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Waldenstrom macroglobulinemia (WM) and its precursor IgM gammopathy are distinct disorders characterized by clonal mature IgM-expressing B-cell outgrowth in the bone marrow. Here, we show by high-dimensional single-cell immunogenomic profiling of patient samples that these disorders originate in the setting of global B-cell compartment alterations, characterized by expansion of genomically aberrant extrafollicular B cells of the nonmalignant clonotype. Alterations in the immune microenvironment preceding malignant clonal expansion include myeloid inflammation and naïve B- and T-cell depletion. Host response to these early lesions involves clone-specific T-cell immunity that may include MYD88 mutation–specific responses. Hematopoietic progenitors carry the oncogenic MYD88 mutations characteristic of the malignant WM clone. These data support a model for WM pathogenesis wherein oncogenic alterations and signaling in progenitors, myeloid inflammation, and global alterations in extrafollicular B cells create the milieu promoting extranodal pattern of growth in differentiated malignant cells.Significance:These data provide evidence that growth of the malignant clone in WM is preceded by expansion of extrafollicular B cells, myeloid inflammation, and immune dysfunction in the preneoplastic phase. These changes may be related in part to MYD88 oncogenic signaling in pre–B progenitor cells and suggest a novel model for WM pathogenesis.This article is highlighted in the In This Issue feature, p. 549

supplementary figs 1-25 and supplementary tables 1-3

Supplementary Data from PDZ Proteins SCRIB and DLG1 Regulate Myeloma Cell Surface CD86 Expression, Growth, and Survival

Purpose:Multiple myeloma is a malignancy of plasma cells. Extensive genetic and transcriptional characterization of myeloma has identified subtypes with prognostic and therapeutic implications. In contrast, relatively little is known about the myeloma epigenome.Experimental Design:CD138+CD38+ myeloma cells were isolated from fresh bone marrow aspirate or the same aspirate after freezing for 1–6 months. Gene expression and chromatin accessibility were compared between fresh and frozen samples by RNA sequencing (RNA-seq) and assay for transpose accessible chromatin sequencing (ATAC-seq). Chromatin accessible regions were used to identify regulatory RNA expression in more than 700 samples from newly diagnosed patients in the Multiple Myeloma Research Foundation CoMMpass trial (NCT01454297).Results:Gene expression and chromatin accessibility of cryopreserved myeloma recapitulated that of freshly isolated samples. ATAC-seq performed on a series of biobanked specimens identified thousands of chromatin accessible regions with hundreds being highly coordinated with gene expression. More than 4,700 of these chromatin accessible regions were transcribed in newly diagnosed myelomas from the CoMMpass trial. Regulatory element activity alone recapitulated myeloma gene expression subtypes, and in particular myeloma subtypes with immunoglobulin heavy chain translocations were defined by transcription of distal regulatory elements. Moreover, enhancer activity predicted oncogene expression implicating gene regulatory mechanisms in aggressive myeloma.Conclusions:These data demonstrate the feasibility of using biobanked specimens for retrospective studies of the myeloma epigenome and illustrate the unique enhancer landscapes of myeloma subtypes that are coupled to gene expression and disease progression.

Enrichment of transcription factor consensus binding motifs in regulatory elements predictive of gene expression associated with poor overall survival.

Correlation of regulatory element transcription and gene expression in CoMMpass specimens.

ATAC-seq data for Emory patients.

Correlation of chromatin accessibility and gene expression for the 5% most variably expressed genes.

Regulatory elements predictive of gene expression for genes prognostic of overall survival in CoMMpass.

Regulatory element transcription in newly diagnosed myelomas from CoMMpass.

Gene set enrichment analysis of transcribed regulatory elements in CoMMpass.

Waldenstrom macroglobulinemia (WM) and its precursor IgM gammopathy are distinct disorders characterized by clonal mature IgM-expressing B-cell outgrowth in the bone marrow. Here, we show by high-dimensional single-cell immunogenomic profiling of patient samples that these disorders originate in the setting of global B-cell compartment alterations, characterized by expansion of genomically aberrant extrafollicular B cells of the nonmalignant clonotype. Alterations in the immune microenvironment preceding malignant clonal expansion include myeloid inflammation and naïve B- and T-cell depletion. Host response to these early lesions involves clone-specific T-cell immunity that may include MYD88 mutation–specific responses. Hematopoietic progenitors carry the oncogenic MYD88 mutations characteristic of the malignant WM clone. These data support a model for WM pathogenesis wherein oncogenic alterations and signaling in progenitors, myeloid inflammation, and global alterations in extrafollicular B cells create the milieu promoting extranodal pattern of growth in differentiated malignant cells.Significance:These data provide evidence that growth of the malignant clone in WM is preceded by expansion of extrafollicular B cells, myeloid inflammation, and immune dysfunction in the preneoplastic phase. These changes may be related in part to MYD88 oncogenic signaling in pre–B progenitor cells and suggest a novel model for WM pathogenesis.This article is highlighted in the In This Issue feature, p. 549

