Benign breast tumors may arise on different immunological backgrounds

Benign breast tumors are a nonthreatening condition defined as abnormal cell growth within the breast without the ability to invade nearby tissue. However, benign lesions hold valuable biological information that can lead us toward better understanding of tumor biology. In this study, we have used two pathway analysis algorithms, Pathifier and gene set variation analysis (GSVA), to identify biological differences between normal breast tissue, benign tumors and malignant tumors in our clinical dataset. Our results revealed that one-third of all pathways that were significantly different between benign and malignant tumors were immune-related pathways, and 227 of them were validated by both methods and in the METABRIC dataset. Furthermore, five of these pathways (all including genes involved in cytokine and interferon signaling) were related to overall survival in cancer patients in both datasets. The cellular moieties that contribute to immune differences in malignant and benign tumors were analyzed using the deconvolution tool, CIBERSORT. The results showed that levels of some immune cells were specifically higher in benign than in malignant tumors, and this was especially the case for resting dendritic cells and follicular T-helper cells. Understanding the distinct immune profiles of benign and malignant breast tumors may aid in developing noninvasive diagnostic methods to differentiate between them in the future.

MiR-18a and miR-18b are expressed in the stroma of oestrogen receptor alpha negative breast cancers

BACKGROUND

Previously, we have shown that miR-18a and miR-18b gene expression strongly correlates with high proliferation, oestrogen receptor -negativity (ER^-), cytokeratin 5/6 positivity and basal-like features of breast cancer.

METHODS

We investigated the expression and localization of miR-18a and -18b in formalin fixed paraffin embedded (FFPE) tissue from lymph node negative breast cancers (n = 40), by chromogenic in situ hybridization (CISH). The expression level and in situ localization of miR-18a and -18b was assessed with respect to the presence of tumour infiltrating lymphocytes (TILs) and immunohistochemical markers for ER, CD4, CD8, CD20, CD68, CD138, PAX5 and actin. Furthermore, in two independent breast cancer cohorts (94 and 377 patients) the correlation between miR-18a and -18b expression and the relative quantification of 22 immune cell types obtained from the CIBERSORT tool was assessed.

RESULTS

CISH demonstrated distinct and specific cytoplasmic staining for both miR-18a and miR-18b, particularly in the intratumoural stroma and the stroma surrounding the tumour margin. Staining by immunohistochemistry revealed some degree of overlap of miR-18a and -18b with CD68 (monocytes/macrophages), CD138 (plasma cells) and the presence of high percentages of TILs. CIBERSORT analysis showed a strong correlation between M1-macrophages and CD4+ memory activated T-cells with mir-18a and -18b.

CONCLUSIONS

Our study demonstrates that miR-18a and miR-18b expression is associated with ER- breast tumours that display a high degree of inflammation. This expression is potentially associated specifically with macrophages. These results suggest that miR-18a and miR-18b may play a role in the systemic immunological response in ER^- tumours.

Abstract 3881: Breast cancer proteogenomics landscape defines subtype specific protein level regulations and reveals proteins coded by pseudogenic loci

The advancement of mass spectrometry (MS) based proteomics has been tremendous in recent years and is expected to continue due to the rapid developments in instrument technology and bioinformatic analysis. These methods have enabled us to discover predictive protein markers for anti-estrogen treatment of estrogen receptor positive breast cancer 1, 2. Recently proteogenomics has emerged as an exciting area, combining proteomics with genomics and transcriptomics. We have published a proteogenomics workflow which can be used to discover new protein coding loci via an unbiased 6 reading frame translation (6-FT) search even in well-annotated higher eukaryotes such as human and mouse3. Herein we present a quantitative proteomics and proteogenomics analysis, using our high resolution isoelectric focusing (HiRIEF) aided proteogenomics method3,4, on breast tumors obtained from five breast cancer subtypes. Protein products from 12645 genes are identified and roughly 10000 proteins are quantified across the entire cohort of 45 breast cancer tissues. The resulting quantitative proteome landscape recapitulates the PAM50 subtypes. The breast cancer proteome defines clusters indicative of stroma, immune response, basal, adipocyte, proliferation, and steroid response related components. Additionally, a proteogenomics search of the 6-FT of the entire human genome reveals novel pseudogenic protein coding regions (n = 150) as well as peptides derived from lncRNA (n = 79). Finally, customized databases including variant peptides derived from SNPs, mutations, and splice junction peptides are used to analyze protein level events related to variants. This proteogenomics analysis for both new open reading frames and sequence variants reveals novel proteins expressed in a tumor specific manner in several studied individuals, with some being related to known sub-types. Taken together, this study reveals the proteome profiles are related to transcriptomics, copy number, and metabolic activity in specific tumors, proving our proteogenomics workflow provides novel information on the breast cancer molecular landscape.

1. Johansson, H.J. et al. Proteomics profiling identify CAPS as a potential predictive marker of tamoxifen resistance in estrogen receptor positive breast cancer. Clinical proteomics 12, 8 (2015).

