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Supplementary Methods

Supplementary Tables 1 and 2, Figures S1-16. Supplementary Table 1: Gene lists from DAVID analysis of genes downregulated in RKIP derived TAMs with a Benjamini p-value < 0.5 Supplementary Table 2: Gene lists from DAVID analysis of genes upregulated in RKIP+CCRL5 derived (rescue) TAMs with a Benjamini p-value < 0.5 Figure S1: Immunoblot validation of RKIP expression in 1833 (BM1), MDA-MB-436, and 4T1.2 cells Figure S2: A schematic describing the method used for RNAseq analysis to compare metastatic BM1 with non-metastatic BM1+RKIP Figure S3: Tumor growth in orthotopic xenograft BM1 tumors, significance compared using a 2-way ANOVA. Figure S4: GO categories enriched in BM1+RKIP tumors from RNAseq analysis. Figure S5: Quantile-quantile plots for all stromal cell types tested between metastatic BM1 and non-metastatic BM1+RKIP tumors. Figure S6: Relative TAM infiltration in MDA-MD-436 tumors determined by %pos staining cells for F4/80. Figure S7: Flow cytometric analysis to determine the purity and heterogeneity of BM1 isolated TAMs. Figure S8: CCL5 levels measured by ELISA from BM1 cells in culture. Figure S9: CCL5 expression by qRT-PCR of MDA-MD-436 and 4T1.2 overexpressing RKIP. Figure S10?: RKIP and CCL5 immunoblotts from 1833 (BM1) tumors overexpressing the vectors shown. Figure S11: Tumor growth, tumor weight, and correlation between tumor weight and TAM infiltration in BM1 tumors treated with the CCR5 inhibitor Maraviroc. Figure S12: Invasion assay for BM1 cells overexpressing RKIP, CCL5, or both. Figure S13: Images of Raybiotech L308 arrays. Figure S14: Gene expression data of TAM secreted factors in human patient data sets. Figure S15: Correlation between CCL5 and TAM secreted factors in human patient data sets. Figure S16: Heatmap identifying data sets where breast cancer metastasis free survival is significantly stratified by classifier

Triple-negative breast cancer (TNBC) patients have the highest risk of recurrence and metastasis. Because they cannot be treated with targeted therapies, and many do not respond to chemotherapy, they represent a clinically underserved group. While physiological inhibitors of metastasis (metastasis suppressors) play key roles in regulating tumor growth, invasion and metastasis, their role in regulating the tumor microenvironment and immune system is unknown. We hypothesized that the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) regulates stromal cells, which then affect tumor invasiveness. Using species-specific RNAseq we determined that expression of RKIP in tumors markedly reduces the number and metastatic potential of infiltrating TAMs. While TAMs isolated from TNBC xenografts drive in vitro invasion, RKIP+ derived TAMs did not drive invasion and had decreased secretion of pro-metastatic factors including SLPI, OPN, MMP-12, Galectin-3, VEGF-A, VEGF-D, TNFR2, and PGRN. We determined that RKIP regulates TAM recruitment by blocking HMGA2, which activates CCL5 expression. CCL5 rescued pro-metastatic TAM infiltration as well as tumor intravasation. We additionally showed that factors decreased in RKIP-derived TAMs were restored in CCL5-derived TAMs. CCL5 derived TAMs were also able to promote metastasis when co-injected with MDA-MB-231 tumors. These tumor cells demonstrated permanent increases in both growth and invasive potential after co-injection with highly pro-metastatic CCL5 derived TAMs. To determine the clinical utility of these TAM genes we combined their expression with RKIP signaling in the tumor to create a signature that strikingly separates TNBC patients based on outcome. Our results demonstrate for the first time that metastasis suppressors can regulate the microenvironment, regulating invasion through TAMs. Our results also suggest aggressive triple negative breast cancers could be controlled by attacking CCL5 derived TAMs crucial for promoting metastasis. Funded by: GM087630, CA184494, and CA192780 Citation Format: Daniel C. Rabe, Casey Frankenberger, Russell Bainer, Devipriya Sankarasharma, Kiran Chada, Thomas Krausz, Yoav Gilad, Lev Becker, Marsha R. Rosner. Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of prometastatic TAMs. [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 1557.