Background/Objectives: Despite intensive multimodal therapy, greater than 50% of children with high-risk neuroblastoma (HR NB) relapse with incurable disease. Next generation sequencing of primary HR NB tumors identified an increase in activating mutations in the RAS/RAF/MAPK pathway. Moreover, gene set enrichment analyses showed a significant decrease in expression of genes suppressed by the Yes-Associated Protein (YAP) at relapse, suggesting increased YAP transcriptional repression. YAP binds with TEAD family transcription factors to regulate gene expression. We have shown that YAP promotes chemotherapy and MEK inhibitor resistance in RAS-mutated NB tumors in vivo by suppressing the expression of Harakiri (HRK), a BH3-only pro-apoptotic protein activated in response to tumor environmental stress such as serum starvation. Our overall objective is to elucidate how YAP represses HRK and tumor suppressor genes globally, and to enhance MEK inhibitor potency by combining MEK inhibition with agents that inhibit YAP or induce HRK to restore the tumor environmental stress response and apoptosis in RAS-mutated NB. Design/Methods: We used publicly available databases to identify TEAD binding sites on the HRK gene locus in NB. To assess the global state of methylation, we treated NB cells, SK-N-AS (NRASQ61K mutation, MYCN non-amplified) and NLF (NF1 deletion, MYCN amplified), with demethylating agent azacitidine and evaluated HRK expression. To identify the specific TEAD (1-4) binding partner to YAP, we performed siRNA and co-immunoprecipitation studies. We further tested novel YAP-TEAD small molecule inhibitors with varying TEAD1-4 inhibition specificity in SK-N-AS and NLF cells in vitro. Results: We observed that TEAD binds near cis-regulatory regions on the HRK gene locus in NB. We found that HRK expression is restored when SK-N-AS and NLF cells are treated with azacitidine despite YAP expression increasing. We also identified TEAD2 as the specific binding partner to YAP in NB and found that TEAD2 is necessary for HRK regulation. Novel YAP-TEAD small molecule inhibitors affect NB cell viability under serum-deprived conditions in vitro, especially the inhibitor with highest specificity against TEAD2, and affect YAP-TEAD downstream targets. Conclusions: YAP-TEAD2 binding is essential for HRK regulation in RAS-mutated NB and thus is a logical therapeutic target to restore therapy response. Further studies are ongoing to test YAP-TEAD small molecule inhibitors in combination with MEK inhibitors and in vivo. Citation Format: Jenny Shim, Andrew Ho, Hunter C. Jonus, Adeiye A. Pilgrim, Benjamin G. Barwick, Tracy T. Tang, Lawrence H. Boise, Kelly C. Goldsmith. YAP-TEAD2 binding mediates therapy resistance in RAS-driven neuroblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3552.

Purpose: Multiple myeloma is a malignancy of plasma cells. Extensive genetic and transcriptional characterization of myeloma has identified subtypes with prognostic and therapeutic implications. In contrast, relatively little is known about the myeloma epigenome. Experimental Design: CD138+CD38+ myeloma cells were isolated from fresh bone marrow aspirate or the same aspirate after freezing for 1–6 months. Gene expression and chromatin accessibility were compared between fresh and frozen samples by RNA sequencing (RNA-seq) and assay for transpose accessible chromatin sequencing (ATAC-seq). Chromatin accessible regions were used to identify regulatory RNA expression in more than 700 samples from newly diagnosed patients in the Multiple Myeloma Research Foundation CoMMpass trial (NCT01454297). Results: Gene expression and chromatin accessibility of cryopreserved myeloma recapitulated that of freshly isolated samples. ATAC-seq performed on a series of biobanked specimens identified thousands of chromatin accessible regions with hundreds being highly coordinated with gene expression. More than 4,700 of these chromatin accessible regions were transcribed in newly diagnosed myelomas from the CoMMpass trial. Regulatory element activity alone recapitulated myeloma gene expression subtypes, and in particular myeloma subtypes with immunoglobulin heavy chain translocations were defined by transcription of distal regulatory elements. Moreover, enhancer activity predicted oncogene expression implicating gene regulatory mechanisms in aggressive myeloma. Conclusions: These data demonstrate the feasibility of using biobanked specimens for retrospective studies of the myeloma epigenome and illustrate the unique enhancer landscapes of myeloma subtypes that are coupled to gene expression and disease progression.

