gene expression features, claudin-low tumors have marked immune and stromal cell infiltration (9,12), but are in many other aspects remarkably heterogeneous. No specific genomic aberrations accurately delineate claudin-low tumors, and there is a greater variation in mutational burden and degree of copy number aberration (CNA) than in the other breast cancer subtypes (13). Claudin-low tumors are, however, often genomically stable, potentially due to a protective effect of the EMT-related transcription factor ZEB1 (14).…”

Re-definition of claudin-low as a breast cancer phenotype

“…Beyond these gene expression features, claudin-low tumors have marked immune and stromal cell infiltration 9,12 , but are in many other aspects remarkably heterogeneous. No specific genomic aberrations accurately delineate claudin-low tumors, and there is a greater variation in mutational burden and degree of copy number aberration (CNA) than in the other breast cancer subtypes 13 . Claudin-low tumors are, however, often genomically stable, potentially due to their less differentiated state and a protective effect mediated by the EMT-related transcription factor ZEB1 14,15 .…”