2. Johansson, H.J. et al. Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer. Nat Commun 4, 2175 (2013).

3. Branca, R.M. et al. HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nature methods 11, 59-62 (2014).

4. Boekel J, et.al. Multi-omic data analysis using Galaxy. Nature Biotechnol. 2015 Feb 6;33(2):137-9.

Citation Format: Henrik Johansson, Yafeng Zhu, Mads Haugland, Kristine Sahlberg, Erik Fredlund, Mikael Huss, Nathaniel Vacanti, Miriam Range Aure, Bengt Sennblad, Sanela Kjellqvist, Lukas Orre, Ola Christian Lingjaerde, Anne-Lise Borresen-Dale, Janne Lehtio. Breast cancer proteogenomics landscape defines subtype specific protein level regulations and reveals proteins coded by pseudogenic loci. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3881.

Thrombin and bradykinin enhance prostaglandin production in human peripheral blood monocytes

Thrombin and bradykinin stimulate production of prostaglandin E2 (PGE2), and 6-keto-prostaglandin F1 alpha (the stable breakdown product of prostacyclin) in isolated human peripheral blood monocytes in a dose- and time-dependent manner. Since PGE2 and prostacyclin can affect the activity of immunocompetent cells and bone resorbing osteoclasts, our finding indicates that thrombin and bradykinin, both of which are formed in inflammatory processes as a consequence of activation of the Hageman factor (coagulation factor XII), may have important roles in the modulation of the inflammatory response and the loss of alveolar bone in periodontitis.

Forskolin sensitizes parathyroid hormone-induced cyclic AMP response, but not the bone resorptive effect, in mouse calvarial bones

The effect of forskolin on parathyroid hormone (PTH) stimulated bone resorption, as assessed in vitro by the release of 45Ca from prelabelled neonatal mouse calvarial bones, and cyclic AMP formation in mouse calvarial bones and osteoblast-like cells was investigated. Much higher concentrations (100-300-times) of PTH were required to stimulate cyclic AMP accumulation than to stimulate mineral mobilization in murine calvarial bones. PTH, in the absence of phosphodiesterase inhibitor, stimulated cyclic AMP formation in mouse calvarial bones at and above concentrations of 3-10 nmol/l with EC50 at 10-15 nmol/l. In the presence of forskolin (1 or 10 mumol/l) the minimal concentration required to obtain a cyclic AMP response to PTH was decreased by a factor of 30-100 and the EC50 value was decreased to 1-2 nmol/l. Similar results were seen in osteoblast-enriched cells. In addition, the magnitude of the PTH-induced cyclic AMP response was substantially potentiated by forskolin, both in calvarial bones and in isolated osteoblasts. Forskolin, in the absence of PTH, stimulated cyclic AMP levels in mouse calvaria at and above 1 mumol/l. In the presence of PTH, the response to forskolin was potentiated over the whole dose-response curve with apparent EC50 value at 1-2 mumol/l of forskolin. Forskolin (1 mumol/l) did not affect the magnitude of the 45Ca release response to PTH in 24 or 48 h cultures. In 96 h cultures, forskolin, in an additive manner, potentiated the effect of PTH on calcium mobilization. These results show that forskolin, in mouse calvarial bones and in isolated osteoblasts, in addition to directly stimulating cyclic AMP, can enhance receptor-mediated activation of adenylate cyclase. The finding that forskolin did not synergistically potentiate PTH-induced bone resorption suggests that there is no simple relationship between PTH-induced cyclic AMP formation and stimulation of bone resorption.

Characterization of adenosine receptors in bone. Studies on the effect of adenosine analogues on cyclic AMP formation and bone resorption in cultured mouse calvaria

The effect of different adenosine analogues on cyclic AMP (cAMP) formation and bone resorption in cultured mouse calvarial bones was investigated. 5'-N-ethylcarboxamidoadenosine (NECA), R-N6-phenylisopropyl-adenosine (PIA), N6-cyclohexyl-adenosine (CHA) and 2-chloroadenosine all stimulated cyclic AMP formation with a threshold close to 1 mumol l-1); NECA was the most potent agonist. Theophylline (10, 100 mumol l-1) inhibited the cAMP accumulation induced by NECA and 2-chloroadenosine (30 and 300 mumol l-1), dose dependently. There was no inhibition of cAMP formation by PIA and CHA in forskolin-treated bone tissue. SQ 22, 536 and 2',5'-dideoxyadenosine (100 mumol l-1) both inhibited rolipram-stimulated cAMP formation. Cyclic AMP accumulation in isolated osteoblast-like cells from neonatal mouse calvarial bones was stimulated by NECA (10 and 100 mumol l-1) and 2-chloroadenosine (100 mumol l-1). 2-chloroadenosine (10 and 30 mumol l-1), but not NECA, PIA nor CHA, caused a dose-dependent stimulation of 45Ca release in both 48- and 120-h culture. The effect of 2-chloroadenosine on 45Ca release could not be antagonized by theophylline. Neither NECA, PIA, CHA nor 2-chloroadenosine could affect PTH-stimulated 45Ca release in short term cultures (6, 24 h). By contrast, stimulation of cAMP formation by forskolin or dibutyryl cAMP caused a rapid (6 h) inhibition of PTH-stimulated bone resorption. The results demonstrate functional A2 and P-site receptors in mouse calvaria and osteoblast-like cells, but no A1-receptor was detected. These adenosine receptors regulate cAMP, but are not intimately linked to bone resorption. The calcium mobilization induced by 2-chloroadenosine appears to be unrelated to adenosine receptors.