Advanced prostate cancer most commonly spreads to bones. Although denosumab or zoledronic acid is recommended for prostate cancer patients with bone metastases to prevent or delay skeletal-related events, no significant benefits in terms of cancer-specific and overall survival have been observed. Some chemotherapies are available for the treatment of bone metastasis, but eventually all such tumors develop resistance. Additionally, the underlying mechanisms of prostate cancer bone metastasis and its resistance to chemotherapy are still poorly understood. In this study, we report that TGF-β-induced acetylation of the basic transcription factor Krüppel-like factor 5 (KLF5) frequently occurred in prostate cancer cells located in both the mouse and human bone microenvironments. Using multiple in vitro and in vivo systems, we demonstrated that tumor cells expressing acetylated KLF5 (Ac-KLF5) enhanced prostate cancer-induced bone lesions by promoting osteoclast differentiation. As revealed by RNA-Seq and ChIP-Seq analyses, Ac-KLF5 transcriptionally activated CXCR4 expression, the silence of which attenuated Ac-KLF5-enhanced osteoclast differentiation. A further screening on the paracrine signaling indicates that IL-11 mediated the promoting effect of the Ac-KLF5/CXCR4 axis on osteoclast differentiation. These findings indicate that the TGF-β/Ac-KLF5/CXCR4/IL-11 signaling axis from bone to tumor and then to bone again is a crucial pathway responsible for TGF-β mediated vicious cycle in bone metastasis. More importantly, targeting CXCR4 using FDA approved drugs AMD3100 selectively sensitizes Ac-KLF5-expressing tumors and bone metastases to docetaxel treatment. These findings provide a rationale for targeting Ac-KLF5/CXCR4 signaling as a novel therapeutic strategy in advanced prostate cancer patients with bone metastases. Citation Format: Baotong Zhang, Yixiang Li, Qiao Wu, Lin Xie, Benjamin Barwick, Jin-Tang Dong. KLF5 acetylation promotes bone metastatic growth of prostate cancer by activating CXCR4/IL-11 and subsequent osteoclast differentiation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3840.

Multiple myeloma is a malignancy of terminally differentiated, antibody secreting B cells known as plasma cells. Normal plasma cell differentiation and cell fate are coupled to epigenetic and transcriptional reprogramming, including a proliferation-dependent global loss of DNA methylation. However, relatively little is known about the epigenetic changes that underlie myelomagenesis and how these contribute to disease etiology. To this end, we have analyzed the DNA methylome of 119 myeloma specimens from the CoMMpass study (NCT01454297) by whole genome bisulfite sequencing (WGBS) and more than 90% of these same specimens were also characterized for structural variants (long-insert whole genome sequencing) and gene expression (RNA-seq). Unsupervised hierarchical clustering grouped together specimens with t(4;14) translocations that upregulate the H3K36 dimethyltransferase NSD2 (also known as MMSET and WHSC1), which likely impacts the DNA methylation state through epigenetic cross-talk. These data also revealed a dramatic genome-wide hypomethylation where myeloma samples had a median global CpG methylation level of 41% as compared to 71% and 89% in normal plasma cells and B cells, respectively. Demethylation of the myeloma methylome occurred in large megabase domains encompassing genes that were devoid of gene expression. Conversely, DNA methylation remained mostly unchanged in the bodies of genes that were highly expressed. Although the majority of these hypomethylated domains were common across myelomas, many regions of variable methylation exist and these differences corresponded with proximal gene expression differences. These variably methylated regions were compared to PFS and OS and this identified 6,314 CpG loci where the level of DNA methylation was prognostic of outcome (P≤0.00001). These loci were clustered into discrete regions and in the majority of cases (79%), reduced DNA methylation at these loci corresponded with poor outcome. For example, several loci in the gene bodies of PRKCE, MGMT, FHIT, WWOX were prognostic of poor survival. Interestingly, myeloma t(14;16) translocations disrupt the tumor suppressor WWOX and induce the oncogene MAF. These data suggest that WWOX expression may also be lost by epigenetic mechanisms. Finally, we analyzed the DNA methylome of primary and relapsed samples for 22 patients, including multiple relapsed samples for 2 patients. These data identified genome-wide DNA methylation remodeling with a median of 1.9 million differential methylated CpGs between the newly diagnosed and relapsed specimens. These relapse differentially methylated loci coincided at the same regions in several patients and significantly overlapped loci where the DNA methylation level was prognostic of outcome. Integrative genetic, epigenetic, and transcriptional analyses for 120 myeloma samples will be presented. Citation Format: Benjamin G. Barwick, Doris R. Powell, Daniel Penaherrera, Sheri Skerget, Jonathan J. Keats, Daniel Auclair, Sagar Lonial, Lawrence H. Boise, Paula M. Vertino. Whole genome DNA methylation analysis of multiple myeloma identifies pervasive hypomethylation and biomarkers of survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 839.

