PD-L1 Expression Correlates with Tumor-Infiltrating Lymphocytes and Response to Neoadjuvant Chemotherapy in Breast Cancer

Programmed death 1 ligand 1 (PD-L1) is an immune regulatory molecule that limits antitumor immune activity. Targeting of PD-L1 and other immune checkpoint proteins has shown therapeutic activity in various tumor types. The expression of PD-L1 and its correlation with response to neoadjuvant chemotherapy in breast cancer has not been studied extensively. Our goal was to assess PD-L1 expression in a cohort of breast cancer patients treated with neoadjuvant chemotherapy. Pretreatment biopsies from 105 patients with breast cancer from Yale New Haven Hospital that subsequently received neoadjuvant chemotherapy were assessed for PD-L1 protein expression by automated quantitative analysis with a rabbit monoclonal antibody (E1L3N) to the cytoplasmic domain of PD-L1. In addition, tumor-infiltrating lymphocytes (TIL) were assessed on hematoxylin and eosin slides. PD-L1 expression was observed in 30% of patients, and it was positively associated with hormone-receptor-negative and triple-negative status and high levels of TILs. Both TILs and PD-L1 measured in the epithelium or stroma predicted pathologic complete response (pCR) to neoadjuvant chemotherapy in univariate and multivariate analyses. However, because they are strongly associated, TILs and PD-L1 cannot both be included in a significant multivariate model. PD-L1 expression is prevalent in breast cancer, particularly hormone-receptor-negative and triple-negative patients, indicating a subset of patients that may benefit from immune therapy. Furthermore, PD-L1 and TILs correlate with pCR, and high PD-L1 predicts pCR in multivariate analysis.

Multiplexed quantitative analysis of CD3, CD8, and CD20 predicts response to neoadjuvant chemotherapy in breast cancer

PURPOSE

Although tumor-infiltrating lymphocytes (TIL) have been associated with response to neoadjuvant therapy, measurement typically is subjective, semiquantitative, and unable to differentiate among subpopulations. Here, we describe a quantitative objective method for analyzing lymphocyte subpopulations and assessing their predictive value.

EXPERIMENTAL DESIGN

We developed a quantitative immunofluorescence assay to measure stromal expression of CD3, CD8, and CD20 on one slide. We validated this assay by comparison with flow cytometry on tonsil specimens and assessed predictive value in breast cancer on a neoadjuvant cohort (n = 95). Then, each marker was tested for prediction of pathologic complete response (pCR) compared with pathologist estimation of the percentage of lymphocyte infiltrate.

RESULTS

The lymphocyte percentage and CD3, CD8, and CD20 proportions were similar between flow cytometry and quantitative immunofluorescence on tonsil specimens. Pathologist TIL count predicted pCR [P = 0.043; OR, 4.77; 95% confidence interval (CI), 1.05-21.6] despite fair interobserver reproducibility (κ = 0.393). Stromal AQUA (automated quantitative analysis) scores for CD3 (P = 0.023; OR, 2.51; 95% CI, 1.13-5.57), CD8 (P = 0.029; OR, 2.00; 95% CI, 1.08-3.72), and CD20 (P = 0.005; OR, 1.80; 95% CI, 1.19-2.72) predicted pCR in univariate analysis. CD20 AQUA score predicted pCR (P = 0.019; OR, 5.37; 95% CI, 1.32-21.8) independently of age, size, nuclear grade, nodal status, ER, PR, HER2, and Ki-67, whereas CD3, CD8, and pathologist estimation did not.

CONCLUSIONS

We have developed and validated an objective, quantitative assay measuring TILs in breast cancer. Although this work provides analytic validity, future larger studies will be required to prove clinical utility.

ERβ splice variant expression in four large cohorts of human breast cancer patient tumors

Though the role of Estrogen Receptor (ER)α in breast cancer has been studied extensively, there is little consensus about the role of alternative ER isoform ERβ in breast cancer biology. ERβ has significant sequence homology to ERα but is located on a different chromosome and maintains both overlapping and unique functional attributes. Five variants exist, resulting from alternative splicing of the C-terminal region of ERβ. The relevance of ERβ variants in breast cancer outcomes and response to therapy is difficult to assess because of conflicting reports in the literature, likely due to variable methods used to assess ERβ in patient tumors. Here, we quantitatively assess expression of ERβ splice variants on over 2,000 breast cancer patient samples. Antibodies against ERβ variants were validated for staining specificity in cell lines by siRNA knockdown of ESR2 and staining reproducibility on formalin-fixed paraffin-embedded tissue by quantitative immunofluorescence (QIF) using AQUA technology. We found antibodies against splice variants ERβ1 and ERβ5, but not ERβ2/cx, which were sensitive, specific, and reproducible. QIF staining of validated antibodies showed both ERβ1 and ERβ5 QIF scores, which have a normal (bell shaped) distribution on most cohorts assessed, and their expression is significantly associated with each other. Extensive survival analyses show that ERβ1 is not a prognostic or predictive biomarker for breast cancer. ERβ5 appears to be a context-dependent marker of worse outcome in HER2-positive and triple-negative patients, suggesting an unknown biological function in the absence of ERα.

