Abstract 4271: Fibroblast transcriptome sequencing reveals different gene expression profiles among distinct subtypes of breast cancer and normal mammary tissue
Authors: Natalia Bromberg, Elisa Napolitano Ferreira, Gustavo Campos Molina, Renato David Puga, Dirce Maria Carraro, Maria Mitzi Brentani
Journal: Cancer Research (2012)

Abstract Cancer associated fibroblasts, CAFs, is believed to actively participate in the growth and invasion of tumor cells by providing a unique tumor microenvironment, rendering increasingly clear that the development of cancer cannot be dissociated from its local microenvironment. However, neither the origin of CAFs nor the criteria to distinguish CAFs from normal fibroblasts has been well established. Moreover, the complex nature of the heterogeneity that exists both within and between breast cancers, particularly as related to gene expression profiling, needs more recognition. It must be appreciated that CAFs from different subtypes of breast cancers have distinct gene expression profiles as well as do CAFs in comparison to normal breast fibroblasts (NAFs). The identification of these differentially expressed genes (DEG) may shed light on the molecular interactions of fibroblasts with carcinoma cells and to further understand their signaling pathways that are actively involved. The advent of next generation sequence technologies and the realization that breast cancer is heterogeneous has shifted the focus to the identification of molecular markers of prognostic relevance. In the present study, we isolated total RNA from fibroblasts of frozen tissue samples of human invasive ductal breast carcinoma luminal A and triple negative subtypes and also from normal surrounding tissue from fibroadenoma lesions using laser capture microdissection. Preparing 3′ fragments cDNA libraries from fibroblast samples and sequencing on the Genome Sequencer FLX Titanium 454 Plataform, we obtained a transcriptional snapshot of CAFs and NAF. Sequencing and filtering (removal of adapter, polyA tail etc) of these sequences resulted in a total of 376,528 high quality reads with an average length of 159.43 bp. A total of 14,950 transcripts were sequenced and corresponded to 10,586 genes, representing 53.72% of the human genome repertoire. The analysis of DEG between the distinct samples was investigated by test on proportions (p value ≤ 0.05 and 2.0 fold change difference in expression level). The comparison of expression in NAFs versus triple negative CAF yielded 192 DEG while NAF versus luminal A CAF revealed 88 DEG and triple negative CAF versus luminal A CAF presented 41 DEG. Gene ontology (GO) assignments and KEGG pathways classifications were performed to gain an overview of the biological processes in which these DEG are involved. The results suggest that highly specific genes are expressed in each breast cancer fibroblast subtype. Taken all together, genes will be selected for validation by RT-qPCR and tissue microarray using independent samples. Further understanding of detailed functional mechanisms of the differentially expressed genes, may thus yield additional candidates for prognostic and therapeutic intervention. Supported by FAPESP:05/60333-7, 09/10088-7. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4271. doi:1538-7445.AM2012-4271