Multiple myeloma is the second most common hematological malignancy with an estimated 30,000 new diagnoses in 2017. Myeloma cells retain numerous characteristics of normal plasma cells including reliance on survival signals in the bone marrow for long term viability. However, they have gained the capacity to proliferate, causing harmful bone lesions in patients, and in advanced stages become extramedullary. Therefore, we are investigating molecular mechanisms of myeloma cells that allow them to survive independently of the bone marrow microenvironment. We have identified syntenin as a protein involved in myeloma cell survival and a potential therapeutic target. Syntenin has been reported to bind to and regulate levels of the plasma cell marker, CD138. We used the CoMMpass dataset, a longitudinal study of myeloma patients following their transcriptomic expression throughout treatment, and discovered that patients expressing in the top quartile for syntenin trend toward lower overall survival, progression-free survival, and shorter response duration than those in the bottom quartile. To determine whether it is involved in myeloma cell survival, we used short hairpin RNA to knock down syntenin (shsyn) in RPMI 8226 and MM1.s myeloma cell lines and determined cell death using Annexin-V staining four days following lentiviral infection. We observed increased death in syntenin-silenced cells compared to our empty vector control in both RPMI 8226 (control=57.83% viable, shsyn=29.47% viable, p=0.04) and MM1.s cell lines (control=91.43% viable, shsyn=70.1% viable, p=0.04) suggesting that syntenin is important for myeloma cell survival. Syntenin is a PDZ-domain containing protein that has been shown to regulate expression of several transmembrane proteins. We, therefore, wanted to look at correlation of syntenin expression with CD138 and CD86, two PDZ-binding domain containing proteins expressed on the surface of myeloma cells. Using the CoMMpass dataset, we found patients with high expression of syntenin had increased expression of CD86 while syntenin-low patients had decreased CD86 expression. This correlation does not exist with CD138 as syntenin-low patients express higher levels of CD138. The correlation with CD86 but not CD138 suggests a previously undescribed role for syntenin in myeloma cells. Our lab has shown that expression of CD86 is necessary for myeloma cell survival, and signals to confer drug resistance. When we silenced syntenin, we observed decreased CD86 expression. Moreover, knockdown of CD86 showed increased expression of syntenin. Taken together, these data suggest that syntenin may regulate CD86 expression on the cell surface. We now show a novel role for syntenin in myeloma cell viability and as a potential regulator of CD86 expression. Syntenin has not previously been explored in multiple myeloma and determining its molecular function is warranted as it may be an effective target for therapeutic treatment of the disease. Citation Format: Tyler Moser-Katz, Catherine M. Gavile, Benjamin G. Barwick, Sagar Lonial, Lawrence H. Boise. Syntenin regulates multiple myeloma cell survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 319.

