Abstract P5-03-02: Three-dimensional (3D) imaging of biomarkers in human core needle biopsies of normal and cancerous breast tissue

Background: The tumor microenvironment is spatially and compositionally very heterogenous, which introduces great challenges to characterize the underlying factors using standard 2D diagnostic methodologies. Capturing high resolution 3D quantitative biomarker data, while simultaneously preserving morphology of the tumor microenvironment, could lead to a better understanding of key spatial relationships and may lead to better prognostic and predictive clinical outcomes. In this study, we utilized a novel technique, CLARITY, to transform core needle biopsies from patients with breast cancer, into optically transparent tissues, followed by multiplex immunostaining and 3D imaging of molecular markers. This data was compared to the conventional methods of immunohistochemistry and immunofluorescence staining on FFPE thin sections.

Methods: Formalin-fixed (less than 24 hours) human breast cancer core needle biopsy tissue pairs (tumor and adjacent normal) were obtained from patients undergoing excisional surgery. Tissues were subsequently embedded in 4% paraformaldehyde containing a 4%/0.05% ratio of acrylamide/BIS for 48 hours, and polymerized to form an intact hydrogel/tissue matrix. The samples were sectioned to a thickness of 200µm, 400 µm, and 1000µm and lipid-cleared in a solution of 0.2M borate buffer containing 8% SDS, pH 8.5 at 45°C. The tissues were then immunostained for various cellular markers (Pan-cytokeratin, Her2, CD3, CD31) and a nuclear marker (Ki67) and counterstained with DAPI. Samples were refractive index matched prior to 3D imaging on a Leica SP8 laser scanning confocal microscope or a LaVision BioTec Ultramicroscope II, light sheet microscope.

Results: During the process, the samples remained intact and the cellular morphology was well preserved suggesting that a pre-fixation step following by hydrogel embedding/Immunostaining was feasible. The average passive lipid-clearing time for breast cancer core needle biopsy tissue was 5-20 days depending on the size of the tumor. The majority of the samples reached visual optical transparency, with the exception of some regions that contained heavy fibrotic tissue. Preliminary results demonstrated that specific staining of various cellular and nuclear markers was successful as evidenced by 3D imaging depth up to 1000 µm. As compared to the images obtained from 2D thin sections, the CLARITY procedure followed by 3D imaging yielded significant imaging depth, with the potential to greatly enhance the understanding of the heterogeneity of the tumor microenvironment.

Conclusion: This is the first study demonstrating that other than fresh or frozen tissues, pre-fixed clinical tissue from patients with breast cancer, can be successfully processed by the CLARITY methods and 3D imaged, indicating the potential power of the technique for core needle biopsy tissue processing and in the identification of biomarkers based on tumor cell heterogeneity.

Citation Format: Chen Y, Shen Q, Goodman LJ, Gökmen-Polar Y, Badve SS. Three-dimensional (3D) imaging of biomarkers in human core needle biopsies of normal and cancerous breast tissue [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-03-02.

Abstract P1-06-02: Impact of heterogeneity of DCIS on immune cell infiltrations

Background: Ductal carcinoma in situ (DCIS) accounts for at least 20% of breast cancers. Factors associated with recurrence of DCIS or progression to invasive carcinoma are not well delineated. The goals of the current study were to profile the epithelial and immune cells using the MultiOmyx hyperplexed immuno-fluorescent based analyses. This was coupled with semi-automated algorithms to characterize the inter-relationships between cell populations within individual DCIS lesions.

Patients and Methods: Analysis for 15 antibody markers (EGFR, Her2, Her4, S6, pMTOR, PCAD, CD44v6, NaKATPase, SLC7A5, CD4, CD8, CD20, CD68, and CD10) was performed on a single FFPE section containing 10-20 distinct ducts from 13 cases of DCIS. Briefly, approximately 40 fields of view (FOV) from digitized sections containing DCIS or normal tissue were sequentially (cyclically) stained for the 15 markers. Each cycle entailed staining with 2-3 markers followed by imaging, dye inactivation, and re-staining. DAPI was used for nuclear demarcation and for registration of the images, while S6, pan-cadherin, Na+K+ATPase and pan-cytokeratin were used for epithelial segmentation. K-means clustering was used to determine patterns of co-expression of markers at the single cell, duct, and patient levels. These clusters were then correlated with immune marker expression by tumor infiltrating lymphocytes (TILs) by marker type (CD4, CD8, and CD20) and tumor compartment (stromal versus intraepithelial).