This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR02) of the Conference Proceedings. Citation Format: Daniel C. Rabe, Casey Frankenberger, Russell Bainer, Devipriya Sankarasharma, Kiran Chada, Thomas Krausz, Yoav Gilad, Lev Becker, Marsha Rich Rosner. Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of pro-metastatic tumor-associated macrophages. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Metastasis; 2015 Nov 30-Dec 3; Austin, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(7 Suppl):Abstract nr A01.

Triple-negative breast cancer (TNBC) patients have the highest risk of recurrence and metastasis. Because they cannot be treated with targeted therapies, and many do not respond to chemotherapy, they represent a clinically underserved group. While physiological inhibitors of metastasis (metastasis suppressors) play key roles in regulating tumor growth, invasion and metastasis, their role in regulating the tumor microenvironment and immune system is unknown. We hypothesized that the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) regulates stromal cells, which then affect tumor invasiveness. Using species-specific RNAseq we determined that expression of RKIP in tumors markedly reduces the number and metastatic potential of infiltrating TAMs. While TAMs isolated from TNBC xenografts drive in vitro invasion, RKIP+ derived TAMs did not drive invasion and had decreased secretion of pro-metastatic factors including SLPI, OPN, MMP-12, Galectin-3, VEGF-A, VEGF-D, TNFR2, and PGRN. We determined that RKIP regulates TAM recruitment by blocking HMGA2, which activates CCL5 expression. CCL5 rescued pro-metastatic TAM infiltration as well as tumor intravasation. We additionally showed that factors decreased in RKIP-derived TAMs were restored in CCL5-derived TAMs. CCL5 derived TAMs were also able to promote metastasis when co-injected with MDA-MB-231 tumors. These tumor cells demonstrated permanent increases in both growth and invasive potential after co-injection with highly pro-metastatic CCL5 derived TAMs. To determine the clinical utility of these TAM genes we combined their expression with RKIP signaling in the tumor to create a signature that strikingly separates TNBC patients based on outcome. Our results demonstrate for the first time that metastasis suppressors can regulate the microenvironment, regulating invasion through TAMs. Our results also suggest aggressive triple negative breast cancers could be controlled by attacking CCL5 derived TAMs crucial for promoting metastasis. Citation Format: Daniel C. Rabe, Casey Frankenberger, Russell Bainer, Devipriya Sankarasharma, Kiran Chada, Thomas Krausz, Yoav Gilad, Lev Becker, Marsha Rich Rosner. Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of pro-metastatic tumor-associated macrophages. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Metastasis; 2015 Nov 30-Dec 3; Austin, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(7 Suppl):Abstract nr PR02.

The molecular interactions between cancer and stromal cells within the tumor microenvironment enable tumor invasion, intravasation, and metastasis at distant sites. However, the degree to which metastatic breast tumors reprogram stromal cells both locally and at distant mammary tissues is not well understood. To address this question, we used species-specific RNA sequencing in a mouse xenograft model to determine how the metastasis suppressor RKIP influences transcription in tumor and stroma tissues. Here we show that metastatic tumors prime mammary tissue at a distant site in a manner that reflects local stromal responses. In addition, gene expression in metastatic breast tumors is pervasively correlated with gene expression in local stroma of both mouse xenografts and human patients. Changes in local and distant stromal gene expression elicited by metastatic tumors are better predictors of subtype and patient survival than tumor gene expression, supporting the use of stromal-based strategies for the diagnosis and prognosis of breast cancer. One mechanism by which changes at contralateral distal mammary breast occur is through exosomes secreted by tumor cells. These results indicate that tumors prime contralateral mammary tissue in a manner that reflects local stromal changes and predicts metastatic disease. This study has future application to our understanding of contralateral breast cancer. Citation Format: Jiyoung Lee, Russell Bainer, Casey Frankenberger, Daniel Rabe, sadiq Saleh, Morag Park, Gary An, Yoav Gilad, Marsha Rich Rosner. Metastatic breast tumors regulate gene expression at distal mammary sites that predicts patient outcome. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr B15.