A plethora of genetic changes occurring in the triple negative (TN) breast tumors (BT) contribute to the different phenotypes exhibited by the tumor cells via deregulation of the specific signaling-pathways. Our group identified a differential upregulation of the Wnt-beta-catenin pathway in TN subset of BT (Barwick etal, 2008, BCS; Dey etal. 2009, AACR) and reported that the poor prognosis and higher incidence of metastasis is associated with this pathway in TNBT (Barwick etal., 2009; PNAS, revised). Of late, we demonstrated a role of the pathway in the control of integrin-mediated migration in TNBT cells (Dey etal. 2009, Adv. BCR). Since integrin-directed migration is instrumental for the invasion (directional movement across extracellular-matrix following matrix degradation) of the tumor cells and TN tumor cells are highly invasive in nature, we hypothesized that the upregulation of Wnt-beta-catenin pathway in TNBT is functionally connected to the control of invasion. Our hypothesis is strengthened by our recent identification of MMP7 (key target-gene of this pathway), as a selective-biomarker of TN subtype (Abramovitz etal, 2009, AACR). In an attempt to define the significance of the pathway in the regulation of invasion, we examined (a) the expression of MMP7 and CTNNB1 in tumor samples and 15 TNBT cell lines, (b) the activity of MMP7 in high MMP7-expressing TNBT cell lines, and (c) effects of pharmacological intervention of the pathway on the invasion of MMP7-expressing TNBT cells. We demonstrated that MMP7 is selectively upregulated in TNBT tumors (our data sets; Montreal-91, Georgia-137) and published data set (MSK-96). We validated the DASL-data by RT-PCR in tumors and cell lines. The expression of MMP7 and beta-catenin (mRNA) in tumor samples from TN patients was comparable to the pattern of expression of MMP7 and beta-catenin (protein) in TNBT cell lines. Zymography of MMP7 demonstrated that the secreted protein is enzymatically active. MDA-MB231, MDA-MB468 and SUM149 TNBT cell lines invaded more in vitro than non-TNBT cells. Administration of sulindac to attenuate the Wnt-beta-catenin pathway showed, 1) a decrease in the levels of beta-catenin (total and active) and MMP7, 2) an inhibition of invasion of cells which corroborated with the integrin-directed cell movement (real-time-video-microscopy), 3) an altered distribution-pattern of filamentous-actin, 4) over 50% attenuation of the activation of RAC1-GTPase and 5) a blockade of migration of TNBT cells. The status of activation of cofilin is directly related to cell migration, invasion, and metastasis in many tumor cells including mammary tumors. We are currently studying the state of phosphorylation of cofilin in the context of fibronectin-dependent activation of the RAC1 (upstream of cofilin) in TNBT cells following the intervention of Wnt-beta-catenin pathway, the results of which will be presented in the meeting. 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 5287.

Clinical Significance: Among 1 million cases of newly diagnosed breast cancer worldwide each year, over 170,000 cases will have a distinct type of triple-negative breast cancer (TNBC), which lacks expression of estrogen (ER), progesterone (PR) and human epidermal growth factor receptor 2 (Her-2/neu). The patients with TNBC are usually detected at the late stage, have an aggressive tumor type, an increased likelihood of local and distant recurrence, and a poorer prognosis compared to women with other types of breast cancer. TNBC patients usually receive neoadjuvant therapy to reduce local and distant recurrence. However, more than 50% of TNBC patients are resistant to conventional chemotherapy. Therefore, novel methods for effective therapy are an urgent need for improving survival of the TNBC patients. Methods: We have developed a targeted therapy for TNBC by systemic delivery of biodegradable theranostic magnetic iron oxide nanoparticles (IONPs) that combine targeted drug delivery and non-invasive tumor imaging capabilities. These theranostic IONPs are targeted to urokinase plasminogen activator receptor (uPAR) by conjugating to the amino-terminal fragment (ATF) of the high affinity receptor binding domain of uPA. Results: 1). Our results from analysis of the gene expressing profile of a cohort of 143 breast cancer tissues revealed that uPAR, a potential cell surface target for the development of targeted therapeutics in TNBC, is highly expressed in the TNBC tissues compared to the luminal type of breast cancer (p < 0.0001). The major advantage of targeting uPAR is that the receptor is highly expressed in tumor cells and angiogenic endothelial cells, which facilitates transporting nanoparticles across the endothelium lining tumor vessels. Internalization of ATF-nanoparticle complexes by tumor cells further increases intracellular drug concentration; 2). We demonstrated that systemic delivery of uPAR-targeted theranostic IONPs carrying a chemotherapy drug, doxorubicin, significantly inhibited the growth of primary tumors through anti-tumor and anti-angiogenesis effects, and delayed local and distant recurrence for 8 weeks as compared mice-treated with free doxorubicin in a TNBC-like 4T1 mouse mammary tumor model. The improved therapeutic effect using these targeted theranostic nanoparticles has also been demonstrated in a human breast cancer xenograft model; 3). Targeting theranostic nanoparticles into tumors allow for monitoring intratumoral drug delivery and therapeutic response in the tumors by MRI; and 4). Targeted delivery of doxorubicin using theranostic IONPs reduces systemic toxicity of the drug in normal organs, such as heart and liver. Conclusion: uPAR-targeted theranostic nanoparticles have potential for targeted therapy, timely assessment of therapeutic response of a given therapy, and ultimately, increased survival of TNBC patients. 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 5482.