Results: Analysis of the epithelial component in each of 13 cases of DCIS (n= 415 ducts) revealed 8 distinct expression patterns (clusters) using a panel of 7 markers (EGFR, Her2, Her4, pmTOR, CD44v6, SLC7A5, and CD10). The frequency and distribution of clusters, annotated at the single cell level, showed that 4 DCIS's were dominated (>80%) by a single cell phenotype represented by cluster groups 3 and 7 (high Her2), cluster 6 (High Her4 and SLC7A5 and low Her2), or cluster 4 (non-descript). In 5 pts, the pattern was more heterogeneous consisting of mixture of cell populations with 50-70% of the cells belonging to cluster 1 (moderate to high levels for all markers except EGFR and CD10). The remaining pts had a strong representation of cluster 4 and 5 (CD44v6 and phospho-mTOR) cells. The distribution of both intra-epithelial and stromal TILs in DCIS cases were either consisted of a mixed B-cell (CD20+) and T-cell response (n=4), or one dominated by T-cells. Cluster 2 (High EGFR and CD10) was associated with a largely T-cell response (rs = 0.83, P value = 0.0004), while Cluster 7 (strong HER2) was associated with a B-cell response (rs = 0.68, P value = is 0.009).

Conclusions: Analysis 15 markers and use of K-means clustering algorithm, shows prominent inter-tumoral (but not intra-tumoral) heterogeneity in DCIS. Furthermore, epithelial cell specific clusters (high HER2 or EGFR) were associated with distinct B or T cell infiltration by TILs. Additional ongoing studies will determine the clinical significance of the clusters with respect to recurrence of DCIS and development of invasive carcinomas.

Citation Format: Badve S, Gökmen-Polar Y, Harris AL, Sui Y, Sevinsky C, Santamaria-Pang A, Ginty F, Tan PH, Gerdes MJ. Impact of heterogeneity of DCIS on immune cell infiltrations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-02.

Abstract P4-12-01: Independent validation of EarlyR gene signature in BIG 1-98: A randomized, double-blind, phase III trial comparing letrozole and tamoxifen as adjuvant endocrine therapy for postmenopausal women with hormone receptor-positive, early breast cancer

Background: EarlyR is a prognostic gene signature score in ER+ breast cancer (BC) computed from the expression values of ESPL1, SPAG5, MKI67, PLK1 and PGR using a novel algorithm. EarlyR has been validated in multiple cohorts profiled on Affymetrix and Illumina microarrays. This study sought to verify prognostic features of EarlyR in a cohort of BIG 1-98.

Patients and Methods: Illumina DASL assay was used to measure gene expression in FFPE tissue of primary BC from a case-cohort sampling subset of postmenopausal women in BIG 1-98 treated with adjuvant endocrine therapy (letrozole or tamoxifen). Chemotherapy treatment was at the discretion of individual physicians and patients. Among the 1218 patients centrally reviewed with sufficient RNA material for the DASL assay, 1174 with ER+ status and assessed for EarlyR are included in the analytic cohort. EarlyR scores and pre-specified risk strata (≤25=low, 26-75=intermediate, >75=high) were computed, while blinded to clinical data. The analysis endpoints included distant recurrence free interval (DRFI) defined as time from randomization to BC recurrence at a distant site within 8 years and BC free-interval (BCFI) defined as time from randomization to first invasive BC recurrence at a local, regional or distant site or invasive contralateral BC within 8 years. Weighted proportional hazards models (univariate and multivariate, stratified by treatment assignment) were used to adjust for Kaplan-Meier, hazard ratio estimates and Wald test statistics to obtain unbiased analyses and to give consistent estimates.

Results: The distribution of the EarlyR risk groups was 67% low, 19% intermediate and 14% high risk in this ER+ cohort. EarlyR was prognostic for 8-year DRFI (P-trend=0.008). Patients with high EarlyR risk score (>75) had significantly increased risk of distant recurrence within 8 years (univariate HR=1.73, 95%CI: 1.14-2.64) compared to low EarlyR risk group (≤25). The estimated 8-year DRFI (95%CI) is 84%(80%-88%) for high risk vs. 91%( 89%-92%) for low risk, corresponding to an absolute DRFI risk reduction of 7% (low vs high). EarlyR is also prognostic of 8-year BCFI in ER+ (P-trend=0.002) with the estimated 8-year BCFI (95%CI) 79%(75%-84%) for high risk vs. 88%( 86%-89%) for low risk. Consistent results were observed in ER+, HER2- (P-trend=0.01 for DRFI, P-trend=0.004 for BCFI), in ER+, LN- (P-trend=0.05 for DRFI, P-trend=0.03 for BCFI) and ER+, LN+ (P-trend=0.08 for DRFI, P-trend=0.03 for BCFI) subsets.