Triple-negative breast cancer (TNBC) patients have the highest risk of recurrence and metastasis. Because they cannot be treated with targeted therapies, and many do not respond to chemotherapy, they represent a clinically underserved group. While physiological inhibitors of metastasis (metastasis suppressors) play key roles in regulating tumor growth, invasion and metastasis, their role in regulating the tumor microenvironment and immune system is unknown. We hypothesized that the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) regulates stromal cells, which then affect tumor invasiveness. Using species-specific RNAseq we determined that expression of RKIP in tumors markedly reduces the number and metastatic potential of infiltrating TAMs. While TAMs isolated from TNBC xenografts drive in vitro invasion, RKIP+ derived TAMs did not drive invasion and had decreased secretion of pro-metastatic factors including SLPI, OPN, MMP-12, Galectin-3, VEGF-A, VEGF-D, TNFR2, and PGRN. We determined that RKIP regulates TAM recruitment by blocking HMGA2, which activates CCL5 expression. CCL5 rescued TAM infiltration as well as tumor intravasation. We additionally showed that factors decreased in RKIP-derived TAMs were restored in CCL5-derived TAMs. Finally, we demonstrated the TAM secreted factor PGRN is both necessary and sufficient for TAM driven invasiveness. To determine the clinical utility of these TAM genes we combined their expression with RKIP signaling in the tumor to create a signature that strikingly separates TNBC patients based on outcome. Our results demonstrate for the first time that metastasis suppressors can regulate the microenvironment, regulating invasion through TAMs. Our results also suggest TNBC patients with decreased RKIP activity and increased TAM infiltration may respond to therapies targeting CCL5 or PGRN. Citation Format: Daniel C. Rabe, Casey Frankenberger, Russell Bainer, Devipriya Sankarasharma, Kiran Chada, Thomas Krausz, Yoav Gilad, Lev Becker, Marsha R. Rosner. Metastasis suppressors regulate the tumor microenvironment by blocking recruitment of pro-metastatic TAMs. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5077. doi:10.1158/1538-7445.AM2015-5077

Triple-negative breast cancer (TNBC) is the most aggressive form of breast cancer. While five-year survival rates have reached 98% in patients treated with anti-ER or anti-HER2 therapies, patients with TNBC have a five-year survival rate of only 24%. Currently, the only form of therapy for these patients is surgery and platinum based chemotherapy. However, patient outcome is generally poor. Additionally, this disease disproportionately affects African-American women and lower income women, with rates seen approximately three times higher in African-American women compared to the rest of the population. An alternative strategy for treating TNBC patients involves targeting the tumor stroma. To better understand interaction between the tumor and stroma necessary for metastasis and invasion, we employed a triple-negative breast cancer (TNBC) model in which the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) controls primary tumor invasiveness. RKIP expression, which converts invasive tumors to non-invasive tumors, dramatically inhibits macrophage infiltration. The mechanism, which is dependent on Let-7 suppression of HMGA2, involves decreased expression of the chemokine CCL5. Furthermore, overexpression of CCL5 partially rescued the infiltration of macrophages into the tumor and intravasation of tumor cells into the blood stream. The relationships of the genes in the RKIP, HMGA2, CCL5, and macrophage pathways were observed in multiple sets of expression array data from breast cancer patients. Regulation of macrophage infiltration was observed in tumors from an HMGA2 knockout mouse model. These results show that RKIP regulates macrophage recruitment by tumors and demonstrate for the first time that metastasis suppressor genes can regulate the tumor microenvironment. Citation Format: Daniel C. Rabe, Casey A. Frankenberger, Russell Bainer, Devipriya Sankarasharma, Kiran Chada, Thomas Krausz, Yoav Gilad, Marsha Rich Rosner. The role of tumor associated macrophages (TAMs) in triple-negative breast cancer (TNBC) invasion revealed by species-specific RNA sequencing. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr B35. doi:10.1158/1538-7445.CHTME14-B35