Abstract P2-10-02: PD-L1 protein expression is a prognostic biomarker in breast cancer

BACKGROUND: Programmed death ligand 1 (PD-L1) and its receptor, PD1, are involved in limiting immune response. In the context of cancer, tumor cells expressing PD-L1 can suppress the immune response of PD1-expressing tumor infiltrating lymphocytes (TILs). Disruption of this pathway with antibodies to either the ligand or the receptor has shown promise in the treatment of non small cell lung cancer, melanoma and renal cell cancer. Here we investigate the pathway in breast cancer.

METHODS: PD-L1 protein expression was assessed on two Yale TMA breast cancer cohorts with two-fold redundancy by quantitative immunofluorescence (QIF) using AQUA technology. Cohort 1 (YTMA201) consists of 400 patients with has extensive follow-up and adjuvant treatment information. Cohort 2 (YTMA128) consists of 245 patients with limited follow-up and no treatment information. The PD-L1 antibody (Lieping Chen, clone 5H1) has been previously validated for specificity and reproducibility using transfected cell models. TILs were assessed by a pathologist for each cohort using a score from 0-3 based on the amount of TILs within the spot. AQUA scores for PD-L1 were used as a continuous variable and also cut at the median for outcome analysis.

RESULTS: PD-L1 protein is positively correlated with TILs (p<0.0001 on cohort 1 and p = 0.0072 on cohort 2) and inversely correlated with estrogen receptor status (p<0.0001 on cohort 1 and p = 0.0188 on cohort 2) on both breast cancer cohorts examined (total n = 594). On cohort 1, PD-L1 protein expression is a marker of good prognosis as a continuous variable (p = 0.0271) as well as when cut at the median (p = 0.0151), particularly in the estrogen receptor positive subset of patients.

CONCLUSIONS: PD-L1 expression in breast cancer is positively associated with TILs and inversely associated with estrogen receptor status on two independent breast cancer cohorts. PD-L1 protein expression shows prognostic value in breast cancer patients, particularly the ER positive subset of patients. Further assessment of PD-1 axis marker expression may be valuable as the associated therapeutics are being tested in breast cancer patients.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P2-10-02.

R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli

Double-stranded DNA ends, often from replication, drive genomic instability, yet their origin in non-replicating cells is unknown. Here we show that transcriptional RNA/DNA hybrids (R-loops) generate DNA ends that underlie stress-induced mutation and amplification. Depleting RNA/DNA hybrids with overproduced RNase HI reduces both genomic changes, indicating RNA/DNA hybrids as intermediates in both. An Mfd requirement and inhibition by translation implicate transcriptional R-loops. R-loops promote instability by generating DNA ends, shown by their dispensability when ends are provided by I-SceI endonuclease. Both R-loops and single-stranded endonuclease TraI are required for end formation, visualized as foci of a fluorescent end-binding protein. The data suggest that R-loops prime replication forks that collapse at single-stranded nicks, producing ends that instigate genomic instability. The results illuminate how DNA ends form in non-replicating cells, identify R-loops as the earliest known mutation/amplification intermediate, and suggest that genomic instability during stress could be targeted to transcribed regions, accelerating adaptation.

Gross chromosomal rearrangement mediated by DNA replication in stressed cells: evidence from Escherichia coli

Gross chromosomal rearrangements (GCRs), or changes in chromosome structure, play central roles in evolution and are central to cancer formation and progression. GCRs underlie copy number variation (CNV), and therefore genomic disorders that stem from CNV. We study amplification in Escherichia coli as a model system to understand mechanisms and circumstances of GCR formation. Here, we summarize observations that led us to postulate that GCR occurs by a replicative mechanism as part of activated stress responses. We report that we do not find RecA to be downregulated by stress on a population basis and that constitutive expression of RecA does not inhibit amplification, as would be expected if downregulation of RecA made cells permissive for nonhomologous recombination. Strains deleted for the genes for three proteins that inhibit RecA activity, psiB, dinI, and recX, all show unaltered amplification, suggesting that if they do downregulate RecA indirectly, this activity does not promote amplification.