Abstract #2027 Background: DASL (cDNA-mediated Annealing, Selection, extension Ligation) is a recently described, RT-PCR-based, multiplex gene expression assay developed by Illumina specifically for use with fragmented RNA prepared from formalin-fixed paraffin-embedded (FFPE) samples. For use with this assay, we have designed a custom 512-gene breast cancer panel, validated this panel with FFPE breast tumor samples, and identified novel genes associated with the triple negative (TN) subtype. Material and Methods: The DASL assay was used to measure mRNA levels from RNA isolated from 5 um FFPE breast tumor sections using the Roche High Pure Kit. Samples that passed our quality control tests were run in the assay. Arrays were imaged using a BeadArray Reader and data was analyzed using BeadStudio software. Differential mRNA regulation was identified by Significance Analysis of Microarrays software using a false discover rate (q-value < 0.01) or Bonferroni correction of the two-tailed Student's t-test. IHC concordance was measured by mRNA expression fold-change for positive versus negative IHC categories. Results: To validate our custom breast cancer panel, we performed the DASL assay on 187 samples from 87 patients with differing receptor status as previously determined by IHC (ER, PR, HER2) and/or FISH (HER2). Correlation between 152 common genes on Illumina's 502-gene standard cancer panel and our custom panel was very high; R2 value of 0.88. Concordance between IHC/FISH and DASL data for ESR1, PGR and ERBB2 was > 90%. We identified 73 genes differentially expressed between TN and the other tumor samples. Of these, 20 were in common between the standard and custom panels, 53 were uniquely expressed on the custom panel. These included genes associated with the TN/Basal subtype identified in previous microarray studies; CXCL1, CDH3, ANXA8, KRT5, TRIM29, KRT17, MFGE8, CX3CL1, FZD7, CHI3L2, B3GNT5 (PNAS 100:8418, 2003) and CDH3, CRABP1, CX3CL1, FOXC1, MMP7 (BMC Genomics 7:96, 2006) further validating both DASL assay and custom panel. In addition, we identified genes not previously linked to the TN subtype, highlighting the potential utility of the custom panel for profiling breast tumor FFPE specimens in the DASL assay. Discussion: We have designed and validated a custom 512-gene breast cancer panel for expression profiling studies using RNA prepared from FFPE tumor specimens on the DASL platform. Thus far, we have identified a 73-gene set with the custom panel (significantly more genes than with the standard panel) that can discriminate TN from other receptor expressing subtypes. We are now applying this platform to samples from clinical trials in order to identify both prognostic and predictive breast tumor gene sets. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2027.