Conclusions: This study confirmed the prognostic significance of EarlyR using FFPE tissue from the BIG 1-98 trial. In analyses of all ER+ patients and subsets LN-, LN+ and HER2-, EarlyR classifies 65%-70% of patients as low risk, 11-16% as high risk, and < 20% as intermediate risk. In these subsets, the size of the low risk group is larger and the size of the intermediate risk group is smaller than those reported for commercially available signatures. EarlyR identifies a set of high-risk patients with relatively poor prognosis who may be considered for additional treatment. The clinical utility of EarlyR requires further study.

Citation Format: Buechler S, Gray KP, Gökmen-Polar Y, Willis S, Thürlimann B, Kammler R, Leyland-Jones B, Badve SS, Regan MM. Independent validation of EarlyR gene signature in BIG 1-98: A randomized, double-blind, phase III trial comparing letrozole and tamoxifen as adjuvant endocrine therapy for postmenopausal women with hormone receptor-positive, early breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-12-01.

Abstract P2-06-05: LINC00478: A novel tumor suppressor in breast cancer

Background:

LncRNAs may play a role in cancer and serve as new potential targets for improving cancer diagnosis, prognosis or treatment. Long intergenic non-protein coding RNA 478 (LINC00478), the miR99a-let-7c cluster host gene, has been shown to be downregulated in estrogen-independent ER-positive (ER+) breast cancer cells. However, its expression in breast tumors and its significance in recurrence has not been well characterized.

Methods:

The clinical relevance of LINC00478 in ER+ breast tumors was first determined by analysis of the expression levels in MiTranscriptome database (RNAseq-based), which contains ∼8000 most differentially expressed lncRNAs for each cancer and/or tissue type. Additionally, the expression of LINC00478 mRNA was determined in a) a cohort of matched pairs of primary and (nodal) metastatic tumors (n=18) (RNA-seq) and b) a cohort of 60 paraffin-embedded ER-positive, node-negative breast carcinomas with Oncotype DX recurrence scores (QRT-PCR).

Results:

LINC00478 was significantly downregulated in patients with ER-positive tumors compared to uninvolved normal breast tissue. In RNA-seq analysis, metastatic tumors had significant low expression as compared to matched primary tumors (FC: -2.2 fold-down; P=0.0027). Quantitative RT-PCR analysis showed that LINC00478 expression was significantly lower in ER+ node-negative patients with Oncotype DX high recurrence score when compared with low recurrence score patients (FC: -4.14-fold down; P=0.02).

Conclusion:

We document for the first time that LINC00478 functions as a tumor suppressor in ER-positive breast cancer. Its loss is associated with tumor progression and recurrence/metastasis. Novel strategies that focus on re-expression of LINC00478 might be useful for targeting breast cancer and preventing the metastases.

Citation Format: Gökmen-Polar Y, Zavodszky M, Chen X, Gu X, Kodira C, Badve S. LINC00478: A novel tumor suppressor in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-06-05.

Abstract P5-09-09: ESRP1 and ESRP2 expression in tamoxifen resistance

Background: Current standard of care therapies with antiestrogens targeting estrogen receptor α (ER) signaling improve disease-free survival (DFS) in early-stage of breast cancer. However a significant number of cases exhibit de novo or acquired endocrine resistance and recur. It is thus important to identify novel targets of resistance and select these patients for additional therapeutic options which might include continued/extended hormonal therapy. The Oncotype Dx recurrence score (RS) in current practice predicts the likelihood of distant recurrence in tamoxifen-treated patients with node-negative, ER+ breast cancer. However, Oncotype Dx does not provide the mechanistic basis for endocrine resistance. In this study, we aimed to investigate the impact of two epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) expression on recurrence and endocrine resistance such as tamoxifen of ER+ breast cancer.

Methods: Publicly available gene expression datasets were analyzed for the overexpression of ESRP1 and ESRP2 in breast cancer. To validate the in silico findings for the ESRP1 and ESRP2 expression, we further performed quantitative real-time RT-PCR (qRT-PCR) in a cohort of 60 paraffin-embedded ER-positive node-negative breast carcinomas with low, intermediate, and high (19, 21, and 20 cases, respectively) Oncotype DX scores. To further determine the correlation between endocrine resistance and ESRP1/ESRP2 expression, we evaluated their expression levels in an established in vitro model of ER+/tamoxifen-resistance (MCF7/LCC2: an acquired tamoxifen resistant model of human breast cancer).