Cancer progression is critically dependent on specific molecular interactions between tumor cells and their microenvironment, but little is known about the global dynamics of this crosstalk within and across individuals. Here, we used an RNA sequencing approach with species-of-origin information in a xenograft mouse model to computationally resolve and compare tumor versus stromal transcriptional changes. Our study employed a triple-negative breast cancer (TNBC) model in which primary tumor invasiveness is controlled by the metastasis suppressor Raf Kinase Inhibitory Protein (RKIP) allowing systemic observation of stromal response to invasive or noninvasive breast tumours at both proximal and distal sites. Initially, we observed that expression levels of gene homologs in human tumor and mouse stroma are highly synchronized. Surprisingly, the set of genes most prognostic for metastasis-free survival in multiple clinical data sets were those whose mRNA expression was inversely correlated between tumor and stroma. These results were confirmed in an independent set of microarray data from tumor and stroma micro-dissected from primary human breast cancer patient tissue. Additionally, we found broad-based and invasion-specific gene expression changes in stromal tissues far from the primary lesion, with these results being confirmed in an independent set of samples. Of note, genes differentially expressed in the tumor-associated stroma were better classifiers of tumor phenotype than genes differentially expressed in the tumor alone. As well, stromal genes differentially expressed both locally and distally, are significant predictors of patient prognosis. These findings demonstrate the potential for using patient tissue remote from the primary tumor as indicators of disease aggressiveness. Furthermore, these results suggest that stromal gene expression, acting to compensate for changes in the tumor, may have both prognostic and therapeutic implications. Citation Format: Casey A. Frankenberger, Russell O. Bainer, Daniel C. Rabe, Sadiq Saleh, Morag Park, Yoav Gilad, Marsha R. Rosner. Systemic tumor-stroma interactions are prognostic indicators of breast tumor invasiveness. [abstract]. In: Abstracts: AACR Special Conference on Cellular Heterogeneity in the Tumor Microenvironment; 2014 Feb 26-Mar 1; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(1 Suppl):Abstract nr A43. doi:10.1158/1538-7445.CHTME14-A43

Tumor invasiveness dysregulates homeostatic processes within tissues, driving both tumor and stroma cells to locally proliferate while also disrupting tissue boundaries and recruiting cells from distal sites to promote metastatic dissemination. Here, we use an RNA sequencing approach in mouse models of invasive and noninvasive breast cancer to directly test whether the transcriptional changes that occur as invasive tumors disrupt their microenvironment can be used to predict tumor subtype and patient outcomes. We find that tumor and stroma gene expression levels are largely synchronized within the tumor microenvironment, but that the expression levels of a subset of genes with high prognostic potential are strongly negatively correlated and may reflect opposing responses of tumor and normal stroma cells to tissue disruption. We clinically validate these observations in multiple human breast tumor gene expression datasets and demonstrate that stromal transcript levels enable superior classification of breast cancer subtypes relative to those expression changes observed between invasive and noninvasive tumor tissue. We show that local stromal remodelling is partially driven by differential recruitment of macrophages to invasive tumor sites by CCL5, and that invasion-specific gene expression changes that are prognostic for metastasis-free survival in human patients are detectable in stromal tissues far from the primary lesion. Our data indicate that dysregulation of tissue homeostasis by invasive tumors generates transcriptional changes both within the tumor microenvironment and in peripheral tissues that have significant diagnostic and prognostic potential and could facilitate novel patient therapeutic strategies. Citation Format: Russell Bainer, Casey Frankenberger, Daniel Rabe, Sadiq Saleh, Morag Park, Kiran Chada, Yoav Gilad, Marsha Rosner. Systemic tumor-stroma interactions are prognostic indicators of breast tumor invasiveness. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-320. doi:10.1158/1538-7445.AM2014-LB-320