Abstract #2089 Background: A disparity in prognosis of triple negative (TN) breast cancer (BC) has been observed between African American (AA) and Caucasian (CAU) race/ethnicities afflicted with this aggressive and invasive BC subtype. Etiological understanding of these differences involves accounting for several factors associated with phenotype and genotype. Here, we address the latter using the Illumina DASL (cDNA mediated, Annealing, Selection, Extension, and Ligation) assay to quantify mRNA expression of 512 breast cancer related genes in a cohort of 24 CAU and 56 AA TN BC tissues sourced from formalin-fixed, paraffin-embedded (FFPE) blocks. Material and Methods: The DASL assay was used to measure mRNA expression levels from FFPE sourced tissues in both cohorts of self-identified patients. CAU BC patients were obtained from St. Mary's Hospital, Montreal, Quebec and AA BC patients were obtained from Grady Hospital, Atlanta, Georgia. RNA extraction used the RNA High Pure Kit (Roche) and was taken from archival FFPE tissues either 5µm tissue sections or cores. Differential mRNA regulation was identified by Significance Analysis of Microarrays (SAM) software using a false discover rate (FDR) less than 1% and a two fold-change criteria to determine differential regulation. Results: In all, 33 genes were found differentially expressed between AA and CAU TN BC tumor samples, 32 of which were upregulated in the AA cohort, only 1 of which was upregulated in the CAU group. The upregulated gene in CAU TN BC was TFF1. Upregulated genes in the AA cohort (order of statistical significance according to SAM software) were KIF20A, EP300, AURKB, FGF4, C14orf155, USP22, EPOR, ZNF668, SCNN1G, MAPT, FLNB, EP400, LTA, ACOT11, RBP3, CSF3, E2F2, TGFB1, CCNE1, L1CAM, NDP, VWF, RHOB, FEN1, BIN1, KRT17, CDC42EP4, SERPINF1, CHI3L2, NES, BCL2, and RERG. Discussion: TFF1 upregulated in the CAU population, has been indicated as biomarker of favorable prognosis in endocrine therapy in clinical studies which is consistent with race/ethnicity disparities. The remaining genes upregulated in the AA cohort include transcription factors E2F2 and RBP3/E2F1 both with cyclin binding domains which may interact with CCNE1, extracellular and adhesion related genes KRT17, L1CAM and FGF4, genes associated with cell cycle AURKB, EP400, and EP300 (activator of HIF-1A). Several RAS related genes were also found differentially expressed in the AA cohort including RHOB, RERG, BIN1, and EPOR. Moreover, it is worth mentioning that BCL2 which is expressed in the aggressive mammary cancer cell line MCF-7 was also found upregulated in the AA cohort. These initial findings suggest that several differentially regulated genes between AA and CAU race/ethnicities may account for the disparity in outcomes resultant in these populations. These initial data warrant further investigation which is currently ongoing. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2089.

Abstract #43 Background: Patients afflicted with triple negative (TN) breast cancer (BC) are typically younger and have the worst prognosis of any BC subtype as a result of its aggressive and invasive phenotype. TN BC has been well studied with respect to the associative and prognostic values of its mRNA expression profiles. We have used the Illumina DASL (cDNA mediated, Annealing, Selection, Extension, and Ligation) platform to characterize 502 genes from 96 BC patients sourced from formalin-fixed, paraffin-embedded (FFPE) tissues. RNA extracted from FFPE tissues is highly fragmented and typically unsuited for expression platforms, but recent advances have allowed for accurate expression profiling of RNA from FFPE tissues. This 96 patient cohort included 21 TN BC patients identified by immunohistochemistry (IHC); differential analysis of TN expression was integrated with known pathway mechanisms and identified activation of the Wnt pathway in TN tumors. Material and Methods: The Illumina DASL assay was used to measure mRNA expression levels from BC patients obtained from St. Mary's Hospital, Montreal, Quebec. RNA was extracted from three 5µm tissue sections from FFPE blocks using the RNA High Pure Kit (Roche). Differential mRNA regulation was identified by Significance Analysis of Microarrays (SAM) software using a false discover rate (FDR, q-value < 0.01) or a Bonferroni corrected two-tailed student's t-test (p-value < 0.05). IHC concordance was measured by mRNA expression fold-change for positive versus negative IHC categories. Results: 165 samples from 96 patients were characterized for mRNA expression on 1,488 probes across 502 genes in the DASL assay. Quality control limited the analysis to 150 samples from 91 patients over 500 genes. Comparison of the TN subtype relative to HER2 positive and hormone positive breast carcinomas identified up-regulation [fold-change] of MMP7 [2.9], MMP9 [2.0], MMP1 [1.8], NOTCH1 [1.5], FZD7 [1.5], PPARD [1.3], CCND2 [1.2], MET [1.3], MYC [1.5], and MYCN [2.0] in the TN subtype. Most of these genes are either a component or downstream target of the Wnt signaling pathway. Down-regulated relevant genes included ESR1 [-8.4], PGR [-3.9], ERBB2 [-3.4] as expected, as well as ERRB3, ERBB4, GLI3, TFF1, LAF4/AFF3, and AR. Discussion: Down-regulation of TFF1 suggests inhibition of the ERK/MAPK pathways which have complex effects on cell-cell adhesion. In combination with over-expression of MMPs 1, 7, and 9, these changes may contribute to the invasive nature of TN BCs. GLI3 down-regulation may attenuate Hedgehog signaling potentially contributing to Wnt activation, further leading to cell migration, invasion, and decrease in cell adhesion to cognate integrin-matrix interaction Up-regulation of both the FZD7 receptor as well as the Wnt targets MMP7, MYC, MYCN, PPARD, and CCND2 strongly suggest Wnt pathway activation in the TN subtype. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 43.