Abstract 689: Validation of antibodies to Estrogen Receptor ≤ and quantitative assessment of ERα1 and ERα5 expression in breast cancer

INTRODUCTION: Estrogen receptors are members of the nuclear hormone receptor family that play an important role in breast carcinogenesis and response to endocrine therapy. Though the role of ERα in breast cancer has been studied extensively, little is known about the alternative isoform ERα. ERα has significant sequence homology to ERα but is located on a different chromosome and maintains both overlapping and unique functional attributes. Five variants resulting from alternative splicing of the C-terminal region of ERα exist. The relevance of ERα variants in breast cancer outcomes and response to therapy is difficult to assess because of conflicting results in the literature, likely due to variable methods used to assess ERα in patient tumors. METHODS: Antibodies against ERα variants (ERα1: ThermoScientific PPG5/10; ERα2/cx: Serotec Clone 57/3; ERα5: Serotec Clone 5/25) were validated for staining specificity by siRNA knockdown of ESR2 as well as staining reproducibility on FFPE tissue by quantitative immunofluorescence (QIF) using AQUA technology (HistoRx). QIF staining of validated antibodies was then assessed on two separate breast cancer cohorts. RESULTS: ERα1 and ERα5, but not ERα2/cx, antibodies were found to be sensitive, specific and reproducible, as shown by reduction in signal after siRNA knockdown in cell lines and reproducible QIF scores on a set of breast cancer control cases. ERα1 and ERα5 expression is significantly associated in both cohorts examined (R*2=.224, p<0.0001). However, ERα1 does not show significant association with patient outcome or response to endocrine therapy. In contrast, ERα5 is associated with worse recurrence free survival (log rank p=0.0500) and, though it shows no association with response to tamoxifen, it predicts response to chemotherapy (log rank p=0.0393). CONCLUSIONS: Validation of ERα antibodies reveals that not all reagents are specific for the expected isoforms. Assessment of breast cancer cohorts using validated reagents show that ERα1 is not associated with outcome while ERα5 is both prognostic and predictive.

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 689. doi:1538-7445.AM2012-689

Abstract 3626: Quantitative analysis of microRNAs by in situ hybridization reveals prognostic value of miRNAs in melanoma and breast cancer

Introduction: Most miRNA measurement methods require total RNA extraction which destroys spatial information and makes standardization a challenge. In situ hybridization (ISH) however, allows the direct assessment of miRNA expression levels in tissue and importantly allows for the evaluation of expression in malignant cells as well as stromal cells. We have developed and validated a novel method for the quantitative analysis of miRNA expression by ISH on formalin fixed paraffin embedded tissue microarrays (TMAs) using miR-21, miR-92a, miR-34a, miR-221, miR-205, and Let-7a. Methods: In order to quantitatively measure miRNA expression by ISH, DIG labeled LNA modified miRNA probes were employed and multiplexed with DAPI and cytokeratin or S100/GP100 immunofluorescence to apply the AQUA technology. This co-localization based, quantitative approach allows for the measurement of miRNA expression in subcellular compartments. The assay allows standardization of miRNA measurement and potential for rapid large cohort assessment. We also assessed protein targets of each miRNA by AQUA to investigate the hypothesized inverse relationship between miRNAs and target proteins. Results: In hundreds of tissue samples a broad dynamic range and a variable expression pattern specific to each miRNA was observed. Specificity of the assay was validated with anti-miR and miRNA mimic transfected cell lines, miR-21 knock out mouse tissue, and blocking oligo experiments. The assays were performed on near serial sections and were found to have high reproducibility with R*2>0.8. miR-221 and miR-205 were found to be prognostic in breast cancer and melanoma respectively (p<0.05). Finally, the inverse relationship between miRNAs and putative targets were not seen in the large population cohorts. Conclusions: This specific and reproducible method for the quantitative analysis of miRNA expression provides proof of concept for the use of miRNAs as tissue biomarkers using quantitative ISH. Future studies will further determine the prognostic value of miR-221 and miR-205, and the relationship between miRNAs and target protein expression.

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 3626. doi:1538-7445.AM2012-3626

Targeting androgen receptor in estrogen receptor-negative breast cancer

Endocrine therapies for breast cancer that target the estrogen receptor (ER) are ineffective in the 25%-30% of cases that are ER negative (ER-). Androgen receptor (AR) is expressed in 60%-70% of breast tumors, independent of ER status. How androgens and AR regulate breast cancer growth remains largely unknown. We find that AR is enriched in ER- breast tumors that overexpress HER2. Through analysis of the AR cistrome and androgen-regulated gene expression in ER-/HER2+ breast cancers we find that AR mediates ligand-dependent activation of Wnt and HER2 signaling pathways through direct transcriptional induction of WNT7B and HER3. Specific targeting of AR, Wnt or HER2 signaling impairs androgen-stimulated tumor cell growth suggesting potential therapeutic approaches for ER-/HER2+ breast cancers.