Results: Using publicly available breast cancer gene expression datasets, we have identified that overexpression of the epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) correlates with worse prognosis in ER+ significantly, but not in ER- breast cancers. qRT-PCR analysis further revealed that ESRP1 and ESRP2 expressions are positively correlated with high Oncotype Dx scores (P <0.05). In vitro, ESRP1 and ESRP2 levels were increased 7.48-fold (P = 0.008) and 2.98-fold (P = 0.0007) in ERα-positive cells with acquired tamoxifen resistance (MCF-7 LCC2), respectively. Thus, ESRP1 expression was slightly elevated more than ESRP2. Furthermore, both ESRP1 and ESRP2 levels did not change in response to E2 alone or E2 and tamoxifen treatment in combination.

Conclusion: These findings suggest a role for the elevated expression of ESRP1 and ESRP2 in tamoxifen resistance and recurrence of ER+ breast cancer. Further studies are ongoing to determine their mechanistic role in ER+ cancer and methods of targeting ESRP1 & 2.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-09-09.

Elevated protein kinase C betaII is an early promotive event in colon carcinogenesis

Protein kinase C (PKC) has been implicated in colon carcinogenesis in humans and in rodent models. However, little is known about the specific role of individual PKC isozymes in this process. We recently demonstrated that elevated expression of PKC betaII in the colonic epithelium induces hyperproliferation in vivo (N. R. Murray et al., J. Cell Biol., 145: 699-711, 1999). Because hyperproliferation is a major risk factor for colon cancer, we assessed whether specific alterations in PKC betaII expression occur during azoxymethane-induced colon carcinogenesis in mice. An increase in PKC betaII expression was observed in preneoplastic lesions (aberrant crypt foci, 3.7-fold) compared with saline-treated animals, and in colon tumors (7.8-fold; P = 0.011) compared with uninvolved colonic epithelium. In contrast, PKC alpha and PKC betaI (a splicing variant of PKC betaII) expression was slightly decreased in aberrant crypt foci and dramatically reduced in colon tumors. Quantitative reverse transcription-PCR analysis revealed that PKC mRNA levels do not directly correlate with PKC protein levels, indicating that PKC isozyme expression is likely regulated at the posttranscriptional/translational level. Finally, transgenic mice expressing elevated PKC betaII in the colonic epithelium exhibit a trend toward increased colon tumor formation after exposure to azoxymethane. Taken together, our results demonstrate that elevated expression of PKC betaII is an important early, promotive event that plays a role in colon cancer development.

Mapping of a molecular determinant for protein kinase C betaII isozyme function

In human erythroleukemia (K562) cells, the highly related protein kinase C (PKC) alpha and PKC betaII isozymes serve distinct functions in cellular differentiation and proliferation, respectively. Previous studies using two domain switch PKC chimera revealed that the catalytic domains of PKC alpha and betaII contain molecular determinants important for isozyme-specific function (Walker, S. D., Murray, N. R., Burns, D. J., and Fields, A. P. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 9156-9160). We have now analyzed a panel of PKC chimeras to determine the specific region within the catalytic domain important for PKC betaII function. A cellular assay for PKC betaII function was devised based on the finding that PKC betaII selectively translocates to the nucleus and phosphorylates nuclear lamin B in response to the PKC activator bryostatin. This response is strictly dependent upon expression of PKC betaII or a PKC chimera that functions like PKC betaII. We demonstrate that a PKC alpha/betaII chimera containing only the carboxyl-terminal 13 amino acids from PKC betaII (betaII V5) is capable of nuclear translocation and lamin B phosphorylation. These results are consistent with our recent observation that the PKC betaII V5 region binds to phosphatidylglycerol (PG), a potent and selective PKC betaII activator present in the nuclear membrane (Murray, N. R., and Fields, A. P. (1998) J. Biol. Chem. 273, 11514-11520). Soluble betaII V5 peptide selectively inhibits PG-stimulated PKC betaII activity in a dose-dependent fashion, indicating that PG-mediated activation of PKC betaII involves interactions with the betaII V5 region of the enzyme. We conclude that betaII V5 is a major determinant for PKC betaII nuclear function and suggest a model in which binding of PG to the betaII V5 region stimulates nuclear PKC betaII activity during G2 phase of the cell cycle.