The ability of cancer cells to survive and grow at primary and metastatic sites is influenced to a large degree by the surrounding cells in the tumor environment. In this process, tumor cells secrete signals that recruit specific cell types to their immediate vicinity and induce these cells to produce factors critical to tumor development, while the surrounding normal tissue, or stroma, detects and responds to developing lesions. While the clinical importance of this complex dialogue between the tumor and the surrounding tissue has long been appreciated, its molecular basis is not well understood. In particular, studies attempting to characterize interactions between tumors and the surrounding tissue have been confounded largely for technical reasons relating to the difficulty of precisely identifying and separating the developing tumor cells from normal cells nearby, and of confidently assigning the factors identified in later analyses to the proper tissue of origin. Recent developments in high-throughput sequencing technology offer an opportunity to overcome these difficulties and precisely identify factors associated with the stromal response to developing tumors on a genomic scale. Using a novel sequencing strategy applied to a xenograft model of triple-negative breast cancer, we are able to unambiguously assign 93.3% of mapped reads to tumor or stromal transcriptomes, with a misassignment rate approaching 0.01%. These methods have allowed us to directly compare transcript levels in stroma containing developing tumors to those levels observed in naive stroma, and to subsequently identify a set of candidate factors likely involved in the stromal response to developing lesions. We then extended this method to contrast stromal responses to near-isogenic tumors with differing metastatic potential and invasive phenotype conferred by expression of the RKIP metastasis suppressor, thereby identifying candidate factors likely to be specifically relevant to metastatic colonization. Surprisingly, we observed significant up-regulation of genes associated with macrophage chemotaxis and macrophage infiltration in the invasive stroma, which was not present in stroma surrounding tumors expressing RKIP. These findings were confirmed by immunohistochemistry using the original cell line as well as parallel experiments in a syngeneic model, suggesting that by utilizing RNA sequencing technology in an innovative way we can increase our understanding of the interplay between tumors and their local environment. Our model allows us to contrast simultaneous high-precision gene expression estimates in tumors and stroma to infer instances of crosstalk. In the invasive microenvironment, we observed coordinated suppression of genes involved in negatively regulating endothelial cell proliferation accompanied by elevated expression of genes whose products bind growth factors in both tumors and stroma. Finally, we extended these analyses to identify candidate paracrine interactions that are likely to be suppressed in noninvasive contexts involving stromal ALK and MDK which may directly contribute to observed differences in cell growth, migration and angiogenesis. Citation Format: Casey A. Frankenberger, Russell O. Bainer, Jyotsana Menon, Claudia Chavarria, Katelyn Michelini, Pàll Melsted, Yoav Gilad, Marsha R. Rosner. Using species-specific RNAseq reveals stromal reprogramming in triple-negative breast cancer xenografts. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr B25.

The transcription factor p53 is a central mediator of the DNA damage response programs controlling cell cycle arrest and apoptosis that are critical to the prevention of oncogenesis. Although p53 has been subject to intense study, the functional consequences of the common proline to arginine coding polymorphism at codon 72 have yet to be fully elucidated. We hypothesized that the previously reported difference in apoptotic potential between cells expressing the two common p53 alleles may be due in part to differences in each variant's ability to transcriptionally regulate downstream target genes. To test this, we used a combination of expression profiling and ChIP-on-chip techniques to identify differences in the transcriptional networks regulated by the alternate alleles of p53 in isogenic cell lines. Our results indicate that although the majority of p53 transcriptional targets are equivalently regulated by both allelic variants, a small number of genes are specifically regulated by the respective versions of p53. Surprisingly, among the genes differentially induced by alternate p53 variants is MDM4 (HDMX), a well-characterized regulator of p53 activity. We subsequently used luciferase expression assays to identify a functional site containing a putative p53 binding element within the MDM4 promoter that discordantly interacts with the two p53 variants. These data provide the first evidence that MDM4 transcription is directly mediated by p53, and suggest a mechanism that could contribute to previously-reported differences in apoptotic potential between the common p53 alleles. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-332.